Mercurial > hg > orthanc-tests
annotate Plugins/WSI/Run.py @ 568:6399d3a1cd30
WSI: fix compatibility with Python 3
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 13 Jul 2023 13:06:38 +0200 |
| parents | 13169c8ddc96 |
| children | 201e69006cff |
| rev | line source |
|---|---|
| 251 | 1 #!/usr/bin/python |
| 2 # -*- coding: utf-8 -*- | |
| 3 | |
| 4 | |
| 5 # Orthanc - A Lightweight, RESTful DICOM Store | |
| 6 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
| 7 # Department, University Hospital of Liege, Belgium | |
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8 # Copyright (C) 2017-2023 Osimis S.A., Belgium |
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9 # Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
| 251 | 10 # |
| 11 # This program is free software: you can redistribute it and/or | |
| 12 # modify it under the terms of the GNU General Public License as | |
| 13 # published by the Free Software Foundation, either version 3 of the | |
| 14 # License, or (at your option) any later version. | |
| 15 # | |
| 16 # This program is distributed in the hope that it will be useful, but | |
| 17 # WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 18 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 19 # General Public License for more details. | |
| 20 # | |
| 21 # You should have received a copy of the GNU General Public License | |
| 22 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 23 | |
| 24 | |
| 25 import argparse | |
| 26 import os | |
| 27 import pprint | |
| 28 import re | |
| 29 import subprocess | |
| 30 import sys | |
| 31 import tempfile | |
| 32 import unittest | |
| 33 from shutil import copyfile | |
| 34 | |
| 35 sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'Tests')) | |
| 36 from Toolbox import * | |
| 37 | |
| 38 | |
| 39 ## | |
| 40 ## Parse the command-line arguments | |
| 41 ## | |
| 42 | |
| 43 parser = argparse.ArgumentParser(description = 'Run the integration tests for the WSI Dicomizer.') | |
| 44 | |
| 45 parser.add_argument('--server', | |
| 46 default = 'localhost', | |
| 47 help = 'Address of the Orthanc server to test') | |
| 48 parser.add_argument('--rest', | |
| 49 type = int, | |
| 50 default = 8042, | |
| 51 help = 'Port to the REST API') | |
| 52 parser.add_argument('--username', | |
| 53 default = 'alice', | |
| 54 help = 'Username to the REST API') | |
| 55 parser.add_argument('--password', | |
| 56 default = 'orthanctest', | |
| 57 help = 'Password to the REST API') | |
| 58 parser.add_argument('--dicomizer', | |
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59 default = os.path.join(os.environ['HOME'], 'Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomizer'), |
| 251 | 60 help = 'Password to the REST API') |
| 61 parser.add_argument('--to-tiff', | |
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62 default = os.path.join(os.environ['HOME'], 'Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomToTiff'), |
| 251 | 63 help = 'Password to the REST API') |
| 252 | 64 parser.add_argument('--valgrind', help = 'Use valgrind while running the DICOM-izer', |
| 65 action = 'store_true') | |
| 251 | 66 parser.add_argument('--force', help = 'Do not warn the user', |
| 67 action = 'store_true') | |
| 68 parser.add_argument('options', metavar = 'N', nargs = '*', | |
| 69 help='Arguments to Python unittest') | |
| 70 | |
| 71 args = parser.parse_args() | |
| 72 | |
| 73 if not args.force: | |
| 74 print(""" | |
| 75 WARNING: This test will remove all the content of your | |
| 76 Orthanc instance running on %s! | |
| 77 | |
| 78 Are you sure ["yes" to go on]?""" % args.server) | |
| 79 | |
| 80 if sys.stdin.readline().strip() != 'yes': | |
| 81 print('Aborting...') | |
| 82 exit(0) | |
| 83 | |
| 84 | |
| 85 | |
| 86 | |
| 87 ## | |
| 88 ## The tests | |
| 89 ## | |
| 90 | |
| 91 ORTHANC = DefineOrthanc(server = args.server, | |
| 92 username = args.username, | |
| 93 password = args.password, | |
| 94 restPort = args.rest) | |
| 95 | |
| 253 | 96 def CallCommand(command): |
| 252 | 97 prefix = [] |
| 98 if args.valgrind: | |
| 99 prefix = [ 'valgrind' ] | |
| 100 | |
| 253 | 101 log = subprocess.check_output(prefix + command, |
| 252 | 102 stderr=subprocess.STDOUT) |
| 253 | 103 |
| 252 | 104 # If using valgrind, only print the lines from the log starting |
| 105 # with '==' (they contain the report from valgrind) | |
| 106 if args.valgrind: | |
| 107 print('\n'.join(filter(lambda x: x.startswith('=='), log.splitlines()))) | |
| 251 | 108 |
| 253 | 109 |
| 110 def CallDicomizer(suffix): | |
| 111 CallCommand([ args.dicomizer, | |
| 460 | 112 '--orthanc=http://%s:%s' % (args.server, args.rest), |
| 253 | 113 '--username=%s' % args.username, |
| 459 | 114 '--password=%s' % args.password ] + suffix |
| 115 ) | |
| 253 | 116 |
| 117 | |
| 118 def CallDicomToTiff(suffix): | |
| 316 | 119 CallCommand([ args.to_tiff, |
| 460 | 120 '--orthanc=http://%s:%s' % (args.server, args.rest), |
| 316 | 121 '--username=%s' % args.username, |
| 122 '--password=%s' % args.password ] + suffix) | |
| 253 | 123 |
| 124 | |
| 125 def CallTiffInfoOnSeries(series): | |
| 126 with tempfile.NamedTemporaryFile(delete = False) as temp: | |
| 127 temp.close() | |
| 128 CallDicomToTiff([ series, temp.name ]) | |
| 316 | 129 try: |
| 130 tiff = subprocess.check_output([ 'tiffinfo', temp.name ]) | |
| 131 except: | |
| 132 print('\ntiffinfo is probably not installed => sudo apt-get install libtiff-tools\n') | |
| 133 tiff = None | |
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134 |
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135 if (tiff != None and sys.version_info >= (3, 0)): |
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136 tiff = tiff.decode('ascii') |
| 316 | 137 |
| 253 | 138 os.unlink(temp.name) |
| 139 | |
| 140 return tiff | |
| 141 | |
| 251 | 142 |
| 143 class Orthanc(unittest.TestCase): | |
| 144 def setUp(self): | |
| 145 if (sys.version_info >= (3, 0)): | |
| 146 # Remove annoying warnings about unclosed socket in Python 3 | |
| 147 import warnings | |
| 148 warnings.simplefilter("ignore", ResourceWarning) | |
| 149 | |
| 150 DropOrthanc(ORTHANC) | |
| 151 | |
| 152 | |
| 153 def test_single(self): | |
| 154 CallDicomizer([ GetDatabasePath('Lena.jpg') ]) | |
| 155 | |
| 156 i = DoGet(ORTHANC, '/instances') | |
| 157 self.assertEqual(1, len(i)) | |
| 158 | |
| 159 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[0]) | |
| 160 self.assertEqual(1, int(tags['NumberOfFrames'])) | |
| 161 self.assertEqual(512, int(tags['Columns'])) | |
| 162 self.assertEqual(512, int(tags['Rows'])) | |
| 163 self.assertEqual('YBR_FULL_422', tags['PhotometricInterpretation']) | |
| 164 | |
| 165 s = DoGet(ORTHANC, '/series') | |
| 166 self.assertEqual(1, len(s)) | |
| 167 | |
| 168 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 169 self.assertEqual(s[0], pyramid['ID']) | |
| 170 self.assertEqual(1, len(pyramid['Resolutions'])) | |
| 171 self.assertEqual(1, len(pyramid['Sizes'])) | |
| 172 self.assertEqual(1, len(pyramid['TilesCount'])) | |
| 173 self.assertEqual(1, pyramid['Resolutions'][0]) | |
| 174 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 175 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
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176 self.assertEqual(1, len(pyramid['TilesSizes'])) |
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177 self.assertEqual(2, len(pyramid['TilesSizes'][0])) |
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178 self.assertEqual(512, pyramid['TilesSizes'][0][0]) |
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179 self.assertEqual(512, pyramid['TilesSizes'][0][1]) |
| 251 | 180 self.assertEqual(512, pyramid['TotalWidth']) |
| 181 self.assertEqual(512, pyramid['TotalHeight']) | |
| 182 self.assertEqual(1, pyramid['TilesCount'][0][0]) | |
| 183 self.assertEqual(1, pyramid['TilesCount'][0][1]) | |
| 184 | |
| 253 | 185 tiff = CallTiffInfoOnSeries(s[0]) |
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186 p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) |
| 253 | 187 self.assertEqual(1, len(p)) |
| 188 self.assertTrue('YCbCr' in p[0]) | |
| 189 | |
| 251 | 190 |
| 191 def test_grayscale_pyramid(self): | |
| 192 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--tile-width=64', '--tile-height=64' ]) | |
| 193 | |
| 194 i = DoGet(ORTHANC, '/instances') | |
| 195 self.assertEqual(4, len(i)) | |
| 196 | |
| 197 for j in range(4): | |
| 198 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[j]) | |
| 199 self.assertEqual(64, int(tags['Columns'])) | |
| 200 self.assertEqual(64, int(tags['Rows'])) | |
| 201 self.assertEqual('MONOCHROME2', tags['PhotometricInterpretation']) | |
| 202 | |
| 203 s = DoGet(ORTHANC, '/series') | |
| 204 self.assertEqual(1, len(s)) | |
| 205 | |
| 206 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 207 self.assertEqual(s[0], pyramid['ID']) | |
| 208 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 209 self.assertEqual(4, len(pyramid['Sizes'])) | |
| 210 self.assertEqual(4, len(pyramid['TilesCount'])) | |
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211 self.assertEqual(4, len(pyramid['TilesSizes'])) |
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212 |
| 251 | 213 self.assertEqual(1, pyramid['Resolutions'][0]) |
| 214 self.assertEqual(2, pyramid['Resolutions'][1]) | |
| 215 self.assertEqual(4, pyramid['Resolutions'][2]) | |
| 216 self.assertEqual(8, pyramid['Resolutions'][3]) | |
| 217 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 218 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
| 219 self.assertEqual(256, pyramid['Sizes'][1][0]) | |
| 220 self.assertEqual(256, pyramid['Sizes'][1][1]) | |
| 221 self.assertEqual(128, pyramid['Sizes'][2][0]) | |
| 222 self.assertEqual(128, pyramid['Sizes'][2][1]) | |
| 223 self.assertEqual(64, pyramid['Sizes'][3][0]) | |
| 224 self.assertEqual(64, pyramid['Sizes'][3][1]) | |
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225 for i in range(4): |
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226 self.assertEqual(2, len(pyramid['TilesSizes'][i])) |
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227 self.assertEqual(64, pyramid['TilesSizes'][i][0]) |
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228 self.assertEqual(64, pyramid['TilesSizes'][i][1]) |
| 251 | 229 self.assertEqual(512, pyramid['TotalWidth']) |
| 230 self.assertEqual(512, pyramid['TotalHeight']) | |
| 231 self.assertEqual(8, pyramid['TilesCount'][0][0]) | |
| 232 self.assertEqual(8, pyramid['TilesCount'][0][1]) | |
| 233 self.assertEqual(4, pyramid['TilesCount'][1][0]) | |
| 234 self.assertEqual(4, pyramid['TilesCount'][1][1]) | |
| 235 self.assertEqual(2, pyramid['TilesCount'][2][0]) | |
| 236 self.assertEqual(2, pyramid['TilesCount'][2][1]) | |
| 237 self.assertEqual(1, pyramid['TilesCount'][3][0]) | |
| 238 self.assertEqual(1, pyramid['TilesCount'][3][1]) | |
| 253 | 239 |
| 240 tiff = CallTiffInfoOnSeries(s[0]) | |
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241 p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) |
| 253 | 242 self.assertEqual(4, len(p)) |
| 243 for j in range(4): | |
| 244 self.assertTrue('min-is-black' in p[j]) | |
| 245 | |
| 246 | |
| 247 def test_import_tiff_grayscale(self): | |
| 248 CallDicomizer([ GetDatabasePath('WSI/LenaGrayscaleJpeg.tiff') ]) | |
| 249 | |
| 250 s = DoGet(ORTHANC, '/series') | |
| 251 self.assertEqual(1, len(s)) | |
| 252 | |
| 253 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 254 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 255 | |
| 256 tiff = CallTiffInfoOnSeries(s[0]) | |
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257 p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) |
| 253 | 258 self.assertEqual(4, len(p)) |
| 259 for j in range(4): | |
| 260 self.assertTrue('min-is-black' in p[j]) | |
| 261 | |
| 262 | |
| 263 def test_import_tiff_ycbcr(self): | |
| 264 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegYCbCr.tiff') ]) | |
| 265 | |
| 266 s = DoGet(ORTHANC, '/series') | |
| 267 self.assertEqual(1, len(s)) | |
| 268 | |
| 269 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 270 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 271 | |
| 272 tiff = CallTiffInfoOnSeries(s[0]) | |
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273 p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) |
| 253 | 274 self.assertEqual(4, len(p)) |
| 275 for j in range(4): | |
| 276 self.assertTrue('YCbCr' in p[j]) | |
| 277 | |
| 278 | |
| 279 def test_import_tiff_rgb(self): | |
| 280 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegRGB.tiff') ]) | |
| 281 | |
| 282 s = DoGet(ORTHANC, '/series') | |
| 283 self.assertEqual(1, len(s)) | |
| 284 | |
| 285 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 286 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 287 | |
| 288 tiff = CallTiffInfoOnSeries(s[0]) | |
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289 p = list(filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines())) |
| 253 | 290 self.assertEqual(4, len(p)) |
| 291 for j in range(4): | |
| 292 self.assertTrue('RGB' in p[j]) | |
| 293 | |
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294 |
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295 def test_concatenation(self): |
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296 # https://bugs.orthanc-server.com/show_bug.cgi?id=145 |
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297 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', ]) |
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298 i = DoGet(ORTHANC, '/instances') |
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299 self.assertEqual(1, len(i)) |
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300 tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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301 self.assertTrue('0020,0242' in tags) # SOP Instance UID of Concatenation Source |
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302 self.assertTrue('0020,9161' in tags) # Concatenation UID |
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303 self.assertTrue('0020,9162' in tags) # In-concatenation Number |
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304 self.assertTrue('0020,9228' in tags) # Concatenation Frame Offset Number |
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305 self.assertEqual('1', tags['0020,9162']) |
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306 self.assertEqual('0', tags['0020,9228']) |
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307 |
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308 DropOrthanc(ORTHANC) |
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309 |
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310 # "--max-size" disables the concatenation |
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311 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', '--max-size=0' ]) |
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312 i = DoGet(ORTHANC, '/instances') |
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313 self.assertEqual(1, len(i)) |
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314 tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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315 self.assertFalse('0020,0242' in tags) |
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316 self.assertFalse('0020,9161' in tags) |
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317 self.assertFalse('0020,9162' in tags) |
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318 self.assertFalse('0020,9228' in tags) |
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319 |
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320 DropOrthanc(ORTHANC) |
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321 |
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322 # This creates a series with 2 instances of roughly 1.5MB (= 2 frames x 512 x 512 x 3 (RGB24) + DICOM overhead) |
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323 CallDicomizer([ GetDatabasePath('WSI/Lena2x2.png'), '--levels=1', '--max-size=1', '--compression=none' ]) |
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324 i = DoGet(ORTHANC, '/instances') |
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325 self.assertEqual(2, len(i)) |
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326 t1 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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327 t2 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[1]) |
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328 self.assertTrue('0020,0242' in t1) |
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329 self.assertTrue('0020,9161' in t1) |
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330 self.assertTrue('0020,9162' in t1) |
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331 self.assertTrue('0020,9228' in t1) |
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332 self.assertEqual(t1['0020,0242'], t2['0020,0242']) |
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333 self.assertEqual(t1['0020,9161'], t2['0020,9161']) |
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334 if t1['0020,9162'] == '1': |
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335 self.assertEqual('1', t1['0020,9162']) |
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336 self.assertEqual('0', t1['0020,9228']) |
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337 self.assertEqual('2', t2['0020,9162']) |
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338 self.assertEqual('2', t2['0020,9228']) |
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339 else: |
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340 self.assertEqual('1', t2['0020,9162']) |
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341 self.assertEqual('0', t2['0020,9228']) |
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342 self.assertEqual('2', t1['0020,9162']) |
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343 self.assertEqual('2', t1['0020,9228']) |
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365
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344 |
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345 |
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346 def test_pixel_spacing(self): |
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347 # https://bugs.orthanc-server.com/show_bug.cgi?id=139 |
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348 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), # Image is 512x512 |
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349 '--levels=4', '--tile-width=64', '--tile-height=64', '--max-size=0', |
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350 '--imaged-width=20', '--imaged-height=10' ]) |
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351 |
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352 instances = DoGet(ORTHANC, '/instances') |
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353 self.assertEqual(4, len(instances)) |
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354 |
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355 spacings = {} |
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356 for i in instances: |
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357 t = DoGet(ORTHANC, '/instances/%s/tags?short' % i) |
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358 spacings[t['0028,0008']] = t['5200,9229'][0]['0028,9110'][0]['0028,0030'] |
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359 |
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360 self.assertEqual(4, len(spacings)) |
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361 for i in range(4): |
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362 s = spacings[str(4 ** i)].split('\\') |
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363 self.assertEqual(2, len(s)) |
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364 self.assertEqual(20.0 / 512.0 * (2.0 ** (3 - i)), float(s[0])) |
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365 self.assertEqual(10.0 / 512.0 * (2.0 ** (3 - i)), float(s[1])) |
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366 |
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567
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367 |
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368 def test_http_accept(self): |
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369 # https://discourse.orthanc-server.org/t/orthanc-wsi-image-quality-issue/3331 |
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370 |
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371 def TestTransferSyntax(s, expected): |
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372 instance = DoGet(ORTHANC, '/series/%s' % s[0]) ['Instances'][0] |
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373 self.assertEqual(expected, DoGet(ORTHANC, '/instances/%s/metadata/TransferSyntax' % instance)) |
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374 |
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375 def TestDefaultAccept(s, mime): |
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376 tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0]) |
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377 self.assertEqual(mime, tile.format) |
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378 |
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379 tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { |
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380 'Accept' : 'text/html,*/*' |
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381 }) |
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382 self.assertEqual(mime, tile.format) |
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383 |
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384 tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { |
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385 'Accept' : 'image/*,text/html' |
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386 }) |
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387 self.assertEqual(mime, tile.format) |
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388 |
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389 tile = DoGetRaw(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], headers = { |
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390 'Accept' : 'text/html' |
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391 }) |
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392 self.assertEqual(406, int(tile[0]['status'])) |
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393 |
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394 def TestForceAccept(s): |
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395 tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { |
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396 'Accept' : 'image/jpeg' |
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397 }) |
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398 self.assertEqual('JPEG', tile.format) |
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399 |
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400 tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { |
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401 'Accept' : 'image/png' |
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402 }) |
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403 self.assertEqual('PNG', tile.format) |
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404 |
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405 tile = GetImage(ORTHANC, '/wsi/tiles/%s/0/0/0' % s[0], { |
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406 'Accept' : 'image/jp2' |
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407 }) |
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408 self.assertEqual('JPEG2000', tile.format) |
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409 |
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410 |
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411 CallDicomizer([ GetDatabasePath('Lena.jpg') ]) |
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412 |
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413 s = DoGet(ORTHANC, '/series') |
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414 self.assertEqual(1, len(s)) |
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415 TestTransferSyntax(s, '1.2.840.10008.1.2.4.50') |
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416 TestDefaultAccept(s, 'JPEG') |
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417 TestForceAccept(s) |
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418 |
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419 DoDelete(ORTHANC, '/series/%s' % s[0]) |
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420 |
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421 CallDicomizer([ GetDatabasePath('Lena.jpg'), '--compression', 'none' ]) |
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422 s = DoGet(ORTHANC, '/series') |
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423 self.assertEqual(1, len(s)) |
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424 |
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425 TestTransferSyntax(s, '1.2.840.10008.1.2') |
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426 TestDefaultAccept(s, 'PNG') |
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427 TestForceAccept(s) |
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428 |
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429 DoDelete(ORTHANC, '/series/%s' % s[0]) |
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430 |
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431 CallDicomizer([ GetDatabasePath('Lena.jpg'), '--compression', 'jpeg2000' ]) |
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432 s = DoGet(ORTHANC, '/series') |
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433 self.assertEqual(1, len(s)) |
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434 |
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435 TestTransferSyntax(s, '1.2.840.10008.1.2.4.90') |
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436 TestDefaultAccept(s, 'PNG') |
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437 TestForceAccept(s) |
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365
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438 |
| 251 | 439 try: |
| 440 print('\nStarting the tests...') | |
| 441 unittest.main(argv = [ sys.argv[0] ] + args.options) | |
| 442 | |
| 443 finally: | |
| 444 print('\nDone') |