[REF] OASIS-to-BIDS create_scans_dict (#1330)

* TODO

* Add new function

* Changes upon suggestions

clinica/iotools/converters/oasis_to_bids/oasis_to_bids.py

@@ -69,8 +69,8 @@ def convert_clinical_data(self, clinical_data_dir: Path, bids_dir: Path):
         cprint("Converting clinical data...", lvl="info")
         bids_ids = get_bids_subjs_list(bids_dir)
         self._create_participants_tsv(clinical_data_dir, bids_dir, bids_ids)
-        sessions = self._create_sessions_tsv(clinical_data_dir, bids_dir, bids_ids)
-        self._create_scans_tsv(clinical_data_dir, bids_dir, bids_ids, sessions)
+        self._create_sessions_tsv(clinical_data_dir, bids_dir, bids_ids)
+        self._create_scans_tsv(bids_dir)
         self._create_modality_agnostic_files(bids_dir)
 
     def _create_participants_tsv(
@@ -107,7 +107,7 @@ def _create_sessions_tsv(
         clinical_data_dir: Path,
         bids_dir: Path,
         bids_ids: list[str],
-    ) -> dict:
+    ) -> None:
         from .oasis_to_bids_utils import create_sessions_dict, write_sessions_tsv
 
         sessions_dict = create_sessions_dict(
@@ -118,31 +118,10 @@ def _create_sessions_tsv(
 
         write_sessions_tsv(bids_dir, sessions_dict)
 
-        return sessions_dict
+    def _create_scans_tsv(self, bids_dir: Path) -> None:
+        from .oasis_to_bids_utils import write_scans_tsv
 
-    def _create_scans_tsv(
-        self,
-        clinical_data_dir: Path,
-        bids_dir: Path,
-        bids_ids: list[str],
-        sessions: dict,
-    ):
-        from clinica.iotools.bids_utils import (
-            StudyName,
-            create_scans_dict,
-            write_scans_tsv,
-        )
-
-        scans_dict = create_scans_dict(
-            clinical_data_dir=clinical_data_dir,
-            study_name=StudyName.OASIS,
-            clinical_specifications_folder=Path(__file__).parents[1] / "specifications",
-            bids_ids=bids_ids,
-            name_column_ids="ID",
-            name_column_ses="",
-            ses_dict=sessions,
-        )
-        write_scans_tsv(bids_dir, bids_ids, scans_dict)
+        write_scans_tsv(bids_dir)
 
     def _create_modality_agnostic_files(self, bids_dir: Path):
         from clinica.iotools.bids_utils import StudyName, write_modality_agnostic_files

clinica/iotools/converters/oasis_to_bids/oasis_to_bids_utils.py

@@ -5,7 +5,7 @@
 
 from clinica.iotools.bids_utils import StudyName, bids_id_factory
 
-__all__ = ["create_sessions_dict", "write_sessions_tsv"]
+__all__ = ["create_sessions_dict", "write_sessions_tsv", "write_scans_tsv"]
 
 
 def create_sessions_dict(
@@ -85,7 +85,6 @@ def write_sessions_tsv(bids_dir: Path, sessions_dict: dict) -> None:
     See also
     --------
     create_sessions_dict
-    write_scans_tsv
     """
     for subject_path in bids_dir.glob("sub-*"):
         if subject_path.name in sessions_dict:
@@ -105,3 +104,29 @@ def write_sessions_tsv(bids_dir: Path, sessions_dict: dict) -> None:
             sep="\t",
             encoding="utf8",
         )
+
+
+def write_scans_tsv(bids_dir: Path) -> None:
+    """
+    Write the scans.tsv file at the root of baseline sessions (ses-M000).
+
+    Parameters
+    ----------
+    bids_dir : Path to the BIDS output
+    """
+    for subject_path in bids_dir.rglob("sub-*"):
+        if subject_path.is_dir():
+            to_write = pd.DataFrame(
+                {
+                    "filename": [
+                        f"{path.parent.name}/{path.name}"
+                        for path in subject_path.rglob("*ses-M000*.nii.gz")
+                    ]
+                }
+            )
+
+            to_write.to_csv(
+                subject_path / "ses-M000" / f"{subject_path.name}_ses-M000_scans.tsv",
+                sep="\t",
+                index=False,
+            )

test/unittests/iotools/converters/oasis_to_bids/test_oasis_to_bids_utils.py

@@ -1,3 +1,4 @@
+from os import write
 from pathlib import Path
 
 import numpy as np
@@ -7,6 +8,7 @@
 
 from clinica.iotools.converters.oasis_to_bids.oasis_to_bids_utils import (
     create_sessions_dict,
+    write_scans_tsv,
     write_sessions_tsv,
 )
 
@@ -179,3 +181,33 @@ def test_write_sessions_tsv(
             check_dtype=False,
         )
         assert file.name == f"{file.parent.name}_sessions.tsv"
+
+
+def test_write_scans_tsv(tmp_path, bids_dir: Path) -> None:
+    image_path = (
+        bids_dir
+        / "sub-OASIS10001"
+        / "ses-M000"
+        / "anat"
+        / "sub-OASIS10001_ses-M000_T1.nii.gz"
+    )
+    image_path.parent.mkdir(parents=True)
+    image_path.touch()
+
+    write_scans_tsv(bids_dir)
+
+    for session_path in bids_dir.rglob("ses-M*"):
+        tsv_path = list(session_path.rglob("*scans.tsv"))
+        if session_path.name != "ses-M000":
+            assert not tsv_path
+        else:
+            assert len(tsv_path) == 1
+            sub = session_path.parent.name
+            assert (
+                tsv_path[0] == bids_dir / sub / "ses-M000" / f"{sub}_ses-M000_scans.tsv"
+            )
+            file = pd.read_csv(tsv_path[0], sep="\t")
+            if sub == "sub-OASIS10001":
+                assert file["filename"].loc[0] == f"anat/{image_path.name}"
+            elif sub == "sub-OASIS10002":
+                assert file.empty