Mercurial > hg > orthanc
view Resources/Samples/Python/AutoClassify.py @ 3786:3801435e34a1 SylvainRouquette/fix-issue169-95b752c
integration Orthanc-1.6.0->SylvainRouquette
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 19 Mar 2020 11:48:30 +0100 |
parents | 94f4a18a79cc |
children |
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#!/usr/bin/python # -*- coding: utf-8 -*- # Orthanc - A Lightweight, RESTful DICOM Store # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics # Department, University Hospital of Liege, Belgium # Copyright (C) 2017-2020 Osimis S.A., 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 time import os import os.path import sys import RestToolbox parser = argparse.ArgumentParser( description = 'Automated classification of DICOM files from Orthanc.', formatter_class = argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('--host', default = '127.0.0.1', help = 'The host address that runs Orthanc') parser.add_argument('--port', type = int, default = '8042', help = 'The port number to which Orthanc is listening for the REST API') parser.add_argument('--target', default = 'OrthancFiles', help = 'The target directory where to store the DICOM files') parser.add_argument('--all', action = 'store_true', help = 'Replay the entire history on startup (disabled by default)') parser.set_defaults(all = False) parser.add_argument('--remove', action = 'store_true', help = 'Remove DICOM files from Orthanc once classified (disabled by default)') parser.set_defaults(remove = False) def FixPath(p): return p.encode('ascii', errors = 'replace').translate(None, r"'\/:*?\"<>|!=").strip() def GetTag(resource, tag): if ('MainDicomTags' in resource and tag in resource['MainDicomTags']): return resource['MainDicomTags'][tag] else: return 'No' + tag def ClassifyInstance(instanceId): # Extract the patient, study, series and instance information instance = RestToolbox.DoGet('%s/instances/%s' % (URL, instanceId)) series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries'])) study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy'])) patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient'])) # Construct a target path a = '%s - %s' % (GetTag(patient, 'PatientID'), GetTag(patient, 'PatientName')) b = GetTag(study, 'StudyDescription') c = '%s - %s' % (GetTag(series, 'Modality'), GetTag(series, 'SeriesDescription')) d = '%s.dcm' % GetTag(instance, 'SOPInstanceUID') p = os.path.join(args.target, FixPath(a), FixPath(b), FixPath(c)) f = os.path.join(p, FixPath(d)) # Copy the DICOM file to the target path print('Writing new DICOM file: %s' % f) try: os.makedirs(p) except: # Already existing directory, ignore the error pass dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, instanceId)) with open(f, 'wb') as g: g.write(dcm) # Parse the arguments args = parser.parse_args() URL = 'http://%s:%d' % (args.host, args.port) print('Connecting to Orthanc on address: %s' % URL) # Compute the starting point for the changes loop if args.all: current = 0 else: current = RestToolbox.DoGet(URL + '/changes?last')['Last'] # Polling loop using the 'changes' API of Orthanc, waiting for the # incoming of new DICOM files while True: r = RestToolbox.DoGet(URL + '/changes', { 'since' : current, 'limit' : 4 # Retrieve at most 4 changes at once }) for change in r['Changes']: # We are only interested in the arrival of new instances if change['ChangeType'] == 'NewInstance': try: ClassifyInstance(change['ID']) # If requested, remove the instance once it has been # properly handled by "ClassifyInstance()". Thanks to # the "try/except" block, the instance is not removed # if the "ClassifyInstance()" function fails. if args.remove: RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID'])) except: print('Unable to write instance %s to the disk' % change['ID']) current = r['Last'] if r['Done']: print('Everything has been processed: Waiting...') time.sleep(1)