Mercurial > hg > orthanc-tests
view Tests/Tests.py @ 308:2565d39dd36c c-get
integration mainline->c-get
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 20 May 2020 16:35:06 +0200 |
| parents | 5be63aef39b1 ed20ead1a8b6 |
| children | 07e2adc4aead |
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#!/usr/bin/env 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 base64 import bz2 import copy import pprint import tempfile import unittest import shutil from PIL import ImageChops from Toolbox import * from xml.dom import minidom _LOCAL = None _REMOTE = None _DOCKER = False def SetOrthancParameters(local, remote, withinDocker): global _LOCAL, _REMOTE, _DOCKER _LOCAL = local _REMOTE = remote _DOCKER = withinDocker def ExtractDicomTags(rawDicom, tags): with tempfile.NamedTemporaryFile(delete = True) as f: f.write(rawDicom) f.flush() data = subprocess.check_output([ FindExecutable('dcm2xml'), f.name ]) result = [] for tag in tags: match = re.search('<element[^>]+name="%s">([^>]*)</element>' % tag, data) if match == None: result.append('') else: result.append(match.group(1)) return result def CompareLists(a, b): if len(a) != len(b): return False for i in range(len(a)): d = a[i] - b[i] if abs(d) >= 0.51: # Add some tolerance for rounding errors return False return True def CompareTags(a, b, tagsToIgnore): for i in tagsToIgnore: if i in a: del a[i] if i in b: del b[i] if a.keys() == b.keys(): return True else: print('Mismatch in tags: %s' % str(set(a.keys()) ^ set(b.keys()))) return False def CallFindScu(args): p = subprocess.Popen([ FindExecutable('findscu'), '-P', '-aec', _REMOTE['DicomAet'], '-aet', _LOCAL['DicomAet'], _REMOTE['Server'], str(_REMOTE['DicomPort']) ] + args, stderr=subprocess.PIPE) return p.communicate()[1] def GetMoveScuCommand(): return [ FindExecutable('movescu'), '--move', _LOCAL['DicomAet'], # Target AET (i.e. storescp) '--call', _REMOTE['DicomAet'], # Called AET (i.e. Orthanc) '--aetitle', _LOCAL['DicomAet'], # Calling AET (i.e. storescp) _REMOTE['Server'], str(_REMOTE['DicomPort']) ] def CallMoveScu(args): try: subprocess.check_call(GetMoveScuCommand() + args, stderr=subprocess.PIPE) except subprocess.CalledProcessError as e: # The error code "69" corresponds to "EXITCODE_CMOVE_ERROR", # that has been introduced in DCMTK 3.6.2. This error code is # expected by some tests that try and C-MOVE non-existing # DICOM instances. # https://groups.google.com/d/msg/orthanc-users/DCRc5NeSCbM/DG-pSWj-BwAJ if e.returncode != 69: raise e def GenerateTestSequence(): return [ { 'StudyDescription': 'Hello^', 'ReferencedStudySequence' : [ { 'StudyDescription': 'Toto', }, { 'StudyDescription': 'Tata', }, ] }, { 'StudyDescription': 'Sébastien^', 'StudyDate' : '19700202', } ] class Orthanc(unittest.TestCase): def setUp(self): if (sys.version_info >= (3, 0)): # Remove annoying warnings about unclosed socket in Python 3 import warnings warnings.simplefilter("ignore", ResourceWarning) DropOrthanc(_LOCAL) DropOrthanc(_REMOTE) UninstallLuaCallbacks(_REMOTE) #print "In test", self._testMethodName def AssertSameImages(self, truth, url): im = GetImage(_REMOTE, url) self.assertTrue(CompareLists(truth, im.getdata())) def test_system(self): self.assertTrue('Version' in DoGet(_REMOTE, '/system')) self.assertEqual('0', DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('0', DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) systemInfo = DoGet(_REMOTE, '/system') if systemInfo["Version"] == "mainline": print "Skipping version checks since you're currently in mainline" return self.assertTrue(IsOrthancVersionAbove(_LOCAL, 0, 8, 6)) self.assertFalse(IsOrthancVersionAbove(_LOCAL, 0, 8, 7)) self.assertTrue(IsOrthancVersionAbove(_LOCAL, 0, 7, 6)) self.assertFalse(IsOrthancVersionAbove(_LOCAL, 0, 9, 6)) self.assertFalse(IsOrthancVersionAbove(_LOCAL, 1, 8, 6)) def test_upload(self): self.assertEqual('0', DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('0', DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) sizeDummyCT = 2472 sizeOverwrite = 2476 instance = '66a662ce-7430e543-bad44d47-0dc5a943-ec7a538d' u = UploadInstance(_REMOTE, 'DummyCT.dcm') self.assertEqual(instance, u['ID']) self.assertEqual('Success', u['Status']) if True: # New test for Orthanc 1.4.3 self.assertEqual('f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe', u['ParentSeries']) self.assertEqual('b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0', u['ParentStudy']) self.assertEqual('6816cb19-844d5aee-85245eba-28e841e6-2414fae2', u['ParentPatient']) j = int(DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/size' % instance)) s = sizeDummyCT + j self.assertEqual('%d' % s, DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('%d' % s, DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) u = UploadInstance(_REMOTE, 'DummyCT.dcm') self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) self.assertEqual('%d' % s, DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('%d' % s, DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) i = DoGet(_REMOTE, '/instances/%s/simplified-tags' % instance) self.assertEqual('20070101', i['StudyDate']) self.assertEqual('KNIX', i['PatientName']) if IsOrthancVersionAbove(_REMOTE, 1, 4, 2): # Overwriting self.assertEqual('Success', u['Status']) else: self.assertEqual('AlreadyStored', u['Status']) u = UploadInstance(_REMOTE, 'DummyCT-overwrite.dcm') self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) if IsOrthancVersionAbove(_REMOTE, 1, 4, 2): # Overwriting self.assertEqual('Success', u['Status']) j2 = int(DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/size' % instance)) s2 = sizeOverwrite + j2 self.assertNotEqual(s, s2) self.assertNotEqual(j, j2) self.assertEqual('%d' % s2, DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('%d' % s2, DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) i = DoGet(_REMOTE, '/instances/%s/simplified-tags' % instance) self.assertEqual('ANOTHER', i['PatientName']) else: self.assertEqual('AlreadyStored', u['Status']) self.assertEqual('%d' % s, DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('%d' % s, DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) def test_upload_2(self): i = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] instance = DoGet(_REMOTE, '/instances/%s' % i) self.assertEqual(i, instance['ID']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7040.1171286242.109', instance['MainDicomTags']['SOPInstanceUID']) series = DoGet(_REMOTE, '/series/%s' % instance['ParentSeries']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.394', series['MainDicomTags']['SeriesInstanceUID']) study = DoGet(_REMOTE, '/studies/%s' % series['ParentStudy']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.390', study['MainDicomTags']['StudyInstanceUID']) patient = DoGet(_REMOTE, '/patients/%s' % study['ParentPatient']) self.assertEqual('ozp00SjY2xG', patient['MainDicomTags']['PatientID']) dicom = DoGet(_REMOTE, '/instances/%s/file' % instance['ID']) self.assertEqual(2472, len(dicom)) self.assertEqual('3e29b869978b6db4886355a2b1132124', ComputeMD5(dicom)) self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/frames' % i))) self.assertEqual('TWINOW', DoGet(_REMOTE, '/instances/%s/simplified-tags' % i)['StationName']) self.assertEqual('TWINOW', DoGet(_REMOTE, '/instances/%s/tags' % i)['0008,1010']['Value']) self.assertEqual('TWINOW', DoGet(_REMOTE, '/instances/%s/tags?simplify' % i)['StationName']) self.assertEqual('TWINOW', DoGet(_REMOTE, '/instances/%s/tags?short' % i)['0008,1010']) def test_images(self): i = UploadInstance(_REMOTE, 'Phenix/IM-0001-0001.dcm')['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/frames' % i))) im = GetImage(_REMOTE, '/instances/%s/preview' % i) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(358, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/image-uint8' % i) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(358, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/image-uint16' % i) self.assertEqual(512, im.size[0]) self.assertEqual(358, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/frames/0/preview' % i) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(358, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/frames/0/image-uint8' % i) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(358, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/frames/0/image-uint16' % i) self.assertEqual(512, im.size[0]) self.assertEqual(358, im.size[1]) # This is Little Endian Explicit self.assertEqual('1.2.840.10008.1.2.1', DoGet(_REMOTE, '/instances/%s/header?simplify' % i)['TransferSyntaxUID']) def test_hierarchy(self): UploadFolder(_REMOTE, 'Brainix/Epi') UploadFolder(_REMOTE, 'Brainix/Flair') UploadFolder(_REMOTE, 'Knee/T1') UploadFolder(_REMOTE, 'Knee/T2') p = DoGet(_REMOTE, '/patients') s = DoGet(_REMOTE, '/studies') t = DoGet(_REMOTE, '/series') self.assertEqual(2, len(p)) self.assertEqual(2, len(s)) self.assertEqual(4, len(t)) self.assertEqual(94, len(DoGet(_REMOTE, '/instances'))) brainixPatient = '16738bc3-e47ed42a-43ce044c-a3414a45-cb069bd0' brainixStudy = '27f7126f-4f66fb14-03f4081b-f9341db2-53925988' brainixEpi = '2ac1316d-3e432022-62eabff2-c59f5475-9b1ac3f8' brainixFlair = '1e2c125c-411b8e86-3f4fe68e-a7584dd3-c6da78f0' kneePatient = 'ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17' kneeStudy = '0a9b3153-2512774b-2d9580de-1fc3dcf6-3bd83918' kneeT1 = '6de73705-c4e65c1b-9d9ea1b5-cabcd8e7-f15e4285' kneeT2 = 'bbf7a453-0d34251a-03663b55-46bb31b9-ffd74c59' self.assertTrue(brainixPatient in p) self.assertTrue(kneePatient in p) self.assertTrue(brainixStudy in s) self.assertTrue(kneeStudy in s) self.assertTrue(brainixEpi in t) self.assertTrue(brainixFlair in t) self.assertTrue(kneeT1 in t) self.assertTrue(kneeT2 in t) self.assertEqual(44, len(DoGet(_REMOTE, '/patients/%s/instances' % brainixPatient))) self.assertEqual(2, len(DoGet(_REMOTE, '/patients/%s/series' % brainixPatient))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients/%s/studies' % brainixPatient))) self.assertEqual(50, len(DoGet(_REMOTE, '/patients/%s/instances' % kneePatient))) self.assertEqual(2, len(DoGet(_REMOTE, '/patients/%s/series' % kneePatient))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients/%s/studies' % kneePatient))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies/%s/series' % brainixStudy))) self.assertEqual(44, len(DoGet(_REMOTE, '/studies/%s/instances' % brainixStudy))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies/%s/series' % kneeStudy))) self.assertEqual(50, len(DoGet(_REMOTE, '/studies/%s/instances' % kneeStudy))) self.assertEqual(22, len(DoGet(_REMOTE, '/series/%s/instances' % brainixEpi))) self.assertEqual(22, len(DoGet(_REMOTE, '/series/%s/instances' % brainixFlair))) self.assertEqual(24, len(DoGet(_REMOTE, '/series/%s/instances' % kneeT1))) self.assertEqual(26, len(DoGet(_REMOTE, '/series/%s/instances' % kneeT2))) for patient in p: for study in DoGet(_REMOTE, '/patients/%s/studies' % patient): self.assertEqual(patient, study['ParentPatient']) for series in DoGet(_REMOTE, '/studies/%s/series' % study['ID']): self.assertEqual(study['ID'], series['ParentStudy']) self.assertEqual('Unknown', series['Status']) for instance in DoGet(_REMOTE, '/series/%s/instances' % series['ID']): self.assertEqual(series['ID'], instance['ParentSeries']) self.assertEqual(json.dumps(DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/data' % instance['ID'])), json.dumps(DoGet(_REMOTE, '/instances/%s/tags' % instance['ID']))) r = DoDelete(_REMOTE, "/studies/%s" % brainixStudy)['RemainingAncestor'] self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(2, len(DoGet(_REMOTE, '/series'))) self.assertEqual(50, len(DoGet(_REMOTE, '/instances'))) self.assertEqual(None, r) r = DoDelete(_REMOTE, "/series/%s" % kneeT2)['RemainingAncestor'] self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(24, len(DoGet(_REMOTE, '/instances'))) self.assertEqual('Study', r['Type']) self.assertEqual(kneeStudy, r['ID']) r = DoDelete(_REMOTE, "/instances/%s" % DoGet(_REMOTE, '/instances')[0])['RemainingAncestor'] self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(23, len(DoGet(_REMOTE, '/instances'))) self.assertEqual('Series', r['Type']) self.assertEqual(kneeT1, r['ID']) r = DoDelete(_REMOTE, "/patients/%s" % kneePatient)['RemainingAncestor'] self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(0, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(0, len(DoGet(_REMOTE, '/series'))) self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) self.assertEqual(None, r) DropOrthanc(_REMOTE) self.assertEqual('0', DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual('0', DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) def test_delete_cascade(self): # make sure deleting the last instance of a study deletes the series, study and patient self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) # make sure orthanc is empty when starting the test a = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) DoDelete(_REMOTE, '/instances/%s' % a) self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) self.assertEqual(0, len(DoGet(_REMOTE, '/series'))) self.assertEqual(0, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) def test_multiframe(self): i = UploadInstance(_REMOTE, 'Multiframe.dcm')['ID'] self.assertEqual(76, len(DoGet(_REMOTE, '/instances/%s/frames' % i))) im = GetImage(_REMOTE, '/instances/%s/frames/0/preview' % i) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(512, im.size[1]) DoGet(_REMOTE, '/instances/%s/frames/0/image-uint8' % i) DoGet(_REMOTE, '/instances/%s/frames/0/image-uint16' % i) DoGet(_REMOTE, '/instances/%s/frames/75/preview' % i) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/frames/aaa/preview' % i)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/frames/76/preview' % i)) def test_changes(self): # Check emptiness c = DoGet(_REMOTE, '/changes') self.assertEqual(0, len(c['Changes'])) #self.assertEqual(0, c['Last']) # Not true anymore for Orthanc >= 1.5.2 self.assertTrue(c['Done']) c = DoGet(_REMOTE, '/changes?last') self.assertEqual(0, len(c['Changes'])) #self.assertEqual(0, c['Last']) # Not true anymore for Orthanc >= 1.5.2 self.assertTrue(c['Done']) # Add 1 instance i = UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] c = DoGet(_REMOTE, '/changes') begin = c['Last'] self.assertEqual(4, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(c['Changes'][-1]['Seq'], c['Last']) c = DoGet(_REMOTE, '/changes?last') self.assertEqual(1, len(c['Changes'])) self.assertEqual(begin, c['Last']) self.assertTrue(c['Done']) c = DoGet(_REMOTE, '/changes?limit=1&since=' + str(begin - 1)) self.assertEqual(1, len(c['Changes'])) self.assertEqual(begin, c['Last']) self.assertTrue(c['Done']) c = DoGet(_REMOTE, '/changes?limit=1&since=' + str(begin - 2)) self.assertEqual(1, len(c['Changes'])) self.assertEqual(begin - 1, c['Last']) self.assertFalse(c['Done']) c = DoGet(_REMOTE, '/changes?limit=1&since=' + str(begin - 3)) self.assertEqual(1, len(c['Changes'])) self.assertEqual(begin - 2, c['Last']) self.assertFalse(c['Done']) UploadFolder(_REMOTE, 'Knee/T1') UploadFolder(_REMOTE, 'Knee/T2') since = begin countPatients = 0 countStudies = 0 countSeries = 0 countInstances = 0 completed = 0 while True: c = DoGet(_REMOTE, '/changes', { 'since' : since, 'limit' : 3 }) since = c['Last'] for i in c['Changes']: if i['ResourceType'] == 'Instance': countInstances += 1 if i['ResourceType'] == 'Patient': countPatients += 1 if i['ResourceType'] == 'Study': countStudies += 1 if i['ResourceType'] == 'Series': countSeries += 1 if i['ChangeType'] == 'NewInstance': countInstances += 1 if i['ChangeType'] == 'NewPatient': countPatients += 1 if i['ChangeType'] == 'NewStudy': countStudies += 1 if i['ChangeType'] == 'NewSeries': countSeries += 1 if i['ChangeType'] == 'CompletedSeries': completed += 1 self.assertTrue('ID' in i) self.assertTrue('Path' in i) self.assertTrue('Seq' in i) if c['Done']: break self.assertEqual(2 * 50, countInstances) self.assertEqual(2 * 1, countPatients) self.assertEqual(2 * 1, countStudies) self.assertEqual(2 * 2, countSeries) self.assertEqual(0, completed) def test_archive(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') knee = 'ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17' z = GetArchive(_REMOTE, '/patients/%s/archive' % knee) self.assertEqual(2, len(z.namelist())) z = GetArchive(_REMOTE, '/studies/%s/archive' % DoGet(_REMOTE, '/studies')[0]) self.assertEqual(2, len(z.namelist())) z = GetArchive(_REMOTE, '/series/%s/archive' % DoGet(_REMOTE, '/series')[0]) self.assertEqual(1, len(z.namelist())) UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') brainix = '16738bc3-e47ed42a-43ce044c-a3414a45-cb069bd0' z = GetArchive(_REMOTE, '/patients/%s/archive' % knee) self.assertEqual(2, len(z.namelist())) z = PostArchive(_REMOTE, '/tools/create-archive', { 'Resources' : [ brainix, knee ] }) self.assertEqual(3, len(z.namelist())) def test_media_archive(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') z = GetArchive(_REMOTE, '/patients/%s/media' % DoGet(_REMOTE, '/patients')[0]) self.assertEqual(3, len(z.namelist())) self.assertTrue('IMAGES/IM0' in z.namelist()) self.assertTrue('IMAGES/IM1' in z.namelist()) self.assertTrue('DICOMDIR' in z.namelist()) try: os.remove('/tmp/DICOMDIR') except: # The file does not exist pass z.extract('DICOMDIR', '/tmp') a = subprocess.check_output([ FindExecutable('dciodvfy'), '/tmp/DICOMDIR' ], stderr = subprocess.STDOUT).split('\n') self.assertEqual(3, len(a)) self.assertTrue(a[0].startswith('Warning')) self.assertEqual('BasicDirectory', a[1]) self.assertEqual('', a[2]) a = subprocess.check_output([ FindExecutable('dcentvfy'), '/tmp/DICOMDIR' ], stderr = subprocess.STDOUT).split('\n') self.assertEqual(1, len(a)) self.assertEqual('', a[0]) a = subprocess.check_output([ FindExecutable('dcm2xml'), '/tmp/DICOMDIR' ]) self.assertTrue(re.search('1.3.46.670589.11.17521.5.0.3124.2008081908590448738', a) != None) self.assertTrue(re.search('1.3.46.670589.11.17521.5.0.3124.2008081909113806560', a) != None) os.remove('/tmp/DICOMDIR') def test_protection(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) a = DoGet(_REMOTE, '/patients')[0] b = DoGet(_REMOTE, '/patients')[1] self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoPut(_REMOTE, '/patients/%s/protected' % a, '0', 'text/plain') self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoPut(_REMOTE, '/patients/%s/protected' % a, '1', 'text/plain') self.assertEqual(1, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoPut(_REMOTE, '/patients/%s/protected' % a, '0', 'text/plain') self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) def test_raw_tags(self): i = UploadInstance(_REMOTE, 'PrivateTags.dcm')['ID'] dicom = DoGet(_REMOTE, '/instances/%s/file' % i) self.assertEqual('1a7c56cb02d6e742cc9c856a8ac182e3', ComputeMD5(dicom)) s = '/instances/%s/content/' % i self.assertEqual('LOGIQBOOK', DoGet(_REMOTE, s + '0008-1010').strip()) self.assertRaises(Exception, lambda: DoGet(_REMOTE, s + '0008-1011')) self.assertEqual('Abdomen', DoGet(_REMOTE, s + '7fe1-1001/0/7fe1-1008/0/7fe1-1057').strip()) self.assertEqual('cla_3c', DoGet(_REMOTE, s + '7fe1-1001/0/7fe1-1008/8/7fe1-1057').strip()) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') for i in DoGet(_REMOTE, '/instances'): aid = DoGet(_REMOTE, '/instances/%s' % i)['MainDicomTags']['SOPInstanceUID'] self.assertEqual(aid, DoGet(_REMOTE, '/instances/%s/content/0008-0018' % i).replace(chr(0), '')) def test_raw_tags_mdn(self): # Bug reported by Cyril Paulus i = UploadInstance(_REMOTE, 'PrivateMDNTags.dcm')['ID'] self.assertAlmostEqual(0.000027, DoGet(_REMOTE, '/instances/%s/content/7053-1000' % i)) def test_modify_instance(self): i = UploadInstance(_REMOTE, 'PrivateTags.dcm')['ID'] modified = DoPost(_REMOTE, '/instances/%s/modify' % i, json.dumps({ "Replace" : { "PatientName" : "hello", #"PatientID" : "world" }, "Remove" : [ "StationName" ], "RemovePrivateTags" : True }), 'application/json') j = DoPost(_REMOTE, '/instances', modified, 'application/dicom')['ID'] self.assertNotEqual('hello', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % i).strip()) #self.assertNotEqual('world', DoGet(_REMOTE, '/instances/%s/content/0010-0020' % i).strip()) self.assertEqual('LOGIQBOOK', DoGet(_REMOTE, '/instances/%s/content/0008-1010' % i).strip()) DoGet(_REMOTE, '/instances/%s/content/6003-1010' % i) # Some private tag self.assertEqual('hello', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % j).strip()) #self.assertEqual('world', DoGet(_REMOTE, '/instances/%s/content/0010-0020' % j).strip()) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/0008-1010' % j)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/6003-1010' % j)) def test_modify_series(self): # Upload 4 images from the same series for i in range(4): UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) origSeries = DoGet(_REMOTE, '/series')[0] newSeries = DoPost(_REMOTE, '/series/%s/modify' % origSeries, '{"Replace":{"PatientName":"Jodogne"}}', 'application/json')['ID'] self.assertEqual(origSeries, DoGet(_REMOTE, '/series/%s' % newSeries)['ModifiedFrom']) instances = DoGet(_REMOTE, '/series/%s' % newSeries)['Instances'] self.assertEqual(4, len(instances)) for i in instances: j = DoGet(_REMOTE, '/instances/%s' % i)['ModifiedFrom'] self.assertEqual(newSeries, DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries']) self.assertEqual(origSeries, DoGet(_REMOTE, '/instances/%s' % j)['ParentSeries']) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % i).strip()) self.assertNotEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % j).strip()) def test_modify_study(self): # Upload 4 images from the 2 series of the same study for i in range(4): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) origStudy = DoGet(_REMOTE, '/studies')[0] newStudy = DoPost(_REMOTE, '/studies/%s/modify' % origStudy, '{"Replace":{"PatientName":"Jodogne"}}', 'application/json')['ID'] self.assertEqual(origStudy, DoGet(_REMOTE, '/studies/%s' % newStudy)['ModifiedFrom']) series = DoGet(_REMOTE, '/studies/%s' % newStudy)['Series'] self.assertEqual(2, len(series)) for s in series: ss = DoGet(_REMOTE, '/series/%s' % s)['ModifiedFrom'] self.assertEqual(newStudy, DoGet(_REMOTE, '/series/%s' % s)['ParentStudy']) self.assertEqual(origStudy, DoGet(_REMOTE, '/series/%s' % ss)['ParentStudy']) instances = DoGet(_REMOTE, '/series/%s' % s)['Instances'] for i in instances: j = DoGet(_REMOTE, '/instances/%s' % i)['ModifiedFrom'] self.assertEqual(s, DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries']) self.assertEqual(ss, DoGet(_REMOTE, '/instances/%s' % j)['ParentSeries']) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % i).strip()) self.assertNotEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % j).strip()) def test_anonymize_series(self): # Upload 4 images from the same series for i in range(4): UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) origSeries = DoGet(_REMOTE, '/series')[0] newSeries = DoPost(_REMOTE, '/series/%s/anonymize' % origSeries, '{}', 'application/json')['ID'] self.assertEqual(origSeries, DoGet(_REMOTE, '/series/%s' % newSeries)['AnonymizedFrom']) instances = DoGet(_REMOTE, '/series/%s' % newSeries)['Instances'] self.assertEqual(4, len(instances)) for i in instances: j = DoGet(_REMOTE, '/instances/%s' % i)['AnonymizedFrom'] self.assertEqual(newSeries, DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries']) self.assertEqual(origSeries, DoGet(_REMOTE, '/instances/%s' % j)['ParentSeries']) DoGet(_REMOTE, '/instances/%s/content/0008-1010' % j) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/0008-1010' % i)) def test_anonymize_study(self): # Upload 4 images from the 2 series of the same study for i in range(4): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) origStudy = DoGet(_REMOTE, '/studies')[0] newStudy = DoPost(_REMOTE,'/studies/%s/anonymize' % origStudy, '{"Replace":{"PatientName":"Jodogne"}}', 'application/json')['ID'] self.assertEqual(origStudy, DoGet(_REMOTE, '/studies/%s' % newStudy)['AnonymizedFrom']) series = DoGet(_REMOTE, '/studies/%s' % newStudy)['Series'] self.assertEqual(2, len(series)) for s in series: ss = DoGet(_REMOTE, '/series/%s' % s)['AnonymizedFrom'] self.assertEqual(newStudy, DoGet(_REMOTE, '/series/%s' % s)['ParentStudy']) self.assertEqual(origStudy, DoGet(_REMOTE, '/series/%s' % ss)['ParentStudy']) instances = DoGet(_REMOTE, '/series/%s' % s)['Instances'] for i in instances: j = DoGet(_REMOTE, '/instances/%s' % i)['AnonymizedFrom'] self.assertEqual(s, DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries']) self.assertEqual(ss, DoGet(_REMOTE, '/instances/%s' % j)['ParentSeries']) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % i).strip()) self.assertNotEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % j).strip()) def test_storescu(self): # Check emptiness e = DoGet(_REMOTE, '/exports') self.assertEqual(0, len(e['Exports'])) self.assertEqual(0, e['Last']) self.assertTrue(e['Done']) e = DoGet(_REMOTE, '/exports?last') self.assertEqual(0, len(e['Exports'])) self.assertEqual(0, e['Last']) self.assertTrue(e['Done']) # Add 1 instance i = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) # Export the instance j = DoPost(_REMOTE, '/modalities/orthanctest/store', str(i), 'text/plain') # instance self.assertEqual(1, len(DoGet(_LOCAL, '/patients'))) self.assertEqual(1, len(DoGet(_LOCAL, '/studies'))) self.assertEqual(1, len(DoGet(_LOCAL, '/series'))) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) e = DoGet(_REMOTE, '/exports') self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], e['Last']) e = DoGet(_REMOTE, '/exports?limit=1') self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], e['Last']) e = DoGet(_REMOTE, '/exports?last') self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], e['Last']) seqInstance = e['Last'] # Export the series j = DoPost(_REMOTE, '/modalities/orthanctest/store', 'f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe', 'text/plain') e = DoGet(_REMOTE, '/exports') self.assertEqual(2, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], e['Last']) seqSeries = e['Last'] self.assertNotEqual(seqInstance, seqSeries) e = DoGet(_REMOTE, '/exports?limit=1&since=0') self.assertEqual(1, len(e['Exports'])) self.assertFalse(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqInstance) e = DoGet(_REMOTE, '/exports?limit=1&since=' + str(seqInstance)) self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqSeries) e = DoGet(_REMOTE, '/exports?last') self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqSeries) # Export the study j = DoPost(_REMOTE, '/modalities/orthanctest/store', 'b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0', 'text/plain') seqStudy = DoGet(_REMOTE, '/exports')['Last'] # Export the patient j = DoPost(_REMOTE, '/modalities/orthanctest/store', '6816cb19-844d5aee-85245eba-28e841e6-2414fae2', 'text/plain') self.assertEqual(1, len(DoGet(_LOCAL, '/patients'))) self.assertEqual(1, len(DoGet(_LOCAL, '/studies'))) self.assertEqual(1, len(DoGet(_LOCAL, '/series'))) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) e = DoGet(_REMOTE, '/exports') self.assertEqual(4, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], e['Last']) seqPatient = e['Last'] self.assertNotEqual(seqInstance, seqSeries) self.assertNotEqual(seqSeries, seqStudy) self.assertNotEqual(seqStudy, seqPatient) self.assertTrue(seqInstance < seqSeries) self.assertTrue(seqSeries < seqStudy) self.assertTrue(seqStudy < seqPatient) e = DoGet(_REMOTE, '/exports?limit=1&since=0') self.assertEqual(1, len(e['Exports'])) self.assertFalse(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqInstance) e = DoGet(_REMOTE, '/exports?limit=1&since=' + str(seqInstance)) self.assertEqual(1, len(e['Exports'])) self.assertFalse(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqSeries) e = DoGet(_REMOTE, '/exports?limit=1&since=' + str(seqSeries)) self.assertEqual(1, len(e['Exports'])) self.assertFalse(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqStudy) e = DoGet(_REMOTE, '/exports?limit=1&since=' + str(seqStudy)) self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqPatient) e = DoGet(_REMOTE, '/exports?last') self.assertEqual(1, len(e['Exports'])) self.assertTrue(e['Done']) self.assertEqual(e['Exports'][-1]['Seq'], seqPatient) # Check the content of the logged information e = DoGet(_REMOTE, '/exports')['Exports'] if 'PatientID' in e[0]: # Since Orthanc 0.8.6 patient = 'PatientID' study = 'StudyInstanceUID' series = 'SeriesInstanceUID' instance = 'SOPInstanceUID' else: # Up to Orthanc 0.8.5 patient = 'PatientId' study = 'StudyInstanceUid' series = 'SeriesInstanceUid' instance = 'SopInstanceUid' for k in range(4): self.assertTrue('Date' in e[k]) self.assertTrue('Seq' in e[k]) self.assertEqual('orthanctest', e[k]['RemoteModality']) self.assertEqual(10, len(e[0])) self.assertEqual('Instance', e[0]['ResourceType']) self.assertEqual('66a662ce-7430e543-bad44d47-0dc5a943-ec7a538d', e[0]['ID']) self.assertEqual('/instances/66a662ce-7430e543-bad44d47-0dc5a943-ec7a538d', e[0]['Path']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7040.1171286242.109', e[0][instance]) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.394', e[0][series]) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.390', e[0][study]) self.assertEqual('ozp00SjY2xG', e[0][patient]) self.assertEqual(9, len(e[1])) self.assertEqual('Series', e[1]['ResourceType']) self.assertEqual('f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe', e[1]['ID']) self.assertEqual('/series/f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe', e[1]['Path']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.394', e[1][series]) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.390', e[1][study]) self.assertEqual('ozp00SjY2xG', e[1][patient]) self.assertEqual(8, len(e[2])) self.assertEqual('Study', e[2]['ResourceType']) self.assertEqual('b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0', e[2]['ID']) self.assertEqual('/studies/b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0', e[2]['Path']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7391.1171285944.390', e[2][study]) self.assertEqual('ozp00SjY2xG', e[2][patient]) self.assertEqual(7, len(e[3])) self.assertEqual('Patient', e[3]['ResourceType']) self.assertEqual('6816cb19-844d5aee-85245eba-28e841e6-2414fae2', e[3]['ID']) self.assertEqual('/patients/6816cb19-844d5aee-85245eba-28e841e6-2414fae2', e[3]['Path']) self.assertEqual('ozp00SjY2xG', e[3][patient]) DropOrthanc(_REMOTE) self.assertEqual(0, len(DoGet(_REMOTE, '/exports')['Exports'])) def test_store_peer(self): self.assertEqual(0, len(DoGet(_LOCAL, '/exports')['Exports'])) self.assertEqual(0, len(DoGet(_REMOTE, '/exports')['Exports'])) i = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) j = DoPost(_REMOTE, '/peers/peer/store', str(i), 'text/plain') self.assertEqual(1, len(DoGet(_LOCAL, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/exports')['Exports'])) DropOrthanc(_REMOTE) self.assertEqual(0, len(DoGet(_REMOTE, '/exports')['Exports'])) def test_bulk_storescu(self): self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) a = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') b = UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') j = DoPost(_REMOTE, '/modalities/orthanctest/store', [ a['ID'], b['ID'] ], 'application/json') self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) DropOrthanc(_LOCAL) # Send using patient's UUID self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) j = DoPost(_REMOTE, '/modalities/orthanctest/store', [ 'ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17' ], 'application/json') self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) def test_color(self): i = UploadInstance(_REMOTE, 'ColorTestMalaterre.dcm')['ID'] im = GetImage(_REMOTE, '/instances/%s/preview' % i) self.assertEqual("RGB", im.mode) self.assertEqual(41, im.size[0]) self.assertEqual(41, im.size[1]) # http://effbot.org/zone/pil-comparing-images.htm truth = Image.open(GetDatabasePath('ColorTestMalaterre.png')) self.assertTrue(ImageChops.difference(im, truth).getbbox() is None) def test_faking_ruby_put(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) a = DoGet(_REMOTE, '/patients')[0] b = DoGet(_REMOTE, '/patients')[1] self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoGet(_REMOTE, '/patients/%s/protected' % a, data = { '_method' : 'PUT' }, body = '0') self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoGet(_REMOTE, '/patients/%s/protected' % a, data = { '_method' : 'PUT' }, body = '1') self.assertEqual(1, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoGet(_REMOTE, '/patients/%s/protected' % a, data = { '_method' : 'PUT' }, body = '0') self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) def test_faking_ruby_delete(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) a = DoGet(_REMOTE, '/patients')[0] b = DoGet(_REMOTE, '/patients')[1] DoGet(_REMOTE, '/patients/%s' % a, data = { '_method' : 'DELETE' }) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) DoGet(_REMOTE, '/patients/%s' % b, data = { '_method' : 'DELETE' }) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) def test_faking_google_put(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) a = DoGet(_REMOTE, '/patients')[0] b = DoGet(_REMOTE, '/patients')[1] self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoPost(_REMOTE, '/patients/%s/protected' % a, headers = { 'X-HTTP-Method-Override' : 'PUT' }, data = '0') self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoPost(_REMOTE, '/patients/%s/protected' % a, headers = { 'X-HTTP-Method-Override' : 'PUT' }, data = '1') self.assertEqual(1, DoGet(_REMOTE, '/patients/%s/protected' % a)) DoPost(_REMOTE, '/patients/%s/protected' % a, headers = { 'X-HTTP-Method-Override' : 'PUT' }, data = '0') self.assertEqual(0, DoGet(_REMOTE, '/patients/%s/protected' % a)) def test_faking_google_delete(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) a = DoGet(_REMOTE, '/patients')[0] b = DoGet(_REMOTE, '/patients')[1] DoPost(_REMOTE, '/patients/%s' % a, headers = { 'X-HTTP-Method-Override' : 'DELETE' }) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) DoPost(_REMOTE, '/patients/%s' % b, headers = { 'X-HTTP-Method-Override' : 'DELETE' }) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) def test_lua(self): self.assertEqual(42, DoPost(_REMOTE, '/tools/execute-script', 'print(42)')) self.assertTrue(IsDefinedInLua(_REMOTE, 'PrintRecursive')) self.assertFalse(IsDefinedInLua(_REMOTE, 'HelloWorld')) def test_metadata(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') p = DoGet(_REMOTE, '/patients')[0] i = DoGet(_REMOTE, '/instances')[0] m = DoGet(_REMOTE, '/patients/%s/metadata' % p) self.assertEqual(1, len(m)) self.assertEqual('LastUpdate', m[0]) m = DoGet(_REMOTE, '/instances/%s/metadata' % i) self.assertEqual(8, len(m)) self.assertTrue('IndexInSeries' in m) self.assertTrue('ReceptionDate' in m) self.assertTrue('RemoteAET' in m) self.assertTrue('Origin' in m) self.assertTrue('TransferSyntax' in m) self.assertTrue('SopClassUid' in m) self.assertTrue('RemoteIP' in m) self.assertTrue('HttpUsername' in m) self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/IndexInSeries' % i), 1) self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/Origin' % i), 'RestApi') self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/RemoteAET' % i), '') # None, received by REST API self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/TransferSyntax' % i), '1.2.840.10008.1.2.4.91') # JPEG2k self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/SopClassUid' % i), '1.2.840.10008.5.1.4.1.1.4') # Play with custom metadata DoPut(_REMOTE, '/patients/%s/metadata/5555' % p, 'coucou') m = DoGet(_REMOTE, '/patients/%s/metadata' % p) self.assertEqual(2, len(m)) self.assertTrue('LastUpdate' in m) self.assertTrue('5555' in m) self.assertEqual('coucou', DoGet(_REMOTE, '/patients/%s/metadata/5555' % p)) DoPut(_REMOTE, '/patients/%s/metadata/5555' % p, 'hello') self.assertEqual('hello', DoGet(_REMOTE, '/patients/%s/metadata/5555' % p)) DoDelete(_REMOTE, '/patients/%s/metadata/5555' % p) m = DoGet(_REMOTE, '/patients/%s/metadata' % p) self.assertEqual(1, len(m)) self.assertTrue('LastUpdate' in m) def test_statistics(self): # Upload 16 instances for i in range(4): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T1/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T2/IM-0001-000%d.dcm' % (i + 1)) s = DoGet(_REMOTE, '/statistics') self.assertEqual(16, s['CountInstances']) self.assertEqual(2, s['CountPatients']) self.assertEqual(2, s['CountStudies']) self.assertEqual(4, s['CountSeries']) d = int(s['TotalUncompressedSize']) e = 0 for patient in DoGet(_REMOTE, '/patients'): s = DoGet(_REMOTE, '/patients/%s/statistics' % patient) self.assertEqual(8, s['CountInstances']) self.assertEqual(1, s['CountStudies']) self.assertEqual(2, s['CountSeries']) e += int(s['UncompressedSize']) for study in DoGet(_REMOTE, '/studies'): s = DoGet(_REMOTE, '/studies/%s/statistics' % study) self.assertEqual(8, s['CountInstances']) self.assertEqual(2, s['CountSeries']) e += int(s['UncompressedSize']) for series in DoGet(_REMOTE, '/series'): s = DoGet(_REMOTE, '/series/%s/statistics' % series) self.assertEqual(4, s['CountInstances']) e += int(s['UncompressedSize']) self.assertEqual(3 * d, e) def test_custom_attachment(self): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') patient = DoGet(_REMOTE, '/patients')[0] instance = DoGet(_REMOTE, '/instances')[0] size = int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']) self.assertEqual(size, int(DoGet(_REMOTE, '/statistics')['TotalDiskSize'])) self.assertEqual(0, len(DoGet(_REMOTE, '/patients/%s/attachments' % patient))) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % instance))) self.assertTrue('dicom' in DoGet(_REMOTE, '/instances/%s/attachments' % instance)) self.assertTrue('dicom-as-json' in DoGet(_REMOTE, '/instances/%s/attachments' % instance)) self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/patients/%s/attachments/22' % patient, 'hello')) hello = 'hellohellohellohellohellohellohellohellohello' DoPut(_REMOTE, '/patients/%s/attachments/1025' % patient, hello) self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), int(DoGet(_REMOTE, '/statistics')['TotalDiskSize'])) self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), size + int(DoGet(_REMOTE, '/patients/%s/attachments/1025/compressed-size' % patient))) DoPut(_REMOTE, '/patients/%s/attachments/1026' % patient, 'world') self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), int(DoGet(_REMOTE, '/statistics')['TotalDiskSize'])) self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), size + int(DoGet(_REMOTE, '/patients/%s/attachments/1025/compressed-size' % patient)) + int(DoGet(_REMOTE, '/patients/%s/attachments/1026/compressed-size' % patient))) self.assertEqual(2, len(DoGet(_REMOTE, '/patients/%s/attachments' % patient))) self.assertEqual(hello, DoGet(_REMOTE, '/patients/%s/attachments/1025/data' % patient)) self.assertEqual('world', DoGet(_REMOTE, '/patients/%s/attachments/1026/data' % patient)) DoPost(_REMOTE, '/patients/%s/attachments/1025/verify-md5' % patient) DoPost(_REMOTE, '/patients/%s/attachments/1026/verify-md5' % patient) DoPut(_REMOTE, '/patients/%s/attachments/1026' % patient, 'world2') self.assertEqual('world2', DoGet(_REMOTE, '/patients/%s/attachments/1026/data' % patient)) self.assertRaises(Exception, lambda: DoDelete(_REMOTE, '/instances/%s/attachments/dicom' % instance)) DoDelete(_REMOTE, '/patients/%s/attachments/1025' % patient) self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), int(DoGet(_REMOTE, '/statistics')['TotalDiskSize'])) self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), size + int(DoGet(_REMOTE, '/patients/%s/attachments/1026/compressed-size' % patient))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients/%s/attachments' % patient))) DoDelete(_REMOTE, '/patients/%s/attachments/1026' % patient) self.assertEqual(0, len(DoGet(_REMOTE, '/patients/%s/attachments' % patient))) self.assertEqual(int(DoGet(_REMOTE, '/patients/%s/statistics' % patient)['DiskSize']), size) self.assertEqual(size, int(DoGet(_REMOTE, '/statistics')['TotalDiskSize'])) def test_incoming_storescu(self): self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) subprocess.check_call([ FindExecutable('storescu'), _REMOTE['Server'], str(_REMOTE['DicomPort']), GetDatabasePath('ColorTestImageJ.dcm') ]) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) i = DoGet(_REMOTE, '/instances') self.assertEqual(1, len(i)) m = DoGet(_REMOTE, '/instances/%s/metadata' % i[0]) self.assertEqual(8, len(m)) self.assertTrue('IndexInSeries' in m) self.assertTrue('ReceptionDate' in m) self.assertTrue('RemoteAET' in m) self.assertTrue('Origin' in m) self.assertTrue('TransferSyntax' in m) self.assertTrue('SopClassUid' in m) self.assertTrue('RemoteIP' in m) self.assertTrue('CalledAET' in m) self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/IndexInSeries' % i[0]), 1) self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/Origin' % i[0]), 'DicomProtocol') self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/RemoteAET' % i[0]), 'STORESCU') self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/TransferSyntax' % i[0]), '1.2.840.10008.1.2.1') self.assertEqual(DoGet(_REMOTE, '/instances/%s/metadata/SopClassUid' % i[0]), '1.2.840.10008.5.1.4.1.1.7') def test_incoming_findscu(self): UploadInstance(_REMOTE, 'Multiframe.dcm') UploadInstance(_REMOTE, 'ColorTestImageJ.dcm') i = CallFindScu([ '-k', '0008,0052=PATIENT', '-k', '0010,0010' ]) patientNames = re.findall('\(0010,0010\).*?\[(.*?)\]', i) self.assertEqual(2, len(patientNames)) self.assertTrue('Test Patient BG ' in patientNames) self.assertTrue('Anonymized' in patientNames) i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', '0008,0021' ]) series = re.findall('\(0008,0021\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(2, len(series)) self.assertTrue('20070208' in series) self.assertTrue('19980312' in series) i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', '0008,0021', '-k', 'ModalitiesInStudy=MR\\XA' ]) series = re.findall('\(0008,0021\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(1, len(series)) self.assertTrue('19980312' in series) i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', 'PatientName=Anonymized' ]) series = re.findall('\(0010,0010\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(1, len(series)) # Test the "CaseSentitivePN" flag (false by default) i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', 'PatientName=anonymized' ]) series = re.findall('\(0010,0010\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(1, len(series)) # Test range search (buggy if Orthanc <= 0.9.6) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'StudyDate=19980312-' ]) studies = re.findall('\(0008,0020\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(2, len(studies)) self.assertTrue('20070208' in studies) self.assertTrue('19980312' in studies) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'StudyDate=19980312-19980312' ]) studies = re.findall('\(0008,0020\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(1, len(studies)) self.assertTrue('19980312' in studies) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'StudyDate=-19980312' ]) studies = re.findall('\(0008,0020\).*?\[\s*(.*?)\s*\]', i) self.assertEqual(1, len(studies)) self.assertTrue('19980312' in studies) def test_incoming_findscu_2(self): # This test fails if "LookupMode_DatabaseOnly" is used # (sequences are not available in this mode, and only main # DICOM tags are returned) UploadInstance(_REMOTE, 'Multiframe.dcm') UploadInstance(_REMOTE, 'ColorTestImageJ.dcm') # Test returning sequence values (only since Orthanc 0.9.5) i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', '0008,2112' ]) # "ColorTestImageJ" has this sequence tag sequences = re.findall('\(0008,2112\)', i) self.assertEqual(1, len(sequences)) # Test returning a non-main DICOM tag, # "SecondaryCaptureDeviceID" (0018,1010), whose value is # "MEDPC" in "ColorTestImageJ.dcm" i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', '0018,1010' ]) tags = re.findall('\(0018,1010\).*MEDPC', i) self.assertEqual(1, len(tags)) def test_incoming_findscu_3(self): # This test fails if "LookupMode_DatabaseOnly" or # "LookupMode_DiskOnAnswer" is used, as # "SecondaryCaptureDeviceID" (0018,1010) is not a main DICOM # tag, as thus a constraint cannot be applied to it UploadInstance(_REMOTE, 'ColorTestImageJ.dcm') i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', '0018,1010=MEDPC' ]) sequences = re.findall('\(0018,1010\)', i) self.assertEqual(1, len(sequences)) def test_incoming_movescu(self): UploadInstance(_REMOTE, 'Multiframe.dcm') # No matching patient, so no job is created self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) CallMoveScu([ '--patient', '-k', '0008,0052=PATIENT', '-k', 'PatientID=none' ]) self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) # 1 Matching patient, track the job self.assertTrue(MonitorJob(_REMOTE, lambda: CallMoveScu([ '--patient', '-k', '0008,0052=PATIENT', '-k', 'PatientID=12345678' ]))) self.assertEqual(1, len(DoGet(_LOCAL, '/patients'))) def test_findscu(self): i = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] j = UploadInstance(_REMOTE, 'Issue22.dcm')['ID'] k = UploadInstance(_REMOTE, 'ColorTestImageJ.dcm')['ID'] DoPost(_REMOTE, '/modalities/orthanctest/store', str(i), 'text/plain') # Test the "find-patient" level p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { }) self.assertEqual(1, len(p)) self.assertEqual('ozp00SjY2xG', p[0]['PatientID']) # Test wildcards constraints. The "LO" value representation # for PatientID is always case-sensitive, but the "PN" for # PatientName might depend on the implementation: # "GenerateConfigurationForTests.py" will force it to be case # insensitive (which was the default until Orthanc 0.8.6). p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientName' : 'K*' }) self.assertEqual(1, len(p)) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientName' : 'k*' }) self.assertEqual(1, len(p)) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientID' : 'ozp*' }) self.assertEqual(1, len(p)) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientID' : 'o?p*' }) self.assertEqual(1, len(p)) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientID' : '0?q*' }) self.assertEqual(0, len(p)) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientName' : 'B*' }) self.assertEqual(0, len(p)) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientName' : 'b*' }) self.assertEqual(0, len(p)) DoPost(_REMOTE, '/modalities/orthanctest/store', str(j), 'text/plain') DoPost(_REMOTE, '/modalities/orthanctest/store', str(k), 'text/plain') DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { }) self.assertEqual(3, len(DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { }))) p = DoPost(_REMOTE, '/modalities/orthanctest/find-patient', { 'PatientName' : 'A*' }) self.assertEqual(2, len(p)) # Test the "find-study" level. This is the instance "ColorTestImageJ.dcm" s = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ' }) self.assertEqual(1, len(s)) self.assertEqual('20070208', s[0]['StudyDate']) # Test range searches t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '-20070101' }) self.assertEqual(0, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '20090101-' }) self.assertEqual(0, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '20070101-' }) self.assertEqual(1, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '-20090101' }) self.assertEqual(1, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '20070207-20070207' }) self.assertEqual(0, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '20070208-20070208' }) self.assertEqual(1, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'StudyDate' : '20070209-20070209' }) self.assertEqual(0, len(t)) # Test the ModalitiesInStudy tag t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'ModalitiesInStudy' : 'US' }) self.assertEqual(0, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'ModalitiesInStudy' : 'CT' }) self.assertEqual(1, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-study', { 'PatientID' : 'B9uTHKOZ', 'ModalitiesInStudy' : 'US\\CT' }) self.assertEqual(1, len(t)) # Test the "find-series" level t = DoPost(_REMOTE, '/modalities/orthanctest/find-series', { 'PatientID' : 'B9uTHKOZ', 'StudyInstanceUID' : s[0]['StudyInstanceUID'] }) self.assertEqual(1, len(t)) # Test "\" separator t = DoPost(_REMOTE, '/modalities/orthanctest/find-series', { 'PatientID' : 'B9uTHKOZ', 'StudyInstanceUID' : s[0]['StudyInstanceUID'], 'Modality' : 'MR\\CT\\US' }) self.assertEqual(1, len(t)) t = DoPost(_REMOTE, '/modalities/orthanctest/find-series', { 'PatientID' : 'B9uTHKOZ', 'StudyInstanceUID' : s[0]['StudyInstanceUID'], 'Modality' : 'MR\\US' }) self.assertEqual(0, len(t)) def test_update_modalities(self): try: DoDelete(_REMOTE, '/modalities/toto') except: pass try: DoDelete(_REMOTE, '/modalities/tata') except: pass self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/modalities/toto')) DoPut(_REMOTE, '/modalities/toto', [ "STORESCP", "localhost", 2000 ]) DoPut(_REMOTE, '/modalities/tata', [ "STORESCP", "localhost", 2000, 'MedInria' ]) # check backward compatiblity with obsolete manufacturer DoDelete(_REMOTE, '/modalities/tata') DoPut(_REMOTE, '/modalities/tata', [ "STORESCP", "localhost", 2000, 'GenericNoUniversalWildcard' ]) DoDelete(_REMOTE, '/modalities/tata') DoPut(_REMOTE, '/modalities/tata', [ "STORESCP", "localhost", 2000, 'GenericNoWildcardInDates' ]) modalitiesReadback = DoGet(_REMOTE, '/modalities?expand') self.assertEqual('STORESCP', modalitiesReadback['tata']['AET']) self.assertEqual('localhost', modalitiesReadback['tata']['Host']) self.assertEqual(2000, modalitiesReadback['tata']['Port']) self.assertEqual('GenericNoWildcardInDates', modalitiesReadback['tata']['Manufacturer']) self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/modalities/toto', [ "STORESCP", "localhost", 2000, 'InvalidManufacturerName' ])) self.assertTrue('store' in DoGet(_REMOTE, '/modalities/toto')) self.assertTrue('store' in DoGet(_REMOTE, '/modalities/tata')) DoDelete(_REMOTE, '/modalities/toto') DoDelete(_REMOTE, '/modalities/tata') self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/modalities/toto')) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/modalities/tata')) def test_update_peers(self): # curl -X PUT http://localhost:8042/peers/toto -d '["http://localhost:8042/"]' -v try: DoDelete(_REMOTE, '/peers/toto') except: pass try: DoDelete(_REMOTE, '/peers/tata') except: pass self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/peers/toto')) DoPut(_REMOTE, '/peers/toto', [ 'http://localhost:8042/' ]) DoPut(_REMOTE, '/peers/tata', { 'Url': 'http://localhost:8042/', 'Username': 'user', 'Password' : 'pass', 'RemoteSelf' : 'self' }) self.assertTrue('tata' in DoGet(_REMOTE, '/peers')) peersReadback = DoGet(_REMOTE, '/peers?expand') self.assertEqual('http://localhost:8042/', peersReadback['tata']['Url']) self.assertEqual('user', peersReadback['tata']['Username']) if IsOrthancVersionAbove(_REMOTE, 1, 5, 4): self.assertEqual(None, peersReadback['tata']['Password']) # make sure no sensitive data is included self.assertFalse(peersReadback['tata']['Pkcs11']) # make sure no sensitive data is included self.assertEqual('self', peersReadback['tata']['RemoteSelf']) else: self.assertFalse('Password' in peersReadback['tata']) # make sure no sensitive data is included self.assertFalse('Pkcs11' in peersReadback['tata']) # make sure no sensitive data is included self.assertFalse('RemoteSelf' in peersReadback['tata']) self.assertFalse('CertificateFile' in peersReadback['tata']) # make sure no sensitive data is included self.assertFalse('CertificateKeyFile' in peersReadback['tata']) # make sure no sensitive data is included self.assertFalse('CertificateKeyPassword' in peersReadback['tata']) # make sure no sensitive data is included self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/peers/toto', [ 'http://localhost:8042/', 'a' ])) self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/peers/toto', [ 'http://localhost:8042/', 'a', 'b', 'c' ])) self.assertTrue('store' in DoGet(_REMOTE, '/peers/toto')) self.assertTrue('store' in DoGet(_REMOTE, '/peers/tata')) DoDelete(_REMOTE, '/peers/toto') DoDelete(_REMOTE, '/peers/tata') self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/peers/toto')) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/peers/tata')) def test_mesterhazy_modification(self): # When I modify a series ( eg. curl # http://localhost:8042/series/uidhere/modify -X POST -d # '{"Replace":{"SeriesDate":"19990101"}}' ) the modified # series is added to a new Study, instead of the existing # Study. Fixed in Orthanc 0.7.5 u = UploadInstance(_REMOTE, 'DummyCT.dcm') study = 'b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0' series = 'f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe' modified = DoPost(_REMOTE, '/series/%s/modify' % series, json.dumps({ "Replace" : { "SeriesDate" : "19990101" }})) self.assertEqual(study, DoGet(_REMOTE, '/series/%s' % modified['ID']) ['ParentStudy']) def test_create(self): i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'PatientName' : 'Jodogne', 'Modality' : 'CT', 'SOPClassUID' : '1.2.840.10008.5.1.4.1.1.1', 'PixelData' : 'data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAUAAAAFCAYAAACNbyblAAAAHElEQVQI12P4//8/w38GIAXDIBKE0DHxgljNBAAO9TXL0Y4OHwAAAABJRU5ErkJggg==' # red dot in RGBA })) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i['ID']).strip()) self.assertEqual('CT', DoGet(_REMOTE, '/instances/%s/content/Modality' % i['ID']).strip()) png = GetImage(_REMOTE, '/instances/%s/preview' % i['ID']) self.assertEqual((5, 5), png.size) j = DoGet(_REMOTE, i['Path']) self.assertEqual('Instance', j['Type']) self.assertEqual(j['ID'], i['ID']) def test_pilates(self): # "SCU failed error when accessing orthanc with osirix" by # Pilates Agentur (Mar 10, 2014 at 9:33 PM) i = UploadInstance(_REMOTE, 'PilatesArgenturGEUltrasoundOsiriX.dcm')['ID'] self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) j = DoPost(_REMOTE, '/modalities/orthanctest/store', str(i), 'text/plain') self.assertEqual(1, len(DoGet(_LOCAL, '/patients'))) def test_shared_tags(self): a = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm')['ID'] b = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0002.dcm')['ID'] p = DoGet(_REMOTE, '/patients')[0] self.assertTrue('0010,0010' in DoGet(_REMOTE, '/patients/%s/shared-tags' % p)) self.assertTrue('PatientName' in DoGet(_REMOTE, '/patients/%s/shared-tags?simplify' % p)) self.assertTrue('0010,0010' in DoGet(_REMOTE, '/patients/%s/shared-tags?short' % p)) self.assertEqual('KNEE', DoGet(_REMOTE, '/patients/%s/shared-tags' % p)['0010,0010']['Value']) self.assertEqual('KNEE', DoGet(_REMOTE, '/patients/%s/shared-tags?simplify' % p)['PatientName']) self.assertEqual('KNEE', DoGet(_REMOTE, '/patients/%s/shared-tags?short' % p)['0010,0010']) self.assertTrue('0008,1030' in DoGet(_REMOTE, '/patients/%s/shared-tags' % p)) self.assertTrue('StudyDescription' in DoGet(_REMOTE, '/patients/%s/shared-tags?simplify' % p)) self.assertTrue('0008,103e' in DoGet(_REMOTE, '/patients/%s/shared-tags' % p)) self.assertTrue('SeriesDescription' in DoGet(_REMOTE, '/patients/%s/shared-tags?simplify' % p)) self.assertFalse('0008,0018' in DoGet(_REMOTE, '/patients/%s/shared-tags' % p)) self.assertFalse('SOPInstanceUID' in DoGet(_REMOTE, '/patients/%s/shared-tags?simplify' % p)) self.assertTrue('0008,0018' in DoGet(_REMOTE, '/instances/%s/tags' % a)) self.assertTrue('SOPInstanceUID' in DoGet(_REMOTE, '/instances/%s/tags?simplify' % a)) def test_modules(self): a = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm')['ID'] p = DoGet(_REMOTE, '/patients')[0] s = DoGet(_REMOTE, '/studies')[0] t = DoGet(_REMOTE, '/series')[0] self.assertTrue('0010,0010' in DoGet(_REMOTE, '/patients/%s/module' % p)) self.assertTrue('PatientName' in DoGet(_REMOTE, '/patients/%s/module?simplify' % p)) self.assertTrue('0010,0010' in DoGet(_REMOTE, '/studies/%s/module-patient' % p)) self.assertTrue('PatientName' in DoGet(_REMOTE, '/studies/%s/module-patient?simplify' % p)) self.assertTrue('0008,1030' in DoGet(_REMOTE, '/studies/%s/module' % s)) self.assertTrue('StudyDescription' in DoGet(_REMOTE, '/studies/%s/module?simplify' % s)) self.assertTrue('0008,103e' in DoGet(_REMOTE, '/series/%s/module' % p)) self.assertTrue('SeriesDescription' in DoGet(_REMOTE, '/series/%s/module?simplify' % p)) self.assertTrue('0008,0018' in DoGet(_REMOTE, '/instances/%s/module' % a)) self.assertTrue('SOPInstanceUID' in DoGet(_REMOTE, '/instances/%s/module?simplify' % a)) def test_auto_directory(self): a = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm')['ID'] self.assertTrue('now' in DoGet(_REMOTE, '/tools')) self.assertTrue('dicom-conformance' in DoGet(_REMOTE, '/tools')) self.assertTrue('invalidate-tags' in DoGet(_REMOTE, '/tools')) self.assertTrue(len(DoGet(_REMOTE, '/tools/dicom-conformance')) > 1000) self.assertTrue('orthanctest' in DoGet(_REMOTE, '/modalities')) self.assertTrue('echo' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('find' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('find-instance' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('find-patient' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('find-series' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('find-study' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('store' in DoGet(_REMOTE, '/modalities/orthanctest')) self.assertTrue('store' in DoGet(_REMOTE, '/peers/peer')) self.assertTrue('matlab' in DoGet(_REMOTE, '/instances/%s/frames/0' % a)) self.assertTrue('raw' in DoGet(_REMOTE, '/instances/%s/frames/0' % a)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/tools/nope')) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/nope')) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/nope/nope.html')) self.assertEqual(404, DoGetRaw(_REMOTE, '/nope')[0].status) self.assertEqual(404, DoGetRaw(_REMOTE, '/nope/nope.html')[0].status) def test_echo(self): DoPost(_REMOTE, '/modalities/orthanctest/echo') def test_xml(self): json = DoGet(_REMOTE, '/tools', headers = { 'accept' : 'application/json' }) xml = minidom.parseString(DoGet(_REMOTE, '/tools', headers = { 'accept' : 'application/xml' })) items = xml.getElementsByTagName('root')[0].getElementsByTagName('item') self.assertEqual(len(items), len(json)) self.assertTrue('dicom-conformance' in json) ok = False for i in items: if i.childNodes[0].data == 'dicom-conformance': ok = True self.assertTrue(ok) def test_googlecode_issue_16(self): i = UploadInstance(_REMOTE, 'Issue16.dcm')['ID'] t = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i)['FrameIncrementPointer'] self.assertEqual('0018,1063', t) def test_googlecode_issue_22(self): s = UploadInstance(_REMOTE, 'Issue22.dcm')['ID'] a = [ "f804691f62197040438f4627c6b994f1", # Frame 0 "c69eee9a51eea3e8611e82e578897254", "315666be83e2d0111c77bc0996d84901", "3e27aa959d911172c48a1436443c72b1", "958642c9e7e9d232d3869faff546058c", "5e7ea8e3e4230cae707d143481355c59", "eda37f83558d858a596175aed8b2ad47", "486713bd2895c4ecbe0e97715ac7f80a", "091ef729eb169e67da8a0faa9631f9a8", "5aa2b8c7ffe0a483efaa8e12417686ca", "e2f39e85896fe58876654b94cd0b5013", "6fd2129e4950abbe1be053bc814d5da8", "c3331a8ba7a757f3d423735ab7fa81f9", "746f808582156734dd6b6fdfd3a0b72c", "8075ea2b227a70c60ea6b7b75a6bb190", "806b8b3e300c615099c11a5ec23465aa", "7c836aa298ba6eef96434579af631a11", "a0357dc9f4f72d73a885c33d7c287446", "f25ba3be1cc7d7fad95706adc199ea7d", "8b114c526b8cbed6cad8a3248b7b480c", "44e6670f127e612a2b4aa60a0d207698", "b8945f90fe02facf2ace24ca1ecbe0a5", "95c796c2fa8f59018b15cf2987b1f79b", "ce0a51ab30224205b44920221dc27351", # Frame 23 ] self.assertEqual(24, len(DoGet(_REMOTE, '/instances/%s/frames' % s))) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/frames/24/preview' % s)) for i in range(len(a)): self.assertEqual(a[i], ComputeMD5(DoGet(_REMOTE, '/instances/%s/frames/%d/preview' % (s, i)))) def test_googlecode_issue_19(self): # This is an image with "YBR_FULL" photometric interpretation, it is not supported by Orthanc # gdcmconv -i /home/jodogne/DICOM/GdcmDatabase/US_DataSet/HDI5000_US/3EAF5E01 -w -o Issue19.dcm a = UploadInstance(_REMOTE, 'Issue19.dcm')['ID'] if not HasGdcmPlugin(_REMOTE): self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/941ad3c8-05d05b88-560459f9-0eae0e20-6cddd533/preview')) def test_googlecode_issue_37(self): # Same test for issues 35 and 37. Fixed in Orthanc 0.9.1 u = UploadInstance(_REMOTE, 'Beaufix/IM-0001-0001.dcm')['ID'] a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Series', 'CaseSensitive' : True, 'Query' : { 'StationName' : 'SMR4-MP3' }}) self.assertEqual(1, len(a)) def test_rest_find(self): # Upload 8 instances for i in range(2): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T1/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T2/IM-0001-000%d.dcm' % (i + 1)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : False, 'Query' : { 'PatientName' : 'BRAINIX' }}) self.assertEqual(1, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : False, 'Query' : { 'PatientName' : 'BRAINIX\\KNEE\\NOPE' }}) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : False, 'Query' : { 'PatientName' : '*n*' }}) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : True, 'Query' : { 'PatientName' : '*n*' }}) self.assertEqual(0, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Expand' : True, 'Level' : 'Patient', 'CaseSensitive' : False, 'Query' : { 'PatientName' : '*ne*' }}) self.assertEqual(1, len(a)) self.assertEqual('20080822', a[0]['MainDicomTags']['PatientBirthDate']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : True, 'Query' : { 'PatientName' : '*ne*' }}) self.assertEqual(0, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'CaseSensitive' : True, 'Query' : { 'PatientName' : '*NE*' }}) self.assertEqual(1, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Series', 'CaseSensitive' : True, 'Query' : { 'PatientName' : '*NE*' }}) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'CaseSensitive' : True, 'Query' : { 'PatientName' : '*NE*' }}) self.assertEqual(4, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'Query' : { }}) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { }}) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Series', 'Query' : { }}) self.assertEqual(4, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { }}) self.assertEqual(8, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '20061201-20061201' }}) self.assertEqual(1, len(a)) self.assertEqual('BRAINIX', a[0]['PatientMainDicomTags']['PatientName']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '20061201-20091201' }}) self.assertEqual(2, len(a)) for i in range(2): self.assertTrue(a[i]['PatientMainDicomTags']['PatientName'] in ['BRAINIX', 'KNEE']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { 'StudyDate' : '20061202-20061202' }}) self.assertEqual(0, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '-20061201' }}) self.assertEqual(1, len(a)) self.assertEqual('BRAINIX', a[0]['PatientMainDicomTags']['PatientName']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '-20051201' }}) self.assertEqual(0, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '20061201-' }}) self.assertEqual(2, len(a)) for i in range(2): self.assertTrue(a[i]['PatientMainDicomTags']['PatientName'] in ['BRAINIX', 'KNEE']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '20061202-' }}) self.assertEqual(1, len(a)) self.assertEqual('KNEE', a[0]['PatientMainDicomTags']['PatientName']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '20080819-' }}) self.assertEqual(1, len(a)) self.assertEqual('KNEE', a[0]['PatientMainDicomTags']['PatientName']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Expand' : True, 'Query' : { 'StudyDate' : '20080820-' }}) self.assertEqual(0, len(a)) def test_rest_query_retrieve(self): self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) # Upload 8 instances for i in range(2): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T1/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T2/IM-0001-000%d.dcm' % (i + 1)) self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) for p in DoGet(_REMOTE, '/patients'): DoPost(_REMOTE, '/modalities/orthanctest/store', p) DoDelete(_REMOTE, '/patients/%s' % p) for q in DoGet(_REMOTE, '/queries'): DoDelete(_REMOTE, '/queries/%s' % q) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(0, len(DoGet(_REMOTE, '/queries'))) a = DoPost(_REMOTE, '/modalities/orthanctest/query', { 'Level' : 'Series', 'Query' : { 'PatientName' : '*NE*', 'StudyDate' : '*', }})['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/queries'))) b = DoGet(_REMOTE, '/queries/%s' % a) self.assertTrue('answers' in b) self.assertTrue('level' in b) self.assertTrue('modality' in b) self.assertTrue('query' in b) self.assertTrue('retrieve' in b) self.assertEqual('Series', DoGet(_REMOTE, '/queries/%s/level' % a)) self.assertEqual('orthanctest', DoGet(_REMOTE, '/queries/%s/modality' % a)) q = DoGet(_REMOTE, '/queries/%s/query?simplify' % a) self.assertEqual(2, len(q)) self.assertTrue('PatientName' in q) self.assertTrue('StudyDate' in q) self.assertEqual('*NE*', q['PatientName']) self.assertEqual('*', q['StudyDate']) self.assertEqual(2, len(DoGet(_REMOTE, '/queries/%s/answers' % a))) s = DoGet(_REMOTE, '/queries/%s/answers/0' % a) self.assertTrue('content' in s) self.assertTrue('retrieve' in s) s = DoGet(_REMOTE, '/queries/%s/answers/0/content?simplify' % a) self.assertEqual('887', s['PatientID']) self.assertEqual('2.16.840.1.113669.632.20.121711.10000160881', s['StudyInstanceUID']) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) DoPost(_REMOTE, '/queries/%s/answers/0/retrieve' % a, 'ORTHANC') self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(2, len(DoGet(_REMOTE, '/instances'))) DoPost(_REMOTE, '/queries/%s/answers/1/retrieve' % a, 'ORTHANC', 'application/json') # make sure the issue #36 is fixed (query/retrieve Rest API: /retrieve route shall accept application/json content type) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(2, len(DoGet(_REMOTE, '/series'))) self.assertEqual(4, len(DoGet(_REMOTE, '/instances'))) # New in Orthanc 1.4.3 s = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % a) self.assertEqual(2, len(s)) for i in range(2): self.assertEqual('SERIES', s[i]['QueryRetrieveLevel']) self.assertEqual('887', s[i]['PatientID']) self.assertEqual('2.16.840.1.113669.632.20.121711.10000160881', s[i]['StudyInstanceUID']) DoDelete(_REMOTE, '/queries/%s' % a) self.assertEqual(0, len(DoGet(_REMOTE, '/queries'))) def test_parent(self): u = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] patient = '6816cb19-844d5aee-85245eba-28e841e6-2414fae2' study = 'b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0' series = 'f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe' instance = '66a662ce-7430e543-bad44d47-0dc5a943-ec7a538d' self.assertEqual(instance, u) a = DoGet(_REMOTE, '/studies/%s/patient' % study) self.assertEqual('Patient', a['Type']) self.assertEqual(patient, a['ID']) a = DoGet(_REMOTE, '/series/%s/patient' % series) self.assertEqual('Patient', a['Type']) self.assertEqual(patient, a['ID']) a = DoGet(_REMOTE, '/series/%s/study' % series) self.assertEqual('Study', a['Type']) self.assertEqual(study, a['ID']) a = DoGet(_REMOTE, '/instances/%s/patient' % instance) self.assertEqual('Patient', a['Type']) self.assertEqual(patient, a['ID']) a = DoGet(_REMOTE, '/instances/%s/study' % instance) self.assertEqual('Study', a['Type']) self.assertEqual(study, a['ID']) a = DoGet(_REMOTE, '/instances/%s/series' % instance) self.assertEqual('Series', a['Type']) self.assertEqual(series, a['ID']) def test_shanon(self): def Anonymize(instance, replacements = {}): return DoPost(_REMOTE, '/instances/%s/anonymize' % instance, { 'Replace' : replacements, 'Force' : True, }, 'application/json') self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) u = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) tags = [ 'PatientID', 'StudyInstanceUID', 'SeriesInstanceUID', 'SOPInstanceUID', 'DeidentificationMethod' ] ids = [ 'ozp00SjY2xG', '1.2.840.113619.2.176.2025.1499492.7391.1171285944.390', '1.2.840.113619.2.176.2025.1499492.7391.1171285944.394', '1.2.840.113619.2.176.2025.1499492.7040.1171286242.109' ] a = ExtractDicomTags(Anonymize(u), tags) for i in range(4): self.assertNotEqual(ids[i], a[i]) self.assertTrue(a[4].startswith('Orthanc')) a = ExtractDicomTags(Anonymize(u, { 'PatientName' : 'toto' }), tags) for i in range(4): self.assertNotEqual(ids[i], a[i]) self.assertFalse(a[4].startswith('Orthanc')) a = ExtractDicomTags(Anonymize(u, { 'SOPInstanceUID' : 'instance' }), tags) self.assertEqual('instance', a[3]) self.assertFalse(a[4].startswith('Orthanc')) a = ExtractDicomTags(Anonymize(u, { 'SeriesInstanceUID' : 'series' }), tags) self.assertEqual('series', a[2]) self.assertFalse(a[4].startswith('Orthanc')) a = ExtractDicomTags(Anonymize(u, { 'StudyInstanceUID' : 'study' }), tags) self.assertEqual('study', a[1]) self.assertFalse(a[4].startswith('Orthanc')) a = ExtractDicomTags(Anonymize(u, { 'PatientID' : 'patient' }), tags) self.assertEqual('patient', a[0]) self.assertFalse(a[4].startswith('Orthanc')) a = ExtractDicomTags(Anonymize(u, { 'PatientID' : 'patient', 'StudyInstanceUID' : 'study', 'SeriesInstanceUID' : 'series', 'SOPInstanceUID' : 'instance' }), tags) self.assertEqual('patient', a[0]) self.assertFalse(a[4].startswith('Orthanc')) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) def test_shanon_2(self): def Modify(instance, replacements = {}): return DoPost(_REMOTE, '/instances/%s/modify' % instance, { 'Replace' : replacements, 'Force': True, }, 'application/json') self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) u = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) tags = [ 'PatientID', 'StudyInstanceUID', 'SeriesInstanceUID', 'SOPInstanceUID', 'DeidentificationMethod' ] ids = [ 'ozp00SjY2xG', '1.2.840.113619.2.176.2025.1499492.7391.1171285944.390', '1.2.840.113619.2.176.2025.1499492.7391.1171285944.394', '1.2.840.113619.2.176.2025.1499492.7040.1171286242.109' ] a = ExtractDicomTags(Modify(u), tags) self.assertEqual(ids[0], a[0]) self.assertEqual(ids[1], a[1]) self.assertEqual(ids[2], a[2]) self.assertNotEqual(ids[3], a[3]) self.assertEqual(0, len(a[4])) a = ExtractDicomTags(Modify(u, { 'SOPInstanceUID' : 'instance' }), tags) self.assertEqual(ids[0], a[0]) self.assertEqual(ids[1], a[1]) self.assertEqual(ids[2], a[2]) self.assertEqual('instance', a[3]) a = ExtractDicomTags(Modify(u, { 'SeriesInstanceUID' : 'series' }), tags) self.assertEqual(ids[0], a[0]) self.assertEqual(ids[1], a[1]) self.assertEqual('series', a[2]) self.assertNotEqual(ids[3], a[3]) a = ExtractDicomTags(Modify(u, { 'StudyInstanceUID' : 'study' }), tags) self.assertEqual(ids[0], a[0]) self.assertEqual('study', a[1]) self.assertNotEqual(ids[2], a[2]) self.assertNotEqual(ids[3], a[3]) a = ExtractDicomTags(Modify(u, { 'PatientID' : 'patient' }), tags) self.assertEqual('patient', a[0]) self.assertNotEqual(ids[1], a[1]) self.assertNotEqual(ids[2], a[2]) self.assertNotEqual(ids[3], a[3]) a = ExtractDicomTags(Modify(u, { 'PatientID' : 'patient', 'StudyInstanceUID' : 'study', 'SeriesInstanceUID' : 'series', 'SOPInstanceUID' : 'instance' }), tags) self.assertEqual('patient', a[0]) self.assertEqual('study', a[1]) self.assertEqual('series', a[2]) self.assertEqual('instance', a[3]) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) def test_instances_tags(self): a = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm')['ID'] b = UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm')['ID'] #a = UploadInstance(_REMOTE, 'Cardiac/MR.X.1.2.276.0.7230010.3.1.4.2831157719.2256.1336386937.676343')['ID'] #b = UploadInstance(_REMOTE, 'Cardiac/MR.X.1.2.276.0.7230010.3.1.4.2831157719.2256.1336386925.676329')['ID'] i = DoGet(_REMOTE, '/patients/%s/instances-tags?simplify' % DoGet(_REMOTE, '/patients')[0]) self.assertEqual(2, len(i)) self.assertEqual('887', i[i.keys()[0]]['PatientID']) self.assertEqual('887', i[i.keys()[1]]['PatientID']) i = DoGet(_REMOTE, '/patients/%s/instances-tags?simplify' % DoGet(_REMOTE, '/studies')[0]) self.assertEqual(2, len(i)) self.assertEqual('887', i[i.keys()[0]]['PatientID']) self.assertEqual('887', i[i.keys()[1]]['PatientID']) self.assertEqual(2, len(DoGet(_REMOTE, '/series'))) i = DoGet(_REMOTE, '/patients/%s/instances-tags?simplify' % DoGet(_REMOTE, '/series')[0]) self.assertEqual(1, len(i)) self.assertEqual('887', i[i.keys()[0]]['PatientID']) i = DoGet(_REMOTE, '/patients/%s/instances-tags?simplify' % DoGet(_REMOTE, '/series')[1]) self.assertEqual(1, len(i)) self.assertEqual('887', i[i.keys()[0]]['PatientID']) i = DoGet(_REMOTE, '/patients/%s/instances-tags?short' % DoGet(_REMOTE, '/series')[1]) self.assertEqual(1, len(i)) self.assertEqual('887', i[i.keys()[0]]['0010,0020']) def test_lookup(self): a = DoPost(_REMOTE, '/tools/lookup', 'ozp00SjY2xG') self.assertEqual(0, len(a)) UploadInstance(_REMOTE, 'DummyCT.dcm') a = DoPost(_REMOTE, '/tools/lookup', 'ozp00SjY2xG') self.assertEqual(1, len(a)) self.assertEqual('Patient', a[0]['Type']) self.assertEqual('6816cb19-844d5aee-85245eba-28e841e6-2414fae2', a[0]['ID']) self.assertEqual('/patients/%s' % a[0]['ID'], a[0]['Path']) a = DoPost(_REMOTE, '/tools/lookup', '1.2.840.113619.2.176.2025.1499492.7391.1171285944.390') self.assertEqual(1, len(a)) self.assertEqual('Study', a[0]['Type']) self.assertEqual('b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0', a[0]['ID']) self.assertEqual('/studies/%s' % a[0]['ID'], a[0]['Path']) a = DoPost(_REMOTE, '/tools/lookup', '1.2.840.113619.2.176.2025.1499492.7391.1171285944.394') self.assertEqual(1, len(a)) self.assertEqual('Series', a[0]['Type']) self.assertEqual('f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe', a[0]['ID']) self.assertEqual('/series/%s' % a[0]['ID'], a[0]['Path']) a = DoPost(_REMOTE, '/tools/lookup', '1.2.840.113619.2.176.2025.1499492.7040.1171286242.109') self.assertEqual(1, len(a)) self.assertEqual('Instance', a[0]['Type']) self.assertEqual('66a662ce-7430e543-bad44d47-0dc5a943-ec7a538d', a[0]['ID']) self.assertEqual('/instances/%s' % a[0]['ID'], a[0]['Path']) DropOrthanc(_REMOTE) a = DoPost(_REMOTE, '/tools/lookup', '3113719P') self.assertEqual(0, len(a)) def test_autorouting(self): knee1 = 'Knee/T1/IM-0001-0001.dcm' knee2 = 'Knee/T2/IM-0001-0002.dcm' other = 'Brainix/Flair/IM-0001-0001.dcm' # Check that this version is >= 0.8.0 self.assertTrue(IsDefinedInLua(_REMOTE, '_InitializeJob')) self.assertTrue('orthanctest' in DoGet(_REMOTE, '/modalities')) UploadInstance(_REMOTE, knee1) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) DropOrthanc(_REMOTE) DropOrthanc(_LOCAL) InstallLuaScriptFromPath(_REMOTE, 'Lua/Autorouting.lua') UploadInstance(_REMOTE, knee1) UploadInstance(_REMOTE, knee2) UploadInstance(_REMOTE, other) WaitEmpty(_REMOTE) UninstallLuaCallbacks(_REMOTE) self.assertEqual(3, len(DoGet(_LOCAL, '/instances'))) DropOrthanc(_REMOTE) DropOrthanc(_LOCAL) InstallLuaScriptFromPath(_REMOTE, 'Lua/AutoroutingConditional.lua') UploadInstance(_REMOTE, knee1) UploadInstance(_REMOTE, knee2) UploadInstance(_REMOTE, other) WaitEmpty(_REMOTE) UninstallLuaCallbacks(_REMOTE) self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) DropOrthanc(_REMOTE) DropOrthanc(_LOCAL) InstallLuaScriptFromPath(_REMOTE, 'Lua/AutoroutingModification.lua') UploadInstance(_REMOTE, knee1) WaitEmpty(_REMOTE) UninstallLuaCallbacks(_REMOTE) i = DoGet(_LOCAL, '/instances') self.assertEqual(1, len(i)) with tempfile.NamedTemporaryFile(delete = True) as f: f.write(DoGet(_LOCAL, '/instances/%s/file' % i[0])) f.flush() routed = subprocess.check_output([ FindExecutable('dcm2xml'), f.name ]) self.assertEqual('My Medical Device', re.search('"StationName">(.*?)<', routed).group(1).strip()) self.assertEqual(None, re.search('"MilitaryRank"', routed)) self.assertEqual(None, re.search('"0051,0010"', routed)) # A private tag def test_storescu_rf(self): i = UploadInstance(_REMOTE, 'KarstenHilbertRF.dcm')['ID'] self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) j = DoPost(_REMOTE, '/modalities/orthanctest/store', str(i), 'text/plain') self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) def test_anonymize_instance(self): def AnonymizeAndUpload(instanceId, parameters): return DoPost(_REMOTE, '/instances', DoPost(_REMOTE, '/instances/%s/anonymize' % instanceId, parameters, 'application/json'), 'application/dicom')['ID'] def ModifyAndUpload(instanceId, parameters): return DoPost(_REMOTE, '/instances', DoPost(_REMOTE, '/instances/%s/modify' % instanceId, parameters, 'application/json'), 'application/dicom')['ID'] a = UploadInstance(_REMOTE, 'PrivateMDNTags.dcm')['ID'] s1 = DoGet(_REMOTE, '/instances/%s/content/PatientName' % a) s2 = DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % a) # Some private tag s3 = DoGet(_REMOTE, '/instances/%s/content/StudyDescription' % a) s4 = DoGet(_REMOTE, '/instances/%s/content/SeriesDescription' % a) s5 = DoGet(_REMOTE, '/instances/%s/content/InstitutionName' % a) b = AnonymizeAndUpload(a, '{}') self.assertNotEqual(s1, DoGet(_REMOTE, '/instances/%s/content/PatientName' % b)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % b)) # Keep private tag (only OK since Orthanc 0.8.0) b = AnonymizeAndUpload(a, '{"Keep":["00e1-10c2"]}') self.assertNotEqual(s1, DoGet(_REMOTE, '/instances/%s/content/PatientName' % b)) self.assertEqual(s2, DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % b)) b = AnonymizeAndUpload(a, '{"Keep":["00e1,10c2","PatientName"]}') self.assertEqual(s1, DoGet(_REMOTE, '/instances/%s/content/PatientName' % b)) self.assertEqual(s2, DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % b)) b = AnonymizeAndUpload(a, '{"Keep":["PatientName"],"Replace":{"00e1,10c2":"Hello"}}') self.assertEqual(s1, DoGet(_REMOTE, '/instances/%s/content/PatientName' % b)) self.assertTrue(DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % b).startswith('Hello')) # Examples from the Wiki b = AnonymizeAndUpload(a, '{"Replace":{"PatientName":"hello","0010-0020":"world"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": true,"Force":true}') self.assertEqual('hello', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % b).strip()) self.assertEqual('world', DoGet(_REMOTE, '/instances/%s/content/PatientID' % b).strip()) self.assertEqual(s3, DoGet(_REMOTE, '/instances/%s/content/0008,1030' % b)) self.assertEqual(s4, DoGet(_REMOTE, '/instances/%s/content/0008,103e' % b)) self.assertEqual(s4, DoGet(_REMOTE, '/instances/%s/content/0008-103E' % b)) self.assertEqual(s2, DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % b)) DoGet(_REMOTE, '/instances/%s/content/InstitutionName' % a) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/InstitutionName' % b)) b = ModifyAndUpload(a, '{"Replace":{"PatientName":"hello","PatientID":"world"},"Remove":["InstitutionName"],"RemovePrivateTags": true,"Force":true}') self.assertEqual('hello', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % b).strip()) self.assertEqual('world', DoGet(_REMOTE, '/instances/%s/content/PatientID' % b).strip()) self.assertEqual(s3, DoGet(_REMOTE, '/instances/%s/content/0008,1030' % b)) self.assertEqual(s4, DoGet(_REMOTE, '/instances/%s/content/0008,103e' % b)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/00e1-10c2' % b)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/InstitutionName' % b)) b = ModifyAndUpload(a, '{"Replace":{"PatientName":"hello","PatientID":"world"},"Force":true}') self.assertEqual('hello', DoGet(_REMOTE, '/instances/%s/content/0010-0010' % b).strip()) self.assertEqual('world', DoGet(_REMOTE, '/instances/%s/content/PatientID' % b).strip()) self.assertEqual(s2, DoGet(_REMOTE, '/instances/%s/content/00e1,10c2' % b)) self.assertEqual(s3, DoGet(_REMOTE, '/instances/%s/content/0008,1030' % b)) self.assertEqual(s4, DoGet(_REMOTE, '/instances/%s/content/0008-103E' % b)) self.assertEqual(s5, DoGet(_REMOTE, '/instances/%s/content/InstitutionName' % b)) # Test modify non-existing i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'PatientName' : 'Jodogne', 'Modality' : 'CT', }))['ID'] self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i).strip()) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/StudyDescription' % i)) self.assertEqual('CT', DoGet(_REMOTE, '/instances/%s/content/Modality' % i).strip()) b = ModifyAndUpload(i, '{"Replace":{"StudyDescription":"hello","Modality":"world"}}') self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % b).strip()) self.assertEqual('hello', DoGet(_REMOTE, '/instances/%s/content/StudyDescription' % b).strip()) self.assertEqual('world', DoGet(_REMOTE, '/instances/%s/content/Modality' % b).strip()) def test_incoming_jpeg(self): def storescu(image, acceptUnknownSopClassUid): if acceptUnknownSopClassUid: tmp = [ '-xf', GetDatabasePath('UnknownSopClassUid.cfg'), 'Default' ] else: tmp = [ '-xs' ] with open(os.devnull, 'w') as FNULL: subprocess.check_call([ FindExecutable('storescu') ] + tmp + [ _REMOTE['Server'], str(_REMOTE['DicomPort']), GetDatabasePath(image) ], stderr = FNULL) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) InstallLuaScriptFromPath(_REMOTE, 'Lua/TransferSyntaxDisable.lua') self.assertRaises(Exception, lambda: storescu('Knix/Loc/IM-0001-0001.dcm', False)) self.assertRaises(Exception, lambda: storescu('UnknownSopClassUid.dcm', True)) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) InstallLuaScriptFromPath(_REMOTE, 'Lua/TransferSyntaxEnable.lua') DoPost(_REMOTE, '/tools/execute-script', "print('All special transfer syntaxes are now accepted')") storescu('Knix/Loc/IM-0001-0001.dcm', False) storescu('UnknownSopClassUid.dcm', True) self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) def test_storescu_jpeg(self): self.assertEqual(0, len(DoGet(_REMOTE, '/exports')['Exports'])) knixStudy = 'b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0' i = UploadInstance(_REMOTE, 'Knix/Loc/IM-0001-0001.dcm')['ID'] # This is JPEG lossless self.assertEqual('1.2.840.10008.1.2.4.70', DoGet(_REMOTE, '/instances/%s/header' % i)['0002,0010']['Value']) self.assertEqual('1.2.840.10008.1.2.4.70', DoGet(_REMOTE, '/instances/%s/header?simplify' % i)['TransferSyntaxUID']) self.assertEqual('1.2.840.10008.1.2.4.70', DoGet(_REMOTE, '/instances/%s/header?short' % i)['0002,0010']) UploadInstance(_REMOTE, 'Knix/Loc/IM-0001-0002.dcm') UploadInstance(_REMOTE, 'Knix/Loc/IM-0001-0003.dcm') a = UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] b = UploadInstance(_REMOTE, 'ColorTestImageJ.dcm')['ID'] self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) DoPost(_REMOTE, '/modalities/orthanctest/store', [ knixStudy, a, b ]) self.assertEqual(5, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(3, len(DoGet(_REMOTE, '/exports')['Exports'])) DropOrthanc(_REMOTE) self.assertEqual(0, len(DoGet(_REMOTE, '/exports')['Exports'])) def test_pixel_data(self): jpeg = UploadInstance(_REMOTE, 'Knix/Loc/IM-0001-0001.dcm')['ID'] color = UploadInstance(_REMOTE, 'ColorTestImageJ.dcm')['ID'] phenix = UploadInstance(_REMOTE, 'Phenix/IM-0001-0001.dcm')['ID'] phenixSize = 358 * 512 * 2 colorSize = 1000 * 1000 * 3 jpegSize = 51918 self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010' % phenix))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010' % color))) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010' % jpeg))) self.assertEqual(0, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010/0' % jpeg))) self.assertEqual(jpegSize, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010/1' % jpeg))) self.assertEqual(phenixSize, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010/0' % phenix))) self.assertEqual(colorSize, len(DoGet(_REMOTE, '/instances/%s/content/7fe0-0010/0' % color))) def test_decode_brainix(self): brainix = [ UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm')['ID'], # (*) UploadInstance(_REMOTE, 'Formats/JpegLossless.dcm')['ID'], # JPEG-LS, same as (*) (since Orthanc 0.7.6) UploadInstance(_REMOTE, 'Formats/Jpeg.dcm')['ID'], # JPEG, same as (*) (since Orthanc 0.7.6) ] h = '6fb11b932d535c2be04beabd99793ff8' maxValue = 426.0 truth = Image.open(GetDatabasePath('Formats/Brainix.png')) for i in brainix: self.AssertSameImages(truth.getdata(), '/instances/%s/image-int16' % i) self.AssertSameImages(truth.getdata(), '/instances/%s/image-uint16' % i) truth2 = map(lambda x: min(255, x), truth.getdata()) for i in brainix: self.AssertSameImages(truth2, '/instances/%s/image-uint8' % i) truth2 = map(lambda x: x * 255.0 / maxValue, truth.getdata()) for i in brainix: self.AssertSameImages(truth2, '/instances/%s/preview' % i) for i in brainix: self.assertEqual(h, ComputeMD5(DoGet(_REMOTE, '/instances/%s/matlab' % i))) def test_decode_color(self): imagej = UploadInstance(_REMOTE, 'ColorTestImageJ.dcm')['ID'] color = UploadInstance(_REMOTE, 'ColorTestMalaterre.dcm')['ID'] for i in [ imagej, color ]: for j in [ 'image-uint8', 'image-uint16', 'image-int16' ]: self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/%s' % (i, j))) self.assertEqual('c14c687f7a1ea9fe022479fc87c67274', ComputeMD5(DoGet(_REMOTE, '/instances/%s/preview' % imagej))) self.assertEqual('a87d122918a56f803bcfe9d2586b9125', ComputeMD5(DoGet(_REMOTE, '/instances/%s/preview' % color))) self.assertEqual('30cc46bfa7aba77a40e4178f6184c25a', ComputeMD5(DoGet(_REMOTE, '/instances/%s/matlab' % imagej))) self.assertEqual('ff195005cef06b59666fd220a9b4cd9a', ComputeMD5(DoGet(_REMOTE, '/instances/%s/matlab' % color))) def test_decode_rf(self): rf = UploadInstance(_REMOTE, 'KarstenHilbertRF.dcm')['ID'] truth = Image.open(GetDatabasePath('Formats/KarstenHilbertRF.png')) self.AssertSameImages(truth.getdata(), '/instances/%s/image-uint8' % rf) self.AssertSameImages(truth.getdata(), '/instances/%s/image-uint16' % rf) self.AssertSameImages(truth.getdata(), '/instances/%s/image-int16' % rf) self.AssertSameImages(truth.getdata(), '/instances/%s/preview' % rf) self.assertEqual('42254d70efd2f4a1b8f3455909689f0e', ComputeMD5(DoGet(_REMOTE, '/instances/%s/matlab' % rf))) def test_decode_multiframe(self): mf = UploadInstance(_REMOTE, 'Multiframe.dcm')['ID'] # Test the first frame truth = Image.open(GetDatabasePath('Formats/Multiframe0.png')) self.AssertSameImages(truth.getdata(), '/instances/%s/image-uint8' % mf) self.AssertSameImages(truth.getdata(), '/instances/%s/image-uint16' % mf) self.AssertSameImages(truth.getdata(), '/instances/%s/image-int16' % mf) self.AssertSameImages(truth.getdata(), '/instances/%s/preview' % mf) self.assertEqual('9812b99d93bbcd4e7684ded089b5dfb3', ComputeMD5(DoGet(_REMOTE, '/instances/%s/matlab' % mf))) self.AssertSameImages(truth.getdata(), '/instances/%s/frames/0/image-uint16' % mf) # Test the last frame truth = Image.open(GetDatabasePath('Formats/Multiframe75.png')) self.AssertSameImages(truth.getdata(), '/instances/%s/frames/75/image-uint16' % mf) def test_decode_signed(self): signed = UploadInstance(_REMOTE, 'SignedCT.dcm')['ID'] minValue = -2000 maxValue = 4042 truth = Image.open(GetDatabasePath('Formats/SignedCT.png')) self.AssertSameImages(truth.getdata(), '/instances/%s/image-int16' % signed) truth2 = map(lambda x: 0 if x >= 32768 else x, truth.getdata()) self.AssertSameImages(truth2, '/instances/%s/image-uint16' % signed) truth3 = map(lambda x: 255 if x >= 256 else x, truth2) self.AssertSameImages(truth3, '/instances/%s/image-uint8' % signed) tmp = map(lambda x: x - 65536 if x >= 32768 else x, truth.getdata()) tmp = map(lambda x: (255.0 * (x - minValue)) / (maxValue - minValue), tmp) self.AssertSameImages(tmp, '/instances/%s/preview' % signed) self.assertEqual('b57e6c872a3da50877c7da689b03a444', ComputeMD5(DoGet(_REMOTE, '/instances/%s/matlab' % signed))) def test_googlecode_issue_32(self): self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/tools/default-encoding', 'nope')) self.assertEqual('Windows1251', DoPut(_REMOTE, '/tools/default-encoding', 'Windows1251')) self.assertEqual('Windows1251', DoGet(_REMOTE, '/tools/default-encoding')) f = UploadInstance(_REMOTE, 'Issue32.dcm')['ID'] tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % f) self.assertEqual(u'Рентгенография', tags['SeriesDescription']) self.assertEqual(u'Таз', tags['BodyPartExamined']) self.assertEqual(u'Прямая', tags['ViewPosition']) # Replay the same test using Latin1 as default encoding: This must fail self.assertEqual('Latin1', DoPut(_REMOTE, '/tools/default-encoding', 'Latin1')) DoDelete(_REMOTE, '/instances/%s' % f) f = UploadInstance(_REMOTE, 'Issue32.dcm')['ID'] tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % f) self.assertNotEqual(u'Рентгенография', tags['SeriesDescription']) def test_encodings(self): # Latin-1 (ISO_IR 100) brainix = UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm')['ID'] tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % brainix) self.assertEqual(u'IRM cérébrale, neuro-crâne', tags['StudyDescription']) # Latin-2 (ISO_IR 101) a = UploadInstance(_REMOTE, 'MarekLatin2.dcm')['ID'] i = DoGet(_REMOTE, '/instances/%s/simplified-tags' % a) # dcm2xml MarekLatin2.dcm | iconv -f latin2 -t utf-8 | xmllint --format - self.assertEqual('Imię i Nazwisko osoby opisującej', i['ContentSequence'][4]['ConceptNameCodeSequence'][0]['CodeMeaning'].encode('utf-8')) def test_storescu_custom_aet(self): # This tests a feature introduced in Orthanc 0.9.1: "Custom # setting of the local AET during C-Store SCU (both in Lua and # in the REST API)." # https://groups.google.com/forum/#!msg/orthanc-users/o5qMULformU/wZjW2iSaMcAJ self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) a = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') b = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0002.dcm') c = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0003.dcm') j = DoPost(_REMOTE, '/modalities/orthanctest/store', { 'LocalAet' : 'YOP', 'Resources' : [ a['ID'], b['ID'] ] }) self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) self.assertEqual('YOP', DoGet(_LOCAL, '/instances/%s/metadata/RemoteAET' % a['ID'])) DropOrthanc(_LOCAL) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) j = DoPost(_REMOTE, '/modalities/orthanctest/store', { 'Resources' : [ c['ID'] ] }) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) self.assertEqual('ORTHANC', DoGet(_LOCAL, '/instances/%s/metadata/RemoteAET' % c['ID'])) DropOrthanc(_REMOTE) DropOrthanc(_LOCAL) InstallLuaScriptFromPath(_REMOTE, 'Lua/AutoroutingChangeAet.lua') DoPost(_REMOTE, '/tools/execute-script', 'aet = "HELLO"', 'application/lua') self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') WaitEmpty(_REMOTE) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) self.assertEqual('HELLO', DoGet(_LOCAL, '/instances/%s/metadata/RemoteAET' % a['ID'])) DoPost(_REMOTE, '/tools/execute-script', 'aet = nill', 'application/lua') UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0002.dcm') WaitEmpty(_REMOTE) self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) self.assertEqual('ORTHANC', DoGet(_LOCAL, '/instances/%s/metadata/RemoteAET' % b['ID'])) def test_resources_since_limit(self): # Upload 16 instances for i in range(4): UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T1/IM-0001-000%d.dcm' % (i + 1)) UploadInstance(_REMOTE, 'Knee/T2/IM-0001-000%d.dcm' % (i + 1)) self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(4, len(DoGet(_REMOTE, '/series'))) self.assertEqual(16, len(DoGet(_REMOTE, '/instances'))) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/patients&since=10' % i)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/patients&limit=10' % i)) self.assertEqual(0, len(DoGet(_REMOTE, '/patients?since=0&limit=0'))) self.assertEqual(2, len(DoGet(_REMOTE, '/patients?since=0&limit=100'))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies?since=0&limit=100'))) self.assertEqual(4, len(DoGet(_REMOTE, '/series?since=0&limit=100'))) self.assertEqual(16, len(DoGet(_REMOTE, '/instances?since=0&limit=100'))) self.assertEqual(1, len(DoGet(_REMOTE, '/patients?since=1&limit=100'))) self.assertEqual(0, len(DoGet(_REMOTE, '/patients?since=2&limit=100'))) self.assertEqual(0, len(DoGet(_REMOTE, '/patients?since=3&limit=100'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies?since=1&limit=100'))) self.assertEqual(3, len(DoGet(_REMOTE, '/series?since=1&limit=100'))) self.assertEqual(2, len(DoGet(_REMOTE, '/series?since=2&limit=100'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series?since=3&limit=100'))) self.assertEqual(0, len(DoGet(_REMOTE, '/series?since=4&limit=100'))) self.assertEqual(0, len(DoGet(_REMOTE, '/series?since=100&limit=100'))) self.assertEqual(15, len(DoGet(_REMOTE, '/instances?since=1&limit=100'))) for limit in [ 1, 2, 3, 7, 16, 17 ]: s = {} since = 0 while True: t = DoGet(_REMOTE, '/instances?since=%d&limit=%d' % (since, limit)) if len(t) == 0: break since += len(t) for i in t: s[i] = None self.assertEqual(16, len(s)) for instance in DoGet(_REMOTE, '/instances'): self.assertTrue(instance in s) def test_create_pdf(self): # Upload 4 instances brainixInstance = UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') brainixPatient = '16738bc3-e47ed42a-43ce044c-a3414a45-cb069bd0' brainixStudy = '27f7126f-4f66fb14-03f4081b-f9341db2-53925988' brainixEpi = '2ac1316d-3e432022-62eabff2-c59f5475-9b1ac3f8' with open(GetDatabasePath('HelloWorld.pdf'), 'rb') as f: pdf = f.read() i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Tags' : { 'PatientName' : 'Jodogne', 'Modality' : 'CT', }, 'Content' : 'data:application/pdf;base64,' + base64.b64encode(pdf) })) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i['ID']).strip()) self.assertEqual('OT', DoGet(_REMOTE, '/instances/%s/content/Modality' % i['ID']).strip()) b = DoGet(_REMOTE, '/instances/%s/content/0042-0011' % i['ID']) self.assertEqual(len(b), len(pdf) + 1) self.assertEqual(ComputeMD5(b), ComputeMD5(pdf + '\0')) self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Parent' : brainixPatient, 'Tags' : { 'PatientName' : 'Jodogne', } }))) i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Parent' : brainixPatient, 'Tags' : { 'StudyDescription' : 'PDF^Patient' }, 'Content' : 'data:application/pdf;base64,' + base64.b64encode(pdf) })) self.assertEqual(brainixPatient, DoGet(_REMOTE, '/instances/%s/patient' % i['ID'])['ID']) i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Parent' : brainixStudy, 'Tags' : { 'SeriesDescription' : 'PDF^Study' }, 'Content' : 'data:application/pdf;base64,' + base64.b64encode(pdf) })) self.assertEqual(brainixStudy, DoGet(_REMOTE, '/instances/%s/study' % i['ID'])['ID']) i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Parent' : brainixEpi, 'Tags' : { 'SpecificCharacterSet' : 'ISO_IR 13' }, 'Content' : 'data:application/pdf;base64,' + base64.b64encode(pdf) })) self.assertEqual(brainixEpi, DoGet(_REMOTE, '/instances/%s/series' % i['ID'])['ID']) b = DoGet(_REMOTE, '/instances/%s/pdf' % i['ID']) self.assertEqual(len(b), len(pdf)) self.assertEqual(ComputeMD5(b), ComputeMD5(pdf)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/pdf' % brainixInstance)) def test_create_series(self): i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Tags' : { 'SpecificCharacterSet' : 'ISO_IR 100', 'PatientName' : 'Sébastien Jodogne', 'Modality' : 'CT', }, 'Content' : [ { 'Content': 'data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAUAAAAFCAYAAACNbyblAAAAHElEQVQI12P4//8/w38GIAXDIBKE0DHxgljNBAAO9TXL0Y4OHwAAAABJRU5ErkJggg==', # red dot in RGBA 'Tags' : { 'ImageComments' : 'Tutu' } }, 'data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAYAAAAf8/9hAAAAoUlEQVQ4jZ2SWw3EIBREjwUsYAELa2EtoAULFUCyXAtroRZqoRbox254BdLC/DZnZjoXWJFgCDg8egW2CBEhEnDzyRk+Ecxz2KP/0AL8S99T+jQccAVs22qKwAuPuq0uyNg9cPLh3am+pe/dkHLZtqJHj6vXJrZ7nvzvxxgemXgUwnGfXqpee09mUwp8m022OYP6bLF7mVuVe0y/umxinsAXRd9z0k1ubWsAAAAASUVORK5CYII=', ] })) s = DoGet(_REMOTE, i['Path']) self.assertEqual('Series', s['Type']) self.assertEqual(s['ID'], i['ID']) self.assertEqual(2, len(s['Instances'])) self.assertEqual(2, s['ExpectedNumberOfInstances']) self.assertEqual('Complete', s['Status']) a = DoGet(_REMOTE, '/instances/%s/tags?simplify' % s['Instances'][0]) b = DoGet(_REMOTE, '/instances/%s/tags?simplify' % s['Instances'][1]) self.assertTrue('ImageComments' in a or 'ImageComments' in b) if 'ImageComments' in a: self.assertEqual('Tutu', a['ImageComments']) else: self.assertEqual('Tutu', b['ImageComments']) patient = DoGet(_REMOTE, '/instances/%s/patient' % s['Instances'][0]) self.assertEqual(patient['MainDicomTags']['PatientName'].encode('utf-8'), 'Sébastien Jodogne') def test_create_binary(self): binary = ''.join(map(chr, range(256))) encoded = 'data:application/octet-stream;base64,' + base64.b64encode(binary) tags = { 'PatientName' : 'Jodogne', '8899-8899' : encoded } i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Tags' : tags, 'PrivateCreator' : 'TestBinary', })) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i['ID']).strip()) self.assertEqual(binary, DoGet(_REMOTE, '/instances/%s/content/8899-8899' % i['ID']).strip()) i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'InterpretBinaryTags' : False, 'Tags' : tags, 'PrivateCreator' : 'TestBinary', })) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i['ID']).strip()) self.assertEqual(encoded, DoGet(_REMOTE, '/instances/%s/content/8899-8899' % i['ID'])[0:-1]) def test_patient_ids_collision(self): # Upload 3 instances from 3 different studies, but with the # same PatientID for i in range(3): UploadInstance(_REMOTE, 'PatientIdsCollision/Image%d.dcm' % (i + 1)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'Query' : { 'PatientName' : '*' }}) self.assertEqual(1, len(a)) self.assertEqual('COMMON', DoGet(_REMOTE, '/patients/%s' % a[0]) ['MainDicomTags']['PatientID']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'CaseSensitive' : True, 'Query' : { 'PatientName' : 'FOO\\HELLO' }}) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Series', 'CaseSensitive' : False, 'Query' : { 'PatientName' : 'Foo' }}) self.assertEqual(1, len(a)) self.assertEqual('FOO^SERIES', DoGet(_REMOTE, '/series/%s/study' % a[0]) ['MainDicomTags']['StudyDescription']) self.assertEqual('FOO', DoGet(_REMOTE, '/series/%s/study' % a[0]) ['PatientMainDicomTags']['PatientName']) self.assertEqual('COMMON', DoGet(_REMOTE, '/series/%s/study' % a[0]) ['PatientMainDicomTags']['PatientID']) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { 'PatientName' : '*' }}) self.assertEqual(3, len(a)) d = map(lambda x: DoGet(_REMOTE, '/studies/%s' % x) ['MainDicomTags']['StudyDescription'], a) self.assertTrue('FOO^SERIES' in d) self.assertTrue('HELLO^SERIES' in d) self.assertTrue('WORLD^SERIES' in d) d = map(lambda x: DoGet(_REMOTE, '/studies/%s' % x) ['PatientMainDicomTags']['PatientID'], a) self.assertEqual(1, len(set(d))) self.assertEqual('COMMON', d[0]) for i in a: d = DoGet(_REMOTE, '/studies/%s' % i) ['MainDicomTags']['StudyDescription'] p = DoGet(_REMOTE, '/studies/%s' % i) ['PatientMainDicomTags']['PatientName'] self.assertEqual('%s^SERIES' % p, d) def test_bitbucket_issue_4(self): UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0002.dcm') UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0003.dcm') UploadInstance(_REMOTE, 'Formats/Jpeg.dcm') UploadInstance(_REMOTE, 'Formats/JpegLossless.dcm') UploadInstance(_REMOTE, 'Formats/Rle.dcm') self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(6, len(DoGet(_REMOTE, '/instances'))) p = DoGet(_REMOTE, '/patients') self.assertEqual(2, len(p)) i1 = map(lambda x: x['ID'], DoGet(_REMOTE, '/patients/%s/instances' % p[0])) i2 = map(lambda x: x['ID'], DoGet(_REMOTE, '/patients/%s/instances' % p[1])) self.assertEqual(3, len(i1)) self.assertEqual(3, len(i2)) j = DoPost(_REMOTE, '/modalities/orthanctest/store', i2[0:1] + i1 + i2[1:3]) self.assertEqual(6, len(DoGet(_LOCAL, '/instances'))) def test_create_sequence(self): i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ 'Tags' : { 'SpecificCharacterSet': 'ISO_IR 100', # Encode using Latin1 'PatientName': 'Jodogne^', 'ReferencedStudySequence': GenerateTestSequence(), } }))['ID'] self.assertEqual('Jodogne^', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i)) self.assertEqual('Hello^', DoGet(_REMOTE, '/instances/%s/content/ReferencedStudySequence/0/StudyDescription' % i)) self.assertEqual('Toto', DoGet(_REMOTE, '/instances/%s/content/ReferencedStudySequence/0/ReferencedStudySequence/0/StudyDescription' % i)) self.assertEqual('Tata', DoGet(_REMOTE, '/instances/%s/content/ReferencedStudySequence/0/ReferencedStudySequence/1/StudyDescription' % i)) self.assertEqual(u'Sébastien^'.encode('latin-1'), DoGet(_REMOTE, '/instances/%s/content/ReferencedStudySequence/1/StudyDescription' % i)) def test_modify_sequence(self): i = UploadInstance(_REMOTE, 'PrivateTags.dcm')['ID'] self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/content/ReferencedStudySequence' % i)) j = DoPost(_REMOTE, '/instances/%s/modify' % i, json.dumps({ "Replace" : { "PatientName" : "hello", 'ReferencedStudySequence': GenerateTestSequence(), }, }), 'application/json') j = DoPost(_REMOTE, '/instances', j, 'application/dicom')['ID'] DoDelete(_REMOTE, '/instances/%s' % i) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/content/ReferencedStudySequence' % j))) def test_compression(self): i = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] data = DoGetRaw(_REMOTE, '/instances/%s/attachments/dicom-as-json/data' % i)[1] # "StorageCompression" is enabled in the Orthanc to be tested, # uncompress the data before running the test if DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/is-compressed' % i) != 0: DoPost(_REMOTE, '/instances/%s/attachments/dicom-as-json/uncompress' % i) cs = DoGet(_REMOTE, '/statistics')['TotalDiskSize'] us = DoGet(_REMOTE, '/statistics')['TotalUncompressedSize'] size = DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/size' % i) md5 = DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/md5' % i) self.assertEqual(data, DoGetRaw(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-data' % i)[1]) self.assertEqual(md5, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-md5' % i)) self.assertEqual(size, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-size' % i)) ops = DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json' % i) self.assertTrue('compress' in ops) self.assertTrue('uncompress' in ops) self.assertTrue('is-compressed' in ops) self.assertEqual(0, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/is-compressed' % i)) DoPost(_REMOTE, '/instances/%s/attachments/dicom-as-json/verify-md5' % i) DoPost(_REMOTE, '/instances/%s/attachments/dicom-as-json/compress' % i) DoPost(_REMOTE, '/instances/%s/attachments/dicom-as-json/verify-md5' % i) self.assertEqual(1, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/is-compressed' % i)) self.assertLess(cs, DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual(us, DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) self.assertGreater(len(data), len(DoGetRaw(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-data' % i)[1])) self.assertGreater(size, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-size' % i)) self.assertEqual(size, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/size' % i)) self.assertEqual(md5, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/md5' % i)) self.assertNotEqual(md5, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-md5' % i)) DoPost(_REMOTE, '/instances/%s/attachments/dicom-as-json/uncompress' % i) DoPost(_REMOTE, '/instances/%s/attachments/dicom-as-json/verify-md5' % i) self.assertEqual(0, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/is-compressed' % i)) self.assertEqual(data, DoGetRaw(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-data' % i)[1]) self.assertEqual(size, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-size' % i)) self.assertEqual(size, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/size' % i)) self.assertEqual(md5, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/md5' % i)) self.assertEqual(md5, DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/compressed-md5' % i)) self.assertEqual(cs, DoGet(_REMOTE, '/statistics')['TotalDiskSize']) self.assertEqual(us, DoGet(_REMOTE, '/statistics')['TotalUncompressedSize']) def test_ordered_slices(self): i = UploadInstance(_REMOTE, 'Multiframe.dcm')['ID'] s = DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries'] o = DoGet(_REMOTE, '/series/%s/ordered-slices' % s) self.assertEqual('Sequence', o['Type']) self.assertEqual(1, len(o['Dicom'])) self.assertEqual('/instances/9e05eb0a-18b6268c-e0d36085-8ddab517-3b5aec02/file', o['Dicom'][0]) self.assertEqual(76, len(o['Slices'])) for j in range(76): self.assertEqual('/instances/9e05eb0a-18b6268c-e0d36085-8ddab517-3b5aec02/frames/%d' % j, o['Slices'][j]) self.assertEqual(1, len(o['SlicesShort'])) self.assertEqual('9e05eb0a-18b6268c-e0d36085-8ddab517-3b5aec02', o['SlicesShort'][0][0]) self.assertEqual(0, o['SlicesShort'][0][1]) self.assertEqual(76, o['SlicesShort'][0][2]) i = UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm')['ID'] j = UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0002.dcm')['ID'] k = UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0003.dcm')['ID'] s = DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries'] o = DoGet(_REMOTE, '/series/%s/ordered-slices' % s) self.assertEqual('Volume', o['Type']) self.assertEqual(3, len(o['Dicom'])) self.assertEqual(3, len(o['Slices'])) self.assertEqual('/instances/%s/file' % i, o['Dicom'][2]) self.assertEqual('/instances/%s/file' % j, o['Dicom'][1]) self.assertEqual('/instances/%s/file' % k, o['Dicom'][0]) self.assertEqual('/instances/%s/frames/0' % i, o['Slices'][2]) self.assertEqual('/instances/%s/frames/0' % j, o['Slices'][1]) self.assertEqual('/instances/%s/frames/0' % k, o['Slices'][0]) self.assertEqual(3, len(o['SlicesShort'])) self.assertEqual(k, o['SlicesShort'][0][0]) self.assertEqual(0, o['SlicesShort'][0][1]) self.assertEqual(1, o['SlicesShort'][0][2]) self.assertEqual(j, o['SlicesShort'][1][0]) self.assertEqual(0, o['SlicesShort'][1][1]) self.assertEqual(1, o['SlicesShort'][1][2]) self.assertEqual(i, o['SlicesShort'][2][0]) self.assertEqual(0, o['SlicesShort'][2][1]) self.assertEqual(1, o['SlicesShort'][2][2]) i = UploadInstance(_REMOTE, 'Beaufix/IM-0001-0001.dcm')['ID'] j = UploadInstance(_REMOTE, 'Beaufix/IM-0001-0002.dcm')['ID'] s = DoGet(_REMOTE, '/instances/%s' % i)['ParentSeries'] o = DoGet(_REMOTE, '/series/%s/ordered-slices' % s) self.assertEqual('Sequence', o['Type']) self.assertEqual(2, len(o['Dicom'])) self.assertEqual(2, len(o['Slices'])) self.assertEqual('/instances/%s/file' % i, o['Dicom'][0]) self.assertEqual('/instances/%s/file' % j, o['Dicom'][1]) self.assertEqual('/instances/%s/frames/0' % i, o['Slices'][0]) self.assertEqual('/instances/%s/frames/0' % j, o['Slices'][1]) self.assertEqual(2, len(o['SlicesShort'])) self.assertEqual(i, o['SlicesShort'][0][0]) self.assertEqual(0, o['SlicesShort'][0][1]) self.assertEqual(1, o['SlicesShort'][0][2]) self.assertEqual(j, o['SlicesShort'][1][0]) self.assertEqual(0, o['SlicesShort'][1][1]) self.assertEqual(1, o['SlicesShort'][1][2]) def test_incoming_movescu_accession(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') # No matching patient, so no job is created self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) CallMoveScu([ '--study', '-k', '0008,0052=STUDY', '-k', 'AccessionNumber=nope' ]) self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) CallMoveScu([ '--study', '-k', '0008,0052=PATIENT', '-k', 'AccessionNumber=A10003245599' ]) self.assertEqual(0, len(DoGet(_LOCAL, '/patients'))) # 1 Matching patient, track the job self.assertTrue(MonitorJob(_REMOTE, lambda: CallMoveScu([ '--study', '-k', '0008,0052=STUDY', '-k', 'AccessionNumber=A10003245599' ]))) self.assertEqual(1, len(DoGet(_LOCAL, '/patients'))) def test_dicom_to_json(self): i = UploadInstance(_REMOTE, 'PrivateMDNTags.dcm')['ID'] j = UploadInstance(_REMOTE, 'PrivateTags.dcm')['ID'] t = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) with open(GetDatabasePath('PrivateMDNTagsSimplify.json'), 'r') as f: self.assertTrue(CompareTags(t, json.loads(f.read()), [ # Tags for compatibility with DCMTK 3.6.0 'RETIRED_OtherPatientIDs', 'OtherPatientIDs', 'ACR_NEMA_2C_VariablePixelDataGroupLength', ])) t = DoGet(_REMOTE, '/instances/%s/tags' % i) with open(GetDatabasePath('PrivateMDNTagsFull.json'), 'r') as f: self.assertTrue(CompareTags(t, json.loads(f.read()), [ ])) t = DoGet(_REMOTE, '/instances/%s/tags?simplify' % j) with open(GetDatabasePath('PrivateTagsSimplify.json'), 'r') as f: self.assertTrue(CompareTags(t, json.loads(f.read()), [ ])) t = DoGet(_REMOTE, '/instances/%s/tags' % j) with open(GetDatabasePath('PrivateTagsFull.json'), 'r') as f: a = json.loads(f.read()) aa = json.dumps(a).replace('2e+022', '2e+22') tt = json.dumps(t).replace('2e+022', '2e+22') self.assertEqual(aa, tt) def test_batch_archive(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0002.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0002.dcm') UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0002.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0002.dcm') s = DoPost(_REMOTE, '/tools/create-archive', [ ]) z = zipfile.ZipFile(StringIO(s), "r") self.assertEqual(0, len(z.namelist())) # One patient s = DoPost(_REMOTE, '/tools/create-archive', [ 'ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17' ]) z = zipfile.ZipFile(StringIO(s), "r") self.assertEqual(4, len(z.namelist())) # One patient + twice its study + one series from other patient s = DoPost(_REMOTE, '/tools/create-archive', [ 'ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17', '0a9b3153-2512774b-2d9580de-1fc3dcf6-3bd83918', '1e2c125c-411b8e86-3f4fe68e-a7584dd3-c6da78f0' ]) z = zipfile.ZipFile(StringIO(s), "r") self.assertEqual(6, len(z.namelist())) # One patient + one series + one instance s = DoPost(_REMOTE, '/tools/create-archive', [ 'ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17', '1e2c125c-411b8e86-3f4fe68e-a7584dd3-c6da78f0', '1d429ccb-bdcc78a1-7d129d6a-ba4966ed-fe4dbd87' ]) z = zipfile.ZipFile(StringIO(s), "r") self.assertEqual(7, len(z.namelist())) def test_decode_brainix_as_jpeg(self): i = UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm')['ID'] j = GetImage(_REMOTE, '/instances/%s/preview' % i) self.assertEqual('PNG', j.format) self.assertEqual(j.size[0], 256) self.assertEqual(j.size[1], 256) j = GetImage(_REMOTE, '/instances/%s/preview' % i, headers = { 'Accept' : '*/*' }) self.assertEqual('PNG', j.format) j = GetImage(_REMOTE, '/instances/%s/preview' % i, headers = { 'Accept' : 'image/*' }) self.assertEqual('PNG', j.format) j = GetImage(_REMOTE, '/instances/%s/preview' % i, headers = { 'Accept' : 'image/png' }) self.assertEqual('PNG', j.format) j = GetImage(_REMOTE, '/instances/%s/preview' % i, headers = { 'Accept' : 'image/jpeg' }) self.assertEqual('JPEG', j.format) self.assertEqual(j.size[0], 256) self.assertEqual(j.size[1], 256) a = len(DoGet(_REMOTE, '/instances/%s/preview?quality=50' % i, headers = { 'Accept' : 'image/jpeg' })) b = len(DoGet(_REMOTE, '/instances/%s/preview' % i, headers = { 'Accept' : 'image/jpeg' })) self.assertLess(a, b) j = GetImage(_REMOTE, '/instances/%s/image-uint8' % i, headers = { 'Accept' : 'image/jpeg' }) self.assertEqual('JPEG', j.format) # 16bit encoding is not supported with JPEG self.assertRaises(Exception, lambda: GetImage(_REMOTE, '/instances/%s/image-uint16' % i, headers = { 'Accept' : 'image/jpeg' })) self.assertRaises(Exception, lambda: GetImage(_REMOTE, '/instances/%s/image-int16' % i, headers = { 'Accept' : 'image/jpeg' })) # No matching content type self.assertRaises(Exception, lambda: GetImage(_REMOTE, '/instances/%s/preview' % i, headers = { 'Accept' : 'application/pdf' })) def test_media_encodings(self): ascii = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm')['ID'] latin1 = UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm')['ID'] latin2 = UploadInstance(_REMOTE, 'MarekLatin2.dcm')['ID'] tmp = DoPost(_REMOTE, '/tools/create-media', [ascii,latin1,latin2]) z = zipfile.ZipFile(StringIO(tmp), "r") self.assertEqual(4, len(z.namelist())) self.assertTrue('IMAGES/IM0' in z.namelist()) self.assertTrue('IMAGES/IM1' in z.namelist()) self.assertTrue('IMAGES/IM2' in z.namelist()) self.assertTrue('DICOMDIR' in z.namelist()) try: os.remove('/tmp/DICOMDIR') except: # The file does not exist pass z.extract('DICOMDIR', '/tmp') a = subprocess.check_output([ FindExecutable('dciodvfy'), '/tmp/DICOMDIR' ], stderr = subprocess.STDOUT).split('\n') a = subprocess.check_output([ FindExecutable('dcentvfy'), '/tmp/DICOMDIR' ], stderr = subprocess.STDOUT).split('\n') self.assertEqual(1, len(a)) self.assertEqual('', a[0]) a = subprocess.check_output([ FindExecutable('dcm2xml'), '/tmp/DICOMDIR' ]) self.assertTrue(re.search('1.3.46.670589.11.17521.5.0.3124.2008081908590448738', a) != None) self.assertTrue(re.search('1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114333648576', a) != None) self.assertTrue(re.search('1.2.826.0.1.3680043.2.1569.1.4.323026757.1700.1399452091.57', a) != None) os.remove('/tmp/DICOMDIR') def test_findscu_counters(self): UploadInstance(_REMOTE, 'Comunix/Ct/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Comunix/Pet/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Comunix/Pet/IM-0001-0002.dcm') i = CallFindScu([ '-k', '0008,0052=PATIENT', '-k', 'NumberOfPatientRelatedStudies' ]) s = re.findall('\(0020,1200\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) self.assertTrue('1 ' in s) i = CallFindScu([ '-k', '0008,0052=PATIENT', '-k', 'NumberOfPatientRelatedSeries' ]) s = re.findall('\(0020,1202\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) self.assertTrue('2 ' in s) i = CallFindScu([ '-k', '0008,0052=PATIENT', '-k', 'NumberOfPatientRelatedInstances' ]) s = re.findall('\(0020,1204\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) self.assertTrue('3 ' in s) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'NumberOfStudyRelatedSeries' ]) s = re.findall('\(0020,1206\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) self.assertTrue('2 ' in s) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'NumberOfStudyRelatedInstances' ]) s = re.findall('\(0020,1208\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) self.assertTrue('3 ' in s) i = CallFindScu([ '-k', '0008,0052=SERIES', '-k', 'NumberOfSeriesRelatedInstances' ]) s = re.findall('\(0020,1209\).*?\[(.*?)\]', i) self.assertEqual(2, len(s)) self.assertTrue('1 ' in s) self.assertTrue('2 ' in s) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'ModalitiesInStudy' ]) s = re.findall('\(0008,0061\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) t = map(lambda x: x.strip(), s[0].split('\\')) self.assertTrue('PT' in t) self.assertTrue('CT' in t) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'SOPClassesInStudy' ]) s = re.findall('\(0008,0062\).*?\[(.*?)\]', i) self.assertEqual(1, len(s)) t = map(lambda x: x.strip('\x00'), s[0].split('\\')) self.assertTrue('1.2.840.10008.5.1.4.1.1.2' in t) self.assertTrue('1.2.840.10008.5.1.4.1.1.128' in t) def test_decode_transfer_syntax(self): def Check(t, md5): i = UploadInstance(_REMOTE, 'TransferSyntaxes/%s.dcm' % t)['ID'] if t != '1.2.840.10008.1.2': # This file has no meta header transferSyntax = DoGet(_REMOTE, '/instances/%s/metadata/TransferSyntax' % i) self.assertEqual(t, transferSyntax) if md5 == None: self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/preview' % i)) else: m = ComputeMD5(DoGet(_REMOTE, '/instances/%s/preview' % i)) self.assertEqual(m, md5) Check('1.2.840.10008.1.2.1', 'fae08d5415c4c0cd2cdbae4522408631') Check('1.2.840.10008.1.2.2', 'f3d9784768b8feb54d6a50b6d5c37682') Check('1.2.840.10008.1.2.4.50', '496326046974eea718dbc16b997c646b') Check('1.2.840.10008.1.2.4.51', 'ccbe75909fe5c9f7361b48416a53fc41') Check('1.2.840.10008.1.2.4.57', '7bbefe11d976b1be4e568915c6a82fc3') Check('1.2.840.10008.1.2.4.70', '7132cfbc457305b04b59787030c785d2') Check('1.2.840.10008.1.2.4.80', '6ff51ae525d362e0d04f550a64075a0e') Check('1.2.840.10008.1.2.4.81', '801579ae7cbf28e604ea74f2c99fa2ca') Check('1.2.840.10008.1.2.5', '6ff51ae525d362e0d04f550a64075a0e') # RLE, supported since Orthanc 1.0.1 Check('1.2.840.10008.1.2', 'd54aed9f67a100984b42942cc2e9939b') # JPEG2k image, not supported without GDCM plugin if not HasGdcmPlugin(_REMOTE): Check('1.2.840.10008.1.2.4.90', None) Check('1.2.840.10008.1.2.4.91', None) def test_raw_frame(self): s = UploadInstance(_REMOTE, 'Issue22.dcm')['ID'] self.assertEqual(24, len(DoGet(_REMOTE, '/instances/%s/frames' % s))) a = DoGet(_REMOTE, '/instances/%s/frames/0/raw' % s) self.assertEqual(512 * 512 * 2, len(a)) self.assertEqual(512 * 512 * 2, len(DoGet(_REMOTE, '/instances/%s/frames/23/raw' % s))) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/frames/24/raw' % s)) self.assertEqual('1914287dc4d958eca21fdaacfb3482fa', ComputeMD5(a)) s = UploadInstance(_REMOTE, 'Multiframe.dcm')['ID'] self.assertEqual(76, len(DoGet(_REMOTE, '/instances/%s/frames' % s))) self.assertEqual(186274, len(DoGet(_REMOTE, '/instances/%s/frames/0/raw' % s))) self.assertEqual(189424, len(DoGet(_REMOTE, '/instances/%s/frames/75/raw' % s))) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/frames/76/raw' % s)) im = GetImage(_REMOTE, '/instances/%s/frames/0/raw' % s) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(512, im.size[1]) # Test an image with 2 JPEG frames spread over multiple fragments s = UploadInstance(_REMOTE, 'LenaTwiceWithFragments.dcm')['ID'] self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/frames' % s))) a = DoGet(_REMOTE, '/instances/%s/frames/0/raw' % s) b = DoGet(_REMOTE, '/instances/%s/frames/1/raw' % s) self.assertEqual(69214, len(a)) self.assertEqual(ComputeMD5(a), ComputeMD5(b)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/frames/2/raw' % s)) im = GetImage(_REMOTE, '/instances/%s/frames/0/raw' % s) self.assertEqual("RGB", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(512, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/frames/0/preview' % s) self.assertEqual("RGB", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(512, im.size[1]) def test_rest_movescu(self): self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) # Upload 4 instances UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0002.dcm') UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) for p in DoGet(_REMOTE, '/patients'): DoPost(_REMOTE, '/modalities/orthanctest/store', p) DoDelete(_REMOTE, '/patients/%s' % p) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) # Upload instance Brainix/Flair/IM-0001-0001.dcm DoPost(_REMOTE, '/modalities/orthanctest/move', { 'Level' : 'Instance', 'Resources' : [ { 'StudyInstanceUID' : '2.16.840.1.113669.632.20.1211.10000357775', 'SeriesInstanceUID' : '1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114285654497', 'SOPInstanceUID' : '1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114314079549', } ]}) # Upload series Brainix/Flair/* self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) DoPost(_REMOTE, '/modalities/orthanctest/move', { 'Level' : 'Series', 'Resources' : [ { 'StudyInstanceUID' : '2.16.840.1.113669.632.20.1211.10000357775', 'SeriesInstanceUID' : '1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114285654497', } ]}) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series'))) self.assertEqual(2, len(DoGet(_REMOTE, '/instances'))) # Upload series Brainix/Epi/* DoPost(_REMOTE, '/modalities/orthanctest/move', { 'Level' : 'Series', 'Resources' : [ { 'StudyInstanceUID' : '2.16.840.1.113669.632.20.1211.10000357775', 'SeriesInstanceUID' : '1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114314125550', } ]}) self.assertEqual(1, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(2, len(DoGet(_REMOTE, '/series'))) self.assertEqual(3, len(DoGet(_REMOTE, '/instances'))) # Upload study Knee/* DoPost(_REMOTE, '/modalities/orthanctest/move', { 'Level' : 'Study', 'Resources' : [ { 'StudyInstanceUID' : '2.16.840.1.113669.632.20.121711.10000160881', } ]}) self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(3, len(DoGet(_REMOTE, '/series'))) self.assertEqual(4, len(DoGet(_REMOTE, '/instances'))) # Reset for p in DoGet(_REMOTE, '/patients'): DoDelete(_REMOTE, '/patients/%s' % p) self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) # Upload all at once DoPost(_REMOTE, '/modalities/orthanctest/move', { 'Level' : 'Study', 'Resources' : [ { 'StudyInstanceUID' : '2.16.840.1.113669.632.20.121711.10000160881', }, { 'StudyInstanceUID' : '2.16.840.1.113669.632.20.1211.10000357775', } ]}) self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(3, len(DoGet(_REMOTE, '/series'))) self.assertEqual(4, len(DoGet(_REMOTE, '/instances'))) def test_reconstruct_json(self): self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) instance = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] first = DoGet(_REMOTE, '/instances/%s/tags' % instance) self.assertEqual('TWINOW', first['0008,1010']['Value']) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % instance))) # Cannot delete the "DICOM" attachment self.assertRaises(Exception, lambda: DoDelete(_REMOTE, '/instances/%s/attachments/dicom' % instance)) # Can delete the "DICOM as JSON" attachment r = DoDelete(_REMOTE, '/instances/%s/attachments/dicom-as-json' % instance) self.assertTrue(type(r) is dict and len(r) == 0) # Only the "DICOM" attachment subsists self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/attachments' % instance))) # Cannot manually reconstruct the "DICOM as JSON" attachment self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/patients/%s/attachments/dicom-as-json' % patient, 'hello')) # Transparently reconstruct the "DICOM as JSON" attachment self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json' % instance)) second = DoGet(_REMOTE, '/instances/%s/tags' % instance) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % instance))) third = DoGet(_REMOTE, '/instances/%s/attachments/dicom-as-json/data' % instance) self.assertEqual(str(first), str(second)) self.assertEqual(str(first), str(third)) def test_reconstruct_json2(self): self.assertEqual(0, len(DoGet(_REMOTE, '/patients'))) a = UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] b = UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm')['ID'] self.assertEqual('BRAINIX', DoGet(_REMOTE, '/instances/%s/tags?simplify' % a)['PatientName']) self.assertEqual('KNEE', DoGet(_REMOTE, '/instances/%s/tags?simplify' % b)['PatientName']) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % a))) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % b))) DoPost(_REMOTE, '/tools/invalidate-tags', '', 'text/plain') self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/attachments' % a))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances/%s/attachments' % b))) self.assertEqual('BRAINIX', DoGet(_REMOTE, '/instances/%s/tags?simplify' % a)['PatientName']) self.assertEqual('KNEE', DoGet(_REMOTE, '/instances/%s/tags?simplify' % b)['PatientName']) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % a))) self.assertEqual(2, len(DoGet(_REMOTE, '/instances/%s/attachments' % b))) def test_private_tags(self): i = UploadInstance(_REMOTE, 'PrivateMDNTags.dcm')['ID'] t = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) self.assertEqual('1.2.840.113704.1.111.6320.1342451261.21', t['PET-CT Multi Modality Name']) self.assertEqual('p37s0_na_ctac.img', t['Original Image Filename']) def test_findscu_encoding(self): # Check out ../Database/Encodings/Generate.sh TEST = u'Test-éüäöòДΘĝדصķћ๛ﾈİ' ENCODINGS = { 'Arabic' : [ 'ISO_IR 127' ], 'Ascii' : [ 'ISO_IR 6' ], # More accurately, ISO 646 'Cyrillic' : [ 'ISO_IR 144' ], 'Greek' : [ 'ISO_IR 126' ], 'Hebrew' : [ 'ISO_IR 138' ], 'Japanese' : [ 'ISO_IR 13', 'shift-jis' ], 'Latin1' : [ 'ISO_IR 100' ], 'Latin2' : [ 'ISO_IR 101' ], 'Latin3' : [ 'ISO_IR 109' ], 'Latin4' : [ 'ISO_IR 110' ], 'Latin5' : [ 'ISO_IR 148' ], 'Thai' : [ 'ISO_IR 166', 'tis-620' ], 'Utf8' : [ 'ISO_IR 192' ], } for name in ENCODINGS.iterkeys(): if len(ENCODINGS[name]) == 1: ENCODINGS[name].append(name.lower()) UploadInstance(_REMOTE, 'Encodings/Lena-utf8.dcm') for name in ENCODINGS.iterkeys(): self.assertEqual(name, DoPut(_REMOTE, '/tools/default-encoding', name)) self.assertEqual(name, DoGet(_REMOTE, '/tools/default-encoding')) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'SpecificCharacterSet', '-k', 'PatientName' ]) characterSet = re.findall('\(0008,0005\).*?\[(.*?)\]', i) self.assertEqual(1, len(characterSet)) self.assertEqual(ENCODINGS[name][0], characterSet[0].strip()) patientName = re.findall('\(0010,0010\).*?\[(.*?)\]', i) self.assertEqual(1, len(patientName)) expected = TEST.encode(ENCODINGS[name][1], 'ignore') self.assertEqual(expected, patientName[0].strip()) #for master in ENCODINGS: for master in [ 'Latin1', 'Utf8', 'Cyrillic' ]: # Shortcut to speedup tests self.assertEqual(master, DoPut(_REMOTE, '/tools/default-encoding', master)) self.assertEqual(master, DoGet(_REMOTE, '/tools/default-encoding')) for name in ENCODINGS: DropOrthanc(_REMOTE) UploadInstance(_REMOTE, 'Encodings/Lena-%s.dcm' % ENCODINGS[name][1]) i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', 'PatientID', '-k', 'SpecificCharacterSet', '-k', 'PatientName' ]) i = i.decode(ENCODINGS[master][1]) characterSet = re.findall('\(0008,0005\).*?\[(.*?)\]', i) self.assertEqual(1, len(characterSet)) self.assertEqual(ENCODINGS[master][0], characterSet[0].strip()) patientId = re.findall('\(0010,0020\).*?\[(.*?)\]', i) self.assertEqual(1, len(patientId)) self.assertEqual(ENCODINGS[name][1], patientId[0].strip()) patientName = re.findall('\(0010,0010\).*?\[(.*?)\]', i) self.assertEqual(1, len(patientName)) tmp = ENCODINGS[name][1] expected = TEST.encode(tmp, 'ignore').decode(tmp) tmp = ENCODINGS[master][1] expected = expected.encode(tmp, 'ignore').decode(tmp) self.assertEqual(expected, patientName[0].strip()) a = DoPost(_REMOTE, '/tools/find', { 'Expand' : True, 'Level' : 'Study', 'Query' : { }}) self.assertEqual(1, len(a)) tmp = ENCODINGS[name][1] self.assertEqual(TEST.encode(tmp, 'ignore').decode(tmp), a[0]["PatientMainDicomTags"]["PatientName"]) def test_reconstruct(self): def CompareMainDicomTag(expected, instance, level, tag): self.assertEqual(expected, DoGet(_REMOTE, '/instances/%s/%s' % (instance, level))['MainDicomTags'][tag].strip()) a = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] studies = DoGet(_REMOTE, '/studies/') self.assertEqual(1, len(DoGet(_REMOTE, '/patients/'))) self.assertEqual(1, len(studies)) self.assertEqual(1, len(DoGet(_REMOTE, '/series/'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances/'))) modified = DoPost(_REMOTE, '/studies/%s/modify' % studies[0], { "Replace" : { "StudyDescription" : "hello", "SeriesDescription" : "world", "SOPClassUID" : "test", "SOPInstanceUID" : "myid", }, "Keep" : [ "StudyInstanceUID", "SeriesInstanceUID" ], "Force" : True }) instances = DoGet(_REMOTE, '/instances/') self.assertEqual(1, len(DoGet(_REMOTE, '/patients/'))) self.assertEqual(1, len(DoGet(_REMOTE, '/studies/'))) self.assertEqual(1, len(DoGet(_REMOTE, '/series/'))) self.assertEqual(2, len(instances)) b = instances[0] if instances[1] == a else instances[1] CompareMainDicomTag('Knee (R)', a, 'study', 'StudyDescription') CompareMainDicomTag('AX. FSE PD', a, 'series', 'SeriesDescription') CompareMainDicomTag('1.2.840.113619.2.176.2025.1499492.7040.1171286242.109', a, '', 'SOPInstanceUID') CompareMainDicomTag('myid', b, '', 'SOPInstanceUID') self.assertEqual('1.2.840.10008.5.1.4.1.1.4', DoGet(_REMOTE, '/instances/%s/metadata/SopClassUid' % a).strip()) self.assertEqual('test', DoGet(_REMOTE, '/instances/%s/metadata/SopClassUid' % b).strip()) DoPost(_REMOTE, '/instances/%s/reconstruct' % b, {}) CompareMainDicomTag('hello', a, 'study', 'StudyDescription') CompareMainDicomTag('world', a, 'series', 'SeriesDescription') CompareMainDicomTag('1.2.840.113619.2.176.2025.1499492.7040.1171286242.109', a, '', 'SOPInstanceUID') def test_httpClient_lua(self): with open(GetDatabasePath('Lua/HttpClient.lua'), 'r') as f: result = DoPost(_REMOTE, '/tools/execute-script', f.read(), 'application/lua') self.assertIn('OK', result) def test_bitbucket_issue_44(self): # https://bitbucket.org/sjodogne/orthanc/issues/44/bad-interpretation-of-photometric UploadInstance(_REMOTE, 'Issue44/Monochrome1.dcm') UploadInstance(_REMOTE, 'Issue44/Monochrome2.dcm') # dcmcjpeg +ua +eb Monochrome1.dcm Monochrome1-Jpeg.dcm UploadInstance(_REMOTE, 'Issue44/Monochrome1-Jpeg.dcm') # dcmcjpeg +ua Monochrome1.dcm Monochrome1-JpegLS.dcm UploadInstance(_REMOTE, 'Issue44/Monochrome1-JpegLS.dcm') monochrome1 = 'bcdd600a-a6a9c522-5f0a6e84-8657c9f3-b76e59b7' monochrome1_jpeg = '9df82121-208a2da8-0038674a-3d7a773b-b7008cd2' monochrome1_jpegls = '0486d1a2-9165573f-b1976b20-e927b016-6b8d67ab' monochrome2 = 'f00947b7-f61f7164-c93414d1-c6fbda6a-9e92ed20' for i in [ monochrome1, monochrome1_jpeg, monochrome1_jpegls ]: im = GetImage(_REMOTE, '/instances/%s/preview' % i) self.assertEqual("L", im.mode) self.assertEqual(2010, im.size[0]) self.assertEqual(2446, im.size[1]) # This is the chest image, with MONOCHROME1. Raw background is # white (255), should be rendered as black (0) => invert if i == monochrome1_jpeg: # Add some tolerance because of JPEG destructive compression self.assertGreater(10, im.getpixel((0,0))) else: self.assertEqual(0, im.getpixel((0,0))) im = GetImage(_REMOTE, '/instances/%s/preview' % monochrome2) self.assertEqual("L", im.mode) self.assertEqual(1572, im.size[0]) self.assertEqual(2010, im.size[1]) # This is the key image, with MONOCHROME2. Raw background is # white (255), should be rendered as white (255) self.assertEqual(255, im.getpixel((0,0))) def test_bitbucket_issue_42(self): # https://bitbucket.org/sjodogne/orthanc/issues/42/fails-to-modify-a-dicom-video-file # This test fails on DCMTK 3.6.0, but succeeds in DCMTK 3.6.1 snapshots and DCMTK 3.6.2 UploadInstance(_REMOTE, 'Issue42.dcm')['ID'] modified = DoPost(_REMOTE, '/patients/da128605-e040d0c4-310615d2-3475da63-df2d1ef4/modify', '{"Replace":{"PatientID":"Hello","PatientName":"Sample patient name"},"Force":true}', 'application/json') self.assertTrue('PatientID' in modified) def test_rest_find_limit(self): # Check the "Since" and "Limit" parameters in URI "/tools/find" # Related to issue 53: https://bitbucket.org/sjodogne/orthanc/issues/53 # Upload 6 instances brainix = [] knee = [] for i in range(2): brainix.append(UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-000%d.dcm' % (i + 1)) ['ID']) brainix.append(UploadInstance(_REMOTE, 'Brainix/Epi/IM-0001-000%d.dcm' % (i + 1)) ['ID']) knee.append(UploadInstance(_REMOTE, 'Knee/T1/IM-0001-000%d.dcm' % (i + 1)) ['ID']) # Check using BRAINIX a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'B*' }, 'Limit' : 10 }) self.assertEqual(4, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'B*' }, 'Limit' : 4 }) self.assertEqual(4, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'B*' }, 'Since' : 2, 'Limit' : 4 }) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'B*' }, 'Limit' : 3 }) self.assertEqual(3, len(a)) b = [] for i in range(4): a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'B*' }, 'Limit' : 1, 'Since' : i }) self.assertEqual(1, len(a)) b.append(a[0]) # Check whether the two sets are equal through symmetric difference self.assertEqual(0, len(set(b) ^ set(brainix))) # Check using KNEE a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'K*' }, 'Limit' : 10 }) self.assertEqual(2, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'K*' }, 'Limit' : 2 }) self.assertEqual(2, len(a)) b = [] for i in range(2): a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Instance', 'Query' : { 'PatientName' : 'K*' }, 'Limit' : 1, 'Since' : i }) self.assertEqual(1, len(a)) b.append(a[0]) self.assertEqual(0, len(set(b) ^ set(knee))) def test_bitbucket_issue_46(self): # "PHI remaining after anonymization" # https://bitbucket.org/sjodogne/orthanc/issues/46 def GetAnonymizedTags(study, version): anonymized = DoPost(_REMOTE, '/studies/%s/anonymize' % study, { 'DicomVersion' : version }, 'application/json') ['ID'] a = DoGet(_REMOTE, '/studies/%s/instances' % anonymized) self.assertEqual(1, len(a)) instance = a[0]['ID'] return (instance, DoGet(_REMOTE, '/instances/%s/tags' % instance)) UploadInstance(_REMOTE, 'Issue44/Monochrome1.dcm') origStudy = '6068a14b-d4df27af-9ec22145-538772d8-74f228ff' # Add the 0032,1033 (Requesting Service) and the 0010,1060 # (Patient's Mother's Birth Name) tags newStudy = DoPost(_REMOTE, '/studies/%s/modify' % origStudy, '{"Replace":{"0010,1060":"OSIMIS","0032,1033":"MOTHER"}}', 'application/json')['ID'] # Use Table E.1-1 from PS 3.15-2008 # https://raw.githubusercontent.com/jodogne/dicom-specification/master/2008/08_15pu.pdf (instance, tags) = GetAnonymizedTags(newStudy, "2008") self.assertTrue('0032,1033' in tags) self.assertTrue('0010,1060' in tags) # Use Table E.1-1 from PS 3.15-2011 (only if Orthanc >= 1.2.1) # https://raw.githubusercontent.com/jodogne/dicom-specification/master/2008/08_15pu.pdf (instance, tags) = GetAnonymizedTags(newStudy, "2017c") self.assertFalse('0032,1033' in tags) self.assertFalse('0010,1060' in tags) t = {} for (key, value) in tags.iteritems(): t[value['Name']] = value['Value'] self.assertEqual('', t['StudyDate']) # Type 1 tag => cleared self.assertEqual('', t['StudyTime']) # Type 1 tag => cleared self.assertEqual('', t['PatientSex']) # Type 1 tag => cleared self.assertFalse('SeriesDate' in t) # Type 3 tag => null self.assertFalse('SeriesTime' in t) # Type 3 tag => null with tempfile.NamedTemporaryFile(delete = True) as f: # Run "dciodvfy" on the anonymized file to be sure it is still valid f.write(DoGet(_REMOTE, '/instances/%s/file' % instance)) f.flush() subprocess.check_output([ FindExecutable('dciodvfy'), f.name ], stderr = subprocess.STDOUT).split('\n') def test_bitbucket_issue_55(self): def Run(modify, query): self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) operation = 'modify' if modify else 'anonymize' self.assertRaises(Exception, lambda: DoPost( _REMOTE, '/studies/%s/%s' % (study, operation), query)) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) query["Force"] = True a = DoPost(_REMOTE, '/studies/%s/%s' % (study, operation), query)['Path'] self.assertEqual(2, len(DoGet(_REMOTE, '/instances'))) DoDelete(_REMOTE, a) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) UploadInstance(_REMOTE, 'DummyCT.dcm') study = 'b9c08539-26f93bde-c81ab0d7-bffaf2cb-a4d0bdd0' Run(True, { "Replace" : { "StudyInstanceUID" : "world" } }) Run(True, { "Replace" : { "SeriesInstanceUID" : "world" } }) Run(True, { "Replace" : { "SOPInstanceUID" : "world" } }) Run(False, { "Keep" : [ "StudyInstanceUID" ]}) Run(False, { "Keep" : [ "SeriesInstanceUID" ]}) Run(False, { "Keep" : [ "SOPInstanceUID" ]}) Run(False, { "Replace" : { "StudyInstanceUID" : "world" } }) Run(False, { "Replace" : { "SeriesInstanceUID" : "world" } }) Run(False, { "Replace" : { "SOPInstanceUID" : "world" } }) def test_bitbucket_issue_56(self): # Case-insensitive matching over accents. This test assumes # that the "CaseSensitivePN" configuration option of Orthanc # is set to "false" (default value). # https://bitbucket.org/sjodogne/orthanc/issues/56 def Check(name, expected, expectedSensitive): a = CallFindScu([ '-k', '0008,0005=ISO_IR 192', # Use UTF-8 '-k', '0008,0052=PATIENT', '-k', 'PatientName=%s' % name ]) patientNames = re.findall('\(0010,0010\).*?\[(.*?)\]', a) self.assertEqual(expected, len(patientNames)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : False, 'Query' : { 'PatientName' : name }}) self.assertEqual(expected, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Patient', 'CaseSensitive' : True, 'Query' : { 'PatientName' : name }}) self.assertEqual(expectedSensitive, len(a)) UploadInstance(_REMOTE, 'Encodings/Lena-latin1.dcm') # WildcardConstraint Check('TeSt*', 1, 0) Check('TeSt-a*', 0, 0) Check('TeSt-É*', 1, 0) Check('TeSt-é*', 1, 0) Check('Test-é*', 1, 1) # ListConstraint Check('Test-éüäöò\\nope', 1, 1) Check('Test-ÉÜÄÖÒ\\nope', 1, 0) # ValueConstraint Check('Test-éüäöò', 1, 1) Check('Test-ÉÜÄÖÒ', 1, 0) def test_gbk_alias(self): # https://groups.google.com/d/msg/orthanc-users/WMM8LMbjpUc/02-1f_yFCgAJ # This test fails on Orthanc <= 1.3.0 i = UploadInstance(_REMOTE, '2017-09-19-GBK-Tumashu.dcm')['ID'] tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) self.assertEqual(tags['PatientName'], u'徐浩凯') self.assertEqual(tags['InstitutionName'], u'灌云县疾病预防控制中心') def test_long_tag(self): i = UploadInstance(_REMOTE, 'DummyCTWithLongTag.dcm')['ID'] series = 'f2635388-f01d497a-15f7c06b-ad7dba06-c4c599fe' tags = DoGet(_REMOTE, '/instances/%s/tags' % i) self.assertTrue('0018,1020' in tags) self.assertEqual('SoftwareVersions', tags['0018,1020']['Name']) self.assertEqual('TooLong', tags['0018,1020']['Type']) self.assertEqual(None, tags['0018,1020']['Value']) tags = DoGet(_REMOTE, '/instances/%s/tags?ignore-length=0018-1020' % i) self.assertTrue('0018,1020' in tags) self.assertEqual('SoftwareVersions', tags['0018,1020']['Name']) self.assertEqual('String', tags['0018,1020']['Type']) self.assertTrue(tags['0018,1020']['Value'].startswith('Lorem ipsum dolor sit amet')) tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) self.assertTrue('SoftwareVersions' in tags) self.assertEqual(None, tags['SoftwareVersions']) self.assertTrue('HeartRate' in tags) self.assertEqual(474, int(tags['HeartRate'])) tags = DoGet(_REMOTE, '/instances/%s/simplified-tags' % i) self.assertTrue('SoftwareVersions' in tags) self.assertEqual(None, tags['SoftwareVersions']) tags = DoGet(_REMOTE, '/instances/%s/tags?simplify&ignore-length=0018-1020' % i) self.assertTrue('SoftwareVersions' in tags) self.assertTrue(tags['SoftwareVersions'].startswith('Lorem ipsum dolor sit amet')) tags = DoGet(_REMOTE, '/instances/%s/tags?simplify&ignore-length=SoftwareVersions' % i) self.assertTrue('SoftwareVersions' in tags) self.assertTrue(tags['SoftwareVersions'].startswith('Lorem ipsum dolor sit amet')) tags = DoGet(_REMOTE, '/series/%s/instances-tags' % series) self.assertEqual(1, len(tags)) self.assertTrue(i in tags.keys()) self.assertTrue('0018,1020' in tags[i]) self.assertEqual('TooLong', tags[i]['0018,1020']['Type']) tags = DoGet(_REMOTE, '/series/%s/instances-tags?ignore-length=SoftwareVersions' % series) self.assertEqual(1, len(tags)) self.assertTrue(i in tags.keys()) self.assertTrue('0018,1020' in tags[i]) self.assertEqual('String', tags[i]['0018,1020']['Type']) self.assertTrue(tags[i]['0018,1020']['Value'].startswith('Lorem ipsum dolor sit amet')) def test_extended_media(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') z = GetArchive(_REMOTE, '/patients/%s/media?extended' % DoGet(_REMOTE, '/patients')[0]) self.assertEqual(2, len(z.namelist())) self.assertTrue('IMAGES/IM0' in z.namelist()) self.assertTrue('DICOMDIR' in z.namelist()) try: os.remove('/tmp/DICOMDIR') except: # The file does not exist pass z.extract('DICOMDIR', '/tmp') a = subprocess.check_output([ FindExecutable('dciodvfy'), '/tmp/DICOMDIR' ], stderr = subprocess.STDOUT).split('\n') self.assertEqual(5, len(a)) self.assertTrue(a[0].startswith('Warning')) self.assertEqual('BasicDirectory', a[1]) self.assertTrue('not present in standard DICOM IOD' in a[2]) self.assertTrue('not present in standard DICOM IOD' in a[3]) self.assertEqual('', a[4]) a = subprocess.check_output([ FindExecutable('dcentvfy'), '/tmp/DICOMDIR' ], stderr = subprocess.STDOUT).split('\n') self.assertEqual(1, len(a)) self.assertEqual('', a[0]) a = subprocess.check_output([ FindExecutable('dcm2xml'), '/tmp/DICOMDIR' ]) self.assertTrue(re.search('1.3.46.670589.11.17521.5.0.3124.2008081908590448738', a) != None) # Check the presence of the series description (extended tag) self.assertTrue(re.search('T1W_aTSE', a) != None) os.remove('/tmp/DICOMDIR') def test_anonymize_relationships_1(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0002.dcm') study = '0a9b3153-2512774b-2d9580de-1fc3dcf6-3bd83918' anonymized = DoPost(_REMOTE, '/studies/%s/anonymize' % study, '{}', 'application/json')['ID'] a = DoGet(_REMOTE, '/studies/%s/instances' % study) self.assertEqual(2, len(a)) a1 = a[0]['ID'] a2 = a[1]['ID'] b = DoGet(_REMOTE, '/studies/%s/instances' % anonymized) self.assertEqual(2, len(b)) b1 = b[0]['ID'] b2 = b[1]['ID'] SEQUENCE = '/instances/%s/content/ReferencedImageSequence' SOP = '/instances/%s/content/ReferencedImageSequence/%d/ReferencedSOPInstanceUID' CLASS = '/instances/%s/content/ReferencedImageSequence/%d/ReferencedSOPClassUID' FRAME = '/instances/%s/content/FrameOfReferenceUID' self.assertEqual(DoGet(_REMOTE, FRAME % a1), DoGet(_REMOTE, FRAME % a2)) self.assertEqual(DoGet(_REMOTE, FRAME % b1), DoGet(_REMOTE, FRAME % b2)) self.assertNotEqual(DoGet(_REMOTE, FRAME % a1), DoGet(_REMOTE, FRAME % b1)) self.assertNotEqual(DoGet(_REMOTE, FRAME % a2), DoGet(_REMOTE, FRAME % b2)) self.assertEqual(3, len(DoGet(_REMOTE, SEQUENCE % a1))) self.assertEqual(3, len(DoGet(_REMOTE, SEQUENCE % a2))) self.assertEqual(3, len(DoGet(_REMOTE, SEQUENCE % b1))) self.assertEqual(3, len(DoGet(_REMOTE, SEQUENCE % b2))) for i in range(3): self.assertEqual(DoGet(_REMOTE, SOP % (a1, i)), DoGet(_REMOTE, SOP % (a2, i))) self.assertEqual(DoGet(_REMOTE, SOP % (b1, i)), DoGet(_REMOTE, SOP % (b2, i))) self.assertNotEqual(DoGet(_REMOTE, SOP % (a1, i)), DoGet(_REMOTE, SOP % (b1, i))) self.assertNotEqual(DoGet(_REMOTE, SOP % (a2, i)), DoGet(_REMOTE, SOP % (b2, i))) self.assertEqual(DoGet(_REMOTE, CLASS % (a1, i)), DoGet(_REMOTE, CLASS % (b1, i))) self.assertEqual(DoGet(_REMOTE, CLASS % (a2, i)), DoGet(_REMOTE, CLASS % (b2, i))) def test_anonymize_relationships_2(self): UploadInstance(_REMOTE, 'Comunix/Ct/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Comunix/Ct/IM-0001-0002.dcm') study = '6c65289b-db2fcb71-7eaf73f4-8e12470c-a4d6d7cf' anonymized = DoPost(_REMOTE, '/studies/%s/anonymize' % study, '{}', 'application/json')['ID'] a = DoGet(_REMOTE, '/studies/%s/instances' % study) self.assertEqual(2, len(a)) a1 = a[0]['ID'] a2 = a[1]['ID'] b = DoGet(_REMOTE, '/studies/%s/instances' % anonymized) self.assertEqual(2, len(b)) b1 = b[0]['ID'] b2 = b[1]['ID'] SEQUENCE = '/instances/%s/content/SourceImageSequence' SOP = '/instances/%s/content/SourceImageSequence/%d/ReferencedSOPInstanceUID' CLASS = '/instances/%s/content/SourceImageSequence/%d/ReferencedSOPClassUID' self.assertEqual(1, len(DoGet(_REMOTE, SEQUENCE % a1))) self.assertEqual(1, len(DoGet(_REMOTE, SEQUENCE % a2))) self.assertEqual(1, len(DoGet(_REMOTE, SEQUENCE % b1))) self.assertEqual(1, len(DoGet(_REMOTE, SEQUENCE % b2))) self.assertEqual(DoGet(_REMOTE, SOP % (a1, 0)), DoGet(_REMOTE, SOP % (a2, 0))) self.assertEqual(DoGet(_REMOTE, SOP % (b1, 0)), DoGet(_REMOTE, SOP % (b2, 0))) self.assertNotEqual(DoGet(_REMOTE, SOP % (a1, 0)), DoGet(_REMOTE, SOP % (b1, 0))) self.assertNotEqual(DoGet(_REMOTE, SOP % (a2, 0)), DoGet(_REMOTE, SOP % (b2, 0))) self.assertEqual(DoGet(_REMOTE, CLASS % (a1, 0)), DoGet(_REMOTE, CLASS % (b1, 0))) self.assertEqual(DoGet(_REMOTE, CLASS % (a2, 0)), DoGet(_REMOTE, CLASS % (b2, 0))) def test_anonymize_relationships_3(self): sr1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/StructuredReports/IM0')['ID'] mr1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/StructuredReports/IM631')['ID'] study = 'ef351eb2-c1147229-062736b8-35a151e3-e32d526b' anonymized = DoPost(_REMOTE, '/studies/%s/anonymize' % study, { "Keep" : [ "ContentSequence" ] }) ['ID'] a = DoGet(_REMOTE, '/studies/%s/instances' % anonymized) self.assertEqual(2, len(a)) if DoGet(_REMOTE, '/instances/%s/content/Modality' % a[0]['ID']) == 'SR': sr2 = a[0]['ID'] mr2 = a[1]['ID'] else: sr2 = a[1]['ID'] mr2 = a[0]['ID'] self.assertEqual(DoGet(_REMOTE, '/instances/%s/content/Modality' % sr1), DoGet(_REMOTE, '/instances/%s/content/Modality' % sr2)) self.assertEqual(DoGet(_REMOTE, '/instances/%s/content/Modality' % mr1), DoGet(_REMOTE, '/instances/%s/content/Modality' % mr2)) mrUid1 = DoGet(_REMOTE, '/instances/%s' % mr1)['MainDicomTags']['SOPInstanceUID'] mrUid2 = DoGet(_REMOTE, '/instances/%s' % mr2)['MainDicomTags']['SOPInstanceUID'] mrSeries1 = DoGet(_REMOTE, '/instances/%s/content/SeriesInstanceUID' % mr1).strip('\x00') mrSeries2 = DoGet(_REMOTE, '/instances/%s/content/SeriesInstanceUID' % mr2).strip('\x00') mrStudy1 = DoGet(_REMOTE, '/instances/%s/content/StudyInstanceUID' % mr1).strip('\x00') mrStudy2 = DoGet(_REMOTE, '/instances/%s/content/StudyInstanceUID' % mr2).strip('\x00') PATH1 = '/instances/%s/content/CurrentRequestedProcedureEvidenceSequence' PATH2 = PATH1 + '/0/ReferencedSeriesSequence' PATH3 = PATH2 + '/0/ReferencedSOPSequence' PATH4 = PATH3 + '/0/ReferencedSOPInstanceUID' PATH5 = PATH3 + '/0/ReferencedSOPClassUID' self.assertEqual(1, len(DoGet(_REMOTE, PATH1 % sr1))) self.assertEqual(1, len(DoGet(_REMOTE, PATH2 % sr1))) self.assertEqual(1, len(DoGet(_REMOTE, PATH3 % sr1))) self.assertEqual(DoGet(_REMOTE, PATH4 % sr1), mrUid1) self.assertEqual(mrSeries1, DoGet(_REMOTE, (PATH2 + '/0/SeriesInstanceUID') % sr1).strip('\x00')) self.assertEqual(mrStudy1, DoGet(_REMOTE, (PATH1 + '/0/StudyInstanceUID') % sr1).strip('\x00')) self.assertEqual(1, len(DoGet(_REMOTE, PATH1 % sr2))) self.assertEqual(1, len(DoGet(_REMOTE, PATH2 % sr2))) self.assertEqual(1, len(DoGet(_REMOTE, PATH3 % sr2))) self.assertEqual(DoGet(_REMOTE, PATH5 % sr1), DoGet(_REMOTE, PATH5 % sr2)) self.assertEqual(mrUid2, DoGet(_REMOTE, PATH4 % sr2).strip('\x00')) self.assertEqual(mrSeries2, DoGet(_REMOTE, (PATH2 + '/0/SeriesInstanceUID') % sr2).strip('\x00')) self.assertEqual(mrStudy2, DoGet(_REMOTE, (PATH1 + '/0/StudyInstanceUID') % sr2).strip('\x00')) content1 = DoGet(_REMOTE, '/instances/%s/tags?simplify' % sr1) ['ContentSequence'] content2 = DoGet(_REMOTE, '/instances/%s/tags?simplify' % sr2) ['ContentSequence'] self.assertEqual(str(content1), str(content2)) def test_bitbucket_issue_94(self): # "a simple instance modification should not modify FrameOfReferenceUID + ..." # https://bitbucket.org/sjodogne/orthanc/issues/94 i = UploadInstance(_REMOTE, 'Issue94.dcm')['ID'] source = DoGet(_REMOTE, '/instances/%s/attachments/dicom/data' % i) modified = DoPost(_REMOTE, '/instances/%s/modify' % i, { "Replace" : {"PatientID" : "toto"}, "Force": True}) anonymized = DoPost(_REMOTE, '/instances/%s/anonymize' % i) a = ExtractDicomTags(source, [ 'FrameOfReferenceUID' ]) self.assertEqual(1, len(a)) b = ExtractDicomTags(modified, [ 'FrameOfReferenceUID' ]) self.assertEqual(1, len(b)) c = ExtractDicomTags(anonymized, [ 'FrameOfReferenceUID' ]) self.assertEqual(1, len(c)) self.assertEqual(a, b) # Modified DICOM self.assertNotEqual(a, c) # Anonymized DICOM def test_metadata_origin(self): # Upload using the REST API i = UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm')['ID'] self.assertEqual('RestApi', DoGet(_REMOTE, '/instances/%s/metadata/Origin' % i)) self.assertEqual('', DoGet(_REMOTE, '/instances/%s/metadata/RemoteAET' % i)) self.assertNotEqual('', DoGet(_REMOTE, '/instances/%s/metadata/RemoteIP' % i)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/metadata/CalledAET' % i)) self.assertEqual('alice', DoGet(_REMOTE, '/instances/%s/metadata/HttpUsername' % i)) m = DoGet(_REMOTE, '/instances/%s/metadata?expand' % i) self.assertEqual('RestApi', m['Origin']) self.assertEqual('', m['RemoteAET']) self.assertNotEqual('', m['RemoteIP']) self.assertFalse('CalledAET' in m) self.assertEqual('alice', m['HttpUsername']) self.assertEqual('1.2.840.10008.1.2.4.91', m['TransferSyntax']) self.assertEqual('1.2.840.10008.5.1.4.1.1.4', m['SopClassUid']) self.assertEqual('1', m['IndexInSeries']) self.assertTrue('ReceptionDate' in m) DoDelete(_REMOTE, '/instances/%s' % i) # Upload using the DICOM protocol subprocess.check_call([ FindExecutable('storescu'), _REMOTE['Server'], str(_REMOTE['DicomPort']), GetDatabasePath('Knee/T1/IM-0001-0001.dcm'), '-xw' ]) # Propose JPEG2000 self.assertEqual('DicomProtocol', DoGet(_REMOTE, '/instances/%s/metadata/Origin' % i)) self.assertEqual('STORESCU', DoGet(_REMOTE, '/instances/%s/metadata/RemoteAET' % i)) self.assertNotEqual('', DoGet(_REMOTE, '/instances/%s/metadata/RemoteIP' % i)) self.assertEqual('ANY-SCP', DoGet(_REMOTE, '/instances/%s/metadata/CalledAET' % i)) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/instances/%s/metadata/HttpUsername' % i)) m = DoGet(_REMOTE, '/instances/%s/metadata?expand' % i) self.assertEqual('DicomProtocol', m['Origin']) self.assertEqual('STORESCU', m['RemoteAET']) self.assertNotEqual('', m['RemoteIP']) self.assertEqual('ANY-SCP', m['CalledAET']) self.assertFalse('HttpUsername' in m) self.assertEqual('1.2.840.10008.1.2.4.91', m['TransferSyntax']) self.assertEqual('1.2.840.10008.5.1.4.1.1.4', m['SopClassUid']) self.assertEqual('1', m['IndexInSeries']) self.assertTrue('ReceptionDate' in m) def test_lua_deadlock(self): # Rana Asim Wajid (2018-07-14): "It does seem that the issue # is with the lua script I'm using for conversion of images to # JPEG2000. When the script is used with 1.4.0 the first # instance appears to be stored and then everything just # halts, ie Orthanc wont respond to anything after that." # https://groups.google.com/d/msg/orthanc-users/Rc-Beb42xc8/JUgdzrmCAgAJ InstallLuaScriptFromPath(_REMOTE, 'Lua/Jpeg2000Conversion.lua') subprocess.check_call([ FindExecutable('storescu'), _REMOTE['Server'], str(_REMOTE['DicomPort']), GetDatabasePath('Brainix/Flair/IM-0001-0001.dcm'), GetDatabasePath('Brainix/Flair/IM-0001-0002.dcm'), ]) instances = DoGet(_REMOTE, '/instances') self.assertEqual(2, len(instances)) t1 = DoGet(_REMOTE, '/instances/%s/metadata/TransferSyntax' % instances[0]) t2 = DoGet(_REMOTE, '/instances/%s/metadata/TransferSyntax' % instances[1]) self.assertEqual('1.2.840.10008.1.2.4.90', t1) # this will fail if libgdcm-tools is not installed self.assertEqual(t1, t2); def test_find_group_length(self): # Orthanc <= 1.4.1 fails to answer C-FIND queries that contain # one of the Generic Group Length tags (*, 0x0000) a = UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] result = CallFindScu([ '-k', '0008,0052=STUDY', '-k', '0008,0000=80' ]) self.assertFalse('UnableToProcess' in result) self.assertFalse('E:' in result) def test_split(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') knee1Sop = '1.3.46.670589.11.17521.5.0.3124.2008081908590448738' knee2Sop = '1.3.46.670589.11.17521.5.0.3124.2008081909113806560' study = '0a9b3153-2512774b-2d9580de-1fc3dcf6-3bd83918' t1 = '6de73705-c4e65c1b-9d9ea1b5-cabcd8e7-f15e4285' t2 = 'bbf7a453-0d34251a-03663b55-46bb31b9-ffd74c59' self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(2, len(DoGet(_REMOTE, '/series'))) info = DoGet(_REMOTE, '/studies/%s' % study) self.assertTrue('ReferringPhysicianName' in info['MainDicomTags']) job = MonitorJob2(_REMOTE, lambda: DoPost (_REMOTE, '/studies/%s/split' % study, { 'Series' : [ t2 ], 'Replace' : { 'PatientName' : 'Hello' }, 'Remove' : [ 'ReferringPhysicianName' ], 'KeepSource' : False, 'Asynchronous' : True })) self.assertNotEqual(None, job) studies = set(DoGet(_REMOTE, '/studies')) self.assertEqual(2, len(studies)) series = set(DoGet(_REMOTE, '/series')) self.assertEqual(2, len(series)) self.assertTrue(t1 in series) study2 = DoGet(_REMOTE, '/jobs/%s' % job)['Content']['TargetStudy'] self.assertTrue(study in studies) self.assertTrue(study2 in studies) info = DoGet(_REMOTE, '/studies/%s' % study2) self.assertTrue('Hello', info['PatientMainDicomTags']['PatientName']) self.assertFalse('ReferringPhysicianName' in info['MainDicomTags']) sopInstanceUids = set() for i in DoGet(_REMOTE, '/instances?expand'): sopInstanceUids.add(i['MainDicomTags']['SOPInstanceUID']) self.assertTrue(knee1Sop in sopInstanceUids) # Fails if Orthanc <= 1.5.7 self.assertFalse(knee2Sop in sopInstanceUids) # Because "KeepSource" is False # One original instance is kept, another one is added because of the split self.assertEqual(2, len(sopInstanceUids)) def test_merge(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') kneeSop = '1.3.46.670589.11.17521.5.0.3124.2008081908590448738' brainixSop = '1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114314079549' knee = '0a9b3153-2512774b-2d9580de-1fc3dcf6-3bd83918' t1 = '6de73705-c4e65c1b-9d9ea1b5-cabcd8e7-f15e4285' brainix = '27f7126f-4f66fb14-03f4081b-f9341db2-53925988' flair = '1e2c125c-411b8e86-3f4fe68e-a7584dd3-c6da78f0' self.assertEqual(2, len(DoGet(_REMOTE, '/studies'))) self.assertEqual(2, len(DoGet(_REMOTE, '/series'))) job = MonitorJob2(_REMOTE, lambda: DoPost (_REMOTE, '/studies/%s/merge' % knee, { 'Resources' : [ brainix ], 'KeepSource' : True, 'Synchronous' : False })) self.assertNotEqual(None, job) studies = set(DoGet(_REMOTE, '/studies')) self.assertEqual(2, len(studies)) self.assertTrue(knee in studies) self.assertTrue(brainix in studies) series = set(DoGet(_REMOTE, '/studies/%s' % knee)['Series']) self.assertTrue(t1 in series) series.remove(t1) self.assertEqual(1, len(series)) instances = DoGet(_REMOTE, '/series/%s' % list(series)[0])['Instances'] self.assertEqual(1, len(instances)) merged = DoGet(_REMOTE, '/instances/%s/tags?simplify' % instances[0]) instances = DoGet(_REMOTE, '/series/%s' % t1)['Instances'] self.assertEqual(1, len(instances)) a = DoGet(_REMOTE, '/instances/%s/tags?simplify' % instances[0]) instances = DoGet(_REMOTE, '/series/%s' % flair)['Instances'] self.assertEqual(1, len(instances)) b = DoGet(_REMOTE, '/instances/%s/tags?simplify' % instances[0]) tags = DoGet(_REMOTE, '/studies/%s' % knee) for key in tags['PatientMainDicomTags']: self.assertEqual(a[key], merged[key]) if (key in b and key != 'PatientSex'): self.assertNotEqual(a[key], b[key]) for key in tags['MainDicomTags']: # Not in the patient/study module if (not key in [ 'InstitutionName', 'RequestingPhysician', 'RequestedProcedureDescription', ]): self.assertEqual(a[key], merged[key]) if (key in b): self.assertNotEqual(a[key], b[key]) sopInstanceUids = set() for i in DoGet(_REMOTE, '/instances?expand'): sopInstanceUids.add(i['MainDicomTags']['SOPInstanceUID']) self.assertTrue(kneeSop in sopInstanceUids) self.assertTrue(brainixSop in sopInstanceUids) # Fails if Orthanc <= 1.5.7 # The 2 original instances are kept, another one is added because of the merge self.assertEqual(3, len(sopInstanceUids)) def test_async_archive(self): # Testing the asynchronous generation of archives/medias (new # in Orthanc 1.4.3) UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Knee/T2/IM-0001-0001.dcm') kneeT1 = '6de73705-c4e65c1b-9d9ea1b5-cabcd8e7-f15e4285' kneeT2 = 'bbf7a453-0d34251a-03663b55-46bb31b9-ffd74c59' job = MonitorJob2(_REMOTE, lambda: DoPost (_REMOTE, '/studies/%s/archive' % kneeT1, { 'Synchronous' : False })) z = GetArchive(_REMOTE, '/jobs/%s/archive' % job) self.assertEqual(1, len(z.namelist())) self.assertFalse('DICOMDIR' in z.namelist()) job2 = MonitorJob2(_REMOTE, lambda: DoPost (_REMOTE, '/studies/%s/media' % kneeT1, { 'Synchronous' : False })) # The archive from the first job has been replaced by the # archive from second job (as MediaArchiveSize == 1) self.assertRaises(Exception, lambda: GetArchive(_REMOTE, '/jobs/%s/archive' % job)) z = GetArchive(_REMOTE, '/jobs/%s/archive' % job2) self.assertEqual(2, len(z.namelist())) self.assertTrue('DICOMDIR' in z.namelist()) job = MonitorJob2(_REMOTE, lambda: DoPost (_REMOTE, '/tools/create-archive', { 'Synchronous' : False, 'Resources' : [ kneeT1, kneeT2 ], })) z = GetArchive(_REMOTE, '/jobs/%s/archive' % job) self.assertEqual(2, len(z.namelist())) self.assertFalse('DICOMDIR' in z.namelist()) job = MonitorJob2(_REMOTE, lambda: DoPost (_REMOTE, '/tools/create-media', { 'Synchronous' : False, 'Resources' : [ kneeT1, kneeT2 ], })) z = GetArchive(_REMOTE, '/jobs/%s/archive' % job) self.assertEqual(3, len(z.namelist())) self.assertTrue('DICOMDIR' in z.namelist()) def test_queries_hierarchy(self): UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') tags = { 'NumberOfPatientRelatedInstances' : '', 'NumberOfPatientRelatedSeries' : '', 'NumberOfPatientRelatedStudies' : '', 'NumberOfStudyRelatedInstances' : '', 'NumberOfStudyRelatedSeries' : '', 'NumberOfSeriesRelatedInstances' : '', } tags2 = copy.copy(tags) tags2['PatientID'] = '887' # Only consider the "Knee" patient patient = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Patient', 'Query' : tags2 }) ['ID'] study = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Study', 'Query' : tags2 }) ['ID'] series = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Series', 'Query' : tags2 }) ['ID'] instance = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Instance', 'Query' : tags2 }) ['ID'] p = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % patient) self.assertEqual(1, len(p)) self.assertEqual('887', p[0]['PatientID']) self.assertEqual('1', p[0]['NumberOfPatientRelatedInstances']) self.assertEqual('1', p[0]['NumberOfPatientRelatedSeries']) self.assertEqual('1', p[0]['NumberOfPatientRelatedStudies']) self.assertFalse('NumberOfStudyRelatedInstances' in p[0]) self.assertFalse('NumberOfStudyRelatedSeries' in p[0]) self.assertFalse('NumberOfSeriesRelatedInstances' in p[0]) p = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % study) self.assertEqual(1, len(p)) self.assertEqual('2.16.840.1.113669.632.20.121711.10000160881', p[0]['StudyInstanceUID']) self.assertEqual('1', p[0]['NumberOfStudyRelatedInstances']) self.assertEqual('1', p[0]['NumberOfStudyRelatedSeries']) self.assertFalse('NumberOfPatientRelatedInstances' in p[0]) self.assertFalse('NumberOfPatientRelatedSeries' in p[0]) self.assertFalse('NumberOfPatientRelatedInstances' in p[0]) self.assertFalse('NumberOfSeriesRelatedInstances' in p[0]) p = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % series) self.assertEqual(1, len(p)) self.assertEqual('1.3.46.670589.11.17521.5.0.3124.2008081908564160709', p[0]['SeriesInstanceUID']) self.assertEqual('1', p[0]['NumberOfSeriesRelatedInstances']) self.assertFalse('NumberOfPatientRelatedInstances' in p[0]) self.assertFalse('NumberOfPatientRelatedSeries' in p[0]) self.assertFalse('NumberOfPatientRelatedInstances' in p[0]) self.assertFalse('NumberOfStudyRelatedInstances' in p[0]) self.assertFalse('NumberOfStudyRelatedSeries' in p[0]) p = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % instance) self.assertEqual(1, len(p)) self.assertEqual('1.3.46.670589.11.17521.5.0.3124.2008081908590448738', p[0]['SOPInstanceUID']) j = DoPost(_REMOTE, '/queries/%s/answers/0/query-studies' % patient, { 'Query' : tags }) ['ID'] self.assertEqual(DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % j), DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % study)) j = DoPost(_REMOTE, '/queries/%s/answers/0/query-series' % patient, { 'Query' : tags }) ['ID'] self.assertEqual(DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % j), DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % series)) j = DoPost(_REMOTE, '/queries/%s/answers/0/query-instances' % patient, { 'Query' : tags }) ['ID'] self.assertEqual(DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % j), DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % instance)) j = DoPost(_REMOTE, '/queries/%s/answers/0/query-series' % study, { 'Query' : tags }) ['ID'] self.assertEqual(DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % j), DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % series)) j = DoPost(_REMOTE, '/queries/%s/answers/0/query-instances' % study, { 'Query' : tags }) ['ID'] self.assertEqual(DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % j), DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % instance)) j = DoPost(_REMOTE, '/queries/%s/answers/0/query-instances' % series, { 'Query' : tags }) ['ID'] self.assertEqual(DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % j), DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % instance)) def test_dicom_disk_size(self): dicomSize = 0 UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm') for i in range(2): p = 'Knee/T%d/IM-0001-0001.dcm' % (i + 1) UploadInstance(_REMOTE, p) dicomSize += os.path.getsize(GetDatabasePath(p)) s = DoGet(_REMOTE, '/patients/ca29faea-b6a0e17f-067743a1-8b778011-a48b2a17/statistics') # Consider Knee patient self.assertEqual(2, s['CountInstances']) self.assertEqual(2, s['CountSeries']) self.assertEqual(1, s['CountStudies']) self.assertEqual(dicomSize, int(s['DicomDiskSize'])) self.assertEqual(dicomSize, int(s['DicomUncompressedSize'])) self.assertLess(dicomSize, int(s['UncompressedSize'])) self.assertEqual(s['UncompressedSize'], s['DiskSize']) def test_changes_2(self): # More consistent behavior since Orthanc 1.5.2 # https://groups.google.com/d/msg/orthanc-users/QhzB6vxYeZ0/YxabgqpfBAAJ # Make sure that this is not the first change self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) a = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) DoDelete(_REMOTE, '/instances/%s' % a) # No more instance, but there were previous changes self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) c = DoGet(_REMOTE, '/changes') self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) seq = c['Last'] c = DoGet(_REMOTE, '/changes?last') self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq, c['Last']) c = DoGet(_REMOTE, '/changes?since=%d' % (seq + 1000)) self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq, c['Last']) # Add one instance UploadInstance(_REMOTE, 'DummyCT.dcm') self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) c = DoGet(_REMOTE, '/changes') self.assertEqual(4, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq + 4, c['Last']) c = DoGet(_REMOTE, '/changes?last') self.assertEqual(1, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq + 4, c['Last']) c = DoGet(_REMOTE, '/changes?since=%d' % (seq + 1000)) self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq + 4, c['Last']) # Remove the uploaded instance DoDelete(_REMOTE, '/instances/%s' % a) self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) c = DoGet(_REMOTE, '/changes') self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq + 4, c['Last']) c = DoGet(_REMOTE, '/changes?last') self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq + 4, c['Last']) c = DoGet(_REMOTE, '/changes?since=%d' % (seq + 1000)) self.assertEqual(0, len(c['Changes'])) self.assertTrue(c['Done']) self.assertEqual(seq + 4, c['Last']) def test_bitbucket_issue_124(self): a = UploadInstance(_REMOTE, 'Issue124.dcm')['ID'] z = GetArchive(_REMOTE, '/patients/%s/media' % a) self.assertEqual(2, len(z.namelist())) def test_invalid_findscp(self): UploadInstance(_REMOTE, 'DummyCT.dcm') findscu = CallFindScu([ '-S', '-k', '8,52=IMAGE', '-k', '8,16', '-k', '2,2' ]) self.assertEqual(0, len(re.findall('\(0002,0002\)', findscu))) def test_bitbucket_issue_90(self): def CountDicomResults(sex): a = CallFindScu([ '-S', '-k', '8,52=STUDY', '-k', sex ]) return len(re.findall('\(0010,0040\)', a)) def CountRestResults(sex): a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { 'PatientSex' : sex } }) return len(a) # Just like the "CR000000.dcm" of the issue, the test image # "DummyCT.dcm" has the tag PatientSex (0010,0040) unset UploadInstance(_REMOTE, 'DummyCT.dcm') # Test that the behavior of DICOM vs. REST API is consistent on missing tags # In wildcard constraints, the patient sex must be set for a match to occur self.assertEqual(0, CountDicomResults('PatientSex=*')) self.assertEqual(0, CountRestResults('*')) # In single-valued constraints, the patient sex must be set self.assertEqual(0, CountDicomResults('PatientSex=F')) self.assertEqual(0, CountDicomResults('PatientSex=M')) self.assertEqual(0, CountRestResults('F')) self.assertEqual(0, CountRestResults('M')) # Empty constraints are only used to ask the actual value of # the tag to be added to the *answer*. The tag should not used # as a filter in such a situation. self.assertEqual(1, CountDicomResults('PatientSex')) self.assertEqual(1, CountDicomResults('PatientSex=')) self.assertEqual(1, CountRestResults('')) # This check fails on Orthanc <= 1.5.2 (issue 90) def test_rest_modalities_in_study(self): # Tests a regression that is present in Orthanc 1.5.2 and 1.5.3 # https://groups.google.com/d/msg/orthanc-users/7lZyG3wpx-M/uOXzAzVCFwAJ UploadInstance(_REMOTE, 'ColorTestImageJ.dcm') a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { 'ModalitiesInStudy' : 'US' }}) self.assertEqual(0, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { 'ModalitiesInStudy' : 'US\\CT' }}) self.assertEqual(1, len(a)) a = DoPost(_REMOTE, '/tools/find', { 'Level' : 'Study', 'Query' : { 'ModalitiesInStudy' : 'CT' }}) self.assertEqual(1, len(a)) def test_series_status(self): def HasCompletedInChanges(): for c in DoGet(_REMOTE, '/changes?limit=1000&since=0')['Changes']: if c['ChangeType'] == 'CompletedSeries': return True; return False UploadInstance(_REMOTE, 'Knix/Loc/IM-0001-0001.dcm') series = '8ea120d7-5057d919-837dfbcc-ccd04e0f-7f3a94aa' self.assertEqual('Unknown', DoGet(_REMOTE, '/series/%s' % series)['Status']) self.assertFalse(HasCompletedInChanges()) series = 'ce25ecb6-ed79d004-5ae43ca7-3fc89bc5-67511614' for i in range(3): UploadInstance(_REMOTE, 'Series/Lena-%d.dcm' % (i + 1)) self.assertEqual('Missing', DoGet(_REMOTE, '/series/%s' % series)['Status']) self.assertFalse(HasCompletedInChanges()) UploadInstance(_REMOTE, 'Series/Lena-4.dcm') self.assertEqual('Complete', DoGet(_REMOTE, '/series/%s' % series)['Status']) self.assertTrue(HasCompletedInChanges()) DoDelete(_REMOTE, '/changes') self.assertFalse(HasCompletedInChanges()) UploadInstance(_REMOTE, 'Series/Lena-5.dcm') self.assertEqual('Inconsistent', DoGet(_REMOTE, '/series/%s' % series)['Status']) self.assertFalse(HasCompletedInChanges()) def test_dicomweb(self): def Compare(dicom, reference): a = UploadInstance(_REMOTE, dicom) ['ID'] b = DoGet(_REMOTE, '/instances/%s/file' % a, headers = { 'Accept' : 'application/dicom+json' }) with open(GetDatabasePath(reference), 'rb') as c: d = json.load(c) AssertAlmostEqualRecursive(self, d, b) Compare('DummyCT.dcm', 'DummyCT.json') Compare('MarekLatin2.dcm', 'MarekLatin2.json') Compare('HierarchicalAnonymization/StructuredReports/IM0', 'HierarchicalAnonymization/StructuredReports/IM0.json') def test_issue_95_encodings(self): # https://bitbucket.org/sjodogne/orthanc/issues/95/server-cant-support-chinese # Check out image: "../Database/Encodings/DavidClunie/charsettests.screenshot.png" # Very useful tool: "file2" from package "file-kanji" def GetPatientName(dicom): i = UploadInstance(_REMOTE, dicom) ['ID'] j = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) return j['PatientName'] def ComparePatientName(name, dicom): self.assertEqual(name, GetPatientName(dicom)) # gdcmraw -t 10,10 -i SCSFREN -o /tmp/tag && uconv -f ISO-IR-100 -t UTF-8 /tmp/tag && echo ComparePatientName(u'Buc^Jérôme', 'Encodings/DavidClunie/SCSFREN') # gdcmraw -t 10,10 -i SCSI2 -o /tmp/tag && uconv -f KOREAN -t UTF-8 /tmp/tag && echo ComparePatientName(u'Hong^Gildong=洪^吉洞=홍^길동', 'Encodings/DavidClunie/SCSI2') # Since Orthanc 1.5.5 # gdcmraw -t 10,10 -i SCSX2 -o /tmp/tag && uconv -f GB18030 -t UTF-8 /tmp/tag && echo ComparePatientName(u'Wang^XiaoDong=王^小东=', 'Encodings/DavidClunie/SCSX2') # gdcmraw -t 10,10 -i SCSX1 -o /tmp/tag && cat /tmp/tag && echo ComparePatientName(u'Wang^XiaoDong=王^小東=', 'Encodings/DavidClunie/SCSX1') # gdcmraw -t 10,10 -i SCSH31 -o /tmp/tag && uconv -f JIS -t UTF-8 /tmp/tag && echo ComparePatientName(u'Yamada^Tarou=山田^太郎=やまだ^たろう', 'Encodings/DavidClunie/SCSH31') # gdcmraw -t 10,10 -i SCSGERM -o /tmp/tag && uconv -f ISO-IR-100 -t UTF-8 /tmp/tag && echo ComparePatientName(u'Äneas^Rüdiger', 'Encodings/DavidClunie/SCSGERM') # gdcmraw -t 10,10 -i SCSGREEK -o /tmp/tag && uconv -f ISO-IR-126 -t UTF-8 /tmp/tag && echo ComparePatientName(u'Διονυσιος', 'Encodings/DavidClunie/SCSGREEK') # gdcmraw -t 10,10 -i SCSRUSS -o /tmp/tag && uconv -f ISO-IR-144 -t UTF-8 /tmp/tag && echo ComparePatientName(u'Люкceмбypг', 'Encodings/DavidClunie/SCSRUSS') # gdcmraw -t 10,10 -i SCSHBRW -o /tmp/tag && uconv -f ISO-IR-138 -t UTF-8 /tmp/tag && echo # NB: Hebrew is a right-to-left encoding, copying/pasting from # Linux console into Emacs automatically reverse the string ComparePatientName(u'שרון^דבורה', 'Encodings/DavidClunie/SCSHBRW') # gdcmraw -t 10,10 -i SCSARAB -o /tmp/tag && uconv -f ISO-IR-127 -t UTF-8 /tmp/tag && echo # NB: Right-to-left as for Hebrew (SCSHBRW), and the Ubuntu console can't display such # characters by default, but copy/paste works with Emacs ComparePatientName(u'قباني^لنزار', 'Encodings/DavidClunie/SCSARAB') # SCSH32: This SpecificCharacterSet is composed of 2 # codepages: "ISO 2022 IR 13" (i.e. "SHIFT_JIS") until the # first equal, then "ISO 2022 IR 87" (i.e. "JIS") for the # remainer. Orthanc only takes into consideration the first # codepage: This is a limitation. # gdcmraw -t 10,10 -i SCSH32 -o /tmp/tag && cut -d '=' -f 1 /tmp/tag | uconv -f SHIFT_JIS -t UTF-8 self.assertTrue(GetPatientName('Encodings/DavidClunie/SCSH32').startswith(u'ﾔﾏﾀﾞ^ﾀﾛｳ=')) def test_findscu_missing_tags(self): # dcmodify -e Rows DummyCTInvalidRows.dcm -gst -gse -gin UploadInstance(_REMOTE, 'DummyCT.dcm') UploadInstance(_REMOTE, 'DummyCTInvalidRows.dcm') i = CallFindScu([ '-k', '0008,0052=IMAGES', '-k', 'Rows', '-k', 'PatientName' ]) # We have 2 instances... patientNames = re.findall('\(0010,0010\).*?\[(.*?)\]', i) self.assertEqual(2, len(patientNames)) self.assertEqual('KNIX', patientNames[0]) self.assertEqual('KNIX', patientNames[1]) # ...but only 1 value for the "Rows" tag rows = re.findall('\(0028,0010\) US ([0-9]+)', i) self.assertEqual(1, len(rows)) self.assertEqual('512', rows[0]) def test_bitbucket_issue_131(self): # "Orthanc PACS silently fails to C-MOVE due to duplicate # StudyInstanceUID in it's database." # https://bitbucket.org/sjodogne/orthanc/issues/131/orthanc-pacs-silently-fails-to-c-move-due # Insert 2 instances, with the same StudyInstanceUID, but with # different patient IDs. Orthanc will create 2 distincts # patients, and the hierarchy of resources above the two # instances will be fully disjoint. UploadInstance(_REMOTE, 'PatientIdsCollision/Issue131-a.dcm') UploadInstance(_REMOTE, 'PatientIdsCollision/Issue131-b.dcm') self.assertEqual(2, len(DoGet(_REMOTE, '/patients'))) self.assertEqual(2, len(DoGet(_REMOTE, '/studies'))) a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Study', 'Query' : {"PatientID": "A" }})['ID'] # 1 study is matched self.assertEqual(1, len(DoGet(_REMOTE, '/queries/%s/answers' % a))) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) WaitAllNewJobsDone(_REMOTE, lambda: DoPost (_REMOTE, '/queries/%s/retrieve' % a, '{"TargetAet":"ORTHANCTEST","Synchronous":false}')) # The two studies are matched, as we made the request at the # Study level, thus the shared StudyInstanceUID is used as the key self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) # Match the 2 studies a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Study', 'Query' : {"StudyInstanceUID": "2.25.123" }})['ID'] self.assertEqual(2, len(DoGet(_REMOTE, '/queries/%s/answers' % a))) DropOrthanc(_LOCAL) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) WaitAllNewJobsDone(_REMOTE, lambda: DoPost (_REMOTE, '/queries/%s/retrieve' % a, '{"TargetAet":"ORTHANCTEST","Synchronous":false}')) self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) # Same test, at the patient level => only 1 instance is transfered a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Patient', 'Query' : {"PatientID": "A" }})['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/queries/%s/answers' % a))) DropOrthanc(_LOCAL) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) WaitAllNewJobsDone(_REMOTE, lambda: DoPost (_REMOTE, '/queries/%s/retrieve' % a, '{"TargetAet":"ORTHANCTEST","Synchronous":false}')) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) # Same test, at the series level => only 1 instance is transfered a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Series', 'Query' : {"PatientID": "A" }})['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/queries/%s/answers' % a))) DropOrthanc(_LOCAL) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) WaitAllNewJobsDone(_REMOTE, lambda: DoPost (_REMOTE, '/queries/%s/retrieve' % a, '{"TargetAet":"ORTHANCTEST","Synchronous":false}')) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) def test_bitbucket_issue_136(self): UploadInstance(_REMOTE, 'Issue137.dcm') i = CallFindScu([ '-k', '0008,0052=STUDY', '-k', '0010,0010', '-k', '0028,0010', '-k', '0040,0275' ]) patientNames = re.findall('\(0010,0010\).*?\[(.*?)\]', i) self.assertEqual(1, len(patientNames)) self.assertEqual('John Doe', patientNames[0]) def test_anonymize_relationships_4(self): # https://groups.google.com/d/msg/orthanc-users/UkcsqyTpszE/bXUpzU0vAAAJ sr1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/2019-03-28/CR000000.dcm')['ID'] mr1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/2019-03-28/PR000000.dcm')['ID'] study = '0c923249-d52121a9-2b7167f7-6b85534f-0943697e' anonymized = DoPost(_REMOTE, '/studies/%s/anonymize' % study, '{}', 'application/json')['ID'] series = DoGet(_REMOTE, '/studies/%s/series' % anonymized) self.assertEqual(2, len(series)) cr = list(filter(lambda x: x['MainDicomTags']['Modality'] == 'CR', series)) pr = list(filter(lambda x: x['MainDicomTags']['Modality'] == 'PR', series)) self.assertEqual(1, len(cr)) self.assertEqual(1, len(pr)) self.assertEqual(1, len(cr[0]['Instances'])) self.assertEqual(1, len(pr[0]['Instances'])) crinstance = DoGet(_REMOTE, '/instances/%s' % cr[0]['Instances'][0]) tags = DoGet(_REMOTE, '/instances/%s/tags?short' % pr[0]['Instances'][0]) self.assertEqual(tags['0008,1115'][0]['0008,1140'][0]['0008,1155'], crinstance['MainDicomTags']['SOPInstanceUID']) self.assertEqual(tags['0008,1115'][0]['0008,1140'][0]['0008,1150'], '1.2.840.10008.5.1.4.1.1.1') # SOP class for CR Image Storage # This fails on Orthanc <= 1.5.6 self.assertEqual(tags['0008,1115'][0]['0020,000e'], cr[0]['MainDicomTags']['SeriesInstanceUID']) def test_anonymize_relationships_5(self): ct1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/RTH/CT01.dcm') rt1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/RTH/RT.dcm') oStudyId = ct1['ParentStudy'] oCtInstanceId = ct1['ID'] oRtInstanceId = rt1['ID'] oCtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % oCtInstanceId) oRtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % oRtInstanceId) # first validate the relationships in the source data oStudyUID = oCtTags['StudyInstanceUID'] oRtSeriesUID = oRtTags['SeriesInstanceUID'] oRtInstanceUID = oRtTags['SOPInstanceUID'] oRtFrameOfReferenceUID = oRtTags['ReferencedFrameOfReferenceSequence'][0]['FrameOfReferenceUID'] oCtSeriesUID = oCtTags['SeriesInstanceUID'] oCtInstanceUID = oCtTags['SOPInstanceUID'] oCtFrameOfReferenceUID = oCtTags['FrameOfReferenceUID'] oContourSequenceCount = len(oRtTags['ROIContourSequence'][0]['ContourSequence']) self.assertEqual(oCtFrameOfReferenceUID, oRtFrameOfReferenceUID) self.assertEqual(oStudyUID, oRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['ReferencedSOPInstanceUID']) self.assertEqual(oCtSeriesUID, oRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['RTReferencedSeriesSequence'][0]['SeriesInstanceUID']) self.assertEqual(oCtInstanceUID, oRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['RTReferencedSeriesSequence'][0]['ContourImageSequence'][0]['ReferencedSOPInstanceUID']) self.assertEqual(oCtInstanceUID, oRtTags['ROIContourSequence'][0]['ContourSequence'][oContourSequenceCount-1]['ContourImageSequence'][0]['ReferencedSOPInstanceUID']) ### anonymize aStudyId = DoPost(_REMOTE, '/studies/%s/anonymize' % oStudyId, '{}', 'application/json')['ID'] ### validate aSeries = DoGet(_REMOTE, '/studies/%s/series' % aStudyId) self.assertEqual(2, len(aSeries)) aCt = list(filter(lambda x: x['MainDicomTags']['Modality'] == 'CT', aSeries)) aRt = list(filter(lambda x: x['MainDicomTags']['Modality'] == 'RTSTRUCT', aSeries)) aCtInstanceId = aCt[0]['Instances'][0] aRtInstanceId = aRt[0]['Instances'][0] aCtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % aCtInstanceId) aRtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % aRtInstanceId) # now validate the relationships in the anonymized data aStudyUID = aCtTags['StudyInstanceUID'] aRtSeriesUID = aRtTags['SeriesInstanceUID'] aRtInstanceUID = aRtTags['SOPInstanceUID'] aRtFrameOfReferenceUID = aRtTags['ReferencedFrameOfReferenceSequence'][0]['FrameOfReferenceUID'] aCtSeriesUID = aCtTags['SeriesInstanceUID'] aCtInstanceUID = aCtTags['SOPInstanceUID'] aCtFrameOfReferenceUID = aCtTags['FrameOfReferenceUID'] aContourSequenceCount = len(aRtTags['ROIContourSequence'][0]['ContourSequence']) # make sure all UIDs have been updated self.assertNotEqual(oStudyUID, aStudyUID) self.assertNotEqual(oRtSeriesUID, aRtSeriesUID) self.assertNotEqual(oRtInstanceUID, aRtInstanceUID) self.assertNotEqual(oRtFrameOfReferenceUID, aRtFrameOfReferenceUID) self.assertNotEqual(oCtSeriesUID, aCtSeriesUID) self.assertNotEqual(oCtInstanceUID, aCtInstanceUID) self.assertNotEqual(oCtFrameOfReferenceUID, aCtFrameOfReferenceUID) # validate the relationships self.assertEqual(oContourSequenceCount, aContourSequenceCount) self.assertEqual(aCtFrameOfReferenceUID, aRtFrameOfReferenceUID) self.assertEqual(aStudyUID, aRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['ReferencedSOPInstanceUID']) self.assertEqual(aCtSeriesUID, aRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['RTReferencedSeriesSequence'][0]['SeriesInstanceUID']) self.assertEqual(aCtInstanceUID, aRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['RTReferencedSeriesSequence'][0]['ContourImageSequence'][0]['ReferencedSOPInstanceUID']) self.assertEqual(aCtInstanceUID, aRtTags['ROIContourSequence'][0]['ContourSequence'][aContourSequenceCount-1]['ContourImageSequence'][0]['ReferencedSOPInstanceUID']) def test_anonymize_relationships_5b(self): # same test as previous one but, this time, we force the StudyInstanceUID ct1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/RTH/CT01.dcm') rt1 = UploadInstance(_REMOTE, 'HierarchicalAnonymization/RTH/RT.dcm') oStudyId = ct1['ParentStudy'] oCtInstanceId = ct1['ID'] oRtInstanceId = rt1['ID'] oCtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % oCtInstanceId) oRtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % oRtInstanceId) ### anonymize while forcing the StudyInstanceUID aStudyId = DoPost(_REMOTE, '/studies/%s/anonymize' % oStudyId, '{ "Replace" : { "StudyInstanceUID" : "1.2.3.4"}, "Force": true}', 'application/json')['ID'] ### validate aSeries = DoGet(_REMOTE, '/studies/%s/series' % aStudyId) self.assertEqual(2, len(aSeries)) aCt = list(filter(lambda x: x['MainDicomTags']['Modality'] == 'CT', aSeries)) aRt = list(filter(lambda x: x['MainDicomTags']['Modality'] == 'RTSTRUCT', aSeries)) aCtInstanceId = aCt[0]['Instances'][0] aRtInstanceId = aRt[0]['Instances'][0] aCtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % aCtInstanceId) aRtTags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % aRtInstanceId) self.assertEqual("1.2.3.4", aCtTags['StudyInstanceUID']) self.assertEqual("1.2.3.4", aRtTags['StudyInstanceUID']) self.assertEqual("1.2.3.4", aRtTags['ReferencedFrameOfReferenceSequence'][0]['RTReferencedStudySequence'][0]['ReferencedSOPInstanceUID']) def test_bitbucket_issue_140(self): # "Modifying private tags with REST API changes VR from LO to # UN." This test fails if DCMTK <= 3.6.1 (e.g. fails on Ubuntu 16.04). # https://bitbucket.org/sjodogne/orthanc/issues/140 source = UploadInstance(_REMOTE, 'Issue140.dcm') ['ID'] series = DoGet(_REMOTE, '/instances/%s' % source) ['ParentSeries'] target = DoPost(_REMOTE, '/series/%s/modify' % series, { 'Replace' : { 'RadioButton3' : 'aaabbbccc' }, 'PrivateCreator' : 'RadioLogic', # <= the trick is here }, 'application/json') ['ID'] instances = DoGet(_REMOTE, '/series/%s/instances' % target) self.assertEqual(1, len(instances)) tags = DoGet(_REMOTE, '/instances/%s/tags' % source) t = tags['4321,1012'] self.assertEqual('String', t['Type']) self.assertEqual('RadioButton3', t['Name']) self.assertEqual('RadioLogic', t['PrivateCreator']) self.assertEqual('jklmopq', t['Value']) tags = DoGet(_REMOTE, '/instances/%s/tags' % instances[0]['ID']) t = tags['4321,1012'] self.assertEqual('String', t['Type']) self.assertEqual('RadioButton3', t['Name']) self.assertEqual('RadioLogic', t['PrivateCreator']) self.assertEqual('aaabbbccc', t['Value']) def test_find_normalize(self): # https://groups.google.com/d/msg/orthanc-users/AIwooGjsh94/YL28MNY4AgAJ UploadInstance(_REMOTE, 'Knee/T1/IM-0001-0001.dcm') a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Instance', 'Query' : { 'Rows' : '42' } }) ['ID'] b = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % a) self.assertEqual(1, len(b)) self.assertFalse('Rows' in b[0]) a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Instance', 'Query' : { 'Rows' : '42' }, 'Normalize' : False }) ['ID'] b = DoGet(_REMOTE, '/queries/%s/answers' % a) self.assertEqual(0, len(b)) a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Instance', 'Query' : { 'Rows' : '512' }, 'Normalize' : False }) ['ID'] b = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % a) self.assertEqual(1, len(b)) self.assertTrue('Rows' in b[0]) self.assertEqual('512', b[0]['Rows']) a = DoPost(_REMOTE, '/modalities/self/query', { 'Level' : 'Instance', 'Query' : { 'Rows' : '' }, 'Normalize' : False }) ['ID'] b = DoGet(_REMOTE, '/queries/%s/answers?expand&simplify' % a) self.assertEqual(1, len(b)) self.assertTrue('Rows' in b[0]) self.assertEqual('512', b[0]['Rows']) self.assertRaises(Exception, lambda: DoPost( _REMOTE, '/modalities/self/query', { 'Level' : 'Instance', 'Query' : { 'Rows' : '*' }, # Out-of-range value 'Normalize' : False })) def test_bitbucket_issue_141(self): # https://bitbucket.org/sjodogne/orthanc/issues/141/ a = UploadInstance(_REMOTE, 'Issue141.dcm') ['ID'] study = '494c8037-b237f263-d8f15075-c8cb2280-daf39bd1' with open(GetDatabasePath('HelloWorld.pdf'), 'rb') as f: pdf = f.read() b = DoPost(_REMOTE, '/tools/create-dicom', { 'Parent' : study, 'Tags' : {}, 'Content' : 'data:application/pdf;base64,' + base64.b64encode(pdf) }) ['ID'] tagsA = DoGet(_REMOTE, '/instances/%s/tags?short' % a) tagsB = DoGet(_REMOTE, '/instances/%s/tags?short' % b) self.assertEqual(tagsA['0008,0005'], tagsB['0008,0005']) self.assertEqual(tagsA['0008,1030'], tagsB['0008,1030']) def test_modifying_missing_patientid(self): # https://groups.google.com/d/msg/orthanc-users/aphG_h1AHVg/rfOTtTPTAgAJ UploadInstance(_REMOTE, '2019-06-17-VedranZdesic.dcm') DoPost(_REMOTE, '/studies/0c4aca1d-c107a241-6659d6aa-594c674a-a468b94a/modify', {}) def test_log_level(self): # https://bitbucket.org/sjodogne/orthanc/issues/65/ original = DoGet(_REMOTE, '/tools/log-level') DoPut(_REMOTE, '/tools/log-level', 'default') self.assertEqual('default', DoGet(_REMOTE, '/tools/log-level')) DoGet(_REMOTE, '/system') DoPut(_REMOTE, '/tools/log-level', 'verbose') self.assertEqual('verbose', DoGet(_REMOTE, '/tools/log-level')) DoGet(_REMOTE, '/system') DoPut(_REMOTE, '/tools/log-level', 'trace') self.assertEqual('trace', DoGet(_REMOTE, '/tools/log-level')) DoGet(_REMOTE, '/system') self.assertRaises(Exception, lambda: DoPut(_REMOTE, '/tools/log-level', 'nope')) # Switch back to the original log level DoPut(_REMOTE, '/tools/log-level', original) def test_upload_compressed(self): # New in Orthanc 1.6.0 with open(GetDatabasePath('DummyCT.dcm.gz'), 'rb') as f: d = f.read() self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/instances', d, 'application/dicom')) self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/instances', d, 'application/dicom', headers = { 'Content-Encoding' : 'nope' })) a = DoPost(_REMOTE, '/instances', d, 'application/dicom', headers = { 'Content-Encoding' : 'gzip' }) self.assertEqual('66a662ce-7430e543-bad44d47-0dc5a943-ec7a538d', a['ID']) def test_study_series_find_inconsistency(self): # https://groups.google.com/forum/#!topic/orthanc-users/bLv6Z11COy0 def CountAnswers(query): a = DoPost(_REMOTE, 'modalities/self/query', query) return len(DoGet(_REMOTE, '%s/answers' % a['Path'])) # This instance has "SeriesDescription" (0008,103e) tag, but no # "ProtocolName" (0018,1030). Both of those tags are part of # the "main DICOM tags" of Orthanc. UploadInstance(_REMOTE, 'Issue137.dcm') self.assertEqual(1, CountAnswers({ 'Level' : 'Study', })) self.assertEqual(1, CountAnswers({ 'Level' : 'Series', })) ## ## "SeriesDescription" is present, and has VR "CS" => wildcard is allowed ## http://dicom.nema.org/medical/dicom/2019e/output/chtml/part04/sect_C.2.2.2.4.html ## # At the study level, the "SeriesDescription" tag is not allowed, but # is wiped out by the normalization self.assertEqual(0, CountAnswers({ 'Level' : 'Study', 'Query' : { 'SeriesDescription' : 'NOPE' }, 'Normalize' : False })) self.assertEqual(0, CountAnswers({ # This test fails on Orthanc <= 1.5.8 'Level' : 'Study', 'Query' : { 'SeriesDescription' : '*' # Wildcard matching => no match, as the tag is absent }, 'Normalize' : False })) self.assertEqual(1, CountAnswers({ 'Level' : 'Study', 'Query' : { 'SeriesDescription' : 'THIS^VALUE^IS^WIPED^OUT' }, 'Normalize' : True })) self.assertEqual(1, CountAnswers({ 'Level' : 'Study', 'Query' : { 'SeriesDescription' : '*' # Matches, as wiped out by the normalization }, 'Normalize' : True })) for normalize in [ True, False ]: # At the series level, the "SeriesDescription" tag is allowed, and # normalization has no effect # "Universal matching" will match all entities, including # those with the missing tag # http://dicom.nema.org/medical/dicom/2019e/output/chtml/part04/sect_C.2.2.2.3.html self.assertEqual(1, CountAnswers({ 'Level' : 'Series', 'Query' : { 'SeriesDescription' : '' # Universal matching }, 'Normalize' : normalize, })) # "Universal matching" will match all entities, including # those with the missing tag # http://dicom.nema.org/medical/dicom/2019e/output/chtml/part04/sect_C.2.2.2.3.html self.assertEqual(1, CountAnswers({ 'Level' : 'Series', 'Query' : { 'SeriesDescription' : '*' # Wildcard matching }, 'Normalize' : normalize, })) self.assertEqual(1, CountAnswers({ 'Level' : 'Series', 'Query' : { 'SeriesDescription' : '*model*' # The actual value is "STL model: intraop Report" }, 'Normalize' : normalize, })) self.assertEqual(0, CountAnswers({ 'Level' : 'Series', 'Query' : { 'SeriesDescription' : '*MISMATCHED^VALUE*' }, 'Normalize' : normalize, })) # Universal matching matches any instance, even if the # query is at the study-level, and thus if "SeriesDescription" # makes no sense self.assertEqual(1, CountAnswers({ 'Level' : 'Study', 'Query' : { 'SeriesDescription' : '' # Universal matching }, 'Normalize' : normalize, })) ## ## "ProtocolName" is absent, and has VR "CS" => wildcard is allowed ## # At the study level, the "ProtocolName" tag is not allowed, but # is wiped out by the normalization self.assertEqual(0, CountAnswers({ 'Level' : 'Study', 'Query' : { 'ProtocolName' : 'NOPE' }, 'Normalize' : False })) self.assertEqual(0, CountAnswers({ 'Level' : 'Study', 'Query' : { 'ProtocolName' : '*' # Wildcard matching => no match, as the tag is absent }, 'Normalize' : False })) self.assertEqual(1, CountAnswers({ 'Level' : 'Study', 'Query' : { 'ProtocolName' : 'THIS^VALUE^IS^WIPED^OUT' }, 'Normalize' : True })) self.assertEqual(1, CountAnswers({ 'Level' : 'Study', 'Query' : { 'ProtocolName' : '*' # Matches, as wiped out by the normalization }, 'Normalize' : True })) for normalize in [ True, False ]: # At the series level, the "ProtocolName" tag is allowed, and # normalization has no effect self.assertEqual(1, CountAnswers({ 'Level' : 'Series', 'Query' : { 'ProtocolName' : '' # Universal matching }, 'Normalize' : normalize, })) self.assertEqual(0, CountAnswers({ 'Level' : 'Series', 'Query' : { 'ProtocolName' : '*' # Wildcard matching => no match, as the tag is absent }, 'Normalize' : normalize, })) self.assertEqual(0, CountAnswers({ 'Level' : 'Series', 'Query' : { 'ProtocolName' : '*MISMATCHED^VALUE*' }, 'Normalize' : normalize, })) self.assertEqual(1, CountAnswers({ 'Level' : 'Study', 'Query' : { 'ProtocolName' : '' # Universal matching }, 'Normalize' : normalize, })) ## ## "StudyInstanceUID" is present, and has VR "UI" => wildcard is not allowed ## for level in [ 'Study', 'Series' ] : for normalize in [ True, False ]: self.assertEqual(1, CountAnswers({ 'Level' : level, 'Query' : { 'StudyInstanceUID' : '' # Universal matching }, 'Normalize' : normalize, })) self.assertEqual(0, CountAnswers({ 'Level' : level, 'Query' : { 'StudyInstanceUID' : 'MISMATCHED^VALUE' }, 'Normalize' : normalize, })) self.assertEqual(1, CountAnswers({ 'Level' : level, 'Query' : { 'StudyInstanceUID' : '4.5.6' # This is the actual value }, 'Normalize' : normalize, })) # Wildcard matching is not allowed for this VR # This test fails on Orthanc <= 1.5.8 self.assertRaises(Exception, lambda: CountAnswers({ 'Level' : level, 'Query' : { 'StudyInstanceUID' : '*' }, 'Normalize' : normalize, })) def test_rendered(self): # New in Orthanc 1.6.0 i = UploadInstance(_REMOTE, 'ColorTestMalaterre.dcm')['ID'] im = GetImage(_REMOTE, '/instances/%s/rendered' % i) self.assertEqual("RGB", im.mode) self.assertEqual(41, im.size[0]) self.assertEqual(41, im.size[1]) # http://effbot.org/zone/pil-comparing-images.htm truth = Image.open(GetDatabasePath('ColorTestMalaterre.png')) self.assertTrue(ImageChops.difference(im, truth).getbbox() is None) im = GetImage(_REMOTE, '/instances/%s/rendered?width=10' % i) self.assertEqual("RGB", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(10, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?height=10' % i) self.assertEqual("RGB", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(10, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?height=128' % i) self.assertEqual("RGB", im.mode) self.assertEqual(128, im.size[0]) self.assertEqual(128, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?height=10&smooth=0' % i) self.assertEqual("RGB", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(10, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?height=10&smooth=1' % i) self.assertEqual("RGB", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(10, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?height=5&width=10' % i) self.assertEqual("RGB", im.mode) self.assertEqual(5, im.size[0]) self.assertEqual(5, im.size[1]) # Grayscale image i = UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] im = GetImage(_REMOTE, '/instances/%s/rendered' % i) self.assertEqual("L", im.mode) self.assertEqual(288, im.size[0]) self.assertEqual(288, im.size[1]) self.assertEqual(0, im.getpixel((0, 0))) # Those are the original windowing parameters that are written # inside the DICOM file im2 = GetImage(_REMOTE, '/instances/%s/rendered?window-center=248.009544468547&window-width=431.351843817788' % i) self.assertEqual("L", im2.mode) self.assertEqual(288, im2.size[0]) self.assertEqual(288, im2.size[1]) self.assertTrue(ImageChops.difference(im, im2).getbbox() is None) im = GetImage(_REMOTE, '/instances/%s/rendered?width=512&smooth=0' % i) self.assertEqual("L", im.mode) self.assertEqual(512, im.size[0]) self.assertEqual(512, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?width=10&smooth=0' % i) self.assertEqual("L", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(10, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?width=10&smooth=1' % i) self.assertEqual("L", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(10, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?width=1&window-center=-1000' % i) self.assertEqual("L", im.mode) self.assertEqual(1, im.size[0]) self.assertEqual(1, im.size[1]) self.assertEqual(255, im.getpixel((0, 0))) im = GetImage(_REMOTE, '/instances/%s/rendered?width=1&window-center=1000' % i) self.assertEqual("L", im.mode) self.assertEqual(1, im.size[0]) self.assertEqual(1, im.size[1]) self.assertEqual(0, im.getpixel((0, 0))) # Test monochrome 1 i = UploadInstance(_REMOTE, 'Issue44/Monochrome1.dcm')['ID'] im = GetImage(_REMOTE, '/instances/%s/rendered' % i) self.assertEqual("L", im.mode) self.assertEqual(2010, im.size[0]) self.assertEqual(2446, im.size[1]) self.assertEqual(0, im.getpixel((0, 0))) im = GetImage(_REMOTE, '/instances/%s/rendered?width=20' % i) self.assertEqual("L", im.mode) self.assertEqual(20, im.size[0]) self.assertEqual(24, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?height=24' % i) self.assertEqual("L", im.mode) self.assertEqual(20, im.size[0]) self.assertEqual(24, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?width=10&height=24' % i) self.assertEqual("L", im.mode) self.assertEqual(10, im.size[0]) self.assertEqual(12, im.size[1]) im = GetImage(_REMOTE, '/instances/%s/rendered?width=40&height=24' % i) self.assertEqual("L", im.mode) self.assertEqual(20, im.size[0]) self.assertEqual(24, im.size[1]) def test_bitbucket_issue_154(self): # "Matching against list of UID-s by C-MOVE" # https://bitbucket.org/sjodogne/orthanc/issues/154/ a = UploadInstance(_REMOTE, 'Issue154-d1.dcm') ['ID'] b = UploadInstance(_REMOTE, 'Issue154-d2.dcm') ['ID'] study = '1.2.826.0.1.3680043.8.498.35214236271657363033644818354280454731' series1 = '1.2.826.0.1.3680043.8.498.12243321927795467590791662266352305113' series2 = '1.2.826.0.1.3680043.8.498.43769499931624584079690260699536473555' # C-FIND is working on list of UIDs i = CallFindScu([ '-k', 'QueryRetrieveLevel=SERIES', '-k', 'StudyInstanceUID=%s' % study, '-k', 'SeriesInstanceUID=%s\\%s' % (series1, series2) ]) series = re.findall('\(0020,000e\).*?\[(.*?)\]', i) self.assertEqual(2, len(series)) self.assertTrue(series1 in series) self.assertTrue(series2 in series) # Individual retrieval is working in Orthanc < 1.6.0 self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) self.assertTrue(MonitorJob(_REMOTE, lambda: CallMoveScu([ '--study', '-k', 'QueryRetrieveLevel=SERIES', '-k', 'StudyInstanceUID=%s' % study, '-k', 'SeriesInstanceUID=%s' % series1, ]))) self.assertTrue(MonitorJob(_REMOTE, lambda: CallMoveScu([ '--study', '-k', 'QueryRetrieveLevel=SERIES', '-k', 'StudyInstanceUID=%s' % study, '-k', 'SeriesInstanceUID=%s' % series2, ]))) self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) DropOrthanc(_LOCAL) # But list matching is working only in Orthanc >= 1.6.0 self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) self.assertTrue(MonitorJob(_REMOTE, lambda: CallMoveScu([ '--study', '-k', 'QueryRetrieveLevel=SERIES', '-k', 'StudyInstanceUID=%s' % study, '-k', 'SeriesInstanceUID=%s\\%s' % (series1, series2), ]))) self.assertEqual(2, len(DoGet(_LOCAL, '/instances'))) def test_storage_commitment_api(self): # Storage commitment is available since Orthanc 1.6.0 def WaitTransaction(uid): while True: s = DoGet(_REMOTE, '/storage-commitment/%s' % uid) if s['Status'] != 'Pending': return s else: time.sleep(0.1) instance = UploadInstance(_REMOTE, 'DummyCT.dcm') sopClassUid = '1.2.840.10008.5.1.4.1.1.4' sopInstanceUid = '1.2.840.113619.2.176.2025.1499492.7040.1171286242.109' # Against self transaction = DoPost(_REMOTE, '/modalities/self/storage-commitment', { "DicomInstances" : [ [ sopClassUid, sopInstanceUid ] ], }) ['ID'] self.assertTrue(transaction.startswith('2.25.')) result = WaitTransaction(transaction) self.assertEqual('ORTHANC', result['RemoteAET']) self.assertEqual('Success', result['Status']) self.assertEqual(1, len(result['Success'])) self.assertEqual(0, len(result['Failures'])) self.assertEqual(sopClassUid, result['Success'][0]['SOPClassUID']) self.assertEqual(sopInstanceUid, result['Success'][0]['SOPInstanceUID']) tmp = DoPost(_REMOTE, '/modalities/self/storage-commitment', { "DicomInstances" : [ { 'SOPClassUID' : sopClassUid, 'SOPInstanceUID' : sopInstanceUid }, ], }) self.assertEqual(tmp['Path'], '/storage-commitment/%s' % tmp['ID']) self.assertEqual(result, WaitTransaction(transaction)) tmp = DoPost(_REMOTE, '/modalities/self/storage-commitment', { "Resources" : [ instance['ID'], instance['ParentSeries'], instance['ParentStudy'], instance['ParentPatient'], ] }) self.assertEqual(tmp['Path'], '/storage-commitment/%s' % tmp['ID']) self.assertEqual(result, WaitTransaction(transaction)) transaction = DoPost(_REMOTE, '/modalities/self/storage-commitment', { "DicomInstances" : [ [ 'nope', 'nope2' ], [ sopClassUid, sopInstanceUid ], ], }) ['ID'] self.assertTrue(transaction.startswith('2.25.')) result = WaitTransaction(transaction) self.assertEqual('ORTHANC', result['RemoteAET']) self.assertEqual('Failure', result['Status']) self.assertEqual(1, len(result['Success'])) self.assertEqual(1, len(result['Failures'])) self.assertEqual(sopClassUid, result['Success'][0]['SOPClassUID']) self.assertEqual(sopInstanceUid, result['Success'][0]['SOPInstanceUID']) self.assertEqual('nope', result['Failures'][0]['SOPClassUID']) self.assertEqual('nope2', result['Failures'][0]['SOPInstanceUID']) self.assertEqual(274, result['Failures'][0]['FailureReason']) # Cannot remove items from a failed storage commitment transaction self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/storage-commitment/%s/remove' % transaction)) # Against Orthanc 0.8.6, that does not support storage commitment self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/modalities/orthanctest/storage-commitment', { "DicomInstances" : [ [ sopClassUid, sopInstanceUid ], ] })) def test_storage_commitment_store(self): # Storage commitment is available since Orthanc 1.6.0 def WaitTransaction(uid): while True: s = DoGet(_REMOTE, '/storage-commitment/%s' % uid) if s['Status'] != 'Pending': return s else: time.sleep(0.1) i = UploadInstance(_REMOTE, 'DummyCT.dcm')['ID'] self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) # The Orthanc 0.8.6 from "_LOCAL" does not support storage commitment self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/modalities/orthanctest/store', { 'Resources' : [ i ], 'StorageCommitment' : True, })) j = DoPost(_REMOTE, '/modalities/orthanctest/store', { 'Resources' : [ i ], 'StorageCommitment' : False, }) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) j = DoPost(_REMOTE, '/modalities/self/store', { 'Resources' : [ i ], 'StorageCommitment' : True, }) transaction = j['StorageCommitmentTransactionUID'] self.assertTrue(transaction.startswith('2.25.')) result = WaitTransaction(transaction) self.assertEqual('ORTHANC', result['RemoteAET']) self.assertEqual('Success', result['Status']) self.assertEqual(1, len(result['Success'])) self.assertEqual(0, len(result['Failures'])) self.assertEqual('1.2.840.10008.5.1.4.1.1.4', result['Success'][0]['SOPClassUID']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7040.1171286242.109', result['Success'][0]['SOPInstanceUID']) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) DoPost(_REMOTE, '/storage-commitment/%s/remove' % transaction) self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) def test_store_straight(self): # New in Orthanc 1.6.1 self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) with open(GetDatabasePath('DummyCT.dcm'), 'rb') as f: dicom = f.read() self.assertRaises(Exception, lambda: DoPost( _REMOTE, '/modalities/orthanctest/store-straight', 'nope', 'nope')) answer = DoPost(_REMOTE, '/modalities/orthanctest/store-straight', dicom, 'nope') self.assertEqual('1.2.840.10008.5.1.4.1.1.4', answer['SOPClassUID']) self.assertEqual('1.2.840.113619.2.176.2025.1499492.7040.1171286242.109', answer['SOPInstanceUID']) self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(0, len(DoGet(_REMOTE, '/instances'))) def test_storescu_transcoding(self): # New in Orthanc 1.7.0 # Add a RLE-encoded DICOM file i = UploadInstance(_REMOTE, 'TransferSyntaxes/1.2.840.10008.1.2.5.dcm')['ID'] self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) rleSize = len(DoGet(_REMOTE, '/instances/%s/file' % i)) # Export the instance, with transcoding: "_REMOTE" is the # Orthanc server being tested try: DoDelete(_REMOTE, '/modalities/toto') except: pass params = DoGet(_REMOTE, '/modalities?expand') ['orthanctest'] DoPut(_REMOTE, '/modalities/toto', params) DoPost(_REMOTE, '/modalities/toto/store', str(i), 'text/plain') j = DoGet(_LOCAL, '/instances') self.assertEqual(1, len(j)) uncompressedSize = len(DoGet(_LOCAL, '/instances/%s/file' % j[0])) self.assertTrue(uncompressedSize > rleSize / 2) # Export, with transcoding disabled => this fails params['AllowTranscoding'] = False DoPut(_REMOTE, '/modalities/toto', params) self.assertRaises(Exception, lambda: DoPost(_REMOTE, '/modalities/toto/store', str(i), 'text/plain')) def test_bitbucket_issue_169(self): with open(GetDatabasePath('Issue169.dcm.bz2'), 'rb') as f: dicom = bz2.decompress(f.read()) self.assertEqual('1.2.840.10008.1.2.1', GetTransferSyntax(dicom)) self.assertEqual(44350560, len(dicom)) i = DoPost(_REMOTE, '/instances', dicom, 'application/dicom') ['ID'] tags = DoGet(_REMOTE, '/instances/%s/tags' % i) self.assertEqual('NORMAL', tags['1337,1001']['Value']) self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) DoPost(_REMOTE, '/modalities/orthanctest/store', str(i), 'text/plain') j = DoGet(_LOCAL, '/instances') self.assertEqual(1, len(j)) # In Orthanc <= 1.6.1, transfer syntax changed from "Explicit # VR Little Endian" (1.2.840.10008.1.2.1) to "Implicit VR # Little Endian" (1.2.840.10008.1.2) self.assertEqual('1.2.840.10008.1.2.1', GetTransferSyntax( DoGet(_LOCAL, '/instances/%s/file' % j[0]))) # In Orthanc <= 1.6.1, the value of the private tags was lost # because of this transcoding tags = DoGet(_LOCAL, '/instances/%s/tags' % j[0]) self.assertEqual('NORMAL', tags['1337,1001']['Value']) def test_modify_transcode_instance(self): i = UploadInstance(_REMOTE, 'KarstenHilbertRF.dcm')['ID'] self.assertEqual('1.2.840.10008.1.2.1', GetTransferSyntax( DoGet(_REMOTE, '/instances/%s/file' % i))) a = ExtractDicomTags(DoGet(_REMOTE, '/instances/%s/file' % i), [ 'SOPInstanceUID' ]) [0] self.assertTrue(len(a) > 20) SYNTAXES = [ '1.2.840.10008.1.2', '1.2.840.10008.1.2.1', #'1.2.840.10008.1.2.1.99', # Deflated Explicit VR Little Endian (cannot be decoded in debug mode if Orthanc is statically linked against DCMTK 3.6.5) '1.2.840.10008.1.2.2', '1.2.840.10008.1.2.4.50', '1.2.840.10008.1.2.4.51', '1.2.840.10008.1.2.4.57', '1.2.840.10008.1.2.4.70', ] if HasGdcmPlugin(_REMOTE): SYNTAXES = SYNTAXES + [ '1.2.840.10008.1.2.4.80', # This makes DCMTK 3.6.2 crash '1.2.840.10008.1.2.4.81', # This makes DCMTK 3.6.2 crash '1.2.840.10008.1.2.4.90', # JPEG2k, unavailable without GDCM '1.2.840.10008.1.2.4.91', # JPEG2k, unavailable without GDCM ] for syntax in SYNTAXES: transcoded = DoPost(_REMOTE, '/instances/%s/modify' % i, { 'Transcode' : syntax, 'Keep' : [ 'SOPInstanceUID' ], 'Force' : True, }) self.assertEqual(syntax, GetTransferSyntax(transcoded)) b = ExtractDicomTags(transcoded, [ 'SOPInstanceUID' ]) [0] self.assertTrue(len(b) > 20) if syntax in [ '1.2.840.10008.1.2.4.50', '1.2.840.10008.1.2.4.51', '1.2.840.10008.1.2.4.81', '1.2.840.10008.1.2.4.91' ]: # Lossy transcoding: The SOP instance UID must have changed self.assertNotEqual(a, b) else: self.assertEqual(a, b) def test_archive_transcode(self): info = UploadInstance(_REMOTE, 'KarstenHilbertRF.dcm') # GET on "/media" z = GetArchive(_REMOTE, '/patients/%s/media' % info['ParentPatient']) self.assertEqual(2, len(z.namelist())) self.assertEqual('1.2.840.10008.1.2.1', GetTransferSyntax(z.read('IMAGES/IM0'))) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/patients/%s/media?transcode=nope' % info['ParentPatient'])) z = GetArchive(_REMOTE, '/patients/%s/media?transcode=1.2.840.10008.1.2.4.50' % info['ParentPatient']) self.assertEqual('1.2.840.10008.1.2.4.50', GetTransferSyntax(z.read('IMAGES/IM0'))) z = GetArchive(_REMOTE, '/studies/%s/media?transcode=1.2.840.10008.1.2.4.51' % info['ParentStudy']) self.assertEqual('1.2.840.10008.1.2.4.51', GetTransferSyntax(z.read('IMAGES/IM0'))) z = GetArchive(_REMOTE, '/series/%s/media?transcode=1.2.840.10008.1.2.4.57' % info['ParentSeries']) self.assertEqual('1.2.840.10008.1.2.4.57', GetTransferSyntax(z.read('IMAGES/IM0'))) # POST on "/media" self.assertRaises(Exception, lambda: PostArchive( _REMOTE, '/patients/%s/media' % info['ParentPatient'], { 'Transcode' : 'nope' })) z = PostArchive(_REMOTE, '/patients/%s/media' % info['ParentPatient'], { 'Transcode' : '1.2.840.10008.1.2.4.50', }) self.assertEqual('1.2.840.10008.1.2.4.50', GetTransferSyntax(z.read('IMAGES/IM0'))) z = PostArchive(_REMOTE, '/studies/%s/media' % info['ParentStudy'], { 'Transcode' : '1.2.840.10008.1.2.4.51', }) self.assertEqual('1.2.840.10008.1.2.4.51', GetTransferSyntax(z.read('IMAGES/IM0'))) z = PostArchive(_REMOTE, '/series/%s/media' % info['ParentSeries'], { 'Transcode' : '1.2.840.10008.1.2.4.57', }) self.assertEqual('1.2.840.10008.1.2.4.57', GetTransferSyntax(z.read('IMAGES/IM0'))) # GET on "/archive" z = GetArchive(_REMOTE, '/patients/%s/archive' % info['ParentPatient']) self.assertEqual(1, len(z.namelist())) self.assertEqual('1.2.840.10008.1.2.1', GetTransferSyntax(z.read(z.namelist()[0]))) self.assertRaises(Exception, lambda: DoGet(_REMOTE, '/patients/%s/archive?transcode=nope' % info['ParentPatient'])) z = GetArchive(_REMOTE, '/patients/%s/archive?transcode=1.2.840.10008.1.2' % info['ParentPatient']) self.assertEqual('1.2.840.10008.1.2', GetTransferSyntax(z.read(z.namelist()[0]))) z = GetArchive(_REMOTE, '/studies/%s/archive?transcode=1.2.840.10008.1.2.2' % info['ParentStudy']) self.assertEqual('1.2.840.10008.1.2.2', GetTransferSyntax(z.read(z.namelist()[0]))) z = GetArchive(_REMOTE, '/series/%s/archive?transcode=1.2.840.10008.1.2.4.70' % info['ParentSeries']) self.assertEqual('1.2.840.10008.1.2.4.70', GetTransferSyntax(z.read(z.namelist()[0]))) # POST on "/archive" self.assertRaises(Exception, lambda: PostArchive( _REMOTE, '/patients/%s/archive' % info['ParentPatient'], { 'Transcode' : 'nope' })) z = PostArchive(_REMOTE, '/patients/%s/archive' % info['ParentPatient'], { 'Transcode' : '1.2.840.10008.1.2.4.50', }) self.assertEqual('1.2.840.10008.1.2.4.50', GetTransferSyntax(z.read(z.namelist()[0]))) z = PostArchive(_REMOTE, '/studies/%s/archive' % info['ParentStudy'], { 'Transcode' : '1.2.840.10008.1.2.4.51', }) self.assertEqual('1.2.840.10008.1.2.4.51', GetTransferSyntax(z.read(z.namelist()[0]))) z = PostArchive(_REMOTE, '/series/%s/archive' % info['ParentSeries'], { 'Transcode' : '1.2.840.10008.1.2.4.57', }) self.assertEqual('1.2.840.10008.1.2.4.57', GetTransferSyntax(z.read(z.namelist()[0]))) # "/tools/create-*" z = PostArchive(_REMOTE, '/tools/create-archive', { 'Resources' : [ info['ParentStudy'] ], 'Transcode' : '1.2.840.10008.1.2.4.50', }) self.assertEqual(1, len(z.namelist())) self.assertEqual('1.2.840.10008.1.2.4.50', GetTransferSyntax(z.read(z.namelist()[0]))) z = PostArchive(_REMOTE, '/tools/create-media', { 'Resources' : [ info['ParentStudy'] ], 'Transcode' : '1.2.840.10008.1.2.4.51', }) self.assertEqual(2, len(z.namelist())) self.assertEqual('1.2.840.10008.1.2.4.51', GetTransferSyntax(z.read('IMAGES/IM0'))) z = PostArchive(_REMOTE, '/tools/create-media-extended', { 'Resources' : [ info['ParentStudy'] ], 'Transcode' : '1.2.840.10008.1.2.4.57', }) self.assertEqual(2, len(z.namelist())) self.assertEqual('1.2.840.10008.1.2.4.57', GetTransferSyntax(z.read('IMAGES/IM0'))) def test_modify_keep_source(self): # https://groups.google.com/d/msg/orthanc-users/CgU-Wg8vDio/BY5ZWcDEAgAJ i = UploadInstance(_REMOTE, 'DummyCT.dcm') self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) j = DoPost(_REMOTE, '/studies/%s/modify' % i['ParentStudy'], { 'Replace' : { 'StationName' : 'TEST', }, 'KeepSource' : True, }) s = DoGet(_REMOTE, '/studies') self.assertEqual(2, len(s)) self.assertTrue(i['ParentStudy'] in s) self.assertTrue(j['ID'] in s) DoDelete(_REMOTE, '/studies/%s' % j['ID']) self.assertEqual(1, len(DoGet(_REMOTE, '/studies'))) j = DoPost(_REMOTE, '/studies/%s/modify' % i['ParentStudy'], { 'Replace' : { 'StationName' : 'TEST', }, 'KeepSource' : False, }) s = DoGet(_REMOTE, '/studies') self.assertEqual(1, len(s)) self.assertFalse(i['ParentStudy'] in s) self.assertTrue(j['ID'] in s) def test_modify_transcode_study(self): i = UploadInstance(_REMOTE, 'KarstenHilbertRF.dcm') self.assertEqual('1.2.840.10008.1.2.1', GetTransferSyntax( DoGet(_REMOTE, '/instances/%s/file' % i['ID']))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) j = DoPost(_REMOTE, '/studies/%s/modify' % i['ParentStudy'], { 'Transcode' : '1.2.840.10008.1.2.4.50', 'KeepSource' : False }) k = DoGet(_REMOTE, '/instances') self.assertEqual(1, len(k)) self.assertEqual(i['ID'], DoGet(_REMOTE, '/instances/%s/metadata?expand' % k[0]) ['ModifiedFrom']) self.assertEqual('1.2.840.10008.1.2.4.50', GetTransferSyntax( DoGet(_REMOTE, '/instances/%s/file' % k[0]))) def test_store_peer_transcoding(self): i = UploadInstance(_REMOTE, 'KarstenHilbertRF.dcm')['ID'] SYNTAXES = [ '1.2.840.10008.1.2', '1.2.840.10008.1.2.1', #'1.2.840.10008.1.2.1.99', # Deflated Explicit VR Little Endian (cannot be decoded in debug mode if Orthanc is statically linked against DCMTK 3.6.5) '1.2.840.10008.1.2.2', '1.2.840.10008.1.2.4.50', '1.2.840.10008.1.2.4.51', '1.2.840.10008.1.2.4.57', '1.2.840.10008.1.2.4.70', ] if HasGdcmPlugin(_REMOTE): SYNTAXES = SYNTAXES + [ '1.2.840.10008.1.2.4.80', # This makes DCMTK 3.6.2 crash '1.2.840.10008.1.2.4.81', # This makes DCMTK 3.6.2 crash '1.2.840.10008.1.2.4.90', # JPEG2k, unavailable without GDCM '1.2.840.10008.1.2.4.91', # JPEG2k, unavailable without GDCM ] for syntax in SYNTAXES: body = { 'Resources' : [ i ], } if syntax != '1.2.840.10008.1.2.1': body['Transcode'] = syntax self.assertEqual(0, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) DoPost(_REMOTE, '/peers/peer/store', body, 'text/plain') self.assertEqual(1, len(DoGet(_LOCAL, '/instances'))) self.assertEqual(1, len(DoGet(_REMOTE, '/instances'))) self.assertEqual(syntax, GetTransferSyntax( DoGet(_LOCAL, '/instances/%s/file' % DoGet(_LOCAL, '/instances') [0]))) DropOrthanc(_LOCAL) def test_getscu(self): def CleanTarget(): if os.path.isdir('/tmp/GETSCU'): shutil.rmtree('/tmp/GETSCU') os.makedirs('/tmp/GETSCU') env = {} if _DOCKER: # This is "getscu" from DCMTK 3.6.5 compiled using LSB, # and running in a GNU/Linux distribution running DCMTK # 3.6.0. Tell "getscu" where it can find the DICOM dictionary. env['DCMDICTPATH'] = '/usr/share/libdcmtk2/dicom.dic' # no transcoding required UploadInstance(_REMOTE, 'Brainix/Flair/IM-0001-0001.dcm')['ID'] CleanTarget() subprocess.check_call([ FindExecutable('getscu'), _REMOTE['Server'], str(_REMOTE['DicomPort']), '-aec', 'ORTHANC', '-aet', 'ORTHANCTEST', # pretend to be the other orthanc '-k', '0020,000d=2.16.840.1.113669.632.20.1211.10000357775', '-k', '0008,0052=STUDY', '--output-directory', '/tmp/GETSCU/' ], env = env) self.assertTrue(os.path.isfile('/tmp/GETSCU/MR.1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114314079549')) CleanTarget() return # transcoding required UploadInstance(_REMOTE, 'Formats/JpegLossless.dcm') subprocess.check_call([ FindExecutable('getscu'), _REMOTE['Server'], str(_REMOTE['DicomPort']), '-aec', 'ORTHANC', '-aet', 'ORTHANCTEST', # pretend to be the other orthanc '-k', '0020,000d=2.16.840.1.113669.632.20.1211.10000357775\\1.2.276.0.7230010.3.1.2.2831176407.19977.1434973482.75580', '-k', '0008,0052=STUDY', '--output-directory', '/tmp/GETSCU/' ], env = env) os.system('ls -l /tmp/GETSCU') self.assertTrue(os.path.isfile('/tmp/GETSCU/MR.1.3.46.670589.11.0.0.11.4.2.0.8743.5.5396.2006120114314079549')) self.assertTrue(os.path.isfile('/tmp/GETSCU/MR.1.2.276.0.7230010.3.1.4.2831176407.19977.1434973482.75579'))