Mercurial > hg > orthanc-tests
annotate Plugins/WSI/Run.py @ 365:27cb0b60f2d3
wsi: test_pixel_spacing
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 13 Jan 2021 16:46:18 +0100 |
| parents | 6fa8218cf8db |
| children | e769bcf2b94f |
| 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) 2017-2021 Osimis S.A., Belgium |
| 251 | 9 # |
| 10 # This program is free software: you can redistribute it and/or | |
| 11 # modify it under the terms of the GNU General Public License as | |
| 12 # published by the Free Software Foundation, either version 3 of the | |
| 13 # License, or (at your option) any later version. | |
| 14 # | |
| 15 # This program is distributed in the hope that it will be useful, but | |
| 16 # WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 18 # General Public License for more details. | |
| 19 # | |
| 20 # You should have received a copy of the GNU General Public License | |
| 21 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 22 | |
| 23 | |
| 24 import argparse | |
| 25 import os | |
| 26 import pprint | |
| 27 import re | |
| 28 import subprocess | |
| 29 import sys | |
| 30 import tempfile | |
| 31 import unittest | |
| 32 from shutil import copyfile | |
| 33 | |
| 34 sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'Tests')) | |
| 35 from Toolbox import * | |
| 36 | |
| 37 | |
| 38 ## | |
| 39 ## Parse the command-line arguments | |
| 40 ## | |
| 41 | |
| 42 parser = argparse.ArgumentParser(description = 'Run the integration tests for the WSI Dicomizer.') | |
| 43 | |
| 44 parser.add_argument('--server', | |
| 45 default = 'localhost', | |
| 46 help = 'Address of the Orthanc server to test') | |
| 47 parser.add_argument('--rest', | |
| 48 type = int, | |
| 49 default = 8042, | |
| 50 help = 'Port to the REST API') | |
| 51 parser.add_argument('--username', | |
| 52 default = 'alice', | |
| 53 help = 'Username to the REST API') | |
| 54 parser.add_argument('--password', | |
| 55 default = 'orthanctest', | |
| 56 help = 'Password to the REST API') | |
| 57 parser.add_argument('--dicomizer', | |
| 58 default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomizer', | |
| 59 help = 'Password to the REST API') | |
| 60 parser.add_argument('--to-tiff', | |
| 61 default = '/home/jodogne/Subversion/orthanc-wsi/Applications/i/OrthancWSIDicomToTiff', | |
| 62 help = 'Password to the REST API') | |
| 252 | 63 parser.add_argument('--valgrind', help = 'Use valgrind while running the DICOM-izer', |
| 64 action = 'store_true') | |
| 251 | 65 parser.add_argument('--force', help = 'Do not warn the user', |
| 66 action = 'store_true') | |
| 67 parser.add_argument('options', metavar = 'N', nargs = '*', | |
| 68 help='Arguments to Python unittest') | |
| 69 | |
| 70 args = parser.parse_args() | |
| 71 | |
| 72 if not args.force: | |
| 73 print(""" | |
| 74 WARNING: This test will remove all the content of your | |
| 75 Orthanc instance running on %s! | |
| 76 | |
| 77 Are you sure ["yes" to go on]?""" % args.server) | |
| 78 | |
| 79 if sys.stdin.readline().strip() != 'yes': | |
| 80 print('Aborting...') | |
| 81 exit(0) | |
| 82 | |
| 83 | |
| 84 | |
| 85 | |
| 86 ## | |
| 87 ## The tests | |
| 88 ## | |
| 89 | |
| 90 ORTHANC = DefineOrthanc(server = args.server, | |
| 91 username = args.username, | |
| 92 password = args.password, | |
| 93 restPort = args.rest) | |
| 94 | |
| 253 | 95 def CallCommand(command): |
| 252 | 96 prefix = [] |
| 97 if args.valgrind: | |
| 98 prefix = [ 'valgrind' ] | |
| 99 | |
| 253 | 100 log = subprocess.check_output(prefix + command, |
| 252 | 101 stderr=subprocess.STDOUT) |
| 253 | 102 |
| 252 | 103 # If using valgrind, only print the lines from the log starting |
| 104 # with '==' (they contain the report from valgrind) | |
| 105 if args.valgrind: | |
| 106 print('\n'.join(filter(lambda x: x.startswith('=='), log.splitlines()))) | |
| 251 | 107 |
| 253 | 108 |
| 109 def CallDicomizer(suffix): | |
| 110 CallCommand([ args.dicomizer, | |
| 111 '--username=%s' % args.username, | |
| 112 '--password=%s' % args.password ] + suffix) | |
| 113 | |
| 114 | |
| 115 def CallDicomToTiff(suffix): | |
| 316 | 116 CallCommand([ args.to_tiff, |
| 117 '--username=%s' % args.username, | |
| 118 '--password=%s' % args.password ] + suffix) | |
| 253 | 119 |
| 120 | |
| 121 def CallTiffInfoOnSeries(series): | |
| 122 with tempfile.NamedTemporaryFile(delete = False) as temp: | |
| 123 temp.close() | |
| 124 CallDicomToTiff([ series, temp.name ]) | |
| 316 | 125 try: |
| 126 tiff = subprocess.check_output([ 'tiffinfo', temp.name ]) | |
| 127 except: | |
| 128 print('\ntiffinfo is probably not installed => sudo apt-get install libtiff-tools\n') | |
| 129 tiff = None | |
| 130 | |
| 253 | 131 os.unlink(temp.name) |
| 132 | |
| 133 return tiff | |
| 134 | |
| 251 | 135 |
| 136 class Orthanc(unittest.TestCase): | |
| 137 def setUp(self): | |
| 138 if (sys.version_info >= (3, 0)): | |
| 139 # Remove annoying warnings about unclosed socket in Python 3 | |
| 140 import warnings | |
| 141 warnings.simplefilter("ignore", ResourceWarning) | |
| 142 | |
| 143 DropOrthanc(ORTHANC) | |
| 144 | |
| 145 | |
| 146 def test_single(self): | |
| 147 CallDicomizer([ GetDatabasePath('Lena.jpg') ]) | |
| 148 | |
| 149 i = DoGet(ORTHANC, '/instances') | |
| 150 self.assertEqual(1, len(i)) | |
| 151 | |
| 152 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[0]) | |
| 153 self.assertEqual(1, int(tags['NumberOfFrames'])) | |
| 154 self.assertEqual(512, int(tags['Columns'])) | |
| 155 self.assertEqual(512, int(tags['Rows'])) | |
| 156 self.assertEqual('YBR_FULL_422', tags['PhotometricInterpretation']) | |
| 157 | |
| 158 s = DoGet(ORTHANC, '/series') | |
| 159 self.assertEqual(1, len(s)) | |
| 160 | |
| 161 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 162 self.assertEqual(s[0], pyramid['ID']) | |
| 163 self.assertEqual(1, len(pyramid['Resolutions'])) | |
| 164 self.assertEqual(1, len(pyramid['Sizes'])) | |
| 165 self.assertEqual(1, len(pyramid['TilesCount'])) | |
| 166 self.assertEqual(1, pyramid['Resolutions'][0]) | |
| 167 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 168 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
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169 self.assertEqual(1, len(pyramid['TilesSizes'])) |
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170 self.assertEqual(2, len(pyramid['TilesSizes'][0])) |
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171 self.assertEqual(512, pyramid['TilesSizes'][0][0]) |
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172 self.assertEqual(512, pyramid['TilesSizes'][0][1]) |
| 251 | 173 self.assertEqual(512, pyramid['TotalWidth']) |
| 174 self.assertEqual(512, pyramid['TotalHeight']) | |
| 175 self.assertEqual(1, pyramid['TilesCount'][0][0]) | |
| 176 self.assertEqual(1, pyramid['TilesCount'][0][1]) | |
| 177 | |
| 253 | 178 tiff = CallTiffInfoOnSeries(s[0]) |
| 179 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 180 self.assertEqual(1, len(p)) | |
| 181 self.assertTrue('YCbCr' in p[0]) | |
| 182 | |
| 251 | 183 |
| 184 def test_grayscale_pyramid(self): | |
| 185 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--tile-width=64', '--tile-height=64' ]) | |
| 186 | |
| 187 i = DoGet(ORTHANC, '/instances') | |
| 188 self.assertEqual(4, len(i)) | |
| 189 | |
| 190 for j in range(4): | |
| 191 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[j]) | |
| 192 self.assertEqual(64, int(tags['Columns'])) | |
| 193 self.assertEqual(64, int(tags['Rows'])) | |
| 194 self.assertEqual('MONOCHROME2', tags['PhotometricInterpretation']) | |
| 195 | |
| 196 s = DoGet(ORTHANC, '/series') | |
| 197 self.assertEqual(1, len(s)) | |
| 198 | |
| 199 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 200 self.assertEqual(s[0], pyramid['ID']) | |
| 201 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 202 self.assertEqual(4, len(pyramid['Sizes'])) | |
| 203 self.assertEqual(4, len(pyramid['TilesCount'])) | |
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204 self.assertEqual(4, len(pyramid['TilesSizes'])) |
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205 |
| 251 | 206 self.assertEqual(1, pyramid['Resolutions'][0]) |
| 207 self.assertEqual(2, pyramid['Resolutions'][1]) | |
| 208 self.assertEqual(4, pyramid['Resolutions'][2]) | |
| 209 self.assertEqual(8, pyramid['Resolutions'][3]) | |
| 210 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 211 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
| 212 self.assertEqual(256, pyramid['Sizes'][1][0]) | |
| 213 self.assertEqual(256, pyramid['Sizes'][1][1]) | |
| 214 self.assertEqual(128, pyramid['Sizes'][2][0]) | |
| 215 self.assertEqual(128, pyramid['Sizes'][2][1]) | |
| 216 self.assertEqual(64, pyramid['Sizes'][3][0]) | |
| 217 self.assertEqual(64, pyramid['Sizes'][3][1]) | |
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218 for i in range(4): |
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219 self.assertEqual(2, len(pyramid['TilesSizes'][i])) |
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220 self.assertEqual(64, pyramid['TilesSizes'][i][0]) |
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221 self.assertEqual(64, pyramid['TilesSizes'][i][1]) |
| 251 | 222 self.assertEqual(512, pyramid['TotalWidth']) |
| 223 self.assertEqual(512, pyramid['TotalHeight']) | |
| 224 self.assertEqual(8, pyramid['TilesCount'][0][0]) | |
| 225 self.assertEqual(8, pyramid['TilesCount'][0][1]) | |
| 226 self.assertEqual(4, pyramid['TilesCount'][1][0]) | |
| 227 self.assertEqual(4, pyramid['TilesCount'][1][1]) | |
| 228 self.assertEqual(2, pyramid['TilesCount'][2][0]) | |
| 229 self.assertEqual(2, pyramid['TilesCount'][2][1]) | |
| 230 self.assertEqual(1, pyramid['TilesCount'][3][0]) | |
| 231 self.assertEqual(1, pyramid['TilesCount'][3][1]) | |
| 253 | 232 |
| 233 tiff = CallTiffInfoOnSeries(s[0]) | |
| 234 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 235 self.assertEqual(4, len(p)) | |
| 236 for j in range(4): | |
| 237 self.assertTrue('min-is-black' in p[j]) | |
| 238 | |
| 239 | |
| 240 def test_import_tiff_grayscale(self): | |
| 241 CallDicomizer([ GetDatabasePath('WSI/LenaGrayscaleJpeg.tiff') ]) | |
| 242 | |
| 243 s = DoGet(ORTHANC, '/series') | |
| 244 self.assertEqual(1, len(s)) | |
| 245 | |
| 246 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 247 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 248 | |
| 249 tiff = CallTiffInfoOnSeries(s[0]) | |
| 250 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 251 self.assertEqual(4, len(p)) | |
| 252 for j in range(4): | |
| 253 self.assertTrue('min-is-black' in p[j]) | |
| 254 | |
| 255 | |
| 256 def test_import_tiff_ycbcr(self): | |
| 257 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegYCbCr.tiff') ]) | |
| 258 | |
| 259 s = DoGet(ORTHANC, '/series') | |
| 260 self.assertEqual(1, len(s)) | |
| 261 | |
| 262 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 263 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 264 | |
| 265 tiff = CallTiffInfoOnSeries(s[0]) | |
| 266 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 267 self.assertEqual(4, len(p)) | |
| 268 for j in range(4): | |
| 269 self.assertTrue('YCbCr' in p[j]) | |
| 270 | |
| 271 | |
| 272 def test_import_tiff_rgb(self): | |
| 273 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegRGB.tiff') ]) | |
| 274 | |
| 275 s = DoGet(ORTHANC, '/series') | |
| 276 self.assertEqual(1, len(s)) | |
| 277 | |
| 278 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 279 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 280 | |
| 281 tiff = CallTiffInfoOnSeries(s[0]) | |
| 282 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 283 self.assertEqual(4, len(p)) | |
| 284 for j in range(4): | |
| 285 self.assertTrue('RGB' in p[j]) | |
| 286 | |
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287 |
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288 def test_concatenation(self): |
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289 # https://bugs.orthanc-server.com/show_bug.cgi?id=145 |
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290 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', ]) |
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291 i = DoGet(ORTHANC, '/instances') |
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292 self.assertEqual(1, len(i)) |
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293 tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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294 self.assertTrue('0020,0242' in tags) # SOP Instance UID of Concatenation Source |
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295 self.assertTrue('0020,9161' in tags) # Concatenation UID |
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296 self.assertTrue('0020,9162' in tags) # In-concatenation Number |
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297 self.assertTrue('0020,9228' in tags) # Concatenation Frame Offset Number |
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298 self.assertEqual('1', tags['0020,9162']) |
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299 self.assertEqual('0', tags['0020,9228']) |
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300 |
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301 DropOrthanc(ORTHANC) |
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302 |
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303 # "--max-size" disables the concatenation |
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304 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--levels=1', '--max-size=0' ]) |
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305 i = DoGet(ORTHANC, '/instances') |
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306 self.assertEqual(1, len(i)) |
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307 tags = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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308 self.assertFalse('0020,0242' in tags) |
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309 self.assertFalse('0020,9161' in tags) |
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310 self.assertFalse('0020,9162' in tags) |
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311 self.assertFalse('0020,9228' in tags) |
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312 |
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313 DropOrthanc(ORTHANC) |
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314 |
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315 # 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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316 CallDicomizer([ GetDatabasePath('WSI/Lena2x2.png'), '--levels=1', '--max-size=1', '--compression=none' ]) |
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317 i = DoGet(ORTHANC, '/instances') |
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318 self.assertEqual(2, len(i)) |
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319 t1 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[0]) |
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320 t2 = DoGet(ORTHANC, '/instances/%s/tags?short' % i[1]) |
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321 self.assertTrue('0020,0242' in t1) |
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322 self.assertTrue('0020,9161' in t1) |
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323 self.assertTrue('0020,9162' in t1) |
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324 self.assertTrue('0020,9228' in t1) |
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325 self.assertEqual(t1['0020,0242'], t2['0020,0242']) |
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326 self.assertEqual(t1['0020,9161'], t2['0020,9161']) |
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327 if t1['0020,9162'] == '1': |
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328 self.assertEqual('1', t1['0020,9162']) |
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329 self.assertEqual('0', t1['0020,9228']) |
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330 self.assertEqual('2', t2['0020,9162']) |
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331 self.assertEqual('2', t2['0020,9228']) |
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332 else: |
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333 self.assertEqual('1', t2['0020,9162']) |
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334 self.assertEqual('0', t2['0020,9228']) |
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335 self.assertEqual('2', t1['0020,9162']) |
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336 self.assertEqual('2', t1['0020,9228']) |
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337 |
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338 |
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339 def test_pixel_spacing(self): |
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340 # https://bugs.orthanc-server.com/show_bug.cgi?id=139 |
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341 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), # Image is 512x512 |
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342 '--levels=4', '--tile-width=64', '--tile-height=64', '--max-size=0', |
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343 '--imaged-width=20', '--imaged-height=10' ]) |
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344 |
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345 instances = DoGet(ORTHANC, '/instances') |
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346 self.assertEqual(4, len(instances)) |
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347 |
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348 spacings = {} |
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349 for i in instances: |
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350 t = DoGet(ORTHANC, '/instances/%s/tags?short' % i) |
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351 spacings[t['0028,0008']] = t['5200,9229'][0]['0028,9110'][0]['0028,0030'] |
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352 |
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353 self.assertEqual(4, len(spacings)) |
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354 for i in range(4): |
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355 s = spacings[str(4 ** i)].split('\\') |
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356 self.assertEqual(2, len(s)) |
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357 self.assertEqual(20.0 / 512.0 * (2.0 ** (3 - i)), float(s[0])) |
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358 self.assertEqual(10.0 / 512.0 * (2.0 ** (3 - i)), float(s[1])) |
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359 |
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360 |
| 251 | 361 try: |
| 362 print('\nStarting the tests...') | |
| 363 unittest.main(argv = [ sys.argv[0] ] + args.options) | |
| 364 | |
| 365 finally: | |
| 366 print('\nDone') |