Mercurial > hg > orthanc-tests
annotate Plugins/WSI/Run.py @ 310:65d5c591fece c-get
closing c-get
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 20 May 2020 16:35:50 +0200 |
| parents | 943166deebcb |
| children | bb01670b3b79 |
| 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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Sebastien Jodogne <s.jodogne@gmail.com>
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8 # Copyright (C) 2017-2020 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): | |
| 116 CallCommand([ args.to_tiff ] + suffix) | |
| 117 | |
| 118 | |
| 119 def CallTiffInfoOnSeries(series): | |
| 120 with tempfile.NamedTemporaryFile(delete = False) as temp: | |
| 121 temp.close() | |
| 122 CallDicomToTiff([ series, temp.name ]) | |
| 123 tiff = subprocess.check_output([ 'tiffinfo', temp.name ]) | |
| 124 os.unlink(temp.name) | |
| 125 | |
| 126 return tiff | |
| 127 | |
| 251 | 128 |
| 129 class Orthanc(unittest.TestCase): | |
| 130 def setUp(self): | |
| 131 if (sys.version_info >= (3, 0)): | |
| 132 # Remove annoying warnings about unclosed socket in Python 3 | |
| 133 import warnings | |
| 134 warnings.simplefilter("ignore", ResourceWarning) | |
| 135 | |
| 136 DropOrthanc(ORTHANC) | |
| 137 | |
| 138 | |
| 139 def test_single(self): | |
| 140 CallDicomizer([ GetDatabasePath('Lena.jpg') ]) | |
| 141 | |
| 142 i = DoGet(ORTHANC, '/instances') | |
| 143 self.assertEqual(1, len(i)) | |
| 144 | |
| 145 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[0]) | |
| 146 self.assertEqual(1, int(tags['NumberOfFrames'])) | |
| 147 self.assertEqual(512, int(tags['Columns'])) | |
| 148 self.assertEqual(512, int(tags['Rows'])) | |
| 149 self.assertEqual('YBR_FULL_422', tags['PhotometricInterpretation']) | |
| 150 | |
| 151 s = DoGet(ORTHANC, '/series') | |
| 152 self.assertEqual(1, len(s)) | |
| 153 | |
| 154 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 155 self.assertEqual(s[0], pyramid['ID']) | |
| 156 self.assertEqual(1, len(pyramid['Resolutions'])) | |
| 157 self.assertEqual(1, len(pyramid['Sizes'])) | |
| 158 self.assertEqual(1, len(pyramid['TilesCount'])) | |
| 159 self.assertEqual(1, pyramid['Resolutions'][0]) | |
| 160 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 161 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
| 162 self.assertEqual(512, pyramid['TileWidth']) | |
| 163 self.assertEqual(512, pyramid['TileHeight']) | |
| 164 self.assertEqual(512, pyramid['TotalWidth']) | |
| 165 self.assertEqual(512, pyramid['TotalHeight']) | |
| 166 self.assertEqual(1, pyramid['TilesCount'][0][0]) | |
| 167 self.assertEqual(1, pyramid['TilesCount'][0][1]) | |
| 168 | |
| 253 | 169 tiff = CallTiffInfoOnSeries(s[0]) |
| 170 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 171 self.assertEqual(1, len(p)) | |
| 172 self.assertTrue('YCbCr' in p[0]) | |
| 173 | |
| 251 | 174 |
| 175 def test_grayscale_pyramid(self): | |
| 176 CallDicomizer([ GetDatabasePath('LenaGrayscale.png'), '--tile-width=64', '--tile-height=64' ]) | |
| 177 | |
| 178 i = DoGet(ORTHANC, '/instances') | |
| 179 self.assertEqual(4, len(i)) | |
| 180 | |
| 181 for j in range(4): | |
| 182 tags = DoGet(ORTHANC, '/instances/%s/tags?simplify' % i[j]) | |
| 183 self.assertEqual(64, int(tags['Columns'])) | |
| 184 self.assertEqual(64, int(tags['Rows'])) | |
| 185 self.assertEqual('MONOCHROME2', tags['PhotometricInterpretation']) | |
| 186 | |
| 187 s = DoGet(ORTHANC, '/series') | |
| 188 self.assertEqual(1, len(s)) | |
| 189 | |
| 190 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 191 self.assertEqual(s[0], pyramid['ID']) | |
| 192 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 193 self.assertEqual(4, len(pyramid['Sizes'])) | |
| 194 self.assertEqual(4, len(pyramid['TilesCount'])) | |
| 195 self.assertEqual(1, pyramid['Resolutions'][0]) | |
| 196 self.assertEqual(2, pyramid['Resolutions'][1]) | |
| 197 self.assertEqual(4, pyramid['Resolutions'][2]) | |
| 198 self.assertEqual(8, pyramid['Resolutions'][3]) | |
| 199 self.assertEqual(512, pyramid['Sizes'][0][0]) | |
| 200 self.assertEqual(512, pyramid['Sizes'][0][1]) | |
| 201 self.assertEqual(256, pyramid['Sizes'][1][0]) | |
| 202 self.assertEqual(256, pyramid['Sizes'][1][1]) | |
| 203 self.assertEqual(128, pyramid['Sizes'][2][0]) | |
| 204 self.assertEqual(128, pyramid['Sizes'][2][1]) | |
| 205 self.assertEqual(64, pyramid['Sizes'][3][0]) | |
| 206 self.assertEqual(64, pyramid['Sizes'][3][1]) | |
| 207 self.assertEqual(64, pyramid['TileWidth']) | |
| 208 self.assertEqual(64, pyramid['TileHeight']) | |
| 209 self.assertEqual(512, pyramid['TotalWidth']) | |
| 210 self.assertEqual(512, pyramid['TotalHeight']) | |
| 211 self.assertEqual(8, pyramid['TilesCount'][0][0]) | |
| 212 self.assertEqual(8, pyramid['TilesCount'][0][1]) | |
| 213 self.assertEqual(4, pyramid['TilesCount'][1][0]) | |
| 214 self.assertEqual(4, pyramid['TilesCount'][1][1]) | |
| 215 self.assertEqual(2, pyramid['TilesCount'][2][0]) | |
| 216 self.assertEqual(2, pyramid['TilesCount'][2][1]) | |
| 217 self.assertEqual(1, pyramid['TilesCount'][3][0]) | |
| 218 self.assertEqual(1, pyramid['TilesCount'][3][1]) | |
| 253 | 219 |
| 220 tiff = CallTiffInfoOnSeries(s[0]) | |
| 221 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 222 self.assertEqual(4, len(p)) | |
| 223 for j in range(4): | |
| 224 self.assertTrue('min-is-black' in p[j]) | |
| 225 | |
| 226 | |
| 227 def test_import_tiff_grayscale(self): | |
| 228 CallDicomizer([ GetDatabasePath('WSI/LenaGrayscaleJpeg.tiff') ]) | |
| 229 | |
| 230 s = DoGet(ORTHANC, '/series') | |
| 231 self.assertEqual(1, len(s)) | |
| 232 | |
| 233 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 234 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 235 | |
| 236 tiff = CallTiffInfoOnSeries(s[0]) | |
| 237 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 238 self.assertEqual(4, len(p)) | |
| 239 for j in range(4): | |
| 240 self.assertTrue('min-is-black' in p[j]) | |
| 241 | |
| 242 | |
| 243 def test_import_tiff_ycbcr(self): | |
| 244 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegYCbCr.tiff') ]) | |
| 245 | |
| 246 s = DoGet(ORTHANC, '/series') | |
| 247 self.assertEqual(1, len(s)) | |
| 248 | |
| 249 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 250 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 251 | |
| 252 tiff = CallTiffInfoOnSeries(s[0]) | |
| 253 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 254 self.assertEqual(4, len(p)) | |
| 255 for j in range(4): | |
| 256 self.assertTrue('YCbCr' in p[j]) | |
| 257 | |
| 258 | |
| 259 def test_import_tiff_rgb(self): | |
| 260 CallDicomizer([ GetDatabasePath('WSI/LenaColorJpegRGB.tiff') ]) | |
| 261 | |
| 262 s = DoGet(ORTHANC, '/series') | |
| 263 self.assertEqual(1, len(s)) | |
| 264 | |
| 265 pyramid = DoGet(ORTHANC, '/wsi/pyramids/%s' % s[0]) | |
| 266 self.assertEqual(4, len(pyramid['Resolutions'])) | |
| 267 | |
| 268 tiff = CallTiffInfoOnSeries(s[0]) | |
| 269 p = filter(lambda x: 'Photometric Interpretation' in x, tiff.splitlines()) | |
| 270 self.assertEqual(4, len(p)) | |
| 271 for j in range(4): | |
| 272 self.assertTrue('RGB' in p[j]) | |
| 273 | |
| 251 | 274 |
| 275 try: | |
| 276 print('\nStarting the tests...') | |
| 277 unittest.main(argv = [ sys.argv[0] ] + args.options) | |
| 278 | |
| 279 finally: | |
| 280 print('\nDone') |