Identify and preprocess dicom items in Girder

dicom_items.py

#!/usr/bin/env python

import argparse
import girder_client
import girder_client.cli
import os
import re


def get_girder_client(opts):
    """
    Log in to Girder and return a reference to the client.

    :param opts: options that include the username, password, and girder api
        url.
    :returns: the girder client.
    """
    gcopts = {k: v for k, v in opts.iteritems() if k in {
        'username', 'password', 'host', 'port', 'apiRoot', 'scheme', 'apiUrl',
        'apiKey', 'sslVerify'}}
    gcopts['username'] = gcopts.get('username') or None
    gcopts['password'] = gcopts.get('password') or None
    return girder_client.cli.GirderCli(**gcopts)


def check_for_dicom(client, regex='.*', simulate=False, **kwargs):
    """
    Enumerate all items in girder.  For any that match a specified regex, check
    if they have been checked if they are DICOM images.  If not, do so.
    """
    pattern = re.compile(regex, re.IGNORECASE | re.UNICODE)
    limit = 100
    offset = 0
    while True:
        items = client.get('resource/search', parameters={
            'q': '', 'mode': 'prefix', 'types': '["item"]', 'level': 0,
            'limit': limit, 'offset': offset})
        if not len(items) or not len(items.get('item', [])):
            break
        offset += limit
        for item in items['item']:
            if not pattern.search(item['name']):
                continue
            if 'dicom' in item:
                continue
            print('Processing %s' % item['name'])
            if simulate:
                result = 'Simulated -- did nothing'
            else:
                try:
                    client.post('item/%s/parseDicom' % item['_id'])
                    item = client.getItem(item['_id'])
                    result = 'Set to DICOM' if 'dicom' in item else 'Not a DICOM'
                except Exception:
                    result = 'Failed to process'
            print('  %s' % result)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(
        description='Check and mark DICOM files.')
    # Standard girder_client CLI options
    parser.add_argument(
        '--apiurl', '--api-url', '--api', '--url', '-a', dest='apiUrl',
        help='The Girder api url (e.g., http://127.0.0.1:8080/api/v1).')
    parser.add_argument(
        '--apikey', '--api-key', '--key', dest='apiKey',
        default=os.environ.get('GIRDER_API_KEY', None),
        help='An API key, defaults to GIRDER_API_KEY environment variable.')
    parser.add_argument(
        '--username', '--user',
        help='The Girder admin username.  If not specified, a prompt is given.')
    parser.add_argument(
        '--password', '--pass', '--passwd', '--pw',
        help='The Girder admin password.  If not specified, a prompt is given.')
    parser.add_argument('--host', help='The Girder API host.')
    parser.add_argument('--scheme', help='The Girder API scheme.')
    parser.add_argument('--port', type=int, help='The Girder API port.')
    parser.add_argument(
        '--apiroot', '--api-root', '--root', dest='apiRoot',
        help='The Girder API root.')
    parser.add_argument(
        '--no-ssl-verify', action='store_false', dest='sslVerify',
        help='Disable SSL verification.')
    parser.add_argument(
        '--certificate', dest='sslVerify', help='A path to SSL certificate')
    # Generic verbose option
    parser.add_argument('--verbose', '-v', action='count', default=0)
    # This program's options
    parser.add_argument(
        'regex', help='A regex used to check items.  Only items whose names '
        'match will be processed.')
    parser.add_argument(
        '--rename', action='store_true',
        help='Rename DICOM items based on their series number and description')
    parser.add_argument(
        '--simulate', '--dry-run', '-n', action='store_true', dest='simulate',
        help='Report what would be done, but don\'t actually make any changes.')

    args = parser.parse_args()
    if args.verbose >= 2:
        print('Parsed arguments: %r' % args)
    client = get_girder_client(vars(args))
    check_for_dicom(client, **vars(args))
    # if args.rename:
    #     rename_dicom_items(client, vars(args))