WIP - gui for bids

nih2mne/make_meg_bids_gui.py

@@ -0,0 +1,197 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jul  5 10:50:57 2024
+
+@author: jstout
+"""
+import PySimpleGUI as sg
+import os,os.path as op
+
+font = ("Arial", 25)
+sg.set_options(font=font)
+
+
+
+class window_opts:
+    def __init__(self):
+        # Button Entries
+        self.anonymize = False
+        self.ignore_mri_checks = False
+
+        # Standard Entries
+        self.bids_dir = op.join(os.getcwd(), 'bids_dir')
+        self.meg_input_dir = None
+        self.bids_session = 1
+        self.subjid_input = None
+        self.bids_id = None
+        self.coreg = 'brainsight'
+
+        ## Afni Coreg:
+        self.mri_brik = None
+
+        ## Brainsight Coreg:
+        self.mri_bsight = None
+        self.mri_bsight_elec = None
+
+        ## Optional Overrides:
+        self.ignore_eroom = None
+        self.autocrop_zeros = None
+        self.freesurfer = None
+        self.eventID_csv = None
+        # Run standardize_eventID_list.py
+
+
+def make_layout(options=None):
+    init_layout = [  
+        [sg.Text('MEG Conversion to BIDS')],
+        [sg.Text('Warning: currently works with {DATE/dsets} format from scanner')]
+        ]
+
+    if options.anonymize==True:
+        l_button_opts = [
+            [sg.Button('Anonymize: Y', key='anonymize', button_color='green')], 
+            ]
+    else:
+        l_button_opts = [
+            [sg.Button('Anonymize: N', key='anonymize', button_color='red')], 
+            ]
+
+    standard_opts = [
+        [sg.Text('Standard Options')], 
+        [sg.Text('BIDS Output Directory'), sg.InputText(key=options.bids_dir)],
+        [sg.Text('BIDS Session'), sg.InputText(default_text=options.bids_session)]
+        ]
+
+    # MRI opts
+    coreg_opts = [
+        [sg.Combo(['BrainSight', 'Afni', 'None'], enable_events=True, readonly=True, k='-COREG-', 
+                  default_value='BrainSight')]
+        ]
+
+    coreg_afni_opts = [
+        [sg.Text('Brik File', key='brik_file')]
+        ]
+
+    coreg_bsight_opts = [
+        [sg.Text('Nifti MRI', key='brik_file')]
+        ]
+
+    layout = init_layout
+    layout.append(l_button_opts)
+    layout.append(standard_opts)
+    if options.ignore_mri_checks != True:
+        layout.append(coreg_opts)
+    layout.append(coreg_afni_opts)
+    layout.append(coreg_bsight_opts)
+    layout.append([sg.Button('EXIT')])
+    return layout
+
+
+def get_window(options=None):
+    layout = make_layout(options=options)
+    window = sg.Window('MEG BIDS conversion', layout, resizable=True, auto_size_buttons=True, 
+                   scaling=True)
+    del layout
+    return window
+
+opts = window_opts()
+window = get_window(opts)
+
+while True:
+    event, values = window.read()
+    if event == 'anonymize': 
+        if opts.anonymize == False:
+            window['anonymize'].update(button_color='green')
+            window['anonymize'].update(text='Anonymize: Y')
+            opts.anonymize = not opts.anonymize
+        else:
+            window['anonymize'].update(button_color='red')
+            window['anonymize'].update(text='Anonymize: N')
+            opts.anonymize = not opts.anonymize
+
+    if event == 'set_coreg_afni':
+        set_coreg_afni = True
+        set_coreg_bsight = False
+    if event == 'set_coreg_bsight':
+        set_coreg_afni = False
+        set_coreg_bsight = True        
+    if event == sg.WIN_CLOSED or event == 'EXIT': # if user closes window or clicks cancel
+        break
+    print('You entered ', values[0])
+    print(f'Anonymize is {opts.anonymize}')
+
+
+window.close()
+
+
+
+
+
+#%% 
+options:
+  -h, --help            show this help message and exit
+  -bids_dir BIDS_DIR    Output bids_dir path
+  -meg_input_dir MEG_INPUT_DIR
+                        Acquisition directory - typically designated by the acquisition date
+  -anonymize            Strip out subject ID information from the MEG data. Currently this does not
+                        anonymize the MRI. Requires the CTF tools.
+  -bids_session BIDS_SESSION
+                        Data acquisition session. This is set to 1 by default. If the same subject had
+                        multiple sessions this must be set manually
+  -subjid_input SUBJID_INPUT
+                        The default subject ID is given by the MEG hash. If more than one subject is
+                        present in a folder, this option can be set to select a single subjects
+                        dataset.
+  -bids_id BIDS_ID      The default subject ID is given by the MEG hash. To override the default
+                        subject ID, use this flag. If -anonymize is used, you must set the subjid
+  -autocrop_zeros       If files are terminated early, leaving zeros at the end of the file - this
+                        will detect and remove the trailing zeros. !!!Files larger than 2G will
+                        Fail!!!
+
+Afni Coreg:
+  -mri_brik MRI_BRIK    Afni coregistered MRI
+
+Brainsight Coreg:
+  -mri_bsight MRI_BSIGHT
+                        Brainsight mri. This should be a .nii file. The exported electrodes text file
+                        must be in the same folder and end in .txt. Otherwise, provide the
+                        mri_sight_elec flag
+  -mri_bsight_elec MRI_BSIGHT_ELEC
+                        Exported electrodes file from brainsight. This has the locations of the
+                        fiducials
+  -ignore_mri_checks
+
+Optional Overrides:
+  -ignore_eroom         If you are Not on Biowulf, use this option to prevent an error. Or if you
+                        collected your own empty room data with your dataset
+  -supplement_eroom     If emptyroom present - ignore, else add emptyroom from the biowulf repository.
+  -freesurfer           Perform recon-all pipeline on the T1w. This is required for the mri_prep
+                        portions below
+  -eventID_csv EVENTID_CSV
+                        Provide the standardized event IDs. This can be produced by running:
+                        standardize_eventID_list.py
+
+UNDER Construction - BIDS PostProcessing:
+  -project PROJECT      Output project name for the mri processing from mri_prep
+  -mri_prep_s           Perform the standard SURFACE processing for meg analysis
+                        (watershed/bem/src/fwd)
+  -mri_prep_v           Perform the standard VOLUME processing for meg analysis
+                        (watershed/bem/src/fwd)
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
+

pyproject.toml

@@ -20,7 +20,7 @@ classifiers=[
         "Operating System :: Linux/Unix",
     ]
 dependencies = [
-'mne<1.6', 'numpy', 'pytest', 'joblib', 'nibabel','mne_bids','pandas', 'wget','nilearn',
+'mne<1.6', 'numpy', 'pytest', 'joblib', 'nibabel','mne_bids','pandas', 'wget','nilearn', 'pysimplegui-4-foss',
 'pyctf-lite @ git+https://github.com/nih-megcore/[email protected]#egg=pyctf-lite' 
 ]
 dynamic = ["version"]