Changes upon suggestions #1

clinica/pipelines/anatomical/freesurfer/longitudinal/correction/pipeline.py

@@ -60,7 +60,10 @@ def _build_input_node(self):
         )
         from clinica.utils.exceptions import ClinicaException
         from clinica.utils.input_files import T1_FS_DESTRIEUX, T1_FS_T_DESTRIEUX
-        from clinica.utils.inputs import _format_errors, clinica_file_reader
+        from clinica.utils.inputs import (
+            clinica_file_reader,
+            format_clinica_file_reader_errors,
+        )
         from clinica.utils.stream import cprint
 
         from .utils import (
@@ -128,7 +131,7 @@ def _build_input_node(self):
         if any(all_errors):
             message = "Clinica faced errors while trying to read files in your CAPS directory.\n"
             for error, info in zip(all_errors, [T1_FS_DESTRIEUX, T1_FS_T_DESTRIEUX]):
-                message += _format_errors(error, info)
+                message += format_clinica_file_reader_errors(error, info)
             raise ClinicaException(message)
 
         save_part_sess_long_ids_to_tsv(

clinica/pipelines/machine_learning_spatial_svm/spatial_svm_pipeline.py

@@ -64,9 +64,9 @@ def _build_input_node(self):
             t1_volume_final_group_template,
         )
         from clinica.utils.inputs import (
-            _format_errors,
             clinica_file_reader,
             clinica_group_reader,
+            format_clinica_file_reader_errors,
         )
         from clinica.utils.ux import print_groups_in_caps_directory
 
@@ -129,7 +129,9 @@ def _build_input_node(self):
             caps_files_information,
         )
         if caps_error:
-            all_errors.append(_format_errors(caps_error, caps_files_information))
+            all_errors.append(
+                format_clinica_file_reader_errors(caps_error, caps_files_information)
+            )
 
         try:
             dartel_input = clinica_group_reader(

clinica/pipelines/pet/linear/pipeline.py

@@ -67,7 +67,10 @@ def _build_input_node(self):
         )
         from clinica.utils.image import get_mni_template
         from clinica.utils.input_files import T1W_NII, T1W_TO_MNI_TRANSFORM
-        from clinica.utils.inputs import _format_errors, clinica_file_reader
+        from clinica.utils.inputs import (
+            clinica_file_reader,
+            format_clinica_file_reader_errors,
+        )
         from clinica.utils.stream import cprint
         from clinica.utils.ux import print_images_to_process
 
@@ -83,15 +86,19 @@ def _build_input_node(self):
         )
         if pet_errors:
             raise ClinicaBIDSError(
-                _format_errors(pet_errors, self._get_pet_scans_query())
+                format_clinica_file_reader_errors(
+                    pet_errors, self._get_pet_scans_query()
+                )
             )
 
         # T1w file:
         t1w_files, t1w_errors = clinica_file_reader(
             self.subjects, self.sessions, self.bids_directory, T1W_NII
         )
         if t1w_errors:
-            raise ClinicaBIDSError(_format_errors(t1w_errors, T1W_NII))
+            raise ClinicaBIDSError(
+                format_clinica_file_reader_errors(t1w_errors, T1W_NII)
+            )
 
         # Inputs from t1-linear pipeline
         # Transformation files from T1w files to MNI:
@@ -100,7 +107,9 @@ def _build_input_node(self):
         )
         if t1w_to_mni_errors:
             raise ClinicaCAPSError(
-                _format_errors(t1w_to_mni_errors, T1W_TO_MNI_TRANSFORM)
+                format_clinica_file_reader_errors(
+                    t1w_to_mni_errors, T1W_TO_MNI_TRANSFORM
+                )
             )
 
         if len(self.subjects):

clinica/pipelines/pet/volume/pipeline.py

@@ -98,10 +98,10 @@ def _build_input_node(self):
             t1_volume_native_tpm_in_mni,
         )
         from clinica.utils.inputs import (
-            _format_errors,
             clinica_file_reader,
             clinica_group_reader,
             clinica_list_of_files_reader,
+            format_clinica_file_reader_errors,
         )
         from clinica.utils.stream import cprint
         from clinica.utils.ux import (
@@ -174,7 +174,7 @@ def _build_input_node(self):
         )
         if flowfields_errors:
             all_errors.append(
-                _format_errors(
+                format_clinica_file_reader_errors(
                     flowfields_errors,
                     t1_volume_deformation_to_template(self.parameters["group_label"]),
                 )

clinica/pipelines/pet_surface/pet_surface_pipeline.py

@@ -78,9 +78,9 @@ def _build_input_node_longitudinal(self):
         )
         from clinica.utils.exceptions import ClinicaException
         from clinica.utils.inputs import (
-            _format_errors,
             clinica_file_reader,
             clinica_list_of_files_reader,
+            format_clinica_file_reader_errors,
         )
 
         read_parameters_node = npe.Node(
@@ -100,7 +100,7 @@ def _build_input_node_longitudinal(self):
             self._get_pet_scans_query(),
         )
         if pet_errors:
-            all_errors.append(_format_errors(pet_errors))
+            all_errors.append(format_clinica_file_reader_errors(pet_errors))
 
         try:
             (
@@ -170,9 +170,9 @@ def _build_input_node_cross_sectional(self):
         )
         from clinica.utils.exceptions import ClinicaException
         from clinica.utils.inputs import (
-            _format_errors,
             clinica_file_reader,
             clinica_list_of_files_reader,
+            format_clinica_file_reader_errors,
         )
 
         read_parameters_node = npe.Node(
@@ -191,7 +191,7 @@ def _build_input_node_cross_sectional(self):
             self._get_pet_scans_query(),
         )
         if pet_errors:
-            all_errors.append(_format_errors(pet_errors))
+            all_errors.append(format_clinica_file_reader_errors(pet_errors))
 
         try:
             (

clinica/pipelines/t1_volume_dartel2mni/t1_volume_dartel2mni_pipeline.py

@@ -58,10 +58,10 @@ def _build_input_node(self):
             t1_volume_native_tpm,
         )
         from clinica.utils.inputs import (
-            _format_errors,
             clinica_file_reader,
             clinica_group_reader,
             clinica_list_of_files_reader,
+            format_clinica_file_reader_errors,
         )
         from clinica.utils.stream import cprint
         from clinica.utils.ux import (
@@ -117,7 +117,7 @@ def _build_input_node(self):
             t1_volume_deformation_to_template(self.parameters["group_label"]),
         )
         if flowfield_errors:
-            all_errors.append(_format_errors(flowfield_errors))
+            all_errors.append(format_clinica_file_reader_errors(flowfield_errors))
 
         # Dartel Template
         # ================

clinica/utils/inputs.py

@@ -271,18 +271,17 @@ def check_caps_folder(caps_directory: Union[str, os.PathLike]) -> None:
         raise ClinicaCAPSError(error_string)
 
 
-def find_sub_ses_pattern_path(
+def find_images_path(
     input_directory: os.PathLike,
     subject: str,
     session: str,
-    error_encountered: list,
-    results: list,
+    errors: List[InvalidSubjectSession],
+    valid_paths: List[str],
     is_bids: bool,
     pattern: str,
 ) -> None:
-    """Appends the output path corresponding to subject, session and pattern in results.
-
-    If an error is encountered, its (subject,session) couple is added to the list `errors_encountered`.
+    """Appends the resulting path corresponding to subject, session and pattern in valid_paths.
+    If an error is encountered, its (subject,session) couple is added to the list `errors`.
 
     Parameters
     ----------
@@ -301,10 +300,10 @@ def find_sub_ses_pattern_path(
     session : str
         Name given to the folder of a session (ex: ses-M00).
 
-    error_encountered : List
+    errors : List
         List to which errors encountered in this function are added.
 
-    results : List
+    valid_paths : List
         List to which the output path corresponding to subject, session
         and pattern is added.
 
@@ -344,14 +343,14 @@ def find_sub_ses_pattern_path(
                 f"Clinica will proceed with the latest run available, that is \n\n-{selected}.",
                 lvl="warning",
             )
-            results.append(selected)
+            valid_paths.append(selected)
         else:
-            error_encountered += [InvalidSubjectSession(subject, session)]
+            errors.append(InvalidSubjectSession(subject, session))
     elif len(current_glob_found) == 0:
-        error_encountered += [InvalidSubjectSession(subject, session)]
+        errors.append(InvalidSubjectSession(subject, session))
     # Otherwise the file found is added to the result
     else:
-        results.append(current_glob_found[0])
+        valid_paths.append(current_glob_found[0])
 
 
 def _are_multiple_runs(files: List[str]) -> bool:
@@ -572,21 +571,23 @@ def clinica_file_filter(
     sessions: List[str],
     input_directory: Path,
     information: Dict,
-    n_procs: Optional[int] = 1,
+    n_procs: int = 1,
 ) -> Tuple[List[str], List[str], List[str]]:
     from clinica.utils.stream import cprint
 
     files, errors = clinica_file_reader(
         subjects, sessions, input_directory, information, n_procs
     )
-    cprint(_format_errors(errors, information), "warning")
+    cprint(format_clinica_file_reader_errors(errors, information), "warning")
     filtered_subjects, filtered_sessions = _remove_sub_ses_from_list(
         subjects, sessions, errors
     )
     return files, filtered_subjects, filtered_sessions
 
 
-def _format_errors(errors: Iterable[InvalidSubjectSession], information: Dict) -> str:
+def format_clinica_file_reader_errors(
+    errors: Iterable[InvalidSubjectSession], information: Dict
+) -> str:
     message = (
         f"Clinica encountered {len(errors)} "
         f"problem(s) while getting {information['description']}:\n"
@@ -606,34 +607,34 @@ def _format_errors(errors: Iterable[InvalidSubjectSession], information: Dict) -
 
 
 def _remove_sub_ses_from_list(
-    list_subjects: List[str],
-    list_sessions: List[str],
-    wrong_sub_ses: Iterable[InvalidSubjectSession],
+    subjects: List[str],
+    sessions: List[str],
+    errors: Iterable[InvalidSubjectSession],
 ) -> Tuple[List[str], List[str]]:
-    list_subjects = list_subjects.copy()
-    list_sessions = list_sessions.copy()
-    for invalid in wrong_sub_ses:
+    subjects = subjects.copy()
+    sessions = sessions.copy()
+    for invalid in errors:
         sub_indexes = [
-            i for i, subject in enumerate(list_subjects) if subject == invalid.subject
+            i for i, subject in enumerate(subjects) if subject == invalid.subject
         ]
         session_indexes = [
-            i for i, session in enumerate(list_sessions) if session == invalid.session
+            i for i, session in enumerate(sessions) if session == invalid.session
         ]
         to_remove = list(set(sub_indexes) & set(session_indexes))
         to_remove.sort(reverse=True)
         for index in to_remove:
-            list_subjects.pop(index)
-            list_sessions.pop(index)
-    return list_subjects, list_sessions
+            subjects.pop(index)
+            sessions.pop(index)
+    return subjects, sessions
 
 
 # todo : generalize
 def clinica_file_reader(
-    subjects: List[str],
-    sessions: List[str],
+    subjects: Iterable[str],
+    sessions: Iterable[str],
     input_directory: os.PathLike,
     information: Dict,
-    n_procs: Optional[int] = 1,
+    n_procs: int = 1,
 ) -> Tuple[List[str], List[InvalidSubjectSession]]:
     """Read files in BIDS or CAPS directory based on participant ID(s).
 
@@ -778,8 +779,8 @@ def clinica_file_reader(
 
 def _read_files_parallel(
     input_directory: os.PathLike,
-    subjects: List[str],
-    sessions: List[str],
+    subjects: Iterable[str],
+    sessions: Iterable[str],
     is_bids: bool,
     pattern: str,
     n_procs: int,
@@ -792,7 +793,7 @@ def _read_files_parallel(
     shared_results = manager.list()
     shared_errors_encountered = manager.list()
     Parallel(n_jobs=n_procs)(
-        delayed(find_sub_ses_pattern_path)(
+        delayed(find_images_path)(
             input_directory,
             sub,
             ses,
@@ -804,23 +805,21 @@ def _read_files_parallel(
         for sub, ses in zip(subjects, sessions)
     )
     results = list(shared_results)
-    errors_encountered = list(
-        shared_errors_encountered
-    )  # todo : "list" needed ? to test
+    errors_encountered = list(shared_errors_encountered)
     return results, errors_encountered
 
 
 def _read_files_sequential(
     input_directory: os.PathLike,
-    subjects: List[str],
-    sessions: List[str],
+    subjects: Iterable[str],
+    sessions: Iterable[str],
     is_bids: bool,
     pattern: str,
     **kwargs,
 ) -> Tuple[List[str], List[InvalidSubjectSession]]:
     errors_encountered, results = [], []
     for sub, ses in zip(subjects, sessions):
-        find_sub_ses_pattern_path(
+        find_images_path(
             input_directory, sub, ses, errors_encountered, results, is_bids, pattern
         )
     return results, errors_encountered
@@ -879,7 +878,7 @@ def clinica_list_of_files_reader(
     if any(all_errors) and raise_exception:
         error_message = "Clinica faced error(s) while trying to read files in your BIDS or CAPS directory.\n"
         for error, info in zip(all_errors, list_information):
-            error_message += _format_errors(error, info)
+            error_message += format_clinica_file_reader_errors(error, info)
         raise ClinicaBIDSError(error_message)
 
     return list_found_files