Merge branch 'main' into documentation

INSTALL.md

@@ -6,7 +6,7 @@
 
 ## 2 - Clone the code
 
-First, install [Datalad](https://www.datalad.org/). This will allow you to access the NARPS data easily, as it is included in the repository as [datalad subdatasets](http://handbook.datalad.org/en/latest/basics/101-106-nesting.html).
+First, install [Datalad](https://handbook.datalad.org/en/latest/intro/installation.html#install-datalad). This will allow you to access the NARPS data easily, as it is included in the repository as [datalad subdatasets](http://handbook.datalad.org/en/latest/basics/101-106-nesting.html).
 
 Then, [clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) the project :
 

narps_open/pipelines/__init__.py

@@ -51,7 +51,7 @@
     'I52Y': None,
     'I9D6': None,
     'IZ20': None,
-    'J7F9': None,
+    'J7F9': 'PipelineTeamJ7F9',
     'K9P0': None,
     'L1A8': None,
     'L3V8': None,

tests/pipelines/test_team_J7F9.py

@@ -0,0 +1,209 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_J7F9' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_J7F9.py
+    pytest -q test_team_J7F9.py -k <selected_test>
+"""
+from os import mkdir
+from os.path import join, exists
+from shutil import rmtree
+from filecmp import cmp
+
+from pytest import helpers, mark, fixture
+from numpy import isclose
+from nipype import Workflow
+from nipype.interfaces.base import Bunch
+
+from narps_open.utils.configuration import Configuration
+from narps_open.pipelines.team_J7F9 import PipelineTeamJ7F9
+
+TEMPORARY_DIR = join(Configuration()['directories']['test_runs'], 'test_J7F9')
+
+@fixture
+def remove_test_dir():
+    """ A fixture to remove temporary directory created by tests """
+
+    rmtree(TEMPORARY_DIR, ignore_errors = True)
+    mkdir(TEMPORARY_DIR)
+    yield # test runs here
+    rmtree(TEMPORARY_DIR, ignore_errors = True)
+
+def compare_float_2d_arrays(array_1, array_2):
+    """ Assert array_1 and array_2 are close enough """
+
+    assert len(array_1) == len(array_2)
+    for reference_array, test_array in zip(array_1, array_2):
+        assert len(reference_array) == len(test_array)
+        assert isclose(reference_array, test_array).all()
+
+class TestPipelinesTeamJ7F9:
+    """ A class that contains all the unit tests for the PipelineTeamJ7F9 class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create():
+        """ Test the creation of a PipelineTeamJ7F9 object """
+
+        pipeline = PipelineTeamJ7F9()
+
+        # 1 - check the parameters
+        assert pipeline.fwhm == 8.0
+        assert pipeline.team_id == 'J7F9'
+
+        # 2 - check workflows
+        assert pipeline.get_preprocessing() is None
+        assert pipeline.get_run_level_analysis() is None
+        assert isinstance(pipeline.get_subject_level_analysis(), Workflow)
+        group_level = pipeline.get_group_level_analysis()
+
+        assert len(group_level) == 3
+        for sub_workflow in group_level:
+            assert isinstance(sub_workflow, Workflow)
+
+    @staticmethod
+    @mark.unit_test
+    def test_outputs():
+        """ Test the expected outputs of a PipelineTeamJ7F9 object """
+        pipeline = PipelineTeamJ7F9()
+        # 1 - 1 subject outputs
+        pipeline.subject_list = ['001']
+        assert len(pipeline.get_preprocessing_outputs()) == 0
+        assert len(pipeline.get_run_level_outputs()) == 0
+        assert len(pipeline.get_subject_level_outputs()) == 7
+        assert len(pipeline.get_group_level_outputs()) == 63
+        assert len(pipeline.get_hypotheses_outputs()) == 18
+
+        # 2 - 4 subjects outputs
+        pipeline.subject_list = ['001', '002', '003', '004']
+        assert len(pipeline.get_preprocessing_outputs()) == 0
+        assert len(pipeline.get_run_level_outputs()) == 0
+        assert len(pipeline.get_subject_level_outputs()) == 28
+        assert len(pipeline.get_group_level_outputs()) == 63
+        assert len(pipeline.get_hypotheses_outputs()) == 18
+
+    @staticmethod
+    @mark.unit_test
+    def test_subject_information():
+        """ Test the get_subject_information method """
+
+        # Get test files
+        test_file = join(Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
+        test_file_2 = join(Configuration()['directories']['test_data'],
+            'pipelines', 'team_J7F9', 'events_resp.tsv')
+
+        # Prepare several scenarii
+        info_missed = PipelineTeamJ7F9.get_subject_information([test_file, test_file])
+        info_ok = PipelineTeamJ7F9.get_subject_information([test_file_2, test_file_2])
+        info_half = PipelineTeamJ7F9.get_subject_information([test_file_2, test_file])
+
+        # Compare bunches to expected
+        bunch = info_missed[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'missed']
+        compare_float_2d_arrays(bunch.onsets, [[4.071, 11.834, 19.535, 27.535, 36.435], [19.535]])
+        compare_float_2d_arrays(bunch.durations, [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0]])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.pmod[0].name == ['gain', 'loss']
+        assert bunch.pmod[0].poly == [1, 1]
+        compare_float_2d_arrays(bunch.pmod[0].param, [[-8.4, 11.6, 15.6, -12.4, -6.4], [-8.2, -0.2, 4.8, 0.8, 2.8]])
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+
+        bunch = info_missed[1]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'missed']
+        compare_float_2d_arrays(bunch.onsets, [[4.071, 11.834, 19.535, 27.535, 36.435], [19.535]])
+        compare_float_2d_arrays(bunch.durations, [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0]])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.pmod[0].name == ['gain', 'loss']
+        assert bunch.pmod[0].poly == [1, 1]
+        compare_float_2d_arrays(bunch.pmod[0].param, [[-8.4, 11.6, 15.6, -12.4, -6.4], [-8.2, -0.2, 4.8, 0.8, 2.8]])
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+
+        bunch = info_ok[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial']
+        compare_float_2d_arrays(bunch.onsets, [[4.071, 11.834, 27.535, 36.435]])
+        compare_float_2d_arrays(bunch.durations, [[0.0, 0.0, 0.0, 0.0]])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.pmod[0].name == ['gain', 'loss']
+        assert bunch.pmod[0].poly == [1, 1]
+        compare_float_2d_arrays(bunch.pmod[0].param, [[-4.5, 15.5, -8.5, -2.5], [-7.0, 1.0, 2.0, 4.0]])
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+
+        bunch = info_ok[1]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial']
+        compare_float_2d_arrays(bunch.onsets, [[4.071, 11.834, 27.535, 36.435]])
+        compare_float_2d_arrays(bunch.durations, [[0.0, 0.0, 0.0, 0.0]])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.pmod[0].name == ['gain', 'loss']
+        assert bunch.pmod[0].poly == [1, 1]
+        compare_float_2d_arrays(bunch.pmod[0].param, [[-4.5, 15.5, -8.5, -2.5], [-7.0, 1.0, 2.0, 4.0]])
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+
+        bunch = info_half[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'missed']
+        compare_float_2d_arrays(bunch.onsets, [[4.071, 11.834, 27.535, 36.435], []])
+        compare_float_2d_arrays(bunch.durations, [[0.0, 0.0, 0.0, 0.0], []])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.pmod[0].name == ['gain', 'loss']
+        assert bunch.pmod[0].poly == [1, 1]
+        compare_float_2d_arrays(bunch.pmod[0].param, [[-6.666666666666668, 13.333333333333332, -10.666666666666668, -4.666666666666668], [-7.666666666666666, 0.3333333333333339, 1.333333333333334, 3.333333333333334]])
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+
+        bunch = info_half[1]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'missed']
+        compare_float_2d_arrays(bunch.onsets, [[4.071, 11.834, 19.535, 27.535, 36.435], [19.535]])
+        compare_float_2d_arrays(bunch.durations, [[0.0, 0.0, 0.0, 0.0, 0.0], [0.0]])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.pmod[0].name == ['gain', 'loss']
+        assert bunch.pmod[0].poly == [1, 1]
+        compare_float_2d_arrays(bunch.pmod[0].param, [[-6.666666666666668, 13.333333333333332, 17.333333333333332, -10.666666666666668, -4.666666666666668], [-7.666666666666666, 0.3333333333333339, 5.333333333333334, 1.333333333333334, 3.333333333333334]])
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+
+    @staticmethod
+    @mark.unit_test
+    def test_confounds_file(remove_test_dir):
+        """ Test the get_confounds_file method """
+
+        confounds_file = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'confounds.tsv')
+        reference_file = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'team_J7F9', 'confounds.tsv')
+
+        # Get new confounds file
+        PipelineTeamJ7F9.get_confounds_file(confounds_file, 'sid', 'rid', TEMPORARY_DIR)
+
+        # Check confounds file was created
+        created_confounds_file = join(
+            TEMPORARY_DIR, 'confounds_files', 'confounds_file_sub-sid_run-rid.tsv')
+        assert exists(created_confounds_file)
+
+        # Check contents
+        assert cmp(reference_file, created_confounds_file)
+
+    @staticmethod
+    @mark.pipeline_test
+    def test_execution():
+        """ Test the execution of a PipelineTeamJ7F9 and compare results """
+        helpers.test_pipeline_evaluation('J7F9')

tests/test_data/pipelines/confounds.tsv

@@ -0,0 +1,4 @@
+CSF	WhiteMatter	GlobalSignal	stdDVARS	non-stdDVARS	vx-wisestdDVARS	FramewiseDisplacement	tCompCor00	tCompCor01	tCompCor02	tCompCor03	tCompCor04	tCompCor05	aCompCor00	aCompCor01	aCompCor02	aCompCor03	aCompCor04	aCompCor05	Cosine00	Cosine01	Cosine02	Cosine03	Cosine04	Cosine05	NonSteadyStateOutlier00	X	Y	Z	RotX	RotY	RotZ
+6551.281999999999	6476.4653	9874.576	n/a	n/a	n/a	n/a	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0	0.0	0.0	-0.0	0.0
+6484.7285	6473.4890000000005	9830.212	1.09046686	52.78273392	1.05943739	0.13527900930999998	0.0263099209	-0.0673065879	0.0934882554	-0.0079328884	0.0338007737	-0.011491083999999999	-0.042411347099999996	0.027736422900000002	0.0453303087	-0.07022609490000001	0.0963618709	-0.0200867957	0.0665186088	0.0665174038	0.0665153954	0.0665125838	0.0665089688	0.06650455059999999	0.0	-0.00996895	-0.0313444	-3.00931e-06	0.00132687	-0.000384193	-0.00016819
+6441.5337	6485.7256	9821.212	1.07520139	52.04382706	1.03821933	0.12437666391	-0.0404820317	0.034150583	0.13661184210000002	0.0745358691	-0.0054829985999999995	-0.0217322686	0.046214115199999996	0.005774624	-0.043909359800000006	-0.075619539	0.17546891539999998	-0.0345256763	0.0665153954	0.06650455059999999	0.06648647719999999	0.0664611772	0.0664286533	0.0663889091	0.0	-2.56954e-05	-0.00923735	0.0549667	0.000997278	-0.00019745	-0.000398988

tests/test_data/pipelines/team_J7F9/confounds.tsv

@@ -0,0 +1,3 @@
+0.0	0.0	0.0	0.0	-0.0	0.0	6551.281999999999	6476.4653	9874.576
+-0.00996895	-0.0313444	-3.00931e-06	0.00132687	-0.000384193	-0.00016819	6484.7285	6473.4890000000005	9830.212
+-2.56954e-05	-0.00923735	0.0549667	0.000997278	-0.00019745	-0.000398988	6441.5337	6485.7256	9821.212

tests/test_data/pipelines/team_J7F9/events_resp.tsv

@@ -0,0 +1,5 @@
+onset	duration	gain	loss	RT	participant_response
+4.071	4	14	6	2.388	weakly_accept
+11.834	4	34	14	2.289	strongly_accept
+27.535	4	10	15	2.08	strongly_reject
+36.435	4	16	17	2.288	weakly_reject