Mercurial > hg > orthanc-tests
changeset 573:31ab8bb2ac5a
merge
author | Alain Mazy <am@osimis.io> |
---|---|
date | Thu, 20 Jul 2023 10:57:39 +0200 |
parents | 3a5260cc6d55 (current diff) e6cee85fe421 (diff) |
children | ee71526e11ed |
files | Tests/Tests.py |
diffstat | 4 files changed, 268 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- a/.hgtags Thu Jul 20 10:52:37 2023 +0200 +++ b/.hgtags Thu Jul 20 10:57:39 2023 +0200 @@ -42,3 +42,4 @@ 8121c8aab919002fef882ac3b33eaeca350b1685 Orthanc-1.10.1 73d41c681568d8b8981fcbf1ee90bf0d558f8f24 Orthanc-1.11.0 86456045ac80545a2eca1fe0d8d7eb337a0b4ceb Orthanc-1.12.0 +855c3720902a1dade9accf91571ee6719e0c1eb6 Orthanc-1.12.1
--- a/GenerateConfigurationForTests.py Thu Jul 20 10:52:37 2023 +0200 +++ b/GenerateConfigurationForTests.py Thu Jul 20 10:57:39 2023 +0200 @@ -227,6 +227,11 @@ 'MaximumConnectionRetries' : 7, } +config['WholeSlideImaging'] = { + 'ServeMirador' : True, + 'ServeOpenSeadragon' : True, +} + # Enable case-insensitive PN (the default on versions <= 0.8.6)
--- a/Plugins/WSI/Run.py Thu Jul 20 10:52:37 2023 +0200 +++ b/Plugins/WSI/Run.py Thu Jul 20 10:57:39 2023 +0200 @@ -56,10 +56,10 @@ default = 'orthanctest', help = 'Password to the REST API') parser.add_argument('--dicomizer', - default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomizer', + default = os.path.join(os.environ['HOME'], 'Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomizer'), help = 'Password to the REST API') parser.add_argument('--to-tiff', - default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomToTiff', + default = os.path.join(os.environ['HOME'], 'Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomToTiff'), help = 'Password to the REST API') parser.add_argument('--valgrind', help = 'Use valgrind while running the DICOM-izer', action = 'store_true') @@ -100,7 +100,10 @@ log = subprocess.check_output(prefix + command, stderr=subprocess.STDOUT) - + + if sys.version_info >= (3, 0): + log = log.decode('ascii') + # If using valgrind, only print the lines from the log starting # with '==' (they contain the report from valgrind) if args.valgrind: @@ -131,6 +134,9 @@ except: print('\ntiffinfo is probably not installed => sudo apt-get install libtiff-tools\n') tiff = None + + if (tiff != None and sys.version_info >= (3, 0)): + tiff = tiff.decode('ascii') os.unlink(temp.name) @@ -180,7 +186,7 @@ self.assertEqual(1, pyramid['TilesCount'][0][1]) tiff = CallTiffInfoOnSeries(s[0]) - p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) + p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) self.assertEqual(1, len(p)) self.assertTrue('YCbCr' in p[0]) @@ -235,7 +241,7 @@ self.assertEqual(1, pyramid['TilesCount'][3][1]) tiff = CallTiffInfoOnSeries(s[0]) - p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) + p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('min-is-black' in p[j]) @@ -251,7 +257,7 @@ self.assertEqual(4, len(pyramid['Resolutions'])) tiff = CallTiffInfoOnSeries(s[0]) - p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) + p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('min-is-black' in p[j]) @@ -267,7 +273,7 @@ self.assertEqual(4, len(pyramid['Resolutions'])) tiff = CallTiffInfoOnSeries(s[0]) - p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) + p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('YCbCr' in p[j]) @@ -283,7 +289,7 @@ self.assertEqual(4, len(pyramid['Resolutions'])) tiff = CallTiffInfoOnSeries(s[0]) - p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) + p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) self.assertEqual(4, len(p)) for j in range(4): self.assertTrue('RGB' in p[j]) @@ -361,7 +367,207 @@ self.assertEqual(20.0 / 512.0 * (2.0 ** (3 - i)), float(s[0])) self.assertEqual(10.0 / 512.0 * (2.0 ** (3 - i)), float(s[1])) + + def test_http_accept(self): + # https://discourse.orthanc-server.org/t/orthanc-wsi-image-quality-issue/3331 + + def TestTransferSyntax(s, expected): + instance = DoGet(ORTHANC, '/series/%s' % s[0]) ['Instances'][0] + self.assertEqual(expected, DoGet(ORTHANC, '/instances/%s/metadata/TransferSyntax' % instance)) + def TestDefaultAccept(s, mime): + tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0]) + self.assertEqual(mime, tile.format) + + tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { + 'Accept' : 'text/html,*/*' + }) + self.assertEqual(mime, tile.format) + + tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { + 'Accept' : 'image/*,text/html' + }) + self.assertEqual(mime, tile.format) + + tile = DoGetRaw(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], headers = { + 'Accept' : 'text/html' + }) + self.assertEqual(406, int(tile[0]['status'])) + + def TestForceAccept(s): + tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { + 'Accept' : 'image/jpeg' + }) + self.assertEqual('JPEG', tile.format) + + tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { + 'Accept' : 'image/png' + }) + self.assertEqual('PNG', tile.format) + + tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { + 'Accept' : 'image/jp2' + }) + self.assertEqual('JPEG2000', tile.format) + + + CallDicomizer([ GetDatabasePath('Lena.jpg') ]) + + s = DoGet(ORTHANC, '/series') + self.assertEqual(1, len(s)) + TestTransferSyntax(s, '1.2.840.10008.1.2.4.50') + TestDefaultAccept(s, 'JPEG') + TestForceAccept(s) + + DoDelete(ORTHANC, '/series/%s' % s[0]) + + CallDicomizer([ GetDatabasePath('Lena.jpg'), '--compression', 'none' ]) + s = DoGet(ORTHANC, '/series') + self.assertEqual(1, len(s)) + + TestTransferSyntax(s, '1.2.840.10008.1.2') + TestDefaultAccept(s, 'PNG') + TestForceAccept(s) + + DoDelete(ORTHANC, '/series/%s' % s[0]) + + CallDicomizer([ GetDatabasePath('Lena.jpg'), '--compression', 'jpeg2000' ]) + s = DoGet(ORTHANC, '/series') + self.assertEqual(1, len(s)) + + TestTransferSyntax(s, '1.2.840.10008.1.2.4.90') + TestDefaultAccept(s, 'PNG') + TestForceAccept(s) + + def test_iiif(self): + CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), # Image is 512x512 + '--levels=3', '--tile-width=128', '--tile-height=128' ]) + + self.assertEqual(3, len(DoGet(ORTHANC, '/instances'))) + + s = DoGet(ORTHANC, '/series') + self.assertEqual(1, len(s)) + + uri = '/wsi/iiif/tiles/%s' % s[0] + info = DoGet(ORTHANC, '%s/info.json' % uri) + self.assertEqual('http://iiif.io/api/image/3/context.json', info['@context']) + self.assertEqual('http://iiif.io/api/image', info['protocol']) + self.assertEqual('http://localhost:8042%s' % uri, info['id']) + self.assertEqual('level0', info['profile']) + self.assertEqual('ImageService3', info['type']) + self.assertEqual(512, info['width']) + self.assertEqual(512, info['height']) + + self.assertEqual(3, len(info['sizes'])) + self.assertEqual(512, info['sizes'][0]['width']) + self.assertEqual(512, info['sizes'][0]['height']) + self.assertEqual(256, info['sizes'][1]['width']) + self.assertEqual(256, info['sizes'][1]['height']) + self.assertEqual(128, info['sizes'][2]['width']) + self.assertEqual(128, info['sizes'][2]['height']) + + self.assertEqual(1, len(info['tiles'])) + self.assertEqual(128, info['tiles'][0]['width']) + self.assertEqual(128, info['tiles'][0]['height']) + self.assertEqual([ 1, 2, 4 ], info['tiles'][0]['scaleFactors']) + + # The list of URIs below was generated by "orthanc-wsi/Resources/TestIIIFTiles.py" + + # Level 0 + GetImage(ORTHANC, '/%s/0,0,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/128,0,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/256,0,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/384,0,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/0,128,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/128,128,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/256,128,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/384,128,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/0,256,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/128,256,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/256,256,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/384,256,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/0,384,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/128,384,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/256,384,128,128/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/384,384,128,128/128,128/0/default.jpg' % uri) + + # Level 1 + GetImage(ORTHANC, '/%s/0,0,256,256/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/256,0,256,256/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/0,256,256,256/128,128/0/default.jpg' % uri) + GetImage(ORTHANC, '/%s/256,256,256,256/128,128/0/default.jpg' % uri) + + # Level 2 + i = GetImage(ORTHANC, '/%s/0,0,512,512/128,128/0/default.jpg' % uri) + self.assertEqual(128, i.width) + self.assertEqual(128, i.height) + + uri2 = '/wsi/iiif/series/%s/manifest.json' % s[0] + manifest = DoGet(ORTHANC, uri2) + self.assertEqual('http://iiif.io/api/presentation/3/context.json', manifest['@context']) + self.assertEqual('http://localhost:8042%s' % uri2, manifest['id']) + + self.assertEqual(1, len(manifest['items'])) + self.assertEqual(1, len(manifest['items'][0]['items'])) + self.assertEqual(1, len(manifest['items'][0]['items'][0]['items'])) + + self.assertEqual('Manifest', manifest['type']) + self.assertEqual('Canvas', manifest['items'][0]['type']) + self.assertEqual('AnnotationPage', manifest['items'][0]['items'][0]['type']) + self.assertEqual('Annotation', manifest['items'][0]['items'][0]['items'][0]['type']) + + self.assertEqual(512, manifest['items'][0]['width']) + self.assertEqual(512, manifest['items'][0]['height']) + + body = manifest['items'][0]['items'][0]['items'][0]['body'] + self.assertEqual(1, len(body['service'])) + self.assertEqual('image/jpeg', body['format']) + self.assertEqual('Image', body['type']) + self.assertEqual(512, body['width']) + self.assertEqual(512, body['height']) + self.assertEqual('level0', body['service'][0]['profile']) + self.assertEqual('ImageService3', body['service'][0]['type']) + self.assertEqual('http://localhost:8042%s' % uri, body['service'][0]['id']) + + def test_iiif_radiology(self): + a = UploadInstance(ORTHANC, 'ColorTestMalaterre.dcm') ['ID'] + b = UploadInstance(ORTHANC, 'Multiframe.dcm') ['ID'] + c = UploadInstance(ORTHANC, 'Brainix/Epi/IM-0001-0001.dcm') ['ID'] + d = UploadInstance(ORTHANC, 'Brainix/Epi/IM-0001-0002.dcm') ['ID'] + + s1 = DoGet(ORTHANC, '/instances/%s/series' % a) ['ID'] + s2 = DoGet(ORTHANC, '/instances/%s/series' % b) ['ID'] + s3 = DoGet(ORTHANC, '/instances/%s/series' % c) ['ID'] + + manifest = DoGet(ORTHANC, '/wsi/iiif/series/%s/manifest.json' % s1) + self.assertEqual(1, len(manifest['items'])) + + manifest = DoGet(ORTHANC, '/wsi/iiif/series/%s/manifest.json' % s2) + self.assertEqual(76, len(manifest['items'])) + + manifest = DoGet(ORTHANC, '/wsi/iiif/series/%s/manifest.json' % s3) + self.assertEqual(2, len(manifest['items'])) + + for (i, width, height) in [ (a, 41, 41), + (b, 512, 512), + (c, 256, 256), + (d, 256, 256) ]: + uri = '/wsi/iiif/frames/%s/0' % i + info = DoGet(ORTHANC, uri + '/info.json') + self.assertEqual(8, len(info)) + self.assertEqual('http://iiif.io/api/image/3/context.json', info['@context']) + self.assertEqual('http://iiif.io/api/image', info['protocol']) + self.assertEqual('http://localhost:8042%s' % uri, info['id']) + self.assertEqual('level0', info['profile']) + self.assertEqual('ImageService3', info['type']) + self.assertEqual(width, info['width']) + self.assertEqual(height, info['height']) + self.assertEqual(1, len(info['tiles'])) + self.assertEqual(3, len(info['tiles'][0])) + self.assertEqual(width, info['tiles'][0]['width']) + self.assertEqual(height, info['tiles'][0]['height']) + self.assertEqual([ 1 ], info['tiles'][0]['scaleFactors']) + try: print('\nStarting the tests...') unittest.main(argv = [ sys.argv[0] ] + args.options)
--- a/Tests/Tests.py Thu Jul 20 10:52:37 2023 +0200 +++ b/Tests/Tests.py Thu Jul 20 10:57:39 2023 +0200 @@ -2885,6 +2885,10 @@ })) self.assertEqual('Jodogne', DoGet(_REMOTE, '/instances/%s/content/PatientName' % i['ID']).strip()) + self.assertEqual('1.2.840.10008.5.1.4.1.1.104.1', DoGet(_REMOTE, '/instances/%s/content/SOPClassUID' % i['ID']).strip('\x00')) + self.assertEqual('WSD', DoGet(_REMOTE, '/instances/%s/content/ConversionType' % i['ID']).strip()) + self.assertEqual('application/pdf', DoGet(_REMOTE, '/instances/%s/content/MIMETypeOfEncapsulatedDocument' % i['ID']).strip()) + # In Orthanc <= 1.9.7, the "CT" would have been replaced by "OT" # https://groups.google.com/g/orthanc-users/c/eNSddNrQDtM/m/wc1HahimAAAJ self.assertEqual('CT', DoGet(_REMOTE, '/instances/%s/content/Modality' % i['ID']).strip()) @@ -2909,6 +2913,10 @@ })) self.assertEqual(brainixPatient, DoGet(_REMOTE, '/instances/%s/patient' % i['ID'])['ID']) + self.assertEqual('1.2.840.10008.5.1.4.1.1.104.1', DoGet(_REMOTE, '/instances/%s/content/SOPClassUID' % i['ID']).strip('\x00')) + self.assertEqual('OT', DoGet(_REMOTE, '/instances/%s/content/Modality' % i['ID']).strip('\x00')) + self.assertEqual('WSD', DoGet(_REMOTE, '/instances/%s/content/ConversionType' % i['ID']).strip()) + self.assertEqual('application/pdf', DoGet(_REMOTE, '/instances/%s/content/MIMETypeOfEncapsulatedDocument' % i['ID']).strip()) i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ @@ -9838,3 +9846,43 @@ Check('TransferSyntaxes/1.2.840.10008.1.2.2.dcm', True, False, 'OB') # Explicit Big Endian, 8bpp Check('TransferSyntaxes/1.2.840.10008.1.2.4.50.dcm', True, False, 'OB') # JPEG Check('Knee/T1/IM-0001-0001.dcm', True, False, 'OB') # JPEG2k + + def test_encapsulate_stl(self): + if IsOrthancVersionAbove(_REMOTE, 1, 12, 1): + stl = b'Hello, world' + + i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ + 'Content' : 'data:model/stl;base64,%s' % base64.b64encode(stl).decode(), + 'Force' : True, + 'Tags' : { + 'PatientName' : 'Jodogne' + } + })) ['ID'] + + tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) + self.assertEqual('Jodogne', tags['PatientName']) + self.assertEqual('M3D', tags['Modality']) + self.assertEqual('model/stl', tags['MIMETypeOfEncapsulatedDocument']) + self.assertEqual('1.2.840.10008.5.1.4.1.1.104.3', tags['SOPClassUID']) + + i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ + 'Content' : 'data:model/mtl;base64,%s' % base64.b64encode(stl).decode(), + 'Tags' : {} + })) ['ID'] + + tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) + self.assertFalse('PatientName' in tags) + self.assertEqual('M3D', tags['Modality']) + self.assertEqual('model/mtl', tags['MIMETypeOfEncapsulatedDocument']) + self.assertEqual('1.2.840.10008.5.1.4.1.1.104.5', tags['SOPClassUID']) + + i = DoPost(_REMOTE, '/tools/create-dicom', json.dumps({ + 'Content' : 'data:model/obj;base64,%s' % base64.b64encode(stl).decode(), + 'Tags' : {} + })) ['ID'] + + tags = DoGet(_REMOTE, '/instances/%s/tags?simplify' % i) + self.assertFalse('PatientName' in tags) + self.assertEqual('M3D', tags['Modality']) + self.assertEqual('model/obj', tags['MIMETypeOfEncapsulatedDocument']) + self.assertEqual('1.2.840.10008.5.1.4.1.1.104.4', tags['SOPClassUID'])