From 583092aefca54bbf8cd968d48947d06aad047b18 Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Thu, 22 Jun 2023 11:38:10 +0200 Subject: [PATCH 01/10] add analysis script + afni_proc script to 6VV2 --- .../pipelines/team_6VV2_AfniProc.simple | 51 +++++++++++++++++++ narps_open/pipelines/team_6VV2_wip.py | 34 +++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 narps_open/pipelines/team_6VV2_AfniProc.simple create mode 100644 narps_open/pipelines/team_6VV2_wip.py diff --git a/narps_open/pipelines/team_6VV2_AfniProc.simple b/narps_open/pipelines/team_6VV2_AfniProc.simple new file mode 100644 index 00000000..1dd8b736 --- /dev/null +++ b/narps_open/pipelines/team_6VV2_AfniProc.simple @@ -0,0 +1,51 @@ +#!/bin/tcsh + +# set subject and group identifiers +set subject = sub-001 +# set data directory +set datadir = /home/jlefortb/narps_open_pipelines/data/original/ds001734 +set expdir = /home/jlefortb/narps_open_pipelines/outputs_6VV2_test_nipype +afni_proc.py \ + -script ${expdir}/proc.${subject}.block \ + -scr_overwrite \ + -subj_id ${subject} \ + -out_dir ${expdir}/${subject}.results.block \ + -dsets ${datadir}/${subject}/func/${subject}_task-MGT_run-01_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-02_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-03_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-04_bold.nii.gz \ + -copy_anat ${datadir}/${subject}/anat/${subject}_T1w.nii.gz \ + -anat_has_skull yes \ + -blocks despike tshift align tlrc volreg blur mask scale regress \ + -despike_new yes \ + -tlrc_base MNI152_T1_2009c+tlrc \ + -tlrc_NL_warp \ + -align_opts_aea \ + -giant_move \ + -cost lpc+ZZ \ + -volreg_align_to MIN_OUTLIER \ + -volreg_tlrc_warp \ + -volreg_align_e2a \ + -blur_in_automask \ + -regress_stim_times \ + ${datadir}/${subject}/func/times+gain.1D \ + ${datadir}/${subject}/func/times+loss.1D \ + -regress_stim_types AM2 \ + -regress_stim_labels \ + GAIN \ + LOSS \ + -regress_basis \ + 'BLOCK(4,1)' \ + -mask_apply anat \ + -regress_motion_per_run \ + -test_stim_files no \ + -regress_opts_3dD \ + -GOFORIT 8 \ + -jobs 6 \ + -regress_censor_motion 0.2 \ + -regress_apply_mot_types demean deriv \ + -regress_censor_first_trs 3 \ + -regress_est_blur_errts \ + -execute + + diff --git a/narps_open/pipelines/team_6VV2_wip.py b/narps_open/pipelines/team_6VV2_wip.py new file mode 100644 index 00000000..c89c7ba1 --- /dev/null +++ b/narps_open/pipelines/team_6VV2_wip.py @@ -0,0 +1,34 @@ + +# last update: June 2023 + +from nipype import Node, Function, Workflow,IdentityInterface +import subprocess +from nipype.interfaces.io import SelectFiles, DataSink +from os.path import abspath +from os.path import join as opj + +# selectfile +templates = {'command_sub1': abspath('outputs_6VV2_test_nipype/6VV2_AfniProc.simple')} +# Create SelectFiles node +files = Node(SelectFiles(templates), + name='files') +# Location of the dataset folder +files.inputs.base_directory = '.' + +# launch afni bash script +def run(command): + import subprocess + subprocess.run([command]) + print("Done") + +afni_proc = Node(Function(input_names=["command"], + output_names=["Adni_proc_ran"], + function=run), + name='afni_proc') + +####### build workflow +wf_run = Workflow(name="Afni_proc_through_nipype") +wf_run.base_dir = '.' +wf_run.connect([(files, afni_proc, [("command_sub1", "command")]) + ]) +wf_run.run() \ No newline at end of file From c391b1d5af6efc682eb5fbc59c786a73181aeb81 Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Fri, 23 Jun 2023 11:58:20 +0200 Subject: [PATCH 02/10] team 6VV2: first level analysis for all subjects --- .../pipelines/team_6VV2_AfniProc.simple | 22 +++-- narps_open/pipelines/team_6VV2_wip.py | 89 ++++++++++++++++--- 2 files changed, 96 insertions(+), 15 deletions(-) mode change 100644 => 100755 narps_open/pipelines/team_6VV2_AfniProc.simple diff --git a/narps_open/pipelines/team_6VV2_AfniProc.simple b/narps_open/pipelines/team_6VV2_AfniProc.simple old mode 100644 new mode 100755 index 1dd8b736..e1196a02 --- a/narps_open/pipelines/team_6VV2_AfniProc.simple +++ b/narps_open/pipelines/team_6VV2_AfniProc.simple @@ -1,10 +1,19 @@ #!/bin/tcsh -# set subject and group identifiers -set subject = sub-001 -# set data directory -set datadir = /home/jlefortb/narps_open_pipelines/data/original/ds001734 -set expdir = /home/jlefortb/narps_open_pipelines/outputs_6VV2_test_nipype +# created by team 6VV2, reproduce by Narps reproducibility team +# creation date: 22 June 2023 +# read and ran by team_6VV2.py script + +# Store arguments +set expdir="$1" +set subject="$2" +set datadir="$3" + +# set expdir = data/results +# set subject = sub-082 +# set datadir = data/original/ds001734 + + afni_proc.py \ -script ${expdir}/proc.${subject}.block \ -scr_overwrite \ @@ -48,4 +57,7 @@ afni_proc.py \ -regress_est_blur_errts \ -execute + + + diff --git a/narps_open/pipelines/team_6VV2_wip.py b/narps_open/pipelines/team_6VV2_wip.py index c89c7ba1..2b502535 100644 --- a/narps_open/pipelines/team_6VV2_wip.py +++ b/narps_open/pipelines/team_6VV2_wip.py @@ -1,4 +1,3 @@ - # last update: June 2023 from nipype import Node, Function, Workflow,IdentityInterface @@ -6,29 +5,99 @@ from nipype.interfaces.io import SelectFiles, DataSink from os.path import abspath from os.path import join as opj +import os + +# define environment +data_dir = "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" +results_dir = "/home/jlefortb/narps_open_pipelines/data/results/" +working_dir = "/home/jlefortb/narps_open_pipelines/" + +# define subject ids +dir_list = os.listdir(data_dir) +# Subject list (to which we will do the analysis) +subject_list = [] +for dirs in dir_list: + if dirs[0:3] == 'sub': + subject_list.append(dirs[-3:]) + + +# Infosource Node - To iterate on subjects + get directoris paths +infosource = Node(interface=IdentityInterface(fields = ['subject_id', 'data_dir', 'results_dir', 'working_dir'], + data_dir = data_dir, + results_dir = results_dir, + working_dir = working_dir), + name = 'infosource') + +infosource.iterables = [('subject_id', subject_list)] + -# selectfile -templates = {'command_sub1': abspath('outputs_6VV2_test_nipype/6VV2_AfniProc.simple')} +templates = {'command': abspath('narps_open/pipelines/team_6VV2_AfniProc.simple')} # Create SelectFiles node files = Node(SelectFiles(templates), name='files') # Location of the dataset folder files.inputs.base_directory = '.' +# create stimuli file the afni way +def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +create_stimuli = Node(Function(input_names=["subject", "data_dir"], + output_names=["Stimuli"], + function=create_stimuli_file), + name='create_stimuli') + + # launch afni bash script -def run(command): - import subprocess - subprocess.run([command]) - print("Done") +def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") -afni_proc = Node(Function(input_names=["command"], +afni_proc = Node(Function(input_names=["command", "results_dir", "subject", "data_dir"], output_names=["Adni_proc_ran"], function=run), name='afni_proc') + + ####### build workflow -wf_run = Workflow(name="Afni_proc_through_nipype") +wf_run = Workflow(base_dir = opj(results_dir, working_dir), name="Afni_proc_through_nipype") wf_run.base_dir = '.' -wf_run.connect([(files, afni_proc, [("command_sub1", "command")]) +wf_run.connect([(infosource, create_stimuli, [('subject_id', 'subject')]), + (infosource, create_stimuli, [("data_dir", "data_dir")]), + (infosource, afni_proc, [('subject_id', 'subject')]), + (infosource, afni_proc, [("results_dir", "results_dir")]), + (infosource, afni_proc, [("data_dir", "data_dir")]), + (files, afni_proc, [("command", "command")]) ]) +# wf_run.write_graph() wf_run.run() \ No newline at end of file From 7706e5c23421bf92d7dcddb47127a39bb2ad7930 Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Fri, 23 Jun 2023 16:54:24 +0200 Subject: [PATCH 03/10] Team 6VV2: Add second level analysis --- ...2_AfniProc.simple => team_6VV2.firstlevel} | 8 +- narps_open/pipelines/team_6VV2.secondlevel | 230 ++++++++++++++++++ narps_open/pipelines/team_6VV2_wip.py | 107 +++++++- 3 files changed, 329 insertions(+), 16 deletions(-) rename narps_open/pipelines/{team_6VV2_AfniProc.simple => team_6VV2.firstlevel} (87%) create mode 100644 narps_open/pipelines/team_6VV2.secondlevel diff --git a/narps_open/pipelines/team_6VV2_AfniProc.simple b/narps_open/pipelines/team_6VV2.firstlevel similarity index 87% rename from narps_open/pipelines/team_6VV2_AfniProc.simple rename to narps_open/pipelines/team_6VV2.firstlevel index e1196a02..e00d4c2a 100755 --- a/narps_open/pipelines/team_6VV2_AfniProc.simple +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -1,18 +1,16 @@ #!/bin/tcsh -# created by team 6VV2, reproduce by Narps reproducibility team +# created by team 6VV2, reproduced by Narps reproducibility team # creation date: 22 June 2023 # read and ran by team_6VV2.py script +# version afni used by the team : AFNI Version 19.0.01 Tiberius +# version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus # Store arguments set expdir="$1" set subject="$2" set datadir="$3" -# set expdir = data/results -# set subject = sub-082 -# set datadir = data/original/ds001734 - afni_proc.py \ -script ${expdir}/proc.${subject}.block \ diff --git a/narps_open/pipelines/team_6VV2.secondlevel b/narps_open/pipelines/team_6VV2.secondlevel new file mode 100644 index 00000000..c4f79e86 --- /dev/null +++ b/narps_open/pipelines/team_6VV2.secondlevel @@ -0,0 +1,230 @@ +#!/bin/tcsh + +# created by team 6VV2, reproduced by Narps reproducibility team +# creation date: 22 June 2023 +# read and ran by team_6VV2.py script +# version afni used by the team : AFNI Version 19.0.01 Tiberius +# version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus + +# Store arguments +set expdir="$1" + +3dLME -prefix expdir -jobs 4 \ +-model 'group*cond' \ +-SS_type 3 \ +-ranEff '~1' \ +-num_glt 5 \ +-gltLabel 1 'GAIN_indiff' -gltCode 1 'group : 1*indiff cond : 1*GAIN' \ +-gltLabel 2 'GAIN_range' -gltCode 2 'group : 1*range cond : 1*GAIN' \ +-gltLabel 3 'LOSS_indiff' -gltCode 3 'group : 1*indiff cond : 1*LOSS' \ +-gltLabel 4 'LOSS_range' -gltCode 4 'group : 1*range cond : 1*LOSS' \ +-gltLabel 5 'LOSS_range-indiff' -gltCode 5 'group : 1*range -1*indiff cond : 1*LOSS' \ +-dataTable +Subj cond group InputFile \ +001 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/sub-001_GAIN.nii \ +001 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/sub-001_LOSS.nii \ +002 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-002.results.block/sub-002_GAIN.nii \ +002 LOSS range 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/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-110.results.block/sub-110_GAIN.nii \ +110 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-110.results.block/sub-110_LOSS.nii \ +112 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-112.results.block/sub-112_GAIN.nii \ +112 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-112.results.block/sub-112_LOSS.nii \ +113 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-113.results.block/sub-113_GAIN.nii \ +113 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-113.results.block/sub-113_LOSS.nii \ +114 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-114.results.block/sub-114_GAIN.nii \ +114 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-114.results.block/sub-114_LOSS.nii \ +115 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-115.results.block/sub-115_GAIN.nii \ +115 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-115.results.block/sub-115_LOSS.nii \ +116 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-116.results.block/sub-116_GAIN.nii \ +116 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-116.results.block/sub-116_LOSS.nii \ +117 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-117.results.block/sub-117_GAIN.nii \ +117 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-117.results.block/sub-117_LOSS.nii \ +118 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-118.results.block/sub-118_GAIN.nii \ +118 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-118.results.block/sub-118_LOSS.nii \ +119 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-119.results.block/sub-119_GAIN.nii \ +119 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-119.results.block/sub-119_LOSS.nii \ +120 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-120.results.block/sub-120_GAIN.nii \ +120 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-120.results.block/sub-120_LOSS.nii \ +121 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-121.results.block/sub-121_GAIN.nii \ +121 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-121.results.block/sub-121_LOSS.nii \ +123 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-123.results.block/sub-123_GAIN.nii \ +123 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-123.results.block/sub-123_LOSS.nii \ +124 GAIN range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-124.results.block/sub-124_GAIN.nii \ +124 LOSS range /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-124.results.block/sub-124_LOSS.nii + + + diff --git a/narps_open/pipelines/team_6VV2_wip.py b/narps_open/pipelines/team_6VV2_wip.py index 2b502535..64525be1 100644 --- a/narps_open/pipelines/team_6VV2_wip.py +++ b/narps_open/pipelines/team_6VV2_wip.py @@ -1,16 +1,24 @@ # last update: June 2023 - from nipype import Node, Function, Workflow,IdentityInterface import subprocess from nipype.interfaces.io import SelectFiles, DataSink from os.path import abspath from os.path import join as opj import os +import pathlib + +######################################################################## +################## FIRST LEVEL ANALYSIS FOR TEAM 6VV2 ################## +######################################################################## -# define environment +# define environment for first level analysis data_dir = "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" -results_dir = "/home/jlefortb/narps_open_pipelines/data/results/" -working_dir = "/home/jlefortb/narps_open_pipelines/" +results_dir = "/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/" + +path = pathlib.Path(results_dir) +path.mkdir(parents=True, exist_ok=True) + + # define subject ids dir_list = os.listdir(data_dir) @@ -22,16 +30,15 @@ # Infosource Node - To iterate on subjects + get directoris paths -infosource = Node(interface=IdentityInterface(fields = ['subject_id', 'data_dir', 'results_dir', 'working_dir'], +infosource = Node(interface=IdentityInterface(fields = ['subject_id', 'data_dir', 'results_dir'], data_dir = data_dir, - results_dir = results_dir, - working_dir = working_dir), + results_dir = results_dir), name = 'infosource') infosource.iterables = [('subject_id', subject_list)] -templates = {'command': abspath('narps_open/pipelines/team_6VV2_AfniProc.simple')} +templates = {'command': abspath('narps_open/pipelines/team_6VV2.firstlevel')} # Create SelectFiles node files = Node(SelectFiles(templates), name='files') @@ -83,14 +90,13 @@ def run(command, results_dir, subject, data_dir): print("Done") afni_proc = Node(Function(input_names=["command", "results_dir", "subject", "data_dir"], - output_names=["Adni_proc_ran"], + output_names=["Adni_1stLevel"], function=run), name='afni_proc') - ####### build workflow -wf_run = Workflow(base_dir = opj(results_dir, working_dir), name="Afni_proc_through_nipype") +wf_run = Workflow(base_dir = results_dir, name="Afni_proc_through_nipype") wf_run.base_dir = '.' wf_run.connect([(infosource, create_stimuli, [('subject_id', 'subject')]), (infosource, create_stimuli, [("data_dir", "data_dir")]), @@ -100,4 +106,83 @@ def run(command, results_dir, subject, data_dir): (files, afni_proc, [("command", "command")]) ]) # wf_run.write_graph() +wf_run.run() + + +######################################################################## +################## SECOND LEVEL ANALYSIS FOR TEAM 6VV2 ################# +######################################################################## + +# define environment for second level analysis +data_dir_firstlevel = "/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/" +results_dir_second_level = "/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/secondlevel/" +path = pathlib.Path(results_dir_second_level) +path.mkdir(parents=True, exist_ok=True) + +# Infosource Node - To iterate on subjects + get directoris paths +infosource = Node(interface=IdentityInterface(fields = ['results_dir_second_level'], + results_dir_second_level = results_dir_second_level), + name = 'infosource') + +templates = {'command': abspath('narps_open/pipelines/team_6VV2.secondlevel')} +# Create SelectFiles node +files = Node(SelectFiles(templates), + name='files') +# Location of the dataset folder +files.inputs.base_directory = '.' + + +# create datatable for afni_proc.py script +def create_dataTable(data_dir_firstlevel): + # subject not analyzed by the team, see pipelines information for more details + not_included = ["016","018","030","088","089","100"] + df_participant = pd.read_csv("data/original/ds001734/participants.tsv", sep="\t") + # replace equalRange and equalIndifference with range and indifference + df_participant["group"] = [i[5:].lower() for i in df_participant["group"].values] + df_participant["participant_id"] = [i[-3:] for i in df_participant["participant_id"].values] + df = pd.DataFrame(columns=["Subj", "cond", "group", "InputFile"]) + for sub in df_participant["participant_id"].values: + if sub in not_included: + continue + size_df = len(df) + sub_group = df_participant["group"][df_participant["participant_id"]==sub].values[0] + df.loc[size_df] = [sub, "GAIN", sub_group, "{}sub-{}/sub-{}_GAIN.nii".format(data_dir_firstlevel, sub, sub)] + size_df = len(df) + df.loc[size_df] = [sub, "LOSS", sub_group, "{}sub-{}/sub-{}_LOSS.nii".format(data_dir_firstlevel, sub, sub)] + dataTable = df + + """ + Should look like + + Subj cond group InputFile \ + 001 GAIN indiff results/sub-001.results.block/sub-001_GAIN.nii \ + 001 LOSS indiff results/sub-001.results.block/sub-001_LOSS.nii \ + … + 124 GAIN range results/sub-124.results.block/sub-124_GAIN.nii \ + 124 LOSS range results/sub-124.results.block/sub-124_LOSS.nii + + + """ + return dataTable + + +# launch afni bash script +def run_secondlevel(command, results_dir_second_level): + import subprocess + subprocess.run([command, results_dir_second_level]) + print("Done") + +afni_proc = Node(Function(input_names=["command", "results_dir_second_level"], + output_names=["Adni_2ndLevel"], + function=run_secondlevel), + name='afni_proc') + + +####### build workflow +wf_run = Workflow(base_dir = results_dir_second_level, name="Afni_proc_2nd_level_through_nipype") +wf_run.base_dir = '.' +wf_run.connect([(infosource, afni_proc, [("results_dir_second_level", "results_dir_second_level")]), + (files, afni_proc, [("command", "command")]) + ]) +# wf_run.write_graph() wf_run.run() \ No newline at end of file From c70fb39de5962c63adaeabcefd51bc946d301eb8 Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Thu, 6 Jul 2023 14:17:46 +0200 Subject: [PATCH 04/10] commenting --- narps_open/pipelines/team_6VV2.firstlevel | 3 +- narps_open/pipelines/team_6VV2.secondlevel | 4 +- narps_open/pipelines/team_6VV2_wip.py | 11 +- narps_open/pipelines/team_I9D6.firstlevel | 175 +++++++++++++++++++++ narps_open/pipelines/team_I9D6_wip.py | 10 ++ 5 files changed, 200 insertions(+), 3 deletions(-) create mode 100644 narps_open/pipelines/team_I9D6.firstlevel create mode 100644 narps_open/pipelines/team_I9D6_wip.py diff --git a/narps_open/pipelines/team_6VV2.firstlevel b/narps_open/pipelines/team_6VV2.firstlevel index e00d4c2a..f76890c7 100755 --- a/narps_open/pipelines/team_6VV2.firstlevel +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -5,8 +5,9 @@ # read and ran by team_6VV2.py script # version afni used by the team : AFNI Version 19.0.01 Tiberius # version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +# Last update: June 2023 -# Store arguments +# Store arguments (directory where to store results, subjects list, directory where data are stored) set expdir="$1" set subject="$2" set datadir="$3" diff --git a/narps_open/pipelines/team_6VV2.secondlevel b/narps_open/pipelines/team_6VV2.secondlevel index c4f79e86..79846071 100644 --- a/narps_open/pipelines/team_6VV2.secondlevel +++ b/narps_open/pipelines/team_6VV2.secondlevel @@ -5,8 +5,10 @@ # read and ran by team_6VV2.py script # version afni used by the team : AFNI Version 19.0.01 Tiberius # version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +# Last update: June 2023 -# Store arguments + +# Store arguments (directory where to store results) set expdir="$1" 3dLME -prefix expdir -jobs 4 \ diff --git a/narps_open/pipelines/team_6VV2_wip.py b/narps_open/pipelines/team_6VV2_wip.py index 64525be1..7c9bf2d3 100644 --- a/narps_open/pipelines/team_6VV2_wip.py +++ b/narps_open/pipelines/team_6VV2_wip.py @@ -1,4 +1,13 @@ -# last update: June 2023 +''' +created by team 6VV2, reproduced by Narps reproducibility team +creation date: 22 June 2023 +needs script "team_6VV2.firstlevel" and "team_6VV2.secondlevel" +the team : AFNI Version 19.0.01 Tiberius +version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +Participants not included 016, 018, 030, 088, 089, 100 +Last update: June 2023 +''' + from nipype import Node, Function, Workflow,IdentityInterface import subprocess from nipype.interfaces.io import SelectFiles, DataSink diff --git a/narps_open/pipelines/team_I9D6.firstlevel b/narps_open/pipelines/team_I9D6.firstlevel new file mode 100644 index 00000000..438a85ae --- /dev/null +++ b/narps_open/pipelines/team_I9D6.firstlevel @@ -0,0 +1,175 @@ +#!/bin/tcsh + +# created by team I9D6, reproduced by Narps reproducibility team +# creation date: 22 June 2023 +# read and ran by team_I9D6.py script +# version afni used by the team : AFNI Version 19.0.24 Tiberius +# version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +# Last update: June 2023 + +# Store arguments (directory where to store results, subjects list, directory where data are stored) +set expdir="$1" +set subject="$2" +set datadir="$3" + +""" +https://osf.io/bvs2f + +Brain extraction and non-linear registration to the MNI152_2009 template were done with AFNI's @SSwarper script. Prior to brain extraction, the images were deobliqued with 3dWarp and intensity normalized with 3dUnifize, so @SSwarper was run with the -unifize_off flag. +1. AFNI's 3dWarp was used to apply the obliquity transformation to the T1's, needed to keep AFNI and FreeSurfer in register. +2. AFNI's 3dUnifize was run to uniform-ize the T1w volume intensities, to provide assistance to FreeSurfer. +3. Freesurfer processing of anatomical T1w datasets, to define white matter and other ROIs +4. AFNI's @SSwarper was applied to skull-strip each anatomical and to estimate a nonlinear warp to a standard space target (MNI152NLin2009cAsym). +5. AFNI's afni_proc.py blocks: +tshift: slice timing alignment on volumes, +align: linear affine alignment of EPI and anatomy, +tlrc: warp anat to standard space (using @SSwarper results), +volreg: EPI registration, plus concatenating and applying 'align' and 'tlrc' transformations to produce the final EPI time series in MNI space, +mask: create a 'brain' mask from the EPI data for later use, +scale: voxelwise scaling of each EPI run mean to 100, for each voxel , +regress: time series regression analysis. + +Freesurfer segmentation with -3T flag: +recon-all -all -sd $cwd -subjid $sid -3T \ + -i $indata_root/$sid/${sid}_T1w-deobl_nu.nii.gz + +The utilized “tissue classes” were specific ROIs selected from the list labeled by FS. These were the ROIs defined to be WM in AFNI’s @SUMA_renumber_FS: Left-Cerebral-White-Matter, Left-Cerebellum-White-Matter, Right-Cerebral-White-Matter, Right-Cerebellum-White-Matter, WM-hypointensities, CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, CC_Anterior. (This WM mask was later used for the ANATICOR calculations.) + +Slice time correction done by AFNI's 3dTshift as setup by the tshift block in the afni_proc.py command, which uses 5th order Lagrange polynomial interpolation. This was done before motion correction. Slice #0 was used for the reference, to keep nominal volume times in sync with stimulus timing. + +Motion correction was done using 3dvolreg using 6-parameter rigid transformations. + +The reference scan is the “MIN_OUTLIER” volume (volume in the time series with fewest number of outliers detected using 3dToutcount, pre-motion correction, to minimize risk of selecting a high-motion time point). + +The similarity metric is weighted least squares, to determine the 6 rigid body motion parameters and the accompanying coordinate transformation matrix for each time point. + +Interpolation type is “cubic” when determining the motion parameters. The interpolation type of "wsinc5" (weighted sinc, ±5 voxel neighborhood) was applied to the EPI when the combined transformation to MNI space was applied: the EPI➝ref➝anat➝(NL)MNI template transformations were combined to allow a single interpolation from the original EPI time series to the MNI analysis space. + +Function-to-structure (T1w) registration done by AFNI's align_epi_anat.py script as setup by the align block in afni_proc.py, with these additional parameters: -giant_move -cost lpc+ZZ -check_flip. These options specify to search a larger range of rotations (giant_move), use a constrained local Pearson correlation cost function (lpc+ZZ: https://www.ncbi.nlm.nih.gov/pubmed/18976717), and check to see if the EPI has been flipped relative to the anatomical (this happens 😟). This transformation is a 12 parameter linear affine matrix. + +T1-weighted volumes were first deobliqued and intensity normalized before brain extraction and non-linear registration to the MNI152_2009 template MNI152NLin2009cAsym space) were done with AFNI's @SSwarper script. Both the subject T1 and template volumes were at 1 mm resolution. +@SSwarper -input \ + $indata_root/$sid/${sid}_T1w-deobl_nu.nii.gz \ + -unifize_off \ + -base MNI152_2009_template_SSW.nii.gz \ + -subid $sid \ + -odir . + +Here are the steps in the @SSwarper script: + #1: Uniform-ize the T1-weighted volume intensity (3dUnifize) - skipped (already done) + #2: Strip the skull (3dSkullStrip), with mildly aggressive settings. + #3: Nonlinearly warp (3dQwarp) the result from #1 to the skull-on + template, driving the warping to a medium level of refinement. + #4: Use a slightly dilated brain mask from the template to + crop off any non-brain tissue resulting from #3 (3dcalc). + #5: Warp the output of #4 back to original anatomical space, + along with the template brain mask, and combine those + with the output of #2 to get a better skull-stripped + result in original space (3dNwarpApply and 3dcalc). + #6: Restart the nonlinear warping, registering the output + of #5 to the skull-off template brain volume (3dQwarp). + #7: Use @snapshot_volreg3 to make pretty pictures for QC. +The nonlinear warp computed in 3dQwarp (and applied to the EPI data in 3dNwarpApply) is computed incrementally using a set of overlapping 3D polynomial patches. As the patches are refined, more parameters are introduced. However, the many thousands of parameters defining the polynomial patches are not saved; rather, the warp is stored as a non-parametric displacement field in a 3-volume NiFTI datasets. Program 3dNwarpApply uses such a warp dataset to transform other 3D datasets in the same fashion (and can catenate warps and matrices on-the-fly); its default interpolation method is weighted sinc, but lower order methods are also available (e.g., NN for warping ROI labels). + +We used AFNI's 3dUnifize for T1w intensity correction. Command: + 3dUnifize -GM -clfrac 0.4 -Urad 30 \ + -input ${sid}_T1w-deobl.nii.gz \ + -prefix ${sid}_T1w-deobl_nu.nii.gz + +We ran Freesurfer with the -3T flag which runs nu intensity correction, in the creation of a white matter mask for each subject. + +The “scale” block was utilized in afni_proc.py, which scales the mean of each EPI voxel time series to 100; that is, the voxels are scaled separately, not the volumes as a whole. The fluctuations in the resulting time series have an interpretation of local (BOLD) % signal change. Values are truncated to a range of [0,200]. + +Nuisance regression was done including the motion parameters and local white matter voxelwise regressors. +The 6 rigid-body motion parameters (estimated in 3dvolreg) were included, one set of 6 per run. + +Local white matter tissue signals were were included in the regression model set up by the afni_proc.py script as specified by the flags “-regress_anaticor_fast” and "-regress_anaticor_fwhm 20”. The local signal from the eroded white matter is computed summing each EPI volume over the nearby white matter voxels weighted by a Gaussian decay, in this case with a full width half max of 20 mm (https://www.ncbi.nlm.nih.gov/pubmed/20420926). Each EPI voxel time series thus gets a separate ANATICOR regressor, in addition to the usual (global) motion parameter regressors. (The time series regression analysis program 3dREMLfit can deal with voxelwise regressors.) + +Censoring is done with AFNI as part of the regress step +Criteria: ++ the Euclidean norm (enorm) of the 6 motion parameters first temporal differences is calculated, and where enorm is greater than a threshold (here, 0.3 ~mm), both that volume and the preceding one are censored. ++ the fraction of outliers in each (automasked) volume is calculated, and where the fraction is greater than a threshold (here, 0.05), that volume is censored from the regression model. +In most cases, censoring due to excessive “outliers” in a volume coincides with censoring due to excessive motion -- but not always. Both methods are used to be safe. + +No spatial smoothing was applied here during single subject processing. + +Spatial smoothing was applied later (to the individual subject-level effect size estimates “betas”) as part of AFNI's ETAC form of running 3dttest++ for group analysis and clustering, where it applied several different blurs (here, 0, 4, 6, and 8mm Gaussian FWHM applied inside the brain mask using an iterative approach), before combining those results to maintain an overall FPR. + +The list of subjects with number of retained TRs, percent of time points censored, and list of censored TRs is available in the spreadsheet here: +https://docs.google.com/spreadsheets/d/1_T_Y7xaaTV4O-AyUd-kN4hACCMJOAYuUFDqSy1WOcTw/edit?usp=sharing +The subjects not including in the group analysis were those shown in the output of: + gen_ss_review_table.py \ + -outlier_sep space \ + -report_outliers 'censor fraction' GE 0.1 \ + -report_outliers 'average censored motion' GE 0.1 \ + -report_outliers 'max censored displacement' GE 8 \ + -infiles sub*/s*.results/out.ss*.txt + + +We modelled the task using a canonical (only) basis function, AFNI's BLOCK model (an integrated gamma variate function), using response times as the individual event durations. HRF peaks varied, according to the convolution with the response times. +We used the following independent variables: +- for trials with a response, BLOCK, with duration equal to response time, and amplitude modulation parameters (leading to automatically generated parametrically modulated regressors) for gain and loss in dollars +- for trials without a response, BLOCK, with duration of 4 s (the total period in which a subject could respond) +Nuisance regressors: +- A Gaussian weighted local neighborhood of white matter (ANATICOR), leading to 1 voxel-dependent regressor +- Six motion parameters (degrees and mm) per run +- The baseline and temporal drift was modeled as Legendre polynomials of order 4, including 5 regressors per run. +- Generalized linear least squares (GLSQ) regression was carried out, with the temporal noise autocovariance modeled with voxelwise ARMA(1,1) parameters estimated from the GLSQ residuals at each voxel (i.e, REML). + + +The 9 hypotheses were evaluated with 4 group-level whole-brain two-sided t-tests and 1 between group test. The 4 whole-brain tests will be: + - Parametric effect of gain in the equal indifference group + - Parametric effect of gain in the equal range group + - Parametric effect of loss in the equal indifference group + - Parametric effect of loss in the equal range group +The between group test was a two-sided test of difference in the parametric effect of loss between the indifference group and the equal range group. + +""" + +afni_proc.py \ + -script ${expdir}/proc.${subject}.block \ + -scr_overwrite \ + -subj_id ${subject} \ + -out_dir ${expdir}/${subject}.results.block \ + -dsets ${datadir}/${subject}/func/${subject}_task-MGT_run-01_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-02_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-03_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-04_bold.nii.gz \ + -copy_anat ${datadir}/${subject}/anat/${subject}_T1w.nii.gz \ + -anat_has_skull yes \ + -blocks tshift align tlrc volreg mask scale regress \ + -despike_new yes \ + -tlrc_base MNI152_T1_2009c+tlrc \ + -tlrc_NL_warp \ + -align_opts_aea \ + -giant_move \ + -cost lpc+ZZ \ + -volreg_align_to MIN_OUTLIER \ + -volreg_tlrc_warp \ + -volreg_align_e2a \ + -blur_in_automask \ + -regress_stim_times \ + ${datadir}/${subject}/func/times+gain.1D \ + ${datadir}/${subject}/func/times+loss.1D \ + -regress_stim_types AM2 \ + -regress_stim_labels \ + GAIN \ + LOSS \ + -regress_basis \ + 'BLOCK(4,1)' \ + -mask_apply anat \ + -regress_motion_per_run \ + -test_stim_files no \ + -regress_opts_3dD \ + -GOFORIT 8 \ + -jobs 6 \ + -regress_censor_motion 0.2 \ + -regress_apply_mot_types demean deriv \ + -regress_censor_first_trs 3 \ + -regress_est_blur_errts \ + -execute + + + + + diff --git a/narps_open/pipelines/team_I9D6_wip.py b/narps_open/pipelines/team_I9D6_wip.py new file mode 100644 index 00000000..39db821c --- /dev/null +++ b/narps_open/pipelines/team_I9D6_wip.py @@ -0,0 +1,10 @@ +''' +created by team I9D6, reproduced by Narps reproducibility team +creation date: 27 June 2023 +needs script "team_I9D6.firstlevel" and "team_I9D6.secondlevel" +the team : AFNI Version 19.0.24 Tiberius +version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +Participants not included 016 +Last update: June 2023 +''' + From 54153acbf060c538f820c88df253e2249c6b8770 Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Tue, 7 Nov 2023 14:24:35 +0100 Subject: [PATCH 05/10] add last updates team 6VV2 repro afni --- narps_open/pipelines/team_6VV2.firstlevel | 8 ++++++-- notes.txt | 1 + 2 files changed, 7 insertions(+), 2 deletions(-) create mode 100644 notes.txt diff --git a/narps_open/pipelines/team_6VV2.firstlevel b/narps_open/pipelines/team_6VV2.firstlevel index f76890c7..f536b331 100755 --- a/narps_open/pipelines/team_6VV2.firstlevel +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -57,6 +57,10 @@ afni_proc.py \ -execute +# extract beta values +3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] +3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] - - +# convert BRIK to nii +3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc +3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc \ No newline at end of file diff --git a/notes.txt b/notes.txt new file mode 100644 index 00000000..8260c233 --- /dev/null +++ b/notes.txt @@ -0,0 +1 @@ +datalad get ./data/original/ds001734/sub-001 From aeff14b31eef619a6d36e97ee3050a02a639c08e Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Mon, 12 Feb 2024 10:25:24 +0100 Subject: [PATCH 06/10] update 6VV2_wip --- ...82c0418a5dc016fe0334a2c8f6_unfinished.json | 25 + .../_subject_id_001/afni_proc/_inputs.pklz | Bin 0 -> 303 bytes .../_subject_id_001/afni_proc/_node.pklz | Bin 0 -> 1294 bytes .../afni_proc/_report/report.rst | 23 + .../_0x4b88c28a232fe352aaa3991b95b3cbfc.json | 14 + .../create_stimuli/_inputs.pklz | Bin 0 -> 589 bytes 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00000000..d8d42f93 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_001/afni_proc/_0x40130b82c0418a5dc016fe0334a2c8f6_unfinished.json @@ -0,0 +1,25 @@ +[ + [ + "command", + [ + "/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel", + "d24bc0377b166d70c1e7e74f97b48e4b" + ] + ], + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def run(command, results_dir, subject, data_dir):\n import subprocess\n subject= \"sub-{}\".format(subject)\n subprocess.run([command, results_dir, subject, data_dir])\n print(\"Done\")\n" + ], + [ + "results_dir", + "/home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/" + ], + [ + "subject", + "001" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_001/afni_proc/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_001/afni_proc/_inputs.pklz new file mode 100644 index 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/home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 001 + diff --git a/Afni_proc_through_nipype/_subject_id_001/create_stimuli/_0x4b88c28a232fe352aaa3991b95b3cbfc.json b/Afni_proc_through_nipype/_subject_id_001/create_stimuli/_0x4b88c28a232fe352aaa3991b95b3cbfc.json new file mode 100644 index 00000000..bbc63a18 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_001/create_stimuli/_0x4b88c28a232fe352aaa3991b95b3cbfc.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "001" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_001/create_stimuli/_inputs.pklz 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(utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a005 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 002 + diff --git a/Afni_proc_through_nipype/_subject_id_002/afni_proc/result_afni_proc.pklz b/Afni_proc_through_nipype/_subject_id_002/afni_proc/result_afni_proc.pklz new file mode 100644 index 0000000000000000000000000000000000000000..6b38ac0ce5dcf8952887ff135b26a90dcfea3145 GIT binary patch literal 2890 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create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), 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b/Afni_proc_through_nipype/_subject_id_002/create_stimuli/_report/report.rst new file mode 100644 index 00000000..7047fcb1 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_002/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a005 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 002 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 002 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.013305 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_002/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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\"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "003" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_003/create_stimuli/_inputs.pklz 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import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 003 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 003 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012411 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_003/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : 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b/Afni_proc_through_nipype/_subject_id_004/create_stimuli/_0x332b1c6e5d406505a41b9862da82d3af.json new file mode 100644 index 00000000..2c2a4c80 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_004/create_stimuli/_0x332b1c6e5d406505a41b9862da82d3af.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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b/Afni_proc_through_nipype/_subject_id_004/create_stimuli/_report/report.rst new file mode 100644 index 00000000..87f3d3d5 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_004/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a004 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 004 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 004 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012438 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_004/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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+ +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 005 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 005 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.074299 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_005/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* 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/dev/null +++ b/Afni_proc_through_nipype/_subject_id_005/create_stimuli/_0x53e9f2ab37b004ea8655a036430b95db.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 005 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 005 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012852 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_005/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome 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pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 006 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 006 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.053228 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_006/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 008 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 008 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073152 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_008/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n 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data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, 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data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 009 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 009 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012112 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_009/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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/home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 010 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 010 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071658 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_010/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : 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"/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "010" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_010/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_010/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..b4db3a46b31e28673e2440838048df6bf562857d GIT binary patch literal 589 zcmV-T0BIV~oa@6Q#B!Bsr9ZKtI4s_cQwsm7F-82kvC5h(HwI$2o?}&CeIV zeqTK6&#trE*JVR;i7Cm1&w(fI^GUE*i z!Aw? z*Ew7qM_mz{S=Z8X?!gbY#loUQAZaP+5@MpiD=LJQrry=9lE~0EGVzU$zR{_^v7v8l z;u{}*<5PVTL*K;2H#zzy|MnefbYw3)SB{q)*2u=BK;LH^k|nYOH&LjZR!vRB@!9*t zac+0;Dw;2XR5e;y+uhsk?kGMCr|OXQS(9FBlDgnwNVl4#4p6lk36$DE1PYlxK!)SU 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literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_010/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_010/create_stimuli/_report/report.rst new file mode 100644 index 00000000..83ecefcb --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_010/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a024 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 010 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 010 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012319 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_010/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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+* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 011 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 011 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.07176 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_011/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* 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b/Afni_proc_through_nipype/_subject_id_011/create_stimuli/_0x562dae15b2074b2c0630186f6a706e0a.json new file mode 100644 index 00000000..2c07b8ca --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_011/create_stimuli/_0x562dae15b2074b2c0630186f6a706e0a.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 011 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 011 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012644 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_011/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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(utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a001 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 013 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 013 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.075128 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_013/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 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--- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_013/create_stimuli/_0xdef586efabfbe19760f7ee91bc0fdaea.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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b/Afni_proc_through_nipype/_subject_id_013/create_stimuli/_report/report.rst new file mode 100644 index 00000000..575005ec --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_013/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a001 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 013 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 013 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.013223 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_013/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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@@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a102 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 014 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 014 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012347 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, 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subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 015 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 015 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012287 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_015/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* 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b/Afni_proc_through_nipype/_subject_id_016/create_stimuli/_0x4506aaa53352c49a81e65aa0d9ecb066.json new file mode 100644 index 00000000..f212a5fd --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_016/create_stimuli/_0x4506aaa53352c49a81e65aa0d9ecb066.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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/dev/null +++ b/Afni_proc_through_nipype/_subject_id_016/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a015 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 016 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 016 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.01247 +* hostname : ptb-03230001.irisa.fr +* prev_wd : 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literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_017/afni_proc/_report/report.rst b/Afni_proc_through_nipype/_subject_id_017/afni_proc/_report/report.rst new file mode 100644 index 00000000..2ba3b7fd --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_017/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a056 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 017 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 017 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.074692 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_017/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "017" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_017/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_017/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..ba67ebb1caaf381e5f8944c1e85e72a1de2f4a2e GIT binary patch literal 589 zcmV-T00Mc`yxR+*8^UZdX{RPLVP;aqQt$zK86VSk@J!m&{UL7G=}_o2=jZzZhtr=g ze*M09)}3u@?_L)T%M|4-l}fZ^xPEYr>TDlw4b0!9|7D z-`6=@90#tXo?6$+a_+$oxB1-SOcG@Qbb%?;-zAsQN)qqtR!L~+8=ClrN8j*N-^kE6 zGVzU$zR{_^v7v8l;u{}*Qw17O~aFs=F{+Gr1>;Fio7#{ zia)l-;BS@4cU^KYyT7vZrt13jN3X5XwHmo-KUtT!l*C0#*q21?f8Cv?Qw6%@a|+ag zGG$vc&Il~ocK7novE4nN1RvVnMX%HDKKV;t5r0(@fU6syVNuJJ*My}ttw~84k-kp% bxu6TmaOvlA0$rlmZyWCqRO{YO_y_<1aFixS literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_017/create_stimuli/_node.pklz b/Afni_proc_through_nipype/_subject_id_017/create_stimuli/_node.pklz new file mode 100644 index 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pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 017 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 017 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012476 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_017/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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Exec ID : create_stimuli.a027 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 018 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 018 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012447 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_018/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* 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Co__@Z literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_019/afni_proc/_report/report.rst b/Afni_proc_through_nipype/_subject_id_019/afni_proc/_report/report.rst new file mode 100644 index 00000000..e766714d --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_019/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a059 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 019 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 019 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072389 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_019/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "020" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_020/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_020/create_stimuli/_inputs.pklz new file mode 100644 index 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 021 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 021 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072532 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_021/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : 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b/Afni_proc_through_nipype/_subject_id_021/create_stimuli/_0x2035f23ddf2da6815786e483128949d6.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 022 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 022 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072042 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_022/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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b/Afni_proc_through_nipype/_subject_id_022/create_stimuli/_0x27d39a75b3df3dee233986845c0d00be.json new file mode 100644 index 00000000..54aac9f4 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_022/create_stimuli/_0x27d39a75b3df3dee233986845c0d00be.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, 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b/Afni_proc_through_nipype/_subject_id_024/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a061 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 024 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 024 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012228 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_024/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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b/Afni_proc_through_nipype/_subject_id_025/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a079 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 025 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 025 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012355 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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Exec ID : afni_proc.a028 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 026 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 026 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073277 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_026/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* 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subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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b/Afni_proc_through_nipype/_subject_id_027/create_stimuli/_0x8535316d7b3edd0392f612e06a6f297b.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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a/Afni_proc_through_nipype/_subject_id_027/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_027/create_stimuli/_report/report.rst new file mode 100644 index 00000000..1622ed0b --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_027/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a084 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 027 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 027 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012305 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_027/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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b/Afni_proc_through_nipype/_subject_id_029/afni_proc/_report/report.rst new file mode 100644 index 00000000..a7aa7a5e --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_029/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a010 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 029 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 029 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073317 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_029/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* 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+ df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 029 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 029 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012369 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_029/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 030 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 030 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.07302 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_030/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = 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ID : create_stimuli.a068 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 030 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 030 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012212 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_030/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* 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file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "033" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_033/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_033/create_stimuli/_inputs.pklz new file mode 100644 index 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\"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "036" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_036/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_036/create_stimuli/_inputs.pklz new file mode 100644 index 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n5%?QMz1KN`7#JY|m<_K|5Z9vBZT{_FndklsAP_X{>JI<_Xs+^7 literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_036/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_036/create_stimuli/_report/report.rst new file mode 100644 index 00000000..b7175d91 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_036/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a099 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 036 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 036 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012482 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_036/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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\"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "037" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_037/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_037/create_stimuli/_inputs.pklz new file mode 100644 index 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b/Afni_proc_through_nipype/_subject_id_037/create_stimuli/_report/report.rst new file mode 100644 index 00000000..13c82a89 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_037/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a088 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 037 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 037 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012266 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_037/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 038 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 038 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073271 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_038/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), 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b/Afni_proc_through_nipype/_subject_id_038/create_stimuli/_report/report.rst new file mode 100644 index 00000000..7093a954 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_038/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a008 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 038 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 038 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.01271 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_038/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 039 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 039 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072638 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_039/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* 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\"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "039" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_039/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_039/create_stimuli/_inputs.pklz new file mode 100644 index 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n1pfEq!JC3W4vdfp%*IzK$ZOH^w)pnfJaGR7+vL)?>JI<_`O@Xj literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_039/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_039/create_stimuli/_report/report.rst new file mode 100644 index 00000000..fc930186 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_039/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a066 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 039 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 039 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.01236 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_039/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a032 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 041 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 041 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012978 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_041/create_stimuli + + +Environment 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"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 043 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 043 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.013179 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_043/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a050 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 044 + diff --git a/Afni_proc_through_nipype/_subject_id_044/afni_proc/result_afni_proc.pklz b/Afni_proc_through_nipype/_subject_id_044/afni_proc/result_afni_proc.pklz new file mode 100644 index 0000000000000000000000000000000000000000..7232492185cd8dbeca24bd734e9b930cc364e82e GIT binary patch literal 2888 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"data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], 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zt#Se?cdfkXAS?#bv~R;+K?f8rUdAlv6v*KhR_+{aQh@QWwk{{5$U{?f~c*(43t zReQw(xoqUUL%LB5Z#~%R^}ODehaWx+dN}O)xa|`!2yhn^xV48nTvcYXgmFyY6mb|6 l_#efCHwA$l7$G5;jjvLW*P`WZ@g2#1_g^-7kQnL@007Ay$P)kn literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_044/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_044/create_stimuli/_report/report.rst new file mode 100644 index 00000000..47d74938 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_044/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a050 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 044 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 044 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012737 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_044/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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+++ b/Afni_proc_through_nipype/_subject_id_045/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a076 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 045 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 045 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012441 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_045/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 046 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 046 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.122185 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_046/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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b/Afni_proc_through_nipype/_subject_id_046/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a006 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 046 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 046 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012248 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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create_stimuli.a039 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 047 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 047 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012221 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_047/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, 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b/Afni_proc_through_nipype/_subject_id_049/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a034 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 049 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 049 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012481 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_049/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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a/Afni_proc_through_nipype/_subject_id_050/afni_proc/_report/report.rst b/Afni_proc_through_nipype/_subject_id_050/afni_proc/_report/report.rst new file mode 100644 index 00000000..0ad397e5 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_050/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a069 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 050 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 050 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072965 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_050/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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b/Afni_proc_through_nipype/_subject_id_050/create_stimuli/_0xc20abc29a7f2cfb3c129121baaa625bb.json new file mode 100644 index 00000000..29ba639e --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_050/create_stimuli/_0xc20abc29a7f2cfb3c129121baaa625bb.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a069 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 050 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 050 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012405 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_050/create_stimuli + + +Environment 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b/Afni_proc_through_nipype/_subject_id_051/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a089 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 051 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 051 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012498 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n 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file mode 100644 index 00000000..73299fa5 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_053/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a012 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 053 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 053 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073039 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_053/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* 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b/Afni_proc_through_nipype/_subject_id_053/create_stimuli/_0xa8b26774dc1bbda1ac991b50707e62e8.json new file mode 100644 index 00000000..b63d1416 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_053/create_stimuli/_0xa8b26774dc1bbda1ac991b50707e62e8.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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b/Afni_proc_through_nipype/_subject_id_053/create_stimuli/_report/report.rst new file mode 100644 index 00000000..d066c13a --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_053/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a012 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 053 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 053 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012302 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_053/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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\"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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+============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a106 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 054 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 054 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.013562 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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+========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a026 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 055 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 055 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071081 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_055/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "055" + ] +] \ No newline at end of file diff --git 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+Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 055 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 055 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012851 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_055/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* 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data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 056 + diff --git a/Afni_proc_through_nipype/_subject_id_056/afni_proc/result_afni_proc.pklz b/Afni_proc_through_nipype/_subject_id_056/afni_proc/result_afni_proc.pklz new file mode 100644 index 0000000000000000000000000000000000000000..67037bd998a8da60d93b6a73ac6c2c5f3e31284f GIT binary patch literal 2894 zcmV-U3$gSciwFpU%z9-4|8iw>b!>EBVP?7if9PxfK;QdUdS;j08A`Sz6o~*~znM96=A1KUX1*EzZuKvJ_;4lpi#~Qt z@61EI=>*6hYC6LFK*NZ~q35}N5J$Hgi*@sg*mRw^et%`I z?nb63jy5i<4g=FNgEM~WYn}(4<7oXTbo78I`Ewkt`Joe-Hj2k9(X|KAFs7rusZWhK zIu^#Rjf58#8iI8L!O?sVtFDI})iXV0nGV82W$2iy=exQZjD0s8jn&i=LB-+V1=0i6 zG*oe?Bxnmku)_#_EwQ8i`9J^m?LYqdpKqfzmQv2t5e(?UQO;?(-Xj;ypR zEvWg47YuS@K`KB)o;Q6HYy1#~x>N7hWaX$KKU6z?rQ28H=-PAiOtj_{8~2W!=a(t&{AO7s$Kj^?;=^k(-- 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\"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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b/Afni_proc_through_nipype/_subject_id_057/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a036 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 057 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 057 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072067 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_057/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* 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\"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "057" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_057/create_stimuli/_inputs.pklz 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"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 057 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 057 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012327 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_057/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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b/Afni_proc_through_nipype/_subject_id_058/create_stimuli/_0x01e5b8dd24756ed0c0fe3629cc71eb3c.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 058 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 058 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012335 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_058/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome 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create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), 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create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a093 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 060 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 060 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012353 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_060/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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/home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 061 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 061 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.07261 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_061/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : 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pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 061 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 061 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012638 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_061/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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\"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "062" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_062/create_stimuli/_inputs.pklz 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+* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 063 + diff --git a/Afni_proc_through_nipype/_subject_id_063/afni_proc/result_afni_proc.pklz b/Afni_proc_through_nipype/_subject_id_063/afni_proc/result_afni_proc.pklz new file mode 100644 index 0000000000000000000000000000000000000000..9ceceeca1b91213446e2ecb7e8638f0c54a558e0 GIT binary patch literal 2891 zcmV-R3$*kfiwFpU%z9-4|8iw>b!>EBVPhMIJNx$J-~ae;w1#Y5#^yvH3cOIr<%L|nDD!)jLaD+Ftgu(! zE0$s`HZeTtiOswrJ*qdGade9t7&Zr?9771Dx+IC6w$iG$tBraujy^XXO*OgDHfEIv zTwu8zD<0N!xXk5+VmZH^z@+`EX3&4wX?A*Yz1IR9cp=gp)A8cytw*9HA9mVuuLD-x zHb%DNAw6^<)OSy64W(6Y_myt1ek7j6(M@QzP!7Duy(ICAdK|6hd7j5L9Z7CiTTt^0 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[ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, 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-0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a055 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 063 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 063 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.01242 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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+--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 064 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 064 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012346 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_064/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 066 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 066 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.078029 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_066/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : 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"/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "066" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_066/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_066/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..1e2913f1022e93d27fd8a59e1e8b9edd531111ef GIT binary patch literal 589 zcmV-T0BIV~oa@6Q#B!Bsr9Zzt{1$=h!~Rj5EE$T@-%sb{!uDx8(LLbhmbRw$P)D4>K{fw}YP z4N&LZAsd7ca}q1xik9K!wMkT=rQjiiyslY}MryWyTv4 zf~l(V6s5>=v9?vz?j>AcDY5Zp>+3i1_xDUf@qPUD%ayJk2VsWRh)Cf{v9`RD@*2v& zuXDIKj=CZ?wXUV*Jb)i=^SMQdK+;ms1;j*uS5ycqO}(o-C6S?TWa1kgeWO!-V?*EA z#5X?r#;5uwhQ5i3Z*ufa{_We>=*V7prW`LhtdWgLfqqOmBnxB*ZlX{*t(uyMnW)kkK$Q9!AC{$aol;3?q~OKWpOG@phik@qH0 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b/Afni_proc_through_nipype/_subject_id_066/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a045 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 066 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 066 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012534 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_066/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n 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Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a022 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 071 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 071 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012329 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_071/create_stimuli + + +Environment 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/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 072 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 072 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071506 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_072/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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b/Afni_proc_through_nipype/_subject_id_074/afni_proc/_report/report.rst new file mode 100644 index 00000000..464fcac4 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_074/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a067 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 074 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 074 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071973 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_074/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* 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pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, 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Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a067 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 074 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 074 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012461 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_074/create_stimuli + + +Environment 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00000000..0a99650d --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_076/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a021 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 076 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 076 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.0755 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_076/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : 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b/Afni_proc_through_nipype/_subject_id_076/create_stimuli/_0x1db59509511bb4dca10d238592ee3904.json new file mode 100644 index 00000000..a6132ae8 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_076/create_stimuli/_0x1db59509511bb4dca10d238592ee3904.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 077 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 077 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.076068 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_077/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : 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new file mode 100644 index 00000000..cec6e98c --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_077/create_stimuli/_0x739c4a8b07a5681b1aaad919d61e986f.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n 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import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 079 + diff --git a/Afni_proc_through_nipype/_subject_id_079/afni_proc/result_afni_proc.pklz b/Afni_proc_through_nipype/_subject_id_079/afni_proc/result_afni_proc.pklz new file mode 100644 index 0000000000000000000000000000000000000000..06e4a159d7ae08a0a71894f89fee38f548509365 GIT binary patch literal 2893 zcmV-T3$pYdiwFpT%z9-4|8iw>b!>EBVPeA9>Rg?N8d(Ue~i9~Hp6vgf;?tCY#G-3$nOZ&KJvKme1z* z3VX$fh)oO+dJ;2lNRMjGW)$8M28Jy_D8~>&sU}H{PFrbJ+Ld~(7logjj;5MIU>mdY z1Hrdkfo~kvGNdeIbA?iNJBD%lRn4IPu+!}HYU!YMlQ40|MC5}>sssreN2K%ha$6O!l*u^9&uzEgvU-9Bk` zs*R&YttWwj4-D(T7zD(zYE619ce=_v&R|FE7&us~HslTj{7$TwXtPz@iNZI#PpeV* z&T=+^ADgT z{7jzDlLB;>o=I}8RaI&ywL_)b0Gn=Pb33^rahAld(`(4jqHz0C{CF$yVOeEP=3}XW zKjxc_O6MpSh40dt=>h2UYIJJW>(!RhthDQpE3j(%65p4PGP^MGk2=KhOEFpROSRsm 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00000000..dc3b8167 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_079/create_stimuli/_0x29b01735ef28de5158cd338cee9a79f8.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "079" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_079/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_079/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..da47a38898aad1e956dca99dda9a8e6ce83baf83 GIT binary patch literal 590 zcmV-U0OLk$p>TVW=j4>KpPL$e`kmOJr0{wt2-OrqV7|Ds#dEic_iU>sUeVk*s-28s^ z=jQB1cQ&oPeOoppmza`FNZx+`r9uTNLCz7BNIk=KQ{k+{6|zNhy+pZmK>;Pq3e26) 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b/Afni_proc_through_nipype/_subject_id_079/create_stimuli/_report/report.rst new file mode 100644 index 00000000..70b979bc --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_079/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a035 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 079 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 079 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012417 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_079/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "080" + ] +] \ No newline at end of file diff --git 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a/Afni_proc_through_nipype/_subject_id_080/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_080/create_stimuli/_report/report.rst new file mode 100644 index 00000000..a3c27acd --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_080/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a107 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 080 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 080 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012766 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_080/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a000 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 082 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 082 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.094263 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_082/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* 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a/Afni_proc_through_nipype/_subject_id_082/create_stimuli/_0xa4f037b6d5ff386c5e97b1d3eb987752.json b/Afni_proc_through_nipype/_subject_id_082/create_stimuli/_0xa4f037b6d5ff386c5e97b1d3eb987752.json new file mode 100644 index 00000000..1fd196b7 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_082/create_stimuli/_0xa4f037b6d5ff386c5e97b1d3eb987752.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "082" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_082/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_082/create_stimuli/_inputs.pklz new file mode 100644 index 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b/Afni_proc_through_nipype/_subject_id_083/create_stimuli/_report/report.rst new file mode 100644 index 00000000..1ce2fb38 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_083/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a086 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 083 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 083 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012327 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_083/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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"/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 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import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n 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pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 085 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 085 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.01371 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_085/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "087" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_087/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_087/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..06777e7df38f726947f74eaac98a264a6c128ab0 GIT binary patch literal 590 zcmV-U0TVW=j4>KpPL$e`kmOJr0{wt2-OrqV7|Ds#dEic_iU>sUeVk*s-28s^ z=jQB1cQ&oPeOoppmza`FNZx+`r9uTNLCz7BNIk=KQ{k+{6|zNhy+pZmK>;Pq3e26) zZ-6@Q_Sqnuf_(wd1z;D(HKSYt21x-0P#;!+E>Ln>11dZQ<)Y78QcQFXWy>z7C^O!W z5KL5+rzl01iHt-%kwB^SM4*uABV;&? zjE0es2{IZ+#>2?i1Q`z_lVN1?A4okPX49ZMoM;+!t7D~4G!4&2noq;Ck>=CzB=X(_ zO8V3qQ-7;SeCU$H>BE(!H&xfKKYDGAuH?uCyUDtMl|U|7sC|j}?$`ZkI#!@dKBWNT zm`K~2Qi9ZyZMU!Y9oy~8;L~}#J?nMa?H7MRYveC0q~P+}Cy+CdQHDsyFhdn4NccM4 cryS2Qft6o~APCRn#BUq#7F|`LGx!Jq08vsKssI20 literal 0 HcmV?d00001 diff --git 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@@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a092 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 087 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 087 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012249 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_087/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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\"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "088" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_088/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_088/create_stimuli/_inputs.pklz new file mode 100644 index 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+--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 088 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 088 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012223 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_088/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 089 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 089 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071698 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_089/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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a/Afni_proc_through_nipype/_subject_id_089/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_089/create_stimuli/_report/report.rst new file mode 100644 index 00000000..f0e50dae --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_089/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a003 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 089 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 089 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.013129 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_089/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 090 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 090 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info 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b/Afni_proc_through_nipype/_subject_id_090/create_stimuli/_0xfc610037c834d75e2eaf02a6b1596ead.json new file mode 100644 index 00000000..3e5f3d52 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_090/create_stimuli/_0xfc610037c834d75e2eaf02a6b1596ead.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 090 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 090 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012333 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_090/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome 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+* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 092 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 092 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.074907 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_092/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "092" + ] +] \ No newline at end of file diff --git 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pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 092 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 092 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.01263 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_092/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : 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E0A(?Hpa1{> literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_093/afni_proc/_report/report.rst b/Afni_proc_through_nipype/_subject_id_093/afni_proc/_report/report.rst new file mode 100644 index 00000000..ee7f7129 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_093/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a020 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 093 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 093 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073071 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_093/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : 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\"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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b/Afni_proc_through_nipype/_subject_id_094/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a065 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 094 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 094 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012521 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_095/create_stimuli/_0x17cd4e6d0f884c5d89823ded883720b8.json b/Afni_proc_through_nipype/_subject_id_095/create_stimuli/_0x17cd4e6d0f884c5d89823ded883720b8.json new file mode 100644 index 00000000..9b003529 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_095/create_stimuli/_0x17cd4e6d0f884c5d89823ded883720b8.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "095" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_095/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_095/create_stimuli/_inputs.pklz new file mode 100644 index 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df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "096" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_096/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_096/create_stimuli/_inputs.pklz new file mode 100644 index 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b/Afni_proc_through_nipype/_subject_id_096/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a025 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 096 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 096 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012373 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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\"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "098" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_098/create_stimuli/_inputs.pklz 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+1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a101 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 098 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 098 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012997 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_098/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 099 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 099 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012344 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_099/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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lA4a{`Ie{1$Apw|;u2K-!qSbBw!`sYr{{z$ndsONV008;9+#dh{ literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_100/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_100/create_stimuli/_report/report.rst new file mode 100644 index 00000000..c2956956 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_100/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a073 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 100 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 100 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012565 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_100/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : 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--git a/Afni_proc_through_nipype/_subject_id_102/afni_proc/_report/report.rst b/Afni_proc_through_nipype/_subject_id_102/afni_proc/_report/report.rst new file mode 100644 index 00000000..c444e66f --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_102/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a051 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 102 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 102 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072565 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_102/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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b/Afni_proc_through_nipype/_subject_id_102/create_stimuli/_0xdd8761564040ddbfdd0333c88f5b5d04.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = 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b/Afni_proc_through_nipype/_subject_id_102/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a051 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 102 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 102 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.035142 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_102/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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+++ b/Afni_proc_through_nipype/_subject_id_103/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a075 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 103 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 103 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012406 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_103/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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zz|mgq_3;<4kH^4A(m8V}?pr*5Bwc$JWXVwX*7z%-S(RWz~t{ydrs}qE6zq1u=k*z2QHrM~S;9D` rZ;CjK3H*=Z{+oh84vdfx%tlu!$ZOW}w)pn1+;{&4$JI<_YB}e< literal 0 HcmV?d00001 diff --git a/Afni_proc_through_nipype/_subject_id_104/create_stimuli/_report/report.rst b/Afni_proc_through_nipype/_subject_id_104/create_stimuli/_report/report.rst new file mode 100644 index 00000000..9485445f --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_104/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a085 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 104 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 104 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.0124 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_104/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* 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command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 105 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 105 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073479 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_105/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* 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b/Afni_proc_through_nipype/_subject_id_105/create_stimuli/_report/report.rst new file mode 100644 index 00000000..72c172ea --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_105/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a043 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 105 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 105 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012343 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_105/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 106 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 106 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071412 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_106/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 106 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 106 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.033148 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_106/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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\"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n 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sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "108" + ] +] \ No 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\"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "109" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_109/create_stimuli/_inputs.pklz 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00000000..5f9aac27 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_109/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a098 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 109 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 109 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012314 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_109/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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b/Afni_proc_through_nipype/_subject_id_110/afni_proc/_report/report.rst new file mode 100644 index 00000000..60e67285 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_110/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a033 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 110 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 110 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.074748 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_110/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* 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\"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "110" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_110/create_stimuli/_inputs.pklz 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b/Afni_proc_through_nipype/_subject_id_112/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a080 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 112 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 112 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012405 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_112/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : 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\"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "113" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_113/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_113/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..b8795e210f69b6f0713c8cc8b65b030f5ae7842c GIT binary patch literal 590 zcmV-U0|d7+$t9*F6Oy-If2dG_N|18|B~s6D-BdU$afKYw+^kV9Jy1XivjTJX z<13)fn?p7T=ipEPbOGqYxMq|~z#u800P4dE&;?3PYe0q1pj-`EYl?}^p={md6lKO6 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import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 113 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 113 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012502 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_113/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : 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function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 114 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 114 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071345 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_114/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m 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b/Afni_proc_through_nipype/_subject_id_114/create_stimuli/_report/report.rst new file mode 100644 index 00000000..66663356 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_114/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a048 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 114 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 114 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012435 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_114/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : 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pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "115" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_115/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_115/create_stimuli/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..aceab530517ff969d20ce3332d0c9c117df659a3 GIT binary patch literal 591 zcmV-V0E$0Dzf1A%ON(7RYf-WE?`n#k;SV`ht+$jkSeM1x9@ZcLB>l+#R zMkc<|!8bbAH#YQ*O?=~nZ~SlHzD7rO!ZYP~&S8aYOmg&d${|@Gd*a3lmC>@Uh&Vj^ z6g$q{4qi#K`6N+|=GJEWezQG@_rs|=Bwg01lNu#1cpTELMu`JdtwsW+))Rq3CXbN8 zFftrQh9<~x7#R&CBNJpajEsko@qZxoe3(sx?r@@M(5;S@KG8Hh8)-fb&qkV0!;{E+ z6Da9ZYfSyEBJrV14rUKmmflodzy9d8HM)``7wjhM9F_vPV5#;c;=5n>r|DRMF8P!K zjAJ5gYeorDOSWxZ?>n~5%OLpJHfOy~+kEwxv_k%>L<%mieF8ZXDP@SH3^P<>f`qTr deai6y6IlAWm`sAtQS7(1cMEVNh+X&y001RN7z_Xa literal 0 HcmV?d00001 diff --git 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import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 115 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 115 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012539 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_115/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 116 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 116 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071015 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_116/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : 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"data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = 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Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a042 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 116 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 116 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.013775 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_116/create_stimuli + + +Environment 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b/Afni_proc_through_nipype/_subject_id_117/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a057 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 117 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 117 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.071836 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_117/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* 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b/Afni_proc_through_nipype/_subject_id_117/create_stimuli/_0xbb6302e2f4b1767c0bfe70340f1011d9.json new file mode 100644 index 00000000..69bcf607 --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_117/create_stimuli/_0xbb6302e2f4b1767c0bfe70340f1011d9.json @@ -0,0 +1,14 @@ +[ + [ + "data_dir", + "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" + ], + [ + "function_str", + "def create_stimuli_file(subject, data_dir):\n # create 1D stimuli file :\n import pandas as pd \n from os.path import join as opj\n df_run1 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-01_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run1 = df_run1[[\"onset\", \"gain\", \"loss\"]].T\n df_run2 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-02_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run2 = df_run2[[\"onset\", \"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 118 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 118 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.073461 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_118/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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/home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 118 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 118 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012219 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_118/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* 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b/Afni_proc_through_nipype/_subject_id_120/create_stimuli/_report/report.rst @@ -0,0 +1,170 @@ +Node: create_stimuli (utility) +============================== + + + Hierarchy : Afni_proc_through_nipype.create_stimuli + Exec ID : create_stimuli.a097 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 120 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 120 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012304 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* 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b/Afni_proc_through_nipype/_subject_id_121/afni_proc/_report/report.rst new file mode 100644 index 00000000..090166bc --- /dev/null +++ b/Afni_proc_through_nipype/_subject_id_121/afni_proc/_report/report.rst @@ -0,0 +1,126 @@ +Node: afni_proc (utility) +========================= + + + Hierarchy : Afni_proc_through_nipype.afni_proc + Exec ID : afni_proc.a031 + + +Original Inputs +--------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 121 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 121 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.076281 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_121/afni_proc + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* 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create_stimuli.a031 + + +Original Inputs +--------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 121 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 121 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012563 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_121/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 123 + + +Execution Inputs +---------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def run(command, results_dir, subject, data_dir): + import subprocess + subject= "sub-{}".format(subject) + subprocess.run([command, results_dir, subject, data_dir]) + print("Done") + +* results_dir : /home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/ +* subject : 123 + + +Execution Outputs +----------------- + + +* Adni_1stLevel : None + + +Runtime info +------------ + + +* duration : 0.072011 +* hostname : ptb-03230001.irisa.fr +* 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\"gain\", \"loss\"]].T\n df_run3 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-03_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run3 = df_run3[[\"onset\", \"gain\", \"loss\"]].T\n df_run4 = pd.read_csv(opj(data_dir, \"sub-{}/func/sub-{}_task-MGT_run-04_events.tsv\".format(subject, subject)), sep=\"\\t\")\n df_run4 = df_run4[[\"onset\", \"gain\", \"loss\"]].T\n\n df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_gain.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)]\n df_gain.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)]\n df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64))\n df_loss.loc[0] = [\"{}*{}\".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[1] = [\"{}*{}\".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[2] = [\"{}*{}\".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)]\n df_loss.loc[3] = [\"{}*{}\".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)]\n\n df_gain.to_csv(opj(data_dir, \"sub-{}/func/times+gain.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n df_loss.to_csv(opj(data_dir, \"sub-{}/func/times+loss.1D\".format(subject)), \n sep='\\t', index=False, header=False)\n print(\"Done\")\n" + ], + [ + "subject", + "124" + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/_subject_id_124/create_stimuli/_inputs.pklz b/Afni_proc_through_nipype/_subject_id_124/create_stimuli/_inputs.pklz new file mode 100644 index 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df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 124 + + +Execution Inputs +---------------- + + +* data_dir : /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +* function_str : def create_stimuli_file(subject, data_dir): + # create 1D stimuli file : + import pandas as pd + from os.path import join as opj + df_run1 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-01_events.tsv".format(subject, subject)), sep="\t") + df_run1 = df_run1[["onset", "gain", "loss"]].T + df_run2 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-02_events.tsv".format(subject, subject)), sep="\t") + df_run2 = df_run2[["onset", "gain", "loss"]].T + df_run3 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-03_events.tsv".format(subject, subject)), sep="\t") + df_run3 = df_run3[["onset", "gain", "loss"]].T + df_run4 = pd.read_csv(opj(data_dir, "sub-{}/func/sub-{}_task-MGT_run-04_events.tsv".format(subject, subject)), sep="\t") + df_run4 = df_run4[["onset", "gain", "loss"]].T + + df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] + df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] + df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) + df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] + df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + df_gain.to_csv(opj(data_dir, "sub-{}/func/times+gain.1D".format(subject)), + sep='\t', index=False, header=False) + df_loss.to_csv(opj(data_dir, "sub-{}/func/times+loss.1D".format(subject)), + sep='\t', index=False, header=False) + print("Done") + +* subject : 124 + + +Execution Outputs +----------------- + + +* Stimuli : None + + +Runtime info +------------ + + +* duration : 0.012064 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/_subject_id_124/create_stimuli + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : 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{ + var i = list.length, array = new Array(i); + while (i--) array[i] = list[i]; + return array; + }; + } + try { + d3_document.createElement("div").style.setProperty("opacity", 0, ""); + } catch (error) { + var d3_element_prototype = d3_window.Element.prototype, d3_element_setAttribute = d3_element_prototype.setAttribute, d3_element_setAttributeNS = d3_element_prototype.setAttributeNS, d3_style_prototype = d3_window.CSSStyleDeclaration.prototype, d3_style_setProperty = d3_style_prototype.setProperty; + d3_element_prototype.setAttribute = function(name, value) { + d3_element_setAttribute.call(this, name, value + ""); + }; + d3_element_prototype.setAttributeNS = function(space, local, value) { + d3_element_setAttributeNS.call(this, space, local, value + ""); + }; + d3_style_prototype.setProperty = function(name, value, priority) { + d3_style_setProperty.call(this, name, value + "", priority); + }; + } + d3.ascending = d3_ascending; + function d3_ascending(a, b) { + return a < b ? -1 : a > b ? 1 : a >= b ? 0 : NaN; + } + d3.descending = function(a, b) { + return b < a ? -1 : b > a ? 1 : b >= a ? 0 : NaN; + }; + d3.min = function(array, f) { + var i = -1, n = array.length, a, b; + if (arguments.length === 1) { + while (++i < n && !((a = array[i]) != null && a <= a)) a = undefined; + while (++i < n) if ((b = array[i]) != null && a > b) a = b; + } else { + while (++i < n && !((a = f.call(array, array[i], i)) != null && a <= a)) a = undefined; + while (++i < n) if ((b = f.call(array, array[i], i)) != null && a > b) a = b; + } + return a; + }; + d3.max = function(array, f) { + var i = -1, n = array.length, a, b; + if (arguments.length === 1) { + while (++i < n && !((a = array[i]) != null && a <= a)) a = undefined; + while (++i < n) if ((b = array[i]) != null && b > a) a = b; + } else { + while (++i < n && !((a = f.call(array, array[i], i)) != null && a <= a)) a = undefined; + while (++i < n) if ((b = f.call(array, array[i], i)) != null && b > a) a = b; + } + return a; + }; + d3.extent = function(array, f) { + var i = -1, n = array.length, a, b, c; + if (arguments.length === 1) { + while (++i < n && !((a = c = array[i]) != null && a <= a)) a = c = undefined; + while (++i < n) if ((b = array[i]) != null) { + if (a > b) a = b; + if (c < b) c = b; + } + } else { + while (++i < n && !((a = c = f.call(array, array[i], i)) != null && a <= a)) a = undefined; + while (++i < n) if ((b = f.call(array, array[i], i)) != null) { + if (a > b) a = b; + if (c < b) c = b; + } + } + return [ a, c ]; + }; + d3.sum = function(array, f) { + var s = 0, n = array.length, a, i = -1; + if (arguments.length === 1) { + while (++i < n) if (!isNaN(a = +array[i])) s += a; + } else { + while (++i < n) if (!isNaN(a = +f.call(array, array[i], i))) s += a; + } + return s; + }; + function d3_number(x) { + return x != null && !isNaN(x); + } + d3.mean = function(array, f) { + var s = 0, n = array.length, a, i = -1, j = n; + if (arguments.length === 1) { + while (++i < n) if (d3_number(a = array[i])) s += a; else --j; + } else { + while (++i < n) if (d3_number(a = f.call(array, array[i], i))) s += a; else --j; + } + return j ? s / j : undefined; + }; + d3.quantile = function(values, p) { + var H = (values.length - 1) * p + 1, h = Math.floor(H), v = +values[h - 1], e = H - h; + return e ? v + e * (values[h] - v) : v; + }; + d3.median = function(array, f) { + if (arguments.length > 1) array = array.map(f); + array = array.filter(d3_number); + return array.length ? d3.quantile(array.sort(d3_ascending), .5) : undefined; + }; + function d3_bisector(compare) { + return { + left: function(a, x, lo, hi) { + if (arguments.length < 3) lo = 0; + if (arguments.length < 4) hi = a.length; + while (lo < hi) { + var mid = lo + hi >>> 1; + if (compare(a[mid], x) < 0) lo = mid + 1; else hi = mid; + } + return lo; + }, + right: function(a, x, lo, hi) { + if (arguments.length < 3) lo = 0; + if (arguments.length < 4) hi = a.length; + while (lo < hi) { + var mid = lo + hi >>> 1; + if (compare(a[mid], x) > 0) hi = mid; else lo = mid + 1; + } + return lo; + } + }; + } + var d3_bisect = d3_bisector(d3_ascending); + d3.bisectLeft = d3_bisect.left; + d3.bisect = d3.bisectRight = d3_bisect.right; + d3.bisector = function(f) { + return d3_bisector(f.length === 1 ? function(d, x) { + return d3_ascending(f(d), x); + } : f); + }; + d3.shuffle = function(array) { + var m = array.length, t, i; + while (m) { + i = Math.random() * m-- | 0; + t = array[m], array[m] = array[i], array[i] = t; + } + return array; + }; + d3.permute = function(array, indexes) { + var i = indexes.length, permutes = new Array(i); + while (i--) permutes[i] = array[indexes[i]]; + return permutes; + }; + d3.pairs = function(array) { + var i = 0, n = array.length - 1, p0, p1 = array[0], pairs = new Array(n < 0 ? 0 : n); + while (i < n) pairs[i] = [ p0 = p1, p1 = array[++i] ]; + return pairs; + }; + d3.zip = function() { + if (!(n = arguments.length)) return []; + for (var i = -1, m = d3.min(arguments, d3_zipLength), zips = new Array(m); ++i < m; ) { + for (var j = -1, n, zip = zips[i] = new Array(n); ++j < n; ) { + zip[j] = arguments[j][i]; + } + } + return zips; + }; + function d3_zipLength(d) { + return d.length; + } + d3.transpose = function(matrix) { + return d3.zip.apply(d3, matrix); + }; + d3.keys = function(map) { + var keys = []; + for (var key in map) keys.push(key); + return keys; + }; + d3.values = function(map) { + var values = []; + for (var key in map) values.push(map[key]); + return values; + }; + d3.entries = function(map) { + var entries = []; + for (var key in map) entries.push({ + key: key, + value: map[key] + }); + return entries; + }; + d3.merge = function(arrays) { + var n = arrays.length, m, i = -1, j = 0, merged, array; + while (++i < n) j += arrays[i].length; + merged = new Array(j); + while (--n >= 0) { + array = arrays[n]; + m = array.length; + while (--m >= 0) { + merged[--j] = array[m]; + } + } + return merged; + }; + var abs = Math.abs; + d3.range = function(start, stop, step) { + if (arguments.length < 3) { + step = 1; + if (arguments.length < 2) { + stop = start; + start = 0; + } + } + if ((stop - start) / step === Infinity) throw new Error("infinite range"); + var range = [], k = d3_range_integerScale(abs(step)), i = -1, j; + start *= k, stop *= k, step *= k; + if (step < 0) while ((j = start + step * ++i) > stop) range.push(j / k); else while ((j = start + step * ++i) < stop) range.push(j / k); + return range; + }; + function d3_range_integerScale(x) { + var k = 1; + while (x * k % 1) k *= 10; + return k; + } + function d3_class(ctor, properties) { + try { + for (var key in properties) { + Object.defineProperty(ctor.prototype, key, { + value: properties[key], + enumerable: false + }); + } + } catch (e) { + ctor.prototype = properties; + } + } + d3.map = function(object) { + var map = new d3_Map(); + if (object instanceof d3_Map) object.forEach(function(key, value) { + map.set(key, value); + }); else for (var key in object) map.set(key, object[key]); + return map; + }; + function d3_Map() {} + d3_class(d3_Map, { + has: d3_map_has, + get: function(key) { + return this[d3_map_prefix + key]; + }, + set: function(key, value) { + return this[d3_map_prefix + key] = value; + }, + remove: d3_map_remove, + keys: d3_map_keys, + values: function() { + var values = []; + this.forEach(function(key, value) { + values.push(value); + }); + return values; + }, + entries: function() { + var entries = []; + this.forEach(function(key, value) { + entries.push({ + key: key, + value: value + }); + }); + return entries; + }, + size: d3_map_size, + empty: d3_map_empty, + forEach: function(f) { + for (var key in this) if (key.charCodeAt(0) === d3_map_prefixCode) f.call(this, key.substring(1), this[key]); + } + }); + var d3_map_prefix = "\x00", d3_map_prefixCode = d3_map_prefix.charCodeAt(0); + function d3_map_has(key) { + return d3_map_prefix + key in this; + } + function d3_map_remove(key) { + key = d3_map_prefix + key; + return key in this && delete this[key]; + } + function d3_map_keys() { + var keys = []; + this.forEach(function(key) { + keys.push(key); + }); + return keys; + } + function d3_map_size() { + var size = 0; + for (var key in this) if (key.charCodeAt(0) === d3_map_prefixCode) ++size; + return size; + } + function d3_map_empty() { + for (var key in this) if (key.charCodeAt(0) === d3_map_prefixCode) return false; + return true; + } + d3.nest = function() { + var nest = {}, keys = [], sortKeys = [], sortValues, rollup; + function map(mapType, array, depth) { + if (depth >= keys.length) return rollup ? rollup.call(nest, array) : sortValues ? array.sort(sortValues) : array; + var i = -1, n = array.length, key = keys[depth++], keyValue, object, setter, valuesByKey = new d3_Map(), values; + while (++i < n) { + if (values = valuesByKey.get(keyValue = key(object = array[i]))) { + values.push(object); + } else { + valuesByKey.set(keyValue, [ object ]); + } + } + if (mapType) { + object = mapType(); + setter = function(keyValue, values) { + object.set(keyValue, map(mapType, values, depth)); + }; + } else { + object = {}; + setter = function(keyValue, values) { + object[keyValue] = map(mapType, values, depth); + }; + } + valuesByKey.forEach(setter); + return object; + } + function entries(map, depth) { + if (depth >= keys.length) return map; + var array = [], sortKey = sortKeys[depth++]; + map.forEach(function(key, keyMap) { + array.push({ + key: key, + values: entries(keyMap, depth) + }); + }); + return sortKey ? array.sort(function(a, b) { + return sortKey(a.key, b.key); + }) : array; + } + nest.map = function(array, mapType) { + return map(mapType, array, 0); + }; + nest.entries = function(array) { + return entries(map(d3.map, array, 0), 0); + }; + nest.key = function(d) { + keys.push(d); + return nest; + }; + nest.sortKeys = function(order) { + sortKeys[keys.length - 1] = order; + return nest; + }; + nest.sortValues = function(order) { + sortValues = order; + return nest; + }; + nest.rollup = function(f) { + rollup = f; + return nest; + }; + return nest; + }; + d3.set = function(array) { + var set = new d3_Set(); + if (array) for (var i = 0, n = array.length; i < n; ++i) set.add(array[i]); + return set; + }; + function d3_Set() {} + d3_class(d3_Set, { + has: d3_map_has, + add: function(value) { + this[d3_map_prefix + value] = true; + return value; + }, + remove: function(value) { + value = d3_map_prefix + value; + return value in this && delete this[value]; + }, + values: d3_map_keys, + size: d3_map_size, + empty: d3_map_empty, + forEach: function(f) { + for (var value in this) if (value.charCodeAt(0) === d3_map_prefixCode) f.call(this, value.substring(1)); + } + }); + d3.behavior = {}; + d3.rebind = function(target, source) { + var i = 1, n = arguments.length, method; + while (++i < n) target[method = arguments[i]] = d3_rebind(target, source, source[method]); + return target; + }; + function d3_rebind(target, source, method) { + return function() { + var value = method.apply(source, arguments); + return value === source ? target : value; + }; + } + function d3_vendorSymbol(object, name) { + if (name in object) return name; + name = name.charAt(0).toUpperCase() + name.substring(1); + for (var i = 0, n = d3_vendorPrefixes.length; i < n; ++i) { + var prefixName = d3_vendorPrefixes[i] + name; + if (prefixName in object) return prefixName; + } + } + var d3_vendorPrefixes = [ "webkit", "ms", "moz", "Moz", "o", "O" ]; + function d3_noop() {} + d3.dispatch = function() { + var dispatch = new d3_dispatch(), i = -1, n = arguments.length; + while (++i < n) dispatch[arguments[i]] = d3_dispatch_event(dispatch); + return dispatch; + }; + function d3_dispatch() {} + d3_dispatch.prototype.on = function(type, listener) { + var i = type.indexOf("."), name = ""; + if (i >= 0) { + name = type.substring(i + 1); + type = type.substring(0, i); + } + if (type) return arguments.length < 2 ? this[type].on(name) : this[type].on(name, listener); + if (arguments.length === 2) { + if (listener == null) for (type in this) { + if (this.hasOwnProperty(type)) this[type].on(name, null); + } + return this; + } + }; + function d3_dispatch_event(dispatch) { + var listeners = [], listenerByName = new d3_Map(); + function event() { + var z = listeners, i = -1, n = z.length, l; + while (++i < n) if (l = z[i].on) l.apply(this, arguments); + return dispatch; + } + event.on = function(name, listener) { + var l = listenerByName.get(name), i; + if (arguments.length < 2) return l && l.on; + if (l) { + l.on = null; + listeners = listeners.slice(0, i = listeners.indexOf(l)).concat(listeners.slice(i + 1)); + listenerByName.remove(name); + } + if (listener) listeners.push(listenerByName.set(name, { + on: listener + })); + return dispatch; + }; + return event; + } + d3.event = null; + function d3_eventPreventDefault() { + d3.event.preventDefault(); + } + function d3_eventSource() { + var e = d3.event, s; + while (s = e.sourceEvent) e = s; + return e; + } + function d3_eventDispatch(target) { + var dispatch = new d3_dispatch(), i = 0, n = arguments.length; + while (++i < n) dispatch[arguments[i]] = d3_dispatch_event(dispatch); + dispatch.of = function(thiz, argumentz) { + return function(e1) { + try { + var e0 = e1.sourceEvent = d3.event; + e1.target = target; + d3.event = e1; + dispatch[e1.type].apply(thiz, argumentz); + } finally { + d3.event = e0; + } + }; + }; + return dispatch; + } + d3.requote = function(s) { + return s.replace(d3_requote_re, "\\$&"); + }; + var d3_requote_re = /[\\\^\$\*\+\?\|\[\]\(\)\.\{\}]/g; + var d3_subclass = {}.__proto__ ? function(object, prototype) { + object.__proto__ = prototype; + } : function(object, prototype) { + for (var property in prototype) object[property] = prototype[property]; + }; + function d3_selection(groups) { + d3_subclass(groups, d3_selectionPrototype); + return groups; + } + var d3_select = function(s, n) { + return n.querySelector(s); + }, d3_selectAll = function(s, n) { + return n.querySelectorAll(s); + }, d3_selectMatcher = d3_documentElement[d3_vendorSymbol(d3_documentElement, "matchesSelector")], d3_selectMatches = function(n, s) { + return d3_selectMatcher.call(n, s); + }; + if (typeof Sizzle === "function") { + d3_select = function(s, n) { + return Sizzle(s, n)[0] || null; + }; + d3_selectAll = Sizzle; + d3_selectMatches = Sizzle.matchesSelector; + } + d3.selection = function() { + return d3_selectionRoot; + }; + var d3_selectionPrototype = d3.selection.prototype = []; + d3_selectionPrototype.select = function(selector) { + var subgroups = [], subgroup, subnode, group, node; + selector = d3_selection_selector(selector); + for (var j = -1, m = this.length; ++j < m; ) { + subgroups.push(subgroup = []); + subgroup.parentNode = (group = this[j]).parentNode; + for (var i = -1, n = group.length; ++i < n; ) { + if (node = group[i]) { + subgroup.push(subnode = selector.call(node, node.__data__, i, j)); + if (subnode && "__data__" in node) subnode.__data__ = node.__data__; + } else { + subgroup.push(null); + } + } + } + return d3_selection(subgroups); + }; + function d3_selection_selector(selector) { + return typeof selector === "function" ? selector : function() { + return d3_select(selector, this); + }; + } + d3_selectionPrototype.selectAll = function(selector) { + var subgroups = [], subgroup, node; + selector = d3_selection_selectorAll(selector); + for (var j = -1, m = this.length; ++j < m; ) { + for (var group = this[j], i = -1, n = group.length; ++i < n; ) { + if (node = group[i]) { + subgroups.push(subgroup = d3_array(selector.call(node, node.__data__, i, j))); + subgroup.parentNode = node; + } + } + } + return d3_selection(subgroups); + }; + function d3_selection_selectorAll(selector) { + return typeof selector === "function" ? selector : function() { + return d3_selectAll(selector, this); + }; + } + var d3_nsPrefix = { + svg: "http://www.w3.org/2000/svg", + xhtml: "http://www.w3.org/1999/xhtml", + xlink: "http://www.w3.org/1999/xlink", + xml: "http://www.w3.org/XML/1998/namespace", + xmlns: "http://www.w3.org/2000/xmlns/" + }; + d3.ns = { + prefix: d3_nsPrefix, + qualify: function(name) { + var i = name.indexOf(":"), prefix = name; + if (i >= 0) { + prefix = name.substring(0, i); + name = name.substring(i + 1); + } + return d3_nsPrefix.hasOwnProperty(prefix) ? { + space: d3_nsPrefix[prefix], + local: name + } : name; + } + }; + d3_selectionPrototype.attr = function(name, value) { + if (arguments.length < 2) { + if (typeof name === "string") { + var node = this.node(); + name = d3.ns.qualify(name); + return name.local ? node.getAttributeNS(name.space, name.local) : node.getAttribute(name); + } + for (value in name) this.each(d3_selection_attr(value, name[value])); + return this; + } + return this.each(d3_selection_attr(name, value)); + }; + function d3_selection_attr(name, value) { + name = d3.ns.qualify(name); + function attrNull() { + this.removeAttribute(name); + } + function attrNullNS() { + this.removeAttributeNS(name.space, name.local); + } + function attrConstant() { + this.setAttribute(name, value); + } + function attrConstantNS() { + this.setAttributeNS(name.space, name.local, value); + } + function attrFunction() { + var x = value.apply(this, arguments); + if (x == null) this.removeAttribute(name); else this.setAttribute(name, x); + } + function attrFunctionNS() { + var x = value.apply(this, arguments); + if (x == null) this.removeAttributeNS(name.space, name.local); else this.setAttributeNS(name.space, name.local, x); + } + return value == null ? name.local ? attrNullNS : attrNull : typeof value === "function" ? name.local ? attrFunctionNS : attrFunction : name.local ? attrConstantNS : attrConstant; + } + function d3_collapse(s) { + return s.trim().replace(/\s+/g, " "); + } + d3_selectionPrototype.classed = function(name, value) { + if (arguments.length < 2) { + if (typeof name === "string") { + var node = this.node(), n = (name = d3_selection_classes(name)).length, i = -1; + if (value = node.classList) { + while (++i < n) if (!value.contains(name[i])) return false; + } else { + value = node.getAttribute("class"); + while (++i < n) if (!d3_selection_classedRe(name[i]).test(value)) return false; + } + return true; + } + for (value in name) this.each(d3_selection_classed(value, name[value])); + return this; + } + return this.each(d3_selection_classed(name, value)); + }; + function d3_selection_classedRe(name) { + return new RegExp("(?:^|\\s+)" + d3.requote(name) + "(?:\\s+|$)", "g"); + } + function d3_selection_classes(name) { + return name.trim().split(/^|\s+/); + } + function d3_selection_classed(name, value) { + name = d3_selection_classes(name).map(d3_selection_classedName); + var n = name.length; + function classedConstant() { + var i = -1; + while (++i < n) name[i](this, value); + } + function classedFunction() { + var i = -1, x = value.apply(this, arguments); + while (++i < n) name[i](this, x); + } + return typeof value === "function" ? classedFunction : classedConstant; + } + function d3_selection_classedName(name) { + var re = d3_selection_classedRe(name); + return function(node, value) { + if (c = node.classList) return value ? c.add(name) : c.remove(name); + var c = node.getAttribute("class") || ""; + if (value) { + re.lastIndex = 0; + if (!re.test(c)) node.setAttribute("class", d3_collapse(c + " " + name)); + } else { + node.setAttribute("class", d3_collapse(c.replace(re, " "))); + } + }; + } + d3_selectionPrototype.style = function(name, value, priority) { + var n = arguments.length; + if (n < 3) { + if (typeof name !== "string") { + if (n < 2) value = ""; + for (priority in name) this.each(d3_selection_style(priority, name[priority], value)); + return this; + } + if (n < 2) return d3_window.getComputedStyle(this.node(), null).getPropertyValue(name); + priority = ""; + } + return this.each(d3_selection_style(name, value, priority)); + }; + function d3_selection_style(name, value, priority) { + function styleNull() { + this.style.removeProperty(name); + } + function styleConstant() { + this.style.setProperty(name, value, priority); + } + function styleFunction() { + var x = value.apply(this, arguments); + if (x == null) this.style.removeProperty(name); else this.style.setProperty(name, x, priority); + } + return value == null ? styleNull : typeof value === "function" ? styleFunction : styleConstant; + } + d3_selectionPrototype.property = function(name, value) { + if (arguments.length < 2) { + if (typeof name === "string") return this.node()[name]; + for (value in name) this.each(d3_selection_property(value, name[value])); + return this; + } + return this.each(d3_selection_property(name, value)); + }; + function d3_selection_property(name, value) { + function propertyNull() { + delete this[name]; + } + function propertyConstant() { + this[name] = value; + } + function propertyFunction() { + var x = value.apply(this, arguments); + if (x == null) delete this[name]; else this[name] = x; + } + return value == null ? propertyNull : typeof value === "function" ? propertyFunction : propertyConstant; + } + d3_selectionPrototype.text = function(value) { + return arguments.length ? this.each(typeof value === "function" ? function() { + var v = value.apply(this, arguments); + this.textContent = v == null ? "" : v; + } : value == null ? function() { + this.textContent = ""; + } : function() { + this.textContent = value; + }) : this.node().textContent; + }; + d3_selectionPrototype.html = function(value) { + return arguments.length ? this.each(typeof value === "function" ? function() { + var v = value.apply(this, arguments); + this.innerHTML = v == null ? "" : v; + } : value == null ? function() { + this.innerHTML = ""; + } : function() { + this.innerHTML = value; + }) : this.node().innerHTML; + }; + d3_selectionPrototype.append = function(name) { + name = d3_selection_creator(name); + return this.select(function() { + return this.appendChild(name.apply(this, arguments)); + }); + }; + function d3_selection_creator(name) { + return typeof name === "function" ? name : (name = d3.ns.qualify(name)).local ? function() { + return this.ownerDocument.createElementNS(name.space, name.local); + } : function() { + return this.ownerDocument.createElementNS(this.namespaceURI, name); + }; + } + d3_selectionPrototype.insert = function(name, before) { + name = d3_selection_creator(name); + before = d3_selection_selector(before); + return this.select(function() { + return this.insertBefore(name.apply(this, arguments), before.apply(this, arguments) || null); + }); + }; + d3_selectionPrototype.remove = function() { + return this.each(function() { + var parent = this.parentNode; + if (parent) parent.removeChild(this); + }); + }; + d3_selectionPrototype.data = function(value, key) { + var i = -1, n = this.length, group, node; + if (!arguments.length) { + value = new Array(n = (group = this[0]).length); + while (++i < n) { + if (node = group[i]) { + value[i] = node.__data__; + } + } + return value; + } + function bind(group, groupData) { + var i, n = group.length, m = groupData.length, n0 = Math.min(n, m), updateNodes = new Array(m), enterNodes = new Array(m), exitNodes = new Array(n), node, nodeData; + if (key) { + var nodeByKeyValue = new d3_Map(), dataByKeyValue = new d3_Map(), keyValues = [], keyValue; + for (i = -1; ++i < n; ) { + keyValue = key.call(node = group[i], node.__data__, i); + if (nodeByKeyValue.has(keyValue)) { + exitNodes[i] = node; + } else { + nodeByKeyValue.set(keyValue, node); + } + keyValues.push(keyValue); + } + for (i = -1; ++i < m; ) { + keyValue = key.call(groupData, nodeData = groupData[i], i); + if (node = nodeByKeyValue.get(keyValue)) { + updateNodes[i] = node; + node.__data__ = nodeData; + } else if (!dataByKeyValue.has(keyValue)) { + enterNodes[i] = d3_selection_dataNode(nodeData); + } + dataByKeyValue.set(keyValue, nodeData); + nodeByKeyValue.remove(keyValue); + } + for (i = -1; ++i < n; ) { + if (nodeByKeyValue.has(keyValues[i])) { + exitNodes[i] = group[i]; + } + } + } else { + for (i = -1; ++i < n0; ) { + node = group[i]; + nodeData = groupData[i]; + if (node) { + node.__data__ = nodeData; + updateNodes[i] = node; + } else { + enterNodes[i] = d3_selection_dataNode(nodeData); + } + } + for (;i < m; ++i) { + enterNodes[i] = d3_selection_dataNode(groupData[i]); + } + for (;i < n; ++i) { + exitNodes[i] = group[i]; + } + } + enterNodes.update = updateNodes; + enterNodes.parentNode = updateNodes.parentNode = exitNodes.parentNode = group.parentNode; + enter.push(enterNodes); + update.push(updateNodes); + exit.push(exitNodes); + } + var enter = d3_selection_enter([]), update = d3_selection([]), exit = d3_selection([]); + if (typeof value === "function") { + while (++i < n) { + bind(group = this[i], value.call(group, group.parentNode.__data__, i)); + } + } else { + while (++i < n) { + bind(group = this[i], value); + } + } + update.enter = function() { + return enter; + }; + update.exit = function() { + return exit; + }; + return update; + }; + function d3_selection_dataNode(data) { + return { + __data__: data + }; + } + d3_selectionPrototype.datum = function(value) { + return arguments.length ? this.property("__data__", value) : this.property("__data__"); + }; + d3_selectionPrototype.filter = function(filter) { + var subgroups = [], subgroup, group, node; + if (typeof filter !== "function") filter = d3_selection_filter(filter); + for (var j = 0, m = this.length; j < m; j++) { + subgroups.push(subgroup = []); + subgroup.parentNode = (group = this[j]).parentNode; + for (var i = 0, n = group.length; i < n; i++) { + if ((node = group[i]) && filter.call(node, node.__data__, i, j)) { + subgroup.push(node); + } + } + } + return d3_selection(subgroups); + }; + function d3_selection_filter(selector) { + return function() { + return d3_selectMatches(this, selector); + }; + } + d3_selectionPrototype.order = function() { + for (var j = -1, m = this.length; ++j < m; ) { + for (var group = this[j], i = group.length - 1, next = group[i], node; --i >= 0; ) { + if (node = group[i]) { + if (next && next !== node.nextSibling) next.parentNode.insertBefore(node, next); + next = node; + } + } + } + return this; + }; + d3_selectionPrototype.sort = function(comparator) { + comparator = d3_selection_sortComparator.apply(this, arguments); + for (var j = -1, m = this.length; ++j < m; ) this[j].sort(comparator); + return this.order(); + }; + function d3_selection_sortComparator(comparator) { + if (!arguments.length) comparator = d3_ascending; + return function(a, b) { + return a && b ? comparator(a.__data__, b.__data__) : !a - !b; + }; + } + d3_selectionPrototype.each = function(callback) { + return d3_selection_each(this, function(node, i, j) { + callback.call(node, node.__data__, i, j); + }); + }; + function d3_selection_each(groups, callback) { + for (var j = 0, m = groups.length; j < m; j++) { + for (var group = groups[j], i = 0, n = group.length, node; i < n; i++) { + if (node = group[i]) callback(node, i, j); + } + } + return groups; + } + d3_selectionPrototype.call = function(callback) { + var args = d3_array(arguments); + callback.apply(args[0] = this, args); + return this; + }; + d3_selectionPrototype.empty = function() { + return !this.node(); + }; + d3_selectionPrototype.node = function() { + for (var j = 0, m = this.length; j < m; j++) { + for (var group = this[j], i = 0, n = group.length; i < n; i++) { + var node = group[i]; + if (node) return node; + } + } + return null; + }; + d3_selectionPrototype.size = function() { + var n = 0; + this.each(function() { + ++n; + }); + return n; + }; + function d3_selection_enter(selection) { + d3_subclass(selection, d3_selection_enterPrototype); + return selection; + } + var d3_selection_enterPrototype = []; + d3.selection.enter = d3_selection_enter; + d3.selection.enter.prototype = d3_selection_enterPrototype; + d3_selection_enterPrototype.append = d3_selectionPrototype.append; + d3_selection_enterPrototype.empty = d3_selectionPrototype.empty; + d3_selection_enterPrototype.node = d3_selectionPrototype.node; + d3_selection_enterPrototype.call = d3_selectionPrototype.call; + d3_selection_enterPrototype.size = d3_selectionPrototype.size; + d3_selection_enterPrototype.select = function(selector) { + var subgroups = [], subgroup, subnode, upgroup, group, node; + for (var j = -1, m = this.length; ++j < m; ) { + upgroup = (group = this[j]).update; + subgroups.push(subgroup = []); + subgroup.parentNode = group.parentNode; + for (var i = -1, n = group.length; ++i < n; ) { + if (node = group[i]) { + subgroup.push(upgroup[i] = subnode = selector.call(group.parentNode, node.__data__, i, j)); + subnode.__data__ = node.__data__; + } else { + subgroup.push(null); + } + } + } + return d3_selection(subgroups); + }; + d3_selection_enterPrototype.insert = function(name, before) { + if (arguments.length < 2) before = d3_selection_enterInsertBefore(this); + return d3_selectionPrototype.insert.call(this, name, before); + }; + function d3_selection_enterInsertBefore(enter) { + var i0, j0; + return function(d, i, j) { + var group = enter[j].update, n = group.length, node; + if (j != j0) j0 = j, i0 = 0; + if (i >= i0) i0 = i + 1; + while (!(node = group[i0]) && ++i0 < n) ; + return node; + }; + } + d3_selectionPrototype.transition = function() { + var id = d3_transitionInheritId || ++d3_transitionId, subgroups = [], subgroup, node, transition = d3_transitionInherit || { + time: Date.now(), + ease: d3_ease_cubicInOut, + delay: 0, + duration: 250 + }; + for (var j = -1, m = this.length; ++j < m; ) { + subgroups.push(subgroup = []); + for (var group = this[j], i = -1, n = group.length; ++i < n; ) { + if (node = group[i]) d3_transitionNode(node, i, id, transition); + subgroup.push(node); + } + } + return d3_transition(subgroups, id); + }; + d3_selectionPrototype.interrupt = function() { + return this.each(d3_selection_interrupt); + }; + function d3_selection_interrupt() { + var lock = this.__transition__; + if (lock) ++lock.active; + } + d3.select = function(node) { + var group = [ typeof node === "string" ? d3_select(node, d3_document) : node ]; + group.parentNode = d3_documentElement; + return d3_selection([ group ]); + }; + d3.selectAll = function(nodes) { + var group = d3_array(typeof nodes === "string" ? d3_selectAll(nodes, d3_document) : nodes); + group.parentNode = d3_documentElement; + return d3_selection([ group ]); + }; + var d3_selectionRoot = d3.select(d3_documentElement); + d3_selectionPrototype.on = function(type, listener, capture) { + var n = arguments.length; + if (n < 3) { + if (typeof type !== "string") { + if (n < 2) listener = false; + for (capture in type) this.each(d3_selection_on(capture, type[capture], listener)); + return this; + } + if (n < 2) return (n = this.node()["__on" + type]) && n._; + capture = false; + } + return this.each(d3_selection_on(type, listener, capture)); + }; + function d3_selection_on(type, listener, capture) { + var name = "__on" + type, i = type.indexOf("."), wrap = d3_selection_onListener; + if (i > 0) type = type.substring(0, i); + var filter = d3_selection_onFilters.get(type); + if (filter) type = filter, wrap = d3_selection_onFilter; + function onRemove() { + var l = this[name]; + if (l) { + this.removeEventListener(type, l, l.$); + delete this[name]; + } + } + function onAdd() { + var l = wrap(listener, d3_array(arguments)); + onRemove.call(this); + this.addEventListener(type, this[name] = l, l.$ = capture); + l._ = listener; + } + function removeAll() { + var re = new RegExp("^__on([^.]+)" + d3.requote(type) + "$"), match; + for (var name in this) { + if (match = name.match(re)) { + var l = this[name]; + this.removeEventListener(match[1], l, l.$); + delete this[name]; + } + } + } + return i ? listener ? onAdd : onRemove : listener ? d3_noop : removeAll; + } + var d3_selection_onFilters = d3.map({ + mouseenter: "mouseover", + mouseleave: "mouseout" + }); + d3_selection_onFilters.forEach(function(k) { + if ("on" + k in d3_document) d3_selection_onFilters.remove(k); + }); + function d3_selection_onListener(listener, argumentz) { + return function(e) { + var o = d3.event; + d3.event = e; + argumentz[0] = this.__data__; + try { + listener.apply(this, argumentz); + } finally { + d3.event = o; + } + }; + } + function d3_selection_onFilter(listener, argumentz) { + var l = d3_selection_onListener(listener, argumentz); + return function(e) { + var target = this, related = e.relatedTarget; + if (!related || related !== target && !(related.compareDocumentPosition(target) & 8)) { + l.call(target, e); + } + }; + } + var d3_event_dragSelect = "onselectstart" in d3_document ? null : d3_vendorSymbol(d3_documentElement.style, "userSelect"), d3_event_dragId = 0; + function d3_event_dragSuppress() { + var name = ".dragsuppress-" + ++d3_event_dragId, click = "click" + name, w = d3.select(d3_window).on("touchmove" + name, d3_eventPreventDefault).on("dragstart" + name, d3_eventPreventDefault).on("selectstart" + name, d3_eventPreventDefault); + if (d3_event_dragSelect) { + var style = d3_documentElement.style, select = style[d3_event_dragSelect]; + style[d3_event_dragSelect] = "none"; + } + return function(suppressClick) { + w.on(name, null); + if (d3_event_dragSelect) style[d3_event_dragSelect] = select; + if (suppressClick) { + function off() { + w.on(click, null); + } + w.on(click, function() { + d3_eventPreventDefault(); + off(); + }, true); + setTimeout(off, 0); + } + }; + } + d3.mouse = function(container) { + return d3_mousePoint(container, d3_eventSource()); + }; + function d3_mousePoint(container, e) { + if (e.changedTouches) e = e.changedTouches[0]; + var svg = container.ownerSVGElement || container; + if (svg.createSVGPoint) { + var point = svg.createSVGPoint(); + point.x = e.clientX, point.y = e.clientY; + point = point.matrixTransform(container.getScreenCTM().inverse()); + return [ point.x, point.y ]; + } + var rect = container.getBoundingClientRect(); + return [ e.clientX - rect.left - container.clientLeft, e.clientY - rect.top - container.clientTop ]; + } + d3.touches = function(container, touches) { + if (arguments.length < 2) touches = d3_eventSource().touches; + return touches ? d3_array(touches).map(function(touch) { + var point = d3_mousePoint(container, touch); + point.identifier = touch.identifier; + return point; + }) : []; + }; + d3.behavior.drag = function() { + var event = d3_eventDispatch(drag, "drag", "dragstart", "dragend"), origin = null, mousedown = dragstart(d3_noop, d3.mouse, d3_behavior_dragMouseSubject, "mousemove", "mouseup"), touchstart = dragstart(d3_behavior_dragTouchId, d3.touch, d3_behavior_dragTouchSubject, "touchmove", "touchend"); + function drag() { + this.on("mousedown.drag", mousedown).on("touchstart.drag", touchstart); + } + function dragstart(id, position, subject, move, end) { + return function() { + var that = this, target = d3.event.target, parent = that.parentNode, dispatch = event.of(that, arguments), dragged = 0, dragId = id(), dragName = ".drag" + (dragId == null ? "" : "-" + dragId), dragOffset, dragSubject = d3.select(subject()).on(move + dragName, moved).on(end + dragName, ended), dragRestore = d3_event_dragSuppress(), position0 = position(parent, dragId); + if (origin) { + dragOffset = origin.apply(that, arguments); + dragOffset = [ dragOffset.x - position0[0], dragOffset.y - position0[1] ]; + } else { + dragOffset = [ 0, 0 ]; + } + dispatch({ + type: "dragstart" + }); + function moved() { + var position1 = position(parent, dragId), dx, dy; + if (!position1) return; + dx = position1[0] - position0[0]; + dy = position1[1] - position0[1]; + dragged |= dx | dy; + position0 = position1; + dispatch({ + type: "drag", + x: position1[0] + dragOffset[0], + y: position1[1] + dragOffset[1], + dx: dx, + dy: dy + }); + } + function ended() { + if (!position(parent, dragId)) return; + dragSubject.on(move + dragName, null).on(end + dragName, null); + dragRestore(dragged && d3.event.target === target); + dispatch({ + type: "dragend" + }); + } + }; + } + drag.origin = function(x) { + if (!arguments.length) return origin; + origin = x; + return drag; + }; + return d3.rebind(drag, event, "on"); + }; + function d3_behavior_dragTouchId() { + return d3.event.changedTouches[0].identifier; + } + function d3_behavior_dragTouchSubject() { + return d3.event.target; + } + function d3_behavior_dragMouseSubject() { + return d3_window; + } + var π = Math.PI, τ = 2 * π, halfπ = π / 2, ε = 1e-6, ε2 = ε * ε, d3_radians = π / 180, d3_degrees = 180 / π; + function d3_sgn(x) { + return x > 0 ? 1 : x < 0 ? -1 : 0; + } + function d3_cross2d(a, b, c) { + return (b[0] - a[0]) * (c[1] - a[1]) - (b[1] - a[1]) * (c[0] - a[0]); + } + function d3_acos(x) { + return x > 1 ? 0 : x < -1 ? π : Math.acos(x); + } + function d3_asin(x) { + return x > 1 ? halfπ : x < -1 ? -halfπ : Math.asin(x); + } + function d3_sinh(x) { + return ((x = Math.exp(x)) - 1 / x) / 2; + } + function d3_cosh(x) { + return ((x = Math.exp(x)) + 1 / x) / 2; + } + function d3_tanh(x) { + return ((x = Math.exp(2 * x)) - 1) / (x + 1); + } + function d3_haversin(x) { + return (x = Math.sin(x / 2)) * x; + } + var ρ = Math.SQRT2, ρ2 = 2, ρ4 = 4; + d3.interpolateZoom = function(p0, p1) { + var ux0 = p0[0], uy0 = p0[1], w0 = p0[2], ux1 = p1[0], uy1 = p1[1], w1 = p1[2]; + var dx = ux1 - ux0, dy = uy1 - uy0, d2 = dx * dx + dy * dy, d1 = Math.sqrt(d2), b0 = (w1 * w1 - w0 * w0 + ρ4 * d2) / (2 * w0 * ρ2 * d1), b1 = (w1 * w1 - w0 * w0 - ρ4 * d2) / (2 * w1 * ρ2 * d1), r0 = Math.log(Math.sqrt(b0 * b0 + 1) - b0), r1 = Math.log(Math.sqrt(b1 * b1 + 1) - b1), dr = r1 - r0, S = (dr || Math.log(w1 / w0)) / ρ; + function interpolate(t) { + var s = t * S; + if (dr) { + var coshr0 = d3_cosh(r0), u = w0 / (ρ2 * d1) * (coshr0 * d3_tanh(ρ * s + r0) - d3_sinh(r0)); + return [ ux0 + u * dx, uy0 + u * dy, w0 * coshr0 / d3_cosh(ρ * s + r0) ]; + } + return [ ux0 + t * dx, uy0 + t * dy, w0 * Math.exp(ρ * s) ]; + } + interpolate.duration = S * 1e3; + return interpolate; + }; + d3.behavior.zoom = function() { + var view = { + x: 0, + y: 0, + k: 1 + }, translate0, center, size = [ 960, 500 ], scaleExtent = d3_behavior_zoomInfinity, mousedown = "mousedown.zoom", mousemove = "mousemove.zoom", mouseup = "mouseup.zoom", mousewheelTimer, touchstart = "touchstart.zoom", touchtime, event = d3_eventDispatch(zoom, "zoomstart", "zoom", "zoomend"), x0, x1, y0, y1; + function zoom(g) { + g.on(mousedown, mousedowned).on(d3_behavior_zoomWheel + ".zoom", mousewheeled).on(mousemove, mousewheelreset).on("dblclick.zoom", dblclicked).on(touchstart, touchstarted); + } + zoom.event = function(g) { + g.each(function() { + var dispatch = event.of(this, arguments), view1 = view; + if (d3_transitionInheritId) { + d3.select(this).transition().each("start.zoom", function() { + view = this.__chart__ || { + x: 0, + y: 0, + k: 1 + }; + zoomstarted(dispatch); + }).tween("zoom:zoom", function() { + var dx = size[0], dy = size[1], cx = dx / 2, cy = dy / 2, i = d3.interpolateZoom([ (cx - view.x) / view.k, (cy - view.y) / view.k, dx / view.k ], [ (cx - view1.x) / view1.k, (cy - view1.y) / view1.k, dx / view1.k ]); + return function(t) { + var l = i(t), k = dx / l[2]; + this.__chart__ = view = { + x: cx - l[0] * k, + y: cy - l[1] * k, + k: k + }; + zoomed(dispatch); + }; + }).each("end.zoom", function() { + zoomended(dispatch); + }); + } else { + this.__chart__ = view; + zoomstarted(dispatch); + zoomed(dispatch); + zoomended(dispatch); + } + }); + }; + zoom.translate = function(_) { + if (!arguments.length) return [ view.x, view.y ]; + view = { + x: +_[0], + y: +_[1], + k: view.k + }; + rescale(); + return zoom; + }; + zoom.scale = function(_) { + if (!arguments.length) return view.k; + view = { + x: view.x, + y: view.y, + k: +_ + }; + rescale(); + return zoom; + }; + zoom.scaleExtent = function(_) { + if (!arguments.length) return scaleExtent; + scaleExtent = _ == null ? d3_behavior_zoomInfinity : [ +_[0], +_[1] ]; + return zoom; + }; + zoom.center = function(_) { + if (!arguments.length) return center; + center = _ && [ +_[0], +_[1] ]; + return zoom; + }; + zoom.size = function(_) { + if (!arguments.length) return size; + size = _ && [ +_[0], +_[1] ]; + return zoom; + }; + zoom.x = function(z) { + if (!arguments.length) return x1; + x1 = z; + x0 = z.copy(); + view = { + x: 0, + y: 0, + k: 1 + }; + return zoom; + }; + zoom.y = function(z) { + if (!arguments.length) return y1; + y1 = z; + y0 = z.copy(); + view = { + x: 0, + y: 0, + k: 1 + }; + return zoom; + }; + function location(p) { + return [ (p[0] - view.x) / view.k, (p[1] - view.y) / view.k ]; + } + function point(l) { + return [ l[0] * view.k + view.x, l[1] * view.k + view.y ]; + } + function scaleTo(s) { + view.k = Math.max(scaleExtent[0], Math.min(scaleExtent[1], s)); + } + function translateTo(p, l) { + l = point(l); + view.x += p[0] - l[0]; + view.y += p[1] - l[1]; + } + function rescale() { + if (x1) x1.domain(x0.range().map(function(x) { + return (x - view.x) / view.k; + }).map(x0.invert)); + if (y1) y1.domain(y0.range().map(function(y) { + return (y - view.y) / view.k; + }).map(y0.invert)); + } + function zoomstarted(dispatch) { + dispatch({ + type: "zoomstart" + }); + } + function zoomed(dispatch) { + rescale(); + dispatch({ + type: "zoom", + scale: view.k, + translate: [ view.x, view.y ] + }); + } + function zoomended(dispatch) { + dispatch({ + type: "zoomend" + }); + } + function mousedowned() { + var that = this, target = d3.event.target, dispatch = event.of(that, arguments), dragged = 0, subject = d3.select(d3_window).on(mousemove, moved).on(mouseup, ended), location0 = location(d3.mouse(that)), dragRestore = d3_event_dragSuppress(); + d3_selection_interrupt.call(that); + zoomstarted(dispatch); + function moved() { + dragged = 1; + translateTo(d3.mouse(that), location0); + zoomed(dispatch); + } + function ended() { + subject.on(mousemove, d3_window === that ? mousewheelreset : null).on(mouseup, null); + dragRestore(dragged && d3.event.target === target); + zoomended(dispatch); + } + } + function touchstarted() { + var that = this, dispatch = event.of(that, arguments), locations0 = {}, distance0 = 0, scale0, zoomName = ".zoom-" + d3.event.changedTouches[0].identifier, touchmove = "touchmove" + zoomName, touchend = "touchend" + zoomName, targets = [], subject = d3.select(that).on(mousedown, null).on(touchstart, started), dragRestore = d3_event_dragSuppress(); + d3_selection_interrupt.call(that); + started(); + zoomstarted(dispatch); + function relocate() { + var touches = d3.touches(that); + scale0 = view.k; + touches.forEach(function(t) { + if (t.identifier in locations0) locations0[t.identifier] = location(t); + }); + return touches; + } + function started() { + var target = d3.event.target; + d3.select(target).on(touchmove, moved).on(touchend, ended); + targets.push(target); + var changed = d3.event.changedTouches; + for (var i = 0, n = changed.length; i < n; ++i) { + locations0[changed[i].identifier] = null; + } + var touches = relocate(), now = Date.now(); + if (touches.length === 1) { + if (now - touchtime < 500) { + var p = touches[0], l = locations0[p.identifier]; + scaleTo(view.k * 2); + translateTo(p, l); + d3_eventPreventDefault(); + zoomed(dispatch); + } + touchtime = now; + } else if (touches.length > 1) { + var p = touches[0], q = touches[1], dx = p[0] - q[0], dy = p[1] - q[1]; + distance0 = dx * dx + dy * dy; + } + } + function moved() { + var touches = d3.touches(that), p0, l0, p1, l1; + for (var i = 0, n = touches.length; i < n; ++i, l1 = null) { + p1 = touches[i]; + if (l1 = locations0[p1.identifier]) { + if (l0) break; + p0 = p1, l0 = l1; + } + } + if (l1) { + var distance1 = (distance1 = p1[0] - p0[0]) * distance1 + (distance1 = p1[1] - p0[1]) * distance1, scale1 = distance0 && Math.sqrt(distance1 / distance0); + p0 = [ (p0[0] + p1[0]) / 2, (p0[1] + p1[1]) / 2 ]; + l0 = [ (l0[0] + l1[0]) / 2, (l0[1] + l1[1]) / 2 ]; + scaleTo(scale1 * scale0); + } + touchtime = null; + translateTo(p0, l0); + zoomed(dispatch); + } + function ended() { + if (d3.event.touches.length) { + var changed = d3.event.changedTouches; + for (var i = 0, n = changed.length; i < n; ++i) { + delete locations0[changed[i].identifier]; + } + for (var identifier in locations0) { + return void relocate(); + } + } + d3.selectAll(targets).on(zoomName, null); + subject.on(mousedown, mousedowned).on(touchstart, touchstarted); + dragRestore(); + zoomended(dispatch); + } + } + function mousewheeled() { + var dispatch = event.of(this, arguments); + if (mousewheelTimer) clearTimeout(mousewheelTimer); else d3_selection_interrupt.call(this), + zoomstarted(dispatch); + mousewheelTimer = setTimeout(function() { + mousewheelTimer = null; + zoomended(dispatch); + }, 50); + d3_eventPreventDefault(); + var point = center || d3.mouse(this); + if (!translate0) translate0 = location(point); + scaleTo(Math.pow(2, d3_behavior_zoomDelta() * .002) * view.k); + translateTo(point, translate0); + zoomed(dispatch); + } + function mousewheelreset() { + translate0 = null; + } + function dblclicked() { + var dispatch = event.of(this, arguments), p = d3.mouse(this), l = location(p), k = Math.log(view.k) / Math.LN2; + zoomstarted(dispatch); + scaleTo(Math.pow(2, d3.event.shiftKey ? Math.ceil(k) - 1 : Math.floor(k) + 1)); + translateTo(p, l); + zoomed(dispatch); + zoomended(dispatch); + } + return d3.rebind(zoom, event, "on"); + }; + var d3_behavior_zoomInfinity = [ 0, Infinity ]; + var d3_behavior_zoomDelta, d3_behavior_zoomWheel = "onwheel" in d3_document ? (d3_behavior_zoomDelta = function() { + return -d3.event.deltaY * (d3.event.deltaMode ? 120 : 1); + }, "wheel") : "onmousewheel" in d3_document ? (d3_behavior_zoomDelta = function() { + return d3.event.wheelDelta; + }, "mousewheel") : (d3_behavior_zoomDelta = function() { + return -d3.event.detail; + }, "MozMousePixelScroll"); + function d3_Color() {} + d3_Color.prototype.toString = function() { + return this.rgb() + ""; + }; + d3.hsl = function(h, s, l) { + return arguments.length === 1 ? h instanceof d3_Hsl ? d3_hsl(h.h, h.s, h.l) : d3_rgb_parse("" + h, d3_rgb_hsl, d3_hsl) : d3_hsl(+h, +s, +l); + }; + function d3_hsl(h, s, l) { + return new d3_Hsl(h, s, l); + } + function d3_Hsl(h, s, l) { + this.h = h; + this.s = s; + this.l = l; + } + var d3_hslPrototype = d3_Hsl.prototype = new d3_Color(); + d3_hslPrototype.brighter = function(k) { + k = Math.pow(.7, arguments.length ? k : 1); + return d3_hsl(this.h, this.s, this.l / k); + }; + d3_hslPrototype.darker = function(k) { + k = Math.pow(.7, arguments.length ? k : 1); + return d3_hsl(this.h, this.s, k * this.l); + }; + d3_hslPrototype.rgb = function() { + return d3_hsl_rgb(this.h, this.s, this.l); + }; + function d3_hsl_rgb(h, s, l) { + var m1, m2; + h = isNaN(h) ? 0 : (h %= 360) < 0 ? h + 360 : h; + s = isNaN(s) ? 0 : s < 0 ? 0 : s > 1 ? 1 : s; + l = l < 0 ? 0 : l > 1 ? 1 : l; + m2 = l <= .5 ? l * (1 + s) : l + s - l * s; + m1 = 2 * l - m2; + function v(h) { + if (h > 360) h -= 360; else if (h < 0) h += 360; + if (h < 60) return m1 + (m2 - m1) * h / 60; + if (h < 180) return m2; + if (h < 240) return m1 + (m2 - m1) * (240 - h) / 60; + return m1; + } + function vv(h) { + return Math.round(v(h) * 255); + } + return d3_rgb(vv(h + 120), vv(h), vv(h - 120)); + } + d3.hcl = function(h, c, l) { + return arguments.length === 1 ? h instanceof d3_Hcl ? d3_hcl(h.h, h.c, h.l) : h instanceof d3_Lab ? d3_lab_hcl(h.l, h.a, h.b) : d3_lab_hcl((h = d3_rgb_lab((h = d3.rgb(h)).r, h.g, h.b)).l, h.a, h.b) : d3_hcl(+h, +c, +l); + }; + function d3_hcl(h, c, l) { + return new d3_Hcl(h, c, l); + } + function d3_Hcl(h, c, l) { + this.h = h; + this.c = c; + this.l = l; + } + var d3_hclPrototype = d3_Hcl.prototype = new d3_Color(); + d3_hclPrototype.brighter = function(k) { + return d3_hcl(this.h, this.c, Math.min(100, this.l + d3_lab_K * (arguments.length ? k : 1))); + }; + d3_hclPrototype.darker = function(k) { + return d3_hcl(this.h, this.c, Math.max(0, this.l - d3_lab_K * (arguments.length ? k : 1))); + }; + d3_hclPrototype.rgb = function() { + return d3_hcl_lab(this.h, this.c, this.l).rgb(); + }; + function d3_hcl_lab(h, c, l) { + if (isNaN(h)) h = 0; + if (isNaN(c)) c = 0; + return d3_lab(l, Math.cos(h *= d3_radians) * c, Math.sin(h) * c); + } + d3.lab = function(l, a, b) { + return arguments.length === 1 ? l instanceof d3_Lab ? d3_lab(l.l, l.a, l.b) : l instanceof d3_Hcl ? d3_hcl_lab(l.l, l.c, l.h) : d3_rgb_lab((l = d3.rgb(l)).r, l.g, l.b) : d3_lab(+l, +a, +b); + }; + function d3_lab(l, a, b) { + return new d3_Lab(l, a, b); + } + function d3_Lab(l, a, b) { + this.l = l; + this.a = a; + this.b = b; + } + var d3_lab_K = 18; + var d3_lab_X = .95047, d3_lab_Y = 1, d3_lab_Z = 1.08883; + var d3_labPrototype = d3_Lab.prototype = new d3_Color(); + d3_labPrototype.brighter = function(k) { + return d3_lab(Math.min(100, this.l + d3_lab_K * (arguments.length ? k : 1)), this.a, this.b); + }; + d3_labPrototype.darker = function(k) { + return d3_lab(Math.max(0, this.l - d3_lab_K * (arguments.length ? k : 1)), this.a, this.b); + }; + d3_labPrototype.rgb = function() { + return d3_lab_rgb(this.l, this.a, this.b); + }; + function d3_lab_rgb(l, a, b) { + var y = (l + 16) / 116, x = y + a / 500, z = y - b / 200; + x = d3_lab_xyz(x) * d3_lab_X; + y = d3_lab_xyz(y) * d3_lab_Y; + z = d3_lab_xyz(z) * d3_lab_Z; + return d3_rgb(d3_xyz_rgb(3.2404542 * x - 1.5371385 * y - .4985314 * z), d3_xyz_rgb(-.969266 * x + 1.8760108 * y + .041556 * z), d3_xyz_rgb(.0556434 * x - .2040259 * y + 1.0572252 * z)); + } + function d3_lab_hcl(l, a, b) { + return l > 0 ? d3_hcl(Math.atan2(b, a) * d3_degrees, Math.sqrt(a * a + b * b), l) : d3_hcl(NaN, NaN, l); + } + function d3_lab_xyz(x) { + return x > .206893034 ? x * x * x : (x - 4 / 29) / 7.787037; + } + function d3_xyz_lab(x) { + return x > .008856 ? Math.pow(x, 1 / 3) : 7.787037 * x + 4 / 29; + } + function d3_xyz_rgb(r) { + return Math.round(255 * (r <= .00304 ? 12.92 * r : 1.055 * Math.pow(r, 1 / 2.4) - .055)); + } + d3.rgb = function(r, g, b) { + return arguments.length === 1 ? r instanceof d3_Rgb ? d3_rgb(r.r, r.g, r.b) : d3_rgb_parse("" + r, d3_rgb, d3_hsl_rgb) : d3_rgb(~~r, ~~g, ~~b); + }; + function d3_rgbNumber(value) { + return d3_rgb(value >> 16, value >> 8 & 255, value & 255); + } + function d3_rgbString(value) { + return d3_rgbNumber(value) + ""; + } + function d3_rgb(r, g, b) { + return new d3_Rgb(r, g, b); + } + function d3_Rgb(r, g, b) { + this.r = r; + this.g = g; + this.b = b; + } + var d3_rgbPrototype = d3_Rgb.prototype = new d3_Color(); + d3_rgbPrototype.brighter = function(k) { + k = Math.pow(.7, arguments.length ? k : 1); + var r = this.r, g = this.g, b = this.b, i = 30; + if (!r && !g && !b) return d3_rgb(i, i, i); + if (r && r < i) r = i; + if (g && g < i) g = i; + if (b && b < i) b = i; + return d3_rgb(Math.min(255, ~~(r / k)), Math.min(255, ~~(g / k)), Math.min(255, ~~(b / k))); + }; + d3_rgbPrototype.darker = function(k) { + k = Math.pow(.7, arguments.length ? k : 1); + return d3_rgb(~~(k * this.r), ~~(k * this.g), ~~(k * this.b)); + }; + d3_rgbPrototype.hsl = function() { + return d3_rgb_hsl(this.r, this.g, this.b); + }; + d3_rgbPrototype.toString = function() { + return "#" + d3_rgb_hex(this.r) + d3_rgb_hex(this.g) + d3_rgb_hex(this.b); + }; + function d3_rgb_hex(v) { + return v < 16 ? "0" + Math.max(0, v).toString(16) : Math.min(255, v).toString(16); + } + function d3_rgb_parse(format, rgb, hsl) { + var r = 0, g = 0, b = 0, m1, m2, color; + m1 = /([a-z]+)\((.*)\)/i.exec(format); + if (m1) { + m2 = m1[2].split(","); + switch (m1[1]) { + case "hsl": + { + return hsl(parseFloat(m2[0]), parseFloat(m2[1]) / 100, parseFloat(m2[2]) / 100); + } + + case "rgb": + { + return rgb(d3_rgb_parseNumber(m2[0]), d3_rgb_parseNumber(m2[1]), d3_rgb_parseNumber(m2[2])); + } + } + } + if (color = d3_rgb_names.get(format)) return rgb(color.r, color.g, color.b); + if (format != null && format.charAt(0) === "#" && !isNaN(color = parseInt(format.substring(1), 16))) { + if (format.length === 4) { + r = (color & 3840) >> 4; + r = r >> 4 | r; + g = color & 240; + g = g >> 4 | g; + b = color & 15; + b = b << 4 | b; + } else if (format.length === 7) { + r = (color & 16711680) >> 16; + g = (color & 65280) >> 8; + b = color & 255; + } + } + return rgb(r, g, b); + } + function d3_rgb_hsl(r, g, b) { + var min = Math.min(r /= 255, g /= 255, b /= 255), max = Math.max(r, g, b), d = max - min, h, s, l = (max + min) / 2; + if (d) { + s = l < .5 ? d / (max + min) : d / (2 - max - min); + if (r == max) h = (g - b) / d + (g < b ? 6 : 0); else if (g == max) h = (b - r) / d + 2; else h = (r - g) / d + 4; + h *= 60; + } else { + h = NaN; + s = l > 0 && l < 1 ? 0 : h; + } + return d3_hsl(h, s, l); + } + function d3_rgb_lab(r, g, b) { + r = d3_rgb_xyz(r); + g = d3_rgb_xyz(g); + b = d3_rgb_xyz(b); + var x = d3_xyz_lab((.4124564 * r + .3575761 * g + .1804375 * b) / d3_lab_X), y = d3_xyz_lab((.2126729 * r + .7151522 * g + .072175 * b) / d3_lab_Y), z = d3_xyz_lab((.0193339 * r + .119192 * g + .9503041 * b) / d3_lab_Z); + return d3_lab(116 * y - 16, 500 * (x - y), 200 * (y - z)); + } + function d3_rgb_xyz(r) { + return (r /= 255) <= .04045 ? r / 12.92 : Math.pow((r + .055) / 1.055, 2.4); + } + function d3_rgb_parseNumber(c) { + var f = parseFloat(c); + return c.charAt(c.length - 1) === "%" ? Math.round(f * 2.55) : f; + } + var d3_rgb_names = d3.map({ + aliceblue: 15792383, + antiquewhite: 16444375, + aqua: 65535, + aquamarine: 8388564, + azure: 15794175, + beige: 16119260, + bisque: 16770244, + black: 0, + blanchedalmond: 16772045, + blue: 255, + blueviolet: 9055202, + brown: 10824234, + burlywood: 14596231, + cadetblue: 6266528, + chartreuse: 8388352, + chocolate: 13789470, + coral: 16744272, + cornflowerblue: 6591981, + cornsilk: 16775388, + crimson: 14423100, + cyan: 65535, + darkblue: 139, + darkcyan: 35723, + darkgoldenrod: 12092939, + darkgray: 11119017, + darkgreen: 25600, + darkgrey: 11119017, + darkkhaki: 12433259, + darkmagenta: 9109643, + darkolivegreen: 5597999, + darkorange: 16747520, + darkorchid: 10040012, + darkred: 9109504, + darksalmon: 15308410, + darkseagreen: 9419919, + darkslateblue: 4734347, + darkslategray: 3100495, + darkslategrey: 3100495, + darkturquoise: 52945, + darkviolet: 9699539, + deeppink: 16716947, + deepskyblue: 49151, + dimgray: 6908265, + dimgrey: 6908265, + dodgerblue: 2003199, + firebrick: 11674146, + floralwhite: 16775920, + forestgreen: 2263842, + fuchsia: 16711935, + gainsboro: 14474460, + ghostwhite: 16316671, + gold: 16766720, + goldenrod: 14329120, + gray: 8421504, + green: 32768, + greenyellow: 11403055, + grey: 8421504, + honeydew: 15794160, + hotpink: 16738740, + indianred: 13458524, + indigo: 4915330, + ivory: 16777200, + khaki: 15787660, + lavender: 15132410, + lavenderblush: 16773365, + lawngreen: 8190976, + lemonchiffon: 16775885, + lightblue: 11393254, + lightcoral: 15761536, + lightcyan: 14745599, + lightgoldenrodyellow: 16448210, + lightgray: 13882323, + lightgreen: 9498256, + lightgrey: 13882323, + lightpink: 16758465, + lightsalmon: 16752762, + lightseagreen: 2142890, + lightskyblue: 8900346, + lightslategray: 7833753, + lightslategrey: 7833753, + lightsteelblue: 11584734, + lightyellow: 16777184, + lime: 65280, + limegreen: 3329330, + linen: 16445670, + magenta: 16711935, + maroon: 8388608, + mediumaquamarine: 6737322, + mediumblue: 205, + mediumorchid: 12211667, + mediumpurple: 9662683, + mediumseagreen: 3978097, + mediumslateblue: 8087790, + mediumspringgreen: 64154, + mediumturquoise: 4772300, + mediumvioletred: 13047173, + midnightblue: 1644912, + mintcream: 16121850, + mistyrose: 16770273, + moccasin: 16770229, + navajowhite: 16768685, + navy: 128, + oldlace: 16643558, + olive: 8421376, + olivedrab: 7048739, + orange: 16753920, + orangered: 16729344, + orchid: 14315734, + palegoldenrod: 15657130, + palegreen: 10025880, + paleturquoise: 11529966, + palevioletred: 14381203, + papayawhip: 16773077, + peachpuff: 16767673, + peru: 13468991, + pink: 16761035, + plum: 14524637, + powderblue: 11591910, + purple: 8388736, + red: 16711680, + rosybrown: 12357519, + royalblue: 4286945, + saddlebrown: 9127187, + salmon: 16416882, + sandybrown: 16032864, + seagreen: 3050327, + seashell: 16774638, + sienna: 10506797, + silver: 12632256, + skyblue: 8900331, + slateblue: 6970061, + slategray: 7372944, + slategrey: 7372944, + snow: 16775930, + springgreen: 65407, + steelblue: 4620980, + tan: 13808780, + teal: 32896, + thistle: 14204888, + tomato: 16737095, + turquoise: 4251856, + violet: 15631086, + wheat: 16113331, + white: 16777215, + whitesmoke: 16119285, + yellow: 16776960, + yellowgreen: 10145074 + }); + d3_rgb_names.forEach(function(key, value) { + d3_rgb_names.set(key, d3_rgbNumber(value)); + }); + function d3_functor(v) { + return typeof v === "function" ? v : function() { + return v; + }; + } + d3.functor = d3_functor; + function d3_identity(d) { + return d; + } + d3.xhr = d3_xhrType(d3_identity); + function d3_xhrType(response) { + return function(url, mimeType, callback) { + if (arguments.length === 2 && typeof mimeType === "function") callback = mimeType, + mimeType = null; + return d3_xhr(url, mimeType, response, callback); + }; + } + function d3_xhr(url, mimeType, response, callback) { + var xhr = {}, dispatch = d3.dispatch("beforesend", "progress", "load", "error"), headers = {}, request = new XMLHttpRequest(), responseType = null; + if (d3_window.XDomainRequest && !("withCredentials" in request) && /^(http(s)?:)?\/\//.test(url)) request = new XDomainRequest(); + "onload" in request ? request.onload = request.onerror = respond : request.onreadystatechange = function() { + request.readyState > 3 && respond(); + }; + function respond() { + var status = request.status, result; + if (!status && request.responseText || status >= 200 && status < 300 || status === 304) { + try { + result = response.call(xhr, request); + } catch (e) { + dispatch.error.call(xhr, e); + return; + } + dispatch.load.call(xhr, result); + } else { + dispatch.error.call(xhr, request); + } + } + request.onprogress = function(event) { + var o = d3.event; + d3.event = event; + try { + dispatch.progress.call(xhr, request); + } finally { + d3.event = o; + } + }; + xhr.header = function(name, value) { + name = (name + "").toLowerCase(); + if (arguments.length < 2) return headers[name]; + if (value == null) delete headers[name]; else headers[name] = value + ""; + return xhr; + }; + xhr.mimeType = function(value) { + if (!arguments.length) return mimeType; + mimeType = value == null ? null : value + ""; + return xhr; + }; + xhr.responseType = function(value) { + if (!arguments.length) return responseType; + responseType = value; + return xhr; + }; + xhr.response = function(value) { + response = value; + return xhr; + }; + [ "get", "post" ].forEach(function(method) { + xhr[method] = function() { + return xhr.send.apply(xhr, [ method ].concat(d3_array(arguments))); + }; + }); + xhr.send = function(method, data, callback) { + if (arguments.length === 2 && typeof data === "function") callback = data, data = null; + request.open(method, url, true); + if (mimeType != null && !("accept" in headers)) headers["accept"] = mimeType + ",*/*"; + if (request.setRequestHeader) for (var name in headers) request.setRequestHeader(name, headers[name]); + if (mimeType != null && request.overrideMimeType) request.overrideMimeType(mimeType); + if (responseType != null) request.responseType = responseType; + if (callback != null) xhr.on("error", callback).on("load", function(request) { + callback(null, request); + }); + dispatch.beforesend.call(xhr, request); + request.send(data == null ? null : data); + return xhr; + }; + xhr.abort = function() { + request.abort(); + return xhr; + }; + d3.rebind(xhr, dispatch, "on"); + return callback == null ? xhr : xhr.get(d3_xhr_fixCallback(callback)); + } + function d3_xhr_fixCallback(callback) { + return callback.length === 1 ? function(error, request) { + callback(error == null ? request : null); + } : callback; + } + d3.dsv = function(delimiter, mimeType) { + var reFormat = new RegExp('["' + delimiter + "\n]"), delimiterCode = delimiter.charCodeAt(0); + function dsv(url, row, callback) { + if (arguments.length < 3) callback = row, row = null; + var xhr = d3_xhr(url, mimeType, row == null ? response : typedResponse(row), callback); + xhr.row = function(_) { + return arguments.length ? xhr.response((row = _) == null ? response : typedResponse(_)) : row; + }; + return xhr; + } + function response(request) { + return dsv.parse(request.responseText); + } + function typedResponse(f) { + return function(request) { + return dsv.parse(request.responseText, f); + }; + } + dsv.parse = function(text, f) { + var o; + return dsv.parseRows(text, function(row, i) { + if (o) return o(row, i - 1); + var a = new Function("d", "return {" + row.map(function(name, i) { + return JSON.stringify(name) + ": d[" + i + "]"; + }).join(",") + "}"); + o = f ? function(row, i) { + return f(a(row), i); + } : a; + }); + }; + dsv.parseRows = function(text, f) { + var EOL = {}, EOF = {}, rows = [], N = text.length, I = 0, n = 0, t, eol; + function token() { + if (I >= N) return EOF; + if (eol) return eol = false, EOL; + var j = I; + if (text.charCodeAt(j) === 34) { + var i = j; + while (i++ < N) { + if (text.charCodeAt(i) === 34) { + if (text.charCodeAt(i + 1) !== 34) break; + ++i; + } + } + I = i + 2; + var c = text.charCodeAt(i + 1); + if (c === 13) { + eol = true; + if (text.charCodeAt(i + 2) === 10) ++I; + } else if (c === 10) { + eol = true; + } + return text.substring(j + 1, i).replace(/""/g, '"'); + } + while (I < N) { + var c = text.charCodeAt(I++), k = 1; + if (c === 10) eol = true; else if (c === 13) { + eol = true; + if (text.charCodeAt(I) === 10) ++I, ++k; + } else if (c !== delimiterCode) continue; + return text.substring(j, I - k); + } + return text.substring(j); + } + while ((t = token()) !== EOF) { + var a = []; + while (t !== EOL && t !== EOF) { + a.push(t); + t = token(); + } + if (f && !(a = f(a, n++))) continue; + rows.push(a); + } + return rows; + }; + dsv.format = function(rows) { + if (Array.isArray(rows[0])) return dsv.formatRows(rows); + var fieldSet = new d3_Set(), fields = []; + rows.forEach(function(row) { + for (var field in row) { + if (!fieldSet.has(field)) { + fields.push(fieldSet.add(field)); + } + } + }); + return [ fields.map(formatValue).join(delimiter) ].concat(rows.map(function(row) { + return fields.map(function(field) { + return formatValue(row[field]); + }).join(delimiter); + })).join("\n"); + }; + dsv.formatRows = function(rows) { + return rows.map(formatRow).join("\n"); + }; + function formatRow(row) { + return row.map(formatValue).join(delimiter); + } + function formatValue(text) { + return reFormat.test(text) ? '"' + text.replace(/\"/g, '""') + '"' : text; + } + return dsv; + }; + d3.csv = d3.dsv(",", "text/csv"); + d3.tsv = d3.dsv(" ", "text/tab-separated-values"); + d3.touch = function(container, touches, identifier) { + if (arguments.length < 3) identifier = touches, touches = d3_eventSource().changedTouches; + if (touches) for (var i = 0, n = touches.length, touch; i < n; ++i) { + if ((touch = touches[i]).identifier === identifier) { + return d3_mousePoint(container, touch); + } + } + }; + var d3_timer_queueHead, d3_timer_queueTail, d3_timer_interval, d3_timer_timeout, d3_timer_active, d3_timer_frame = d3_window[d3_vendorSymbol(d3_window, "requestAnimationFrame")] || function(callback) { + setTimeout(callback, 17); + }; + d3.timer = function(callback, delay, then) { + var n = arguments.length; + if (n < 2) delay = 0; + if (n < 3) then = Date.now(); + var time = then + delay, timer = { + c: callback, + t: time, + f: false, + n: null + }; + if (d3_timer_queueTail) d3_timer_queueTail.n = timer; else d3_timer_queueHead = timer; + d3_timer_queueTail = timer; + if (!d3_timer_interval) { + d3_timer_timeout = clearTimeout(d3_timer_timeout); + d3_timer_interval = 1; + d3_timer_frame(d3_timer_step); + } + }; + function d3_timer_step() { + var now = d3_timer_mark(), delay = d3_timer_sweep() - now; + if (delay > 24) { + if (isFinite(delay)) { + clearTimeout(d3_timer_timeout); + d3_timer_timeout = setTimeout(d3_timer_step, delay); + } + d3_timer_interval = 0; + } else { + d3_timer_interval = 1; + d3_timer_frame(d3_timer_step); + } + } + d3.timer.flush = function() { + d3_timer_mark(); + d3_timer_sweep(); + }; + function d3_timer_mark() { + var now = Date.now(); + d3_timer_active = d3_timer_queueHead; + while (d3_timer_active) { + if (now >= d3_timer_active.t) d3_timer_active.f = d3_timer_active.c(now - d3_timer_active.t); + d3_timer_active = d3_timer_active.n; + } + return now; + } + function d3_timer_sweep() { + var t0, t1 = d3_timer_queueHead, time = Infinity; + while (t1) { + if (t1.f) { + t1 = t0 ? t0.n = t1.n : d3_timer_queueHead = t1.n; + } else { + if (t1.t < time) time = t1.t; + t1 = (t0 = t1).n; + } + } + d3_timer_queueTail = t0; + return time; + } + function d3_format_precision(x, p) { + return p - (x ? Math.ceil(Math.log(x) / Math.LN10) : 1); + } + d3.round = function(x, n) { + return n ? Math.round(x * (n = Math.pow(10, n))) / n : Math.round(x); + }; + var d3_formatPrefixes = [ "y", "z", "a", "f", "p", "n", "µ", "m", "", "k", "M", "G", "T", "P", "E", "Z", "Y" ].map(d3_formatPrefix); + d3.formatPrefix = function(value, precision) { + var i = 0; + if (value) { + if (value < 0) value *= -1; + if (precision) value = d3.round(value, d3_format_precision(value, precision)); + i = 1 + Math.floor(1e-12 + Math.log(value) / Math.LN10); + i = Math.max(-24, Math.min(24, Math.floor((i - 1) / 3) * 3)); + } + return d3_formatPrefixes[8 + i / 3]; + }; + function d3_formatPrefix(d, i) { + var k = Math.pow(10, abs(8 - i) * 3); + return { + scale: i > 8 ? function(d) { + return d / k; + } : function(d) { + return d * k; + }, + symbol: d + }; + } + function d3_locale_numberFormat(locale) { + var locale_decimal = locale.decimal, locale_thousands = locale.thousands, locale_grouping = locale.grouping, locale_currency = locale.currency, formatGroup = locale_grouping ? function(value) { + var i = value.length, t = [], j = 0, g = locale_grouping[0]; + while (i > 0 && g > 0) { + t.push(value.substring(i -= g, i + g)); + g = locale_grouping[j = (j + 1) % locale_grouping.length]; + } + return t.reverse().join(locale_thousands); + } : d3_identity; + return function(specifier) { + var match = d3_format_re.exec(specifier), fill = match[1] || " ", align = match[2] || ">", sign = match[3] || "", symbol = match[4] || "", zfill = match[5], width = +match[6], comma = match[7], precision = match[8], type = match[9], scale = 1, prefix = "", suffix = "", integer = false; + if (precision) precision = +precision.substring(1); + if (zfill || fill === "0" && align === "=") { + zfill = fill = "0"; + align = "="; + if (comma) width -= Math.floor((width - 1) / 4); + } + switch (type) { + case "n": + comma = true; + type = "g"; + break; + + case "%": + scale = 100; + suffix = "%"; + type = "f"; + break; + + case "p": + scale = 100; + suffix = "%"; + type = "r"; + break; + + case "b": + case "o": + case "x": + case "X": + if (symbol === "#") prefix = "0" + type.toLowerCase(); + + case "c": + case "d": + integer = true; + precision = 0; + break; + + case "s": + scale = -1; + type = "r"; + break; + } + if (symbol === "$") prefix = locale_currency[0], suffix = locale_currency[1]; + if (type == "r" && !precision) type = "g"; + if (precision != null) { + if (type == "g") precision = Math.max(1, Math.min(21, precision)); else if (type == "e" || type == "f") precision = Math.max(0, Math.min(20, precision)); + } + type = d3_format_types.get(type) || d3_format_typeDefault; + var zcomma = zfill && comma; + return function(value) { + var fullSuffix = suffix; + if (integer && value % 1) return ""; + var negative = value < 0 || value === 0 && 1 / value < 0 ? (value = -value, "-") : sign; + if (scale < 0) { + var unit = d3.formatPrefix(value, precision); + value = unit.scale(value); + fullSuffix = unit.symbol + suffix; + } else { + value *= scale; + } + value = type(value, precision); + var i = value.lastIndexOf("."), before = i < 0 ? value : value.substring(0, i), after = i < 0 ? "" : locale_decimal + value.substring(i + 1); + if (!zfill && comma) before = formatGroup(before); + var length = prefix.length + before.length + after.length + (zcomma ? 0 : negative.length), padding = length < width ? new Array(length = width - length + 1).join(fill) : ""; + if (zcomma) before = formatGroup(padding + before); + negative += prefix; + value = before + after; + return (align === "<" ? negative + value + padding : align === ">" ? padding + negative + value : align === "^" ? padding.substring(0, length >>= 1) + negative + value + padding.substring(length) : negative + (zcomma ? value : padding + value)) + fullSuffix; + }; + }; + } + var d3_format_re = /(?:([^{])?([<>=^]))?([+\- ])?([$#])?(0)?(\d+)?(,)?(\.-?\d+)?([a-z%])?/i; + var d3_format_types = d3.map({ + b: function(x) { + return x.toString(2); + }, + c: function(x) { + return String.fromCharCode(x); + }, + o: function(x) { + return x.toString(8); + }, + x: function(x) { + return x.toString(16); + }, + X: function(x) { + return x.toString(16).toUpperCase(); + }, + g: function(x, p) { + return x.toPrecision(p); + }, + e: function(x, p) { + return x.toExponential(p); + }, + f: function(x, p) { + return x.toFixed(p); + }, + r: function(x, p) { + return (x = d3.round(x, d3_format_precision(x, p))).toFixed(Math.max(0, Math.min(20, d3_format_precision(x * (1 + 1e-15), p)))); + } + }); + function d3_format_typeDefault(x) { + return x + ""; + } + var d3_time = d3.time = {}, d3_date = Date; + function d3_date_utc() { + this._ = new Date(arguments.length > 1 ? Date.UTC.apply(this, arguments) : arguments[0]); + } + d3_date_utc.prototype = { + getDate: function() { + return this._.getUTCDate(); + }, + getDay: function() { + return this._.getUTCDay(); + }, + getFullYear: function() { + return this._.getUTCFullYear(); + }, + getHours: function() { + return this._.getUTCHours(); + }, + getMilliseconds: function() { + return this._.getUTCMilliseconds(); + }, + getMinutes: function() { + return this._.getUTCMinutes(); + }, + getMonth: function() { + return this._.getUTCMonth(); + }, + getSeconds: function() { + return this._.getUTCSeconds(); + }, + getTime: function() { + return this._.getTime(); + }, + getTimezoneOffset: function() { + return 0; + }, + valueOf: function() { + return this._.valueOf(); + }, + setDate: function() { + d3_time_prototype.setUTCDate.apply(this._, arguments); + }, + setDay: function() { + d3_time_prototype.setUTCDay.apply(this._, arguments); + }, + setFullYear: function() { + d3_time_prototype.setUTCFullYear.apply(this._, arguments); + }, + setHours: function() { + d3_time_prototype.setUTCHours.apply(this._, arguments); + }, + setMilliseconds: function() { + d3_time_prototype.setUTCMilliseconds.apply(this._, arguments); + }, + setMinutes: function() { + d3_time_prototype.setUTCMinutes.apply(this._, arguments); + }, + setMonth: function() { + d3_time_prototype.setUTCMonth.apply(this._, arguments); + }, + setSeconds: function() { + d3_time_prototype.setUTCSeconds.apply(this._, arguments); + }, + setTime: function() { + d3_time_prototype.setTime.apply(this._, arguments); + } + }; + var d3_time_prototype = Date.prototype; + function d3_time_interval(local, step, number) { + function round(date) { + var d0 = local(date), d1 = offset(d0, 1); + return date - d0 < d1 - date ? d0 : d1; + } + function ceil(date) { + step(date = local(new d3_date(date - 1)), 1); + return date; + } + function offset(date, k) { + step(date = new d3_date(+date), k); + return date; + } + function range(t0, t1, dt) { + var time = ceil(t0), times = []; + if (dt > 1) { + while (time < t1) { + if (!(number(time) % dt)) times.push(new Date(+time)); + step(time, 1); + } + } else { + while (time < t1) times.push(new Date(+time)), step(time, 1); + } + return times; + } + function range_utc(t0, t1, dt) { + try { + d3_date = d3_date_utc; + var utc = new d3_date_utc(); + utc._ = t0; + return range(utc, t1, dt); + } finally { + d3_date = Date; + } + } + local.floor = local; + local.round = round; + local.ceil = ceil; + local.offset = offset; + local.range = range; + var utc = local.utc = d3_time_interval_utc(local); + utc.floor = utc; + utc.round = d3_time_interval_utc(round); + utc.ceil = d3_time_interval_utc(ceil); + utc.offset = d3_time_interval_utc(offset); + utc.range = range_utc; + return local; + } + function d3_time_interval_utc(method) { + return function(date, k) { + try { + d3_date = d3_date_utc; + var utc = new d3_date_utc(); + utc._ = date; + return method(utc, k)._; + } finally { + d3_date = Date; + } + }; + } + d3_time.year = d3_time_interval(function(date) { + date = d3_time.day(date); + date.setMonth(0, 1); + return date; + }, function(date, offset) { + date.setFullYear(date.getFullYear() + offset); + }, function(date) { + return date.getFullYear(); + }); + d3_time.years = d3_time.year.range; + d3_time.years.utc = d3_time.year.utc.range; + d3_time.day = d3_time_interval(function(date) { + var day = new d3_date(2e3, 0); + day.setFullYear(date.getFullYear(), date.getMonth(), date.getDate()); + return day; + }, function(date, offset) { + date.setDate(date.getDate() + offset); + }, function(date) { + return date.getDate() - 1; + }); + d3_time.days = d3_time.day.range; + d3_time.days.utc = d3_time.day.utc.range; + d3_time.dayOfYear = function(date) { + var year = d3_time.year(date); + return Math.floor((date - year - (date.getTimezoneOffset() - year.getTimezoneOffset()) * 6e4) / 864e5); + }; + [ "sunday", "monday", "tuesday", "wednesday", "thursday", "friday", "saturday" ].forEach(function(day, i) { + i = 7 - i; + var interval = d3_time[day] = d3_time_interval(function(date) { + (date = d3_time.day(date)).setDate(date.getDate() - (date.getDay() + i) % 7); + return date; + }, function(date, offset) { + date.setDate(date.getDate() + Math.floor(offset) * 7); + }, function(date) { + var day = d3_time.year(date).getDay(); + return Math.floor((d3_time.dayOfYear(date) + (day + i) % 7) / 7) - (day !== i); + }); + d3_time[day + "s"] = interval.range; + d3_time[day + "s"].utc = interval.utc.range; + d3_time[day + "OfYear"] = function(date) { + var day = d3_time.year(date).getDay(); + return Math.floor((d3_time.dayOfYear(date) + (day + i) % 7) / 7); + }; + }); + d3_time.week = d3_time.sunday; + d3_time.weeks = d3_time.sunday.range; + d3_time.weeks.utc = d3_time.sunday.utc.range; + d3_time.weekOfYear = d3_time.sundayOfYear; + function d3_locale_timeFormat(locale) { + var locale_dateTime = locale.dateTime, locale_date = locale.date, locale_time = locale.time, locale_periods = locale.periods, locale_days = locale.days, locale_shortDays = locale.shortDays, locale_months = locale.months, locale_shortMonths = locale.shortMonths; + function d3_time_format(template) { + var n = template.length; + function format(date) { + var string = [], i = -1, j = 0, c, p, f; + while (++i < n) { + if (template.charCodeAt(i) === 37) { + string.push(template.substring(j, i)); + if ((p = d3_time_formatPads[c = template.charAt(++i)]) != null) c = template.charAt(++i); + if (f = d3_time_formats[c]) c = f(date, p == null ? c === "e" ? " " : "0" : p); + string.push(c); + j = i + 1; + } + } + string.push(template.substring(j, i)); + return string.join(""); + } + format.parse = function(string) { + var d = { + y: 1900, + m: 0, + d: 1, + H: 0, + M: 0, + S: 0, + L: 0, + Z: null + }, i = d3_time_parse(d, template, string, 0); + if (i != string.length) return null; + if ("p" in d) d.H = d.H % 12 + d.p * 12; + var localZ = d.Z != null && d3_date !== d3_date_utc, date = new (localZ ? d3_date_utc : d3_date)(); + if ("j" in d) date.setFullYear(d.y, 0, d.j); else if ("w" in d && ("W" in d || "U" in d)) { + date.setFullYear(d.y, 0, 1); + date.setFullYear(d.y, 0, "W" in d ? (d.w + 6) % 7 + d.W * 7 - (date.getDay() + 5) % 7 : d.w + d.U * 7 - (date.getDay() + 6) % 7); + } else date.setFullYear(d.y, d.m, d.d); + date.setHours(d.H + Math.floor(d.Z / 100), d.M + d.Z % 100, d.S, d.L); + return localZ ? date._ : date; + }; + format.toString = function() { + return template; + }; + return format; + } + function d3_time_parse(date, template, string, j) { + var c, p, t, i = 0, n = template.length, m = string.length; + while (i < n) { + if (j >= m) return -1; + c = template.charCodeAt(i++); + if (c === 37) { + t = template.charAt(i++); + p = d3_time_parsers[t in d3_time_formatPads ? template.charAt(i++) : t]; + if (!p || (j = p(date, string, j)) < 0) return -1; + } else if (c != string.charCodeAt(j++)) { + return -1; + } + } + return j; + } + d3_time_format.utc = function(template) { + var local = d3_time_format(template); + function format(date) { + try { + d3_date = d3_date_utc; + var utc = new d3_date(); + utc._ = date; + return local(utc); + } finally { + d3_date = Date; + } + } + format.parse = function(string) { + try { + d3_date = d3_date_utc; + var date = local.parse(string); + return date && date._; + } finally { + d3_date = Date; + } + }; + format.toString = local.toString; + return format; + }; + d3_time_format.multi = d3_time_format.utc.multi = d3_time_formatMulti; + var d3_time_periodLookup = d3.map(), d3_time_dayRe = d3_time_formatRe(locale_days), d3_time_dayLookup = d3_time_formatLookup(locale_days), d3_time_dayAbbrevRe = d3_time_formatRe(locale_shortDays), d3_time_dayAbbrevLookup = d3_time_formatLookup(locale_shortDays), d3_time_monthRe = d3_time_formatRe(locale_months), d3_time_monthLookup = d3_time_formatLookup(locale_months), d3_time_monthAbbrevRe = d3_time_formatRe(locale_shortMonths), d3_time_monthAbbrevLookup = d3_time_formatLookup(locale_shortMonths); + locale_periods.forEach(function(p, i) { + d3_time_periodLookup.set(p.toLowerCase(), i); + }); + var d3_time_formats = { + a: function(d) { + return locale_shortDays[d.getDay()]; + }, + A: function(d) { + return locale_days[d.getDay()]; + }, + b: function(d) { + return locale_shortMonths[d.getMonth()]; + }, + B: function(d) { + return locale_months[d.getMonth()]; + }, + c: d3_time_format(locale_dateTime), + d: function(d, p) { + return d3_time_formatPad(d.getDate(), p, 2); + }, + e: function(d, p) { + return d3_time_formatPad(d.getDate(), p, 2); + }, + H: function(d, p) { + return d3_time_formatPad(d.getHours(), p, 2); + }, + I: function(d, p) { + return d3_time_formatPad(d.getHours() % 12 || 12, p, 2); + }, + j: function(d, p) { + return d3_time_formatPad(1 + d3_time.dayOfYear(d), p, 3); + }, + L: function(d, p) { + return d3_time_formatPad(d.getMilliseconds(), p, 3); + }, + m: function(d, p) { + return d3_time_formatPad(d.getMonth() + 1, p, 2); + }, + M: function(d, p) { + return d3_time_formatPad(d.getMinutes(), p, 2); + }, + p: function(d) { + return locale_periods[+(d.getHours() >= 12)]; + }, + S: function(d, p) { + return d3_time_formatPad(d.getSeconds(), p, 2); + }, + U: function(d, p) { + return d3_time_formatPad(d3_time.sundayOfYear(d), p, 2); + }, + w: function(d) { + return d.getDay(); + }, + W: function(d, p) { + return d3_time_formatPad(d3_time.mondayOfYear(d), p, 2); + }, + x: d3_time_format(locale_date), + X: d3_time_format(locale_time), + y: function(d, p) { + return d3_time_formatPad(d.getFullYear() % 100, p, 2); + }, + Y: function(d, p) { + return d3_time_formatPad(d.getFullYear() % 1e4, p, 4); + }, + Z: d3_time_zone, + "%": function() { + return "%"; + } + }; + var d3_time_parsers = { + a: d3_time_parseWeekdayAbbrev, + A: d3_time_parseWeekday, + b: d3_time_parseMonthAbbrev, + B: d3_time_parseMonth, + c: d3_time_parseLocaleFull, + d: d3_time_parseDay, + e: d3_time_parseDay, + H: d3_time_parseHour24, + I: d3_time_parseHour24, + j: d3_time_parseDayOfYear, + L: d3_time_parseMilliseconds, + m: d3_time_parseMonthNumber, + M: d3_time_parseMinutes, + p: d3_time_parseAmPm, + S: d3_time_parseSeconds, + U: d3_time_parseWeekNumberSunday, + w: d3_time_parseWeekdayNumber, + W: d3_time_parseWeekNumberMonday, + x: d3_time_parseLocaleDate, + X: d3_time_parseLocaleTime, + y: d3_time_parseYear, + Y: d3_time_parseFullYear, + Z: d3_time_parseZone, + "%": d3_time_parseLiteralPercent + }; + function d3_time_parseWeekdayAbbrev(date, string, i) { + d3_time_dayAbbrevRe.lastIndex = 0; + var n = d3_time_dayAbbrevRe.exec(string.substring(i)); + return n ? (date.w = d3_time_dayAbbrevLookup.get(n[0].toLowerCase()), i + n[0].length) : -1; + } + function d3_time_parseWeekday(date, string, i) { + d3_time_dayRe.lastIndex = 0; + var n = d3_time_dayRe.exec(string.substring(i)); + return n ? (date.w = d3_time_dayLookup.get(n[0].toLowerCase()), i + n[0].length) : -1; + } + function d3_time_parseMonthAbbrev(date, string, i) { + d3_time_monthAbbrevRe.lastIndex = 0; + var n = d3_time_monthAbbrevRe.exec(string.substring(i)); + return n ? (date.m = d3_time_monthAbbrevLookup.get(n[0].toLowerCase()), i + n[0].length) : -1; + } + function d3_time_parseMonth(date, string, i) { + d3_time_monthRe.lastIndex = 0; + var n = d3_time_monthRe.exec(string.substring(i)); + return n ? (date.m = d3_time_monthLookup.get(n[0].toLowerCase()), i + n[0].length) : -1; + } + function d3_time_parseLocaleFull(date, string, i) { + return d3_time_parse(date, d3_time_formats.c.toString(), string, i); + } + function d3_time_parseLocaleDate(date, string, i) { + return d3_time_parse(date, d3_time_formats.x.toString(), string, i); + } + function d3_time_parseLocaleTime(date, string, i) { + return d3_time_parse(date, d3_time_formats.X.toString(), string, i); + } + function d3_time_parseAmPm(date, string, i) { + var n = d3_time_periodLookup.get(string.substring(i, i += 2).toLowerCase()); + return n == null ? -1 : (date.p = n, i); + } + return d3_time_format; + } + var d3_time_formatPads = { + "-": "", + _: " ", + "0": "0" + }, d3_time_numberRe = /^\s*\d+/, d3_time_percentRe = /^%/; + function d3_time_formatPad(value, fill, width) { + var sign = value < 0 ? "-" : "", string = (sign ? -value : value) + "", length = string.length; + return sign + (length < width ? new Array(width - length + 1).join(fill) + string : string); + } + function d3_time_formatRe(names) { + return new RegExp("^(?:" + names.map(d3.requote).join("|") + ")", "i"); + } + function d3_time_formatLookup(names) { + var map = new d3_Map(), i = -1, n = names.length; + while (++i < n) map.set(names[i].toLowerCase(), i); + return map; + } + function d3_time_parseWeekdayNumber(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 1)); + return n ? (date.w = +n[0], i + n[0].length) : -1; + } + function d3_time_parseWeekNumberSunday(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i)); + return n ? (date.U = +n[0], i + n[0].length) : -1; + } + function d3_time_parseWeekNumberMonday(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i)); + return n ? (date.W = +n[0], i + n[0].length) : -1; + } + function d3_time_parseFullYear(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 4)); + return n ? (date.y = +n[0], i + n[0].length) : -1; + } + function d3_time_parseYear(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 2)); + return n ? (date.y = d3_time_expandYear(+n[0]), i + n[0].length) : -1; + } + function d3_time_parseZone(date, string, i) { + return /^[+-]\d{4}$/.test(string = string.substring(i, i + 5)) ? (date.Z = -string, + i + 5) : -1; + } + function d3_time_expandYear(d) { + return d + (d > 68 ? 1900 : 2e3); + } + function d3_time_parseMonthNumber(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 2)); + return n ? (date.m = n[0] - 1, i + n[0].length) : -1; + } + function d3_time_parseDay(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 2)); + return n ? (date.d = +n[0], i + n[0].length) : -1; + } + function d3_time_parseDayOfYear(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 3)); + return n ? (date.j = +n[0], i + n[0].length) : -1; + } + function d3_time_parseHour24(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 2)); + return n ? (date.H = +n[0], i + n[0].length) : -1; + } + function d3_time_parseMinutes(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 2)); + return n ? (date.M = +n[0], i + n[0].length) : -1; + } + function d3_time_parseSeconds(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 2)); + return n ? (date.S = +n[0], i + n[0].length) : -1; + } + function d3_time_parseMilliseconds(date, string, i) { + d3_time_numberRe.lastIndex = 0; + var n = d3_time_numberRe.exec(string.substring(i, i + 3)); + return n ? (date.L = +n[0], i + n[0].length) : -1; + } + function d3_time_zone(d) { + var z = d.getTimezoneOffset(), zs = z > 0 ? "-" : "+", zh = ~~(abs(z) / 60), zm = abs(z) % 60; + return zs + d3_time_formatPad(zh, "0", 2) + d3_time_formatPad(zm, "0", 2); + } + function d3_time_parseLiteralPercent(date, string, i) { + d3_time_percentRe.lastIndex = 0; + var n = d3_time_percentRe.exec(string.substring(i, i + 1)); + return n ? i + n[0].length : -1; + } + function d3_time_formatMulti(formats) { + var n = formats.length, i = -1; + while (++i < n) formats[i][0] = this(formats[i][0]); + return function(date) { + var i = 0, f = formats[i]; + while (!f[1](date)) f = formats[++i]; + return f[0](date); + }; + } + d3.locale = function(locale) { + return { + numberFormat: d3_locale_numberFormat(locale), + timeFormat: d3_locale_timeFormat(locale) + }; + }; + var d3_locale_enUS = d3.locale({ + decimal: ".", + thousands: ",", + grouping: [ 3 ], + currency: [ "$", "" ], + dateTime: "%a %b %e %X %Y", + date: "%m/%d/%Y", + time: "%H:%M:%S", + periods: [ "AM", "PM" ], + days: [ "Sunday", "Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday" ], + shortDays: [ "Sun", "Mon", "Tue", "Wed", "Thu", "Fri", "Sat" ], + months: [ "January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December" ], + shortMonths: [ "Jan", "Feb", "Mar", "Apr", "May", "Jun", "Jul", "Aug", "Sep", "Oct", "Nov", "Dec" ] + }); + d3.format = d3_locale_enUS.numberFormat; + d3.geo = {}; + function d3_adder() {} + d3_adder.prototype = { + s: 0, + t: 0, + add: function(y) { + d3_adderSum(y, this.t, d3_adderTemp); + d3_adderSum(d3_adderTemp.s, this.s, this); + if (this.s) this.t += d3_adderTemp.t; else this.s = d3_adderTemp.t; + }, + reset: function() { + this.s = this.t = 0; + }, + valueOf: function() { + return this.s; + } + }; + var d3_adderTemp = new d3_adder(); + function d3_adderSum(a, b, o) { + var x = o.s = a + b, bv = x - a, av = x - bv; + o.t = a - av + (b - bv); + } + d3.geo.stream = function(object, listener) { + if (object && d3_geo_streamObjectType.hasOwnProperty(object.type)) { + d3_geo_streamObjectType[object.type](object, listener); + } else { + d3_geo_streamGeometry(object, listener); + } + }; + function d3_geo_streamGeometry(geometry, listener) { + if (geometry && d3_geo_streamGeometryType.hasOwnProperty(geometry.type)) { + d3_geo_streamGeometryType[geometry.type](geometry, listener); + } + } + var d3_geo_streamObjectType = { + Feature: function(feature, listener) { + d3_geo_streamGeometry(feature.geometry, listener); + }, + FeatureCollection: function(object, listener) { + var features = object.features, i = -1, n = features.length; + while (++i < n) d3_geo_streamGeometry(features[i].geometry, listener); + } + }; + var d3_geo_streamGeometryType = { + Sphere: function(object, listener) { + listener.sphere(); + }, + Point: function(object, listener) { + object = object.coordinates; + listener.point(object[0], object[1], object[2]); + }, + MultiPoint: function(object, listener) { + var coordinates = object.coordinates, i = -1, n = coordinates.length; + while (++i < n) object = coordinates[i], listener.point(object[0], object[1], object[2]); + }, + LineString: function(object, listener) { + d3_geo_streamLine(object.coordinates, listener, 0); + }, + MultiLineString: function(object, listener) { + var coordinates = object.coordinates, i = -1, n = coordinates.length; + while (++i < n) d3_geo_streamLine(coordinates[i], listener, 0); + }, + Polygon: function(object, listener) { + d3_geo_streamPolygon(object.coordinates, listener); + }, + MultiPolygon: function(object, listener) { + var coordinates = object.coordinates, i = -1, n = coordinates.length; + while (++i < n) d3_geo_streamPolygon(coordinates[i], listener); + }, + GeometryCollection: function(object, listener) { + var geometries = object.geometries, i = -1, n = geometries.length; + while (++i < n) d3_geo_streamGeometry(geometries[i], listener); + } + }; + function d3_geo_streamLine(coordinates, listener, closed) { + var i = -1, n = coordinates.length - closed, coordinate; + listener.lineStart(); + while (++i < n) coordinate = coordinates[i], listener.point(coordinate[0], coordinate[1], coordinate[2]); + listener.lineEnd(); + } + function d3_geo_streamPolygon(coordinates, listener) { + var i = -1, n = coordinates.length; + listener.polygonStart(); + while (++i < n) d3_geo_streamLine(coordinates[i], listener, 1); + listener.polygonEnd(); + } + d3.geo.area = function(object) { + d3_geo_areaSum = 0; + d3.geo.stream(object, d3_geo_area); + return d3_geo_areaSum; + }; + var d3_geo_areaSum, d3_geo_areaRingSum = new d3_adder(); + var d3_geo_area = { + sphere: function() { + d3_geo_areaSum += 4 * π; + }, + point: d3_noop, + lineStart: d3_noop, + lineEnd: d3_noop, + polygonStart: function() { + d3_geo_areaRingSum.reset(); + d3_geo_area.lineStart = d3_geo_areaRingStart; + }, + polygonEnd: function() { + var area = 2 * d3_geo_areaRingSum; + d3_geo_areaSum += area < 0 ? 4 * π + area : area; + d3_geo_area.lineStart = d3_geo_area.lineEnd = d3_geo_area.point = d3_noop; + } + }; + function d3_geo_areaRingStart() { + var λ00, φ00, λ0, cosφ0, sinφ0; + d3_geo_area.point = function(λ, φ) { + d3_geo_area.point = nextPoint; + λ0 = (λ00 = λ) * d3_radians, cosφ0 = Math.cos(φ = (φ00 = φ) * d3_radians / 2 + π / 4), + sinφ0 = Math.sin(φ); + }; + function nextPoint(λ, φ) { + λ *= d3_radians; + φ = φ * d3_radians / 2 + π / 4; + var dλ = λ - λ0, sdλ = dλ >= 0 ? 1 : -1, adλ = sdλ * dλ, cosφ = Math.cos(φ), sinφ = Math.sin(φ), k = sinφ0 * sinφ, u = cosφ0 * cosφ + k * Math.cos(adλ), v = k * sdλ * Math.sin(adλ); + d3_geo_areaRingSum.add(Math.atan2(v, u)); + λ0 = λ, cosφ0 = cosφ, sinφ0 = sinφ; + } + d3_geo_area.lineEnd = function() { + nextPoint(λ00, φ00); + }; + } + function d3_geo_cartesian(spherical) { + var λ = spherical[0], φ = spherical[1], cosφ = Math.cos(φ); + return [ cosφ * Math.cos(λ), cosφ * Math.sin(λ), Math.sin(φ) ]; + } + function d3_geo_cartesianDot(a, b) { + return a[0] * b[0] + a[1] * b[1] + a[2] * b[2]; + } + function d3_geo_cartesianCross(a, b) { + return [ a[1] * b[2] - a[2] * b[1], a[2] * b[0] - a[0] * b[2], a[0] * b[1] - a[1] * b[0] ]; + } + function d3_geo_cartesianAdd(a, b) { + a[0] += b[0]; + a[1] += b[1]; + a[2] += b[2]; + } + function d3_geo_cartesianScale(vector, k) { + return [ vector[0] * k, vector[1] * k, vector[2] * k ]; + } + function d3_geo_cartesianNormalize(d) { + var l = Math.sqrt(d[0] * d[0] + d[1] * d[1] + d[2] * d[2]); + d[0] /= l; + d[1] /= l; + d[2] /= l; + } + function d3_geo_spherical(cartesian) { + return [ Math.atan2(cartesian[1], cartesian[0]), d3_asin(cartesian[2]) ]; + } + function d3_geo_sphericalEqual(a, b) { + return abs(a[0] - b[0]) < ε && abs(a[1] - b[1]) < ε; + } + d3.geo.bounds = function() { + var λ0, φ0, λ1, φ1, λ_, λ__, φ__, p0, dλSum, ranges, range; + var bound = { + point: point, + lineStart: lineStart, + lineEnd: lineEnd, + polygonStart: function() { + bound.point = ringPoint; + bound.lineStart = ringStart; + bound.lineEnd = ringEnd; + dλSum = 0; + d3_geo_area.polygonStart(); + }, + polygonEnd: function() { + d3_geo_area.polygonEnd(); + bound.point = point; + bound.lineStart = lineStart; + bound.lineEnd = lineEnd; + if (d3_geo_areaRingSum < 0) λ0 = -(λ1 = 180), φ0 = -(φ1 = 90); else if (dλSum > ε) φ1 = 90; else if (dλSum < -ε) φ0 = -90; + range[0] = λ0, range[1] = λ1; + } + }; + function point(λ, φ) { + ranges.push(range = [ λ0 = λ, λ1 = λ ]); + if (φ < φ0) φ0 = φ; + if (φ > φ1) φ1 = φ; + } + function linePoint(λ, φ) { + var p = d3_geo_cartesian([ λ * d3_radians, φ * d3_radians ]); + if (p0) { + var normal = d3_geo_cartesianCross(p0, p), equatorial = [ normal[1], -normal[0], 0 ], inflection = d3_geo_cartesianCross(equatorial, normal); + d3_geo_cartesianNormalize(inflection); + inflection = d3_geo_spherical(inflection); + var dλ = λ - λ_, s = dλ > 0 ? 1 : -1, λi = inflection[0] * d3_degrees * s, antimeridian = abs(dλ) > 180; + if (antimeridian ^ (s * λ_ < λi && λi < s * λ)) { + var φi = inflection[1] * d3_degrees; + if (φi > φ1) φ1 = φi; + } else if (λi = (λi + 360) % 360 - 180, antimeridian ^ (s * λ_ < λi && λi < s * λ)) { + var φi = -inflection[1] * d3_degrees; + if (φi < φ0) φ0 = φi; + } else { + if (φ < φ0) φ0 = φ; + if (φ > φ1) φ1 = φ; + } + if (antimeridian) { + if (λ < λ_) { + if (angle(λ0, λ) > angle(λ0, λ1)) λ1 = λ; + } else { + if (angle(λ, λ1) > angle(λ0, λ1)) λ0 = λ; + } + } else { + if (λ1 >= λ0) { + if (λ < λ0) λ0 = λ; + if (λ > λ1) λ1 = λ; + } else { + if (λ > λ_) { + if (angle(λ0, λ) > angle(λ0, λ1)) λ1 = λ; + } else { + if (angle(λ, λ1) > angle(λ0, λ1)) λ0 = λ; + } + } + } + } else { + point(λ, φ); + } + p0 = p, λ_ = λ; + } + function lineStart() { + bound.point = linePoint; + } + function lineEnd() { + range[0] = λ0, range[1] = λ1; + bound.point = point; + p0 = null; + } + function ringPoint(λ, φ) { + if (p0) { + var dλ = λ - λ_; + dλSum += abs(dλ) > 180 ? dλ + (dλ > 0 ? 360 : -360) : dλ; + } else λ__ = λ, φ__ = φ; + d3_geo_area.point(λ, φ); + linePoint(λ, φ); + } + function ringStart() { + d3_geo_area.lineStart(); + } + function ringEnd() { + ringPoint(λ__, φ__); + d3_geo_area.lineEnd(); + if (abs(dλSum) > ε) λ0 = -(λ1 = 180); + range[0] = λ0, range[1] = λ1; + p0 = null; + } + function angle(λ0, λ1) { + return (λ1 -= λ0) < 0 ? λ1 + 360 : λ1; + } + function compareRanges(a, b) { + return a[0] - b[0]; + } + function withinRange(x, range) { + return range[0] <= range[1] ? range[0] <= x && x <= range[1] : x < range[0] || range[1] < x; + } + return function(feature) { + φ1 = λ1 = -(λ0 = φ0 = Infinity); + ranges = []; + d3.geo.stream(feature, bound); + var n = ranges.length; + if (n) { + ranges.sort(compareRanges); + for (var i = 1, a = ranges[0], b, merged = [ a ]; i < n; ++i) { + b = ranges[i]; + if (withinRange(b[0], a) || withinRange(b[1], a)) { + if (angle(a[0], b[1]) > angle(a[0], a[1])) a[1] = b[1]; + if (angle(b[0], a[1]) > angle(a[0], a[1])) a[0] = b[0]; + } else { + merged.push(a = b); + } + } + var best = -Infinity, dλ; + for (var n = merged.length - 1, i = 0, a = merged[n], b; i <= n; a = b, ++i) { + b = merged[i]; + if ((dλ = angle(a[1], b[0])) > best) best = dλ, λ0 = b[0], λ1 = a[1]; + } + } + ranges = range = null; + return λ0 === Infinity || φ0 === Infinity ? [ [ NaN, NaN ], [ NaN, NaN ] ] : [ [ λ0, φ0 ], [ λ1, φ1 ] ]; + }; + }(); + d3.geo.centroid = function(object) { + d3_geo_centroidW0 = d3_geo_centroidW1 = d3_geo_centroidX0 = d3_geo_centroidY0 = d3_geo_centroidZ0 = d3_geo_centroidX1 = d3_geo_centroidY1 = d3_geo_centroidZ1 = d3_geo_centroidX2 = d3_geo_centroidY2 = d3_geo_centroidZ2 = 0; + d3.geo.stream(object, d3_geo_centroid); + var x = d3_geo_centroidX2, y = d3_geo_centroidY2, z = d3_geo_centroidZ2, m = x * x + y * y + z * z; + if (m < ε2) { + x = d3_geo_centroidX1, y = d3_geo_centroidY1, z = d3_geo_centroidZ1; + if (d3_geo_centroidW1 < ε) x = d3_geo_centroidX0, y = d3_geo_centroidY0, z = d3_geo_centroidZ0; + m = x * x + y * y + z * z; + if (m < ε2) return [ NaN, NaN ]; + } + return [ Math.atan2(y, x) * d3_degrees, d3_asin(z / Math.sqrt(m)) * d3_degrees ]; + }; + var d3_geo_centroidW0, d3_geo_centroidW1, d3_geo_centroidX0, d3_geo_centroidY0, d3_geo_centroidZ0, d3_geo_centroidX1, d3_geo_centroidY1, d3_geo_centroidZ1, d3_geo_centroidX2, d3_geo_centroidY2, d3_geo_centroidZ2; + var d3_geo_centroid = { + sphere: d3_noop, + point: d3_geo_centroidPoint, + lineStart: d3_geo_centroidLineStart, + lineEnd: d3_geo_centroidLineEnd, + polygonStart: function() { + d3_geo_centroid.lineStart = d3_geo_centroidRingStart; + }, + polygonEnd: function() { + d3_geo_centroid.lineStart = d3_geo_centroidLineStart; + } + }; + function d3_geo_centroidPoint(λ, φ) { + λ *= d3_radians; + var cosφ = Math.cos(φ *= d3_radians); + d3_geo_centroidPointXYZ(cosφ * Math.cos(λ), cosφ * Math.sin(λ), Math.sin(φ)); + } + function d3_geo_centroidPointXYZ(x, y, z) { + ++d3_geo_centroidW0; + d3_geo_centroidX0 += (x - d3_geo_centroidX0) / d3_geo_centroidW0; + d3_geo_centroidY0 += (y - d3_geo_centroidY0) / d3_geo_centroidW0; + d3_geo_centroidZ0 += (z - d3_geo_centroidZ0) / d3_geo_centroidW0; + } + function d3_geo_centroidLineStart() { + var x0, y0, z0; + d3_geo_centroid.point = function(λ, φ) { + λ *= d3_radians; + var cosφ = Math.cos(φ *= d3_radians); + x0 = cosφ * Math.cos(λ); + y0 = cosφ * Math.sin(λ); + z0 = Math.sin(φ); + d3_geo_centroid.point = nextPoint; + d3_geo_centroidPointXYZ(x0, y0, z0); + }; + function nextPoint(λ, φ) { + λ *= d3_radians; + var cosφ = Math.cos(φ *= d3_radians), x = cosφ * Math.cos(λ), y = cosφ * Math.sin(λ), z = Math.sin(φ), w = Math.atan2(Math.sqrt((w = y0 * z - z0 * y) * w + (w = z0 * x - x0 * z) * w + (w = x0 * y - y0 * x) * w), x0 * x + y0 * y + z0 * z); + d3_geo_centroidW1 += w; + d3_geo_centroidX1 += w * (x0 + (x0 = x)); + d3_geo_centroidY1 += w * (y0 + (y0 = y)); + d3_geo_centroidZ1 += w * (z0 + (z0 = z)); + d3_geo_centroidPointXYZ(x0, y0, z0); + } + } + function d3_geo_centroidLineEnd() { + d3_geo_centroid.point = d3_geo_centroidPoint; + } + function d3_geo_centroidRingStart() { + var λ00, φ00, x0, y0, z0; + d3_geo_centroid.point = function(λ, φ) { + λ00 = λ, φ00 = φ; + d3_geo_centroid.point = nextPoint; + λ *= d3_radians; + var cosφ = Math.cos(φ *= d3_radians); + x0 = cosφ * Math.cos(λ); + y0 = cosφ * Math.sin(λ); + z0 = Math.sin(φ); + d3_geo_centroidPointXYZ(x0, y0, z0); + }; + d3_geo_centroid.lineEnd = function() { + nextPoint(λ00, φ00); + d3_geo_centroid.lineEnd = d3_geo_centroidLineEnd; + d3_geo_centroid.point = d3_geo_centroidPoint; + }; + function nextPoint(λ, φ) { + λ *= d3_radians; + var cosφ = Math.cos(φ *= d3_radians), x = cosφ * Math.cos(λ), y = cosφ * Math.sin(λ), z = Math.sin(φ), cx = y0 * z - z0 * y, cy = z0 * x - x0 * z, cz = x0 * y - y0 * x, m = Math.sqrt(cx * cx + cy * cy + cz * cz), u = x0 * x + y0 * y + z0 * z, v = m && -d3_acos(u) / m, w = Math.atan2(m, u); + d3_geo_centroidX2 += v * cx; + d3_geo_centroidY2 += v * cy; + d3_geo_centroidZ2 += v * cz; + d3_geo_centroidW1 += w; + d3_geo_centroidX1 += w * (x0 + (x0 = x)); + d3_geo_centroidY1 += w * (y0 + (y0 = y)); + d3_geo_centroidZ1 += w * (z0 + (z0 = z)); + d3_geo_centroidPointXYZ(x0, y0, z0); + } + } + function d3_true() { + return true; + } + function d3_geo_clipPolygon(segments, compare, clipStartInside, interpolate, listener) { + var subject = [], clip = []; + segments.forEach(function(segment) { + if ((n = segment.length - 1) <= 0) return; + var n, p0 = segment[0], p1 = segment[n]; + if (d3_geo_sphericalEqual(p0, p1)) { + listener.lineStart(); + for (var i = 0; i < n; ++i) listener.point((p0 = segment[i])[0], p0[1]); + listener.lineEnd(); + return; + } + var a = new d3_geo_clipPolygonIntersection(p0, segment, null, true), b = new d3_geo_clipPolygonIntersection(p0, null, a, false); + a.o = b; + subject.push(a); + clip.push(b); + a = new d3_geo_clipPolygonIntersection(p1, segment, null, false); + b = new d3_geo_clipPolygonIntersection(p1, null, a, true); + a.o = b; + subject.push(a); + clip.push(b); + }); + clip.sort(compare); + d3_geo_clipPolygonLinkCircular(subject); + d3_geo_clipPolygonLinkCircular(clip); + if (!subject.length) return; + for (var i = 0, entry = clipStartInside, n = clip.length; i < n; ++i) { + clip[i].e = entry = !entry; + } + var start = subject[0], points, point; + while (1) { + var current = start, isSubject = true; + while (current.v) if ((current = current.n) === start) return; + points = current.z; + listener.lineStart(); + do { + current.v = current.o.v = true; + if (current.e) { + if (isSubject) { + for (var i = 0, n = points.length; i < n; ++i) listener.point((point = points[i])[0], point[1]); + } else { + interpolate(current.x, current.n.x, 1, listener); + } + current = current.n; + } else { + if (isSubject) { + points = current.p.z; + for (var i = points.length - 1; i >= 0; --i) listener.point((point = points[i])[0], point[1]); + } else { + interpolate(current.x, current.p.x, -1, listener); + } + current = current.p; + } + current = current.o; + points = current.z; + isSubject = !isSubject; + } while (!current.v); + listener.lineEnd(); + } + } + function d3_geo_clipPolygonLinkCircular(array) { + if (!(n = array.length)) return; + var n, i = 0, a = array[0], b; + while (++i < n) { + a.n = b = array[i]; + b.p = a; + a = b; + } + a.n = b = array[0]; + b.p = a; + } + function d3_geo_clipPolygonIntersection(point, points, other, entry) { + this.x = point; + this.z = points; + this.o = other; + this.e = entry; + this.v = false; + this.n = this.p = null; + } + function d3_geo_clip(pointVisible, clipLine, interpolate, clipStart) { + return function(rotate, listener) { + var line = clipLine(listener), rotatedClipStart = rotate.invert(clipStart[0], clipStart[1]); + var clip = { + point: point, + lineStart: lineStart, + lineEnd: lineEnd, + polygonStart: function() { + clip.point = pointRing; + clip.lineStart = ringStart; + clip.lineEnd = ringEnd; + segments = []; + polygon = []; + }, + polygonEnd: function() { + clip.point = point; + clip.lineStart = lineStart; + clip.lineEnd = lineEnd; + segments = d3.merge(segments); + var clipStartInside = d3_geo_pointInPolygon(rotatedClipStart, polygon); + if (segments.length) { + if (!polygonStarted) listener.polygonStart(), polygonStarted = true; + d3_geo_clipPolygon(segments, d3_geo_clipSort, clipStartInside, interpolate, listener); + } else if (clipStartInside) { + if (!polygonStarted) listener.polygonStart(), polygonStarted = true; + listener.lineStart(); + interpolate(null, null, 1, listener); + listener.lineEnd(); + } + if (polygonStarted) listener.polygonEnd(), polygonStarted = false; + segments = polygon = null; + }, + sphere: function() { + listener.polygonStart(); + listener.lineStart(); + interpolate(null, null, 1, listener); + listener.lineEnd(); + listener.polygonEnd(); + } + }; + function point(λ, φ) { + var point = rotate(λ, φ); + if (pointVisible(λ = point[0], φ = point[1])) listener.point(λ, φ); + } + function pointLine(λ, φ) { + var point = rotate(λ, φ); + line.point(point[0], point[1]); + } + function lineStart() { + clip.point = pointLine; + line.lineStart(); + } + function lineEnd() { + clip.point = point; + line.lineEnd(); + } + var segments; + var buffer = d3_geo_clipBufferListener(), ringListener = clipLine(buffer), polygonStarted = false, polygon, ring; + function pointRing(λ, φ) { + ring.push([ λ, φ ]); + var point = rotate(λ, φ); + ringListener.point(point[0], point[1]); + } + function ringStart() { + ringListener.lineStart(); + ring = []; + } + function ringEnd() { + pointRing(ring[0][0], ring[0][1]); + ringListener.lineEnd(); + var clean = ringListener.clean(), ringSegments = buffer.buffer(), segment, n = ringSegments.length; + ring.pop(); + polygon.push(ring); + ring = null; + if (!n) return; + if (clean & 1) { + segment = ringSegments[0]; + var n = segment.length - 1, i = -1, point; + if (n > 0) { + if (!polygonStarted) listener.polygonStart(), polygonStarted = true; + listener.lineStart(); + while (++i < n) listener.point((point = segment[i])[0], point[1]); + listener.lineEnd(); + } + return; + } + if (n > 1 && clean & 2) ringSegments.push(ringSegments.pop().concat(ringSegments.shift())); + segments.push(ringSegments.filter(d3_geo_clipSegmentLength1)); + } + return clip; + }; + } + function d3_geo_clipSegmentLength1(segment) { + return segment.length > 1; + } + function d3_geo_clipBufferListener() { + var lines = [], line; + return { + lineStart: function() { + lines.push(line = []); + }, + point: function(λ, φ) { + line.push([ λ, φ ]); + }, + lineEnd: d3_noop, + buffer: function() { + var buffer = lines; + lines = []; + line = null; + return buffer; + }, + rejoin: function() { + if (lines.length > 1) lines.push(lines.pop().concat(lines.shift())); + } + }; + } + function d3_geo_clipSort(a, b) { + return ((a = a.x)[0] < 0 ? a[1] - halfπ - ε : halfπ - a[1]) - ((b = b.x)[0] < 0 ? b[1] - halfπ - ε : halfπ - b[1]); + } + function d3_geo_pointInPolygon(point, polygon) { + var meridian = point[0], parallel = point[1], meridianNormal = [ Math.sin(meridian), -Math.cos(meridian), 0 ], polarAngle = 0, winding = 0; + d3_geo_areaRingSum.reset(); + for (var i = 0, n = polygon.length; i < n; ++i) { + var ring = polygon[i], m = ring.length; + if (!m) continue; + var point0 = ring[0], λ0 = point0[0], φ0 = point0[1] / 2 + π / 4, sinφ0 = Math.sin(φ0), cosφ0 = Math.cos(φ0), j = 1; + while (true) { + if (j === m) j = 0; + point = ring[j]; + var λ = point[0], φ = point[1] / 2 + π / 4, sinφ = Math.sin(φ), cosφ = Math.cos(φ), dλ = λ - λ0, sdλ = dλ >= 0 ? 1 : -1, adλ = sdλ * dλ, antimeridian = adλ > π, k = sinφ0 * sinφ; + d3_geo_areaRingSum.add(Math.atan2(k * sdλ * Math.sin(adλ), cosφ0 * cosφ + k * Math.cos(adλ))); + polarAngle += antimeridian ? dλ + sdλ * τ : dλ; + if (antimeridian ^ λ0 >= meridian ^ λ >= meridian) { + var arc = d3_geo_cartesianCross(d3_geo_cartesian(point0), d3_geo_cartesian(point)); + d3_geo_cartesianNormalize(arc); + var intersection = d3_geo_cartesianCross(meridianNormal, arc); + d3_geo_cartesianNormalize(intersection); + var φarc = (antimeridian ^ dλ >= 0 ? -1 : 1) * d3_asin(intersection[2]); + if (parallel > φarc || parallel === φarc && (arc[0] || arc[1])) { + winding += antimeridian ^ dλ >= 0 ? 1 : -1; + } + } + if (!j++) break; + λ0 = λ, sinφ0 = sinφ, cosφ0 = cosφ, point0 = point; + } + } + return (polarAngle < -ε || polarAngle < ε && d3_geo_areaRingSum < 0) ^ winding & 1; + } + var d3_geo_clipAntimeridian = d3_geo_clip(d3_true, d3_geo_clipAntimeridianLine, d3_geo_clipAntimeridianInterpolate, [ -π, -π / 2 ]); + function d3_geo_clipAntimeridianLine(listener) { + var λ0 = NaN, φ0 = NaN, sλ0 = NaN, clean; + return { + lineStart: function() { + listener.lineStart(); + clean = 1; + }, + point: function(λ1, φ1) { + var sλ1 = λ1 > 0 ? π : -π, dλ = abs(λ1 - λ0); + if (abs(dλ - π) < ε) { + listener.point(λ0, φ0 = (φ0 + φ1) / 2 > 0 ? halfπ : -halfπ); + listener.point(sλ0, φ0); + listener.lineEnd(); + listener.lineStart(); + listener.point(sλ1, φ0); + listener.point(λ1, φ0); + clean = 0; + } else if (sλ0 !== sλ1 && dλ >= π) { + if (abs(λ0 - sλ0) < ε) λ0 -= sλ0 * ε; + if (abs(λ1 - sλ1) < ε) λ1 -= sλ1 * ε; + φ0 = d3_geo_clipAntimeridianIntersect(λ0, φ0, λ1, φ1); + listener.point(sλ0, φ0); + listener.lineEnd(); + listener.lineStart(); + listener.point(sλ1, φ0); + clean = 0; + } + listener.point(λ0 = λ1, φ0 = φ1); + sλ0 = sλ1; + }, + lineEnd: function() { + listener.lineEnd(); + λ0 = φ0 = NaN; + }, + clean: function() { + return 2 - clean; + } + }; + } + function d3_geo_clipAntimeridianIntersect(λ0, φ0, λ1, φ1) { + var cosφ0, cosφ1, sinλ0_λ1 = Math.sin(λ0 - λ1); + return abs(sinλ0_λ1) > ε ? Math.atan((Math.sin(φ0) * (cosφ1 = Math.cos(φ1)) * Math.sin(λ1) - Math.sin(φ1) * (cosφ0 = Math.cos(φ0)) * Math.sin(λ0)) / (cosφ0 * cosφ1 * sinλ0_λ1)) : (φ0 + φ1) / 2; + } + function d3_geo_clipAntimeridianInterpolate(from, to, direction, listener) { + var φ; + if (from == null) { + φ = direction * halfπ; + listener.point(-π, φ); + listener.point(0, φ); + listener.point(π, φ); + listener.point(π, 0); + listener.point(π, -φ); + listener.point(0, -φ); + listener.point(-π, -φ); + listener.point(-π, 0); + listener.point(-π, φ); + } else if (abs(from[0] - to[0]) > ε) { + var s = from[0] < to[0] ? π : -π; + φ = direction * s / 2; + listener.point(-s, φ); + listener.point(0, φ); + listener.point(s, φ); + } else { + listener.point(to[0], to[1]); + } + } + function d3_geo_clipCircle(radius) { + var cr = Math.cos(radius), smallRadius = cr > 0, notHemisphere = abs(cr) > ε, interpolate = d3_geo_circleInterpolate(radius, 6 * d3_radians); + return d3_geo_clip(visible, clipLine, interpolate, smallRadius ? [ 0, -radius ] : [ -π, radius - π ]); + function visible(λ, φ) { + return Math.cos(λ) * Math.cos(φ) > cr; + } + function clipLine(listener) { + var point0, c0, v0, v00, clean; + return { + lineStart: function() { + v00 = v0 = false; + clean = 1; + }, + point: function(λ, φ) { + var point1 = [ λ, φ ], point2, v = visible(λ, φ), c = smallRadius ? v ? 0 : code(λ, φ) : v ? code(λ + (λ < 0 ? π : -π), φ) : 0; + if (!point0 && (v00 = v0 = v)) listener.lineStart(); + if (v !== v0) { + point2 = intersect(point0, point1); + if (d3_geo_sphericalEqual(point0, point2) || d3_geo_sphericalEqual(point1, point2)) { + point1[0] += ε; + point1[1] += ε; + v = visible(point1[0], point1[1]); + } + } + if (v !== v0) { + clean = 0; + if (v) { + listener.lineStart(); + point2 = intersect(point1, point0); + listener.point(point2[0], point2[1]); + } else { + point2 = intersect(point0, point1); + listener.point(point2[0], point2[1]); + listener.lineEnd(); + } + point0 = point2; + } else if (notHemisphere && point0 && smallRadius ^ v) { + var t; + if (!(c & c0) && (t = intersect(point1, point0, true))) { + clean = 0; + if (smallRadius) { + listener.lineStart(); + listener.point(t[0][0], t[0][1]); + listener.point(t[1][0], t[1][1]); + listener.lineEnd(); + } else { + listener.point(t[1][0], t[1][1]); + listener.lineEnd(); + listener.lineStart(); + listener.point(t[0][0], t[0][1]); + } + } + } + if (v && (!point0 || !d3_geo_sphericalEqual(point0, point1))) { + listener.point(point1[0], point1[1]); + } + point0 = point1, v0 = v, c0 = c; + }, + lineEnd: function() { + if (v0) listener.lineEnd(); + point0 = null; + }, + clean: function() { + return clean | (v00 && v0) << 1; + } + }; + } + function intersect(a, b, two) { + var pa = d3_geo_cartesian(a), pb = d3_geo_cartesian(b); + var n1 = [ 1, 0, 0 ], n2 = d3_geo_cartesianCross(pa, pb), n2n2 = d3_geo_cartesianDot(n2, n2), n1n2 = n2[0], determinant = n2n2 - n1n2 * n1n2; + if (!determinant) return !two && a; + var c1 = cr * n2n2 / determinant, c2 = -cr * n1n2 / determinant, n1xn2 = d3_geo_cartesianCross(n1, n2), A = d3_geo_cartesianScale(n1, c1), B = d3_geo_cartesianScale(n2, c2); + d3_geo_cartesianAdd(A, B); + var u = n1xn2, w = d3_geo_cartesianDot(A, u), uu = d3_geo_cartesianDot(u, u), t2 = w * w - uu * (d3_geo_cartesianDot(A, A) - 1); + if (t2 < 0) return; + var t = Math.sqrt(t2), q = d3_geo_cartesianScale(u, (-w - t) / uu); + d3_geo_cartesianAdd(q, A); + q = d3_geo_spherical(q); + if (!two) return q; + var λ0 = a[0], λ1 = b[0], φ0 = a[1], φ1 = b[1], z; + if (λ1 < λ0) z = λ0, λ0 = λ1, λ1 = z; + var δλ = λ1 - λ0, polar = abs(δλ - π) < ε, meridian = polar || δλ < ε; + if (!polar && φ1 < φ0) z = φ0, φ0 = φ1, φ1 = z; + if (meridian ? polar ? φ0 + φ1 > 0 ^ q[1] < (abs(q[0] - λ0) < ε ? φ0 : φ1) : φ0 <= q[1] && q[1] <= φ1 : δλ > π ^ (λ0 <= q[0] && q[0] <= λ1)) { + var q1 = d3_geo_cartesianScale(u, (-w + t) / uu); + d3_geo_cartesianAdd(q1, A); + return [ q, d3_geo_spherical(q1) ]; + } + } + function code(λ, φ) { + var r = smallRadius ? radius : π - radius, code = 0; + if (λ < -r) code |= 1; else if (λ > r) code |= 2; + if (φ < -r) code |= 4; else if (φ > r) code |= 8; + return code; + } + } + function d3_geom_clipLine(x0, y0, x1, y1) { + return function(line) { + var a = line.a, b = line.b, ax = a.x, ay = a.y, bx = b.x, by = b.y, t0 = 0, t1 = 1, dx = bx - ax, dy = by - ay, r; + r = x0 - ax; + if (!dx && r > 0) return; + r /= dx; + if (dx < 0) { + if (r < t0) return; + if (r < t1) t1 = r; + } else if (dx > 0) { + if (r > t1) return; + if (r > t0) t0 = r; + } + r = x1 - ax; + if (!dx && r < 0) return; + r /= dx; + if (dx < 0) { + if (r > t1) return; + if (r > t0) t0 = r; + } else if (dx > 0) { + if (r < t0) return; + if (r < t1) t1 = r; + } + r = y0 - ay; + if (!dy && r > 0) return; + r /= dy; + if (dy < 0) { + if (r < t0) return; + if (r < t1) t1 = r; + } else if (dy > 0) { + if (r > t1) return; + if (r > t0) t0 = r; + } + r = y1 - ay; + if (!dy && r < 0) return; + r /= dy; + if (dy < 0) { + if (r > t1) return; + if (r > t0) t0 = r; + } else if (dy > 0) { + if (r < t0) return; + if (r < t1) t1 = r; + } + if (t0 > 0) line.a = { + x: ax + t0 * dx, + y: ay + t0 * dy + }; + if (t1 < 1) line.b = { + x: ax + t1 * dx, + y: ay + t1 * dy + }; + return line; + }; + } + var d3_geo_clipExtentMAX = 1e9; + d3.geo.clipExtent = function() { + var x0, y0, x1, y1, stream, clip, clipExtent = { + stream: function(output) { + if (stream) stream.valid = false; + stream = clip(output); + stream.valid = true; + return stream; + }, + extent: function(_) { + if (!arguments.length) return [ [ x0, y0 ], [ x1, y1 ] ]; + clip = d3_geo_clipExtent(x0 = +_[0][0], y0 = +_[0][1], x1 = +_[1][0], y1 = +_[1][1]); + if (stream) stream.valid = false, stream = null; + return clipExtent; + } + }; + return clipExtent.extent([ [ 0, 0 ], [ 960, 500 ] ]); + }; + function d3_geo_clipExtent(x0, y0, x1, y1) { + return function(listener) { + var listener_ = listener, bufferListener = d3_geo_clipBufferListener(), clipLine = d3_geom_clipLine(x0, y0, x1, y1), segments, polygon, ring; + var clip = { + point: point, + lineStart: lineStart, + lineEnd: lineEnd, + polygonStart: function() { + listener = bufferListener; + segments = []; + polygon = []; + clean = true; + }, + polygonEnd: function() { + listener = listener_; + segments = d3.merge(segments); + var clipStartInside = insidePolygon([ x0, y1 ]), inside = clean && clipStartInside, visible = segments.length; + if (inside || visible) { + listener.polygonStart(); + if (inside) { + listener.lineStart(); + interpolate(null, null, 1, listener); + listener.lineEnd(); + } + if (visible) { + d3_geo_clipPolygon(segments, compare, clipStartInside, interpolate, listener); + } + listener.polygonEnd(); + } + segments = polygon = ring = null; + } + }; + function insidePolygon(p) { + var wn = 0, n = polygon.length, y = p[1]; + for (var i = 0; i < n; ++i) { + for (var j = 1, v = polygon[i], m = v.length, a = v[0], b; j < m; ++j) { + b = v[j]; + if (a[1] <= y) { + if (b[1] > y && d3_cross2d(a, b, p) > 0) ++wn; + } else { + if (b[1] <= y && d3_cross2d(a, b, p) < 0) --wn; + } + a = b; + } + } + return wn !== 0; + } + function interpolate(from, to, direction, listener) { + var a = 0, a1 = 0; + if (from == null || (a = corner(from, direction)) !== (a1 = corner(to, direction)) || comparePoints(from, to) < 0 ^ direction > 0) { + do { + listener.point(a === 0 || a === 3 ? x0 : x1, a > 1 ? y1 : y0); + } while ((a = (a + direction + 4) % 4) !== a1); + } else { + listener.point(to[0], to[1]); + } + } + function pointVisible(x, y) { + return x0 <= x && x <= x1 && y0 <= y && y <= y1; + } + function point(x, y) { + if (pointVisible(x, y)) listener.point(x, y); + } + var x__, y__, v__, x_, y_, v_, first, clean; + function lineStart() { + clip.point = linePoint; + if (polygon) polygon.push(ring = []); + first = true; + v_ = false; + x_ = y_ = NaN; + } + function lineEnd() { + if (segments) { + linePoint(x__, y__); + if (v__ && v_) bufferListener.rejoin(); + segments.push(bufferListener.buffer()); + } + clip.point = point; + if (v_) listener.lineEnd(); + } + function linePoint(x, y) { + x = Math.max(-d3_geo_clipExtentMAX, Math.min(d3_geo_clipExtentMAX, x)); + y = Math.max(-d3_geo_clipExtentMAX, Math.min(d3_geo_clipExtentMAX, y)); + var v = pointVisible(x, y); + if (polygon) ring.push([ x, y ]); + if (first) { + x__ = x, y__ = y, v__ = v; + first = false; + if (v) { + listener.lineStart(); + listener.point(x, y); + } + } else { + if (v && v_) listener.point(x, y); else { + var l = { + a: { + x: x_, + y: y_ + }, + b: { + x: x, + y: y + } + }; + if (clipLine(l)) { + if (!v_) { + listener.lineStart(); + listener.point(l.a.x, l.a.y); + } + listener.point(l.b.x, l.b.y); + if (!v) listener.lineEnd(); + clean = false; + } else if (v) { + listener.lineStart(); + listener.point(x, y); + clean = false; + } + } + } + x_ = x, y_ = y, v_ = v; + } + return clip; + }; + function corner(p, direction) { + return abs(p[0] - x0) < ε ? direction > 0 ? 0 : 3 : abs(p[0] - x1) < ε ? direction > 0 ? 2 : 1 : abs(p[1] - y0) < ε ? direction > 0 ? 1 : 0 : direction > 0 ? 3 : 2; + } + function compare(a, b) { + return comparePoints(a.x, b.x); + } + function comparePoints(a, b) { + var ca = corner(a, 1), cb = corner(b, 1); + return ca !== cb ? ca - cb : ca === 0 ? b[1] - a[1] : ca === 1 ? a[0] - b[0] : ca === 2 ? a[1] - b[1] : b[0] - a[0]; + } + } + function d3_geo_compose(a, b) { + function compose(x, y) { + return x = a(x, y), b(x[0], x[1]); + } + if (a.invert && b.invert) compose.invert = function(x, y) { + return x = b.invert(x, y), x && a.invert(x[0], x[1]); + }; + return compose; + } + function d3_geo_conic(projectAt) { + var φ0 = 0, φ1 = π / 3, m = d3_geo_projectionMutator(projectAt), p = m(φ0, φ1); + p.parallels = function(_) { + if (!arguments.length) return [ φ0 / π * 180, φ1 / π * 180 ]; + return m(φ0 = _[0] * π / 180, φ1 = _[1] * π / 180); + }; + return p; + } + function d3_geo_conicEqualArea(φ0, φ1) { + var sinφ0 = Math.sin(φ0), n = (sinφ0 + Math.sin(φ1)) / 2, C = 1 + sinφ0 * (2 * n - sinφ0), ρ0 = Math.sqrt(C) / n; + function forward(λ, φ) { + var ρ = Math.sqrt(C - 2 * n * Math.sin(φ)) / n; + return [ ρ * Math.sin(λ *= n), ρ0 - ρ * Math.cos(λ) ]; + } + forward.invert = function(x, y) { + var ρ0_y = ρ0 - y; + return [ Math.atan2(x, ρ0_y) / n, d3_asin((C - (x * x + ρ0_y * ρ0_y) * n * n) / (2 * n)) ]; + }; + return forward; + } + (d3.geo.conicEqualArea = function() { + return d3_geo_conic(d3_geo_conicEqualArea); + }).raw = d3_geo_conicEqualArea; + d3.geo.albers = function() { + return d3.geo.conicEqualArea().rotate([ 96, 0 ]).center([ -.6, 38.7 ]).parallels([ 29.5, 45.5 ]).scale(1070); + }; + d3.geo.albersUsa = function() { + var lower48 = d3.geo.albers(); + var alaska = d3.geo.conicEqualArea().rotate([ 154, 0 ]).center([ -2, 58.5 ]).parallels([ 55, 65 ]); + var hawaii = d3.geo.conicEqualArea().rotate([ 157, 0 ]).center([ -3, 19.9 ]).parallels([ 8, 18 ]); + var point, pointStream = { + point: function(x, y) { + point = [ x, y ]; + } + }, lower48Point, alaskaPoint, hawaiiPoint; + function albersUsa(coordinates) { + var x = coordinates[0], y = coordinates[1]; + point = null; + (lower48Point(x, y), point) || (alaskaPoint(x, y), point) || hawaiiPoint(x, y); + return point; + } + albersUsa.invert = function(coordinates) { + var k = lower48.scale(), t = lower48.translate(), x = (coordinates[0] - t[0]) / k, y = (coordinates[1] - t[1]) / k; + return (y >= .12 && y < .234 && x >= -.425 && x < -.214 ? alaska : y >= .166 && y < .234 && x >= -.214 && x < -.115 ? hawaii : lower48).invert(coordinates); + }; + albersUsa.stream = function(stream) { + var lower48Stream = lower48.stream(stream), alaskaStream = alaska.stream(stream), hawaiiStream = hawaii.stream(stream); + return { + point: function(x, y) { + lower48Stream.point(x, y); + alaskaStream.point(x, y); + hawaiiStream.point(x, y); + }, + sphere: function() { + lower48Stream.sphere(); + alaskaStream.sphere(); + hawaiiStream.sphere(); + }, + lineStart: function() { + lower48Stream.lineStart(); + alaskaStream.lineStart(); + hawaiiStream.lineStart(); + }, + lineEnd: function() { + lower48Stream.lineEnd(); + alaskaStream.lineEnd(); + hawaiiStream.lineEnd(); + }, + polygonStart: function() { + lower48Stream.polygonStart(); + alaskaStream.polygonStart(); + hawaiiStream.polygonStart(); + }, + polygonEnd: function() { + lower48Stream.polygonEnd(); + alaskaStream.polygonEnd(); + hawaiiStream.polygonEnd(); + } + }; + }; + albersUsa.precision = function(_) { + if (!arguments.length) return lower48.precision(); + lower48.precision(_); + alaska.precision(_); + hawaii.precision(_); + return albersUsa; + }; + albersUsa.scale = function(_) { + if (!arguments.length) return lower48.scale(); + lower48.scale(_); + alaska.scale(_ * .35); + hawaii.scale(_); + return albersUsa.translate(lower48.translate()); + }; + albersUsa.translate = function(_) { + if (!arguments.length) return lower48.translate(); + var k = lower48.scale(), x = +_[0], y = +_[1]; + lower48Point = lower48.translate(_).clipExtent([ [ x - .455 * k, y - .238 * k ], [ x + .455 * k, y + .238 * k ] ]).stream(pointStream).point; + alaskaPoint = alaska.translate([ x - .307 * k, y + .201 * k ]).clipExtent([ [ x - .425 * k + ε, y + .12 * k + ε ], [ x - .214 * k - ε, y + .234 * k - ε ] ]).stream(pointStream).point; + hawaiiPoint = hawaii.translate([ x - .205 * k, y + .212 * k ]).clipExtent([ [ x - .214 * k + ε, y + .166 * k + ε ], [ x - .115 * k - ε, y + .234 * k - ε ] ]).stream(pointStream).point; + return albersUsa; + }; + return albersUsa.scale(1070); + }; + var d3_geo_pathAreaSum, d3_geo_pathAreaPolygon, d3_geo_pathArea = { + point: d3_noop, + lineStart: d3_noop, + lineEnd: d3_noop, + polygonStart: function() { + d3_geo_pathAreaPolygon = 0; + d3_geo_pathArea.lineStart = d3_geo_pathAreaRingStart; + }, + polygonEnd: function() { + d3_geo_pathArea.lineStart = d3_geo_pathArea.lineEnd = d3_geo_pathArea.point = d3_noop; + d3_geo_pathAreaSum += abs(d3_geo_pathAreaPolygon / 2); + } + }; + function d3_geo_pathAreaRingStart() { + var x00, y00, x0, y0; + d3_geo_pathArea.point = function(x, y) { + d3_geo_pathArea.point = nextPoint; + x00 = x0 = x, y00 = y0 = y; + }; + function nextPoint(x, y) { + d3_geo_pathAreaPolygon += y0 * x - x0 * y; + x0 = x, y0 = y; + } + d3_geo_pathArea.lineEnd = function() { + nextPoint(x00, y00); + }; + } + var d3_geo_pathBoundsX0, d3_geo_pathBoundsY0, d3_geo_pathBoundsX1, d3_geo_pathBoundsY1; + var d3_geo_pathBounds = { + point: d3_geo_pathBoundsPoint, + lineStart: d3_noop, + lineEnd: d3_noop, + polygonStart: d3_noop, + polygonEnd: d3_noop + }; + function d3_geo_pathBoundsPoint(x, y) { + if (x < d3_geo_pathBoundsX0) d3_geo_pathBoundsX0 = x; + if (x > d3_geo_pathBoundsX1) d3_geo_pathBoundsX1 = x; + if (y < d3_geo_pathBoundsY0) d3_geo_pathBoundsY0 = y; + if (y > d3_geo_pathBoundsY1) d3_geo_pathBoundsY1 = y; + } + function d3_geo_pathBuffer() { + var pointCircle = d3_geo_pathBufferCircle(4.5), buffer = []; + var stream = { + point: point, + lineStart: function() { + stream.point = pointLineStart; + }, + lineEnd: lineEnd, + polygonStart: function() { + stream.lineEnd = lineEndPolygon; + }, + polygonEnd: function() { + stream.lineEnd = lineEnd; + stream.point = point; + }, + pointRadius: function(_) { + pointCircle = d3_geo_pathBufferCircle(_); + return stream; + }, + result: function() { + if (buffer.length) { + var result = buffer.join(""); + buffer = []; + return result; + } + } + }; + function point(x, y) { + buffer.push("M", x, ",", y, pointCircle); + } + function pointLineStart(x, y) { + buffer.push("M", x, ",", y); + stream.point = pointLine; + } + function pointLine(x, y) { + buffer.push("L", x, ",", y); + } + function lineEnd() { + stream.point = point; + } + function lineEndPolygon() { + buffer.push("Z"); + } + return stream; + } + function d3_geo_pathBufferCircle(radius) { + return "m0," + radius + "a" + radius + "," + radius + " 0 1,1 0," + -2 * radius + "a" + radius + "," + radius + " 0 1,1 0," + 2 * radius + "z"; + } + var d3_geo_pathCentroid = { + point: d3_geo_pathCentroidPoint, + lineStart: d3_geo_pathCentroidLineStart, + lineEnd: d3_geo_pathCentroidLineEnd, + polygonStart: function() { + d3_geo_pathCentroid.lineStart = d3_geo_pathCentroidRingStart; + }, + polygonEnd: function() { + d3_geo_pathCentroid.point = d3_geo_pathCentroidPoint; + d3_geo_pathCentroid.lineStart = d3_geo_pathCentroidLineStart; + d3_geo_pathCentroid.lineEnd = d3_geo_pathCentroidLineEnd; + } + }; + function d3_geo_pathCentroidPoint(x, y) { + d3_geo_centroidX0 += x; + d3_geo_centroidY0 += y; + ++d3_geo_centroidZ0; + } + function d3_geo_pathCentroidLineStart() { + var x0, y0; + d3_geo_pathCentroid.point = function(x, y) { + d3_geo_pathCentroid.point = nextPoint; + d3_geo_pathCentroidPoint(x0 = x, y0 = y); + }; + function nextPoint(x, y) { + var dx = x - x0, dy = y - y0, z = Math.sqrt(dx * dx + dy * dy); + d3_geo_centroidX1 += z * (x0 + x) / 2; + d3_geo_centroidY1 += z * (y0 + y) / 2; + d3_geo_centroidZ1 += z; + d3_geo_pathCentroidPoint(x0 = x, y0 = y); + } + } + function d3_geo_pathCentroidLineEnd() { + d3_geo_pathCentroid.point = d3_geo_pathCentroidPoint; + } + function d3_geo_pathCentroidRingStart() { + var x00, y00, x0, y0; + d3_geo_pathCentroid.point = function(x, y) { + d3_geo_pathCentroid.point = nextPoint; + d3_geo_pathCentroidPoint(x00 = x0 = x, y00 = y0 = y); + }; + function nextPoint(x, y) { + var dx = x - x0, dy = y - y0, z = Math.sqrt(dx * dx + dy * dy); + d3_geo_centroidX1 += z * (x0 + x) / 2; + d3_geo_centroidY1 += z * (y0 + y) / 2; + d3_geo_centroidZ1 += z; + z = y0 * x - x0 * y; + d3_geo_centroidX2 += z * (x0 + x); + d3_geo_centroidY2 += z * (y0 + y); + d3_geo_centroidZ2 += z * 3; + d3_geo_pathCentroidPoint(x0 = x, y0 = y); + } + d3_geo_pathCentroid.lineEnd = function() { + nextPoint(x00, y00); + }; + } + function d3_geo_pathContext(context) { + var pointRadius = 4.5; + var stream = { + point: point, + lineStart: function() { + stream.point = pointLineStart; + }, + lineEnd: lineEnd, + polygonStart: function() { + stream.lineEnd = lineEndPolygon; + }, + polygonEnd: function() { + stream.lineEnd = lineEnd; + stream.point = point; + }, + pointRadius: function(_) { + pointRadius = _; + return stream; + }, + result: d3_noop + }; + function point(x, y) { + context.moveTo(x, y); + context.arc(x, y, pointRadius, 0, τ); + } + function pointLineStart(x, y) { + context.moveTo(x, y); + stream.point = pointLine; + } + function pointLine(x, y) { + context.lineTo(x, y); + } + function lineEnd() { + stream.point = point; + } + function lineEndPolygon() { + context.closePath(); + } + return stream; + } + function d3_geo_resample(project) { + var δ2 = .5, cosMinDistance = Math.cos(30 * d3_radians), maxDepth = 16; + function resample(stream) { + return (maxDepth ? resampleRecursive : resampleNone)(stream); + } + function resampleNone(stream) { + return d3_geo_transformPoint(stream, function(x, y) { + x = project(x, y); + stream.point(x[0], x[1]); + }); + } + function resampleRecursive(stream) { + var λ00, φ00, x00, y00, a00, b00, c00, λ0, x0, y0, a0, b0, c0; + var resample = { + point: point, + lineStart: lineStart, + lineEnd: lineEnd, + polygonStart: function() { + stream.polygonStart(); + resample.lineStart = ringStart; + }, + polygonEnd: function() { + stream.polygonEnd(); + resample.lineStart = lineStart; + } + }; + function point(x, y) { + x = project(x, y); + stream.point(x[0], x[1]); + } + function lineStart() { + x0 = NaN; + resample.point = linePoint; + stream.lineStart(); + } + function linePoint(λ, φ) { + var c = d3_geo_cartesian([ λ, φ ]), p = project(λ, φ); + resampleLineTo(x0, y0, λ0, a0, b0, c0, x0 = p[0], y0 = p[1], λ0 = λ, a0 = c[0], b0 = c[1], c0 = c[2], maxDepth, stream); + stream.point(x0, y0); + } + function lineEnd() { + resample.point = point; + stream.lineEnd(); + } + function ringStart() { + lineStart(); + resample.point = ringPoint; + resample.lineEnd = ringEnd; + } + function ringPoint(λ, φ) { + linePoint(λ00 = λ, φ00 = φ), x00 = x0, y00 = y0, a00 = a0, b00 = b0, c00 = c0; + resample.point = linePoint; + } + function ringEnd() { + resampleLineTo(x0, y0, λ0, a0, b0, c0, x00, y00, λ00, a00, b00, c00, maxDepth, stream); + resample.lineEnd = lineEnd; + lineEnd(); + } + return resample; + } + function resampleLineTo(x0, y0, λ0, a0, b0, c0, x1, y1, λ1, a1, b1, c1, depth, stream) { + var dx = x1 - x0, dy = y1 - y0, d2 = dx * dx + dy * dy; + if (d2 > 4 * δ2 && depth--) { + var a = a0 + a1, b = b0 + b1, c = c0 + c1, m = Math.sqrt(a * a + b * b + c * c), φ2 = Math.asin(c /= m), λ2 = abs(abs(c) - 1) < ε || abs(λ0 - λ1) < ε ? (λ0 + λ1) / 2 : Math.atan2(b, a), p = project(λ2, φ2), x2 = p[0], y2 = p[1], dx2 = x2 - x0, dy2 = y2 - y0, dz = dy * dx2 - dx * dy2; + if (dz * dz / d2 > δ2 || abs((dx * dx2 + dy * dy2) / d2 - .5) > .3 || a0 * a1 + b0 * b1 + c0 * c1 < cosMinDistance) { + resampleLineTo(x0, y0, λ0, a0, b0, c0, x2, y2, λ2, a /= m, b /= m, c, depth, stream); + stream.point(x2, y2); + resampleLineTo(x2, y2, λ2, a, b, c, x1, y1, λ1, a1, b1, c1, depth, stream); + } + } + } + resample.precision = function(_) { + if (!arguments.length) return Math.sqrt(δ2); + maxDepth = (δ2 = _ * _) > 0 && 16; + return resample; + }; + return resample; + } + d3.geo.path = function() { + var pointRadius = 4.5, projection, context, projectStream, contextStream, cacheStream; + function path(object) { + if (object) { + if (typeof pointRadius === "function") contextStream.pointRadius(+pointRadius.apply(this, arguments)); + if (!cacheStream || !cacheStream.valid) cacheStream = projectStream(contextStream); + d3.geo.stream(object, cacheStream); + } + return contextStream.result(); + } + path.area = function(object) { + d3_geo_pathAreaSum = 0; + d3.geo.stream(object, projectStream(d3_geo_pathArea)); + return d3_geo_pathAreaSum; + }; + path.centroid = function(object) { + d3_geo_centroidX0 = d3_geo_centroidY0 = d3_geo_centroidZ0 = d3_geo_centroidX1 = d3_geo_centroidY1 = d3_geo_centroidZ1 = d3_geo_centroidX2 = d3_geo_centroidY2 = d3_geo_centroidZ2 = 0; + d3.geo.stream(object, projectStream(d3_geo_pathCentroid)); + return d3_geo_centroidZ2 ? [ d3_geo_centroidX2 / d3_geo_centroidZ2, d3_geo_centroidY2 / d3_geo_centroidZ2 ] : d3_geo_centroidZ1 ? [ d3_geo_centroidX1 / d3_geo_centroidZ1, d3_geo_centroidY1 / d3_geo_centroidZ1 ] : d3_geo_centroidZ0 ? [ d3_geo_centroidX0 / d3_geo_centroidZ0, d3_geo_centroidY0 / d3_geo_centroidZ0 ] : [ NaN, NaN ]; + }; + path.bounds = function(object) { + d3_geo_pathBoundsX1 = d3_geo_pathBoundsY1 = -(d3_geo_pathBoundsX0 = d3_geo_pathBoundsY0 = Infinity); + d3.geo.stream(object, projectStream(d3_geo_pathBounds)); + return [ [ d3_geo_pathBoundsX0, d3_geo_pathBoundsY0 ], [ d3_geo_pathBoundsX1, d3_geo_pathBoundsY1 ] ]; + }; + path.projection = function(_) { + if (!arguments.length) return projection; + projectStream = (projection = _) ? _.stream || d3_geo_pathProjectStream(_) : d3_identity; + return reset(); + }; + path.context = function(_) { + if (!arguments.length) return context; + contextStream = (context = _) == null ? new d3_geo_pathBuffer() : new d3_geo_pathContext(_); + if (typeof pointRadius !== "function") contextStream.pointRadius(pointRadius); + return reset(); + }; + path.pointRadius = function(_) { + if (!arguments.length) return pointRadius; + pointRadius = typeof _ === "function" ? _ : (contextStream.pointRadius(+_), +_); + return path; + }; + function reset() { + cacheStream = null; + return path; + } + return path.projection(d3.geo.albersUsa()).context(null); + }; + function d3_geo_pathProjectStream(project) { + var resample = d3_geo_resample(function(x, y) { + return project([ x * d3_degrees, y * d3_degrees ]); + }); + return function(stream) { + return d3_geo_projectionRadians(resample(stream)); + }; + } + d3.geo.transform = function(methods) { + return { + stream: function(stream) { + var transform = new d3_geo_transform(stream); + for (var k in methods) transform[k] = methods[k]; + return transform; + } + }; + }; + function d3_geo_transform(stream) { + this.stream = stream; + } + d3_geo_transform.prototype = { + point: function(x, y) { + this.stream.point(x, y); + }, + sphere: function() { + this.stream.sphere(); + }, + lineStart: function() { + this.stream.lineStart(); + }, + lineEnd: function() { + this.stream.lineEnd(); + }, + polygonStart: function() { + this.stream.polygonStart(); + }, + polygonEnd: function() { + this.stream.polygonEnd(); + } + }; + function d3_geo_transformPoint(stream, point) { + return { + point: point, + sphere: function() { + stream.sphere(); + }, + lineStart: function() { + stream.lineStart(); + }, + lineEnd: function() { + stream.lineEnd(); + }, + polygonStart: function() { + stream.polygonStart(); + }, + polygonEnd: function() { + stream.polygonEnd(); + } + }; + } + d3.geo.projection = d3_geo_projection; + d3.geo.projectionMutator = d3_geo_projectionMutator; + function d3_geo_projection(project) { + return d3_geo_projectionMutator(function() { + return project; + })(); + } + function d3_geo_projectionMutator(projectAt) { + var project, rotate, projectRotate, projectResample = d3_geo_resample(function(x, y) { + x = project(x, y); + return [ x[0] * k + δx, δy - x[1] * k ]; + }), k = 150, x = 480, y = 250, λ = 0, φ = 0, δλ = 0, δφ = 0, δγ = 0, δx, δy, preclip = d3_geo_clipAntimeridian, postclip = d3_identity, clipAngle = null, clipExtent = null, stream; + function projection(point) { + point = projectRotate(point[0] * d3_radians, point[1] * d3_radians); + return [ point[0] * k + δx, δy - point[1] * k ]; + } + function invert(point) { + point = projectRotate.invert((point[0] - δx) / k, (δy - point[1]) / k); + return point && [ point[0] * d3_degrees, point[1] * d3_degrees ]; + } + projection.stream = function(output) { + if (stream) stream.valid = false; + stream = d3_geo_projectionRadians(preclip(rotate, projectResample(postclip(output)))); + stream.valid = true; + return stream; + }; + projection.clipAngle = function(_) { + if (!arguments.length) return clipAngle; + preclip = _ == null ? (clipAngle = _, d3_geo_clipAntimeridian) : d3_geo_clipCircle((clipAngle = +_) * d3_radians); + return invalidate(); + }; + projection.clipExtent = function(_) { + if (!arguments.length) return clipExtent; + clipExtent = _; + postclip = _ ? d3_geo_clipExtent(_[0][0], _[0][1], _[1][0], _[1][1]) : d3_identity; + return invalidate(); + }; + projection.scale = function(_) { + if (!arguments.length) return k; + k = +_; + return reset(); + }; + projection.translate = function(_) { + if (!arguments.length) return [ x, y ]; + x = +_[0]; + y = +_[1]; + return reset(); + }; + projection.center = function(_) { + if (!arguments.length) return [ λ * d3_degrees, φ * d3_degrees ]; + λ = _[0] % 360 * d3_radians; + φ = _[1] % 360 * d3_radians; + return reset(); + }; + projection.rotate = function(_) { + if (!arguments.length) return [ δλ * d3_degrees, δφ * d3_degrees, δγ * d3_degrees ]; + δλ = _[0] % 360 * d3_radians; + δφ = _[1] % 360 * d3_radians; + δγ = _.length > 2 ? _[2] % 360 * d3_radians : 0; + return reset(); + }; + d3.rebind(projection, projectResample, "precision"); + function reset() { + projectRotate = d3_geo_compose(rotate = d3_geo_rotation(δλ, δφ, δγ), project); + var center = project(λ, φ); + δx = x - center[0] * k; + δy = y + center[1] * k; + return invalidate(); + } + function invalidate() { + if (stream) stream.valid = false, stream = null; + return projection; + } + return function() { + project = projectAt.apply(this, arguments); + projection.invert = project.invert && invert; + return reset(); + }; + } + function d3_geo_projectionRadians(stream) { + return d3_geo_transformPoint(stream, function(x, y) { + stream.point(x * d3_radians, y * d3_radians); + }); + } + function d3_geo_equirectangular(λ, φ) { + return [ λ, φ ]; + } + (d3.geo.equirectangular = function() { + return d3_geo_projection(d3_geo_equirectangular); + }).raw = d3_geo_equirectangular.invert = d3_geo_equirectangular; + d3.geo.rotation = function(rotate) { + rotate = d3_geo_rotation(rotate[0] % 360 * d3_radians, rotate[1] * d3_radians, rotate.length > 2 ? rotate[2] * d3_radians : 0); + function forward(coordinates) { + coordinates = rotate(coordinates[0] * d3_radians, coordinates[1] * d3_radians); + return coordinates[0] *= d3_degrees, coordinates[1] *= d3_degrees, coordinates; + } + forward.invert = function(coordinates) { + coordinates = rotate.invert(coordinates[0] * d3_radians, coordinates[1] * d3_radians); + return coordinates[0] *= d3_degrees, coordinates[1] *= d3_degrees, coordinates; + }; + return forward; + }; + function d3_geo_identityRotation(λ, φ) { + return [ λ > π ? λ - τ : λ < -π ? λ + τ : λ, φ ]; + } + d3_geo_identityRotation.invert = d3_geo_equirectangular; + function d3_geo_rotation(δλ, δφ, δγ) { + return δλ ? δφ || δγ ? d3_geo_compose(d3_geo_rotationλ(δλ), d3_geo_rotationφγ(δφ, δγ)) : d3_geo_rotationλ(δλ) : δφ || δγ ? d3_geo_rotationφγ(δφ, δγ) : d3_geo_identityRotation; + } + function d3_geo_forwardRotationλ(δλ) { + return function(λ, φ) { + return λ += δλ, [ λ > π ? λ - τ : λ < -π ? λ + τ : λ, φ ]; + }; + } + function d3_geo_rotationλ(δλ) { + var rotation = d3_geo_forwardRotationλ(δλ); + rotation.invert = d3_geo_forwardRotationλ(-δλ); + return rotation; + } + function d3_geo_rotationφγ(δφ, δγ) { + var cosδφ = Math.cos(δφ), sinδφ = Math.sin(δφ), cosδγ = Math.cos(δγ), sinδγ = Math.sin(δγ); + function rotation(λ, φ) { + var cosφ = Math.cos(φ), x = Math.cos(λ) * cosφ, y = Math.sin(λ) * cosφ, z = Math.sin(φ), k = z * cosδφ + x * sinδφ; + return [ Math.atan2(y * cosδγ - k * sinδγ, x * cosδφ - z * sinδφ), d3_asin(k * cosδγ + y * sinδγ) ]; + } + rotation.invert = function(λ, φ) { + var cosφ = Math.cos(φ), x = Math.cos(λ) * cosφ, y = Math.sin(λ) * cosφ, z = Math.sin(φ), k = z * cosδγ - y * sinδγ; + return [ Math.atan2(y * cosδγ + z * sinδγ, x * cosδφ + k * sinδφ), d3_asin(k * cosδφ - x * sinδφ) ]; + }; + return rotation; + } + d3.geo.circle = function() { + var origin = [ 0, 0 ], angle, precision = 6, interpolate; + function circle() { + var center = typeof origin === "function" ? origin.apply(this, arguments) : origin, rotate = d3_geo_rotation(-center[0] * d3_radians, -center[1] * d3_radians, 0).invert, ring = []; + interpolate(null, null, 1, { + point: function(x, y) { + ring.push(x = rotate(x, y)); + x[0] *= d3_degrees, x[1] *= d3_degrees; + } + }); + return { + type: "Polygon", + coordinates: [ ring ] + }; + } + circle.origin = function(x) { + if (!arguments.length) return origin; + origin = x; + return circle; + }; + circle.angle = function(x) { + if (!arguments.length) return angle; + interpolate = d3_geo_circleInterpolate((angle = +x) * d3_radians, precision * d3_radians); + return circle; + }; + circle.precision = function(_) { + if (!arguments.length) return precision; + interpolate = d3_geo_circleInterpolate(angle * d3_radians, (precision = +_) * d3_radians); + return circle; + }; + return circle.angle(90); + }; + function d3_geo_circleInterpolate(radius, precision) { + var cr = Math.cos(radius), sr = Math.sin(radius); + return function(from, to, direction, listener) { + var step = direction * precision; + if (from != null) { + from = d3_geo_circleAngle(cr, from); + to = d3_geo_circleAngle(cr, to); + if (direction > 0 ? from < to : from > to) from += direction * τ; + } else { + from = radius + direction * τ; + to = radius - .5 * step; + } + for (var point, t = from; direction > 0 ? t > to : t < to; t -= step) { + listener.point((point = d3_geo_spherical([ cr, -sr * Math.cos(t), -sr * Math.sin(t) ]))[0], point[1]); + } + }; + } + function d3_geo_circleAngle(cr, point) { + var a = d3_geo_cartesian(point); + a[0] -= cr; + d3_geo_cartesianNormalize(a); + var angle = d3_acos(-a[1]); + return ((-a[2] < 0 ? -angle : angle) + 2 * Math.PI - ε) % (2 * Math.PI); + } + d3.geo.distance = function(a, b) { + var Δλ = (b[0] - a[0]) * d3_radians, φ0 = a[1] * d3_radians, φ1 = b[1] * d3_radians, sinΔλ = Math.sin(Δλ), cosΔλ = Math.cos(Δλ), sinφ0 = Math.sin(φ0), cosφ0 = Math.cos(φ0), sinφ1 = Math.sin(φ1), cosφ1 = Math.cos(φ1), t; + return Math.atan2(Math.sqrt((t = cosφ1 * sinΔλ) * t + (t = cosφ0 * sinφ1 - sinφ0 * cosφ1 * cosΔλ) * t), sinφ0 * sinφ1 + cosφ0 * cosφ1 * cosΔλ); + }; + d3.geo.graticule = function() { + var x1, x0, X1, X0, y1, y0, Y1, Y0, dx = 10, dy = dx, DX = 90, DY = 360, x, y, X, Y, precision = 2.5; + function graticule() { + return { + type: "MultiLineString", + coordinates: lines() + }; + } + function lines() { + return d3.range(Math.ceil(X0 / DX) * DX, X1, DX).map(X).concat(d3.range(Math.ceil(Y0 / DY) * DY, Y1, DY).map(Y)).concat(d3.range(Math.ceil(x0 / dx) * dx, x1, dx).filter(function(x) { + return abs(x % DX) > ε; + }).map(x)).concat(d3.range(Math.ceil(y0 / dy) * dy, y1, dy).filter(function(y) { + return abs(y % DY) > ε; + }).map(y)); + } + graticule.lines = function() { + return lines().map(function(coordinates) { + return { + type: "LineString", + coordinates: coordinates + }; + }); + }; + graticule.outline = function() { + return { + type: "Polygon", + coordinates: [ X(X0).concat(Y(Y1).slice(1), X(X1).reverse().slice(1), Y(Y0).reverse().slice(1)) ] + }; + }; + graticule.extent = function(_) { + if (!arguments.length) return graticule.minorExtent(); + return graticule.majorExtent(_).minorExtent(_); + }; + graticule.majorExtent = function(_) { + if (!arguments.length) return [ [ X0, Y0 ], [ X1, Y1 ] ]; + X0 = +_[0][0], X1 = +_[1][0]; + Y0 = +_[0][1], Y1 = +_[1][1]; + if (X0 > X1) _ = X0, X0 = X1, X1 = _; + if (Y0 > Y1) _ = Y0, Y0 = Y1, Y1 = _; + return graticule.precision(precision); + }; + graticule.minorExtent = function(_) { + if (!arguments.length) return [ [ x0, y0 ], [ x1, y1 ] ]; + x0 = +_[0][0], x1 = +_[1][0]; + y0 = +_[0][1], y1 = +_[1][1]; + if (x0 > x1) _ = x0, x0 = x1, x1 = _; + if (y0 > y1) _ = y0, y0 = y1, y1 = _; + return graticule.precision(precision); + }; + graticule.step = function(_) { + if (!arguments.length) return graticule.minorStep(); + return graticule.majorStep(_).minorStep(_); + }; + graticule.majorStep = function(_) { + if (!arguments.length) return [ DX, DY ]; + DX = +_[0], DY = +_[1]; + return graticule; + }; + graticule.minorStep = function(_) { + if (!arguments.length) return [ dx, dy ]; + dx = +_[0], dy = +_[1]; + return graticule; + }; + graticule.precision = function(_) { + if (!arguments.length) return precision; + precision = +_; + x = d3_geo_graticuleX(y0, y1, 90); + y = d3_geo_graticuleY(x0, x1, precision); + X = d3_geo_graticuleX(Y0, Y1, 90); + Y = d3_geo_graticuleY(X0, X1, precision); + return graticule; + }; + return graticule.majorExtent([ [ -180, -90 + ε ], [ 180, 90 - ε ] ]).minorExtent([ [ -180, -80 - ε ], [ 180, 80 + ε ] ]); + }; + function d3_geo_graticuleX(y0, y1, dy) { + var y = d3.range(y0, y1 - ε, dy).concat(y1); + return function(x) { + return y.map(function(y) { + return [ x, y ]; + }); + }; + } + function d3_geo_graticuleY(x0, x1, dx) { + var x = d3.range(x0, x1 - ε, dx).concat(x1); + return function(y) { + return x.map(function(x) { + return [ x, y ]; + }); + }; + } + function d3_source(d) { + return d.source; + } + function d3_target(d) { + return d.target; + } + d3.geo.greatArc = function() { + var source = d3_source, source_, target = d3_target, target_; + function greatArc() { + return { + type: "LineString", + coordinates: [ source_ || source.apply(this, arguments), target_ || target.apply(this, arguments) ] + }; + } + greatArc.distance = function() { + return d3.geo.distance(source_ || source.apply(this, arguments), target_ || target.apply(this, arguments)); + }; + greatArc.source = function(_) { + if (!arguments.length) return source; + source = _, source_ = typeof _ === "function" ? null : _; + return greatArc; + }; + greatArc.target = function(_) { + if (!arguments.length) return target; + target = _, target_ = typeof _ === "function" ? null : _; + return greatArc; + }; + greatArc.precision = function() { + return arguments.length ? greatArc : 0; + }; + return greatArc; + }; + d3.geo.interpolate = function(source, target) { + return d3_geo_interpolate(source[0] * d3_radians, source[1] * d3_radians, target[0] * d3_radians, target[1] * d3_radians); + }; + function d3_geo_interpolate(x0, y0, x1, y1) { + var cy0 = Math.cos(y0), sy0 = Math.sin(y0), cy1 = Math.cos(y1), sy1 = Math.sin(y1), kx0 = cy0 * Math.cos(x0), ky0 = cy0 * Math.sin(x0), kx1 = cy1 * Math.cos(x1), ky1 = cy1 * Math.sin(x1), d = 2 * Math.asin(Math.sqrt(d3_haversin(y1 - y0) + cy0 * cy1 * d3_haversin(x1 - x0))), k = 1 / Math.sin(d); + var interpolate = d ? function(t) { + var B = Math.sin(t *= d) * k, A = Math.sin(d - t) * k, x = A * kx0 + B * kx1, y = A * ky0 + B * ky1, z = A * sy0 + B * sy1; + return [ Math.atan2(y, x) * d3_degrees, Math.atan2(z, Math.sqrt(x * x + y * y)) * d3_degrees ]; + } : function() { + return [ x0 * d3_degrees, y0 * d3_degrees ]; + }; + interpolate.distance = d; + return interpolate; + } + d3.geo.length = function(object) { + d3_geo_lengthSum = 0; + d3.geo.stream(object, d3_geo_length); + return d3_geo_lengthSum; + }; + var d3_geo_lengthSum; + var d3_geo_length = { + sphere: d3_noop, + point: d3_noop, + lineStart: d3_geo_lengthLineStart, + lineEnd: d3_noop, + polygonStart: d3_noop, + polygonEnd: d3_noop + }; + function d3_geo_lengthLineStart() { + var λ0, sinφ0, cosφ0; + d3_geo_length.point = function(λ, φ) { + λ0 = λ * d3_radians, sinφ0 = Math.sin(φ *= d3_radians), cosφ0 = Math.cos(φ); + d3_geo_length.point = nextPoint; + }; + d3_geo_length.lineEnd = function() { + d3_geo_length.point = d3_geo_length.lineEnd = d3_noop; + }; + function nextPoint(λ, φ) { + var sinφ = Math.sin(φ *= d3_radians), cosφ = Math.cos(φ), t = abs((λ *= d3_radians) - λ0), cosΔλ = Math.cos(t); + d3_geo_lengthSum += Math.atan2(Math.sqrt((t = cosφ * Math.sin(t)) * t + (t = cosφ0 * sinφ - sinφ0 * cosφ * cosΔλ) * t), sinφ0 * sinφ + cosφ0 * cosφ * cosΔλ); + λ0 = λ, sinφ0 = sinφ, cosφ0 = cosφ; + } + } + function d3_geo_azimuthal(scale, angle) { + function azimuthal(λ, φ) { + var cosλ = Math.cos(λ), cosφ = Math.cos(φ), k = scale(cosλ * cosφ); + return [ k * cosφ * Math.sin(λ), k * Math.sin(φ) ]; + } + azimuthal.invert = function(x, y) { + var ρ = Math.sqrt(x * x + y * y), c = angle(ρ), sinc = Math.sin(c), cosc = Math.cos(c); + return [ Math.atan2(x * sinc, ρ * cosc), Math.asin(ρ && y * sinc / ρ) ]; + }; + return azimuthal; + } + var d3_geo_azimuthalEqualArea = d3_geo_azimuthal(function(cosλcosφ) { + return Math.sqrt(2 / (1 + cosλcosφ)); + }, function(ρ) { + return 2 * Math.asin(ρ / 2); + }); + (d3.geo.azimuthalEqualArea = function() { + return d3_geo_projection(d3_geo_azimuthalEqualArea); + }).raw = d3_geo_azimuthalEqualArea; + var d3_geo_azimuthalEquidistant = d3_geo_azimuthal(function(cosλcosφ) { + var c = Math.acos(cosλcosφ); + return c && c / Math.sin(c); + }, d3_identity); + (d3.geo.azimuthalEquidistant = function() { + return d3_geo_projection(d3_geo_azimuthalEquidistant); + }).raw = d3_geo_azimuthalEquidistant; + function d3_geo_conicConformal(φ0, φ1) { + var cosφ0 = Math.cos(φ0), t = function(φ) { + return Math.tan(π / 4 + φ / 2); + }, n = φ0 === φ1 ? Math.sin(φ0) : Math.log(cosφ0 / Math.cos(φ1)) / Math.log(t(φ1) / t(φ0)), F = cosφ0 * Math.pow(t(φ0), n) / n; + if (!n) return d3_geo_mercator; + function forward(λ, φ) { + if (F > 0) { + if (φ < -halfπ + ε) φ = -halfπ + ε; + } else { + if (φ > halfπ - ε) φ = halfπ - ε; + } + var ρ = F / Math.pow(t(φ), n); + return [ ρ * Math.sin(n * λ), F - ρ * Math.cos(n * λ) ]; + } + forward.invert = function(x, y) { + var ρ0_y = F - y, ρ = d3_sgn(n) * Math.sqrt(x * x + ρ0_y * ρ0_y); + return [ Math.atan2(x, ρ0_y) / n, 2 * Math.atan(Math.pow(F / ρ, 1 / n)) - halfπ ]; + }; + return forward; + } + (d3.geo.conicConformal = function() { + return d3_geo_conic(d3_geo_conicConformal); + }).raw = d3_geo_conicConformal; + function d3_geo_conicEquidistant(φ0, φ1) { + var cosφ0 = Math.cos(φ0), n = φ0 === φ1 ? Math.sin(φ0) : (cosφ0 - Math.cos(φ1)) / (φ1 - φ0), G = cosφ0 / n + φ0; + if (abs(n) < ε) return d3_geo_equirectangular; + function forward(λ, φ) { + var ρ = G - φ; + return [ ρ * Math.sin(n * λ), G - ρ * Math.cos(n * λ) ]; + } + forward.invert = function(x, y) { + var ρ0_y = G - y; + return [ Math.atan2(x, ρ0_y) / n, G - d3_sgn(n) * Math.sqrt(x * x + ρ0_y * ρ0_y) ]; + }; + return forward; + } + (d3.geo.conicEquidistant = function() { + return d3_geo_conic(d3_geo_conicEquidistant); + }).raw = d3_geo_conicEquidistant; + var d3_geo_gnomonic = d3_geo_azimuthal(function(cosλcosφ) { + return 1 / cosλcosφ; + }, Math.atan); + (d3.geo.gnomonic = function() { + return d3_geo_projection(d3_geo_gnomonic); + }).raw = d3_geo_gnomonic; + function d3_geo_mercator(λ, φ) { + return [ λ, Math.log(Math.tan(π / 4 + φ / 2)) ]; + } + d3_geo_mercator.invert = function(x, y) { + return [ x, 2 * Math.atan(Math.exp(y)) - halfπ ]; + }; + function d3_geo_mercatorProjection(project) { + var m = d3_geo_projection(project), scale = m.scale, translate = m.translate, clipExtent = m.clipExtent, clipAuto; + m.scale = function() { + var v = scale.apply(m, arguments); + return v === m ? clipAuto ? m.clipExtent(null) : m : v; + }; + m.translate = function() { + var v = translate.apply(m, arguments); + return v === m ? clipAuto ? m.clipExtent(null) : m : v; + }; + m.clipExtent = function(_) { + var v = clipExtent.apply(m, arguments); + if (v === m) { + if (clipAuto = _ == null) { + var k = π * scale(), t = translate(); + clipExtent([ [ t[0] - k, t[1] - k ], [ t[0] + k, t[1] + k ] ]); + } + } else if (clipAuto) { + v = null; + } + return v; + }; + return m.clipExtent(null); + } + (d3.geo.mercator = function() { + return d3_geo_mercatorProjection(d3_geo_mercator); + }).raw = d3_geo_mercator; + var d3_geo_orthographic = d3_geo_azimuthal(function() { + return 1; + }, Math.asin); + (d3.geo.orthographic = function() { + return d3_geo_projection(d3_geo_orthographic); + }).raw = d3_geo_orthographic; + var d3_geo_stereographic = d3_geo_azimuthal(function(cosλcosφ) { + return 1 / (1 + cosλcosφ); + }, function(ρ) { + return 2 * Math.atan(ρ); + }); + (d3.geo.stereographic = function() { + return d3_geo_projection(d3_geo_stereographic); + }).raw = d3_geo_stereographic; + function d3_geo_transverseMercator(λ, φ) { + return [ Math.log(Math.tan(π / 4 + φ / 2)), -λ ]; + } + d3_geo_transverseMercator.invert = function(x, y) { + return [ -y, 2 * Math.atan(Math.exp(x)) - halfπ ]; + }; + (d3.geo.transverseMercator = function() { + var projection = d3_geo_mercatorProjection(d3_geo_transverseMercator), center = projection.center, rotate = projection.rotate; + projection.center = function(_) { + return _ ? center([ -_[1], _[0] ]) : (_ = center(), [ -_[1], _[0] ]); + }; + projection.rotate = function(_) { + return _ ? rotate([ _[0], _[1], _.length > 2 ? _[2] + 90 : 90 ]) : (_ = rotate(), + [ _[0], _[1], _[2] - 90 ]); + }; + return projection.rotate([ 0, 0 ]); + }).raw = d3_geo_transverseMercator; + d3.geom = {}; + function d3_geom_pointX(d) { + return d[0]; + } + function d3_geom_pointY(d) { + return d[1]; + } + d3.geom.hull = function(vertices) { + var x = d3_geom_pointX, y = d3_geom_pointY; + if (arguments.length) return hull(vertices); + function hull(data) { + if (data.length < 3) return []; + var fx = d3_functor(x), fy = d3_functor(y), i, n = data.length, points = [], flippedPoints = []; + for (i = 0; i < n; i++) { + points.push([ +fx.call(this, data[i], i), +fy.call(this, data[i], i), i ]); + } + points.sort(d3_geom_hullOrder); + for (i = 0; i < n; i++) flippedPoints.push([ points[i][0], -points[i][1] ]); + var upper = d3_geom_hullUpper(points), lower = d3_geom_hullUpper(flippedPoints); + var skipLeft = lower[0] === upper[0], skipRight = lower[lower.length - 1] === upper[upper.length - 1], polygon = []; + for (i = upper.length - 1; i >= 0; --i) polygon.push(data[points[upper[i]][2]]); + for (i = +skipLeft; i < lower.length - skipRight; ++i) polygon.push(data[points[lower[i]][2]]); + return polygon; + } + hull.x = function(_) { + return arguments.length ? (x = _, hull) : x; + }; + hull.y = function(_) { + return arguments.length ? (y = _, hull) : y; + }; + return hull; + }; + function d3_geom_hullUpper(points) { + var n = points.length, hull = [ 0, 1 ], hs = 2; + for (var i = 2; i < n; i++) { + while (hs > 1 && d3_cross2d(points[hull[hs - 2]], points[hull[hs - 1]], points[i]) <= 0) --hs; + hull[hs++] = i; + } + return hull.slice(0, hs); + } + function d3_geom_hullOrder(a, b) { + return a[0] - b[0] || a[1] - b[1]; + } + d3.geom.polygon = function(coordinates) { + d3_subclass(coordinates, d3_geom_polygonPrototype); + return coordinates; + }; + var d3_geom_polygonPrototype = d3.geom.polygon.prototype = []; + d3_geom_polygonPrototype.area = function() { + var i = -1, n = this.length, a, b = this[n - 1], area = 0; + while (++i < n) { + a = b; + b = this[i]; + area += a[1] * b[0] - a[0] * b[1]; + } + return area * .5; + }; + d3_geom_polygonPrototype.centroid = function(k) { + var i = -1, n = this.length, x = 0, y = 0, a, b = this[n - 1], c; + if (!arguments.length) k = -1 / (6 * this.area()); + while (++i < n) { + a = b; + b = this[i]; + c = a[0] * b[1] - b[0] * a[1]; + x += (a[0] + b[0]) * c; + y += (a[1] + b[1]) * c; + } + return [ x * k, y * k ]; + }; + d3_geom_polygonPrototype.clip = function(subject) { + var input, closed = d3_geom_polygonClosed(subject), i = -1, n = this.length - d3_geom_polygonClosed(this), j, m, a = this[n - 1], b, c, d; + while (++i < n) { + input = subject.slice(); + subject.length = 0; + b = this[i]; + c = input[(m = input.length - closed) - 1]; + j = -1; + while (++j < m) { + d = input[j]; + if (d3_geom_polygonInside(d, a, b)) { + if (!d3_geom_polygonInside(c, a, b)) { + subject.push(d3_geom_polygonIntersect(c, d, a, b)); + } + subject.push(d); + } else if (d3_geom_polygonInside(c, a, b)) { + subject.push(d3_geom_polygonIntersect(c, d, a, b)); + } + c = d; + } + if (closed) subject.push(subject[0]); + a = b; + } + return subject; + }; + function d3_geom_polygonInside(p, a, b) { + return (b[0] - a[0]) * (p[1] - a[1]) < (b[1] - a[1]) * (p[0] - a[0]); + } + function d3_geom_polygonIntersect(c, d, a, b) { + var x1 = c[0], x3 = a[0], x21 = d[0] - x1, x43 = b[0] - x3, y1 = c[1], y3 = a[1], y21 = d[1] - y1, y43 = b[1] - y3, ua = (x43 * (y1 - y3) - y43 * (x1 - x3)) / (y43 * x21 - x43 * y21); + return [ x1 + ua * x21, y1 + ua * y21 ]; + } + function d3_geom_polygonClosed(coordinates) { + var a = coordinates[0], b = coordinates[coordinates.length - 1]; + return !(a[0] - b[0] || a[1] - b[1]); + } + var d3_geom_voronoiEdges, d3_geom_voronoiCells, d3_geom_voronoiBeaches, d3_geom_voronoiBeachPool = [], d3_geom_voronoiFirstCircle, d3_geom_voronoiCircles, d3_geom_voronoiCirclePool = []; + function d3_geom_voronoiBeach() { + d3_geom_voronoiRedBlackNode(this); + this.edge = this.site = this.circle = null; + } + function d3_geom_voronoiCreateBeach(site) { + var beach = d3_geom_voronoiBeachPool.pop() || new d3_geom_voronoiBeach(); + beach.site = site; + return beach; + } + function d3_geom_voronoiDetachBeach(beach) { + d3_geom_voronoiDetachCircle(beach); + d3_geom_voronoiBeaches.remove(beach); + d3_geom_voronoiBeachPool.push(beach); + d3_geom_voronoiRedBlackNode(beach); + } + function d3_geom_voronoiRemoveBeach(beach) { + var circle = beach.circle, x = circle.x, y = circle.cy, vertex = { + x: x, + y: y + }, previous = beach.P, next = beach.N, disappearing = [ beach ]; + d3_geom_voronoiDetachBeach(beach); + var lArc = previous; + while (lArc.circle && abs(x - lArc.circle.x) < ε && abs(y - lArc.circle.cy) < ε) { + previous = lArc.P; + disappearing.unshift(lArc); + d3_geom_voronoiDetachBeach(lArc); + lArc = previous; + } + disappearing.unshift(lArc); + d3_geom_voronoiDetachCircle(lArc); + var rArc = next; + while (rArc.circle && abs(x - rArc.circle.x) < ε && abs(y - rArc.circle.cy) < ε) { + next = rArc.N; + disappearing.push(rArc); + d3_geom_voronoiDetachBeach(rArc); + rArc = next; + } + disappearing.push(rArc); + d3_geom_voronoiDetachCircle(rArc); + var nArcs = disappearing.length, iArc; + for (iArc = 1; iArc < nArcs; ++iArc) { + rArc = disappearing[iArc]; + lArc = disappearing[iArc - 1]; + d3_geom_voronoiSetEdgeEnd(rArc.edge, lArc.site, rArc.site, vertex); + } + lArc = disappearing[0]; + rArc = disappearing[nArcs - 1]; + rArc.edge = d3_geom_voronoiCreateEdge(lArc.site, rArc.site, null, vertex); + d3_geom_voronoiAttachCircle(lArc); + d3_geom_voronoiAttachCircle(rArc); + } + function d3_geom_voronoiAddBeach(site) { + var x = site.x, directrix = site.y, lArc, rArc, dxl, dxr, node = d3_geom_voronoiBeaches._; + while (node) { + dxl = d3_geom_voronoiLeftBreakPoint(node, directrix) - x; + if (dxl > ε) node = node.L; else { + dxr = x - d3_geom_voronoiRightBreakPoint(node, directrix); + if (dxr > ε) { + if (!node.R) { + lArc = node; + break; + } + node = node.R; + } else { + if (dxl > -ε) { + lArc = node.P; + rArc = node; + } else if (dxr > -ε) { + lArc = node; + rArc = node.N; + } else { + lArc = rArc = node; + } + break; + } + } + } + var newArc = d3_geom_voronoiCreateBeach(site); + d3_geom_voronoiBeaches.insert(lArc, newArc); + if (!lArc && !rArc) return; + if (lArc === rArc) { + d3_geom_voronoiDetachCircle(lArc); + rArc = d3_geom_voronoiCreateBeach(lArc.site); + d3_geom_voronoiBeaches.insert(newArc, rArc); + newArc.edge = rArc.edge = d3_geom_voronoiCreateEdge(lArc.site, newArc.site); + d3_geom_voronoiAttachCircle(lArc); + d3_geom_voronoiAttachCircle(rArc); + return; + } + if (!rArc) { + newArc.edge = d3_geom_voronoiCreateEdge(lArc.site, newArc.site); + return; + } + d3_geom_voronoiDetachCircle(lArc); + d3_geom_voronoiDetachCircle(rArc); + var lSite = lArc.site, ax = lSite.x, ay = lSite.y, bx = site.x - ax, by = site.y - ay, rSite = rArc.site, cx = rSite.x - ax, cy = rSite.y - ay, d = 2 * (bx * cy - by * cx), hb = bx * bx + by * by, hc = cx * cx + cy * cy, vertex = { + x: (cy * hb - by * hc) / d + ax, + y: (bx * hc - cx * hb) / d + ay + }; + d3_geom_voronoiSetEdgeEnd(rArc.edge, lSite, rSite, vertex); + newArc.edge = d3_geom_voronoiCreateEdge(lSite, site, null, vertex); + rArc.edge = d3_geom_voronoiCreateEdge(site, rSite, null, vertex); + d3_geom_voronoiAttachCircle(lArc); + d3_geom_voronoiAttachCircle(rArc); + } + function d3_geom_voronoiLeftBreakPoint(arc, directrix) { + var site = arc.site, rfocx = site.x, rfocy = site.y, pby2 = rfocy - directrix; + if (!pby2) return rfocx; + var lArc = arc.P; + if (!lArc) return -Infinity; + site = lArc.site; + var lfocx = site.x, lfocy = site.y, plby2 = lfocy - directrix; + if (!plby2) return lfocx; + var hl = lfocx - rfocx, aby2 = 1 / pby2 - 1 / plby2, b = hl / plby2; + if (aby2) return (-b + Math.sqrt(b * b - 2 * aby2 * (hl * hl / (-2 * plby2) - lfocy + plby2 / 2 + rfocy - pby2 / 2))) / aby2 + rfocx; + return (rfocx + lfocx) / 2; + } + function d3_geom_voronoiRightBreakPoint(arc, directrix) { + var rArc = arc.N; + if (rArc) return d3_geom_voronoiLeftBreakPoint(rArc, directrix); + var site = arc.site; + return site.y === directrix ? site.x : Infinity; + } + function d3_geom_voronoiCell(site) { + this.site = site; + this.edges = []; + } + d3_geom_voronoiCell.prototype.prepare = function() { + var halfEdges = this.edges, iHalfEdge = halfEdges.length, edge; + while (iHalfEdge--) { + edge = halfEdges[iHalfEdge].edge; + if (!edge.b || !edge.a) halfEdges.splice(iHalfEdge, 1); + } + halfEdges.sort(d3_geom_voronoiHalfEdgeOrder); + return halfEdges.length; + }; + function d3_geom_voronoiCloseCells(extent) { + var x0 = extent[0][0], x1 = extent[1][0], y0 = extent[0][1], y1 = extent[1][1], x2, y2, x3, y3, cells = d3_geom_voronoiCells, iCell = cells.length, cell, iHalfEdge, halfEdges, nHalfEdges, start, end; + while (iCell--) { + cell = cells[iCell]; + if (!cell || !cell.prepare()) continue; + halfEdges = cell.edges; + nHalfEdges = halfEdges.length; + iHalfEdge = 0; + while (iHalfEdge < nHalfEdges) { + end = halfEdges[iHalfEdge].end(), x3 = end.x, y3 = end.y; + start = halfEdges[++iHalfEdge % nHalfEdges].start(), x2 = start.x, y2 = start.y; + if (abs(x3 - x2) > ε || abs(y3 - y2) > ε) { + halfEdges.splice(iHalfEdge, 0, new d3_geom_voronoiHalfEdge(d3_geom_voronoiCreateBorderEdge(cell.site, end, abs(x3 - x0) < ε && y1 - y3 > ε ? { + x: x0, + y: abs(x2 - x0) < ε ? y2 : y1 + } : abs(y3 - y1) < ε && x1 - x3 > ε ? { + x: abs(y2 - y1) < ε ? x2 : x1, + y: y1 + } : abs(x3 - x1) < ε && y3 - y0 > ε ? { + x: x1, + y: abs(x2 - x1) < ε ? y2 : y0 + } : abs(y3 - y0) < ε && x3 - x0 > ε ? { + x: abs(y2 - y0) < ε ? x2 : x0, + y: y0 + } : null), cell.site, null)); + ++nHalfEdges; + } + } + } + } + function d3_geom_voronoiHalfEdgeOrder(a, b) { + return b.angle - a.angle; + } + function d3_geom_voronoiCircle() { + d3_geom_voronoiRedBlackNode(this); + this.x = this.y = this.arc = this.site = this.cy = null; + } + function d3_geom_voronoiAttachCircle(arc) { + var lArc = arc.P, rArc = arc.N; + if (!lArc || !rArc) return; + var lSite = lArc.site, cSite = arc.site, rSite = rArc.site; + if (lSite === rSite) return; + var bx = cSite.x, by = cSite.y, ax = lSite.x - bx, ay = lSite.y - by, cx = rSite.x - bx, cy = rSite.y - by; + var d = 2 * (ax * cy - ay * cx); + if (d >= -ε2) return; + var ha = ax * ax + ay * ay, hc = cx * cx + cy * cy, x = (cy * ha - ay * hc) / d, y = (ax * hc - cx * ha) / d, cy = y + by; + var circle = d3_geom_voronoiCirclePool.pop() || new d3_geom_voronoiCircle(); + circle.arc = arc; + circle.site = cSite; + circle.x = x + bx; + circle.y = cy + Math.sqrt(x * x + y * y); + circle.cy = cy; + arc.circle = circle; + var before = null, node = d3_geom_voronoiCircles._; + while (node) { + if (circle.y < node.y || circle.y === node.y && circle.x <= node.x) { + if (node.L) node = node.L; else { + before = node.P; + break; + } + } else { + if (node.R) node = node.R; else { + before = node; + break; + } + } + } + d3_geom_voronoiCircles.insert(before, circle); + if (!before) d3_geom_voronoiFirstCircle = circle; + } + function d3_geom_voronoiDetachCircle(arc) { + var circle = arc.circle; + if (circle) { + if (!circle.P) d3_geom_voronoiFirstCircle = circle.N; + d3_geom_voronoiCircles.remove(circle); + d3_geom_voronoiCirclePool.push(circle); + d3_geom_voronoiRedBlackNode(circle); + arc.circle = null; + } + } + function d3_geom_voronoiClipEdges(extent) { + var edges = d3_geom_voronoiEdges, clip = d3_geom_clipLine(extent[0][0], extent[0][1], extent[1][0], extent[1][1]), i = edges.length, e; + while (i--) { + e = edges[i]; + if (!d3_geom_voronoiConnectEdge(e, extent) || !clip(e) || abs(e.a.x - e.b.x) < ε && abs(e.a.y - e.b.y) < ε) { + e.a = e.b = null; + edges.splice(i, 1); + } + } + } + function d3_geom_voronoiConnectEdge(edge, extent) { + var vb = edge.b; + if (vb) return true; + var va = edge.a, x0 = extent[0][0], x1 = extent[1][0], y0 = extent[0][1], y1 = extent[1][1], lSite = edge.l, rSite = edge.r, lx = lSite.x, ly = lSite.y, rx = rSite.x, ry = rSite.y, fx = (lx + rx) / 2, fy = (ly + ry) / 2, fm, fb; + if (ry === ly) { + if (fx < x0 || fx >= x1) return; + if (lx > rx) { + if (!va) va = { + x: fx, + y: y0 + }; else if (va.y >= y1) return; + vb = { + x: fx, + y: y1 + }; + } else { + if (!va) va = { + x: fx, + y: y1 + }; else if (va.y < y0) return; + vb = { + x: fx, + y: y0 + }; + } + } else { + fm = (lx - rx) / (ry - ly); + fb = fy - fm * fx; + if (fm < -1 || fm > 1) { + if (lx > rx) { + if (!va) va = { + x: (y0 - fb) / fm, + y: y0 + }; else if (va.y >= y1) return; + vb = { + x: (y1 - fb) / fm, + y: y1 + }; + } else { + if (!va) va = { + x: (y1 - fb) / fm, + y: y1 + }; else if (va.y < y0) return; + vb = { + x: (y0 - fb) / fm, + y: y0 + }; + } + } else { + if (ly < ry) { + if (!va) va = { + x: x0, + y: fm * x0 + fb + }; else if (va.x >= x1) return; + vb = { + x: x1, + y: fm * x1 + fb + }; + } else { + if (!va) va = { + x: x1, + y: fm * x1 + fb + }; else if (va.x < x0) return; + vb = { + x: x0, + y: fm * x0 + fb + }; + } + } + } + edge.a = va; + edge.b = vb; + return true; + } + function d3_geom_voronoiEdge(lSite, rSite) { + this.l = lSite; + this.r = rSite; + this.a = this.b = null; + } + function d3_geom_voronoiCreateEdge(lSite, rSite, va, vb) { + var edge = new d3_geom_voronoiEdge(lSite, rSite); + d3_geom_voronoiEdges.push(edge); + if (va) d3_geom_voronoiSetEdgeEnd(edge, lSite, rSite, va); + if (vb) d3_geom_voronoiSetEdgeEnd(edge, rSite, lSite, vb); + d3_geom_voronoiCells[lSite.i].edges.push(new d3_geom_voronoiHalfEdge(edge, lSite, rSite)); + d3_geom_voronoiCells[rSite.i].edges.push(new d3_geom_voronoiHalfEdge(edge, rSite, lSite)); + return edge; + } + function d3_geom_voronoiCreateBorderEdge(lSite, va, vb) { + var edge = new d3_geom_voronoiEdge(lSite, null); + edge.a = va; + edge.b = vb; + d3_geom_voronoiEdges.push(edge); + return edge; + } + function d3_geom_voronoiSetEdgeEnd(edge, lSite, rSite, vertex) { + if (!edge.a && !edge.b) { + edge.a = vertex; + edge.l = lSite; + edge.r = rSite; + } else if (edge.l === rSite) { + edge.b = vertex; + } else { + edge.a = vertex; + } + } + function d3_geom_voronoiHalfEdge(edge, lSite, rSite) { + var va = edge.a, vb = edge.b; + this.edge = edge; + this.site = lSite; + this.angle = rSite ? Math.atan2(rSite.y - lSite.y, rSite.x - lSite.x) : edge.l === lSite ? Math.atan2(vb.x - va.x, va.y - vb.y) : Math.atan2(va.x - vb.x, vb.y - va.y); + } + d3_geom_voronoiHalfEdge.prototype = { + start: function() { + return this.edge.l === this.site ? this.edge.a : this.edge.b; + }, + end: function() { + return this.edge.l === this.site ? this.edge.b : this.edge.a; + } + }; + function d3_geom_voronoiRedBlackTree() { + this._ = null; + } + function d3_geom_voronoiRedBlackNode(node) { + node.U = node.C = node.L = node.R = node.P = node.N = null; + } + d3_geom_voronoiRedBlackTree.prototype = { + insert: function(after, node) { + var parent, grandpa, uncle; + if (after) { + node.P = after; + node.N = after.N; + if (after.N) after.N.P = node; + after.N = node; + if (after.R) { + after = after.R; + while (after.L) after = after.L; + after.L = node; + } else { + after.R = node; + } + parent = after; + } else if (this._) { + after = d3_geom_voronoiRedBlackFirst(this._); + node.P = null; + node.N = after; + after.P = after.L = node; + parent = after; + } else { + node.P = node.N = null; + this._ = node; + parent = null; + } + node.L = node.R = null; + node.U = parent; + node.C = true; + after = node; + while (parent && parent.C) { + grandpa = parent.U; + if (parent === grandpa.L) { + uncle = grandpa.R; + if (uncle && uncle.C) { + parent.C = uncle.C = false; + grandpa.C = true; + after = grandpa; + } else { + if (after === parent.R) { + d3_geom_voronoiRedBlackRotateLeft(this, parent); + after = parent; + parent = after.U; + } + parent.C = false; + grandpa.C = true; + d3_geom_voronoiRedBlackRotateRight(this, grandpa); + } + } else { + uncle = grandpa.L; + if (uncle && uncle.C) { + parent.C = uncle.C = false; + grandpa.C = true; + after = grandpa; + } else { + if (after === parent.L) { + d3_geom_voronoiRedBlackRotateRight(this, parent); + after = parent; + parent = after.U; + } + parent.C = false; + grandpa.C = true; + d3_geom_voronoiRedBlackRotateLeft(this, grandpa); + } + } + parent = after.U; + } + this._.C = false; + }, + remove: function(node) { + if (node.N) node.N.P = node.P; + if (node.P) node.P.N = node.N; + node.N = node.P = null; + var parent = node.U, sibling, left = node.L, right = node.R, next, red; + if (!left) next = right; else if (!right) next = left; else next = d3_geom_voronoiRedBlackFirst(right); + if (parent) { + if (parent.L === node) parent.L = next; else parent.R = next; + } else { + this._ = next; + } + if (left && right) { + red = next.C; + next.C = node.C; + next.L = left; + left.U = next; + if (next !== right) { + parent = next.U; + next.U = node.U; + node = next.R; + parent.L = node; + next.R = right; + right.U = next; + } else { + next.U = parent; + parent = next; + node = next.R; + } + } else { + red = node.C; + node = next; + } + if (node) node.U = parent; + if (red) return; + if (node && node.C) { + node.C = false; + return; + } + do { + if (node === this._) break; + if (node === parent.L) { + sibling = parent.R; + if (sibling.C) { + sibling.C = false; + parent.C = true; + d3_geom_voronoiRedBlackRotateLeft(this, parent); + sibling = parent.R; + } + if (sibling.L && sibling.L.C || sibling.R && sibling.R.C) { + if (!sibling.R || !sibling.R.C) { + sibling.L.C = false; + sibling.C = true; + d3_geom_voronoiRedBlackRotateRight(this, sibling); + sibling = parent.R; + } + sibling.C = parent.C; + parent.C = sibling.R.C = false; + d3_geom_voronoiRedBlackRotateLeft(this, parent); + node = this._; + break; + } + } else { + sibling = parent.L; + if (sibling.C) { + sibling.C = false; + parent.C = true; + d3_geom_voronoiRedBlackRotateRight(this, parent); + sibling = parent.L; + } + if (sibling.L && sibling.L.C || sibling.R && sibling.R.C) { + if (!sibling.L || !sibling.L.C) { + sibling.R.C = false; + sibling.C = true; + d3_geom_voronoiRedBlackRotateLeft(this, sibling); + sibling = parent.L; + } + sibling.C = parent.C; + parent.C = sibling.L.C = false; + d3_geom_voronoiRedBlackRotateRight(this, parent); + node = this._; + break; + } + } + sibling.C = true; + node = parent; + parent = parent.U; + } while (!node.C); + if (node) node.C = false; + } + }; + function d3_geom_voronoiRedBlackRotateLeft(tree, node) { + var p = node, q = node.R, parent = p.U; + if (parent) { + if (parent.L === p) parent.L = q; else parent.R = q; + } else { + tree._ = q; + } + q.U = parent; + p.U = q; + p.R = q.L; + if (p.R) p.R.U = p; + q.L = p; + } + function d3_geom_voronoiRedBlackRotateRight(tree, node) { + var p = node, q = node.L, parent = p.U; + if (parent) { + if (parent.L === p) parent.L = q; else parent.R = q; + } else { + tree._ = q; + } + q.U = parent; + p.U = q; + p.L = q.R; + if (p.L) p.L.U = p; + q.R = p; + } + function d3_geom_voronoiRedBlackFirst(node) { + while (node.L) node = node.L; + return node; + } + function d3_geom_voronoi(sites, bbox) { + var site = sites.sort(d3_geom_voronoiVertexOrder).pop(), x0, y0, circle; + d3_geom_voronoiEdges = []; + d3_geom_voronoiCells = new Array(sites.length); + d3_geom_voronoiBeaches = new d3_geom_voronoiRedBlackTree(); + d3_geom_voronoiCircles = new d3_geom_voronoiRedBlackTree(); + while (true) { + circle = d3_geom_voronoiFirstCircle; + if (site && (!circle || site.y < circle.y || site.y === circle.y && site.x < circle.x)) { + if (site.x !== x0 || site.y !== y0) { + d3_geom_voronoiCells[site.i] = new d3_geom_voronoiCell(site); + d3_geom_voronoiAddBeach(site); + x0 = site.x, y0 = site.y; + } + site = sites.pop(); + } else if (circle) { + d3_geom_voronoiRemoveBeach(circle.arc); + } else { + break; + } + } + if (bbox) d3_geom_voronoiClipEdges(bbox), d3_geom_voronoiCloseCells(bbox); + var diagram = { + cells: d3_geom_voronoiCells, + edges: d3_geom_voronoiEdges + }; + d3_geom_voronoiBeaches = d3_geom_voronoiCircles = d3_geom_voronoiEdges = d3_geom_voronoiCells = null; + return diagram; + } + function d3_geom_voronoiVertexOrder(a, b) { + return b.y - a.y || b.x - a.x; + } + d3.geom.voronoi = function(points) { + var x = d3_geom_pointX, y = d3_geom_pointY, fx = x, fy = y, clipExtent = d3_geom_voronoiClipExtent; + if (points) return voronoi(points); + function voronoi(data) { + var polygons = new Array(data.length), x0 = clipExtent[0][0], y0 = clipExtent[0][1], x1 = clipExtent[1][0], y1 = clipExtent[1][1]; + d3_geom_voronoi(sites(data), clipExtent).cells.forEach(function(cell, i) { + var edges = cell.edges, site = cell.site, polygon = polygons[i] = edges.length ? edges.map(function(e) { + var s = e.start(); + return [ s.x, s.y ]; + }) : site.x >= x0 && site.x <= x1 && site.y >= y0 && site.y <= y1 ? [ [ x0, y1 ], [ x1, y1 ], [ x1, y0 ], [ x0, y0 ] ] : []; + polygon.point = data[i]; + }); + return polygons; + } + function sites(data) { + return data.map(function(d, i) { + return { + x: Math.round(fx(d, i) / ε) * ε, + y: Math.round(fy(d, i) / ε) * ε, + i: i + }; + }); + } + voronoi.links = function(data) { + return d3_geom_voronoi(sites(data)).edges.filter(function(edge) { + return edge.l && edge.r; + }).map(function(edge) { + return { + source: data[edge.l.i], + target: data[edge.r.i] + }; + }); + }; + voronoi.triangles = function(data) { + var triangles = []; + d3_geom_voronoi(sites(data)).cells.forEach(function(cell, i) { + var site = cell.site, edges = cell.edges.sort(d3_geom_voronoiHalfEdgeOrder), j = -1, m = edges.length, e0, s0, e1 = edges[m - 1].edge, s1 = e1.l === site ? e1.r : e1.l; + while (++j < m) { + e0 = e1; + s0 = s1; + e1 = edges[j].edge; + s1 = e1.l === site ? e1.r : e1.l; + if (i < s0.i && i < s1.i && d3_geom_voronoiTriangleArea(site, s0, s1) < 0) { + triangles.push([ data[i], data[s0.i], data[s1.i] ]); + } + } + }); + return triangles; + }; + voronoi.x = function(_) { + return arguments.length ? (fx = d3_functor(x = _), voronoi) : x; + }; + voronoi.y = function(_) { + return arguments.length ? (fy = d3_functor(y = _), voronoi) : y; + }; + voronoi.clipExtent = function(_) { + if (!arguments.length) return clipExtent === d3_geom_voronoiClipExtent ? null : clipExtent; + clipExtent = _ == null ? d3_geom_voronoiClipExtent : _; + return voronoi; + }; + voronoi.size = function(_) { + if (!arguments.length) return clipExtent === d3_geom_voronoiClipExtent ? null : clipExtent && clipExtent[1]; + return voronoi.clipExtent(_ && [ [ 0, 0 ], _ ]); + }; + return voronoi; + }; + var d3_geom_voronoiClipExtent = [ [ -1e6, -1e6 ], [ 1e6, 1e6 ] ]; + function d3_geom_voronoiTriangleArea(a, b, c) { + return (a.x - c.x) * (b.y - a.y) - (a.x - b.x) * (c.y - a.y); + } + d3.geom.delaunay = function(vertices) { + return d3.geom.voronoi().triangles(vertices); + }; + d3.geom.quadtree = function(points, x1, y1, x2, y2) { + var x = d3_geom_pointX, y = d3_geom_pointY, compat; + if (compat = arguments.length) { + x = d3_geom_quadtreeCompatX; + y = d3_geom_quadtreeCompatY; + if (compat === 3) { + y2 = y1; + x2 = x1; + y1 = x1 = 0; + } + return quadtree(points); + } + function quadtree(data) { + var d, fx = d3_functor(x), fy = d3_functor(y), xs, ys, i, n, x1_, y1_, x2_, y2_; + if (x1 != null) { + x1_ = x1, y1_ = y1, x2_ = x2, y2_ = y2; + } else { + x2_ = y2_ = -(x1_ = y1_ = Infinity); + xs = [], ys = []; + n = data.length; + if (compat) for (i = 0; i < n; ++i) { + d = data[i]; + if (d.x < x1_) x1_ = d.x; + if (d.y < y1_) y1_ = d.y; + if (d.x > x2_) x2_ = d.x; + if (d.y > y2_) y2_ = d.y; + xs.push(d.x); + ys.push(d.y); + } else for (i = 0; i < n; ++i) { + var x_ = +fx(d = data[i], i), y_ = +fy(d, i); + if (x_ < x1_) x1_ = x_; + if (y_ < y1_) y1_ = y_; + if (x_ > x2_) x2_ = x_; + if (y_ > y2_) y2_ = y_; + xs.push(x_); + ys.push(y_); + } + } + var dx = x2_ - x1_, dy = y2_ - y1_; + if (dx > dy) y2_ = y1_ + dx; else x2_ = x1_ + dy; + function insert(n, d, x, y, x1, y1, x2, y2) { + if (isNaN(x) || isNaN(y)) return; + if (n.leaf) { + var nx = n.x, ny = n.y; + if (nx != null) { + if (abs(nx - x) + abs(ny - y) < .01) { + insertChild(n, d, x, y, x1, y1, x2, y2); + } else { + var nPoint = n.point; + n.x = n.y = n.point = null; + insertChild(n, nPoint, nx, ny, x1, y1, x2, y2); + insertChild(n, d, x, y, x1, y1, x2, y2); + } + } else { + n.x = x, n.y = y, n.point = d; + } + } else { + insertChild(n, d, x, y, x1, y1, x2, y2); + } + } + function insertChild(n, d, x, y, x1, y1, x2, y2) { + var sx = (x1 + x2) * .5, sy = (y1 + y2) * .5, right = x >= sx, bottom = y >= sy, i = (bottom << 1) + right; + n.leaf = false; + n = n.nodes[i] || (n.nodes[i] = d3_geom_quadtreeNode()); + if (right) x1 = sx; else x2 = sx; + if (bottom) y1 = sy; else y2 = sy; + insert(n, d, x, y, x1, y1, x2, y2); + } + var root = d3_geom_quadtreeNode(); + root.add = function(d) { + insert(root, d, +fx(d, ++i), +fy(d, i), x1_, y1_, x2_, y2_); + }; + root.visit = function(f) { + d3_geom_quadtreeVisit(f, root, x1_, y1_, x2_, y2_); + }; + i = -1; + if (x1 == null) { + while (++i < n) { + insert(root, data[i], xs[i], ys[i], x1_, y1_, x2_, y2_); + } + --i; + } else data.forEach(root.add); + xs = ys = data = d = null; + return root; + } + quadtree.x = function(_) { + return arguments.length ? (x = _, quadtree) : x; + }; + quadtree.y = function(_) { + return arguments.length ? (y = _, quadtree) : y; + }; + quadtree.extent = function(_) { + if (!arguments.length) return x1 == null ? null : [ [ x1, y1 ], [ x2, y2 ] ]; + if (_ == null) x1 = y1 = x2 = y2 = null; else x1 = +_[0][0], y1 = +_[0][1], x2 = +_[1][0], + y2 = +_[1][1]; + return quadtree; + }; + quadtree.size = function(_) { + if (!arguments.length) return x1 == null ? null : [ x2 - x1, y2 - y1 ]; + if (_ == null) x1 = y1 = x2 = y2 = null; else x1 = y1 = 0, x2 = +_[0], y2 = +_[1]; + return quadtree; + }; + return quadtree; + }; + function d3_geom_quadtreeCompatX(d) { + return d.x; + } + function d3_geom_quadtreeCompatY(d) { + return d.y; + } + function d3_geom_quadtreeNode() { + return { + leaf: true, + nodes: [], + point: null, + x: null, + y: null + }; + } + function d3_geom_quadtreeVisit(f, node, x1, y1, x2, y2) { + if (!f(node, x1, y1, x2, y2)) { + var sx = (x1 + x2) * .5, sy = (y1 + y2) * .5, children = node.nodes; + if (children[0]) d3_geom_quadtreeVisit(f, children[0], x1, y1, sx, sy); + if (children[1]) d3_geom_quadtreeVisit(f, children[1], sx, y1, x2, sy); + if (children[2]) d3_geom_quadtreeVisit(f, children[2], x1, sy, sx, y2); + if (children[3]) d3_geom_quadtreeVisit(f, children[3], sx, sy, x2, y2); + } + } + d3.interpolateRgb = d3_interpolateRgb; + function d3_interpolateRgb(a, b) { + a = d3.rgb(a); + b = d3.rgb(b); + var ar = a.r, ag = a.g, ab = a.b, br = b.r - ar, bg = b.g - ag, bb = b.b - ab; + return function(t) { + return "#" + d3_rgb_hex(Math.round(ar + br * t)) + d3_rgb_hex(Math.round(ag + bg * t)) + d3_rgb_hex(Math.round(ab + bb * t)); + }; + } + d3.interpolateObject = d3_interpolateObject; + function d3_interpolateObject(a, b) { + var i = {}, c = {}, k; + for (k in a) { + if (k in b) { + i[k] = d3_interpolate(a[k], b[k]); + } else { + c[k] = a[k]; + } + } + for (k in b) { + if (!(k in a)) { + c[k] = b[k]; + } + } + return function(t) { + for (k in i) c[k] = i[k](t); + return c; + }; + } + d3.interpolateNumber = d3_interpolateNumber; + function d3_interpolateNumber(a, b) { + b -= a = +a; + return function(t) { + return a + b * t; + }; + } + d3.interpolateString = d3_interpolateString; + function d3_interpolateString(a, b) { + var bi = d3_interpolate_numberA.lastIndex = d3_interpolate_numberB.lastIndex = 0, am, bm, bs, i = -1, s = [], q = []; + a = a + "", b = b + ""; + while ((am = d3_interpolate_numberA.exec(a)) && (bm = d3_interpolate_numberB.exec(b))) { + if ((bs = bm.index) > bi) { + bs = b.substring(bi, bs); + if (s[i]) s[i] += bs; else s[++i] = bs; + } + if ((am = am[0]) === (bm = bm[0])) { + if (s[i]) s[i] += bm; else s[++i] = bm; + } else { + s[++i] = null; + q.push({ + i: i, + x: d3_interpolateNumber(am, bm) + }); + } + bi = d3_interpolate_numberB.lastIndex; + } + if (bi < b.length) { + bs = b.substring(bi); + if (s[i]) s[i] += bs; else s[++i] = bs; + } + return s.length < 2 ? q[0] ? (b = q[0].x, function(t) { + return b(t) + ""; + }) : function() { + return b; + } : (b = q.length, function(t) { + for (var i = 0, o; i < b; ++i) s[(o = q[i]).i] = o.x(t); + return s.join(""); + }); + } + var d3_interpolate_numberA = /[-+]?(?:\d+\.?\d*|\.?\d+)(?:[eE][-+]?\d+)?/g, d3_interpolate_numberB = new RegExp(d3_interpolate_numberA.source, "g"); + d3.interpolate = d3_interpolate; + function d3_interpolate(a, b) { + var i = d3.interpolators.length, f; + while (--i >= 0 && !(f = d3.interpolators[i](a, b))) ; + return f; + } + d3.interpolators = [ function(a, b) { + var t = typeof b; + return (t === "string" ? d3_rgb_names.has(b) || /^(#|rgb\(|hsl\()/.test(b) ? d3_interpolateRgb : d3_interpolateString : b instanceof d3_Color ? d3_interpolateRgb : Array.isArray(b) ? d3_interpolateArray : t === "object" && isNaN(b) ? d3_interpolateObject : d3_interpolateNumber)(a, b); + } ]; + d3.interpolateArray = d3_interpolateArray; + function d3_interpolateArray(a, b) { + var x = [], c = [], na = a.length, nb = b.length, n0 = Math.min(a.length, b.length), i; + for (i = 0; i < n0; ++i) x.push(d3_interpolate(a[i], b[i])); + for (;i < na; ++i) c[i] = a[i]; + for (;i < nb; ++i) c[i] = b[i]; + return function(t) { + for (i = 0; i < n0; ++i) c[i] = x[i](t); + return c; + }; + } + var d3_ease_default = function() { + return d3_identity; + }; + var d3_ease = d3.map({ + linear: d3_ease_default, + poly: d3_ease_poly, + quad: function() { + return d3_ease_quad; + }, + cubic: function() { + return d3_ease_cubic; + }, + sin: function() { + return d3_ease_sin; + }, + exp: function() { + return d3_ease_exp; + }, + circle: function() { + return d3_ease_circle; + }, + elastic: d3_ease_elastic, + back: d3_ease_back, + bounce: function() { + return d3_ease_bounce; + } + }); + var d3_ease_mode = d3.map({ + "in": d3_identity, + out: d3_ease_reverse, + "in-out": d3_ease_reflect, + "out-in": function(f) { + return d3_ease_reflect(d3_ease_reverse(f)); + } + }); + d3.ease = function(name) { + var i = name.indexOf("-"), t = i >= 0 ? name.substring(0, i) : name, m = i >= 0 ? name.substring(i + 1) : "in"; + t = d3_ease.get(t) || d3_ease_default; + m = d3_ease_mode.get(m) || d3_identity; + return d3_ease_clamp(m(t.apply(null, d3_arraySlice.call(arguments, 1)))); + }; + function d3_ease_clamp(f) { + return function(t) { + return t <= 0 ? 0 : t >= 1 ? 1 : f(t); + }; + } + function d3_ease_reverse(f) { + return function(t) { + return 1 - f(1 - t); + }; + } + function d3_ease_reflect(f) { + return function(t) { + return .5 * (t < .5 ? f(2 * t) : 2 - f(2 - 2 * t)); + }; + } + function d3_ease_quad(t) { + return t * t; + } + function d3_ease_cubic(t) { + return t * t * t; + } + function d3_ease_cubicInOut(t) { + if (t <= 0) return 0; + if (t >= 1) return 1; + var t2 = t * t, t3 = t2 * t; + return 4 * (t < .5 ? t3 : 3 * (t - t2) + t3 - .75); + } + function d3_ease_poly(e) { + return function(t) { + return Math.pow(t, e); + }; + } + function d3_ease_sin(t) { + return 1 - Math.cos(t * halfπ); + } + function d3_ease_exp(t) { + return Math.pow(2, 10 * (t - 1)); + } + function d3_ease_circle(t) { + return 1 - Math.sqrt(1 - t * t); + } + function d3_ease_elastic(a, p) { + var s; + if (arguments.length < 2) p = .45; + if (arguments.length) s = p / τ * Math.asin(1 / a); else a = 1, s = p / 4; + return function(t) { + return 1 + a * Math.pow(2, -10 * t) * Math.sin((t - s) * τ / p); + }; + } + function d3_ease_back(s) { + if (!s) s = 1.70158; + return function(t) { + return t * t * ((s + 1) * t - s); + }; + } + function d3_ease_bounce(t) { + return t < 1 / 2.75 ? 7.5625 * t * t : t < 2 / 2.75 ? 7.5625 * (t -= 1.5 / 2.75) * t + .75 : t < 2.5 / 2.75 ? 7.5625 * (t -= 2.25 / 2.75) * t + .9375 : 7.5625 * (t -= 2.625 / 2.75) * t + .984375; + } + d3.interpolateHcl = d3_interpolateHcl; + function d3_interpolateHcl(a, b) { + a = d3.hcl(a); + b = d3.hcl(b); + var ah = a.h, ac = a.c, al = a.l, bh = b.h - ah, bc = b.c - ac, bl = b.l - al; + if (isNaN(bc)) bc = 0, ac = isNaN(ac) ? b.c : ac; + if (isNaN(bh)) bh = 0, ah = isNaN(ah) ? b.h : ah; else if (bh > 180) bh -= 360; else if (bh < -180) bh += 360; + return function(t) { + return d3_hcl_lab(ah + bh * t, ac + bc * t, al + bl * t) + ""; + }; + } + d3.interpolateHsl = d3_interpolateHsl; + function d3_interpolateHsl(a, b) { + a = d3.hsl(a); + b = d3.hsl(b); + var ah = a.h, as = a.s, al = a.l, bh = b.h - ah, bs = b.s - as, bl = b.l - al; + if (isNaN(bs)) bs = 0, as = isNaN(as) ? b.s : as; + if (isNaN(bh)) bh = 0, ah = isNaN(ah) ? b.h : ah; else if (bh > 180) bh -= 360; else if (bh < -180) bh += 360; + return function(t) { + return d3_hsl_rgb(ah + bh * t, as + bs * t, al + bl * t) + ""; + }; + } + d3.interpolateLab = d3_interpolateLab; + function d3_interpolateLab(a, b) { + a = d3.lab(a); + b = d3.lab(b); + var al = a.l, aa = a.a, ab = a.b, bl = b.l - al, ba = b.a - aa, bb = b.b - ab; + return function(t) { + return d3_lab_rgb(al + bl * t, aa + ba * t, ab + bb * t) + ""; + }; + } + d3.interpolateRound = d3_interpolateRound; + function d3_interpolateRound(a, b) { + b -= a; + return function(t) { + return Math.round(a + b * t); + }; + } + d3.transform = function(string) { + var g = d3_document.createElementNS(d3.ns.prefix.svg, "g"); + return (d3.transform = function(string) { + if (string != null) { + g.setAttribute("transform", string); + var t = g.transform.baseVal.consolidate(); + } + return new d3_transform(t ? t.matrix : d3_transformIdentity); + })(string); + }; + function d3_transform(m) { + var r0 = [ m.a, m.b ], r1 = [ m.c, m.d ], kx = d3_transformNormalize(r0), kz = d3_transformDot(r0, r1), ky = d3_transformNormalize(d3_transformCombine(r1, r0, -kz)) || 0; + if (r0[0] * r1[1] < r1[0] * r0[1]) { + r0[0] *= -1; + r0[1] *= -1; + kx *= -1; + kz *= -1; + } + this.rotate = (kx ? Math.atan2(r0[1], r0[0]) : Math.atan2(-r1[0], r1[1])) * d3_degrees; + this.translate = [ m.e, m.f ]; + this.scale = [ kx, ky ]; + this.skew = ky ? Math.atan2(kz, ky) * d3_degrees : 0; + } + d3_transform.prototype.toString = function() { + return "translate(" + this.translate + ")rotate(" + this.rotate + ")skewX(" + this.skew + ")scale(" + this.scale + ")"; + }; + function d3_transformDot(a, b) { + return a[0] * b[0] + a[1] * b[1]; + } + function d3_transformNormalize(a) { + var k = Math.sqrt(d3_transformDot(a, a)); + if (k) { + a[0] /= k; + a[1] /= k; + } + return k; + } + function d3_transformCombine(a, b, k) { + a[0] += k * b[0]; + a[1] += k * b[1]; + return a; + } + var d3_transformIdentity = { + a: 1, + b: 0, + c: 0, + d: 1, + e: 0, + f: 0 + }; + d3.interpolateTransform = d3_interpolateTransform; + function d3_interpolateTransform(a, b) { + var s = [], q = [], n, A = d3.transform(a), B = d3.transform(b), ta = A.translate, tb = B.translate, ra = A.rotate, rb = B.rotate, wa = A.skew, wb = B.skew, ka = A.scale, kb = B.scale; + if (ta[0] != tb[0] || ta[1] != tb[1]) { + s.push("translate(", null, ",", null, ")"); + q.push({ + i: 1, + x: d3_interpolateNumber(ta[0], tb[0]) + }, { + i: 3, + x: d3_interpolateNumber(ta[1], tb[1]) + }); + } else if (tb[0] || tb[1]) { + s.push("translate(" + tb + ")"); + } else { + s.push(""); + } + if (ra != rb) { + if (ra - rb > 180) rb += 360; else if (rb - ra > 180) ra += 360; + q.push({ + i: s.push(s.pop() + "rotate(", null, ")") - 2, + x: d3_interpolateNumber(ra, rb) + }); + } else if (rb) { + s.push(s.pop() + "rotate(" + rb + ")"); + } + if (wa != wb) { + q.push({ + i: s.push(s.pop() + "skewX(", null, ")") - 2, + x: d3_interpolateNumber(wa, wb) + }); + } else if (wb) { + s.push(s.pop() + "skewX(" + wb + ")"); + } + if (ka[0] != kb[0] || ka[1] != kb[1]) { + n = s.push(s.pop() + "scale(", null, ",", null, ")"); + q.push({ + i: n - 4, + x: d3_interpolateNumber(ka[0], kb[0]) + }, { + i: n - 2, + x: d3_interpolateNumber(ka[1], kb[1]) + }); + } else if (kb[0] != 1 || kb[1] != 1) { + s.push(s.pop() + "scale(" + kb + ")"); + } + n = q.length; + return function(t) { + var i = -1, o; + while (++i < n) s[(o = q[i]).i] = o.x(t); + return s.join(""); + }; + } + function d3_uninterpolateNumber(a, b) { + b = b - (a = +a) ? 1 / (b - a) : 0; + return function(x) { + return (x - a) * b; + }; + } + function d3_uninterpolateClamp(a, b) { + b = b - (a = +a) ? 1 / (b - a) : 0; + return function(x) { + return Math.max(0, Math.min(1, (x - a) * b)); + }; + } + d3.layout = {}; + d3.layout.bundle = function() { + return function(links) { + var paths = [], i = -1, n = links.length; + while (++i < n) paths.push(d3_layout_bundlePath(links[i])); + return paths; + }; + }; + function d3_layout_bundlePath(link) { + var start = link.source, end = link.target, lca = d3_layout_bundleLeastCommonAncestor(start, end), points = [ start ]; + while (start !== lca) { + start = start.parent; + points.push(start); + } + var k = points.length; + while (end !== lca) { + points.splice(k, 0, end); + end = end.parent; + } + return points; + } + function d3_layout_bundleAncestors(node) { + var ancestors = [], parent = node.parent; + while (parent != null) { + ancestors.push(node); + node = parent; + parent = parent.parent; + } + ancestors.push(node); + return ancestors; + } + function d3_layout_bundleLeastCommonAncestor(a, b) { + if (a === b) return a; + var aNodes = d3_layout_bundleAncestors(a), bNodes = d3_layout_bundleAncestors(b), aNode = aNodes.pop(), bNode = bNodes.pop(), sharedNode = null; + while (aNode === bNode) { + sharedNode = aNode; + aNode = aNodes.pop(); + bNode = bNodes.pop(); + } + return sharedNode; + } + d3.layout.chord = function() { + var chord = {}, chords, groups, matrix, n, padding = 0, sortGroups, sortSubgroups, sortChords; + function relayout() { + var subgroups = {}, groupSums = [], groupIndex = d3.range(n), subgroupIndex = [], k, x, x0, i, j; + chords = []; + groups = []; + k = 0, i = -1; + while (++i < n) { + x = 0, j = -1; + while (++j < n) { + x += matrix[i][j]; + } + groupSums.push(x); + subgroupIndex.push(d3.range(n)); + k += x; + } + if (sortGroups) { + groupIndex.sort(function(a, b) { + return sortGroups(groupSums[a], groupSums[b]); + }); + } + if (sortSubgroups) { + subgroupIndex.forEach(function(d, i) { + d.sort(function(a, b) { + return sortSubgroups(matrix[i][a], matrix[i][b]); + }); + }); + } + k = (τ - padding * n) / k; + x = 0, i = -1; + while (++i < n) { + x0 = x, j = -1; + while (++j < n) { + var di = groupIndex[i], dj = subgroupIndex[di][j], v = matrix[di][dj], a0 = x, a1 = x += v * k; + subgroups[di + "-" + dj] = { + index: di, + subindex: dj, + startAngle: a0, + endAngle: a1, + value: v + }; + } + groups[di] = { + index: di, + startAngle: x0, + endAngle: x, + value: (x - x0) / k + }; + x += padding; + } + i = -1; + while (++i < n) { + j = i - 1; + while (++j < n) { + var source = subgroups[i + "-" + j], target = subgroups[j + "-" + i]; + if (source.value || target.value) { + chords.push(source.value < target.value ? { + source: target, + target: source + } : { + source: source, + target: target + }); + } + } + } + if (sortChords) resort(); + } + function resort() { + chords.sort(function(a, b) { + return sortChords((a.source.value + a.target.value) / 2, (b.source.value + b.target.value) / 2); + }); + } + chord.matrix = function(x) { + if (!arguments.length) return matrix; + n = (matrix = x) && matrix.length; + chords = groups = null; + return chord; + }; + chord.padding = function(x) { + if (!arguments.length) return padding; + padding = x; + chords = groups = null; + return chord; + }; + chord.sortGroups = function(x) { + if (!arguments.length) return sortGroups; + sortGroups = x; + chords = groups = null; + return chord; + }; + chord.sortSubgroups = function(x) { + if (!arguments.length) return sortSubgroups; + sortSubgroups = x; + chords = null; + return chord; + }; + chord.sortChords = function(x) { + if (!arguments.length) return sortChords; + sortChords = x; + if (chords) resort(); + return chord; + }; + chord.chords = function() { + if (!chords) relayout(); + return chords; + }; + chord.groups = function() { + if (!groups) relayout(); + return groups; + }; + return chord; + }; + d3.layout.force = function() { + var force = {}, event = d3.dispatch("start", "tick", "end"), size = [ 1, 1 ], drag, alpha, friction = .9, linkDistance = d3_layout_forceLinkDistance, linkStrength = d3_layout_forceLinkStrength, charge = -30, chargeDistance2 = d3_layout_forceChargeDistance2, gravity = .1, theta2 = .64, nodes = [], links = [], distances, strengths, charges; + function repulse(node) { + return function(quad, x1, _, x2) { + if (quad.point !== node) { + var dx = quad.cx - node.x, dy = quad.cy - node.y, dw = x2 - x1, dn = dx * dx + dy * dy; + if (dw * dw / theta2 < dn) { + if (dn < chargeDistance2) { + var k = quad.charge / dn; + node.px -= dx * k; + node.py -= dy * k; + } + return true; + } + if (quad.point && dn && dn < chargeDistance2) { + var k = quad.pointCharge / dn; + node.px -= dx * k; + node.py -= dy * k; + } + } + return !quad.charge; + }; + } + force.tick = function() { + if ((alpha *= .99) < .005) { + event.end({ + type: "end", + alpha: alpha = 0 + }); + return true; + } + var n = nodes.length, m = links.length, q, i, o, s, t, l, k, x, y; + for (i = 0; i < m; ++i) { + o = links[i]; + s = o.source; + t = o.target; + x = t.x - s.x; + y = t.y - s.y; + if (l = x * x + y * y) { + l = alpha * strengths[i] * ((l = Math.sqrt(l)) - distances[i]) / l; + x *= l; + y *= l; + t.x -= x * (k = s.weight / (t.weight + s.weight)); + t.y -= y * k; + s.x += x * (k = 1 - k); + s.y += y * k; + } + } + if (k = alpha * gravity) { + x = size[0] / 2; + y = size[1] / 2; + i = -1; + if (k) while (++i < n) { + o = nodes[i]; + o.x += (x - o.x) * k; + o.y += (y - o.y) * k; + } + } + if (charge) { + d3_layout_forceAccumulate(q = d3.geom.quadtree(nodes), alpha, charges); + i = -1; + while (++i < n) { + if (!(o = nodes[i]).fixed) { + q.visit(repulse(o)); + } + } + } + i = -1; + while (++i < n) { + o = nodes[i]; + if (o.fixed) { + o.x = o.px; + o.y = o.py; + } else { + o.x -= (o.px - (o.px = o.x)) * friction; + o.y -= (o.py - (o.py = o.y)) * friction; + } + } + event.tick({ + type: "tick", + alpha: alpha + }); + }; + force.nodes = function(x) { + if (!arguments.length) return nodes; + nodes = x; + return force; + }; + force.links = function(x) { + if (!arguments.length) return links; + links = x; + return force; + }; + force.size = function(x) { + if (!arguments.length) return size; + size = x; + return force; + }; + force.linkDistance = function(x) { + if (!arguments.length) return linkDistance; + linkDistance = typeof x === "function" ? x : +x; + return force; + }; + force.distance = force.linkDistance; + force.linkStrength = function(x) { + if (!arguments.length) return linkStrength; + linkStrength = typeof x === "function" ? x : +x; + return force; + }; + force.friction = function(x) { + if (!arguments.length) return friction; + friction = +x; + return force; + }; + force.charge = function(x) { + if (!arguments.length) return charge; + charge = typeof x === "function" ? x : +x; + return force; + }; + force.chargeDistance = function(x) { + if (!arguments.length) return Math.sqrt(chargeDistance2); + chargeDistance2 = x * x; + return force; + }; + force.gravity = function(x) { + if (!arguments.length) return gravity; + gravity = +x; + return force; + }; + force.theta = function(x) { + if (!arguments.length) return Math.sqrt(theta2); + theta2 = x * x; + return force; + }; + force.alpha = function(x) { + if (!arguments.length) return alpha; + x = +x; + if (alpha) { + if (x > 0) alpha = x; else alpha = 0; + } else if (x > 0) { + event.start({ + type: "start", + alpha: alpha = x + }); + d3.timer(force.tick); + } + return force; + }; + force.start = function() { + var i, n = nodes.length, m = links.length, w = size[0], h = size[1], neighbors, o; + for (i = 0; i < n; ++i) { + (o = nodes[i]).index = i; + o.weight = 0; + } + for (i = 0; i < m; ++i) { + o = links[i]; + if (typeof o.source == "number") o.source = nodes[o.source]; + if (typeof o.target == "number") o.target = nodes[o.target]; + ++o.source.weight; + ++o.target.weight; + } + for (i = 0; i < n; ++i) { + o = nodes[i]; + if (isNaN(o.x)) o.x = position("x", w); + if (isNaN(o.y)) o.y = position("y", h); + if (isNaN(o.px)) o.px = o.x; + if (isNaN(o.py)) o.py = o.y; + } + distances = []; + if (typeof linkDistance === "function") for (i = 0; i < m; ++i) distances[i] = +linkDistance.call(this, links[i], i); else for (i = 0; i < m; ++i) distances[i] = linkDistance; + strengths = []; + if (typeof linkStrength === "function") for (i = 0; i < m; ++i) strengths[i] = +linkStrength.call(this, links[i], i); else for (i = 0; i < m; ++i) strengths[i] = linkStrength; + charges = []; + if (typeof charge === "function") for (i = 0; i < n; ++i) charges[i] = +charge.call(this, nodes[i], i); else for (i = 0; i < n; ++i) charges[i] = charge; + function position(dimension, size) { + if (!neighbors) { + neighbors = new Array(n); + for (j = 0; j < n; ++j) { + neighbors[j] = []; + } + for (j = 0; j < m; ++j) { + var o = links[j]; + neighbors[o.source.index].push(o.target); + neighbors[o.target.index].push(o.source); + } + } + var candidates = neighbors[i], j = -1, m = candidates.length, x; + while (++j < m) if (!isNaN(x = candidates[j][dimension])) return x; + return Math.random() * size; + } + return force.resume(); + }; + force.resume = function() { + return force.alpha(.1); + }; + force.stop = function() { + return force.alpha(0); + }; + force.drag = function() { + if (!drag) drag = d3.behavior.drag().origin(d3_identity).on("dragstart.force", d3_layout_forceDragstart).on("drag.force", dragmove).on("dragend.force", d3_layout_forceDragend); + if (!arguments.length) return drag; + this.on("mouseover.force", d3_layout_forceMouseover).on("mouseout.force", d3_layout_forceMouseout).call(drag); + }; + function dragmove(d) { + d.px = d3.event.x, d.py = d3.event.y; + force.resume(); + } + return d3.rebind(force, event, "on"); + }; + function d3_layout_forceDragstart(d) { + d.fixed |= 2; + } + function d3_layout_forceDragend(d) { + d.fixed &= ~6; + } + function d3_layout_forceMouseover(d) { + d.fixed |= 4; + d.px = d.x, d.py = d.y; + } + function d3_layout_forceMouseout(d) { + d.fixed &= ~4; + } + function d3_layout_forceAccumulate(quad, alpha, charges) { + var cx = 0, cy = 0; + quad.charge = 0; + if (!quad.leaf) { + var nodes = quad.nodes, n = nodes.length, i = -1, c; + while (++i < n) { + c = nodes[i]; + if (c == null) continue; + d3_layout_forceAccumulate(c, alpha, charges); + quad.charge += c.charge; + cx += c.charge * c.cx; + cy += c.charge * c.cy; + } + } + if (quad.point) { + if (!quad.leaf) { + quad.point.x += Math.random() - .5; + quad.point.y += Math.random() - .5; + } + var k = alpha * charges[quad.point.index]; + quad.charge += quad.pointCharge = k; + cx += k * quad.point.x; + cy += k * quad.point.y; + } + quad.cx = cx / quad.charge; + quad.cy = cy / quad.charge; + } + var d3_layout_forceLinkDistance = 20, d3_layout_forceLinkStrength = 1, d3_layout_forceChargeDistance2 = Infinity; + d3.layout.hierarchy = function() { + var sort = d3_layout_hierarchySort, children = d3_layout_hierarchyChildren, value = d3_layout_hierarchyValue; + function hierarchy(root) { + var stack = [ root ], nodes = [], node; + root.depth = 0; + while ((node = stack.pop()) != null) { + nodes.push(node); + if ((childs = children.call(hierarchy, node, node.depth)) && (n = childs.length)) { + var n, childs, child; + while (--n >= 0) { + stack.push(child = childs[n]); + child.parent = node; + child.depth = node.depth + 1; + } + if (value) node.value = 0; + node.children = childs; + } else { + if (value) node.value = +value.call(hierarchy, node, node.depth) || 0; + delete node.children; + } + } + d3_layout_hierarchyVisitAfter(root, function(node) { + var childs, parent; + if (sort && (childs = node.children)) childs.sort(sort); + if (value && (parent = node.parent)) parent.value += node.value; + }); + return nodes; + } + hierarchy.sort = function(x) { + if (!arguments.length) return sort; + sort = x; + return hierarchy; + }; + hierarchy.children = function(x) { + if (!arguments.length) return children; + children = x; + return hierarchy; + }; + hierarchy.value = function(x) { + if (!arguments.length) return value; + value = x; + return hierarchy; + }; + hierarchy.revalue = function(root) { + if (value) { + d3_layout_hierarchyVisitBefore(root, function(node) { + if (node.children) node.value = 0; + }); + d3_layout_hierarchyVisitAfter(root, function(node) { + var parent; + if (!node.children) node.value = +value.call(hierarchy, node, node.depth) || 0; + if (parent = node.parent) parent.value += node.value; + }); + } + return root; + }; + return hierarchy; + }; + function d3_layout_hierarchyRebind(object, hierarchy) { + d3.rebind(object, hierarchy, "sort", "children", "value"); + object.nodes = object; + object.links = d3_layout_hierarchyLinks; + return object; + } + function d3_layout_hierarchyVisitBefore(node, callback) { + var nodes = [ node ]; + while ((node = nodes.pop()) != null) { + callback(node); + if ((children = node.children) && (n = children.length)) { + var n, children; + while (--n >= 0) nodes.push(children[n]); + } + } + } + function d3_layout_hierarchyVisitAfter(node, callback) { + var nodes = [ node ], nodes2 = []; + while ((node = nodes.pop()) != null) { + nodes2.push(node); + if ((children = node.children) && (n = children.length)) { + var i = -1, n, children; + while (++i < n) nodes.push(children[i]); + } + } + while ((node = nodes2.pop()) != null) { + callback(node); + } + } + function d3_layout_hierarchyChildren(d) { + return d.children; + } + function d3_layout_hierarchyValue(d) { + return d.value; + } + function d3_layout_hierarchySort(a, b) { + return b.value - a.value; + } + function d3_layout_hierarchyLinks(nodes) { + return d3.merge(nodes.map(function(parent) { + return (parent.children || []).map(function(child) { + return { + source: parent, + target: child + }; + }); + })); + } + d3.layout.partition = function() { + var hierarchy = d3.layout.hierarchy(), size = [ 1, 1 ]; + function position(node, x, dx, dy) { + var children = node.children; + node.x = x; + node.y = node.depth * dy; + node.dx = dx; + node.dy = dy; + if (children && (n = children.length)) { + var i = -1, n, c, d; + dx = node.value ? dx / node.value : 0; + while (++i < n) { + position(c = children[i], x, d = c.value * dx, dy); + x += d; + } + } + } + function depth(node) { + var children = node.children, d = 0; + if (children && (n = children.length)) { + var i = -1, n; + while (++i < n) d = Math.max(d, depth(children[i])); + } + return 1 + d; + } + function partition(d, i) { + var nodes = hierarchy.call(this, d, i); + position(nodes[0], 0, size[0], size[1] / depth(nodes[0])); + return nodes; + } + partition.size = function(x) { + if (!arguments.length) return size; + size = x; + return partition; + }; + return d3_layout_hierarchyRebind(partition, hierarchy); + }; + d3.layout.pie = function() { + var value = Number, sort = d3_layout_pieSortByValue, startAngle = 0, endAngle = τ; + function pie(data) { + var values = data.map(function(d, i) { + return +value.call(pie, d, i); + }); + var a = +(typeof startAngle === "function" ? startAngle.apply(this, arguments) : startAngle); + var k = ((typeof endAngle === "function" ? endAngle.apply(this, arguments) : endAngle) - a) / d3.sum(values); + var index = d3.range(data.length); + if (sort != null) index.sort(sort === d3_layout_pieSortByValue ? function(i, j) { + return values[j] - values[i]; + } : function(i, j) { + return sort(data[i], data[j]); + }); + var arcs = []; + index.forEach(function(i) { + var d; + arcs[i] = { + data: data[i], + value: d = values[i], + startAngle: a, + endAngle: a += d * k + }; + }); + return arcs; + } + pie.value = function(x) { + if (!arguments.length) return value; + value = x; + return pie; + }; + pie.sort = function(x) { + if (!arguments.length) return sort; + sort = x; + return pie; + }; + pie.startAngle = function(x) { + if (!arguments.length) return startAngle; + startAngle = x; + return pie; + }; + pie.endAngle = function(x) { + if (!arguments.length) return endAngle; + endAngle = x; + return pie; + }; + return pie; + }; + var d3_layout_pieSortByValue = {}; + d3.layout.stack = function() { + var values = d3_identity, order = d3_layout_stackOrderDefault, offset = d3_layout_stackOffsetZero, out = d3_layout_stackOut, x = d3_layout_stackX, y = d3_layout_stackY; + function stack(data, index) { + var series = data.map(function(d, i) { + return values.call(stack, d, i); + }); + var points = series.map(function(d) { + return d.map(function(v, i) { + return [ x.call(stack, v, i), y.call(stack, v, i) ]; + }); + }); + var orders = order.call(stack, points, index); + series = d3.permute(series, orders); + points = d3.permute(points, orders); + var offsets = offset.call(stack, points, index); + var n = series.length, m = series[0].length, i, j, o; + for (j = 0; j < m; ++j) { + out.call(stack, series[0][j], o = offsets[j], points[0][j][1]); + for (i = 1; i < n; ++i) { + out.call(stack, series[i][j], o += points[i - 1][j][1], points[i][j][1]); + } + } + return data; + } + stack.values = function(x) { + if (!arguments.length) return values; + values = x; + return stack; + }; + stack.order = function(x) { + if (!arguments.length) return order; + order = typeof x === "function" ? x : d3_layout_stackOrders.get(x) || d3_layout_stackOrderDefault; + return stack; + }; + stack.offset = function(x) { + if (!arguments.length) return offset; + offset = typeof x === "function" ? x : d3_layout_stackOffsets.get(x) || d3_layout_stackOffsetZero; + return stack; + }; + stack.x = function(z) { + if (!arguments.length) return x; + x = z; + return stack; + }; + stack.y = function(z) { + if (!arguments.length) return y; + y = z; + return stack; + }; + stack.out = function(z) { + if (!arguments.length) return out; + out = z; + return stack; + }; + return stack; + }; + function d3_layout_stackX(d) { + return d.x; + } + function d3_layout_stackY(d) { + return d.y; + } + function d3_layout_stackOut(d, y0, y) { + d.y0 = y0; + d.y = y; + } + var d3_layout_stackOrders = d3.map({ + "inside-out": function(data) { + var n = data.length, i, j, max = data.map(d3_layout_stackMaxIndex), sums = data.map(d3_layout_stackReduceSum), index = d3.range(n).sort(function(a, b) { + return max[a] - max[b]; + }), top = 0, bottom = 0, tops = [], bottoms = []; + for (i = 0; i < n; ++i) { + j = index[i]; + if (top < bottom) { + top += sums[j]; + tops.push(j); + } else { + bottom += sums[j]; + bottoms.push(j); + } + } + return bottoms.reverse().concat(tops); + }, + reverse: function(data) { + return d3.range(data.length).reverse(); + }, + "default": d3_layout_stackOrderDefault + }); + var d3_layout_stackOffsets = d3.map({ + silhouette: function(data) { + var n = data.length, m = data[0].length, sums = [], max = 0, i, j, o, y0 = []; + for (j = 0; j < m; ++j) { + for (i = 0, o = 0; i < n; i++) o += data[i][j][1]; + if (o > max) max = o; + sums.push(o); + } + for (j = 0; j < m; ++j) { + y0[j] = (max - sums[j]) / 2; + } + return y0; + }, + wiggle: function(data) { + var n = data.length, x = data[0], m = x.length, i, j, k, s1, s2, s3, dx, o, o0, y0 = []; + y0[0] = o = o0 = 0; + for (j = 1; j < m; ++j) { + for (i = 0, s1 = 0; i < n; ++i) s1 += data[i][j][1]; + for (i = 0, s2 = 0, dx = x[j][0] - x[j - 1][0]; i < n; ++i) { + for (k = 0, s3 = (data[i][j][1] - data[i][j - 1][1]) / (2 * dx); k < i; ++k) { + s3 += (data[k][j][1] - data[k][j - 1][1]) / dx; + } + s2 += s3 * data[i][j][1]; + } + y0[j] = o -= s1 ? s2 / s1 * dx : 0; + if (o < o0) o0 = o; + } + for (j = 0; j < m; ++j) y0[j] -= o0; + return y0; + }, + expand: function(data) { + var n = data.length, m = data[0].length, k = 1 / n, i, j, o, y0 = []; + for (j = 0; j < m; ++j) { + for (i = 0, o = 0; i < n; i++) o += data[i][j][1]; + if (o) for (i = 0; i < n; i++) data[i][j][1] /= o; else for (i = 0; i < n; i++) data[i][j][1] = k; + } + for (j = 0; j < m; ++j) y0[j] = 0; + return y0; + }, + zero: d3_layout_stackOffsetZero + }); + function d3_layout_stackOrderDefault(data) { + return d3.range(data.length); + } + function d3_layout_stackOffsetZero(data) { + var j = -1, m = data[0].length, y0 = []; + while (++j < m) y0[j] = 0; + return y0; + } + function d3_layout_stackMaxIndex(array) { + var i = 1, j = 0, v = array[0][1], k, n = array.length; + for (;i < n; ++i) { + if ((k = array[i][1]) > v) { + j = i; + v = k; + } + } + return j; + } + function d3_layout_stackReduceSum(d) { + return d.reduce(d3_layout_stackSum, 0); + } + function d3_layout_stackSum(p, d) { + return p + d[1]; + } + d3.layout.histogram = function() { + var frequency = true, valuer = Number, ranger = d3_layout_histogramRange, binner = d3_layout_histogramBinSturges; + function histogram(data, i) { + var bins = [], values = data.map(valuer, this), range = ranger.call(this, values, i), thresholds = binner.call(this, range, values, i), bin, i = -1, n = values.length, m = thresholds.length - 1, k = frequency ? 1 : 1 / n, x; + while (++i < m) { + bin = bins[i] = []; + bin.dx = thresholds[i + 1] - (bin.x = thresholds[i]); + bin.y = 0; + } + if (m > 0) { + i = -1; + while (++i < n) { + x = values[i]; + if (x >= range[0] && x <= range[1]) { + bin = bins[d3.bisect(thresholds, x, 1, m) - 1]; + bin.y += k; + bin.push(data[i]); + } + } + } + return bins; + } + histogram.value = function(x) { + if (!arguments.length) return valuer; + valuer = x; + return histogram; + }; + histogram.range = function(x) { + if (!arguments.length) return ranger; + ranger = d3_functor(x); + return histogram; + }; + histogram.bins = function(x) { + if (!arguments.length) return binner; + binner = typeof x === "number" ? function(range) { + return d3_layout_histogramBinFixed(range, x); + } : d3_functor(x); + return histogram; + }; + histogram.frequency = function(x) { + if (!arguments.length) return frequency; + frequency = !!x; + return histogram; + }; + return histogram; + }; + function d3_layout_histogramBinSturges(range, values) { + return d3_layout_histogramBinFixed(range, Math.ceil(Math.log(values.length) / Math.LN2 + 1)); + } + function d3_layout_histogramBinFixed(range, n) { + var x = -1, b = +range[0], m = (range[1] - b) / n, f = []; + while (++x <= n) f[x] = m * x + b; + return f; + } + function d3_layout_histogramRange(values) { + return [ d3.min(values), d3.max(values) ]; + } + d3.layout.pack = function() { + var hierarchy = d3.layout.hierarchy().sort(d3_layout_packSort), padding = 0, size = [ 1, 1 ], radius; + function pack(d, i) { + var nodes = hierarchy.call(this, d, i), root = nodes[0], w = size[0], h = size[1], r = radius == null ? Math.sqrt : typeof radius === "function" ? radius : function() { + return radius; + }; + root.x = root.y = 0; + d3_layout_hierarchyVisitAfter(root, function(d) { + d.r = +r(d.value); + }); + d3_layout_hierarchyVisitAfter(root, d3_layout_packSiblings); + if (padding) { + var dr = padding * (radius ? 1 : Math.max(2 * root.r / w, 2 * root.r / h)) / 2; + d3_layout_hierarchyVisitAfter(root, function(d) { + d.r += dr; + }); + d3_layout_hierarchyVisitAfter(root, d3_layout_packSiblings); + d3_layout_hierarchyVisitAfter(root, function(d) { + d.r -= dr; + }); + } + d3_layout_packTransform(root, w / 2, h / 2, radius ? 1 : 1 / Math.max(2 * root.r / w, 2 * root.r / h)); + return nodes; + } + pack.size = function(_) { + if (!arguments.length) return size; + size = _; + return pack; + }; + pack.radius = function(_) { + if (!arguments.length) return radius; + radius = _ == null || typeof _ === "function" ? _ : +_; + return pack; + }; + pack.padding = function(_) { + if (!arguments.length) return padding; + padding = +_; + return pack; + }; + return d3_layout_hierarchyRebind(pack, hierarchy); + }; + function d3_layout_packSort(a, b) { + return a.value - b.value; + } + function d3_layout_packInsert(a, b) { + var c = a._pack_next; + a._pack_next = b; + b._pack_prev = a; + b._pack_next = c; + c._pack_prev = b; + } + function d3_layout_packSplice(a, b) { + a._pack_next = b; + b._pack_prev = a; + } + function d3_layout_packIntersects(a, b) { + var dx = b.x - a.x, dy = b.y - a.y, dr = a.r + b.r; + return .999 * dr * dr > dx * dx + dy * dy; + } + function d3_layout_packSiblings(node) { + if (!(nodes = node.children) || !(n = nodes.length)) return; + var nodes, xMin = Infinity, xMax = -Infinity, yMin = Infinity, yMax = -Infinity, a, b, c, i, j, k, n; + function bound(node) { + xMin = Math.min(node.x - node.r, xMin); + xMax = Math.max(node.x + node.r, xMax); + yMin = Math.min(node.y - node.r, yMin); + yMax = Math.max(node.y + node.r, yMax); + } + nodes.forEach(d3_layout_packLink); + a = nodes[0]; + a.x = -a.r; + a.y = 0; + bound(a); + if (n > 1) { + b = nodes[1]; + b.x = b.r; + b.y = 0; + bound(b); + if (n > 2) { + c = nodes[2]; + d3_layout_packPlace(a, b, c); + bound(c); + d3_layout_packInsert(a, c); + a._pack_prev = c; + d3_layout_packInsert(c, b); + b = a._pack_next; + for (i = 3; i < n; i++) { + d3_layout_packPlace(a, b, c = nodes[i]); + var isect = 0, s1 = 1, s2 = 1; + for (j = b._pack_next; j !== b; j = j._pack_next, s1++) { + if (d3_layout_packIntersects(j, c)) { + isect = 1; + break; + } + } + if (isect == 1) { + for (k = a._pack_prev; k !== j._pack_prev; k = k._pack_prev, s2++) { + if (d3_layout_packIntersects(k, c)) { + break; + } + } + } + if (isect) { + if (s1 < s2 || s1 == s2 && b.r < a.r) d3_layout_packSplice(a, b = j); else d3_layout_packSplice(a = k, b); + i--; + } else { + d3_layout_packInsert(a, c); + b = c; + bound(c); + } + } + } + } + var cx = (xMin + xMax) / 2, cy = (yMin + yMax) / 2, cr = 0; + for (i = 0; i < n; i++) { + c = nodes[i]; + c.x -= cx; + c.y -= cy; + cr = Math.max(cr, c.r + Math.sqrt(c.x * c.x + c.y * c.y)); + } + node.r = cr; + nodes.forEach(d3_layout_packUnlink); + } + function d3_layout_packLink(node) { + node._pack_next = node._pack_prev = node; + } + function d3_layout_packUnlink(node) { + delete node._pack_next; + delete node._pack_prev; + } + function d3_layout_packTransform(node, x, y, k) { + var children = node.children; + node.x = x += k * node.x; + node.y = y += k * node.y; + node.r *= k; + if (children) { + var i = -1, n = children.length; + while (++i < n) d3_layout_packTransform(children[i], x, y, k); + } + } + function d3_layout_packPlace(a, b, c) { + var db = a.r + c.r, dx = b.x - a.x, dy = b.y - a.y; + if (db && (dx || dy)) { + var da = b.r + c.r, dc = dx * dx + dy * dy; + da *= da; + db *= db; + var x = .5 + (db - da) / (2 * dc), y = Math.sqrt(Math.max(0, 2 * da * (db + dc) - (db -= dc) * db - da * da)) / (2 * dc); + c.x = a.x + x * dx + y * dy; + c.y = a.y + x * dy - y * dx; + } else { + c.x = a.x + db; + c.y = a.y; + } + } + d3.layout.tree = function() { + var hierarchy = d3.layout.hierarchy().sort(null).value(null), separation = d3_layout_treeSeparation, size = [ 1, 1 ], nodeSize = null; + function tree(d, i) { + var nodes = hierarchy.call(this, d, i), root0 = nodes[0], root1 = wrapTree(root0); + d3_layout_hierarchyVisitAfter(root1, firstWalk), root1.parent.m = -root1.z; + d3_layout_hierarchyVisitBefore(root1, secondWalk); + if (nodeSize) d3_layout_hierarchyVisitBefore(root0, sizeNode); else { + var left = root0, right = root0, bottom = root0; + d3_layout_hierarchyVisitBefore(root0, function(node) { + if (node.x < left.x) left = node; + if (node.x > right.x) right = node; + if (node.depth > bottom.depth) bottom = node; + }); + var tx = separation(left, right) / 2 - left.x, kx = size[0] / (right.x + separation(right, left) / 2 + tx), ky = size[1] / (bottom.depth || 1); + d3_layout_hierarchyVisitBefore(root0, function(node) { + node.x = (node.x + tx) * kx; + node.y = node.depth * ky; + }); + } + return nodes; + } + function wrapTree(root0) { + var root1 = { + A: null, + children: [ root0 ] + }, queue = [ root1 ], node1; + while ((node1 = queue.pop()) != null) { + for (var children = node1.children, child, i = 0, n = children.length; i < n; ++i) { + queue.push((children[i] = child = { + _: children[i], + parent: node1, + children: (child = children[i].children) && child.slice() || [], + A: null, + a: null, + z: 0, + m: 0, + c: 0, + s: 0, + t: null, + i: i + }).a = child); + } + } + return root1.children[0]; + } + function firstWalk(v) { + var children = v.children, siblings = v.parent.children, w = v.i ? siblings[v.i - 1] : null; + if (children.length) { + d3_layout_treeShift(v); + var midpoint = (children[0].z + children[children.length - 1].z) / 2; + if (w) { + v.z = w.z + separation(v._, w._); + v.m = v.z - midpoint; + } else { + v.z = midpoint; + } + } else if (w) { + v.z = w.z + separation(v._, w._); + } + v.parent.A = apportion(v, w, v.parent.A || siblings[0]); + } + function secondWalk(v) { + v._.x = v.z + v.parent.m; + v.m += v.parent.m; + } + function apportion(v, w, ancestor) { + if (w) { + var vip = v, vop = v, vim = w, vom = vip.parent.children[0], sip = vip.m, sop = vop.m, sim = vim.m, som = vom.m, shift; + while (vim = d3_layout_treeRight(vim), vip = d3_layout_treeLeft(vip), vim && vip) { + vom = d3_layout_treeLeft(vom); + vop = d3_layout_treeRight(vop); + vop.a = v; + shift = vim.z + sim - vip.z - sip + separation(vim._, vip._); + if (shift > 0) { + d3_layout_treeMove(d3_layout_treeAncestor(vim, v, ancestor), v, shift); + sip += shift; + sop += shift; + } + sim += vim.m; + sip += vip.m; + som += vom.m; + sop += vop.m; + } + if (vim && !d3_layout_treeRight(vop)) { + vop.t = vim; + vop.m += sim - sop; + } + if (vip && !d3_layout_treeLeft(vom)) { + vom.t = vip; + vom.m += sip - som; + ancestor = v; + } + } + return ancestor; + } + function sizeNode(node) { + node.x *= size[0]; + node.y = node.depth * size[1]; + } + tree.separation = function(x) { + if (!arguments.length) return separation; + separation = x; + return tree; + }; + tree.size = function(x) { + if (!arguments.length) return nodeSize ? null : size; + nodeSize = (size = x) == null ? sizeNode : null; + return tree; + }; + tree.nodeSize = function(x) { + if (!arguments.length) return nodeSize ? size : null; + nodeSize = (size = x) == null ? null : sizeNode; + return tree; + }; + return d3_layout_hierarchyRebind(tree, hierarchy); + }; + function d3_layout_treeSeparation(a, b) { + return a.parent == b.parent ? 1 : 2; + } + function d3_layout_treeLeft(v) { + var children = v.children; + return children.length ? children[0] : v.t; + } + function d3_layout_treeRight(v) { + var children = v.children, n; + return (n = children.length) ? children[n - 1] : v.t; + } + function d3_layout_treeMove(wm, wp, shift) { + var change = shift / (wp.i - wm.i); + wp.c -= change; + wp.s += shift; + wm.c += change; + wp.z += shift; + wp.m += shift; + } + function d3_layout_treeShift(v) { + var shift = 0, change = 0, children = v.children, i = children.length, w; + while (--i >= 0) { + w = children[i]; + w.z += shift; + w.m += shift; + shift += w.s + (change += w.c); + } + } + function d3_layout_treeAncestor(vim, v, ancestor) { + return vim.a.parent === v.parent ? vim.a : ancestor; + } + d3.layout.cluster = function() { + var hierarchy = d3.layout.hierarchy().sort(null).value(null), separation = d3_layout_treeSeparation, size = [ 1, 1 ], nodeSize = false; + function cluster(d, i) { + var nodes = hierarchy.call(this, d, i), root = nodes[0], previousNode, x = 0; + d3_layout_hierarchyVisitAfter(root, function(node) { + var children = node.children; + if (children && children.length) { + node.x = d3_layout_clusterX(children); + node.y = d3_layout_clusterY(children); + } else { + node.x = previousNode ? x += separation(node, previousNode) : 0; + node.y = 0; + previousNode = node; + } + }); + var left = d3_layout_clusterLeft(root), right = d3_layout_clusterRight(root), x0 = left.x - separation(left, right) / 2, x1 = right.x + separation(right, left) / 2; + d3_layout_hierarchyVisitAfter(root, nodeSize ? function(node) { + node.x = (node.x - root.x) * size[0]; + node.y = (root.y - node.y) * size[1]; + } : function(node) { + node.x = (node.x - x0) / (x1 - x0) * size[0]; + node.y = (1 - (root.y ? node.y / root.y : 1)) * size[1]; + }); + return nodes; + } + cluster.separation = function(x) { + if (!arguments.length) return separation; + separation = x; + return cluster; + }; + cluster.size = function(x) { + if (!arguments.length) return nodeSize ? null : size; + nodeSize = (size = x) == null; + return cluster; + }; + cluster.nodeSize = function(x) { + if (!arguments.length) return nodeSize ? size : null; + nodeSize = (size = x) != null; + return cluster; + }; + return d3_layout_hierarchyRebind(cluster, hierarchy); + }; + function d3_layout_clusterY(children) { + return 1 + d3.max(children, function(child) { + return child.y; + }); + } + function d3_layout_clusterX(children) { + return children.reduce(function(x, child) { + return x + child.x; + }, 0) / children.length; + } + function d3_layout_clusterLeft(node) { + var children = node.children; + return children && children.length ? d3_layout_clusterLeft(children[0]) : node; + } + function d3_layout_clusterRight(node) { + var children = node.children, n; + return children && (n = children.length) ? d3_layout_clusterRight(children[n - 1]) : node; + } + d3.layout.treemap = function() { + var hierarchy = d3.layout.hierarchy(), round = Math.round, size = [ 1, 1 ], padding = null, pad = d3_layout_treemapPadNull, sticky = false, stickies, mode = "squarify", ratio = .5 * (1 + Math.sqrt(5)); + function scale(children, k) { + var i = -1, n = children.length, child, area; + while (++i < n) { + area = (child = children[i]).value * (k < 0 ? 0 : k); + child.area = isNaN(area) || area <= 0 ? 0 : area; + } + } + function squarify(node) { + var children = node.children; + if (children && children.length) { + var rect = pad(node), row = [], remaining = children.slice(), child, best = Infinity, score, u = mode === "slice" ? rect.dx : mode === "dice" ? rect.dy : mode === "slice-dice" ? node.depth & 1 ? rect.dy : rect.dx : Math.min(rect.dx, rect.dy), n; + scale(remaining, rect.dx * rect.dy / node.value); + row.area = 0; + while ((n = remaining.length) > 0) { + row.push(child = remaining[n - 1]); + row.area += child.area; + if (mode !== "squarify" || (score = worst(row, u)) <= best) { + remaining.pop(); + best = score; + } else { + row.area -= row.pop().area; + position(row, u, rect, false); + u = Math.min(rect.dx, rect.dy); + row.length = row.area = 0; + best = Infinity; + } + } + if (row.length) { + position(row, u, rect, true); + row.length = row.area = 0; + } + children.forEach(squarify); + } + } + function stickify(node) { + var children = node.children; + if (children && children.length) { + var rect = pad(node), remaining = children.slice(), child, row = []; + scale(remaining, rect.dx * rect.dy / node.value); + row.area = 0; + while (child = remaining.pop()) { + row.push(child); + row.area += child.area; + if (child.z != null) { + position(row, child.z ? rect.dx : rect.dy, rect, !remaining.length); + row.length = row.area = 0; + } + } + children.forEach(stickify); + } + } + function worst(row, u) { + var s = row.area, r, rmax = 0, rmin = Infinity, i = -1, n = row.length; + while (++i < n) { + if (!(r = row[i].area)) continue; + if (r < rmin) rmin = r; + if (r > rmax) rmax = r; + } + s *= s; + u *= u; + return s ? Math.max(u * rmax * ratio / s, s / (u * rmin * ratio)) : Infinity; + } + function position(row, u, rect, flush) { + var i = -1, n = row.length, x = rect.x, y = rect.y, v = u ? round(row.area / u) : 0, o; + if (u == rect.dx) { + if (flush || v > rect.dy) v = rect.dy; + while (++i < n) { + o = row[i]; + o.x = x; + o.y = y; + o.dy = v; + x += o.dx = Math.min(rect.x + rect.dx - x, v ? round(o.area / v) : 0); + } + o.z = true; + o.dx += rect.x + rect.dx - x; + rect.y += v; + rect.dy -= v; + } else { + if (flush || v > rect.dx) v = rect.dx; + while (++i < n) { + o = row[i]; + o.x = x; + o.y = y; + o.dx = v; + y += o.dy = Math.min(rect.y + rect.dy - y, v ? round(o.area / v) : 0); + } + o.z = false; + o.dy += rect.y + rect.dy - y; + rect.x += v; + rect.dx -= v; + } + } + function treemap(d) { + var nodes = stickies || hierarchy(d), root = nodes[0]; + root.x = 0; + root.y = 0; + root.dx = size[0]; + root.dy = size[1]; + if (stickies) hierarchy.revalue(root); + scale([ root ], root.dx * root.dy / root.value); + (stickies ? stickify : squarify)(root); + if (sticky) stickies = nodes; + return nodes; + } + treemap.size = function(x) { + if (!arguments.length) return size; + size = x; + return treemap; + }; + treemap.padding = function(x) { + if (!arguments.length) return padding; + function padFunction(node) { + var p = x.call(treemap, node, node.depth); + return p == null ? d3_layout_treemapPadNull(node) : d3_layout_treemapPad(node, typeof p === "number" ? [ p, p, p, p ] : p); + } + function padConstant(node) { + return d3_layout_treemapPad(node, x); + } + var type; + pad = (padding = x) == null ? d3_layout_treemapPadNull : (type = typeof x) === "function" ? padFunction : type === "number" ? (x = [ x, x, x, x ], + padConstant) : padConstant; + return treemap; + }; + treemap.round = function(x) { + if (!arguments.length) return round != Number; + round = x ? Math.round : Number; + return treemap; + }; + treemap.sticky = function(x) { + if (!arguments.length) return sticky; + sticky = x; + stickies = null; + return treemap; + }; + treemap.ratio = function(x) { + if (!arguments.length) return ratio; + ratio = x; + return treemap; + }; + treemap.mode = function(x) { + if (!arguments.length) return mode; + mode = x + ""; + return treemap; + }; + return d3_layout_hierarchyRebind(treemap, hierarchy); + }; + function d3_layout_treemapPadNull(node) { + return { + x: node.x, + y: node.y, + dx: node.dx, + dy: node.dy + }; + } + function d3_layout_treemapPad(node, padding) { + var x = node.x + padding[3], y = node.y + padding[0], dx = node.dx - padding[1] - padding[3], dy = node.dy - padding[0] - padding[2]; + if (dx < 0) { + x += dx / 2; + dx = 0; + } + if (dy < 0) { + y += dy / 2; + dy = 0; + } + return { + x: x, + y: y, + dx: dx, + dy: dy + }; + } + d3.random = { + normal: function(µ, σ) { + var n = arguments.length; + if (n < 2) σ = 1; + if (n < 1) µ = 0; + return function() { + var x, y, r; + do { + x = Math.random() * 2 - 1; + y = Math.random() * 2 - 1; + r = x * x + y * y; + } while (!r || r > 1); + return µ + σ * x * Math.sqrt(-2 * Math.log(r) / r); + }; + }, + logNormal: function() { + var random = d3.random.normal.apply(d3, arguments); + return function() { + return Math.exp(random()); + }; + }, + bates: function(m) { + var random = d3.random.irwinHall(m); + return function() { + return random() / m; + }; + }, + irwinHall: function(m) { + return function() { + for (var s = 0, j = 0; j < m; j++) s += Math.random(); + return s; + }; + } + }; + d3.scale = {}; + function d3_scaleExtent(domain) { + var start = domain[0], stop = domain[domain.length - 1]; + return start < stop ? [ start, stop ] : [ stop, start ]; + } + function d3_scaleRange(scale) { + return scale.rangeExtent ? scale.rangeExtent() : d3_scaleExtent(scale.range()); + } + function d3_scale_bilinear(domain, range, uninterpolate, interpolate) { + var u = uninterpolate(domain[0], domain[1]), i = interpolate(range[0], range[1]); + return function(x) { + return i(u(x)); + }; + } + function d3_scale_nice(domain, nice) { + var i0 = 0, i1 = domain.length - 1, x0 = domain[i0], x1 = domain[i1], dx; + if (x1 < x0) { + dx = i0, i0 = i1, i1 = dx; + dx = x0, x0 = x1, x1 = dx; + } + domain[i0] = nice.floor(x0); + domain[i1] = nice.ceil(x1); + return domain; + } + function d3_scale_niceStep(step) { + return step ? { + floor: function(x) { + return Math.floor(x / step) * step; + }, + ceil: function(x) { + return Math.ceil(x / step) * step; + } + } : d3_scale_niceIdentity; + } + var d3_scale_niceIdentity = { + floor: d3_identity, + ceil: d3_identity + }; + function d3_scale_polylinear(domain, range, uninterpolate, interpolate) { + var u = [], i = [], j = 0, k = Math.min(domain.length, range.length) - 1; + if (domain[k] < domain[0]) { + domain = domain.slice().reverse(); + range = range.slice().reverse(); + } + while (++j <= k) { + u.push(uninterpolate(domain[j - 1], domain[j])); + i.push(interpolate(range[j - 1], range[j])); + } + return function(x) { + var j = d3.bisect(domain, x, 1, k) - 1; + return i[j](u[j](x)); + }; + } + d3.scale.linear = function() { + return d3_scale_linear([ 0, 1 ], [ 0, 1 ], d3_interpolate, false); + }; + function d3_scale_linear(domain, range, interpolate, clamp) { + var output, input; + function rescale() { + var linear = Math.min(domain.length, range.length) > 2 ? d3_scale_polylinear : d3_scale_bilinear, uninterpolate = clamp ? d3_uninterpolateClamp : d3_uninterpolateNumber; + output = linear(domain, range, uninterpolate, interpolate); + input = linear(range, domain, uninterpolate, d3_interpolate); + return scale; + } + function scale(x) { + return output(x); + } + scale.invert = function(y) { + return input(y); + }; + scale.domain = function(x) { + if (!arguments.length) return domain; + domain = x.map(Number); + return rescale(); + }; + scale.range = function(x) { + if (!arguments.length) return range; + range = x; + return rescale(); + }; + scale.rangeRound = function(x) { + return scale.range(x).interpolate(d3_interpolateRound); + }; + scale.clamp = function(x) { + if (!arguments.length) return clamp; + clamp = x; + return rescale(); + }; + scale.interpolate = function(x) { + if (!arguments.length) return interpolate; + interpolate = x; + return rescale(); + }; + scale.ticks = function(m) { + return d3_scale_linearTicks(domain, m); + }; + scale.tickFormat = function(m, format) { + return d3_scale_linearTickFormat(domain, m, format); + }; + scale.nice = function(m) { + d3_scale_linearNice(domain, m); + return rescale(); + }; + scale.copy = function() { + return d3_scale_linear(domain, range, interpolate, clamp); + }; + return rescale(); + } + function d3_scale_linearRebind(scale, linear) { + return d3.rebind(scale, linear, "range", "rangeRound", "interpolate", "clamp"); + } + function d3_scale_linearNice(domain, m) { + return d3_scale_nice(domain, d3_scale_niceStep(d3_scale_linearTickRange(domain, m)[2])); + } + function d3_scale_linearTickRange(domain, m) { + if (m == null) m = 10; + var extent = d3_scaleExtent(domain), span = extent[1] - extent[0], step = Math.pow(10, Math.floor(Math.log(span / m) / Math.LN10)), err = m / span * step; + if (err <= .15) step *= 10; else if (err <= .35) step *= 5; else if (err <= .75) step *= 2; + extent[0] = Math.ceil(extent[0] / step) * step; + extent[1] = Math.floor(extent[1] / step) * step + step * .5; + extent[2] = step; + return extent; + } + function d3_scale_linearTicks(domain, m) { + return d3.range.apply(d3, d3_scale_linearTickRange(domain, m)); + } + function d3_scale_linearTickFormat(domain, m, format) { + var range = d3_scale_linearTickRange(domain, m); + if (format) { + var match = d3_format_re.exec(format); + match.shift(); + if (match[8] === "s") { + var prefix = d3.formatPrefix(Math.max(abs(range[0]), abs(range[1]))); + if (!match[7]) match[7] = "." + d3_scale_linearPrecision(prefix.scale(range[2])); + match[8] = "f"; + format = d3.format(match.join("")); + return function(d) { + return format(prefix.scale(d)) + prefix.symbol; + }; + } + if (!match[7]) match[7] = "." + d3_scale_linearFormatPrecision(match[8], range); + format = match.join(""); + } else { + format = ",." + d3_scale_linearPrecision(range[2]) + "f"; + } + return d3.format(format); + } + var d3_scale_linearFormatSignificant = { + s: 1, + g: 1, + p: 1, + r: 1, + e: 1 + }; + function d3_scale_linearPrecision(value) { + return -Math.floor(Math.log(value) / Math.LN10 + .01); + } + function d3_scale_linearFormatPrecision(type, range) { + var p = d3_scale_linearPrecision(range[2]); + return type in d3_scale_linearFormatSignificant ? Math.abs(p - d3_scale_linearPrecision(Math.max(abs(range[0]), abs(range[1])))) + +(type !== "e") : p - (type === "%") * 2; + } + d3.scale.log = function() { + return d3_scale_log(d3.scale.linear().domain([ 0, 1 ]), 10, true, [ 1, 10 ]); + }; + function d3_scale_log(linear, base, positive, domain) { + function log(x) { + return (positive ? Math.log(x < 0 ? 0 : x) : -Math.log(x > 0 ? 0 : -x)) / Math.log(base); + } + function pow(x) { + return positive ? Math.pow(base, x) : -Math.pow(base, -x); + } + function scale(x) { + return linear(log(x)); + } + scale.invert = function(x) { + return pow(linear.invert(x)); + }; + scale.domain = function(x) { + if (!arguments.length) return domain; + positive = x[0] >= 0; + linear.domain((domain = x.map(Number)).map(log)); + return scale; + }; + scale.base = function(_) { + if (!arguments.length) return base; + base = +_; + linear.domain(domain.map(log)); + return scale; + }; + scale.nice = function() { + var niced = d3_scale_nice(domain.map(log), positive ? Math : d3_scale_logNiceNegative); + linear.domain(niced); + domain = niced.map(pow); + return scale; + }; + scale.ticks = function() { + var extent = d3_scaleExtent(domain), ticks = [], u = extent[0], v = extent[1], i = Math.floor(log(u)), j = Math.ceil(log(v)), n = base % 1 ? 2 : base; + if (isFinite(j - i)) { + if (positive) { + for (;i < j; i++) for (var k = 1; k < n; k++) ticks.push(pow(i) * k); + ticks.push(pow(i)); + } else { + ticks.push(pow(i)); + for (;i++ < j; ) for (var k = n - 1; k > 0; k--) ticks.push(pow(i) * k); + } + for (i = 0; ticks[i] < u; i++) {} + for (j = ticks.length; ticks[j - 1] > v; j--) {} + ticks = ticks.slice(i, j); + } + return ticks; + }; + scale.tickFormat = function(n, format) { + if (!arguments.length) return d3_scale_logFormat; + if (arguments.length < 2) format = d3_scale_logFormat; else if (typeof format !== "function") format = d3.format(format); + var k = Math.max(.1, n / scale.ticks().length), f = positive ? (e = 1e-12, Math.ceil) : (e = -1e-12, + Math.floor), e; + return function(d) { + return d / pow(f(log(d) + e)) <= k ? format(d) : ""; + }; + }; + scale.copy = function() { + return d3_scale_log(linear.copy(), base, positive, domain); + }; + return d3_scale_linearRebind(scale, linear); + } + var d3_scale_logFormat = d3.format(".0e"), d3_scale_logNiceNegative = { + floor: function(x) { + return -Math.ceil(-x); + }, + ceil: function(x) { + return -Math.floor(-x); + } + }; + d3.scale.pow = function() { + return d3_scale_pow(d3.scale.linear(), 1, [ 0, 1 ]); + }; + function d3_scale_pow(linear, exponent, domain) { + var powp = d3_scale_powPow(exponent), powb = d3_scale_powPow(1 / exponent); + function scale(x) { + return linear(powp(x)); + } + scale.invert = function(x) { + return powb(linear.invert(x)); + }; + scale.domain = function(x) { + if (!arguments.length) return domain; + linear.domain((domain = x.map(Number)).map(powp)); + return scale; + }; + scale.ticks = function(m) { + return d3_scale_linearTicks(domain, m); + }; + scale.tickFormat = function(m, format) { + return d3_scale_linearTickFormat(domain, m, format); + }; + scale.nice = function(m) { + return scale.domain(d3_scale_linearNice(domain, m)); + }; + scale.exponent = function(x) { + if (!arguments.length) return exponent; + powp = d3_scale_powPow(exponent = x); + powb = d3_scale_powPow(1 / exponent); + linear.domain(domain.map(powp)); + return scale; + }; + scale.copy = function() { + return d3_scale_pow(linear.copy(), exponent, domain); + }; + return d3_scale_linearRebind(scale, linear); + } + function d3_scale_powPow(e) { + return function(x) { + return x < 0 ? -Math.pow(-x, e) : Math.pow(x, e); + }; + } + d3.scale.sqrt = function() { + return d3.scale.pow().exponent(.5); + }; + d3.scale.ordinal = function() { + return d3_scale_ordinal([], { + t: "range", + a: [ [] ] + }); + }; + function d3_scale_ordinal(domain, ranger) { + var index, range, rangeBand; + function scale(x) { + return range[((index.get(x) || (ranger.t === "range" ? index.set(x, domain.push(x)) : NaN)) - 1) % range.length]; + } + function steps(start, step) { + return d3.range(domain.length).map(function(i) { + return start + step * i; + }); + } + scale.domain = function(x) { + if (!arguments.length) return domain; + domain = []; + index = new d3_Map(); + var i = -1, n = x.length, xi; + while (++i < n) if (!index.has(xi = x[i])) index.set(xi, domain.push(xi)); + return scale[ranger.t].apply(scale, ranger.a); + }; + scale.range = function(x) { + if (!arguments.length) return range; + range = x; + rangeBand = 0; + ranger = { + t: "range", + a: arguments + }; + return scale; + }; + scale.rangePoints = function(x, padding) { + if (arguments.length < 2) padding = 0; + var start = x[0], stop = x[1], step = (stop - start) / (Math.max(1, domain.length - 1) + padding); + range = steps(domain.length < 2 ? (start + stop) / 2 : start + step * padding / 2, step); + rangeBand = 0; + ranger = { + t: "rangePoints", + a: arguments + }; + return scale; + }; + scale.rangeBands = function(x, padding, outerPadding) { + if (arguments.length < 2) padding = 0; + if (arguments.length < 3) outerPadding = padding; + var reverse = x[1] < x[0], start = x[reverse - 0], stop = x[1 - reverse], step = (stop - start) / (domain.length - padding + 2 * outerPadding); + range = steps(start + step * outerPadding, step); + if (reverse) range.reverse(); + rangeBand = step * (1 - padding); + ranger = { + t: "rangeBands", + a: arguments + }; + return scale; + }; + scale.rangeRoundBands = function(x, padding, outerPadding) { + if (arguments.length < 2) padding = 0; + if (arguments.length < 3) outerPadding = padding; + var reverse = x[1] < x[0], start = x[reverse - 0], stop = x[1 - reverse], step = Math.floor((stop - start) / (domain.length - padding + 2 * outerPadding)), error = stop - start - (domain.length - padding) * step; + range = steps(start + Math.round(error / 2), step); + if (reverse) range.reverse(); + rangeBand = Math.round(step * (1 - padding)); + ranger = { + t: "rangeRoundBands", + a: arguments + }; + return scale; + }; + scale.rangeBand = function() { + return rangeBand; + }; + scale.rangeExtent = function() { + return d3_scaleExtent(ranger.a[0]); + }; + scale.copy = function() { + return d3_scale_ordinal(domain, ranger); + }; + return scale.domain(domain); + } + d3.scale.category10 = function() { + return d3.scale.ordinal().range(d3_category10); + }; + d3.scale.category20 = function() { + return d3.scale.ordinal().range(d3_category20); + }; + d3.scale.category20b = function() { + return d3.scale.ordinal().range(d3_category20b); + }; + d3.scale.category20c = function() { + return d3.scale.ordinal().range(d3_category20c); + }; + var d3_category10 = [ 2062260, 16744206, 2924588, 14034728, 9725885, 9197131, 14907330, 8355711, 12369186, 1556175 ].map(d3_rgbString); + var d3_category20 = [ 2062260, 11454440, 16744206, 16759672, 2924588, 10018698, 14034728, 16750742, 9725885, 12955861, 9197131, 12885140, 14907330, 16234194, 8355711, 13092807, 12369186, 14408589, 1556175, 10410725 ].map(d3_rgbString); + var d3_category20b = [ 3750777, 5395619, 7040719, 10264286, 6519097, 9216594, 11915115, 13556636, 9202993, 12426809, 15186514, 15190932, 8666169, 11356490, 14049643, 15177372, 8077683, 10834324, 13528509, 14589654 ].map(d3_rgbString); + var d3_category20c = [ 3244733, 7057110, 10406625, 13032431, 15095053, 16616764, 16625259, 16634018, 3253076, 7652470, 10607003, 13101504, 7695281, 10394312, 12369372, 14342891, 6513507, 9868950, 12434877, 14277081 ].map(d3_rgbString); + d3.scale.quantile = function() { + return d3_scale_quantile([], []); + }; + function d3_scale_quantile(domain, range) { + var thresholds; + function rescale() { + var k = 0, q = range.length; + thresholds = []; + while (++k < q) thresholds[k - 1] = d3.quantile(domain, k / q); + return scale; + } + function scale(x) { + if (!isNaN(x = +x)) return range[d3.bisect(thresholds, x)]; + } + scale.domain = function(x) { + if (!arguments.length) return domain; + domain = x.filter(d3_number).sort(d3_ascending); + return rescale(); + }; + scale.range = function(x) { + if (!arguments.length) return range; + range = x; + return rescale(); + }; + scale.quantiles = function() { + return thresholds; + }; + scale.invertExtent = function(y) { + y = range.indexOf(y); + return y < 0 ? [ NaN, NaN ] : [ y > 0 ? thresholds[y - 1] : domain[0], y < thresholds.length ? thresholds[y] : domain[domain.length - 1] ]; + }; + scale.copy = function() { + return d3_scale_quantile(domain, range); + }; + return rescale(); + } + d3.scale.quantize = function() { + return d3_scale_quantize(0, 1, [ 0, 1 ]); + }; + function d3_scale_quantize(x0, x1, range) { + var kx, i; + function scale(x) { + return range[Math.max(0, Math.min(i, Math.floor(kx * (x - x0))))]; + } + function rescale() { + kx = range.length / (x1 - x0); + i = range.length - 1; + return scale; + } + scale.domain = function(x) { + if (!arguments.length) return [ x0, x1 ]; + x0 = +x[0]; + x1 = +x[x.length - 1]; + return rescale(); + }; + scale.range = function(x) { + if (!arguments.length) return range; + range = x; + return rescale(); + }; + scale.invertExtent = function(y) { + y = range.indexOf(y); + y = y < 0 ? NaN : y / kx + x0; + return [ y, y + 1 / kx ]; + }; + scale.copy = function() { + return d3_scale_quantize(x0, x1, range); + }; + return rescale(); + } + d3.scale.threshold = function() { + return d3_scale_threshold([ .5 ], [ 0, 1 ]); + }; + function d3_scale_threshold(domain, range) { + function scale(x) { + if (x <= x) return range[d3.bisect(domain, x)]; + } + scale.domain = function(_) { + if (!arguments.length) return domain; + domain = _; + return scale; + }; + scale.range = function(_) { + if (!arguments.length) return range; + range = _; + return scale; + }; + scale.invertExtent = function(y) { + y = range.indexOf(y); + return [ domain[y - 1], domain[y] ]; + }; + scale.copy = function() { + return d3_scale_threshold(domain, range); + }; + return scale; + } + d3.scale.identity = function() { + return d3_scale_identity([ 0, 1 ]); + }; + function d3_scale_identity(domain) { + function identity(x) { + return +x; + } + identity.invert = identity; + identity.domain = identity.range = function(x) { + if (!arguments.length) return domain; + domain = x.map(identity); + return identity; + }; + identity.ticks = function(m) { + return d3_scale_linearTicks(domain, m); + }; + identity.tickFormat = function(m, format) { + return d3_scale_linearTickFormat(domain, m, format); + }; + identity.copy = function() { + return d3_scale_identity(domain); + }; + return identity; + } + d3.svg = {}; + d3.svg.arc = function() { + var innerRadius = d3_svg_arcInnerRadius, outerRadius = d3_svg_arcOuterRadius, startAngle = d3_svg_arcStartAngle, endAngle = d3_svg_arcEndAngle; + function arc() { + var r0 = innerRadius.apply(this, arguments), r1 = outerRadius.apply(this, arguments), a0 = startAngle.apply(this, arguments) + d3_svg_arcOffset, a1 = endAngle.apply(this, arguments) + d3_svg_arcOffset, da = (a1 < a0 && (da = a0, + a0 = a1, a1 = da), a1 - a0), df = da < π ? "0" : "1", c0 = Math.cos(a0), s0 = Math.sin(a0), c1 = Math.cos(a1), s1 = Math.sin(a1); + return da >= d3_svg_arcMax ? r0 ? "M0," + r1 + "A" + r1 + "," + r1 + " 0 1,1 0," + -r1 + "A" + r1 + "," + r1 + " 0 1,1 0," + r1 + "M0," + r0 + "A" + r0 + "," + r0 + " 0 1,0 0," + -r0 + "A" + r0 + "," + r0 + " 0 1,0 0," + r0 + "Z" : "M0," + r1 + "A" + r1 + "," + r1 + " 0 1,1 0," + -r1 + "A" + r1 + "," + r1 + " 0 1,1 0," + r1 + "Z" : r0 ? "M" + r1 * c0 + "," + r1 * s0 + "A" + r1 + "," + r1 + " 0 " + df + ",1 " + r1 * c1 + "," + r1 * s1 + "L" + r0 * c1 + "," + r0 * s1 + "A" + r0 + "," + r0 + " 0 " + df + ",0 " + r0 * c0 + "," + r0 * s0 + "Z" : "M" + r1 * c0 + "," + r1 * s0 + "A" + r1 + "," + r1 + " 0 " + df + ",1 " + r1 * c1 + "," + r1 * s1 + "L0,0" + "Z"; + } + arc.innerRadius = function(v) { + if (!arguments.length) return innerRadius; + innerRadius = d3_functor(v); + return arc; + }; + arc.outerRadius = function(v) { + if (!arguments.length) return outerRadius; + outerRadius = d3_functor(v); + return arc; + }; + arc.startAngle = function(v) { + if (!arguments.length) return startAngle; + startAngle = d3_functor(v); + return arc; + }; + arc.endAngle = function(v) { + if (!arguments.length) return endAngle; + endAngle = d3_functor(v); + return arc; + }; + arc.centroid = function() { + var r = (innerRadius.apply(this, arguments) + outerRadius.apply(this, arguments)) / 2, a = (startAngle.apply(this, arguments) + endAngle.apply(this, arguments)) / 2 + d3_svg_arcOffset; + return [ Math.cos(a) * r, Math.sin(a) * r ]; + }; + return arc; + }; + var d3_svg_arcOffset = -halfπ, d3_svg_arcMax = τ - ε; + function d3_svg_arcInnerRadius(d) { + return d.innerRadius; + } + function d3_svg_arcOuterRadius(d) { + return d.outerRadius; + } + function d3_svg_arcStartAngle(d) { + return d.startAngle; + } + function d3_svg_arcEndAngle(d) { + return d.endAngle; + } + function d3_svg_line(projection) { + var x = d3_geom_pointX, y = d3_geom_pointY, defined = d3_true, interpolate = d3_svg_lineLinear, interpolateKey = interpolate.key, tension = .7; + function line(data) { + var segments = [], points = [], i = -1, n = data.length, d, fx = d3_functor(x), fy = d3_functor(y); + function segment() { + segments.push("M", interpolate(projection(points), tension)); + } + while (++i < n) { + if (defined.call(this, d = data[i], i)) { + points.push([ +fx.call(this, d, i), +fy.call(this, d, i) ]); + } else if (points.length) { + segment(); + points = []; + } + } + if (points.length) segment(); + return segments.length ? segments.join("") : null; + } + line.x = function(_) { + if (!arguments.length) return x; + x = _; + return line; + }; + line.y = function(_) { + if (!arguments.length) return y; + y = _; + return line; + }; + line.defined = function(_) { + if (!arguments.length) return defined; + defined = _; + return line; + }; + line.interpolate = function(_) { + if (!arguments.length) return interpolateKey; + if (typeof _ === "function") interpolateKey = interpolate = _; else interpolateKey = (interpolate = d3_svg_lineInterpolators.get(_) || d3_svg_lineLinear).key; + return line; + }; + line.tension = function(_) { + if (!arguments.length) return tension; + tension = _; + return line; + }; + return line; + } + d3.svg.line = function() { + return d3_svg_line(d3_identity); + }; + var d3_svg_lineInterpolators = d3.map({ + linear: d3_svg_lineLinear, + "linear-closed": d3_svg_lineLinearClosed, + step: d3_svg_lineStep, + "step-before": d3_svg_lineStepBefore, + "step-after": d3_svg_lineStepAfter, + basis: d3_svg_lineBasis, + "basis-open": d3_svg_lineBasisOpen, + "basis-closed": d3_svg_lineBasisClosed, + bundle: d3_svg_lineBundle, + cardinal: d3_svg_lineCardinal, + "cardinal-open": d3_svg_lineCardinalOpen, + "cardinal-closed": d3_svg_lineCardinalClosed, + monotone: d3_svg_lineMonotone + }); + d3_svg_lineInterpolators.forEach(function(key, value) { + value.key = key; + value.closed = /-closed$/.test(key); + }); + function d3_svg_lineLinear(points) { + return points.join("L"); + } + function d3_svg_lineLinearClosed(points) { + return d3_svg_lineLinear(points) + "Z"; + } + function d3_svg_lineStep(points) { + var i = 0, n = points.length, p = points[0], path = [ p[0], ",", p[1] ]; + while (++i < n) path.push("H", (p[0] + (p = points[i])[0]) / 2, "V", p[1]); + if (n > 1) path.push("H", p[0]); + return path.join(""); + } + function d3_svg_lineStepBefore(points) { + var i = 0, n = points.length, p = points[0], path = [ p[0], ",", p[1] ]; + while (++i < n) path.push("V", (p = points[i])[1], "H", p[0]); + return path.join(""); + } + function d3_svg_lineStepAfter(points) { + var i = 0, n = points.length, p = points[0], path = [ p[0], ",", p[1] ]; + while (++i < n) path.push("H", (p = points[i])[0], "V", p[1]); + return path.join(""); + } + function d3_svg_lineCardinalOpen(points, tension) { + return points.length < 4 ? d3_svg_lineLinear(points) : points[1] + d3_svg_lineHermite(points.slice(1, points.length - 1), d3_svg_lineCardinalTangents(points, tension)); + } + function d3_svg_lineCardinalClosed(points, tension) { + return points.length < 3 ? d3_svg_lineLinear(points) : points[0] + d3_svg_lineHermite((points.push(points[0]), + points), d3_svg_lineCardinalTangents([ points[points.length - 2] ].concat(points, [ points[1] ]), tension)); + } + function d3_svg_lineCardinal(points, tension) { + return points.length < 3 ? d3_svg_lineLinear(points) : points[0] + d3_svg_lineHermite(points, d3_svg_lineCardinalTangents(points, tension)); + } + function d3_svg_lineHermite(points, tangents) { + if (tangents.length < 1 || points.length != tangents.length && points.length != tangents.length + 2) { + return d3_svg_lineLinear(points); + } + var quad = points.length != tangents.length, path = "", p0 = points[0], p = points[1], t0 = tangents[0], t = t0, pi = 1; + if (quad) { + path += "Q" + (p[0] - t0[0] * 2 / 3) + "," + (p[1] - t0[1] * 2 / 3) + "," + p[0] + "," + p[1]; + p0 = points[1]; + pi = 2; + } + if (tangents.length > 1) { + t = tangents[1]; + p = points[pi]; + pi++; + path += "C" + (p0[0] + t0[0]) + "," + (p0[1] + t0[1]) + "," + (p[0] - t[0]) + "," + (p[1] - t[1]) + "," + p[0] + "," + p[1]; + for (var i = 2; i < tangents.length; i++, pi++) { + p = points[pi]; + t = tangents[i]; + path += "S" + (p[0] - t[0]) + "," + (p[1] - t[1]) + "," + p[0] + "," + p[1]; + } + } + if (quad) { + var lp = points[pi]; + path += "Q" + (p[0] + t[0] * 2 / 3) + "," + (p[1] + t[1] * 2 / 3) + "," + lp[0] + "," + lp[1]; + } + return path; + } + function d3_svg_lineCardinalTangents(points, tension) { + var tangents = [], a = (1 - tension) / 2, p0, p1 = points[0], p2 = points[1], i = 1, n = points.length; + while (++i < n) { + p0 = p1; + p1 = p2; + p2 = points[i]; + tangents.push([ a * (p2[0] - p0[0]), a * (p2[1] - p0[1]) ]); + } + return tangents; + } + function d3_svg_lineBasis(points) { + if (points.length < 3) return d3_svg_lineLinear(points); + var i = 1, n = points.length, pi = points[0], x0 = pi[0], y0 = pi[1], px = [ x0, x0, x0, (pi = points[1])[0] ], py = [ y0, y0, y0, pi[1] ], path = [ x0, ",", y0, "L", d3_svg_lineDot4(d3_svg_lineBasisBezier3, px), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier3, py) ]; + points.push(points[n - 1]); + while (++i <= n) { + pi = points[i]; + px.shift(); + px.push(pi[0]); + py.shift(); + py.push(pi[1]); + d3_svg_lineBasisBezier(path, px, py); + } + points.pop(); + path.push("L", pi); + return path.join(""); + } + function d3_svg_lineBasisOpen(points) { + if (points.length < 4) return d3_svg_lineLinear(points); + var path = [], i = -1, n = points.length, pi, px = [ 0 ], py = [ 0 ]; + while (++i < 3) { + pi = points[i]; + px.push(pi[0]); + py.push(pi[1]); + } + path.push(d3_svg_lineDot4(d3_svg_lineBasisBezier3, px) + "," + d3_svg_lineDot4(d3_svg_lineBasisBezier3, py)); + --i; + while (++i < n) { + pi = points[i]; + px.shift(); + px.push(pi[0]); + py.shift(); + py.push(pi[1]); + d3_svg_lineBasisBezier(path, px, py); + } + return path.join(""); + } + function d3_svg_lineBasisClosed(points) { + var path, i = -1, n = points.length, m = n + 4, pi, px = [], py = []; + while (++i < 4) { + pi = points[i % n]; + px.push(pi[0]); + py.push(pi[1]); + } + path = [ d3_svg_lineDot4(d3_svg_lineBasisBezier3, px), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier3, py) ]; + --i; + while (++i < m) { + pi = points[i % n]; + px.shift(); + px.push(pi[0]); + py.shift(); + py.push(pi[1]); + d3_svg_lineBasisBezier(path, px, py); + } + return path.join(""); + } + function d3_svg_lineBundle(points, tension) { + var n = points.length - 1; + if (n) { + var x0 = points[0][0], y0 = points[0][1], dx = points[n][0] - x0, dy = points[n][1] - y0, i = -1, p, t; + while (++i <= n) { + p = points[i]; + t = i / n; + p[0] = tension * p[0] + (1 - tension) * (x0 + t * dx); + p[1] = tension * p[1] + (1 - tension) * (y0 + t * dy); + } + } + return d3_svg_lineBasis(points); + } + function d3_svg_lineDot4(a, b) { + return a[0] * b[0] + a[1] * b[1] + a[2] * b[2] + a[3] * b[3]; + } + var d3_svg_lineBasisBezier1 = [ 0, 2 / 3, 1 / 3, 0 ], d3_svg_lineBasisBezier2 = [ 0, 1 / 3, 2 / 3, 0 ], d3_svg_lineBasisBezier3 = [ 0, 1 / 6, 2 / 3, 1 / 6 ]; + function d3_svg_lineBasisBezier(path, x, y) { + path.push("C", d3_svg_lineDot4(d3_svg_lineBasisBezier1, x), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier1, y), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier2, x), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier2, y), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier3, x), ",", d3_svg_lineDot4(d3_svg_lineBasisBezier3, y)); + } + function d3_svg_lineSlope(p0, p1) { + return (p1[1] - p0[1]) / (p1[0] - p0[0]); + } + function d3_svg_lineFiniteDifferences(points) { + var i = 0, j = points.length - 1, m = [], p0 = points[0], p1 = points[1], d = m[0] = d3_svg_lineSlope(p0, p1); + while (++i < j) { + m[i] = (d + (d = d3_svg_lineSlope(p0 = p1, p1 = points[i + 1]))) / 2; + } + m[i] = d; + return m; + } + function d3_svg_lineMonotoneTangents(points) { + var tangents = [], d, a, b, s, m = d3_svg_lineFiniteDifferences(points), i = -1, j = points.length - 1; + while (++i < j) { + d = d3_svg_lineSlope(points[i], points[i + 1]); + if (abs(d) < ε) { + m[i] = m[i + 1] = 0; + } else { + a = m[i] / d; + b = m[i + 1] / d; + s = a * a + b * b; + if (s > 9) { + s = d * 3 / Math.sqrt(s); + m[i] = s * a; + m[i + 1] = s * b; + } + } + } + i = -1; + while (++i <= j) { + s = (points[Math.min(j, i + 1)][0] - points[Math.max(0, i - 1)][0]) / (6 * (1 + m[i] * m[i])); + tangents.push([ s || 0, m[i] * s || 0 ]); + } + return tangents; + } + function d3_svg_lineMonotone(points) { + return points.length < 3 ? d3_svg_lineLinear(points) : points[0] + d3_svg_lineHermite(points, d3_svg_lineMonotoneTangents(points)); + } + d3.svg.line.radial = function() { + var line = d3_svg_line(d3_svg_lineRadial); + line.radius = line.x, delete line.x; + line.angle = line.y, delete line.y; + return line; + }; + function d3_svg_lineRadial(points) { + var point, i = -1, n = points.length, r, a; + while (++i < n) { + point = points[i]; + r = point[0]; + a = point[1] + d3_svg_arcOffset; + point[0] = r * Math.cos(a); + point[1] = r * Math.sin(a); + } + return points; + } + function d3_svg_area(projection) { + var x0 = d3_geom_pointX, x1 = d3_geom_pointX, y0 = 0, y1 = d3_geom_pointY, defined = d3_true, interpolate = d3_svg_lineLinear, interpolateKey = interpolate.key, interpolateReverse = interpolate, L = "L", tension = .7; + function area(data) { + var segments = [], points0 = [], points1 = [], i = -1, n = data.length, d, fx0 = d3_functor(x0), fy0 = d3_functor(y0), fx1 = x0 === x1 ? function() { + return x; + } : d3_functor(x1), fy1 = y0 === y1 ? function() { + return y; + } : d3_functor(y1), x, y; + function segment() { + segments.push("M", interpolate(projection(points1), tension), L, interpolateReverse(projection(points0.reverse()), tension), "Z"); + } + while (++i < n) { + if (defined.call(this, d = data[i], i)) { + points0.push([ x = +fx0.call(this, d, i), y = +fy0.call(this, d, i) ]); + points1.push([ +fx1.call(this, d, i), +fy1.call(this, d, i) ]); + } else if (points0.length) { + segment(); + points0 = []; + points1 = []; + } + } + if (points0.length) segment(); + return segments.length ? segments.join("") : null; + } + area.x = function(_) { + if (!arguments.length) return x1; + x0 = x1 = _; + return area; + }; + area.x0 = function(_) { + if (!arguments.length) return x0; + x0 = _; + return area; + }; + area.x1 = function(_) { + if (!arguments.length) return x1; + x1 = _; + return area; + }; + area.y = function(_) { + if (!arguments.length) return y1; + y0 = y1 = _; + return area; + }; + area.y0 = function(_) { + if (!arguments.length) return y0; + y0 = _; + return area; + }; + area.y1 = function(_) { + if (!arguments.length) return y1; + y1 = _; + return area; + }; + area.defined = function(_) { + if (!arguments.length) return defined; + defined = _; + return area; + }; + area.interpolate = function(_) { + if (!arguments.length) return interpolateKey; + if (typeof _ === "function") interpolateKey = interpolate = _; else interpolateKey = (interpolate = d3_svg_lineInterpolators.get(_) || d3_svg_lineLinear).key; + interpolateReverse = interpolate.reverse || interpolate; + L = interpolate.closed ? "M" : "L"; + return area; + }; + area.tension = function(_) { + if (!arguments.length) return tension; + tension = _; + return area; + }; + return area; + } + d3_svg_lineStepBefore.reverse = d3_svg_lineStepAfter; + d3_svg_lineStepAfter.reverse = d3_svg_lineStepBefore; + d3.svg.area = function() { + return d3_svg_area(d3_identity); + }; + d3.svg.area.radial = function() { + var area = d3_svg_area(d3_svg_lineRadial); + area.radius = area.x, delete area.x; + area.innerRadius = area.x0, delete area.x0; + area.outerRadius = area.x1, delete area.x1; + area.angle = area.y, delete area.y; + area.startAngle = area.y0, delete area.y0; + area.endAngle = area.y1, delete area.y1; + return area; + }; + d3.svg.chord = function() { + var source = d3_source, target = d3_target, radius = d3_svg_chordRadius, startAngle = d3_svg_arcStartAngle, endAngle = d3_svg_arcEndAngle; + function chord(d, i) { + var s = subgroup(this, source, d, i), t = subgroup(this, target, d, i); + return "M" + s.p0 + arc(s.r, s.p1, s.a1 - s.a0) + (equals(s, t) ? curve(s.r, s.p1, s.r, s.p0) : curve(s.r, s.p1, t.r, t.p0) + arc(t.r, t.p1, t.a1 - t.a0) + curve(t.r, t.p1, s.r, s.p0)) + "Z"; + } + function subgroup(self, f, d, i) { + var subgroup = f.call(self, d, i), r = radius.call(self, subgroup, i), a0 = startAngle.call(self, subgroup, i) + d3_svg_arcOffset, a1 = endAngle.call(self, subgroup, i) + d3_svg_arcOffset; + return { + r: r, + a0: a0, + a1: a1, + p0: [ r * Math.cos(a0), r * Math.sin(a0) ], + p1: [ r * Math.cos(a1), r * Math.sin(a1) ] + }; + } + function equals(a, b) { + return a.a0 == b.a0 && a.a1 == b.a1; + } + function arc(r, p, a) { + return "A" + r + "," + r + " 0 " + +(a > π) + ",1 " + p; + } + function curve(r0, p0, r1, p1) { + return "Q 0,0 " + p1; + } + chord.radius = function(v) { + if (!arguments.length) return radius; + radius = d3_functor(v); + return chord; + }; + chord.source = function(v) { + if (!arguments.length) return source; + source = d3_functor(v); + return chord; + }; + chord.target = function(v) { + if (!arguments.length) return target; + target = d3_functor(v); + return chord; + }; + chord.startAngle = function(v) { + if (!arguments.length) return startAngle; + startAngle = d3_functor(v); + return chord; + }; + chord.endAngle = function(v) { + if (!arguments.length) return endAngle; + endAngle = d3_functor(v); + return chord; + }; + return chord; + }; + function d3_svg_chordRadius(d) { + return d.radius; + } + d3.svg.diagonal = function() { + var source = d3_source, target = d3_target, projection = d3_svg_diagonalProjection; + function diagonal(d, i) { + var p0 = source.call(this, d, i), p3 = target.call(this, d, i), m = (p0.y + p3.y) / 2, p = [ p0, { + x: p0.x, + y: m + }, { + x: p3.x, + y: m + }, p3 ]; + p = p.map(projection); + return "M" + p[0] + "C" + p[1] + " " + p[2] + " " + p[3]; + } + diagonal.source = function(x) { + if (!arguments.length) return source; + source = d3_functor(x); + return diagonal; + }; + diagonal.target = function(x) { + if (!arguments.length) return target; + target = d3_functor(x); + return diagonal; + }; + diagonal.projection = function(x) { + if (!arguments.length) return projection; + projection = x; + return diagonal; + }; + return diagonal; + }; + function d3_svg_diagonalProjection(d) { + return [ d.x, d.y ]; + } + d3.svg.diagonal.radial = function() { + var diagonal = d3.svg.diagonal(), projection = d3_svg_diagonalProjection, projection_ = diagonal.projection; + diagonal.projection = function(x) { + return arguments.length ? projection_(d3_svg_diagonalRadialProjection(projection = x)) : projection; + }; + return diagonal; + }; + function d3_svg_diagonalRadialProjection(projection) { + return function() { + var d = projection.apply(this, arguments), r = d[0], a = d[1] + d3_svg_arcOffset; + return [ r * Math.cos(a), r * Math.sin(a) ]; + }; + } + d3.svg.symbol = function() { + var type = d3_svg_symbolType, size = d3_svg_symbolSize; + function symbol(d, i) { + return (d3_svg_symbols.get(type.call(this, d, i)) || d3_svg_symbolCircle)(size.call(this, d, i)); + } + symbol.type = function(x) { + if (!arguments.length) return type; + type = d3_functor(x); + return symbol; + }; + symbol.size = function(x) { + if (!arguments.length) return size; + size = d3_functor(x); + return symbol; + }; + return symbol; + }; + function d3_svg_symbolSize() { + return 64; + } + function d3_svg_symbolType() { + return "circle"; + } + function d3_svg_symbolCircle(size) { + var r = Math.sqrt(size / π); + return "M0," + r + "A" + r + "," + r + " 0 1,1 0," + -r + "A" + r + "," + r + " 0 1,1 0," + r + "Z"; + } + var d3_svg_symbols = d3.map({ + circle: d3_svg_symbolCircle, + cross: function(size) { + var r = Math.sqrt(size / 5) / 2; + return "M" + -3 * r + "," + -r + "H" + -r + "V" + -3 * r + "H" + r + "V" + -r + "H" + 3 * r + "V" + r + "H" + r + "V" + 3 * r + "H" + -r + "V" + r + "H" + -3 * r + "Z"; + }, + diamond: function(size) { + var ry = Math.sqrt(size / (2 * d3_svg_symbolTan30)), rx = ry * d3_svg_symbolTan30; + return "M0," + -ry + "L" + rx + ",0" + " 0," + ry + " " + -rx + ",0" + "Z"; + }, + square: function(size) { + var r = Math.sqrt(size) / 2; + return "M" + -r + "," + -r + "L" + r + "," + -r + " " + r + "," + r + " " + -r + "," + r + "Z"; + }, + "triangle-down": function(size) { + var rx = Math.sqrt(size / d3_svg_symbolSqrt3), ry = rx * d3_svg_symbolSqrt3 / 2; + return "M0," + ry + "L" + rx + "," + -ry + " " + -rx + "," + -ry + "Z"; + }, + "triangle-up": function(size) { + var rx = Math.sqrt(size / d3_svg_symbolSqrt3), ry = rx * d3_svg_symbolSqrt3 / 2; + return "M0," + -ry + "L" + rx + "," + ry + " " + -rx + "," + ry + "Z"; + } + }); + d3.svg.symbolTypes = d3_svg_symbols.keys(); + var d3_svg_symbolSqrt3 = Math.sqrt(3), d3_svg_symbolTan30 = Math.tan(30 * d3_radians); + function d3_transition(groups, id) { + d3_subclass(groups, d3_transitionPrototype); + groups.id = id; + return groups; + } + var d3_transitionPrototype = [], d3_transitionId = 0, d3_transitionInheritId, d3_transitionInherit; + d3_transitionPrototype.call = d3_selectionPrototype.call; + d3_transitionPrototype.empty = d3_selectionPrototype.empty; + d3_transitionPrototype.node = d3_selectionPrototype.node; + d3_transitionPrototype.size = d3_selectionPrototype.size; + d3.transition = function(selection) { + return arguments.length ? d3_transitionInheritId ? selection.transition() : selection : d3_selectionRoot.transition(); + }; + d3.transition.prototype = d3_transitionPrototype; + d3_transitionPrototype.select = function(selector) { + var id = this.id, subgroups = [], subgroup, subnode, node; + selector = d3_selection_selector(selector); + for (var j = -1, m = this.length; ++j < m; ) { + subgroups.push(subgroup = []); + for (var group = this[j], i = -1, n = group.length; ++i < n; ) { + if ((node = group[i]) && (subnode = selector.call(node, node.__data__, i, j))) { + if ("__data__" in node) subnode.__data__ = node.__data__; + d3_transitionNode(subnode, i, id, node.__transition__[id]); + subgroup.push(subnode); + } else { + subgroup.push(null); + } + } + } + return d3_transition(subgroups, id); + }; + d3_transitionPrototype.selectAll = function(selector) { + var id = this.id, subgroups = [], subgroup, subnodes, node, subnode, transition; + selector = d3_selection_selectorAll(selector); + for (var j = -1, m = this.length; ++j < m; ) { + for (var group = this[j], i = -1, n = group.length; ++i < n; ) { + if (node = group[i]) { + transition = node.__transition__[id]; + subnodes = selector.call(node, node.__data__, i, j); + subgroups.push(subgroup = []); + for (var k = -1, o = subnodes.length; ++k < o; ) { + if (subnode = subnodes[k]) d3_transitionNode(subnode, k, id, transition); + subgroup.push(subnode); + } + } + } + } + return d3_transition(subgroups, id); + }; + d3_transitionPrototype.filter = function(filter) { + var subgroups = [], subgroup, group, node; + if (typeof filter !== "function") filter = d3_selection_filter(filter); + for (var j = 0, m = this.length; j < m; j++) { + subgroups.push(subgroup = []); + for (var group = this[j], i = 0, n = group.length; i < n; i++) { + if ((node = group[i]) && filter.call(node, node.__data__, i, j)) { + subgroup.push(node); + } + } + } + return d3_transition(subgroups, this.id); + }; + d3_transitionPrototype.tween = function(name, tween) { + var id = this.id; + if (arguments.length < 2) return this.node().__transition__[id].tween.get(name); + return d3_selection_each(this, tween == null ? function(node) { + node.__transition__[id].tween.remove(name); + } : function(node) { + node.__transition__[id].tween.set(name, tween); + }); + }; + function d3_transition_tween(groups, name, value, tween) { + var id = groups.id; + return d3_selection_each(groups, typeof value === "function" ? function(node, i, j) { + node.__transition__[id].tween.set(name, tween(value.call(node, node.__data__, i, j))); + } : (value = tween(value), function(node) { + node.__transition__[id].tween.set(name, value); + })); + } + d3_transitionPrototype.attr = function(nameNS, value) { + if (arguments.length < 2) { + for (value in nameNS) this.attr(value, nameNS[value]); + return this; + } + var interpolate = nameNS == "transform" ? d3_interpolateTransform : d3_interpolate, name = d3.ns.qualify(nameNS); + function attrNull() { + this.removeAttribute(name); + } + function attrNullNS() { + this.removeAttributeNS(name.space, name.local); + } + function attrTween(b) { + return b == null ? attrNull : (b += "", function() { + var a = this.getAttribute(name), i; + return a !== b && (i = interpolate(a, b), function(t) { + this.setAttribute(name, i(t)); + }); + }); + } + function attrTweenNS(b) { + return b == null ? attrNullNS : (b += "", function() { + var a = this.getAttributeNS(name.space, name.local), i; + return a !== b && (i = interpolate(a, b), function(t) { + this.setAttributeNS(name.space, name.local, i(t)); + }); + }); + } + return d3_transition_tween(this, "attr." + nameNS, value, name.local ? attrTweenNS : attrTween); + }; + d3_transitionPrototype.attrTween = function(nameNS, tween) { + var name = d3.ns.qualify(nameNS); + function attrTween(d, i) { + var f = tween.call(this, d, i, this.getAttribute(name)); + return f && function(t) { + this.setAttribute(name, f(t)); + }; + } + function attrTweenNS(d, i) { + var f = tween.call(this, d, i, this.getAttributeNS(name.space, name.local)); + return f && function(t) { + this.setAttributeNS(name.space, name.local, f(t)); + }; + } + return this.tween("attr." + nameNS, name.local ? attrTweenNS : attrTween); + }; + d3_transitionPrototype.style = function(name, value, priority) { + var n = arguments.length; + if (n < 3) { + if (typeof name !== "string") { + if (n < 2) value = ""; + for (priority in name) this.style(priority, name[priority], value); + return this; + } + priority = ""; + } + function styleNull() { + this.style.removeProperty(name); + } + function styleString(b) { + return b == null ? styleNull : (b += "", function() { + var a = d3_window.getComputedStyle(this, null).getPropertyValue(name), i; + return a !== b && (i = d3_interpolate(a, b), function(t) { + this.style.setProperty(name, i(t), priority); + }); + }); + } + return d3_transition_tween(this, "style." + name, value, styleString); + }; + d3_transitionPrototype.styleTween = function(name, tween, priority) { + if (arguments.length < 3) priority = ""; + function styleTween(d, i) { + var f = tween.call(this, d, i, d3_window.getComputedStyle(this, null).getPropertyValue(name)); + return f && function(t) { + this.style.setProperty(name, f(t), priority); + }; + } + return this.tween("style." + name, styleTween); + }; + d3_transitionPrototype.text = function(value) { + return d3_transition_tween(this, "text", value, d3_transition_text); + }; + function d3_transition_text(b) { + if (b == null) b = ""; + return function() { + this.textContent = b; + }; + } + d3_transitionPrototype.remove = function() { + return this.each("end.transition", function() { + var p; + if (this.__transition__.count < 2 && (p = this.parentNode)) p.removeChild(this); + }); + }; + d3_transitionPrototype.ease = function(value) { + var id = this.id; + if (arguments.length < 1) return this.node().__transition__[id].ease; + if (typeof value !== "function") value = d3.ease.apply(d3, arguments); + return d3_selection_each(this, function(node) { + node.__transition__[id].ease = value; + }); + }; + d3_transitionPrototype.delay = function(value) { + var id = this.id; + if (arguments.length < 1) return this.node().__transition__[id].delay; + return d3_selection_each(this, typeof value === "function" ? function(node, i, j) { + node.__transition__[id].delay = +value.call(node, node.__data__, i, j); + } : (value = +value, function(node) { + node.__transition__[id].delay = value; + })); + }; + d3_transitionPrototype.duration = function(value) { + var id = this.id; + if (arguments.length < 1) return this.node().__transition__[id].duration; + return d3_selection_each(this, typeof value === "function" ? function(node, i, j) { + node.__transition__[id].duration = Math.max(1, value.call(node, node.__data__, i, j)); + } : (value = Math.max(1, value), function(node) { + node.__transition__[id].duration = value; + })); + }; + d3_transitionPrototype.each = function(type, listener) { + var id = this.id; + if (arguments.length < 2) { + var inherit = d3_transitionInherit, inheritId = d3_transitionInheritId; + d3_transitionInheritId = id; + d3_selection_each(this, function(node, i, j) { + d3_transitionInherit = node.__transition__[id]; + type.call(node, node.__data__, i, j); + }); + d3_transitionInherit = inherit; + d3_transitionInheritId = inheritId; + } else { + d3_selection_each(this, function(node) { + var transition = node.__transition__[id]; + (transition.event || (transition.event = d3.dispatch("start", "end"))).on(type, listener); + }); + } + return this; + }; + d3_transitionPrototype.transition = function() { + var id0 = this.id, id1 = ++d3_transitionId, subgroups = [], subgroup, group, node, transition; + for (var j = 0, m = this.length; j < m; j++) { + subgroups.push(subgroup = []); + for (var group = this[j], i = 0, n = group.length; i < n; i++) { + if (node = group[i]) { + transition = Object.create(node.__transition__[id0]); + transition.delay += transition.duration; + d3_transitionNode(node, i, id1, transition); + } + subgroup.push(node); + } + } + return d3_transition(subgroups, id1); + }; + function d3_transitionNode(node, i, id, inherit) { + var lock = node.__transition__ || (node.__transition__ = { + active: 0, + count: 0 + }), transition = lock[id]; + if (!transition) { + var time = inherit.time; + transition = lock[id] = { + tween: new d3_Map(), + time: time, + ease: inherit.ease, + delay: inherit.delay, + duration: inherit.duration + }; + ++lock.count; + d3.timer(function(elapsed) { + var d = node.__data__, ease = transition.ease, delay = transition.delay, duration = transition.duration, timer = d3_timer_active, tweened = []; + timer.t = delay + time; + if (delay <= elapsed) return start(elapsed - delay); + timer.c = start; + function start(elapsed) { + if (lock.active > id) return stop(); + lock.active = id; + transition.event && transition.event.start.call(node, d, i); + transition.tween.forEach(function(key, value) { + if (value = value.call(node, d, i)) { + tweened.push(value); + } + }); + d3.timer(function() { + timer.c = tick(elapsed || 1) ? d3_true : tick; + return 1; + }, 0, time); + } + function tick(elapsed) { + if (lock.active !== id) return stop(); + var t = elapsed / duration, e = ease(t), n = tweened.length; + while (n > 0) { + tweened[--n].call(node, e); + } + if (t >= 1) { + transition.event && transition.event.end.call(node, d, i); + return stop(); + } + } + function stop() { + if (--lock.count) delete lock[id]; else delete node.__transition__; + return 1; + } + }, 0, time); + } + } + d3.svg.axis = function() { + var scale = d3.scale.linear(), orient = d3_svg_axisDefaultOrient, innerTickSize = 6, outerTickSize = 6, tickPadding = 3, tickArguments_ = [ 10 ], tickValues = null, tickFormat_; + function axis(g) { + g.each(function() { + var g = d3.select(this); + var scale0 = this.__chart__ || scale, scale1 = this.__chart__ = scale.copy(); + var ticks = tickValues == null ? scale1.ticks ? scale1.ticks.apply(scale1, tickArguments_) : scale1.domain() : tickValues, tickFormat = tickFormat_ == null ? scale1.tickFormat ? scale1.tickFormat.apply(scale1, tickArguments_) : d3_identity : tickFormat_, tick = g.selectAll(".tick").data(ticks, scale1), tickEnter = tick.enter().insert("g", ".domain").attr("class", "tick").style("opacity", ε), tickExit = d3.transition(tick.exit()).style("opacity", ε).remove(), tickUpdate = d3.transition(tick.order()).style("opacity", 1), tickTransform; + var range = d3_scaleRange(scale1), path = g.selectAll(".domain").data([ 0 ]), pathUpdate = (path.enter().append("path").attr("class", "domain"), + d3.transition(path)); + tickEnter.append("line"); + tickEnter.append("text"); + var lineEnter = tickEnter.select("line"), lineUpdate = tickUpdate.select("line"), text = tick.select("text").text(tickFormat), textEnter = tickEnter.select("text"), textUpdate = tickUpdate.select("text"); + switch (orient) { + case "bottom": + { + tickTransform = d3_svg_axisX; + lineEnter.attr("y2", innerTickSize); + textEnter.attr("y", Math.max(innerTickSize, 0) + tickPadding); + lineUpdate.attr("x2", 0).attr("y2", innerTickSize); + textUpdate.attr("x", 0).attr("y", Math.max(innerTickSize, 0) + tickPadding); + text.attr("dy", ".71em").style("text-anchor", "middle"); + pathUpdate.attr("d", "M" + range[0] + "," + outerTickSize + "V0H" + range[1] + "V" + outerTickSize); + break; + } + + case "top": + { + tickTransform = d3_svg_axisX; + lineEnter.attr("y2", -innerTickSize); + textEnter.attr("y", -(Math.max(innerTickSize, 0) + tickPadding)); + lineUpdate.attr("x2", 0).attr("y2", -innerTickSize); + textUpdate.attr("x", 0).attr("y", -(Math.max(innerTickSize, 0) + tickPadding)); + text.attr("dy", "0em").style("text-anchor", "middle"); + pathUpdate.attr("d", "M" + range[0] + "," + -outerTickSize + "V0H" + range[1] + "V" + -outerTickSize); + break; + } + + case "left": + { + tickTransform = d3_svg_axisY; + lineEnter.attr("x2", -innerTickSize); + textEnter.attr("x", -(Math.max(innerTickSize, 0) + tickPadding)); + lineUpdate.attr("x2", -innerTickSize).attr("y2", 0); + textUpdate.attr("x", -(Math.max(innerTickSize, 0) + tickPadding)).attr("y", 0); + text.attr("dy", ".32em").style("text-anchor", "end"); + pathUpdate.attr("d", "M" + -outerTickSize + "," + range[0] + "H0V" + range[1] + "H" + -outerTickSize); + break; + } + + case "right": + { + tickTransform = d3_svg_axisY; + lineEnter.attr("x2", innerTickSize); + textEnter.attr("x", Math.max(innerTickSize, 0) + tickPadding); + lineUpdate.attr("x2", innerTickSize).attr("y2", 0); + textUpdate.attr("x", Math.max(innerTickSize, 0) + tickPadding).attr("y", 0); + text.attr("dy", ".32em").style("text-anchor", "start"); + pathUpdate.attr("d", "M" + outerTickSize + "," + range[0] + "H0V" + range[1] + "H" + outerTickSize); + break; + } + } + if (scale1.rangeBand) { + var x = scale1, dx = x.rangeBand() / 2; + scale0 = scale1 = function(d) { + return x(d) + dx; + }; + } else if (scale0.rangeBand) { + scale0 = scale1; + } else { + tickExit.call(tickTransform, scale1); + } + tickEnter.call(tickTransform, scale0); + tickUpdate.call(tickTransform, scale1); + }); + } + axis.scale = function(x) { + if (!arguments.length) return scale; + scale = x; + return axis; + }; + axis.orient = function(x) { + if (!arguments.length) return orient; + orient = x in d3_svg_axisOrients ? x + "" : d3_svg_axisDefaultOrient; + return axis; + }; + axis.ticks = function() { + if (!arguments.length) return tickArguments_; + tickArguments_ = arguments; + return axis; + }; + axis.tickValues = function(x) { + if (!arguments.length) return tickValues; + tickValues = x; + return axis; + }; + axis.tickFormat = function(x) { + if (!arguments.length) return tickFormat_; + tickFormat_ = x; + return axis; + }; + axis.tickSize = function(x) { + var n = arguments.length; + if (!n) return innerTickSize; + innerTickSize = +x; + outerTickSize = +arguments[n - 1]; + return axis; + }; + axis.innerTickSize = function(x) { + if (!arguments.length) return innerTickSize; + innerTickSize = +x; + return axis; + }; + axis.outerTickSize = function(x) { + if (!arguments.length) return outerTickSize; + outerTickSize = +x; + return axis; + }; + axis.tickPadding = function(x) { + if (!arguments.length) return tickPadding; + tickPadding = +x; + return axis; + }; + axis.tickSubdivide = function() { + return arguments.length && axis; + }; + return axis; + }; + var d3_svg_axisDefaultOrient = "bottom", d3_svg_axisOrients = { + top: 1, + right: 1, + bottom: 1, + left: 1 + }; + function d3_svg_axisX(selection, x) { + selection.attr("transform", function(d) { + return "translate(" + x(d) + ",0)"; + }); + } + function d3_svg_axisY(selection, y) { + selection.attr("transform", function(d) { + return "translate(0," + y(d) + ")"; + }); + } + d3.svg.brush = function() { + var event = d3_eventDispatch(brush, "brushstart", "brush", "brushend"), x = null, y = null, xExtent = [ 0, 0 ], yExtent = [ 0, 0 ], xExtentDomain, yExtentDomain, xClamp = true, yClamp = true, resizes = d3_svg_brushResizes[0]; + function brush(g) { + g.each(function() { + var g = d3.select(this).style("pointer-events", "all").style("-webkit-tap-highlight-color", "rgba(0,0,0,0)").on("mousedown.brush", brushstart).on("touchstart.brush", brushstart); + var background = g.selectAll(".background").data([ 0 ]); + background.enter().append("rect").attr("class", "background").style("visibility", "hidden").style("cursor", "crosshair"); + g.selectAll(".extent").data([ 0 ]).enter().append("rect").attr("class", "extent").style("cursor", "move"); + var resize = g.selectAll(".resize").data(resizes, d3_identity); + resize.exit().remove(); + resize.enter().append("g").attr("class", function(d) { + return "resize " + d; + }).style("cursor", function(d) { + return d3_svg_brushCursor[d]; + }).append("rect").attr("x", function(d) { + return /[ew]$/.test(d) ? -3 : null; + }).attr("y", function(d) { + return /^[ns]/.test(d) ? -3 : null; + }).attr("width", 6).attr("height", 6).style("visibility", "hidden"); + resize.style("display", brush.empty() ? "none" : null); + var gUpdate = d3.transition(g), backgroundUpdate = d3.transition(background), range; + if (x) { + range = d3_scaleRange(x); + backgroundUpdate.attr("x", range[0]).attr("width", range[1] - range[0]); + redrawX(gUpdate); + } + if (y) { + range = d3_scaleRange(y); + backgroundUpdate.attr("y", range[0]).attr("height", range[1] - range[0]); + redrawY(gUpdate); + } + redraw(gUpdate); + }); + } + brush.event = function(g) { + g.each(function() { + var event_ = event.of(this, arguments), extent1 = { + x: xExtent, + y: yExtent, + i: xExtentDomain, + j: yExtentDomain + }, extent0 = this.__chart__ || extent1; + this.__chart__ = extent1; + if (d3_transitionInheritId) { + d3.select(this).transition().each("start.brush", function() { + xExtentDomain = extent0.i; + yExtentDomain = extent0.j; + xExtent = extent0.x; + yExtent = extent0.y; + event_({ + type: "brushstart" + }); + }).tween("brush:brush", function() { + var xi = d3_interpolateArray(xExtent, extent1.x), yi = d3_interpolateArray(yExtent, extent1.y); + xExtentDomain = yExtentDomain = null; + return function(t) { + xExtent = extent1.x = xi(t); + yExtent = extent1.y = yi(t); + event_({ + type: "brush", + mode: "resize" + }); + }; + }).each("end.brush", function() { + xExtentDomain = extent1.i; + yExtentDomain = extent1.j; + event_({ + type: "brush", + mode: "resize" + }); + event_({ + type: "brushend" + }); + }); + } else { + event_({ + type: "brushstart" + }); + event_({ + type: "brush", + mode: "resize" + }); + event_({ + type: "brushend" + }); + } + }); + }; + function redraw(g) { + g.selectAll(".resize").attr("transform", function(d) { + return "translate(" + xExtent[+/e$/.test(d)] + "," + yExtent[+/^s/.test(d)] + ")"; + }); + } + function redrawX(g) { + g.select(".extent").attr("x", xExtent[0]); + g.selectAll(".extent,.n>rect,.s>rect").attr("width", xExtent[1] - xExtent[0]); + } + function redrawY(g) { + g.select(".extent").attr("y", yExtent[0]); + g.selectAll(".extent,.e>rect,.w>rect").attr("height", yExtent[1] - yExtent[0]); + } + function brushstart() { + var target = this, eventTarget = d3.select(d3.event.target), event_ = event.of(target, arguments), g = d3.select(target), resizing = eventTarget.datum(), resizingX = !/^(n|s)$/.test(resizing) && x, resizingY = !/^(e|w)$/.test(resizing) && y, dragging = eventTarget.classed("extent"), dragRestore = d3_event_dragSuppress(), center, origin = d3.mouse(target), offset; + var w = d3.select(d3_window).on("keydown.brush", keydown).on("keyup.brush", keyup); + if (d3.event.changedTouches) { + w.on("touchmove.brush", brushmove).on("touchend.brush", brushend); + } else { + w.on("mousemove.brush", brushmove).on("mouseup.brush", brushend); + } + g.interrupt().selectAll("*").interrupt(); + if (dragging) { + origin[0] = xExtent[0] - origin[0]; + origin[1] = yExtent[0] - origin[1]; + } else if (resizing) { + var ex = +/w$/.test(resizing), ey = +/^n/.test(resizing); + offset = [ xExtent[1 - ex] - origin[0], yExtent[1 - ey] - origin[1] ]; + origin[0] = xExtent[ex]; + origin[1] = yExtent[ey]; + } else if (d3.event.altKey) center = origin.slice(); + g.style("pointer-events", "none").selectAll(".resize").style("display", null); + d3.select("body").style("cursor", eventTarget.style("cursor")); + event_({ + type: "brushstart" + }); + brushmove(); + function keydown() { + if (d3.event.keyCode == 32) { + if (!dragging) { + center = null; + origin[0] -= xExtent[1]; + origin[1] -= yExtent[1]; + dragging = 2; + } + d3_eventPreventDefault(); + } + } + function keyup() { + if (d3.event.keyCode == 32 && dragging == 2) { + origin[0] += xExtent[1]; + origin[1] += yExtent[1]; + dragging = 0; + d3_eventPreventDefault(); + } + } + function brushmove() { + var point = d3.mouse(target), moved = false; + if (offset) { + point[0] += offset[0]; + point[1] += offset[1]; + } + if (!dragging) { + if (d3.event.altKey) { + if (!center) center = [ (xExtent[0] + xExtent[1]) / 2, (yExtent[0] + yExtent[1]) / 2 ]; + origin[0] = xExtent[+(point[0] < center[0])]; + origin[1] = yExtent[+(point[1] < center[1])]; + } else center = null; + } + if (resizingX && move1(point, x, 0)) { + redrawX(g); + moved = true; + } + if (resizingY && move1(point, y, 1)) { + redrawY(g); + moved = true; + } + if (moved) { + redraw(g); + event_({ + type: "brush", + mode: dragging ? "move" : "resize" + }); + } + } + function move1(point, scale, i) { + var range = d3_scaleRange(scale), r0 = range[0], r1 = range[1], position = origin[i], extent = i ? yExtent : xExtent, size = extent[1] - extent[0], min, max; + if (dragging) { + r0 -= position; + r1 -= size + position; + } + min = (i ? yClamp : xClamp) ? Math.max(r0, Math.min(r1, point[i])) : point[i]; + if (dragging) { + max = (min += position) + size; + } else { + if (center) position = Math.max(r0, Math.min(r1, 2 * center[i] - min)); + if (position < min) { + max = min; + min = position; + } else { + max = position; + } + } + if (extent[0] != min || extent[1] != max) { + if (i) yExtentDomain = null; else xExtentDomain = null; + extent[0] = min; + extent[1] = max; + return true; + } + } + function brushend() { + brushmove(); + g.style("pointer-events", "all").selectAll(".resize").style("display", brush.empty() ? "none" : null); + d3.select("body").style("cursor", null); + w.on("mousemove.brush", null).on("mouseup.brush", null).on("touchmove.brush", null).on("touchend.brush", null).on("keydown.brush", null).on("keyup.brush", null); + dragRestore(); + event_({ + type: "brushend" + }); + } + } + brush.x = function(z) { + if (!arguments.length) return x; + x = z; + resizes = d3_svg_brushResizes[!x << 1 | !y]; + return brush; + }; + brush.y = function(z) { + if (!arguments.length) return y; + y = z; + resizes = d3_svg_brushResizes[!x << 1 | !y]; + return brush; + }; + brush.clamp = function(z) { + if (!arguments.length) return x && y ? [ xClamp, yClamp ] : x ? xClamp : y ? yClamp : null; + if (x && y) xClamp = !!z[0], yClamp = !!z[1]; else if (x) xClamp = !!z; else if (y) yClamp = !!z; + return brush; + }; + brush.extent = function(z) { + var x0, x1, y0, y1, t; + if (!arguments.length) { + if (x) { + if (xExtentDomain) { + x0 = xExtentDomain[0], x1 = xExtentDomain[1]; + } else { + x0 = xExtent[0], x1 = xExtent[1]; + if (x.invert) x0 = x.invert(x0), x1 = x.invert(x1); + if (x1 < x0) t = x0, x0 = x1, x1 = t; + } + } + if (y) { + if (yExtentDomain) { + y0 = yExtentDomain[0], y1 = yExtentDomain[1]; + } else { + y0 = yExtent[0], y1 = yExtent[1]; + if (y.invert) y0 = y.invert(y0), y1 = y.invert(y1); + if (y1 < y0) t = y0, y0 = y1, y1 = t; + } + } + return x && y ? [ [ x0, y0 ], [ x1, y1 ] ] : x ? [ x0, x1 ] : y && [ y0, y1 ]; + } + if (x) { + x0 = z[0], x1 = z[1]; + if (y) x0 = x0[0], x1 = x1[0]; + xExtentDomain = [ x0, x1 ]; + if (x.invert) x0 = x(x0), x1 = x(x1); + if (x1 < x0) t = x0, x0 = x1, x1 = t; + if (x0 != xExtent[0] || x1 != xExtent[1]) xExtent = [ x0, x1 ]; + } + if (y) { + y0 = z[0], y1 = z[1]; + if (x) y0 = y0[1], y1 = y1[1]; + yExtentDomain = [ y0, y1 ]; + if (y.invert) y0 = y(y0), y1 = y(y1); + if (y1 < y0) t = y0, y0 = y1, y1 = t; + if (y0 != yExtent[0] || y1 != yExtent[1]) yExtent = [ y0, y1 ]; + } + return brush; + }; + brush.clear = function() { + if (!brush.empty()) { + xExtent = [ 0, 0 ], yExtent = [ 0, 0 ]; + xExtentDomain = yExtentDomain = null; + } + return brush; + }; + brush.empty = function() { + return !!x && xExtent[0] == xExtent[1] || !!y && yExtent[0] == yExtent[1]; + }; + return d3.rebind(brush, event, "on"); + }; + var d3_svg_brushCursor = { + n: "ns-resize", + e: "ew-resize", + s: "ns-resize", + w: "ew-resize", + nw: "nwse-resize", + ne: "nesw-resize", + se: "nwse-resize", + sw: "nesw-resize" + }; + var d3_svg_brushResizes = [ [ "n", "e", "s", "w", "nw", "ne", "se", "sw" ], [ "e", "w" ], [ "n", "s" ], [] ]; + var d3_time_format = d3_time.format = d3_locale_enUS.timeFormat; + var d3_time_formatUtc = d3_time_format.utc; + var d3_time_formatIso = d3_time_formatUtc("%Y-%m-%dT%H:%M:%S.%LZ"); + d3_time_format.iso = Date.prototype.toISOString && +new Date("2000-01-01T00:00:00.000Z") ? d3_time_formatIsoNative : d3_time_formatIso; + function d3_time_formatIsoNative(date) { + return date.toISOString(); + } + d3_time_formatIsoNative.parse = function(string) { + var date = new Date(string); + return isNaN(date) ? null : date; + }; + d3_time_formatIsoNative.toString = d3_time_formatIso.toString; + d3_time.second = d3_time_interval(function(date) { + return new d3_date(Math.floor(date / 1e3) * 1e3); + }, function(date, offset) { + date.setTime(date.getTime() + Math.floor(offset) * 1e3); + }, function(date) { + return date.getSeconds(); + }); + d3_time.seconds = d3_time.second.range; + d3_time.seconds.utc = d3_time.second.utc.range; + d3_time.minute = d3_time_interval(function(date) { + return new d3_date(Math.floor(date / 6e4) * 6e4); + }, function(date, offset) { + date.setTime(date.getTime() + Math.floor(offset) * 6e4); + }, function(date) { + return date.getMinutes(); + }); + d3_time.minutes = d3_time.minute.range; + d3_time.minutes.utc = d3_time.minute.utc.range; + d3_time.hour = d3_time_interval(function(date) { + var timezone = date.getTimezoneOffset() / 60; + return new d3_date((Math.floor(date / 36e5 - timezone) + timezone) * 36e5); + }, function(date, offset) { + date.setTime(date.getTime() + Math.floor(offset) * 36e5); + }, function(date) { + return date.getHours(); + }); + d3_time.hours = d3_time.hour.range; + d3_time.hours.utc = d3_time.hour.utc.range; + d3_time.month = d3_time_interval(function(date) { + date = d3_time.day(date); + date.setDate(1); + return date; + }, function(date, offset) { + date.setMonth(date.getMonth() + offset); + }, function(date) { + return date.getMonth(); + }); + d3_time.months = d3_time.month.range; + d3_time.months.utc = d3_time.month.utc.range; + function d3_time_scale(linear, methods, format) { + function scale(x) { + return linear(x); + } + scale.invert = function(x) { + return d3_time_scaleDate(linear.invert(x)); + }; + scale.domain = function(x) { + if (!arguments.length) return linear.domain().map(d3_time_scaleDate); + linear.domain(x); + return scale; + }; + function tickMethod(extent, count) { + var span = extent[1] - extent[0], target = span / count, i = d3.bisect(d3_time_scaleSteps, target); + return i == d3_time_scaleSteps.length ? [ methods.year, d3_scale_linearTickRange(extent.map(function(d) { + return d / 31536e6; + }), count)[2] ] : !i ? [ d3_time_scaleMilliseconds, d3_scale_linearTickRange(extent, count)[2] ] : methods[target / d3_time_scaleSteps[i - 1] < d3_time_scaleSteps[i] / target ? i - 1 : i]; + } + scale.nice = function(interval, skip) { + var domain = scale.domain(), extent = d3_scaleExtent(domain), method = interval == null ? tickMethod(extent, 10) : typeof interval === "number" && tickMethod(extent, interval); + if (method) interval = method[0], skip = method[1]; + function skipped(date) { + return !isNaN(date) && !interval.range(date, d3_time_scaleDate(+date + 1), skip).length; + } + return scale.domain(d3_scale_nice(domain, skip > 1 ? { + floor: function(date) { + while (skipped(date = interval.floor(date))) date = d3_time_scaleDate(date - 1); + return date; + }, + ceil: function(date) { + while (skipped(date = interval.ceil(date))) date = d3_time_scaleDate(+date + 1); + return date; + } + } : interval)); + }; + scale.ticks = function(interval, skip) { + var extent = d3_scaleExtent(scale.domain()), method = interval == null ? tickMethod(extent, 10) : typeof interval === "number" ? tickMethod(extent, interval) : !interval.range && [ { + range: interval + }, skip ]; + if (method) interval = method[0], skip = method[1]; + return interval.range(extent[0], d3_time_scaleDate(+extent[1] + 1), skip < 1 ? 1 : skip); + }; + scale.tickFormat = function() { + return format; + }; + scale.copy = function() { + return d3_time_scale(linear.copy(), methods, format); + }; + return d3_scale_linearRebind(scale, linear); + } + function d3_time_scaleDate(t) { + return new Date(t); + } + var d3_time_scaleSteps = [ 1e3, 5e3, 15e3, 3e4, 6e4, 3e5, 9e5, 18e5, 36e5, 108e5, 216e5, 432e5, 864e5, 1728e5, 6048e5, 2592e6, 7776e6, 31536e6 ]; + var d3_time_scaleLocalMethods = [ [ d3_time.second, 1 ], [ d3_time.second, 5 ], [ d3_time.second, 15 ], [ d3_time.second, 30 ], [ d3_time.minute, 1 ], [ d3_time.minute, 5 ], [ d3_time.minute, 15 ], [ d3_time.minute, 30 ], [ d3_time.hour, 1 ], [ d3_time.hour, 3 ], [ d3_time.hour, 6 ], [ d3_time.hour, 12 ], [ d3_time.day, 1 ], [ d3_time.day, 2 ], [ d3_time.week, 1 ], [ d3_time.month, 1 ], [ d3_time.month, 3 ], [ d3_time.year, 1 ] ]; + var d3_time_scaleLocalFormat = d3_time_format.multi([ [ ".%L", function(d) { + return d.getMilliseconds(); + } ], [ ":%S", function(d) { + return d.getSeconds(); + } ], [ "%I:%M", function(d) { + return d.getMinutes(); + } ], [ "%I %p", function(d) { + return d.getHours(); + } ], [ "%a %d", function(d) { + return d.getDay() && d.getDate() != 1; + } ], [ "%b %d", function(d) { + return d.getDate() != 1; + } ], [ "%B", function(d) { + return d.getMonth(); + } ], [ "%Y", d3_true ] ]); + var d3_time_scaleMilliseconds = { + range: function(start, stop, step) { + return d3.range(Math.ceil(start / step) * step, +stop, step).map(d3_time_scaleDate); + }, + floor: d3_identity, + ceil: d3_identity + }; + d3_time_scaleLocalMethods.year = d3_time.year; + d3_time.scale = function() { + return d3_time_scale(d3.scale.linear(), d3_time_scaleLocalMethods, d3_time_scaleLocalFormat); + }; + var d3_time_scaleUtcMethods = d3_time_scaleLocalMethods.map(function(m) { + return [ m[0].utc, m[1] ]; + }); + var d3_time_scaleUtcFormat = d3_time_formatUtc.multi([ [ ".%L", function(d) { + return d.getUTCMilliseconds(); + } ], [ ":%S", function(d) { + return d.getUTCSeconds(); + } ], [ "%I:%M", function(d) { + return d.getUTCMinutes(); + } ], [ "%I %p", function(d) { + return d.getUTCHours(); + } ], [ "%a %d", function(d) { + return d.getUTCDay() && d.getUTCDate() != 1; + } ], [ "%b %d", function(d) { + return d.getUTCDate() != 1; + } ], [ "%B", function(d) { + return d.getUTCMonth(); + } ], [ "%Y", d3_true ] ]); + d3_time_scaleUtcMethods.year = d3_time.year.utc; + d3_time.scale.utc = function() { + return d3_time_scale(d3.scale.linear(), d3_time_scaleUtcMethods, d3_time_scaleUtcFormat); + }; + d3.text = d3_xhrType(function(request) { + return request.responseText; + }); + d3.json = function(url, callback) { + return d3_xhr(url, "application/json", d3_json, callback); + }; + function d3_json(request) { + return JSON.parse(request.responseText); + } + d3.html = function(url, callback) { + return d3_xhr(url, "text/html", d3_html, callback); + }; + function d3_html(request) { + var range = d3_document.createRange(); + range.selectNode(d3_document.body); + return range.createContextualFragment(request.responseText); + } + d3.xml = d3_xhrType(function(request) { + return request.responseXML; + }); + if (typeof define === "function" && define.amd) { + define(d3); + } else if (typeof module === "object" && module.exports) { + module.exports = d3; + } else { + this.d3 = d3; + } +}(); diff --git a/Afni_proc_through_nipype/files/_0x2a29d196401e292490f5a331c7b8bf30.json b/Afni_proc_through_nipype/files/_0x2a29d196401e292490f5a331c7b8bf30.json new file mode 100644 index 00000000..8e2b9c7c --- /dev/null +++ b/Afni_proc_through_nipype/files/_0x2a29d196401e292490f5a331c7b8bf30.json @@ -0,0 +1,24 @@ +[ + [ + "base_directory", + "." + ], + [ + "force_lists", + false + ], + [ + "raise_on_empty", + true + ], + [ + "sort_filelist", + true + ], + [ + "needed_outputs", + [ + "command" + ] + ] +] \ No newline at end of file diff --git a/Afni_proc_through_nipype/files/_inputs.pklz b/Afni_proc_through_nipype/files/_inputs.pklz new file mode 100644 index 0000000000000000000000000000000000000000..9f9f79e4480627e60c30f9b4364366f0b4399ed2 GIT binary patch literal 116 zcmV-)0E_=0iwFo&%z9-4|6gftaCLNZE^upXdMbHA;e%HCv{=(-7+jN-$$}&U|HcQ&wztc?@@%C}MR#Y-QXLD};?`k>DkEEV5NfVO5@$&q|&oOixFQmI=d?1u3JK{Orj>eVDYnH$! z%v?IWcas$mDEHa|_TEvYYdU%(X{4>sV%SOnPP|3z*5LH`*-5|ON2$qbwdWr8jg#1f zZMvi!fV65c@8*`^WR?u>0SIrKlrFd2RYg;qS>0d$H{Frq);OjODYobVi0xMRh}GmP zUBs~MMNQ80+Qe}9MrWu<30G0Ul0!Ghw(%4njfo5s$~4}s>fM(*=aRJ-<`w1RCA5Q@ zdn2`%B4ZiP$E1+!?(?!lXN+vn4gC2LfH-hJwp8m0u_TNoeS+2!eKwD1l%kxRx6~9v}(01s4 zLW-+=O=_PQZZR)VC)AWkTM_ZlXepVKsbfWBc`Ku^F@#_)C!-9NU$Q9|sPLmfKdC5n zZk2p?OA~f#twd_Xd~iB|kVz`m;5o=95oYPvhExv4Zw#P%*VJ|D5I3gn`{KsUnMST5 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+Execution Outputs +----------------- + + +* command : /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel + + +Runtime info +------------ + + +* duration : 0.000182 +* hostname : ptb-03230001.irisa.fr +* prev_wd : /home/jlefortb/narps_open_pipelines +* working_dir : /home/jlefortb/narps_open_pipelines/Afni_proc_through_nipype/files + + +Environment +~~~~~~~~~~~ + + +* COLORTERM : truecolor +* DBUS_SESSION_BUS_ADDRESS : unix:path=/run/user/670967/bus +* DEBUGINFOD_URLS : https://debuginfod.fedoraproject.org/ +* DESKTOP_SESSION : gnome +* DISPLAY : :0 +* EDITOR : /usr/bin/nano +* FSLDIR : /usr/local/fsl +* FSLGECUDAQ : cuda.q +* FSLMULTIFILEQUIT : TRUE +* FSLOUTPUTTYPE : NIFTI_GZ +* FSLTCLSH : /usr/local/fsl/bin/fsltclsh +* FSLWISH : /usr/local/fsl/bin/fslwish +* FSL_LOAD_NIFTI_EXTENSIONS : 0 +* FSL_SKIP_GLOBAL : 0 +* GDMSESSION : gnome +* GDM_LANG : en_US.UTF-8 +* GNOME_SETUP_DISPLAY : :1 +* GNOME_TERMINAL_SCREEN : /org/gnome/Terminal/screen/3627c221_9f8a_4ca7_a192_68617ea35d25 +* GNOME_TERMINAL_SERVICE : :1.180 +* GUESTFISH_INIT : \e[1;34m +* GUESTFISH_OUTPUT : \e[0m +* GUESTFISH_PS1 : \[\e[1;32m\]>\[\e[0;31m\] +* GUESTFISH_RESTORE : \e[0m +* HISTCONTROL : ignoredups +* HISTSIZE : 1000 +* HOME : /home/jlefortb +* HOSTNAME : ptb-03230001.irisa.fr +* KDEDIRS : /usr +* LANG : en_US.UTF-8 +* LESSOPEN : ||/usr/bin/lesspipe.sh %s +* LOGNAME : jlefortb +* LS_COLORS : 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+ Flare imports
+ hierarchical edge bundling +

+
tension: +
+ + + + + diff --git a/narps_open/pipelines/team_6VV2_wip.py b/narps_open/pipelines/team_6VV2_wip.py index 7c9bf2d3..201290af 100644 --- a/narps_open/pipelines/team_6VV2_wip.py +++ b/narps_open/pipelines/team_6VV2_wip.py @@ -15,6 +15,11 @@ from os.path import join as opj import os import pathlib +from glob import glob +from nilearn import plotting +import matplotlib.pyplot as plt +from nilearn import image +import pandas as pd ######################################################################## ################## FIRST LEVEL ANALYSIS FOR TEAM 6VV2 ################## @@ -22,7 +27,7 @@ # define environment for first level analysis data_dir = "/home/jlefortb/narps_open_pipelines/data/original/ds001734/" -results_dir = "/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/" +results_dir = "/home/jlefortb/narps_open_pipelines/data/results/derived/team_6VV2_afni/firstlevel/" path = pathlib.Path(results_dir) path.mkdir(parents=True, exist_ok=True) @@ -38,6 +43,8 @@ subject_list.append(dirs[-3:]) + + # Infosource Node - To iterate on subjects + get directoris paths infosource = Node(interface=IdentityInterface(fields = ['subject_id', 'data_dir', 'results_dir'], data_dir = data_dir, @@ -117,6 +124,33 @@ def run(command, results_dir, subject, data_dir): # wf_run.write_graph() wf_run.run() +#### +# to do: relaunch sub 1 and launch sub 2, then launch part 2 to check which data are mandatory and which we can delete +# because taking a bunch of space (60G) +#### + +# convert BRIK to nii +command = "3dAFNItoNIFTI" +for Afni_file in glob("/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/*.HEAD"): + file_name = Afni_file.split('/')[-1] + nifti_file_name = file_name[:-5] + results_dir = "/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/results_as_nifti/" + prefixname = opj(results_dir, nifti_file_name) + subprocess.run([command, "-prefix", prefixname, Afni_file]) + +# visualise nifti +for nifi_file in glob("/home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/results_as_nifti/*"): + shape = image.load_img(nifi_file).shape + print("shape: ", shape) + if len(shape) > 3: + plotting.plot_stat_map(image.index_img(nifi_file, 0), annotate=False, title=nifi_file.split('/')[-1] + " ind 0", colorbar=True, cut_coords=(-24, -10, 4, 18, 32, 52, 64), display_mode='z', cmap='coolwarm') + plotting.plot_stat_map(image.index_img(nifi_file, 30), annotate=False, title=nifi_file.split('/')[-1] + " ind 30", colorbar=True, cut_coords=(-24, -10, 4, 18, 32, 52, 64), display_mode='z', cmap='coolwarm') + plotting.plot_stat_map(image.index_img(nifi_file, 60), annotate=False, title=nifi_file.split('/')[-1] + " ind 60", colorbar=True, cut_coords=(-24, -10, 4, 18, 32, 52, 64), display_mode='z', cmap='coolwarm') + plt.show() + else: + plotting.plot_stat_map(nifi_file, annotate=False, title=nifi_file.split('/')[-1], colorbar=True, cut_coords=(-24, -10, 4, 18, 32, 52, 64), display_mode='z', cmap='coolwarm') + plt.show() + ######################################################################## ################## SECOND LEVEL ANALYSIS FOR TEAM 6VV2 ################# From c59657d84a22580e1ec635fbc6a51cf276ab699a Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Mon, 12 Feb 2024 14:49:06 +0100 Subject: [PATCH 07/10] add stuff --- narps_open/pipelines/team_27SS.firstlevel | 66 +++++++++++++++++++++++ narps_open/pipelines/team_6VV2.firstlevel | 10 ++++ 2 files changed, 76 insertions(+) create mode 100755 narps_open/pipelines/team_27SS.firstlevel diff --git a/narps_open/pipelines/team_27SS.firstlevel b/narps_open/pipelines/team_27SS.firstlevel new file mode 100755 index 00000000..f536b331 --- /dev/null +++ b/narps_open/pipelines/team_27SS.firstlevel @@ -0,0 +1,66 @@ +#!/bin/tcsh + +# created by team 6VV2, reproduced by Narps reproducibility team +# creation date: 22 June 2023 +# read and ran by team_6VV2.py script +# version afni used by the team : AFNI Version 19.0.01 Tiberius +# version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus +# Last update: June 2023 + +# Store arguments (directory where to store results, subjects list, directory where data are stored) +set expdir="$1" +set subject="$2" +set datadir="$3" + + +afni_proc.py \ + -script ${expdir}/proc.${subject}.block \ + -scr_overwrite \ + -subj_id ${subject} \ + -out_dir ${expdir}/${subject}.results.block \ + -dsets ${datadir}/${subject}/func/${subject}_task-MGT_run-01_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-02_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-03_bold.nii.gz \ + ${datadir}/${subject}/func/${subject}_task-MGT_run-04_bold.nii.gz \ + -copy_anat ${datadir}/${subject}/anat/${subject}_T1w.nii.gz \ + -anat_has_skull yes \ + -blocks despike tshift align tlrc volreg blur mask scale regress \ + -despike_new yes \ + -tlrc_base MNI152_T1_2009c+tlrc \ + -tlrc_NL_warp \ + -align_opts_aea \ + -giant_move \ + -cost lpc+ZZ \ + -volreg_align_to MIN_OUTLIER \ + -volreg_tlrc_warp \ + -volreg_align_e2a \ + -blur_in_automask \ + -regress_stim_times \ + ${datadir}/${subject}/func/times+gain.1D \ + ${datadir}/${subject}/func/times+loss.1D \ + -regress_stim_types AM2 \ + -regress_stim_labels \ + GAIN \ + LOSS \ + -regress_basis \ + 'BLOCK(4,1)' \ + -mask_apply anat \ + -regress_motion_per_run \ + -test_stim_files no \ + -regress_opts_3dD \ + -GOFORIT 8 \ + -jobs 6 \ + -regress_censor_motion 0.2 \ + -regress_apply_mot_types demean deriv \ + -regress_censor_first_trs 3 \ + -regress_est_blur_errts \ + -execute + + +# extract beta values +3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] +3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] + +# convert BRIK to nii +3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc +3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc \ No newline at end of file diff --git a/narps_open/pipelines/team_6VV2.firstlevel b/narps_open/pipelines/team_6VV2.firstlevel index f536b331..41a56649 100755 --- a/narps_open/pipelines/team_6VV2.firstlevel +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -7,6 +7,16 @@ # version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus # Last update: June 2023 +""" +exemple run: +In a terminal, path /home/jlefortb/narps_open_pipelines, run: +/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/, sub-001, /home/jlefortb/narps_open_pipelines/data/original/ds001734/ + + +""" + + + # Store arguments (directory where to store results, subjects list, directory where data are stored) set expdir="$1" set subject="$2" From f41f63040b31dfa44eaa44b62f693a3a524cf48f Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Tue, 13 Feb 2024 11:48:49 +0100 Subject: [PATCH 08/10] update 27SS file to compare with 6VV2 --- narps_open/pipelines/team_27SS.firstlevel | 95 +++++++++++++++++------ 1 file changed, 70 insertions(+), 25 deletions(-) diff --git a/narps_open/pipelines/team_27SS.firstlevel b/narps_open/pipelines/team_27SS.firstlevel index f536b331..9d1ba399 100755 --- a/narps_open/pipelines/team_27SS.firstlevel +++ b/narps_open/pipelines/team_27SS.firstlevel @@ -1,11 +1,20 @@ #!/bin/tcsh -# created by team 6VV2, reproduced by Narps reproducibility team -# creation date: 22 June 2023 -# read and ran by team_6VV2.py script -# version afni used by the team : AFNI Version 19.0.01 Tiberius -# version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus -# Last update: June 2023 +# Reproduction of 27SS pipeline by the Narps reproducibility team +# creation date: 13 February 2024 +# version afni used by the team: AFNI 18.3.12 +# version afni used by the reproducibility team: AFNI Version 23.0.02 Commodus + +# Store arguments (directory where to store results, subjects list, directory where data are stored) +set expdir="$1" # /home/jlefortb/narps_open_pipelines/data/results/team_27SS_afni/firstlevel/ +set subject="$2" # sub-001 +set datadir="$3" # /home/jlefortb/narps_open_pipelines/data/original/ds001734/ + +# In a terminal, path /home/jlefortb/narps_open_pipelines, run: +# /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_27SS.firstlevel /home/jlefortb/narps_open_pipelines/data/results/team_27SS_afni/firstlevel/, sub-001, /home/jlefortb/narps_open_pipelines/data/original/ds001734/ + + + # Store arguments (directory where to store results, subjects list, directory where data are stored) set expdir="$1" @@ -14,53 +23,89 @@ set datadir="$3" afni_proc.py \ + # Spécification du script de sortie -script ${expdir}/proc.${subject}.block \ + # Autoriser l'écrasement du script existant -scr_overwrite \ + # Spécification de l'identifiant du sujet -subj_id ${subject} \ + # Spécification du répertoire de sortie -out_dir ${expdir}/${subject}.results.block \ + # Spécification des ensembles de données EPI -dsets ${datadir}/${subject}/func/${subject}_task-MGT_run-01_bold.nii.gz \ ${datadir}/${subject}/func/${subject}_task-MGT_run-02_bold.nii.gz \ ${datadir}/${subject}/func/${subject}_task-MGT_run-03_bold.nii.gz \ ${datadir}/${subject}/func/${subject}_task-MGT_run-04_bold.nii.gz \ + # Copie de l'image anatomique -copy_anat ${datadir}/${subject}/anat/${subject}_T1w.nii.gz \ + # Spécification de la présence du crâne dans l'image anatomique -anat_has_skull yes \ + # Blocs de prétraitement inclus dans le pipeline -blocks despike tshift align tlrc volreg blur mask scale regress \ + # Option de déspike -despike_new yes \ + # Spécification de la base TLRC -tlrc_base MNI152_T1_2009c+tlrc \ - -tlrc_NL_warp \ + # Specify blur size + -blur_size 6.0 \ + # Options d'alignement -align_opts_aea \ + # Déplacement géant -giant_move \ + # Coût de l'alignement -cost lpc+ZZ \ + # Options for temporal shift + -tshift_opts_ts -quintic \ + # Alignement des volumes EPI sur l'outlier minimal -volreg_align_to MIN_OUTLIER \ - -volreg_tlrc_warp \ + # Interpolation method for volume registration + -volreg_interp cubic \ + # Alignement EPI vers anatomique -volreg_align_e2a \ + # Flou dans le masque automatique -blur_in_automask \ + # Model motion per run + -regress_motion_per_run \ + # Censor motion outliers with framewise displacement greater than 1.5 mm + -regress_censor_motion 1.5 \ + # Specify the regressors and their corresponding labels -regress_stim_times \ ${datadir}/${subject}/func/times+gain.1D \ ${datadir}/${subject}/func/times+loss.1D \ - -regress_stim_types AM2 \ - -regress_stim_labels \ - GAIN \ - LOSS \ - -regress_basis \ - 'BLOCK(4,1)' \ + -regress_stim_labels task nuisance \ + # Modélisation des régresseurs de stimulus + -regress_basis 'BLOCK(4,1)' \ + # Application du masque anatomique -mask_apply anat \ - -regress_motion_per_run \ - -test_stim_files no \ + # Options supplémentaires pour 3dDeconvolve -regress_opts_3dD \ -GOFORIT 8 \ -jobs 6 \ - -regress_censor_motion 0.2 \ - -regress_apply_mot_types demean deriv \ + -ortvec ${datadir}/${subject}/func/motion_parameters.1D motion_params \ + -allzero_OK \ + # Application des types de mouvement pour la régression + -regress_apply_mot_types demean \ + # Censure des premiers TRs -regress_censor_first_trs 3 \ + # Estimation des erreurs de flou + # Estimate the blur epochs + -regress_est_blur_epits \ + # Estimate the blur error times -regress_est_blur_errts \ - -execute + # Exécution du pipeline directement après création du script TCSH + # No gradient distortion correction specified + # No distortion correction specified + # No intensity correction specified + # No intensity normalization specified + # No spatial smoothing specified + # Execute the pipeline script +# -execute -# extract beta values -3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] -3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] +# # extract beta values +# 3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] +# 3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] -# convert BRIK to nii -3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc -3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc \ No newline at end of file +# # convert BRIK to nii +# 3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc +# 3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc \ No newline at end of file From c83679882f02f389202b88944200fd93040a4add Mon Sep 17 00:00:00 2001 From: jlefortbesnard Date: Tue, 13 Feb 2024 14:18:04 +0100 Subject: [PATCH 09/10] false manip cancelled --- narps_open/pipelines/team_6VV2.firstlevel | 53 ++++++++++++++++++----- 1 file changed, 42 insertions(+), 11 deletions(-) diff --git a/narps_open/pipelines/team_6VV2.firstlevel b/narps_open/pipelines/team_6VV2.firstlevel index 41a56649..435d6324 100755 --- a/narps_open/pipelines/team_6VV2.firstlevel +++ b/narps_open/pipelines/team_6VV2.firstlevel @@ -7,13 +7,11 @@ # version afni used by the reproducibility team :AFNI Version 23.0.02 Commodus # Last update: June 2023 -""" -exemple run: -In a terminal, path /home/jlefortb/narps_open_pipelines, run: -/home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/, sub-001, /home/jlefortb/narps_open_pipelines/data/original/ds001734/ +# exemple run: +# In a terminal, path /home/jlefortb/narps_open_pipelines, run: +# tcsh /home/jlefortb/narps_open_pipelines/narps_open/pipelines/team_6VV2.firstlevel /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/, sub-001, /home/jlefortb/narps_open_pipelines/data/original/ds001734/ -""" @@ -67,10 +65,43 @@ afni_proc.py \ -execute -# extract beta values -3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] -3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] +# # extract beta values +# 3dbucket -prefix GAIN ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[3] +# 3dbucket -prefix LOSS ${expdir}/${subject}.results.block/stats.sub-001+tlrc.BRIK[8] -# convert BRIK to nii -3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc -3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc \ No newline at end of file +# # convert BRIK to nii +# 3dAFNItoNIFTI -prefix GAIN ${subject}_GAIN+tlrc +# 3dAFNItoNIFTI -prefix LOSS ${subject}_LOSS+tlrc + + + +# run this file with "tcsh 6VV2_afni_proc.simple" + +# create 1D stimuli file : +# import pandas as pd + +# df_run1 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-01_events.tsv", sep="\t") +# df_run1 = df_run1[["onset", "gain", "loss"]].T +# df_run2 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-02_events.tsv", sep="\t") +# df_run2 = df_run2[["onset", "gain", "loss"]].T +# df_run3 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-03_events.tsv", sep="\t") +# df_run3 = df_run3[["onset", "gain", "loss"]].T +# df_run4 = pd.read_csv("/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/sub-001_task-MGT_run-04_events.tsv", sep="\t") +# df_run4 = df_run4[["onset", "gain", "loss"]].T + +# df_gain = pd.DataFrame(index=range(0,4), columns=range(0,64)) +# df_gain.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['gain']) for col in range(0, 64)] +# df_gain.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['gain']) for col in range(0, 64)] +# df_gain.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['gain']) for col in range(0, 64)] +# df_gain.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['gain']) for col in range(0, 64)] +# df_loss = pd.DataFrame(index=range(0,4), columns=range(0,64)) +# df_loss.loc[0] = ["{}*{}".format(df_run1[col].loc['onset'], df_run1[col].loc['loss']) for col in range(0, 64)] +# df_loss.loc[1] = ["{}*{}".format(df_run2[col].loc['onset'], df_run2[col].loc['loss']) for col in range(0, 64)] +# df_loss.loc[2] = ["{}*{}".format(df_run3[col].loc['onset'], df_run3[col].loc['loss']) for col in range(0, 64)] +# df_loss.loc[3] = ["{}*{}".format(df_run4[col].loc['onset'], df_run4[col].loc['loss']) for col in range(0, 64)] + + +# df_gain.to_csv('/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/times+gain.1D', +# sep='\t', index=False, header=False) +# df_loss.to_csv('/home/jlefortb/narps_open_pipelines/data/original/ds001734/sub-001/func/times+loss.1D', +# sep='\t', index=False, header=False) From e08499408b70550314c07509c5f62e198ef9fb05 Mon Sep 17 00:00:00 2001 From: Jeremy Lefort-Besnard <21123003+JLefortBesnard@users.noreply.github.com> Date: Thu, 20 Jun 2024 15:51:26 +0900 Subject: [PATCH 10/10] add a missing \ in team_6VV2.secondlevel --- narps_open/pipelines/team_6VV2.secondlevel | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/narps_open/pipelines/team_6VV2.secondlevel b/narps_open/pipelines/team_6VV2.secondlevel index 79846071..390b8b85 100644 --- a/narps_open/pipelines/team_6VV2.secondlevel +++ b/narps_open/pipelines/team_6VV2.secondlevel @@ -21,7 +21,7 @@ set expdir="$1" -gltLabel 3 'LOSS_indiff' -gltCode 3 'group : 1*indiff cond : 1*LOSS' \ -gltLabel 4 'LOSS_range' -gltCode 4 'group : 1*range cond : 1*LOSS' \ -gltLabel 5 'LOSS_range-indiff' -gltCode 5 'group : 1*range -1*indiff cond : 1*LOSS' \ --dataTable +-dataTable \ Subj cond group InputFile \ 001 GAIN indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/sub-001_GAIN.nii \ 001 LOSS indifference /home/jlefortb/narps_open_pipelines/data/results/team_6VV2_afni/firstlevel/sub-001.results.block/sub-001_LOSS.nii \