Simplifying select files [skip ci]

bclenet · May 29, 2024 · eb7cca4 · eb7cca4
1 parent 57739e1
commit eb7cca4
Showing 1 changed file with 18 additions and 30 deletions.
diff --git a/narps_open/pipelines/team_0ED6.py b/narps_open/pipelines/team_0ED6.py
@@ -58,53 +58,41 @@ def get_preprocessing(self):
             base_dir = self.directories.working_dir,
             name = 'preprocessing')
 
-        # IDENTITY INTERFACE - To iterate on subjects
-        information_source_subjects = Node(IdentityInterface(
-            fields = ['subject_id']),
-            name = 'information_source_subjects')
-        information_source_subjects.iterables = [('subject_id', self.subject_list)]
-
-        # IDENTITY INTERFACE - To iterate on runs
-        information_source_runs = Node(IdentityInterface(
-            fields = ['run_id']),
-            name = 'information_source_runs')
-        information_source_runs.iterables = [('run_id', self.run_list)]
+        # IDENTITY INTERFACE - To iterate on subjects and runs
+        information_source = Node(IdentityInterface(
+            fields = ['subject_id', 'run_id']),
+            name = 'information_source')
+        information_source.iterables = [
+            ('subject_id', self.subject_list),
+            ('run_id', self.run_list)
+            ]
 
-        # SELECT FILES - Select subject_related files
+        # SELECT FILES - Select input files
         templates = {
             'anat' : join('sub-{subject_id}', 'anat', 'sub-{subject_id}_T1w.nii.gz'),
             'magnitude' : join('sub-{subject_id}', 'fmap', 'sub-{subject_id}_magnitude1.nii.gz'),
             'phase' : join('sub-{subject_id}', 'fmap', 'sub-{subject_id}_phasediff.nii.gz'),
-        }
-        select_subject_files = Node(SelectFiles(templates), name = 'select_subject_files')
-        select_subject_files.inputs.base_directory = self.directories.dataset_dir
-        preprocessing.connect(
-            information_source_subjects, 'subject_id', select_subject_files, 'subject_id')
-
-        # SELECT FILES - Select run related files
-        templates = {
             'func' : join('sub-{subject_id}', 'func',
                 'sub-{subject_id}_task-MGT_run-{run_id}_bold.nii.gz'),
             'sbref' : join('sub-{subject_id}', 'func',
                 'sub-{subject_id}_task-MGT_run-{run_id}_sbref.nii.gz')
         }
-        select_run_files = Node(SelectFiles(templates), name = 'select_run_files')
-        select_run_files.inputs.base_directory = self.directories.dataset_dir
-        preprocessing.connect(information_source_runs, 'run_id', select_run_files, 'run_id')
-        preprocessing.connect(
-            information_source_subjects, 'subject_id', select_run_files, 'subject_id')
+        select_files = Node(SelectFiles(templates), name = 'select_files')
+        select_files.inputs.base_directory = self.directories.dataset_dir
+        preprocessing.connect(information_source, 'subject_id', select_files, 'subject_id')
+        preprocessing.connect(information_source, 'run_id', select_files, 'run_id')
 
         # GUNZIP - gunzip files because SPM do not use .nii.gz files
         gunzip_anat = Node(Gunzip(), name = 'gunzip_anat')
         gunzip_func = Node(Gunzip(), name = 'gunzip_func')
         gunzip_sbref = Node(Gunzip(), name = 'gunzip_sbref')
         gunzip_magnitude = Node(Gunzip(), name = 'gunzip_magnitude')
         gunzip_phase = Node(Gunzip(), name = 'gunzip_phase')
-        preprocessing.connect(select_subject_files, 'anat', gunzip_anat, 'in_file')
-        preprocessing.connect(select_run_files, 'func', gunzip_func, 'in_file')
-        preprocessing.connect(select_run_files, 'sbref', gunzip_sbref, 'in_file')
-        preprocessing.connect(select_subject_files, 'magnitude', gunzip_magnitude, 'in_file')
-        preprocessing.connect(select_subject_files, 'phase', gunzip_phase, 'in_file')
+        preprocessing.connect(select_files, 'anat', gunzip_anat, 'in_file')
+        preprocessing.connect(select_files, 'func', gunzip_func, 'in_file')
+        preprocessing.connect(select_files, 'sbref', gunzip_sbref, 'in_file')
+        preprocessing.connect(select_files, 'magnitude', gunzip_magnitude, 'in_file')
+        preprocessing.connect(select_files, 'phase', gunzip_phase, 'in_file')
 
         # FIELD MAP - Compute a voxel displacement map from magnitude and phase data
         fieldmap = Node(FieldMap(), name = 'fieldmap')