Mercurial > hg > orthanc-tests
annotate Plugins/WSI/Run.py @ 527:86456045ac80 Orthanc-1.12.0
added test_numeric_metadata
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 14 Apr 2023 12:12:44 +0200 |
| parents | 933fe1bbce4f |
| children | 13169c8ddc96 |
| rev | line source |
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| 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', | |
| 59 default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomizer', | |
| 60 help = 'Password to the REST API') | |
| 61 parser.add_argument('--to-tiff', | |
| 62 default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomToTiff', | |
| 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 | |
| 134 | |
| 253 | 135 os.unlink(temp.name) |
| 136 | |
| 137 return tiff | |
| 138 | |
| 251 | 139 |
| 140 class Orthanc(unittest.TestCase): | |
| 141 def setUp(self): | |
| 142 if (sys.version_info >= (3, 0)): | |
| 143 # Remove annoying warnings about unclosed socket in Python 3 | |
| 144 import warnings | |
| 145 warnings.simplefilter("ignore", ResourceWarning) | |
| 146 | |
| 147 DropOrthanc(ORTHANC) | |
| 148 | |
| 149 | |
| 150 def test_single(self): | |
| 151 CallDicomizer([ GetDatabasePath('Lena.jpg') ]) | |
| 152 | |
| 153 i = DoGet(ORTHANC, '/instances') | |
| 154 self.assertEqual(1, len(i)) | |
| 155 | |
| 156 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[0]) | |
| 157 self.assertEqual(1, int(tags['NumberOfFrames'])) | |
| 158 self.assertEqual(512, int(tags['Columns'])) | |
| 159 self.assertEqual(512, int(tags['Rows'])) | |
| 160 self.assertEqual('YBR_FULL_422', tags['PhotometricInterpretation']) | |
| 161 | |
| 162 s = DoGet(ORTHANC, '/series') | |
| 163 self.assertEqual(1, len(s)) | |
| 164 | |
| 165 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 166 self.assertEqual(s[0], pyramid['ID']) | |
| 167 self.assertEqual(1, len(pyramid['Resolutions'])) | |
| 168 self.assertEqual(1, len(pyramid['Sizes'])) | |
| 169 self.assertEqual(1, len(pyramid['TilesCount'])) | |
| 170 self.assertEqual(1, pyramid['Resolutions'][0]) | |
| 171 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 172 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
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173 self.assertEqual(1, len(pyramid['TilesSizes'])) |
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174 self.assertEqual(2, len(pyramid['TilesSizes'][0])) |
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175 self.assertEqual(512, pyramid['TilesSizes'][0][0]) |
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176 self.assertEqual(512, pyramid['TilesSizes'][0][1]) |
| 251 | 177 self.assertEqual(512, pyramid['TotalWidth']) |
| 178 self.assertEqual(512, pyramid['TotalHeight']) | |
| 179 self.assertEqual(1, pyramid['TilesCount'][0][0]) | |
| 180 self.assertEqual(1, pyramid['TilesCount'][0][1]) | |
| 181 | |
| 253 | 182 tiff = CallTiffInfoOnSeries(s[0]) |
| 183 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 184 self.assertEqual(1, len(p)) | |
| 185 self.assertTrue('YCbCr' in p[0]) | |
| 186 | |
| 251 | 187 |
| 188 def test_grayscale_pyramid(self): | |
| 189 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--tile-width=64', '--tile-height=64' ]) | |
| 190 | |
| 191 i = DoGet(ORTHANC, '/instances') | |
| 192 self.assertEqual(4, len(i)) | |
| 193 | |
| 194 for j in range(4): | |
| 195 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[j]) | |
| 196 self.assertEqual(64, int(tags['Columns'])) | |
| 197 self.assertEqual(64, int(tags['Rows'])) | |
| 198 self.assertEqual('MONOCHROME2', tags['PhotometricInterpretation']) | |
| 199 | |
| 200 s = DoGet(ORTHANC, '/series') | |
| 201 self.assertEqual(1, len(s)) | |
| 202 | |
| 203 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 204 self.assertEqual(s[0], pyramid['ID']) | |
| 205 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 206 self.assertEqual(4, len(pyramid['Sizes'])) | |
| 207 self.assertEqual(4, len(pyramid['TilesCount'])) | |
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208 self.assertEqual(4, len(pyramid['TilesSizes'])) |
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209 |
| 251 | 210 self.assertEqual(1, pyramid['Resolutions'][0]) |
| 211 self.assertEqual(2, pyramid['Resolutions'][1]) | |
| 212 self.assertEqual(4, pyramid['Resolutions'][2]) | |
| 213 self.assertEqual(8, pyramid['Resolutions'][3]) | |
| 214 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 215 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
| 216 self.assertEqual(256, pyramid['Sizes'][1][0]) | |
| 217 self.assertEqual(256, pyramid['Sizes'][1][1]) | |
| 218 self.assertEqual(128, pyramid['Sizes'][2][0]) | |
| 219 self.assertEqual(128, pyramid['Sizes'][2][1]) | |
| 220 self.assertEqual(64, pyramid['Sizes'][3][0]) | |
| 221 self.assertEqual(64, pyramid['Sizes'][3][1]) | |
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222 for i in range(4): |
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223 self.assertEqual(2, len(pyramid['TilesSizes'][i])) |
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224 self.assertEqual(64, pyramid['TilesSizes'][i][0]) |
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225 self.assertEqual(64, pyramid['TilesSizes'][i][1]) |
| 251 | 226 self.assertEqual(512, pyramid['TotalWidth']) |
| 227 self.assertEqual(512, pyramid['TotalHeight']) | |
| 228 self.assertEqual(8, pyramid['TilesCount'][0][0]) | |
| 229 self.assertEqual(8, pyramid['TilesCount'][0][1]) | |
| 230 self.assertEqual(4, pyramid['TilesCount'][1][0]) | |
| 231 self.assertEqual(4, pyramid['TilesCount'][1][1]) | |
| 232 self.assertEqual(2, pyramid['TilesCount'][2][0]) | |
| 233 self.assertEqual(2, pyramid['TilesCount'][2][1]) | |
| 234 self.assertEqual(1, pyramid['TilesCount'][3][0]) | |
| 235 self.assertEqual(1, pyramid['TilesCount'][3][1]) | |
| 253 | 236 |
| 237 tiff = CallTiffInfoOnSeries(s[0]) | |
| 238 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 239 self.assertEqual(4, len(p)) | |
| 240 for j in range(4): | |
| 241 self.assertTrue('min-is-black' in p[j]) | |
| 242 | |
| 243 | |
| 244 def test_import_tiff_grayscale(self): | |
| 245 CallDicomizer([ GetDatabasePath('WSI/LenaGrayscaleJpeg.tiff') ]) | |
| 246 | |
| 247 s = DoGet(ORTHANC, '/series') | |
| 248 self.assertEqual(1, len(s)) | |
| 249 | |
| 250 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 251 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 252 | |
| 253 tiff = CallTiffInfoOnSeries(s[0]) | |
| 254 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 255 self.assertEqual(4, len(p)) | |
| 256 for j in range(4): | |
| 257 self.assertTrue('min-is-black' in p[j]) | |
| 258 | |
| 259 | |
| 260 def test_import_tiff_ycbcr(self): | |
| 261 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegYCbCr.tiff') ]) | |
| 262 | |
| 263 s = DoGet(ORTHANC, '/series') | |
| 264 self.assertEqual(1, len(s)) | |
| 265 | |
| 266 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 267 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 268 | |
| 269 tiff = CallTiffInfoOnSeries(s[0]) | |
| 270 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 271 self.assertEqual(4, len(p)) | |
| 272 for j in range(4): | |
| 273 self.assertTrue('YCbCr' in p[j]) | |
| 274 | |
| 275 | |
| 276 def test_import_tiff_rgb(self): | |
| 277 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegRGB.tiff') ]) | |
| 278 | |
| 279 s = DoGet(ORTHANC, '/series') | |
| 280 self.assertEqual(1, len(s)) | |
| 281 | |
| 282 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 283 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 284 | |
| 285 tiff = CallTiffInfoOnSeries(s[0]) | |
| 286 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 287 self.assertEqual(4, len(p)) | |
| 288 for j in range(4): | |
| 289 self.assertTrue('RGB' in p[j]) | |
| 290 | |
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291 |
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292 def test_concatenation(self): |
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293 # https://bugs.orthanc-server.com/show_bug.cgi?id=145 |
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294 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', ]) |
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295 i = DoGet(ORTHANC, '/instances') |
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296 self.assertEqual(1, len(i)) |
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297 tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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298 self.assertTrue('0020,0242' in tags) # SOP Instance UID of Concatenation Source |
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299 self.assertTrue('0020,9161' in tags) # Concatenation UID |
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300 self.assertTrue('0020,9162' in tags) # In-concatenation Number |
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301 self.assertTrue('0020,9228' in tags) # Concatenation Frame Offset Number |
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302 self.assertEqual('1', tags['0020,9162']) |
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303 self.assertEqual('0', tags['0020,9228']) |
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304 |
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305 DropOrthanc(ORTHANC) |
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306 |
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307 # "--max-size" disables the concatenation |
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308 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', '--max-size=0' ]) |
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309 i = DoGet(ORTHANC, '/instances') |
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310 self.assertEqual(1, len(i)) |
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311 tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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312 self.assertFalse('0020,0242' in tags) |
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313 self.assertFalse('0020,9161' in tags) |
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314 self.assertFalse('0020,9162' in tags) |
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315 self.assertFalse('0020,9228' in tags) |
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316 |
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317 DropOrthanc(ORTHANC) |
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318 |
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319 # 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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320 CallDicomizer([ GetDatabasePath('WSI/Lena2x2.png'), '--levels=1', '--max-size=1', '--compression=none' ]) |
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321 i = DoGet(ORTHANC, '/instances') |
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322 self.assertEqual(2, len(i)) |
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323 t1 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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324 t2 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[1]) |
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325 self.assertTrue('0020,0242' in t1) |
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326 self.assertTrue('0020,9161' in t1) |
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327 self.assertTrue('0020,9162' in t1) |
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328 self.assertTrue('0020,9228' in t1) |
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329 self.assertEqual(t1['0020,0242'], t2['0020,0242']) |
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330 self.assertEqual(t1['0020,9161'], t2['0020,9161']) |
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331 if t1['0020,9162'] == '1': |
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332 self.assertEqual('1', t1['0020,9162']) |
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333 self.assertEqual('0', t1['0020,9228']) |
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334 self.assertEqual('2', t2['0020,9162']) |
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335 self.assertEqual('2', t2['0020,9228']) |
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336 else: |
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337 self.assertEqual('1', t2['0020,9162']) |
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338 self.assertEqual('0', t2['0020,9228']) |
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339 self.assertEqual('2', t1['0020,9162']) |
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340 self.assertEqual('2', t1['0020,9228']) |
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341 |
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342 |
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343 def test_pixel_spacing(self): |
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344 # https://bugs.orthanc-server.com/show_bug.cgi?id=139 |
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345 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), # Image is 512x512 |
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346 '--levels=4', '--tile-width=64', '--tile-height=64', '--max-size=0', |
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347 '--imaged-width=20', '--imaged-height=10' ]) |
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348 |
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349 instances = DoGet(ORTHANC, '/instances') |
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350 self.assertEqual(4, len(instances)) |
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351 |
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352 spacings = {} |
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353 for i in instances: |
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354 t = DoGet(ORTHANC, '/instances/%s/tags?short' % i) |
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355 spacings[t['0028,0008']] = t['5200,9229'][0]['0028,9110'][0]['0028,0030'] |
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356 |
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357 self.assertEqual(4, len(spacings)) |
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358 for i in range(4): |
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359 s = spacings[str(4 ** i)].split('\\') |
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360 self.assertEqual(2, len(s)) |
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361 self.assertEqual(20.0 / 512.0 * (2.0 ** (3 - i)), float(s[0])) |
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362 self.assertEqual(10.0 / 512.0 * (2.0 ** (3 - i)), float(s[1])) |
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363 |
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364 |
| 251 | 365 try: |
| 366 print('\nStarting the tests...') | |
| 367 unittest.main(argv = [ sys.argv[0] ] + args.options) | |
| 368 | |
| 369 finally: | |
| 370 print('\nDone') |