Refac pipeline

narps_open/pipelines/team_C88N.py

@@ -378,6 +378,33 @@ def get_subject_level_analysis(self):
 
         return l1_analysis
 
+    def get_subject_level_outputs(self):
+        """ Return the names of the files the subject level analysis is supposed to generate. """
+
+        # 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
+
     # @staticmethod # Starting python 3.10, staticmethod should be used here
     # Otherwise it produces a TypeError: 'staticmethod' object is not callable
     def get_subset_contrasts(file_list, subject_list, participants_file):
@@ -413,72 +440,6 @@ def get_subset_contrasts(file_list, subject_list, participants_file):
 
         return equal_indifference_id, equal_range_id, equal_indifference_files, equal_range_files
 
-    # @staticmethod # Starting python 3.10, staticmethod should be used here
-    # Otherwise it produces a TypeError: 'staticmethod' object is not callable
-    def reorganize_results(team_id, nb_sub, output_dir, results_dir):
-        """ Reorganize the results to analyze them.
-
-        Parameters:
-            - results_dir: str, directory where results will be stored
-            - output_dir: str, name of the sub-directory for final results
-            - nb_sub: float, number of subject used for the analysis
-            - team_id: str, ID of the team to reorganize results
-        """
-        from os import mkdir
-        from os.path import join, isdir
-        from shutil import copyfile
-
-        hypotheses = [
-            join(output_dir,
-                f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_contrast_id_1_model_type_gain'),
-            join(output_dir,
-                f'l2_analysis_equalRange_nsub_{nb_sub}', '_contrast_id_1_model_type_gain'),
-            join(output_dir,
-                f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_contrast_id_1_model_type_gain'),
-            join(output_dir,
-                f'l2_analysis_equalRange_nsub_{nb_sub}', '_contrast_id_1_model_type_gain'),
-            join(output_dir,
-                f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_contrast_id_1_model_type_loss'),
-            join(output_dir,
-                f'l2_analysis_equalRange_nsub_{nb_sub}', '_contrast_id_1_model_type_loss'),
-            join(output_dir,
-                f'l2_analysis_equalIndifference_nsub_{nb_sub}', '_contrast_id_1_model_type_loss'),
-            join(output_dir,
-                f'l2_analysis_equalRange_nsub_{nb_sub}', '_contrast_id_1_model_type_loss'),
-            join(output_dir,
-                f'l2_analysis_groupComp_nsub_{nb_sub}', '_contrast_id_1_model_type_loss')
-        ]
-
-        # Build lists of files for unthresholded and thresholded maps
-        repro_unthresh = []
-        repro_thresh = []
-        for file_id, filename in enumerate(hypotheses):
-            if file_id in [4,5]:
-                repro_unthresh.append(join(filename, 'spmT_0002.nii'))
-                repro_thresh.append(join(filename, '_threshold1', 'spmT_0002_thr.nii'))
-            else:
-                repro_unthresh.append(join(filename, 'spmT_0001.nii'))
-                repro_thresh.append(join(filename, '_threshold0', 'spmT_0001_thr.nii'))
-
-        if not isdir(join(results_dir, "NARPS-reproduction")):
-            mkdir(join(results_dir, "NARPS-reproduction"))
-
-        for file_id, filename in enumerate(repro_unthresh):
-            f_in = filename
-            f_out = join(results_dir,
-                'NARPS-reproduction',
-                f'team_{team_id}_nsub_{nb_sub}_hypo{file_id + 1}_unthresholded.nii')
-            copyfile(f_in, f_out)
-
-        for file_id, filename in enumerate(repro_thresh):
-            f_in = filename
-            f_out = join(results_dir,
-                'NARPS-reproduction',
-                f'team_{team_id}_nsub_{nb_sub}_hypo{file_id + 1}_thresholded.nii')
-            copyfile(f_in, f_out)
-
-        print(f'Results files of team {team_id} reorganized.')
-
     def get_group_level_analysis(self):
         """
         Return all workflows for the group level analysis.