Automatic tests failing due to ITK errors about inability to load seg.vtm file
Closed this issue · 10 comments
23 automatic tests have been failing since October 29 due to error messages about seg.vtm files. These are the first failures:
http://slicer.cdash.org/viewTest.php?onlyfailed&buildid=1734159
These failing tests prevent us from seeing any regressions in DVH and segment comparisons modules, so these would need to be fixed asap.
I don't find any commit obviously suspicious from that time. There is one that is related to segmentation storage, but it seems to be unrelated after a quick glance.
This is the actual error:
ERROR: In D:\D\P\Slicer-0\Libs\vtkITK\vtkITKArchetypeImageSeriesReader.cxx, line 622
vtkITKArchetypeImageSeriesVectorReaderFile (0000000003BFEFD0): vtkITKArchetypeImageSeriesReader::ExecuteInformation: Cannot open D:/D/P/S-0-E-b/SlicerRT/Testing/Data/EclipseEnt_Structures.seg.vtm. ITK exception info: error in unknown: Could not create IO object for reading file D:/D/P/S-0-E-b/SlicerRT/Testing/Data/EclipseEnt_Structures.seg.vtm
Tried to create one of the following:
BMPImageIO
BioRadImageIO
DCMTKImageIO
GDCMImageIO
GiplImageIO
JPEGImageIO
LSMImageIO
MGHImageIO
MINCImageIO
MRCImageIO
MetaImageIO
NiftiImageIO
NrrdImageIO
PNGImageIO
StimulateImageIO
TIFFImageIO
VTKImageIO
MRMLIDImageIO
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
ERROR: In D:\D\P\Slicer-0-build\VTK\Common\ExecutionModel\vtkExecutive.cxx, line 782
vtkCompositeDataPipeline (0000000003C307E0): Algorithm vtkITKArchetypeImageSeriesVectorReaderFile(0000000003BFEFD0) returned failure for request: vtkInformation (0000000003C28A40)
Debug: Off
Modified Time: 4891
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
FORWARD_DIRECTION: 0
ALGORITHM_AFTER_FORWARD: 1
ERROR: In D:\D\P\Slicer-0\Libs\MRML\Core\vtkMRMLSegmentationStorageNode.cxx, line 537
vtkMRMLSegmentationStorageNode (0000000003BFDA30): ReadBinaryLabelmapRepresentation: Error reading image!
Somewhat related: there is one further test that is failing due to changes in Slicer core, namely the DICOM widgets.
http://slicer.cdash.org/testDetails.php?test=9814070&build=1733317
The issue here seems easy to fix:
Traceback (most recent call last): File "/Volumes/Dashboards/Preview/S-0-E-b/SlicerRT/DicomRtImportExport/Testing/Python/DicomRtImportTest.py", line 37, in test_DicomRtImportTest_FullTest1 self.TestSection_OpenTempDatabase() File "/Volumes/Dashboards/Preview/S-0-E-b/SlicerRT/DicomRtImportExport/Testing/Python/DicomRtImportTest.py", line 87, in TestSection_OpenTempDatabase self.dicomWidget.onDatabaseDirectoryChanged(self.dicomDatabaseDir) AttributeError: 'DICOMWidget' object has no attribute 'onDatabaseDirectoryChanged'
Copied from email:
The first issue has to do with loading polydata segmentations, and the WIP fix is in this pull request: Slicer/Slicer#1269
I haven't looked into the DICOM error yet, but I will look at it soon.
Thanks! Do you know why the tests started failing on Oct 29 though? There does not seem to be any related change (neither an ITK update nor any change around vtkITKArchetype...).
This commit: Slicer/Slicer@81b762a.
We didn't use vtkITKArchetypeImageSeriesVectorReaderFile prior to this.
Ah, not having used the archetype reader is the reason! Thanks.
Having 22 out of 70 tests failing because of this is very bad, so please if you have the chance finish the pull request. It will be very hard to track down regressions like this, especially that now we have an active contributor.
Updated the pull request, Tests should pass again once it is integrated.
Thank you very much, @Sunderlandkyl, I really appreciate the quick action!
@Sunderlandkyl's fix is integrated in Slicer/Slicer@8ea6945
All tests related to the vtkITKArchetype reader are now passing.
Only py_DicomRtImportTest is now failing.
Indeed, thank you very much!