Mercurial > hg > orthanc
changeset 1182:d74ac5d0bcaf
New sample: Automated classification of DICOM files
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Thu, 09 Oct 2014 17:11:00 +0200 |
parents | 17302d83abfd |
children | 6ef2c81581cd |
files | Resources/Samples/Python/AutoClassify.py |
diffstat | 1 files changed, 113 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Resources/Samples/Python/AutoClassify.py Thu Oct 09 17:11:00 2014 +0200 @@ -0,0 +1,113 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- + +# Orthanc - A Lightweight, RESTful DICOM Store +# Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, +# 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 RestToolbox + +parser = argparse.ArgumentParser( + description = 'Automated classification of DICOM files from Orthanc.', + formatter_class = argparse.ArgumentDefaultsHelpFormatter) + +parser.add_argument('--host', default = 'localhost', + 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) + + +# 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 interested in the arrival of new instances + if change['ChangeType'] == 'NewInstance': + # Extract the patient, study, series and instance information + instance = RestToolbox.DoGet('%s/instances/%s' % (URL, change['ID'])) + 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' % (patient['MainDicomTags']['PatientID'], + patient['MainDicomTags']['PatientName']) + b = study['MainDicomTags']['StudyDescription'] + c = '%s - %s' % (series['MainDicomTags']['Modality'], + series['MainDicomTags']['SeriesDescription']) + d = '%s.dcm' % instance['MainDicomTags']['SOPInstanceUID'] + + p = os.path.join( + args.target, + a.encode('ascii', 'ignore'), + b.encode('ascii', 'ignore'), + c.encode('ascii', 'ignore') + ) + + f = os.path.join(p, d.encode('ascii', 'ignore')) + + + # 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, change['ID'])) + with open(f, 'wb') as g: + g.write(dcm) + + # If requested, remove the instance once it has been copied + if args.remove: + RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID'])) + + current = r['Last'] + + if r['Done']: + print "Everything has been processed: Waiting..." + time.sleep(1)