[CI] OASIS-to-BIDS : Add option --subjects-list and its functionality for oasis-to-bids converter

clinica/converters/_utils.py

@@ -22,6 +22,7 @@
     "validate_input_path",
     "viscode_to_session",
     "load_clinical_csv",
+    "get_subjects_list_from_file",
 ]
 
 
@@ -571,3 +572,19 @@ def load_clinical_csv(clinical_dir: Path, filename: str) -> pd.DataFrame:
             f"File {str(files_matching_pattern[0])} was found but could not "
             "be loaded as a DataFrame. Please check your data."
         )
+
+
+def get_subjects_list_from_file(subjects_list_path: Path) -> list[str]:
+    """Gets the list of subjects from a subjects list file.
+
+    Parameters
+    ----------
+    subjects_list_path : Path
+        The path to the subjects list file.
+
+    Returns
+    -------
+    list[str] :
+        List of subjects.
+    """
+    return subjects_list_path.read_text().splitlines()

clinica/converters/ixi_to_bids/_utils.py

@@ -41,10 +41,6 @@ def _get_subjects_list_from_data(data_directory: Path) -> List[str]:
     )
 
 
-def _get_subjects_list_from_file(subjs_list_path: Path) -> List[str]:
-    return subjs_list_path.read_text().splitlines()
-
-
 def define_participants(
     data_directory: Path,
     subjs_list_path: Optional[Path] = None,
@@ -65,11 +61,13 @@ def define_participants(
 
     """
 
+    from .._utils import get_subjects_list_from_file
+
     list_from_data = _get_subjects_list_from_data(data_directory)
     if subjs_list_path is None:
         return sorted(list_from_data)
     cprint("Loading a subjects list provided by the user...")
-    list_from_file = _get_subjects_list_from_file(subjs_list_path)
+    list_from_file = get_subjects_list_from_file(subjs_list_path)
     list_filtered = [subject for subject in list_from_file if subject in list_from_data]
     invalid_subjects = list(set(list_from_file) - set(list_filtered))
     if invalid_subjects:

clinica/converters/oasis_to_bids/_converter.py

@@ -30,17 +30,13 @@ def convert(
     bids_dir = validate_input_path(bids_dir, check_exist=False)
     path_to_clinical = validate_input_path(path_to_clinical)
     if subjects:
-        cprint(
-            (
-                f"Subject filtering is not yet implemented in {get_converter_name(StudyName.OASIS)} converter. "
-                "All subjects available will be converted."
-            ),
-            lvl="warning",
-        )
+        subjects = validate_input_path(subjects)
+
     OasisToBids().convert(
         path_to_dataset,
         bids_dir,
         path_to_clinical,
+        subjects=subjects,
         n_procs=n_procs,
     )
 
@@ -51,10 +47,13 @@ def convert(
         source_dir: Path,
         destination_dir: Path,
         clinical_data_dir: Path,
+        subjects: Optional[Path] = None,
         n_procs: Optional[int] = 1,
     ):
         self._create_modality_agnostic_files(destination_dir)
-        self.convert_images(source_dir, destination_dir, n_procs=n_procs)
+        self.convert_images(
+            source_dir, destination_dir, subjects=subjects, n_procs=n_procs
+        )
         self.convert_clinical_data(clinical_data_dir, destination_dir)
 
     def convert_clinical_data(self, clinical_data_dir: Path, bids_dir: Path):
@@ -183,7 +182,11 @@ def convert_single_subject(subj_folder: Path, dest_dir: Path):
         )
 
     def convert_images(
-        self, source_dir: Path, dest_dir: Path, n_procs: Optional[int] = 1
+        self,
+        source_dir: Path,
+        dest_dir: Path,
+        subjects: Optional[Path] = None,
+        n_procs: Optional[int] = 1,
     ):
         """Convert T1w images to BIDS.
 
@@ -193,6 +196,8 @@ def convert_images(
 
         dest_dir: path to the BIDS directory
 
+        subjects: path to list of subjects to process
+
         n_procs : int, optional
             The requested number of processes.
             If specified, it should be between 1 and the number of available CPUs.
@@ -206,14 +211,13 @@ def convert_images(
         from functools import partial
         from multiprocessing import Pool
 
+        from ._utils import get_subjects_list
+
         if not dest_dir.exists():
             dest_dir.mkdir(parents=True)
 
-        subjects_folders = [
-            path
-            for path in source_dir.rglob("OAS1_*")
-            if path.is_dir() and path.name.endswith("_MR1")
-        ]
+        subjects_folders = get_subjects_list(source_dir, subjects)
+
         func = partial(self.convert_single_subject, dest_dir=dest_dir)
         # If n_procs==1 do not rely on a Process Pool to enable classical debugging
         if n_procs == 1:

clinica/converters/oasis_to_bids/_utils.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Iterable, Union
+from typing import Iterable, Optional, Union
 
 import nibabel as nb
 import numpy as np
@@ -8,6 +8,7 @@
 from clinica.converters.study_models import StudyName, bids_id_factory
 
 __all__ = [
+    "get_subjects_list",
     "create_sessions_df",
     "write_sessions_tsv",
     "write_scans_tsv",
@@ -16,6 +17,61 @@
 ]
 
 
+def _get_subjects_list_from_data(source_dir: Path) -> list[str]:
+    return [
+        folder.name
+        for folder in source_dir.iterdir()
+        if not folder.name.startswith(".")
+    ]
+
+
+def _filter_oasis_subjects(source_dir: Path, subjects_list: list[str]) -> list[Path]:
+    import re
+
+    rgx = re.compile(r"OAS1_\d{4}_MR1")
+
+    return list(
+        filter(
+            lambda path: path.is_dir(),
+            [
+                source_dir / subj
+                for subj in filter(
+                    rgx.fullmatch,
+                    subjects_list,
+                )
+            ],
+        )
+    )
+
+
+def get_subjects_list(
+    source_dir: Path, subjs_list_path: Optional[Path] = None
+) -> list[Path]:
+    """Gets the list of paths to the subjects folders.
+
+    Parameters
+    ----------
+    source_dir : Path
+        The path to the input dataset folder.
+
+    subjs_list_path : Optional[Path]
+        The path to the subjects list file.
+
+    Returns
+    -------
+    list[Path] :
+        List of paths to the subjects folders.
+    """
+    from .._utils import get_subjects_list_from_file
+
+    if subjs_list_path:
+        return _filter_oasis_subjects(
+            source_dir, get_subjects_list_from_file(subjs_list_path)
+        )
+
+    return _filter_oasis_subjects(source_dir, _get_subjects_list_from_data(source_dir))
+
+
 def _convert_cdr_to_diagnosis(cdr: Union[int, str]) -> str:
     if cdr == 0:
         return "CN"

clinica/converters/oasis_to_bids/cli.py

@@ -1,3 +1,4 @@
+from pathlib import Path
 from typing import Optional
 
 import click
@@ -10,12 +11,14 @@
 @cli_param.dataset_directory
 @cli_param.clinical_data_directory
 @cli_param.bids_directory
+@cli_param.subjects_list
 @option.global_option_group
 @option.n_procs
 def cli(
     dataset_directory: str,
     clinical_data_directory: str,
     bids_directory: str,
+    subjects_list: Optional[Path] = None,
     n_procs: Optional[int] = None,
 ) -> None:
     """OASIS to BIDS converter.
@@ -30,6 +33,7 @@ def cli(
         dataset_directory,
         bids_directory,
         clinical_data_directory,
+        subjects=subjects_list,
         n_procs=n_procs,
     )
 

test/unittests/converters/test_converter_utils.py

@@ -413,3 +413,15 @@ def test_viscode_to_session_with_custom_baseline_identifiers():
     assert viscode_to_session("foo", baseline_identifiers={"base", "foo"}) == "ses-M000"
     with pytest.raises(ValueError, match="The viscode bl is not correctly formatted."):
         viscode_to_session("bl", baseline_identifiers={"base", "foo"})
+
+
+def test_get_subjects_list_from_file(tmp_path):
+    from clinica.converters._utils import get_subjects_list_from_file
+
+    with open(tmp_path / "subjects.txt", "w") as f:
+        f.write("IXI123\nIXI001")
+
+    assert get_subjects_list_from_file(tmp_path / "subjects.txt") == [
+        "IXI123",
+        "IXI001",
+    ]

test/unittests/converters/test_ixi_to_bids_utils.py

@@ -29,18 +29,6 @@ def test_get_subjects_list_from_data(tmp_path):
     assert _get_subjects_list_from_data(tmp_path) == ["IXI123"]
 
 
-def test_get_subjects_list_from_file(tmp_path):
-    from clinica.converters.ixi_to_bids._utils import _get_subjects_list_from_file
-
-    with open(tmp_path / "subjects.txt", "w") as f:
-        f.write("IXI123\nIXI001")
-
-    assert _get_subjects_list_from_file(tmp_path / "subjects.txt") == [
-        "IXI123",
-        "IXI001",
-    ]
-
-
 def test_define_participants_filter(tmp_path):
     from clinica.converters.ixi_to_bids._utils import define_participants
 

test/unittests/converters/test_oasis_to_bids_utils.py

@@ -244,7 +244,7 @@ def test_write_scans_tsv(tmp_path, bids_dir: Path) -> None:
                 assert file.empty
 
 
-def test_get_first_image(tmp_path: Path) -> None:
+def test_get_first_image(tmp_path) -> None:
     from clinica.converters.oasis_to_bids._utils import get_first_image
 
     folder_path = tmp_path / "folder"
@@ -256,7 +256,7 @@ def test_get_first_image(tmp_path: Path) -> None:
     assert get_first_image(folder_path) == (folder_path / "file_2.img")
 
 
-def test_get_first_image_not_found_error(tmp_path: Path) -> None:
+def test_get_first_image_not_found_error(tmp_path) -> None:
     from clinica.converters.oasis_to_bids._utils import get_first_image
 
     folder_path = tmp_path / "folder"
@@ -270,7 +270,7 @@ def test_get_first_image_not_found_error(tmp_path: Path) -> None:
         get_first_image(folder_path)
 
 
-def test_get_image_with_good_orientation(tmp_path: Path) -> None:
+def test_get_image_with_good_orientation(tmp_path) -> None:
     from clinica.converters.oasis_to_bids._utils import get_image_with_good_orientation
 
     folder_path = tmp_path / "folder"
@@ -310,6 +310,61 @@ def test_get_image_with_good_orientation(tmp_path: Path) -> None:
     assert len(image.shape) == 3  # the image dimension should be 3D
 
 
+def test_get_subjects_list_from_data(tmp_path) -> None:
+    from clinica.converters.oasis_to_bids._utils import get_subjects_list
+
+    source_dir = tmp_path / "dataset"
+    source_dir.mkdir()
+
+    for filename in (
+        "OAS1_0001_MR1",
+        "OAS2_0002_MR1",
+        "OAS1_0003_MR2",
+        "OAS1_004_MR1",
+        "foo",
+    ):
+        (source_dir / filename).mkdir()
+
+    (source_dir / "OAS1_0005_MR1").touch()
+
+    assert get_subjects_list(source_dir) == [source_dir / "OAS1_0001_MR1"]
+
+
+def test_get_subjects_list_from_file(tmp_path) -> None:
+    from clinica.converters.oasis_to_bids._utils import get_subjects_list
+
+    source_dir = tmp_path / "dataset"
+    source_dir.mkdir()
+
+    lines = [
+        "OAS1_0001_MR1\n",
+        "OAS2_0002_MR1\n",
+        "OAS1_0003_MR2\n",
+        "OAS1_004_MR1\n",
+        "foo\n",
+    ]
+
+    for filename in lines:
+        (source_dir / filename[:-1]).mkdir()
+
+    (source_dir / "OAS1_0005_MR1").touch()
+
+    lines.append("OAS1_0005_MR1\n")
+
+    subjects_list_dir = tmp_path / "subjects_list_dir"
+    subjects_list_dir.mkdir()
+
+    subjects_list = subjects_list_dir / "subjects_list.txt"
+    subjects_list.touch()
+
+    with open(str(subjects_list), "a") as file:
+        file.writelines(lines)
+
+    assert get_subjects_list(source_dir, subjects_list) == [
+        source_dir / "OAS1_0001_MR1"
+    ]
+
+
 @pytest.mark.parametrize(
     "cdr,diagnosis",
     [