WIP 2

aramis-lab · Sep 27, 2024 · 3273a8b · 3273a8b
1 parent 246f1b5
commit 3273a8b
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Showing 6 changed files with 22 additions and 31 deletions.
diff --git a/clinica/pipelines/anatomical/freesurfer/atlas/pipeline.py b/clinica/pipelines/anatomical/freesurfer/atlas/pipeline.py
@@ -81,10 +81,16 @@ def get_to_process_with_atlases(
                     - set(t1_freesurfer_longitudinal_output_atlas)
                 )
                 t1_freesurfer_output, _ = clinica_file_reader(
-                    subjects, sessions, caps_directory, T1_FS_DESTRIEUX, False
+                    subjects,
+                    sessions,
+                    caps_directory,
+                    T1_FS_DESTRIEUX,
                 )
                 t1_freesurfer_files, _ = clinica_file_reader(
-                    subjects, sessions, caps_directory, atlas_info, False
+                    subjects,
+                    sessions,
+                    caps_directory,
+                    atlas_info,
                 )
                 image_ids = extract_image_ids(t1_freesurfer_files)
                 image_ids_2 = extract_image_ids(t1_freesurfer_output)

diff --git a/clinica/pipelines/anatomical/freesurfer/longitudinal/template/pipeline.py b/clinica/pipelines/anatomical/freesurfer/longitudinal/template/pipeline.py
@@ -32,11 +32,7 @@ def get_processed_images(
         image_ids: List[str] = []
         if caps_directory.is_dir():
             t1_freesurfer_files, _ = clinica_file_reader(
-                list_participant_id,
-                list_long_id,
-                caps_directory,
-                T1_FS_T_DESTRIEUX,
-                False,
+                list_participant_id, list_long_id, caps_directory, T1_FS_T_DESTRIEUX
             )
             image_ids = [
                 re.search(r"(sub-[a-zA-Z0-9]+)_(long-[a-zA-Z0-9]+)", file).group()
@@ -95,7 +91,7 @@ def _build_input_node(self):
         from clinica.utils.exceptions import ClinicaCAPSError, ClinicaException
         from clinica.utils.filemanip import extract_subjects_sessions_from_filename
         from clinica.utils.input_files import T1_FS_DESTRIEUX
-        from clinica.utils.inputs import clinica_file_reader
+        from clinica.utils.inputs import clinica_file_filter
         from clinica.utils.longitudinal import (
             get_long_id,
             get_participants_long_id,
@@ -153,16 +149,10 @@ def _build_input_node(self):
                 self.subjects, self.sessions = extract_subjects_sessions_from_filename(
                     to_process_ids
                 )
-        try:
-            clinica_file_reader(
-                self.subjects, self.sessions, self.caps_directory, T1_FS_DESTRIEUX
-            )
-        except ClinicaException as e:
-            err_msg = (
-                "Clinica faced error(s) while trying to read files in your CAPS directory.\n"
-                + str(e)
-            )
-            raise ClinicaCAPSError(err_msg)
+
+        _, self.subjects, self.sessions = clinica_file_filter(
+            self.subjects, self.sessions, self.caps_directory, T1_FS_DESTRIEUX
+        )
 
         long_ids = get_participants_long_id(self.subjects, self.sessions)
         save_part_sess_long_ids_to_tsv(

diff --git a/clinica/pipelines/anatomical/freesurfer/t1/pipeline.py b/clinica/pipelines/anatomical/freesurfer/t1/pipeline.py
@@ -27,7 +27,7 @@ def get_processed_images(
         image_ids: List[str] = []
         if caps_directory.is_dir():
             t1_freesurfer_files, _ = clinica_file_reader(
-                subjects, sessions, caps_directory, T1_FS_DESTRIEUX, False
+                subjects, sessions, caps_directory, T1_FS_DESTRIEUX
             )
             image_ids = extract_image_ids(t1_freesurfer_files)
         return image_ids
@@ -97,7 +97,7 @@ def _build_input_node(self):
             save_participants_sessions,
         )
         from clinica.utils.input_files import T1W_NII
-        from clinica.utils.inputs import clinica_file_reader
+        from clinica.utils.inputs import clinica_file_filter
         from clinica.utils.stream import cprint
         from clinica.utils.ux import print_images_to_process
 
@@ -130,17 +130,10 @@ def _build_input_node(self):
                     to_process_ids
                 )
 
-        t1w_files, error_message = clinica_file_reader(
-            self.subjects,
-            self.sessions,
-            self.bids_directory,
-            T1W_NII,
-            raise_exception=False,
+        t1w_files, self.subjects, self.sessions = clinica_file_filter(
+            self.subjects, self.sessions, self.bids_directory, T1W_NII
         )
 
-        if error_message:
-            cprint(error_message, lvl="warning")
-
         if not t1w_files:
             raise ClinicaException("Empty dataset or already processed")
 

diff --git a/clinica/pipelines/dwi/preprocessing/fmap/pipeline.py b/clinica/pipelines/dwi/preprocessing/fmap/pipeline.py
@@ -36,7 +36,7 @@ def get_processed_images(
         image_ids: List[str] = []
         if caps_directory.is_dir():
             preproc_files, _ = clinica_file_reader(
-                subjects, sessions, caps_directory, DWI_PREPROC_NII, False
+                subjects, sessions, caps_directory, DWI_PREPROC_NII
             )
             image_ids = extract_image_ids(preproc_files)
         return image_ids

diff --git a/clinica/pipelines/dwi/preprocessing/t1/pipeline.py b/clinica/pipelines/dwi/preprocessing/t1/pipeline.py
@@ -40,7 +40,7 @@ def get_processed_images(
         image_ids: List[str] = []
         if caps_directory.is_dir():
             preproc_files, _ = clinica_file_reader(
-                subjects, sessions, caps_directory, DWI_PREPROC_NII, False
+                subjects, sessions, caps_directory, DWI_PREPROC_NII
             )
             image_ids = extract_image_ids(preproc_files)
         return image_ids

diff --git a/clinica/utils/inputs.py b/clinica/utils/inputs.py
@@ -627,6 +627,7 @@ def _remove_sub_ses_from_list(
     return list_subjects, list_sessions
 
 
+# todo : generalize
 def clinica_file_reader(
     subjects: List[str],
     sessions: List[str],
@@ -825,6 +826,7 @@ def _read_files_sequential(
     return results, errors_encountered
 
 
+# todo : generalize
 def clinica_list_of_files_reader(
     participant_ids: List[str],
     session_ids: List[str],