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  1. ============================= test session starts ==============================
  2. platform linux -- Python 3.7.4, pytest-5.1.2, py-1.8.0, pluggy-0.13.0
  3. rootdir: /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests
  4. collected 558 items
  5.  
  6. test_PypeS/test_pype.py ....x... [ 1%]
  7. test_PypeS/test_pypes.py . [ 1%]
  8. test_vmtkScripts/test_importvmtkscripts.py . [ 1%]
  9. test_vmtkScripts/test_vmtkbifurcationprofiles.py ....................... [ 5%]
  10. . [ 6%]
  11. test_vmtkScripts/test_vmtkbifurcationreferencesystems.py ............ [ 8%]
  12. test_vmtkScripts/test_vmtkbifurcationsections.py ...............FFFFFFFF [ 12%]
  13. FFFFFFFFFFFFFF............ [ 17%]
  14. test_vmtkScripts/test_vmtkbifurcationvectors.py ........................ [ 21%]
  15. ... [ 21%]
  16. test_vmtkScripts/test_vmtkbranchclipper.py .......... [ 23%]
  17. test_vmtkScripts/test_vmtkbranchextractor.py ....FFF.FFF................ [ 28%]
  18. ......... [ 30%]
  19. test_vmtkScripts/test_vmtkbranchgeometry.py ............. [ 32%]
  20. test_vmtkScripts/test_vmtkbranchmetrics.py .. [ 32%]
  21. test_vmtkScripts/test_vmtkbranchsections.py ..FFFFFFFFFFFFFF............ [ 37%]
  22. ........................................................................ [ 50%]
  23. ........................... [ 55%]
  24. test_vmtkScripts/test_vmtkcenterlineattributes.py .. [ 55%]
  25. test_vmtkScripts/test_vmtkcenterlinegeometry.py . [ 56%]
  26. test_vmtkScripts/test_vmtkcenterlineimage.py F [ 56%]
  27. test_vmtkScripts/test_vmtkcenterlineinterpolation.py ... [ 56%]
  28. test_vmtkScripts/test_vmtkcenterlinemodeller.py ... [ 57%]
  29. test_vmtkScripts/test_vmtkcenterlineoffsetattributes.py .. [ 57%]
  30. test_vmtkScripts/test_vmtkcenterlineresampling.py . [ 57%]
  31. test_vmtkScripts/test_vmtkcenterlines.py ... [ 58%]
  32. test_vmtkScripts/test_vmtkcenterlinesmoothing.py ..... [ 59%]
  33. test_vmtkScripts/test_vmtkcenterlinesnetwork.py F [ 59%]
  34. test_vmtkScripts/test_vmtkimagebinarize.py ..... [ 60%]
  35. test_vmtkScripts/test_vmtkimagecast.py .... [ 61%]
  36. test_vmtkScripts/test_vmtkimagecompare.py .. [ 61%]
  37. test_vmtkScripts/test_vmtkimagecompose.py ..... [ 62%]
  38. test_vmtkScripts/test_vmtkimagefeatures.py ........FF [ 64%]
  39. test_vmtkScripts/test_vmtkimageinitialization.py ....... [ 65%]
  40. test_vmtkScripts/test_vmtkimagemorphology.py ..... [ 66%]
  41. test_vmtkScripts/test_vmtkimagenormalize.py . [ 66%]
  42. test_vmtkScripts/test_vmtkimageobjectenhancement.py .......... [ 68%]
  43. test_vmtkScripts/test_vmtkimageotsuthresholds.py .... [ 68%]
  44. test_vmtkScripts/test_vmtkimagereader.py ... [ 69%]
  45. test_vmtkScripts/test_vmtkimageshiftscale.py ................... [ 72%]
  46. test_vmtkScripts/test_vmtkimagesmoother.py ......... [ 74%]
  47. test_vmtkScripts/test_vmtkimagevesselenhancement.py .............sssssss [ 78%]
  48. sss [ 78%]
  49. test_vmtkScripts/test_vmtkimagevoipainter.py s [ 78%]
  50. test_vmtkScripts/test_vmtkimagevoiselector.py . [ 79%]
  51. test_vmtkScripts/test_vmtkimagevolumeviewer.py EEEEEEEEEEEEEEEEEEEEEEEE [ 83%]
  52. test_vmtkScripts/test_vmtklevelsetsegmentation.py ....... [ 84%]
  53. test_vmtkScripts/test_vmtkmarchingcubes.py . [ 84%]
  54. test_vmtkScripts/test_vmtksurfaceappend.py . [ 84%]
  55. test_vmtkScripts/test_vmtksurfacebooleanoperation.py ...... [ 86%]
  56. test_vmtkScripts/test_vmtksurfacecapper.py sssssssss [ 87%]
  57. test_vmtkScripts/test_vmtksurfacecelldatatopointdata.py ................ [ 90%]
  58. .. [ 90%]
  59. test_vmtkScripts/test_vmtksurfaceconnectivity.py ... [ 91%]
  60. test_vmtkScripts/test_vmtksurfacedecimation.py .. [ 91%]
  61. test_vmtkScripts/test_vmtksurfacekiteremoval.py .. [ 92%]
  62. test_vmtkScripts/test_vmtksurfacemassproperties.py . [ 92%]
  63. test_vmtkScripts/test_vmtksurfacemodeller.py ... [ 92%]
  64. test_vmtkScripts/test_vmtksurfacenormals.py ... [ 93%]
  65. test_vmtkScripts/test_vmtksurfacereader.py .. [ 93%]
  66. test_vmtkScripts/test_vmtksurfaceremeshing.py ........... [ 95%]
  67. test_vmtkScripts/test_vmtksurfacescaling.py ....... [ 96%]
  68. test_vmtkScripts/test_vmtksurfacesmoothing.py .... [ 97%]
  69. test_vmtkScripts/test_vmtksurfacesubdivision.py ...... [ 98%]
  70. test_vmtkScripts/test_vmtksurfacetobinaryimage.py FFFFF [ 99%]
  71. test_vmtkScripts/test_vmtksurfacetransformtoras.py EE [100%]
  72.  
  73. ==================================== ERRORS ====================================
  74. __________ ERROR at setup of test_volume_viewer_preset_values[CT-AAA] __________
  75.  
  76. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  77.  
  78. @pytest.fixture(scope='module')
  79. def expected_results_dict(input_datadir):
  80. from json import load
  81. import os
  82. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  83. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  84.  
  85. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  86. ---------------------------- Captured stdout setup -----------------------------
  87. Spacing 0.878906 0.878906 1.500090
  88. Origin 156.445000 24.609400 0.000000
  89. Dimensions 157 393 34
  90. _________ ERROR at setup of test_volume_viewer_preset_values[CT-AAA2] __________
  91.  
  92. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  93.  
  94. @pytest.fixture(scope='module')
  95. def expected_results_dict(input_datadir):
  96. from json import load
  97. import os
  98. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  99. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  100.  
  101. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  102. _________ ERROR at setup of test_volume_viewer_preset_values[CT-Bone] __________
  103.  
  104. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  105.  
  106. @pytest.fixture(scope='module')
  107. def expected_results_dict(input_datadir):
  108. from json import load
  109. import os
  110. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  111. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  112.  
  113. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  114. _________ ERROR at setup of test_volume_viewer_preset_values[CT-Bones] _________
  115.  
  116. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  117.  
  118. @pytest.fixture(scope='module')
  119. def expected_results_dict(input_datadir):
  120. from json import load
  121. import os
  122. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  123. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  124.  
  125. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  126. ________ ERROR at setup of test_volume_viewer_preset_values[CT-Cardiac] ________
  127.  
  128. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  129.  
  130. @pytest.fixture(scope='module')
  131. def expected_results_dict(input_datadir):
  132. from json import load
  133. import os
  134. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  135. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  136.  
  137. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  138. _______ ERROR at setup of test_volume_viewer_preset_values[CT-Cardiac2] ________
  139.  
  140. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  141.  
  142. @pytest.fixture(scope='module')
  143. def expected_results_dict(input_datadir):
  144. from json import load
  145. import os
  146. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  147. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  148.  
  149. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  150. _______ ERROR at setup of test_volume_viewer_preset_values[CT-Cardiac3] ________
  151.  
  152. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  153.  
  154. @pytest.fixture(scope='module')
  155. def expected_results_dict(input_datadir):
  156. from json import load
  157. import os
  158. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  159. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  160.  
  161. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  162. _ ERROR at setup of test_volume_viewer_preset_values[CT-Chest-Contrast-Enhanced] _
  163.  
  164. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  165.  
  166. @pytest.fixture(scope='module')
  167. def expected_results_dict(input_datadir):
  168. from json import load
  169. import os
  170. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  171. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  172.  
  173. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  174. _____ ERROR at setup of test_volume_viewer_preset_values[CT-Chest-Vessels] _____
  175.  
  176. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  177.  
  178. @pytest.fixture(scope='module')
  179. def expected_results_dict(input_datadir):
  180. from json import load
  181. import os
  182. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  183. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  184.  
  185. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  186. ___ ERROR at setup of test_volume_viewer_preset_values[CT-Coronary-Arteries] ___
  187.  
  188. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  189.  
  190. @pytest.fixture(scope='module')
  191. def expected_results_dict(input_datadir):
  192. from json import load
  193. import os
  194. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  195. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  196.  
  197. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  198. __ ERROR at setup of test_volume_viewer_preset_values[CT-Coronary-Arteries-2] __
  199.  
  200. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  201.  
  202. @pytest.fixture(scope='module')
  203. def expected_results_dict(input_datadir):
  204. from json import load
  205. import os
  206. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  207. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  208.  
  209. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  210. __ ERROR at setup of test_volume_viewer_preset_values[CT-Coronary-Arteries-3] __
  211.  
  212. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  213.  
  214. @pytest.fixture(scope='module')
  215. def expected_results_dict(input_datadir):
  216. from json import load
  217. import os
  218. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  219. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  220.  
  221. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  222. __ ERROR at setup of test_volume_viewer_preset_values[CT-Cropped-Volume-Bone] __
  223.  
  224. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  225.  
  226. @pytest.fixture(scope='module')
  227. def expected_results_dict(input_datadir):
  228. from json import load
  229. import os
  230. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  231. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  232.  
  233. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  234. __________ ERROR at setup of test_volume_viewer_preset_values[CT-Fat] __________
  235.  
  236. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  237.  
  238. @pytest.fixture(scope='module')
  239. def expected_results_dict(input_datadir):
  240. from json import load
  241. import os
  242. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  243. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  244.  
  245. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  246. ___ ERROR at setup of test_volume_viewer_preset_values[CT-Liver-Vasculature] ___
  247.  
  248. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  249.  
  250. @pytest.fixture(scope='module')
  251. def expected_results_dict(input_datadir):
  252. from json import load
  253. import os
  254. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  255. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  256.  
  257. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  258. _________ ERROR at setup of test_volume_viewer_preset_values[CT-Lung] __________
  259.  
  260. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  261.  
  262. @pytest.fixture(scope='module')
  263. def expected_results_dict(input_datadir):
  264. from json import load
  265. import os
  266. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  267. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  268.  
  269. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  270. __________ ERROR at setup of test_volume_viewer_preset_values[CT-MIP] __________
  271.  
  272. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  273.  
  274. @pytest.fixture(scope='module')
  275. def expected_results_dict(input_datadir):
  276. from json import load
  277. import os
  278. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  279. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  280.  
  281. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  282. ________ ERROR at setup of test_volume_viewer_preset_values[CT-Muscle] _________
  283.  
  284. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  285.  
  286. @pytest.fixture(scope='module')
  287. def expected_results_dict(input_datadir):
  288. from json import load
  289. import os
  290. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  291. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  292.  
  293. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  294. __ ERROR at setup of test_volume_viewer_preset_values[CT-Pulmonary-Arteries] ___
  295.  
  296. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  297.  
  298. @pytest.fixture(scope='module')
  299. def expected_results_dict(input_datadir):
  300. from json import load
  301. import os
  302. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  303. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  304.  
  305. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  306. ______ ERROR at setup of test_volume_viewer_preset_values[CT-Soft-Tissue] ______
  307.  
  308. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  309.  
  310. @pytest.fixture(scope='module')
  311. def expected_results_dict(input_datadir):
  312. from json import load
  313. import os
  314. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  315. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  316.  
  317. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  318. _________ ERROR at setup of test_volume_viewer_preset_values[MR-Angio] _________
  319.  
  320. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  321.  
  322. @pytest.fixture(scope='module')
  323. def expected_results_dict(input_datadir):
  324. from json import load
  325. import os
  326. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  327. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  328.  
  329. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  330. ________ ERROR at setup of test_volume_viewer_preset_values[MR-Default] ________
  331.  
  332. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  333.  
  334. @pytest.fixture(scope='module')
  335. def expected_results_dict(input_datadir):
  336. from json import load
  337. import os
  338. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  339. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  340.  
  341. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  342. __________ ERROR at setup of test_volume_viewer_preset_values[MR-MIP] __________
  343.  
  344. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  345.  
  346. @pytest.fixture(scope='module')
  347. def expected_results_dict(input_datadir):
  348. from json import load
  349. import os
  350. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  351. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  352.  
  353. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  354. _______ ERROR at setup of test_volume_viewer_preset_values[MR-T2-Brain] ________
  355.  
  356. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  357.  
  358. @pytest.fixture(scope='module')
  359. def expected_results_dict(input_datadir):
  360. from json import load
  361. import os
  362. > with open(os.path.join(input_datadir, 'vmtkimagevolumeviewer_testresults.json'), 'r') as f:
  363. E FileNotFoundError: [Errno 2] No such file or directory: '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/vmtkimagevolumeviewer_testresults.json'
  364.  
  365. test_vmtkScripts/test_vmtkimagevolumeviewer.py:25: FileNotFoundError
  366. __________________ ERROR at setup of test_default_parameters ___________________
  367.  
  368. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  369.  
  370. @pytest.fixture(scope='module')
  371. def transform_image(input_datadir):
  372. import vmtk.vmtkimagereader as imagereader
  373. reader = imagereader.vmtkImageReader()
  374. reader.InputFileName = os.path.join(input_datadir, 'image-test-transform.nrrd')
  375. > reader.Execute()
  376.  
  377. test_vmtkScripts/test_vmtksurfacetransformtoras.py:26:
  378. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
  379. /scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/vmtk/vmtkimagereader.py:266: in Execute
  380. self.ReadITKIO()
  381. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
  382.  
  383. self = <vmtk.vmtkimagereader.vmtkImageReader object at 0x2ab226052b10>
  384.  
  385. def ReadITKIO(self):
  386. if self.InputFileName == '':
  387. self.PrintError('Error: no InputFileName.')
  388. reader = vtkvmtk.vtkvmtkITKArchetypeImageSeriesScalarReader()
  389. reader.SetArchetype(self.InputFileName)
  390. reader.SetDefaultDataSpacing(self.DataSpacing)
  391. reader.SetDefaultDataOrigin(self.DataOrigin)
  392. reader.SetOutputScalarTypeToNative()
  393. if self.DesiredOrientation == 'native':
  394. reader.SetDesiredCoordinateOrientationToNative()
  395. elif self.DesiredOrientation == 'axial':
  396. reader.SetDesiredCoordinateOrientationToAxial()
  397. elif self.DesiredOrientation == 'coronal':
  398. reader.SetDesiredCoordinateOrientationToCoronal()
  399. elif self.DesiredOrientation == 'sagittal':
  400. reader.SetDesiredCoordinateOrientationToSagittal()
  401. reader.SetSingleFile(0)
  402. reader.Update()
  403. self.Image = vtk.vtkImageData()
  404. self.Image.DeepCopy(reader.GetOutput())
  405. matrix = reader.GetRasToIjkMatrix()
  406. self.RasToIjkMatrixCoefficients = [
  407. > matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
  408. matrix.GetElement(1,0), matrix.GetElement(1,1), matrix.GetElement(1,2), matrix.GetElement(1,3),
  409. matrix.GetElement(2,0), matrix.GetElement(2,1), matrix.GetElement(2,2), matrix.GetElement(2,3),
  410. matrix.GetElement(3,0), matrix.GetElement(3,1), matrix.GetElement(3,2), matrix.GetElement(3,3)]
  411. E AttributeError: 'NoneType' object has no attribute 'GetElement'
  412.  
  413. /scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/vmtk/vmtkimagereader.py:203: AttributeError
  414. ---------------------------- Captured stderr setup -----------------------------
  415. ERROR: In /tmp/vsc43810/easybuild/build/VMTK/1.4.0/foss-2019b-Python-3.7.4/vmtk-63a3b990328d8dfaa6ffd31968fc341cad9dbe67/vtkVmtk/Utilities/vtkvmtkITK/vtkvmtkITKArchetypeImageSeriesReader.cxx, line 220
  416. vtkvmtkITKArchetypeImageSeriesScalarReader (0x4b12530): vtkvmtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input/image-test-transform.nrrd does not exist.
  417.  
  418. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  419. vtkCompositeDataPipeline (0x4d320e0): Algorithm vtkvmtkITKArchetypeImageSeriesScalarReader(0x4b12530) returned failure for request: vtkInformation (0x4217ef0)
  420. Debug: Off
  421. Modified Time: 39217731
  422. Reference Count: 1
  423. Registered Events: (none)
  424. Request: REQUEST_INFORMATION
  425. ALGORITHM_AFTER_FORWARD: 1
  426. FORWARD_DIRECTION: 0
  427.  
  428.  
  429.  
  430. _______________________ ERROR at setup of test_invert_on _______________________
  431.  
  432. input_datadir = '/vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/input'
  433.  
  434. @pytest.fixture(scope='module')
  435. def transform_image(input_datadir):
  436. import vmtk.vmtkimagereader as imagereader
  437. reader = imagereader.vmtkImageReader()
  438. reader.InputFileName = os.path.join(input_datadir, 'image-test-transform.nrrd')
  439. > reader.Execute()
  440.  
  441. test_vmtkScripts/test_vmtksurfacetransformtoras.py:26:
  442. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
  443. /scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/vmtk/vmtkimagereader.py:266: in Execute
  444. self.ReadITKIO()
  445. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
  446.  
  447. self = <vmtk.vmtkimagereader.vmtkImageReader object at 0x2ab226052b10>
  448.  
  449. def ReadITKIO(self):
  450. if self.InputFileName == '':
  451. self.PrintError('Error: no InputFileName.')
  452. reader = vtkvmtk.vtkvmtkITKArchetypeImageSeriesScalarReader()
  453. reader.SetArchetype(self.InputFileName)
  454. reader.SetDefaultDataSpacing(self.DataSpacing)
  455. reader.SetDefaultDataOrigin(self.DataOrigin)
  456. reader.SetOutputScalarTypeToNative()
  457. if self.DesiredOrientation == 'native':
  458. reader.SetDesiredCoordinateOrientationToNative()
  459. elif self.DesiredOrientation == 'axial':
  460. reader.SetDesiredCoordinateOrientationToAxial()
  461. elif self.DesiredOrientation == 'coronal':
  462. reader.SetDesiredCoordinateOrientationToCoronal()
  463. elif self.DesiredOrientation == 'sagittal':
  464. reader.SetDesiredCoordinateOrientationToSagittal()
  465. reader.SetSingleFile(0)
  466. reader.Update()
  467. self.Image = vtk.vtkImageData()
  468. self.Image.DeepCopy(reader.GetOutput())
  469. matrix = reader.GetRasToIjkMatrix()
  470. self.RasToIjkMatrixCoefficients = [
  471. > matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
  472. matrix.GetElement(1,0), matrix.GetElement(1,1), matrix.GetElement(1,2), matrix.GetElement(1,3),
  473. matrix.GetElement(2,0), matrix.GetElement(2,1), matrix.GetElement(2,2), matrix.GetElement(2,3),
  474. matrix.GetElement(3,0), matrix.GetElement(3,1), matrix.GetElement(3,2), matrix.GetElement(3,3)]
  475. E AttributeError: 'NoneType' object has no attribute 'GetElement'
  476.  
  477. /scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/vmtk/vmtkimagereader.py:203: AttributeError
  478. =================================== FAILURES ===================================
  479. _ test_bifurcation_section_group_ids_correct[bifur_sections_one_sphere-expectedValue0] _
  480. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  481. but are created automatically when test functions request them as parameters.
  482. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  483. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  484. _ test_bifurcation_section_group_ids_correct[bifur_sections_two_spheres-expectedValue1] _
  485. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  486. but are created automatically when test functions request them as parameters.
  487. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  488. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  489. _ test_bifurcation_section_bifurcation_group_ids_correct[bifur_sections_one_sphere-expectedValue0] _
  490. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  491. but are created automatically when test functions request them as parameters.
  492. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  493. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  494. _ test_bifurcation_section_bifurcation_group_ids_correct[bifur_sections_two_spheres-expectedValue1] _
  495. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  496. but are created automatically when test functions request them as parameters.
  497. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  498. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  499. _ test_bifurcation_section_point_correct[bifur_sections_one_sphere-expectedValue0] _
  500. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  501. but are created automatically when test functions request them as parameters.
  502. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  503. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  504. _ test_bifurcation_section_point_correct[bifur_sections_two_spheres-expectedValue1] _
  505. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  506. but are created automatically when test functions request them as parameters.
  507. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  508. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  509. _ test_bifurcation_section_normal_correct[bifur_sections_one_sphere-expectedValue0] _
  510. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  511. but are created automatically when test functions request them as parameters.
  512. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  513. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  514. _ test_bifurcation_section_normal_correct[bifur_sections_two_spheres-expectedValue1] _
  515. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  516. but are created automatically when test functions request them as parameters.
  517. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  518. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  519. _ test_bifurcation_section_area_correct[bifur_sections_one_sphere-expectedValue0] _
  520. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  521. but are created automatically when test functions request them as parameters.
  522. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  523. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  524. _ test_bifurcation_section_area_correct[bifur_sections_two_spheres-expectedValue1] _
  525. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  526. but are created automatically when test functions request them as parameters.
  527. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  528. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  529. _ test_bifurcation_section_min_size_correct[bifur_sections_one_sphere-expectedValue0] _
  530. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  531. but are created automatically when test functions request them as parameters.
  532. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  533. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  534. _ test_bifurcation_section_min_size_correct[bifur_sections_two_spheres-expectedValue1] _
  535. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  536. but are created automatically when test functions request them as parameters.
  537. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  538. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  539. _ test_bifurcation_section_max_size_correct[bifur_sections_one_sphere-expectedValue0] _
  540. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  541. but are created automatically when test functions request them as parameters.
  542. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  543. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  544. _ test_bifurcation_section_max_size_correct[bifur_sections_two_spheres-expectedValue1] _
  545. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  546. but are created automatically when test functions request them as parameters.
  547. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  548. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  549. _ test_bifurcation_section_shape_correct[bifur_sections_one_sphere-expectedValue0] _
  550. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  551. but are created automatically when test functions request them as parameters.
  552. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  553. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  554. _ test_bifurcation_section_shape_correct[bifur_sections_two_spheres-expectedValue1] _
  555. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  556. but are created automatically when test functions request them as parameters.
  557. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  558. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  559. _ test_bifurcation_section_closed_correct[bifur_sections_one_sphere-expectedValue0] _
  560. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  561. but are created automatically when test functions request them as parameters.
  562. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  563. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  564. _ test_bifurcation_section_closed_correct[bifur_sections_two_spheres-expectedValue1] _
  565. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  566. but are created automatically when test functions request them as parameters.
  567. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  568. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  569. _ test_bifurcation_section_orientation_correct[bifur_sections_one_sphere-expectedValue0] _
  570. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  571. but are created automatically when test functions request them as parameters.
  572. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  573. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  574. _ test_bifurcation_section_orientation_correct[bifur_sections_two_spheres-expectedValue1] _
  575. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  576. but are created automatically when test functions request them as parameters.
  577. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  578. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  579. _ test_bifurcation_section_distance_to_spheres_correct[bifur_sections_one_sphere-expectedValue0] _
  580. Fixture "bifur_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  581. but are created automatically when test functions request them as parameters.
  582. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  583. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  584. _ test_bifurcation_section_distance_to_spheres_correct[bifur_sections_two_spheres-expectedValue1] _
  585. Fixture "bifur_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  586. but are created automatically when test functions request them as parameters.
  587. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  588. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  589. _________________ test_cell_data_array_names[CenterlineIds-0] __________________
  590.  
  591. centerline_branches = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036d00
  592. expectedname = 'CenterlineIds', paramid = 0
  593.  
  594. @pytest.mark.parametrize("expectedname,paramid", [
  595. ("CenterlineIds", 0),
  596. ("TractIds", 1),
  597. ("Blanking", 2),
  598. ("GroupIds", 3)
  599. ])
  600. def test_cell_data_array_names(centerline_branches, expectedname, paramid):
  601. > assert centerline_branches.GetCellData().GetArrayName(paramid) == expectedname
  602. E AssertionError: assert 'Blanking' == 'CenterlineIds'
  603. E - Blanking
  604. E + CenterlineIds
  605.  
  606. test_vmtkScripts/test_vmtkbranchextractor.py:57: AssertionError
  607. ____________________ test_cell_data_array_names[TractIds-1] ____________________
  608.  
  609. centerline_branches = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036d00
  610. expectedname = 'TractIds', paramid = 1
  611.  
  612. @pytest.mark.parametrize("expectedname,paramid", [
  613. ("CenterlineIds", 0),
  614. ("TractIds", 1),
  615. ("Blanking", 2),
  616. ("GroupIds", 3)
  617. ])
  618. def test_cell_data_array_names(centerline_branches, expectedname, paramid):
  619. > assert centerline_branches.GetCellData().GetArrayName(paramid) == expectedname
  620. E AssertionError: assert 'CenterlineIds' == 'TractIds'
  621. E - CenterlineIds
  622. E + TractIds
  623.  
  624. test_vmtkScripts/test_vmtkbranchextractor.py:57: AssertionError
  625. ____________________ test_cell_data_array_names[Blanking-2] ____________________
  626.  
  627. centerline_branches = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036d00
  628. expectedname = 'Blanking', paramid = 2
  629.  
  630. @pytest.mark.parametrize("expectedname,paramid", [
  631. ("CenterlineIds", 0),
  632. ("TractIds", 1),
  633. ("Blanking", 2),
  634. ("GroupIds", 3)
  635. ])
  636. def test_cell_data_array_names(centerline_branches, expectedname, paramid):
  637. > assert centerline_branches.GetCellData().GetArrayName(paramid) == expectedname
  638. E AssertionError: assert 'TractIds' == 'Blanking'
  639. E - TractIds
  640. E + Blanking
  641.  
  642. test_vmtkScripts/test_vmtkbranchextractor.py:57: AssertionError
  643. ________________ test_cell_data_array_values[expectedvalue0-0] _________________
  644.  
  645. centerline_branches = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036d00
  646. expectedvalue = [0, 0, 0, 1, 1, 1], paramid = 0
  647.  
  648. @pytest.mark.parametrize("expectedvalue,paramid", [
  649. ([0, 0, 0, 1, 1, 1], 0),
  650. ([0, 1, 2, 0, 1, 2], 1),
  651. ([0, 1, 0, 0, 1, 0], 2),
  652. ([0, 1, 2, 0, 1, 3], 3)
  653. ])
  654. def test_cell_data_array_values(centerline_branches, expectedvalue, paramid):
  655. centerline_branches_wrapped = dsa.WrapDataObject(centerline_branches)
  656. > assert centerline_branches_wrapped.CellData.GetArray(paramid).tolist() == expectedvalue
  657. E assert [0, 1, 0, 0, 1, 0] == [0, 0, 0, 1, 1, 1]
  658. E At index 1 diff: 1 != 0
  659. E Use -v to get the full diff
  660.  
  661. test_vmtkScripts/test_vmtkbranchextractor.py:68: AssertionError
  662. ________________ test_cell_data_array_values[expectedvalue1-1] _________________
  663.  
  664. centerline_branches = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036d00
  665. expectedvalue = [0, 1, 2, 0, 1, 2], paramid = 1
  666.  
  667. @pytest.mark.parametrize("expectedvalue,paramid", [
  668. ([0, 0, 0, 1, 1, 1], 0),
  669. ([0, 1, 2, 0, 1, 2], 1),
  670. ([0, 1, 0, 0, 1, 0], 2),
  671. ([0, 1, 2, 0, 1, 3], 3)
  672. ])
  673. def test_cell_data_array_values(centerline_branches, expectedvalue, paramid):
  674. centerline_branches_wrapped = dsa.WrapDataObject(centerline_branches)
  675. > assert centerline_branches_wrapped.CellData.GetArray(paramid).tolist() == expectedvalue
  676. E assert [0, 0, 0, 1, 1, 1] == [0, 1, 2, 0, 1, 2]
  677. E At index 1 diff: 0 != 1
  678. E Use -v to get the full diff
  679.  
  680. test_vmtkScripts/test_vmtkbranchextractor.py:68: AssertionError
  681. ________________ test_cell_data_array_values[expectedvalue2-2] _________________
  682.  
  683. centerline_branches = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036d00
  684. expectedvalue = [0, 1, 0, 0, 1, 0], paramid = 2
  685.  
  686. @pytest.mark.parametrize("expectedvalue,paramid", [
  687. ([0, 0, 0, 1, 1, 1], 0),
  688. ([0, 1, 2, 0, 1, 2], 1),
  689. ([0, 1, 0, 0, 1, 0], 2),
  690. ([0, 1, 2, 0, 1, 3], 3)
  691. ])
  692. def test_cell_data_array_values(centerline_branches, expectedvalue, paramid):
  693. centerline_branches_wrapped = dsa.WrapDataObject(centerline_branches)
  694. > assert centerline_branches_wrapped.CellData.GetArray(paramid).tolist() == expectedvalue
  695. E assert [0, 1, 2, 0, 1, 2] == [0, 1, 0, 0, 1, 0]
  696. E At index 2 diff: 2 != 0
  697. E Use -v to get the full diff
  698.  
  699. test_vmtkScripts/test_vmtkbranchextractor.py:68: AssertionError
  700. _ test_branch_section_group_ids_correct[branch_sections_one_sphere-expectedValue0] _
  701. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  702. but are created automatically when test functions request them as parameters.
  703. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  704. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  705. _ test_branch_section_group_ids_correct[branch_sections_two_spheres-expectedValue1] _
  706. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  707. but are created automatically when test functions request them as parameters.
  708. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  709. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  710. _ test_branch_section_area_correct[branch_sections_one_sphere-expectedValue0] __
  711. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  712. but are created automatically when test functions request them as parameters.
  713. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  714. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  715. _ test_branch_section_area_correct[branch_sections_two_spheres-expectedValue1] _
  716. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  717. but are created automatically when test functions request them as parameters.
  718. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  719. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  720. _ test_branch_section_min_size_correct[branch_sections_one_sphere-expectedValue0] _
  721. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  722. but are created automatically when test functions request them as parameters.
  723. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  724. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  725. _ test_branch_section_min_size_correct[branch_sections_two_spheres-expectedValue1] _
  726. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  727. but are created automatically when test functions request them as parameters.
  728. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  729. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  730. _ test_branch_section_max_size_correct[branch_sections_one_sphere-expectedValue0] _
  731. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  732. but are created automatically when test functions request them as parameters.
  733. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  734. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  735. _ test_branch_section_max_size_correct[branch_sections_two_spheres-expectedValue1] _
  736. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  737. but are created automatically when test functions request them as parameters.
  738. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  739. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  740. _ test_branch_section_shape_correct[branch_sections_one_sphere-expectedValue0] _
  741. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  742. but are created automatically when test functions request them as parameters.
  743. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  744. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  745. _ test_branch_section_shape_correct[branch_sections_two_spheres-expectedValue1] _
  746. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  747. but are created automatically when test functions request them as parameters.
  748. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  749. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  750. _ test_branch_section_closed_correct[branch_sections_one_sphere-expectedValue0] _
  751. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  752. but are created automatically when test functions request them as parameters.
  753. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  754. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  755. _ test_branch_section_closed_correct[branch_sections_two_spheres-expectedValue1] _
  756. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  757. but are created automatically when test functions request them as parameters.
  758. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  759. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  760. _ test_branch_section_distance_to_spheres_correct[branch_sections_one_sphere-expectedValue0] _
  761. Fixture "branch_sections_one_sphere" called directly. Fixtures are not meant to be called directly,
  762. but are created automatically when test functions request them as parameters.
  763. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  764. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  765. _ test_branch_section_distance_to_spheres_correct[branch_sections_two_spheres-expectedValue1] _
  766. Fixture "branch_sections_two_spheres" called directly. Fixtures are not meant to be called directly,
  767. but are created automatically when test functions request them as parameters.
  768. See https://docs.pytest.org/en/latest/fixture.html for more information about fixtures, and
  769. https://docs.pytest.org/en/latest/deprecations.html#calling-fixtures-directly about how to update your code.
  770. ___________________________ test_default_parameters ____________________________
  771.  
  772. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab226036590
  773. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab225fbfd40>
  774. per_system_compare_image_name = 'test_vmtkcenterlineimage_test_default_parameters_linux.vti'
  775.  
  776. def test_default_parameters(aorta_surface, compare_images, per_system_compare_image_name):
  777. centImage = centerlineimage.vmtkCenterlineImage()
  778. centImage.Surface = aorta_surface
  779. centImage.Execute()
  780.  
  781. > assert compare_images(centImage.Image, per_system_compare_image_name) == True
  782. E AssertionError: assert False == True
  783. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab225fbfd40>((vtkCommonDataModelPython.vtkImageData)0x2ab225febb40, 'test_vmtkcenterlineimage_test_default_parameters_linux.vti')
  784. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab225febb40 = <vmtk.vmtkcenterlineimage.vmtkCenterlineImage object at 0x2ab2260a4c10>.Image
  785.  
  786. test_vmtkScripts/test_vmtkcenterlineimage.py:37: AssertionError
  787. ---------------------------- Captured stdout setup -----------------------------
  788. Reading VTK XML surface file.
  789. ----------------------------- Captured stdout call -----------------------------
  790. Converting Surface to Image Mask
  791. Extracting Centerline Skeleton from Image Mask...
  792. Reading VTK XML image file.
  793. Spacing 1.000000 1.000000 1.000000
  794. Origin 0.000000 0.000000 0.000000
  795. Dimensions 0 0 0
  796. Image Points: 2479400Reference Image Points: 0
  797. ----------------------------- Captured stderr call -----------------------------
  798. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/IO/XML/vtkXMLReader.cxx, line 271
  799. vtkXMLImageDataReader (0x44e5070): Error opening file /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/imagereference/test_vmtkcenterlineimage_test_default_parameters_linux.vti
  800.  
  801. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  802. vtkCompositeDataPipeline (0x27c72d0): Algorithm vtkXMLImageDataReader(0x44e5070) returned failure for request: vtkInformation (0x2a8c180)
  803. Debug: Off
  804. Modified Time: 2894420
  805. Reference Count: 1
  806. Registered Events: (none)
  807. Request: REQUEST_INFORMATION
  808. ALGORITHM_AFTER_FORWARD: 1
  809. FORWARD_DIRECTION: 0
  810.  
  811.  
  812.  
  813. _______________ test_centerline_extraction_surface_with_no_hole ________________
  814.  
  815. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab225feb590
  816.  
  817. def test_centerline_extraction_surface_with_no_hole(aorta_surface):
  818. clnetwork = centerlinesnetwork.vmtkCenterlinesNetwork()
  819. clnetwork.Surface = aorta_surface
  820. > clnetwork.Execute()
  821.  
  822. test_vmtkScripts/test_vmtkcenterlinesnetwork.py:24:
  823. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
  824.  
  825. self = <vmtk.vmtkcenterlinesnetwork.vmtkCenterlinesNetwork object at 0x2ab2260bf5d0>
  826.  
  827. def Execute(self):
  828. if self.Surface == None:
  829. self.PrintError('Error: No input surface.')
  830.  
  831. # feature edges are used to find any holes in the surface.
  832. fedges = vtk.vtkFeatureEdges()
  833. fedges.BoundaryEdgesOn()
  834. fedges.FeatureEdgesOff()
  835. fedges.ManifoldEdgesOff()
  836. fedges.SetInputData(self.Surface)
  837. fedges.Update()
  838. ofedges = fedges.GetOutput()
  839.  
  840. # if numEdges is not 0, then there are holes which need to be capped
  841. numEdges = ofedges.GetNumberOfPoints()
  842. if numEdges != 0:
  843. tempcapper = vmtksurfacecapper.vmtkSurfaceCapper()
  844. tempcapper.Surface = self.Surface
  845. tempcapper.Interactive = 0
  846. tempcapper.Execute()
  847.  
  848. networkSurface = tempcapper.Surface
  849. else:
  850. networkSurface = self.Surface
  851.  
  852. # randomly select one cell to delete so that there is an opening for
  853. # vmtkNetworkExtraction to use.
  854. numCells = self.Surface.GetNumberOfCells()
  855. cellToDelete = random.randrange(0, numCells-1)
  856. networkSurface.BuildLinks()
  857. networkSurface.DeleteCell(cellToDelete)
  858. networkSurface.RemoveDeletedCells()
  859.  
  860. # extract the network of approximated centerlines
  861. net = vmtknetworkextraction.vmtkNetworkExtraction()
  862. net.Surface = networkSurface
  863. net.AdvancementRatio = 1.001
  864. net.Execute()
  865. network = net.Network
  866.  
  867. convert = vmtkcenterlinestonumpy.vmtkCenterlinesToNumpy()
  868. convert.Centerlines = network
  869. convert.LogOn = False
  870. convert.Execute()
  871. ad = convert.ArrayDict
  872. cellDataTopology = ad['CellData']['Topology']
  873.  
  874. # the network topology identifies an the input segment with the "0" id.
  875. # since we artificially created this segment, we don't want to use the
  876. # ends of the segment as source/target points of the centerline calculation
  877. nodeIndexToIgnore = np.where(cellDataTopology[:,0] == 0)[0][0]
  878. keepCellConnectivityList = []
  879. pointIdxToKeep = np.array([])
  880. # we remove the cell, points, and point data which are associated with the
  881. # segment we want to ignore
  882. for loopIdx, cellConnectivityList in enumerate(ad['CellData']['CellPointIds']):
  883. if loopIdx == nodeIndexToIgnore:
  884. removeCellStartIdx = cellConnectivityList[0]
  885. removeCellEndIdx = cellConnectivityList[-1]
  886. removeCellLength = cellConnectivityList.size
  887. if (removeCellEndIdx + 1) - removeCellStartIdx != removeCellLength:
  888. raise(ValueError)
  889. continue
  890. else:
  891. > rescaledCellConnectivity = np.subtract(cellConnectivityList, removeCellLength, where=cellConnectivityList >= removeCellLength)
  892. E UnboundLocalError: local variable 'removeCellLength' referenced before assignment
  893.  
  894. /scratch/gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/lib/python3.7/site-packages/vmtk/vmtkcenterlinesnetwork.py:174: UnboundLocalError
  895. ---------------------------- Captured stdout setup -----------------------------
  896. Reading VTK XML surface file.
  897. ----------------------------- Captured stdout call -----------------------------
  898.  
  899. Progress: 100%Progress: 100%
  900. _________________ test_upwind_factor_values_for_upwind[0.0-0] __________________
  901.  
  902. aorta_image = (vtkCommonDataModelPython.vtkImageData)0x2ab22608ed70
  903. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab22609f560>
  904. upwindValue = 0.0, paramid = '0'
  905. write_image = <function write_image.<locals>.make_write_image at 0x2ab22609f170>
  906.  
  907. @pytest.mark.parametrize("upwindValue,paramid", [
  908. (0.0, '0'),
  909. (0.3, '1'),
  910. ])
  911. def test_upwind_factor_values_for_upwind(aorta_image, compare_images, upwindValue, paramid, write_image):
  912. name = __name__ + '_test_upwind_factor_values_for_upwind_' + paramid + '.mha'
  913. featurer = imagefeatures.vmtkImageFeatures()
  914. featurer.Image = aorta_image
  915. featurer.FeatureImageType = 'upwind'
  916. featurer.UpwindFactor = upwindValue
  917. featurer.Execute()
  918.  
  919. > assert compare_images(featurer.Image, name) == True
  920. E AssertionError: assert False == True
  921. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab22609f560>((vtkCommonDataModelPython.vtkImageData)0x2ab2260aa280, 'test_vmtkimagefeatures_test_upwind_factor_values_for_upwind_0.mha')
  922. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab2260aa280 = <vmtk.vmtkimagefeatures.vmtkImageFeatures object at 0x2ab225ffe610>.Image
  923.  
  924. test_vmtkScripts/test_vmtkimagefeatures.py:80: AssertionError
  925. ----------------------------- Captured stdout call -----------------------------
  926. Spacing 0.878906 0.878906 1.500090
  927. Origin 156.445000 24.609400 0.000000
  928. Dimensions 157 393 34
  929. Image Points: 2097834Reference Image Points: 2097834Difference Range: (-0.9947620630264282, 0.0)
  930. _________________ test_upwind_factor_values_for_upwind[0.3-1] __________________
  931.  
  932. aorta_image = (vtkCommonDataModelPython.vtkImageData)0x2ab22608ed70
  933. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab22609f560>
  934. upwindValue = 0.3, paramid = '1'
  935. write_image = <function write_image.<locals>.make_write_image at 0x2ab22609f170>
  936.  
  937. @pytest.mark.parametrize("upwindValue,paramid", [
  938. (0.0, '0'),
  939. (0.3, '1'),
  940. ])
  941. def test_upwind_factor_values_for_upwind(aorta_image, compare_images, upwindValue, paramid, write_image):
  942. name = __name__ + '_test_upwind_factor_values_for_upwind_' + paramid + '.mha'
  943. featurer = imagefeatures.vmtkImageFeatures()
  944. featurer.Image = aorta_image
  945. featurer.FeatureImageType = 'upwind'
  946. featurer.UpwindFactor = upwindValue
  947. featurer.Execute()
  948.  
  949. > assert compare_images(featurer.Image, name) == True
  950. E AssertionError: assert False == True
  951. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab22609f560>((vtkCommonDataModelPython.vtkImageData)0x2ab2260aaa60, 'test_vmtkimagefeatures_test_upwind_factor_values_for_upwind_1.mha')
  952. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab2260aaa60 = <vmtk.vmtkimagefeatures.vmtkImageFeatures object at 0x2ab226052310>.Image
  953.  
  954. test_vmtkScripts/test_vmtkimagefeatures.py:80: AssertionError
  955. ----------------------------- Captured stdout call -----------------------------
  956. Spacing 0.878906 0.878906 1.500090
  957. Origin 156.445000 24.609400 0.000000
  958. Dimensions 157 393 34
  959. Image Points: 2097834Reference Image Points: 2097834Difference Range: (-0.9925339818000793, 0.0)
  960. ____________________ test_set_inside_outside_values[1-0-0] _____________________
  961.  
  962. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab2260aae50
  963. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>
  964. insidevalue = 1, outsidevalue = 0, paramid = '0'
  965.  
  966. @pytest.mark.parametrize("insidevalue,outsidevalue,paramid", [
  967. (1, 0 ,'0'),
  968. (255, 0, '1'),
  969. (255, 1, '2'),
  970. (1, 255, '3'),
  971. ])
  972. def test_set_inside_outside_values(aorta_surface, compare_images,
  973. insidevalue, outsidevalue, paramid):
  974. name = __name__ + '_test_set_inside_outside_values_' + paramid + '.vti'
  975. surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
  976. surfToImage.Surface = aorta_surface
  977. surfToImage.InsideValue = insidevalue
  978. surfToImage.OutsideValue = outsidevalue
  979. surfToImage.Execute()
  980.  
  981. > assert compare_images(surfToImage.Image, name) == True
  982. E AssertionError: assert False == True
  983. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>((vtkCommonDataModelPython.vtkImageData)0x2ab225feb910, 'test_vmtksurfacetobinaryimage_test_set_inside_outside_values_0.vti')
  984. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab225feb910 = <vmtk.vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage object at 0x2ab2260529d0>.Image
  985.  
  986. test_vmtkScripts/test_vmtksurfacetobinaryimage.py:35: AssertionError
  987. ---------------------------- Captured stdout setup -----------------------------
  988. Reading VTK XML surface file.
  989. ----------------------------- Captured stdout call -----------------------------
  990. Reading VTK XML image file.
  991. Spacing 1.000000 1.000000 1.000000
  992. Origin 0.000000 0.000000 0.000000
  993. Dimensions 0 0 0
  994. Image Points: 2479400Reference Image Points: 0
  995. ----------------------------- Captured stderr call -----------------------------
  996. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/IO/XML/vtkXMLReader.cxx, line 271
  997. vtkXMLImageDataReader (0x2abb180): Error opening file /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/imagereference/test_vmtksurfacetobinaryimage_test_set_inside_outside_values_0.vti
  998.  
  999. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  1000. vtkCompositeDataPipeline (0x542bd60): Algorithm vtkXMLImageDataReader(0x2abb180) returned failure for request: vtkInformation (0x323c2d0)
  1001. Debug: Off
  1002. Modified Time: 39207558
  1003. Reference Count: 1
  1004. Registered Events: (none)
  1005. Request: REQUEST_INFORMATION
  1006. ALGORITHM_AFTER_FORWARD: 1
  1007. FORWARD_DIRECTION: 0
  1008.  
  1009.  
  1010.  
  1011. ___________________ test_set_inside_outside_values[255-0-1] ____________________
  1012.  
  1013. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab2260aae50
  1014. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>
  1015. insidevalue = 255, outsidevalue = 0, paramid = '1'
  1016.  
  1017. @pytest.mark.parametrize("insidevalue,outsidevalue,paramid", [
  1018. (1, 0 ,'0'),
  1019. (255, 0, '1'),
  1020. (255, 1, '2'),
  1021. (1, 255, '3'),
  1022. ])
  1023. def test_set_inside_outside_values(aorta_surface, compare_images,
  1024. insidevalue, outsidevalue, paramid):
  1025. name = __name__ + '_test_set_inside_outside_values_' + paramid + '.vti'
  1026. surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
  1027. surfToImage.Surface = aorta_surface
  1028. surfToImage.InsideValue = insidevalue
  1029. surfToImage.OutsideValue = outsidevalue
  1030. surfToImage.Execute()
  1031.  
  1032. > assert compare_images(surfToImage.Image, name) == True
  1033. E AssertionError: assert False == True
  1034. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>((vtkCommonDataModelPython.vtkImageData)0x2ab2260aa910, 'test_vmtksurfacetobinaryimage_test_set_inside_outside_values_1.vti')
  1035. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab2260aa910 = <vmtk.vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage object at 0x2ab22616c610>.Image
  1036.  
  1037. test_vmtkScripts/test_vmtksurfacetobinaryimage.py:35: AssertionError
  1038. ----------------------------- Captured stdout call -----------------------------
  1039. Reading VTK XML image file.
  1040. Spacing 1.000000 1.000000 1.000000
  1041. Origin 0.000000 0.000000 0.000000
  1042. Dimensions 0 0 0
  1043. Image Points: 2479400Reference Image Points: 0
  1044. ----------------------------- Captured stderr call -----------------------------
  1045. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/IO/XML/vtkXMLReader.cxx, line 271
  1046. vtkXMLImageDataReader (0x52468b0): Error opening file /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/imagereference/test_vmtksurfacetobinaryimage_test_set_inside_outside_values_1.vti
  1047.  
  1048. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  1049. vtkCompositeDataPipeline (0x524b7b0): Algorithm vtkXMLImageDataReader(0x52468b0) returned failure for request: vtkInformation (0x2c4dda0)
  1050. Debug: Off
  1051. Modified Time: 39210253
  1052. Reference Count: 1
  1053. Registered Events: (none)
  1054. Request: REQUEST_INFORMATION
  1055. ALGORITHM_AFTER_FORWARD: 1
  1056. FORWARD_DIRECTION: 0
  1057.  
  1058.  
  1059.  
  1060. ___________________ test_set_inside_outside_values[255-1-2] ____________________
  1061.  
  1062. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab2260aae50
  1063. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>
  1064. insidevalue = 255, outsidevalue = 1, paramid = '2'
  1065.  
  1066. @pytest.mark.parametrize("insidevalue,outsidevalue,paramid", [
  1067. (1, 0 ,'0'),
  1068. (255, 0, '1'),
  1069. (255, 1, '2'),
  1070. (1, 255, '3'),
  1071. ])
  1072. def test_set_inside_outside_values(aorta_surface, compare_images,
  1073. insidevalue, outsidevalue, paramid):
  1074. name = __name__ + '_test_set_inside_outside_values_' + paramid + '.vti'
  1075. surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
  1076. surfToImage.Surface = aorta_surface
  1077. surfToImage.InsideValue = insidevalue
  1078. surfToImage.OutsideValue = outsidevalue
  1079. surfToImage.Execute()
  1080.  
  1081. > assert compare_images(surfToImage.Image, name) == True
  1082. E AssertionError: assert False == True
  1083. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>((vtkCommonDataModelPython.vtkImageData)0x2ab225d02670, 'test_vmtksurfacetobinaryimage_test_set_inside_outside_values_2.vti')
  1084. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab225d02670 = <vmtk.vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage object at 0x2ab22614cc10>.Image
  1085.  
  1086. test_vmtkScripts/test_vmtksurfacetobinaryimage.py:35: AssertionError
  1087. ----------------------------- Captured stdout call -----------------------------
  1088. Reading VTK XML image file.
  1089. Spacing 1.000000 1.000000 1.000000
  1090. Origin 0.000000 0.000000 0.000000
  1091. Dimensions 0 0 0
  1092. Image Points: 2479400Reference Image Points: 0
  1093. ----------------------------- Captured stderr call -----------------------------
  1094. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/IO/XML/vtkXMLReader.cxx, line 271
  1095. vtkXMLImageDataReader (0x4de7390): Error opening file /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/imagereference/test_vmtksurfacetobinaryimage_test_set_inside_outside_values_2.vti
  1096.  
  1097. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  1098. vtkCompositeDataPipeline (0x524e8f0): Algorithm vtkXMLImageDataReader(0x4de7390) returned failure for request: vtkInformation (0x523a8f0)
  1099. Debug: Off
  1100. Modified Time: 39212856
  1101. Reference Count: 1
  1102. Registered Events: (none)
  1103. Request: REQUEST_INFORMATION
  1104. ALGORITHM_AFTER_FORWARD: 1
  1105. FORWARD_DIRECTION: 0
  1106.  
  1107.  
  1108.  
  1109. ___________________ test_set_inside_outside_values[1-255-3] ____________________
  1110.  
  1111. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab2260aae50
  1112. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>
  1113. insidevalue = 1, outsidevalue = 255, paramid = '3'
  1114.  
  1115. @pytest.mark.parametrize("insidevalue,outsidevalue,paramid", [
  1116. (1, 0 ,'0'),
  1117. (255, 0, '1'),
  1118. (255, 1, '2'),
  1119. (1, 255, '3'),
  1120. ])
  1121. def test_set_inside_outside_values(aorta_surface, compare_images,
  1122. insidevalue, outsidevalue, paramid):
  1123. name = __name__ + '_test_set_inside_outside_values_' + paramid + '.vti'
  1124. surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
  1125. surfToImage.Surface = aorta_surface
  1126. surfToImage.InsideValue = insidevalue
  1127. surfToImage.OutsideValue = outsidevalue
  1128. surfToImage.Execute()
  1129.  
  1130. > assert compare_images(surfToImage.Image, name) == True
  1131. E AssertionError: assert False == True
  1132. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>((vtkCommonDataModelPython.vtkImageData)0x2ab226161520, 'test_vmtksurfacetobinaryimage_test_set_inside_outside_values_3.vti')
  1133. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab226161520 = <vmtk.vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage object at 0x2ab226188b90>.Image
  1134.  
  1135. test_vmtkScripts/test_vmtksurfacetobinaryimage.py:35: AssertionError
  1136. ----------------------------- Captured stdout call -----------------------------
  1137. Reading VTK XML image file.
  1138. Spacing 1.000000 1.000000 1.000000
  1139. Origin 0.000000 0.000000 0.000000
  1140. Dimensions 0 0 0
  1141. Image Points: 2479400Reference Image Points: 0
  1142. ----------------------------- Captured stderr call -----------------------------
  1143. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/IO/XML/vtkXMLReader.cxx, line 271
  1144. vtkXMLImageDataReader (0x4b21b40): Error opening file /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/imagereference/test_vmtksurfacetobinaryimage_test_set_inside_outside_values_3.vti
  1145.  
  1146. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  1147. vtkCompositeDataPipeline (0x52405a0): Algorithm vtkXMLImageDataReader(0x4b21b40) returned failure for request: vtkInformation (0x4d28380)
  1148. Debug: Off
  1149. Modified Time: 39215489
  1150. Reference Count: 1
  1151. Registered Events: (none)
  1152. Request: REQUEST_INFORMATION
  1153. ALGORITHM_AFTER_FORWARD: 1
  1154. FORWARD_DIRECTION: 0
  1155.  
  1156.  
  1157.  
  1158. _____________________________ test_change_spacing ______________________________
  1159.  
  1160. aorta_surface = (vtkCommonDataModelPython.vtkPolyData)0x2ab2260aae50
  1161. compare_images = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>
  1162.  
  1163. def test_change_spacing(aorta_surface, compare_images):
  1164. name = __name__ + '_test_change_spacing.vti'
  1165. surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
  1166. surfToImage.Surface = aorta_surface
  1167. surfToImage.PolyDataToImageDataSpacing = [0.4, 0.4, 0.4]
  1168. surfToImage.Execute()
  1169.  
  1170. > assert compare_images(surfToImage.Image, name) == True
  1171. E AssertionError: assert False == True
  1172. E + where False = <function compare_images.<locals>.make_compare_images at 0x2ab226145170>((vtkCommonDataModelPython.vtkImageData)0x2ab2261614b0, 'test_vmtksurfacetobinaryimage_test_change_spacing.vti')
  1173. E + where (vtkCommonDataModelPython.vtkImageData)0x2ab2261614b0 = <vmtk.vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage object at 0x2ab22617b450>.Image
  1174.  
  1175. test_vmtkScripts/test_vmtksurfacetobinaryimage.py:45: AssertionError
  1176. ----------------------------- Captured stdout call -----------------------------
  1177. Reading VTK XML image file.
  1178. Spacing 1.000000 1.000000 1.000000
  1179. Origin 0.000000 0.000000 0.000000
  1180. Dimensions 0 0 0
  1181. Image Points: 1047480Reference Image Points: 0
  1182. ----------------------------- Captured stderr call -----------------------------
  1183. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/IO/XML/vtkXMLReader.cxx, line 271
  1184. vtkXMLImageDataReader (0x6c55600): Error opening file /vscmnt/gent_kyukon_scratch/_kyukon_scratch_gent/vo/001/gvo00117/easybuild/CO7/skylake-eth/software/VMTK/1.4.0-foss-2019b-Python-3.7.4/tests/vmtk-test-data/imagereference/test_vmtksurfacetobinaryimage_test_change_spacing.vti
  1185.  
  1186. ERROR: In /tmp/vsc40003/easybuild/VTK/8.2.0/foss-2019b-Python-3.7.4/VTK-8.2.0/Common/ExecutionModel/vtkExecutive.cxx, line 782
  1187. vtkCompositeDataPipeline (0x490f9c0): Algorithm vtkXMLImageDataReader(0x6c55600) returned failure for request: vtkInformation (0x149d510)
  1188. Debug: Off
  1189. Modified Time: 39217618
  1190. Reference Count: 1
  1191. Registered Events: (none)
  1192. Request: REQUEST_INFORMATION
  1193. ALGORITHM_AFTER_FORWARD: 1
  1194. FORWARD_DIRECTION: 0
  1195.  
  1196.  
  1197.  
  1198. == 51 failed, 460 passed, 20 skipped, 1 xfailed, 26 error in 98.89s (0:01:38) ==
  1199.  
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