Mercurial > hg > orthanc
view OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 5044:6fed78e13233
Refactored DicomMap to handle sequences when needed
author | Alain Mazy <am@osimis.io> |
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date | Tue, 28 Jun 2022 17:45:09 +0200 |
parents | 17c91e054636 |
children | 0ea402b4d901 |
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#!/usr/bin/env python # Orthanc - A Lightweight, RESTful DICOM Store # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics # Department, University Hospital of Liege, Belgium # Copyright (C) 2017-2022 Osimis S.A., Belgium # Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium # # This program is free software: you can redistribute it and/or # modify it under the terms of the GNU General Public License as # published by the Free Software Foundation, either version 3 of the # License, or (at your option) any later version. # # This program is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see <http://www.gnu.org/licenses/>. import argparse import bz2 import gzip import json import os import requests import sys import tarfile import zipfile from requests.auth import HTTPBasicAuth parser = argparse.ArgumentParser(description = 'Command-line tool to import files or archives into Orthanc.') parser.add_argument('--url', default = 'http://localhost:8042', help = 'URL to the REST API of the Orthanc server') parser.add_argument('--username', default = 'orthanc', help = 'Username to the REST API') parser.add_argument('--password', default = 'orthanc', help = 'Password to the REST API') parser.add_argument('--force', help = 'Do not warn the user about deletion', action = 'store_true') parser.add_argument('--clear', help = 'Remove the content of the Orthanc database', action = 'store_true') parser.add_argument('--verbose', help = 'Be verbose', action = 'store_true') parser.add_argument('--ignore-errors', help = 'Do not stop if encountering non-DICOM files', action = 'store_true') parser.add_argument('files', metavar = 'N', nargs = '*', help = 'Files to import') args = parser.parse_args() if args.clear and not args.force: print(""" WARNING: This script will remove all the content of your Orthanc instance running on %s! Are you sure ["yes" to go on]?""" % args.url) if sys.stdin.readline().strip() != 'yes': print('Aborting...') exit(0) IMPORTED_STUDIES = set() COUNT_ERROR = 0 COUNT_DICOM = 0 COUNT_JSON = 0 def IsJson(content): try: if (sys.version_info >= (3, 0)): json.loads(content.decode()) return True else: json.loads(content) return True except: return False def UploadBuffer(dicom): global IMPORTED_STUDIES global COUNT_ERROR global COUNT_DICOM global COUNT_JSON if IsJson(dicom): COUNT_JSON += 1 return auth = HTTPBasicAuth(args.username, args.password) r = requests.post('%s/instances' % args.url, auth = auth, data = dicom) try: r.raise_for_status() except: COUNT_ERROR += 1 if args.ignore_errors: if args.verbose: print(' not a valid DICOM file, ignoring it') return else: raise info = r.json() COUNT_DICOM += 1 if (isinstance(info, dict) and not info['ParentStudy'] in IMPORTED_STUDIES): IMPORTED_STUDIES.add(info['ParentStudy']) r2 = requests.get('%s/instances/%s/tags?short' % (args.url, info['ID']), auth = auth) r2.raise_for_status() tags = r2.json() print('') print('New imported study:') print(' Orthanc ID of the patient: %s' % info['ParentPatient']) print(' Orthanc ID of the study: %s' % info['ParentStudy']) print(' DICOM Patient ID: %s' % ( tags['0010,0020'] if '0010,0020' in tags else '(empty)')) print(' DICOM Study Instance UID: %s' % ( tags['0020,000d'] if '0020,000d' in tags else '(empty)')) print('') def UploadFile(path): with open(path, 'rb') as f: dicom = f.read() if args.verbose: print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024))) UploadBuffer(dicom) def UploadBzip2(path): with bz2.BZ2File(path, 'rb') as f: dicom = f.read() if args.verbose: print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024))) UploadBuffer(dicom) def UploadGzip(path): with gzip.open(path, 'rb') as f: dicom = f.read() if args.verbose: print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024))) UploadBuffer(dicom) def UploadTar(path, decoder): if args.verbose: print('Uncompressing tar archive: %s' % path) with tarfile.open(path, decoder) as tar: for item in tar: if item.isreg(): f = tar.extractfile(item) dicom = f.read() f.close() if args.verbose: print('Uploading: %s (%dMB)' % (item.name, len(dicom) / (1024 * 1024))) UploadBuffer(dicom) def UploadZip(path): if args.verbose: print('Uncompressing ZIP archive: %s' % path) with zipfile.ZipFile(path, 'r') as zip: for item in zip.infolist(): # WARNING - "item.is_dir()" would be better, but is not available in Python 2.7 if item.file_size > 0: dicom = zip.read(item.filename) if args.verbose: print('Uploading: %s (%dMB)' % (item.filename, len(dicom) / (1024 * 1024))) UploadBuffer(dicom) def DecodeFile(path): extension = os.path.splitext(path) [1] if path.endswith('.tar.bz2'): UploadTar(path, 'r:bz2') elif path.endswith('.tar.gz'): UploadTar(path, 'r:gz') elif extension == '.zip': UploadZip(path) elif extension == '.tar': UploadTar(path, 'r') elif extension == '.bz2': UploadBzip2(path) elif extension == '.gz': UploadGzip(path) else: UploadFile(path) if args.clear: print('Removing the content of Orthanc') auth = HTTPBasicAuth(args.username, args.password) r = requests.get('%s/studies' % args.url, auth = auth) r.raise_for_status() print(' %d studies are being removed...' % len(r.json())) for study in r.json(): requests.delete('%s/studies/%s' % (args.url, study), auth = auth).raise_for_status() print('Orthanc is now empty') print('') for path in args.files: if os.path.isfile(path): DecodeFile(path) elif os.path.isdir(path): for root, dirs, files in os.walk(path): for name in files: DecodeFile(os.path.join(root, name)) else: raise Exception('Missing file or directory: %s' % path) print('') if COUNT_ERROR == 0: print('SUCCESS:') else: print('WARNING:') print(' %d DICOM instances properly imported' % COUNT_DICOM) print(' %d DICOM studies properly imported' % len(IMPORTED_STUDIES)) print(' %d JSON files ignored' % COUNT_JSON) print(' Error in %d files' % COUNT_ERROR) print('')