Testing - 2811

clinica/iotools/bids_utils.py

@@ -557,7 +557,6 @@ def write_modality_agnostic_files(
     _write_bidsignore(bids_dir)
 
 
-# todo : test + open issue for usability across converters (though may not be useful if json from dicom)
 def _get_pet_tracer_from_filename(filename: str) -> Tracer:
     """Return the PET tracer from the provided filename.
 

clinica/iotools/converters/aibl_to_bids/utils/clinical.py

@@ -512,12 +512,13 @@ def write_scans_tsv(bids_dir: Path, scans_dict: dict) -> None:
 
     supported_modalities = ("anat", "dwi", "func", "pet")
 
+    # todo : what happens now is if it is not a recognized modality it will still write something... not worth it
+
     for sub in scans_dict.keys():
         for session in scans_dict[sub].keys():
             scans_df = pd.DataFrame()
             tsv_file = bids_dir / sub / session / f"{sub}_{session}_scans.tsv"
             tsv_file.unlink(missing_ok=True)
-
             for mod in (bids_dir / sub / session).glob("*"):
                 if mod.name in supported_modalities:
                     for file in [

test/unittests/iotools/test_bids_utils.py

@@ -8,10 +8,12 @@
 
 from clinica.iotools.bids_utils import (
     StudyName,
+    _get_pet_tracer_from_filename,
     _write_bids_validator_config,
     _write_bidsignore,
     _write_readme,
 )
+from clinica.utils.pet import Tracer
 
 MODALITY_AGNOSTIC_FILE_WRITERS = {
     #    "readme": _write_readme,
@@ -41,6 +43,37 @@
 )
 
 
+@pytest.mark.parametrize(
+    "filename, expected",
+    [
+        ("sub-1_ses-1_trc-18FFDG_pet.nii.gz", Tracer.FDG),
+        ("sub-1_ses-1_acq-18FFDG_pet.nii.gz", Tracer.FDG),
+        ("sub-1_ses-1_trc-18FFDG_acq-18FFDG_pet.nii.gz", Tracer.FDG),
+        ("sub-1_ses-1_trc-11CPIB_pet.nii.gz", Tracer.PIB),
+        ("sub-1_ses-1_trc-18FFBB_pet.nii.gz", Tracer.FBB),
+        ("sub-1_ses-1_trc-18FFMM_pet.nii.gz", Tracer.FMM),
+        ("sub-1_ses-1_trc-18FAV1451_pet.nii.gz", Tracer.AV1451),
+        ("sub-1_ses-1_trc-18FAV45_pet.nii.gz", Tracer.AV45),
+    ],
+)
+def test_get_pet_tracer_from_filename_success(filename, expected):
+    assert expected == _get_pet_tracer_from_filename(filename)
+
+
+@pytest.mark.parametrize(
+    "filename",
+    [
+        "sub-1_ses-1_trc18FFDG_pet.nii.gz",
+        "sub-1_ses-1_trc-///_pet.nii.gz",
+        "sub-1_ses-1_trc-foo_pet.nii.gz",
+        "sub-1_ses-1_pet.nii.gz",
+    ],
+)
+def test_get_pet_tracer_from_filename_error(filename):
+    with pytest.raises(ValueError):
+        _get_pet_tracer_from_filename(filename)
+
+
 @pytest.mark.parametrize(
     "study,study_id,expected",
     [