change API

clinica/iotools/converters/adni_to_bids/adni_to_bids.py

@@ -208,20 +208,15 @@ def convert_images(
         import clinica.iotools.converters.adni_to_bids.adni_modalities.adni_pib_pet as adni_pib
         import clinica.iotools.converters.adni_to_bids.adni_modalities.adni_t1 as adni_t1
         import clinica.iotools.converters.adni_to_bids.adni_modalities.adni_tau_pet as adni_tau
-        from clinica.iotools.converters.adni_to_bids.adni_utils import (
-            check_subjects_list,
-            define_subjects_list,
-        )
+        from clinica.iotools.converters.adni_to_bids.adni_utils import get_subjects_list
         from clinica.utils.stream import cprint
 
         modalities = modalities or self.get_modalities_supported()
 
         if subjs_list_path:
             subjs_list_path = Path(subjs_list_path)
 
-        subjs_list = check_subjects_list(
-            define_subjects_list(Path(source_dir), subjs_list_path), clinical_dir
-        )
+        subjs_list = get_subjects_list(Path(source_dir), subjs_list_path, clinical_dir)
 
         # Create the output folder if is not already existing
         os.makedirs(dest_dir, exist_ok=True)

clinica/iotools/converters/adni_to_bids/adni_utils.py

@@ -29,7 +29,7 @@ def from_string(cls, study_name: str):
         )
 
 
-def define_subjects_list(
+def _define_subjects_list(
     source_dir: Path,
     subjs_list_path: Optional[Path] = None,
 ) -> List[str]:
@@ -47,16 +47,16 @@ def define_subjects_list(
     return list(filter(rgx.fullmatch, [folder.name for folder in source_dir.iterdir()]))
 
 
-def check_subjects_list(
+def _check_subjects_list(
     subjs_list: List[str],
-    clinical_dir: str,
+    clinical_dir: Path,
 ) -> List[str]:
     from copy import copy
 
     from clinica.utils.stream import cprint
 
     subjs_list_copy = copy(subjs_list)
-    adni_merge = load_clinical_csv(clinical_dir, "ADNIMERGE")
+    adni_merge = load_clinical_csv(str(clinical_dir), "ADNIMERGE")
     # Check that there are no errors in subjs_list given by the user
     for subj in subjs_list_copy:
         adnimerge_subj = adni_merge[adni_merge.PTID == subj]
@@ -75,6 +75,16 @@ def check_subjects_list(
     return subjs_list
 
 
+def get_subjects_list(
+    source_dir: Path,
+    clinical_dir: Path,
+    subjs_list_path: Optional[Path] = None,
+) -> List[str]:
+    return _check_subjects_list(
+        _define_subjects_list(source_dir, subjs_list_path), clinical_dir
+    )
+
+
 def visits_to_timepoints(
     subject,
     mri_list_subj,

test/unittests/iotools/converters/adni_to_bids/test_adni_utils.py

@@ -16,27 +16,27 @@
     ],
 )
 def test_define_subjects_list_directory(tmp_path, input, expected):
-    from clinica.iotools.converters.adni_to_bids.adni_utils import define_subjects_list
+    from clinica.iotools.converters.adni_to_bids.adni_utils import _define_subjects_list
 
     source_dir = tmp_path / "source_dir"
     source_dir.mkdir()
 
     for subject in input:
         (source_dir / subject).touch()
 
-    assert set(define_subjects_list(source_dir)) == expected
+    assert set(_define_subjects_list(source_dir)) == expected
 
 
 def test_define_subjects_list_txt(tmp_path):
-    from clinica.iotools.converters.adni_to_bids.adni_utils import define_subjects_list
+    from clinica.iotools.converters.adni_to_bids.adni_utils import _define_subjects_list
 
     source_dir = tmp_path / "source_dir"
     subjs_list_path = tmp_path / "subjects_list.txt"
     input = {"001_S_0001", "001_S_00022", "001S0003"}
     with open(subjs_list_path, "w") as f:
         f.write("\n".join(input))
 
-    assert set(define_subjects_list(source_dir, subjs_list_path)) == input
+    assert set(_define_subjects_list(source_dir, subjs_list_path)) == input
 
 
 @pytest.mark.parametrize(
@@ -47,7 +47,7 @@ def test_define_subjects_list_txt(tmp_path):
     ],
 )
 def test_check_subjects_list(tmp_path, write_all, input, expected):
-    from clinica.iotools.converters.adni_to_bids.adni_utils import check_subjects_list
+    from clinica.iotools.converters.adni_to_bids.adni_utils import _check_subjects_list
 
     clinical_dir = tmp_path / "clinical_dir"
     clinical_dir.mkdir()
@@ -58,7 +58,7 @@ def test_check_subjects_list(tmp_path, write_all, input, expected):
     adni_df = pd.DataFrame(columns=["PTID"], data=input)
     adni_df.to_csv(clinical_dir / "ADNIMERGE.csv")
 
-    assert set(check_subjects_list(input, str(clinical_dir))) == expected
+    assert set(_check_subjects_list(input, clinical_dir)) == expected
 
 
 @pytest.mark.parametrize(