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Find DICOMs

imgtools.dicom.find_dicoms 

find_dicoms(
    directory: pathlib.Path,
    recursive: bool,
    check_header: bool,
    extension: typing.Optional[str] = None,
    limit: typing.Optional[int] = None,
    search_input: typing.Optional[typing.List[str]] = None,
) -> typing.List[pathlib.Path]

Locate DICOM files in a specified directory.

This function scans a directory for files matching the specified extension and validates them as DICOM files based on the provided options. It supports recursive search and optional header validation to confirm file validity.

Parameters:

Name Type Description Default

directory

pathlib.Path

The directory in which to search for DICOM files.

 required

recursive

bool

Whether to include subdirectories in the search

 required

check_header

bool

Whether to validate files by checking for a valid DICOM header. - If True, perform DICOM header validation (slower but more accurate). - If False, skip header validation and rely on extension.

 required

extension

str

File extension to search for (e.g., "dcm"). If None, consider all files regardless of extension.

 None

limit

int

Maximum number of DICOM files to return. If None, return all found files.

 None

Returns:

Type Description
typing.List[pathlib.Path]

A list of valid DICOM file paths found in the directory.
Notes
  • If check_header is enabled, the function checks each file for a valid DICOM header, which may slow down the search process.

Examples:

Setup

>>> from pathlib import (
...     Path,
... )
>>> from imgtools.dicom.utils import (
...     find_dicoms,
... )

Find DICOM files recursively without header validation:

>>> find_dicoms(
...     Path("/data"),
...     recursive=True,
...     check_header=False,
... )
[PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm'), PosixPath('/data/subdir/scan3.dcm')]

Suppose that scan3.dcm is not a valid DICOM file. Find DICOM files with header validation:

>>> find_dicoms(
...     Path("/data"),
...     recursive=True,
...     check_header=True,
... )
[PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]

Find DICOM files without recursion:

>>> find_dicoms(
...     Path("/data"),
...     recursive=False,
...     check_header=False,
... )
[PosixPath('/data/scan1.dcm')]

Find DICOM files with a specific extension:

>>> find_dicoms(
...     Path("/data"),
...     recursive=True,
...     check_header=False,
...     extension="dcm",
... )
[PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]

Find DICOM files with a search input:

>>> find_dicoms(
...     Path("/data"),
...     recursive=True,
...     check_header=False,
...     search_input=[
...         "scan1",
...         "scan2",
...     ],
... )
[PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]

Find DICOM files with a limit:

>>> find_dicoms(
...     Path("/data"),
...     recursive=True,
...     check_header=False,
...     limit=1,
... )
[PosixPath('/data/scan1.dcm')]

Find DICOM files with all options:

>>> find_dicoms(
...     Path("/data"),
...     recursive=True,
...     check_header=True,
...     extension="dcm",
...     limit=2,
...     search_input=["scan"],
... )
[PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]
Source code in src/imgtools/dicom/utils.py 
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def find_dicoms(
    directory: Path,
    recursive: bool,
    check_header: bool,
    extension: Optional[str] = None,
    limit: Optional[int] = None,
    search_input: Optional[List[str]] = None,
) -> List[Path]:
    """Locate DICOM files in a specified directory.

    This function scans a directory for files matching the specified extension
    and validates them as DICOM files based on the provided options. It supports
    recursive search and optional header validation to confirm file validity.

    Parameters
    ----------
    directory : Path
        The directory in which to search for DICOM files.
    recursive : bool
        Whether to include subdirectories in the search
    check_header : bool
        Whether to validate files by checking for a valid DICOM header.
            - If `True`, perform DICOM header validation (slower but more accurate).
            - If `False`, skip header validation and rely on extension.

    extension : str, optional
        File extension to search for (e.g., "dcm"). If `None`, consider all files
        regardless of extension.

    limit : int, optional
        Maximum number of DICOM files to return. If `None`, return all found files.

    Returns
    -------
    List[Path]
        A list of valid DICOM file paths found in the directory.

    Notes
    -----
    - If `check_header` is enabled, the function checks each file for a valid
        DICOM header, which may slow down the search process.

    Examples
    --------
    Setup

    >>> from pathlib import (
    ...     Path,
    ... )
    >>> from imgtools.dicom.utils import (
    ...     find_dicoms,
    ... )

    Find DICOM files recursively without header validation:

    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=True,
    ...     check_header=False,
    ... )
    [PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm'), PosixPath('/data/subdir/scan3.dcm')]

    Suppose that `scan3.dcm` is not a valid DICOM file. Find DICOM files with header validation:

    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=True,
    ...     check_header=True,
    ... )
    [PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]

    Find DICOM files without recursion:
    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=False,
    ...     check_header=False,
    ... )
    [PosixPath('/data/scan1.dcm')]

    Find DICOM files with a specific extension:
    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=True,
    ...     check_header=False,
    ...     extension="dcm",
    ... )
    [PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]

    Find DICOM files with a search input:
    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=True,
    ...     check_header=False,
    ...     search_input=[
    ...         "scan1",
    ...         "scan2",
    ...     ],
    ... )
    [PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]

    Find DICOM files with a limit:
    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=True,
    ...     check_header=False,
    ...     limit=1,
    ... )
    [PosixPath('/data/scan1.dcm')]

    Find DICOM files with all options:
    >>> find_dicoms(
    ...     Path("/data"),
    ...     recursive=True,
    ...     check_header=True,
    ...     extension="dcm",
    ...     limit=2,
    ...     search_input=["scan"],
    ... )
    [PosixPath('/data/scan1.dcm'), PosixPath('/data/subdir/scan2.dcm')]
    """
    pattern = f"*.{extension}" if extension else "*"

    glob_method = directory.rglob if recursive else directory.glob

    logger.debug(
        "Looking for DICOM files",
        directory=directory,
        recursive=recursive,
        search_pattern=pattern,
        check_header=check_header,
        limit=limit,
        search_input=search_input,
    )

    files = (
        file.absolute()
        for file in glob_method(pattern)
        if (
            not search_input
            or all(term in str(file.as_posix()) for term in search_input)
        )
        and _is_valid_dicom(file, check_header)
    )

    return list(islice(files, limit)) if limit else list(files)