Merge branch 'main' into 51PW_reproduction

Inria-Empenn · Feb 7, 2024 · 2156ff0 · 2156ff0
2 parents 7eac2af + f87cf70
commit 2156ff0
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diff --git a/.github/workflows/code_quality.yml b/.github/workflows/code_quality.yml
@@ -46,7 +46,7 @@ jobs:
 
     - name: Analyse the code with pylint
       run: |
-        pylint --fail-under 8 --ignore-paths narps_open/pipelines/ narps_open > pylint_report_narps_open.txt
+        pylint --fail-under 8 narps_open > pylint_report_narps_open.txt
         pylint --fail-under 8 tests > pylint_report_tests.txt
 
     - name: Archive pylint results

diff --git a/narps_open/pipelines/__init__.py b/narps_open/pipelines/__init__.py
@@ -69,12 +69,12 @@
     'R9K3': None,
     'SM54': None,
     'T54A': 'PipelineTeamT54A',
-    'U26C': None,
+    'U26C': 'PipelineTeamU26C',
     'UI76': None,
     'UK24': None,
     'V55J': None,
     'VG39': None,
-    'X19V': None,
+    'X19V': 'PipelineTeamX19V',
     'X1Y5': None,
     'X1Z4': None,
     'XU70': None

diff --git a/narps_open/pipelines/__main__.py b/narps_open/pipelines/__main__.py
diff --git a/narps_open/pipelines/team_08MQ.py b/narps_open/pipelines/team_08MQ.py
@@ -386,23 +386,24 @@ def get_preprocessing_outputs(self):
         parameters = {
             'subject_id': self.subject_list,
             'run_id': self.run_list,
-            'file': [
-                'components_file.txt',
-                'sub-{subject_id}_task-MGT_run-{run_id}_bold_brain_mcf.nii.gz.par',
-                'sub-{subject_id}_task-MGT_run-{run_id}_bold_brain_mcf_st_smooth_flirt_wtsimt.nii.gz',
-                'sub-{subject_id}_task-MGT_run-{run_id}_bold_brain_mask_flirt_wtsimt.nii.gz'
-            ]
         }
         parameter_sets = product(*parameters.values())
-        template = join(
+        output_dir = join(
             self.directories.output_dir,
             'preprocessing',
-            '_run_id_{run_id}_subject_id_{subject_id}',
-            '{file}'
-            )
+            '_run_id_{run_id}_subject_id_{subject_id}'
+        )
+        templates = [
+            join(output_dir, 'components_file.txt'),
+            join(output_dir, 'sub-{subject_id}_task-MGT_run-{run_id}_bold_brain_mcf.nii.gz.par'),
+            join(output_dir,
+                'sub-{subject_id}_task-MGT_run-{run_id}_bold_brain_mcf_st_smooth_flirt_wtsimt.nii.gz'),
+            join(output_dir,
+                'sub-{subject_id}_task-MGT_run-{run_id}_bold_brain_mask_flirt_wtsimt.nii.gz')
+        ]
 
         return [template.format(**dict(zip(parameters.keys(), parameter_values)))\
-            for parameter_values in parameter_sets]
+            for parameter_values in parameter_sets for template in templates]
 
     def get_subject_information(event_file):
         """
@@ -586,21 +587,20 @@ def get_run_level_outputs(self):
             'run_id' : self.run_list,
             'subject_id' : self.subject_list,
             'contrast_id' : self.contrast_list,
-            'file' : [
-                join('results', 'cope{contrast_id}.nii.gz'),
-                join('results', 'tstat{contrast_id}.nii.gz'),
-                join('results', 'varcope{contrast_id}.nii.gz'),
-                join('results', 'zstat{contrast_id}.nii.gz'),
-            ]
         }
         parameter_sets = product(*parameters.values())
-        template = join(
+        output_dir = join(
             self.directories.output_dir,
-            'run_level_analysis', '_run_id_{run_id}_subject_id_{subject_id}','{file}'
+            'run_level_analysis', '_run_id_{run_id}_subject_id_{subject_id}'
             )
-
+        templates = [
+            join(output_dir, 'results', 'cope{contrast_id}.nii.gz'),
+            join(output_dir, 'results', 'tstat{contrast_id}.nii.gz'),
+            join(output_dir, 'results', 'varcope{contrast_id}.nii.gz'),
+            join(output_dir, 'results', 'zstat{contrast_id}.nii.gz'),
+        ]
         return_list += [template.format(**dict(zip(parameters.keys(), parameter_values)))\
-            for parameter_values in parameter_sets]
+            for parameter_values in parameter_sets for template in templates]
 
         return return_list
 
@@ -1005,6 +1005,57 @@ def get_group_level_analysis_sub_workflow(self, method):
 
         return group_level_analysis
 
+    def get_group_level_outputs(self):
+        """ Return all names for the files the group level analysis is supposed to generate. """
+
+        # Handle equalRange and equalIndifference
+        parameters = {
+            'contrast_id': self.contrast_list,
+            'method': ['equalRange', 'equalIndifference'],
+            'file': [
+                'randomise_tfce_corrp_tstat1.nii.gz',
+                'randomise_tfce_corrp_tstat2.nii.gz',
+                'randomise_tstat1.nii.gz',
+                'randomise_tstat2.nii.gz',
+                'tstat1.nii.gz',
+                'tstat2.nii.gz',
+                'zstat1.nii.gz',
+                'zstat2.nii.gz'
+                ],
+            'nb_subjects' : [str(len(self.subject_list))]
+        }
+        parameter_sets = product(*parameters.values())
+        template = join(
+            self.directories.output_dir,
+            'group_level_analysis_{method}_nsub_{nb_subjects}',
+            '_contrast_id_{contrast_id}',
+            '{file}'
+            )
+
+        return_list = [template.format(**dict(zip(parameters.keys(), parameter_values)))\
+            for parameter_values in parameter_sets]
+
+        # Handle groupComp
+        parameters = {
+            'contrast_id': self.contrast_list,
+            'file': [
+                'randomise_tfce_corrp_tstat1.nii.gz',
+                'randomise_tstat1.nii.gz',
+                'zstat1.nii.gz',
+                'tstat1.nii.gz'
+            ]
+        }
+        parameter_sets = product(*parameters.values())
+        template = join(
+            self.directories.output_dir,
+            f'group_level_analysis_groupComp_nsub_{len(self.subject_list)}',
+            '_contrast_id_{contrast_id}', '{file}')
+
+        return_list += [template.format(**dict(zip(parameters.keys(), parameter_values)))\
+            for parameter_values in parameter_sets]
+
+        return return_list
+
     def get_hypotheses_outputs(self):
         """ Return the names of the files used by the team to answer the hypotheses of NARPS. """
 

diff --git a/narps_open/pipelines/team_0I4U_debug.py b/narps_open/pipelines/team_0I4U_debug.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.spm import (Coregister, Smooth, OneSampleTTestDesign, EstimateModel, EstimateContrast, 
                                    Level1Design, TwoSampleTTestDesign, RealignUnwarp, FieldMap, NewSegment, 
                                    Normalize12, Reslice)

diff --git a/narps_open/pipelines/team_1KB2_debug.py b/narps_open/pipelines/team_1KB2_debug.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (BET, FAST, MCFLIRT, FLIRT, FNIRT, ApplyWarp, SUSAN, 
                                    Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr,Cluster,  FILMGLS, Randomise, MultipleRegressDesign)

diff --git a/narps_open/pipelines/team_43FJ_debug.py b/narps_open/pipelines/team_43FJ_debug.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (BET, FAST, MCFLIRT, FLIRT, FNIRT, ApplyWarp, SUSAN, MotionOutliers,
                                    Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr, FILMGLS, Randomise, MultipleRegressDesign)

diff --git a/narps_open/pipelines/team_4TQ6_wip.py b/narps_open/pipelines/team_4TQ6_wip.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.fsl import (BET, ICA_AROMA, FAST, MCFLIRT, FLIRT, FNIRT, ApplyWarp, SUSAN, 
                                    Info, ImageMaths, IsotropicSmooth, Threshold, Level1Design, FEATModel, 
                                    L2Model, Merge, FLAMEO, ContrastMgr,Cluster,  FILMGLS, Randomise, MultipleRegressDesign)

diff --git a/narps_open/pipelines/team_98BT.py b/narps_open/pipelines/team_98BT.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 from nipype.interfaces.spm import (Coregister, Smooth, OneSampleTTestDesign, EstimateModel, EstimateContrast, 
                                    Level1Design, TwoSampleTTestDesign, RealignUnwarp, NewSegment, SliceTiming,
                                   DARTEL, DARTELNorm2MNI, FieldMap)

diff --git a/narps_open/pipelines/team_Q6O0.py b/narps_open/pipelines/team_Q6O0.py
@@ -468,11 +468,14 @@ def get_subject_level_outputs(self):
             )
 
         # Formatting templates and returning it as a list of files
-        output_files = [contrast_map_template.format(**dict(zip(parameters.keys(), parameter_values)))\
+        output_files = [
+            contrast_map_template.format(**dict(zip(parameters.keys(), parameter_values)))\
             for parameter_values in parameter_sets]
-        output_files += [mat_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
+        output_files += [
+            mat_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
             for parameter_values in parameter_sets]
-        output_files += [spmt_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
+        output_files += [
+            spmt_file_template.format(**dict(zip(parameters.keys(), parameter_values)))\
             for parameter_values in parameter_sets]
 
         return output_files
@@ -698,23 +701,41 @@ def get_hypotheses_outputs(self):
         """ Return all hypotheses output file names. """
         nb_sub = len(self.subject_list)
         files = [
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_gain', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', 'spmT_0002.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', 'spmT_0002.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_model_type_loss', 'spmT_0001.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_equalRange_nsub_{nb_sub}', '_model_type_loss', 'spmT_0001.nii'),
-            join(f'l2_analysis_groupComp_nsub_{nb_sub}', '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
-            join(f'l2_analysis_groupComp_nsub_{nb_sub}', '_model_type_loss', 'spmT_0001.nii')
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_gain', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0002.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold1', 'spmT_0002_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0002.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalIndifference_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0001.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_equalRange_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0001.nii'),
+            join(f'l2_analysis_groupComp_nsub_{nb_sub}',
+                '_model_type_loss', '_threshold0', 'spmT_0001_thr.nii'),
+            join(f'l2_analysis_groupComp_nsub_{nb_sub}',
+                '_model_type_loss', 'spmT_0001.nii')
         ]
         return [join(self.directories.output_dir, f) for f in files]
diff --git a/narps_open/pipelines/team_R9K3_wip.py b/narps_open/pipelines/team_R9K3_wip.py
@@ -1,3 +1,4 @@
+# pylint: skip-file
 # THIS IS A TEMPLATE THAT CAN BE USE TO REPRODUCE A NEW PIPELINE
 
 import os

diff --git a/narps_open/pipelines/team_T54A.py b/narps_open/pipelines/team_T54A.py
@@ -765,17 +765,22 @@ def get_group_level_outputs(self):
             for parameter_values in parameter_sets]
 
         # Handle groupComp
-        files = [
-            'randomise_tfce_corrp_tstat1.nii.gz',
-            'randomise_tstat1.nii.gz',
-            'zstat1.nii.gz',
-            'tstat1.nii.gz'
+        parameters = {
+            'contrast_id': self.contrast_list,
+            'file': [
+                'randomise_tfce_corrp_tstat1.nii.gz',
+                'randomise_tstat1.nii.gz',
+                'zstat1.nii.gz',
+                'tstat1.nii.gz'
             ]
-
-        return_list += [join(
+        }
+        parameter_sets = product(*parameters.values())
+        template = join(
             self.directories.output_dir,
             f'group_level_analysis_groupComp_nsub_{len(self.subject_list)}',
-            '_contrast_id_2', f'{file}') for file in files]
+            '_contrast_id_{contrast_id}', '{file}')
+        return_list += [template.format(**dict(zip(parameters.keys(), parameter_values)))\
+            for parameter_values in parameter_sets]
 
         return return_list