Creates links to DICOM files.

lndicom.py

#!/usr/bin/env python
"""Creates links to DICOM files."""

import sys
import os
import argparse
import dicom
from dicom.filereader import InvalidDicomError


DCM_EXT = '.dcm'
"""The standard DICOM file extension."""


def main(argv=sys.argv):
    # Parse the command line arguments.
    parser = argparse.ArgumentParser()
    parser.add_argument('source', help='the DICOM input directory',
                        metavar='DIR')
    parser.add_argument('dest', help='the destination directory',
                        metavar='DIR')
    args = parser.parse_args()

    # Link the input DICOM files in the destination directory.
    for src_file in dicom_files(args.source):
        # The link name does not have spaces and has a .dcm extension.
        _, src_base = os.path.split(src_file)
        src_root, src_ext = os.path.splitext(src_base)
        tgt_root = src_root.replace(' ', '_')
        tgt_base = tgt_root + DCM_EXT
        tgt_file = os.path.join(args.dest, tgt_base)
        # Link the DICOM file in the destination directory.
        os.symlink(src_file, tgt_file)


def dicom_files(path):
    """
    Recursively iterates over the DICOM files in the given directory.
    
    :param path: the directory containing DICOM files
    :yield: each DICOM file in the directory
    """
    # The full input directory path.
    src_dir = os.path.abspath(path)
    # Iterate over each file with a DICOM header.
    for root, _, files in os.walk(src_dir):
        for f in files:
            # Skip hidden files.
            if f.startswith('.'):
                continue
            # The file path.
            src_file = os.path.join(root, f)
            # If the file has a DICOM header, then we have a
            # winner. Otherwise, ignore the file.
            try:
                # Read only the header.
                dicom.read_file(src_file, defer_size=256,
                                stop_before_pixels=True)
                yield src_file
            except InvalidDicomError:
                pass


if __name__ == '__main__':
    sys.exit(main())