Group analysis workflow bug

narps_open/pipelines/team_08MQ.py

@@ -267,15 +267,38 @@ def get_preprocessing(self):
 
     def get_preprocessing_outputs(self):
         """ Return a list of the files generated by the preprocessing """
-        return []
+
+        # Contrat maps
+        templates = [join(
+            self.directories.output_dir,
+            'l1_analysis', '_subject_id_{subject_id}', f'con_{contrast_id}.nii')\
+            for contrast_id in self.contrast_list]
+
+        # SPM.mat file
+        templates += [join(
+            self.directories.output_dir,
+            'l1_analysis', '_subject_id_{subject_id}', 'SPM.mat')]
+
+        # spmT maps
+        templates += [join(
+            self.directories.output_dir,
+            'l1_analysis', '_subject_id_{subject_id}', f'spmT_{contrast_id}.nii')\
+            for contrast_id in self.contrast_list]
+
+        # Format with subject_ids
+        return_list = []
+        for template in templates:
+            return_list += [template.format(subject_id = s) for s in self.subject_list]
+
+        return return_list
 
     def get_run_level_analysis(self):
         """ Return a Nipype workflow describing the run level analysis part of the pipeline """
         return None
 
     def get_run_level_outputs(self):
         """ Return a list of the files generated by the run level analysis """
-        return []
+        return ['fake_file']
 
     def get_subject_information(event_file: str):
         """
@@ -507,7 +530,7 @@ def get_subject_level_analysis(self):
 
     def get_subject_level_outputs(self):
         """ Return a list of the files generated by the subject level analysis """
-        return []
+        return ['fake_file']
 
     def get_subgroups_contrasts(
         copes, varcopes, subject_list: list, participants_file: str
@@ -642,6 +665,7 @@ def get_group_level_analysis(self):
         Returns;
             - a list of nipype.WorkFlow
         """
+        return None
 
         methods = ['equalRange', 'equalIndifference', 'groupComp']
         return [self.get_group_level_analysis_sub_workflow(method) for method in methods]
@@ -736,12 +760,6 @@ def get_group_level_analysis_sub_workflow(self, method):
         )
         group_level_analysis.connect([
             (info_source, select_files, [('contrast_id', 'contrast_id')])
-            """(info_source, subgroups_contrasts, [('subject_list', 'subject_ids')]),
-            (select_files, subgroups_contrasts, [
-                ('cope', 'copes'),
-                ('varcope', 'varcopes'),
-                ('participants', 'participants_file'),
-            ])"""
         ])
 
         # [INFO] Here we define the contrasts used for the group level analysis, depending on the
@@ -759,8 +777,48 @@ def get_group_level_analysis_sub_workflow(self, method):
 
     def get_group_level_outputs(self):
         """ Return a list of the files generated by the group level analysis """
-        return []
+        return ['fake_file']
 
     def get_hypotheses_outputs(self):
         """ Return the names of the files used by the team to answer the hypotheses of NARPS. """
-        return []
+
+        nb_sub = len(self.subject_list)
+        files = [
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'zstat1.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'zstat1.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'zstat1.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_pgain', 'zstat1.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'randomise_tfce_corrp_tstat2.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'zstat2.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'randomise_tfce_corrp_tstat2.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'zstat2.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_equalIndifference_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'zstat1.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_equalRange_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'zstat1.nii.gz'),
+            join(f'l3_analysis_groupComp_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'randomise_tfce_corrp_tstat1.nii.gz'),
+            join(f'l3_analysis_groupComp_nsub_{nb_sub}',
+                '_contrast_id_ploss', 'zstat1.nii.gz')
+        ]
+        return [join(self.directories.output_dir, f) for f in files]