GENFI to BIDS converter

clinica/iotools/bids_utils.py

@@ -906,6 +906,80 @@ def run_dcm2niix(
         )
 
 
+def identify_modality(filename: str) -> Optional[str]:
+    """Identifies the modality of a file given its name.
+
+    Parameters
+    ----------
+    filename: str
+        Input filename
+
+    Returns
+    -------
+    Optional[str]:
+        Modality or None if parsing uns
+    """
+    filename = filename.lower()
+    if "dwi" in filename:
+        return "dwi"
+    if "t1" in filename:
+        return "T1"
+    if "t2" in filename:
+        return "T2w"
+    if "fieldmap" in filename:
+        return "fieldmap"
+    if "fmri" in filename:
+        return "rsfmri"
+    else:
+        return None
+
+
+def parse_description(filepath: PathLike, start_line: int, end_line: int) -> str:
+    """Parse the description of the dataset from the readme in the documentation.
+
+    Parameters
+    ----------
+    filepath : PathLike
+        Path to the readme file from which to extract the description.
+
+    start_line : int
+        Line number where the description starts.
+
+    end_line : int
+        Line number where the description ends.
+
+    Returns
+    -------
+    str :
+        The description extracted from the readme file.
+    """
+    with open(filepath, "r") as fp:
+        txt = fp.readlines()
+    return "\n".join(txt[start_line:end_line])
+
+
+def parse_url(filepath: PathLike) -> List[str]:
+    """Parse the URLs from the readme in the documentation.
+
+    Parameters
+    ----------
+    filepath : PathLike
+        Path to the readme file from which to extract the URLs.
+
+    Returns
+    -------
+    List[str] :
+        The list of found URLs.
+    """
+    import re
+
+    with open(filepath, "r") as fp:
+        txt = fp.readlines()
+    txt = "".join(txt)
+    url_extract_pattern = "https?:\\/\\/(?:www\\.)?[-a-zA-Z0-9@:%._\\+~#=]{1,256}\\.[a-zA-Z0-9()]{1,6}\\b(?:[-a-zA-Z0-9()@:%_\\+.~#?&\\/=]*)"
+    return re.findall(url_extract_pattern, txt)
+
+
 def write_to_tsv(df: DataFrame, buffer: Union[PathLike, BinaryIO]) -> None:
     """Save dataframe as a BIDS-compliant TSV file.
 

clinica/iotools/converters/cli.py

@@ -2,6 +2,7 @@
 
 from .adni_to_bids import adni_to_bids_cli
 from .aibl_to_bids import aibl_to_bids_cli
+from .genfi_to_bids import genfi_to_bids_cli
 from .habs_to_bids import habs_to_bids_cli
 from .nifd_to_bids import nifd_to_bids_cli
 from .oasis3_to_bids import oasis3_to_bids_cli
@@ -22,6 +23,7 @@ def cli() -> None:
 cli.add_command(oasis_to_bids_cli.cli)
 cli.add_command(oasis3_to_bids_cli.cli)
 cli.add_command(ukb_to_bids_cli.cli)
+cli.add_command(genfi_to_bids_cli.cli)
 
 if __name__ == "__main__":
     cli()

clinica/iotools/converters/genfi_to_bids/genfi_to_bids.py

@@ -0,0 +1,95 @@
+"""Convert the GENFI dataset into BIDS."""
+
+from os import PathLike
+from typing import Optional
+
+
+def convert_images(
+    path_to_dataset: PathLike,
+    bids_dir: PathLike,
+    path_to_clinical: Optional[PathLike],
+    gif: bool,
+) -> None:
+    """Convert the entire dataset to BIDS.
+
+    Scans available files in the path_to_dataset,
+    identifies the patients that have images described by the JSON file,
+    converts the image with the highest quality for each category.
+
+    Parameters
+    ----------
+    path_to_dataset: PathLike
+        Path to the raw images
+
+    bids_dir: PathLike
+        Path to directory where the bids will be written
+
+    path_to_clinical: PathLike, optional
+        Path to the clinical data associated with the dataset.
+        If None, the clinical data won't be converted.
+
+    gif: bool
+        If True, indicates the user wants to have the values of the gif parcellation
+    """
+    import os
+
+    import clinica.iotools.bids_utils as bids
+
+    from .genfi_to_bids_utils import (
+        complete_clinical_data,
+        dataset_to_bids,
+        find_clinical_data,
+        intersect_data,
+        merge_imaging_data,
+        read_imaging_data,
+        write_bids,
+    )
+
+    # read the clinical data files
+    if path_to_clinical:
+        df_demographics, df_imaging, df_clinical = find_clinical_data(path_to_clinical)
+    # makes a df of the imaging data
+    imaging_data = read_imaging_data(path_to_dataset)
+
+    # complete the data extracted
+    imaging_data = merge_imaging_data(imaging_data)
+
+    # complete clinical data
+    if path_to_clinical:
+        df_clinical_complete = complete_clinical_data(
+            df_demographics, df_imaging, df_clinical
+        )
+
+    # intersect the data
+    if path_to_clinical:
+        df_complete = intersect_data(imaging_data, df_clinical_complete)
+    else:
+        df_complete = imaging_data
+    # build the tsv
+    results = dataset_to_bids(df_complete, gif)
+
+    write_bids(
+        to=bids_dir,
+        participants=results["participants"],
+        sessions=results["sessions"],
+        scans=results["scans"],
+    )
+    # fetch data for readme from markdown
+    readme_path = os.path.join(
+        os.path.dirname(
+            os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(__file__))))
+        ),
+        "docs",
+        "Converters",
+        "GENFItoBIDS.md",
+    )
+    try:
+        readme_data = {
+            "link": bids.parse_url(readme_path)[0],
+            "desc": bids.parse_description(readme_path, 4, 5),
+        }
+    except IndexError:
+        raise ValueError("Could not parse information for dataset.")
+    bids.write_modality_agnostic_files(
+        study_name="GENFI", readme_data=readme_data, bids_dir=bids_dir
+    )

clinica/iotools/converters/genfi_to_bids/genfi_to_bids_cli.py

@@ -0,0 +1,49 @@
+from os import PathLike
+from typing import Optional
+
+import click
+
+from clinica.iotools.converters import cli_param
+
+clinical_data_directory = click.option(
+    "-cdd",
+    "--clinical-data-dir",
+    "clinical_data_directory",
+    type=click.Path(exists=True, file_okay=False, resolve_path=True),
+    help="Path to the clinical data directory",
+)
+
+gif = click.option("-gif", is_flag=True, help="Add values from gif to session.tsv")
+
+
+@click.command(name="genfi-to-bids")
+@cli_param.dataset_directory
+@cli_param.bids_directory
+@clinical_data_directory
+@gif
+def cli(
+    dataset_directory: PathLike,
+    bids_directory: PathLike,
+    clinical_data_directory: Optional[PathLike] = None,
+    gif: bool = False,
+) -> None:
+    """GENFI to BIDS converter.
+
+    Convert the imaging and clinical data of GENFI, located in DATASET_DIRECTORY and
+    CLINICAL_DATA_DIRECTORY respectively, to a BIDS dataset in the target BIDS_DIRECTORY.
+    """
+    from clinica.iotools.bids_utils import _write_bidsignore
+    from clinica.iotools.converters.genfi_to_bids.genfi_to_bids import convert_images
+    from clinica.utils.check_dependency import check_dcm2niix
+    from clinica.utils.stream import cprint
+
+    check_dcm2niix()
+
+    convert_images(dataset_directory, bids_directory, clinical_data_directory, gif)
+    _write_bidsignore(str(bids_directory))
+
+    cprint("Conversion to BIDS succeeded.")
+
+
+if __name__ == "__main__":
+    cli()