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Find DICOMs

imgtools.dicom.utils.find_dicoms 

find_dicoms(directory: Path, recursive: bool, check_header: bool, extension: Optional[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:

Name Type Description Default

directory

Path

The directory in which to search for DICOM files.

 required

recursive

bool

Whether to include subdirectories in the search.

  • If True, recursively search all subdirectories.
  • If False, search only the specified directory.
 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

Returns:

Type Description
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')]
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,
) -> 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.

	    - If `True`, recursively search all subdirectories.
	    - If `False`, search only the specified directory.
	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.

	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')]
	"""

	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,
	)

	return [file.resolve() for file in glob_method(pattern) if _is_valid_dicom(file, check_header)]