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Hmm, that is weird. I agree it doesn't look like an out-of-memory situation, but it's possibly related.
I'm able to replicate the issue on my machine by pasting in the code below and then trying to use the editor.
Looks like it's an issue with the undo/redo code, probably something in the zlib helper library used to compress undo stnapshots.
I get the following error on the console before the program exits:
Zlib error while compressing data.
This come from a worker thread so the main threads' stack dump appears to happen at a random spot.
import SampleData
sdl = SampleData.SampleDataLogic()
sdl.downloadMRHead()
id = vtk.vtkImageData()
id.SetDimensions(1500,1500,1074)
id.AllocateScalars(vtk.VTK_FLOAT, 1)
head = slicer.util.getNode('MRHead')
head.SetAndObserveImageData(id) |
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Hey Steve,
I am fairly new to using 3D slicer. I tried copying and pasting the above into the python interactor and then trying to use the brush on it produced the crash as well. Sorry for teh long log file. I loaded the tiffs briefly before resetting the scene and trying the above. I am not necessarily seeing the Zlib error (though let me know if its in another location I should be looking at). I might point out, though it very well may be unrelated, that I notice that on mac this only ever works on a single core of my 12 whereas on windows it seems to work across all as I would expect from its description. I just thought I would mention it since memory addressing is in play and in my admittedly very limited experience maybe it has something to do with that.
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Session start time .......: 2016-03-17 16:31:08
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Slicer version ...........: 4.5.0-1 (revision 24735) macosx-amd64 - installed
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Operating system .........: Mac OS X / 10.10.5 / 14F1605 - 64-bit
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Memory ...................: 131072 MB physical, 0 MB virtual
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - CPU ......................: GenuineIntel 2.700 MHz, 12 cores
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Developer mode enabled ...: no
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Prefer executable CLI ....: yes
[DEBUG][Qt] 17.03.2016 16:31:08 [] (unknown:0) - Additional module paths ..: (none)
[CRITICAL][Qt] 17.03.2016 16:31:11 [] (unknown:0) - Error(s):
Cannot load library /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libPerformMetricTestLib.dylib: (dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libPerformMetricTestLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Package/Slicer-450-package/ITKv4-build/lib/libITKCommon-4.8.1.dylib
Referenced from: /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libPerformMetricTestLib.dylib
Reason: image not found)
[CRITICAL][Qt] 17.03.2016 16:31:12 [] (unknown:0) - Error(s):
Cannot load library /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libVBRAINSDemonWarpLib.dylib: (dlopen(/Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libVBRAINSDemonWarpLib.dylib, 5): Library not loaded: /Users/kitware/Dashboards/Package/Slicer-450-package/ITKv4-build/lib/libITKIOBMP-4.8.1.dylib
Referenced from: /Applications/Slicer.app/Contents/lib/Slicer-4.5/cli-modules/libVBRAINSDemonWarpLib.dylib
Reason: image not found)
[DEBUG][Qt] 17.03.2016 16:31:12 [] (unknown:0) - Number of registered modules: 141
[DEBUG][Qt] 17.03.2016 16:31:18 [] (unknown:0) - Number of instantiated modules: 141
[DEBUG][Qt] 17.03.2016 16:31:19 [] (unknown:0) - Number of loaded modules: 141
[DEBUG][Qt] 17.03.2016 16:31:19 [] (unknown:0) - Switch to module: "Welcome"
[DEBUG][Qt] 17.03.2016 16:34:06 [] (unknown:0) - Python console user input: import SampleData
[DEBUG][Qt] 17.03.2016 16:34:06 [] (unknown:0) - Python console user input: sdl = SampleData.SampleDataLogic()
[DEBUG][Qt] 17.03.2016 16:34:06 [] (unknown:0) - Python console user input: sdl.downloadMRHead()
[INFO][Stream] 17.03.2016 16:34:06 [] (unknown:0) - <b>Requesting download</b> <i>MR-head.nrrd</i> from http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd...
[INFO][Stream] 17.03.2016 16:34:06 [] (unknown:0) -
[INFO][Stream] 17.03.2016 16:34:08 [] (unknown:0) - <i>Downloaded 648.0 KB (10% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:08 [] (unknown:0) - <i>Downloaded 1.3 MB (20% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:09 [] (unknown:0) - <i>Downloaded 1.9 MB (30% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:09 [] (unknown:0) - <i>Downloaded 2.5 MB (40% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:09 [] (unknown:0) - <i>Downloaded 3.2 MB (50% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:10 [] (unknown:0) - <i>Downloaded 3.8 MB (60% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:10 [] (unknown:0) - <i>Downloaded 4.4 MB (70% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:10 [] (unknown:0) - <i>Downloaded 5.0 MB (80% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) - <i>Downloaded 5.7 MB (90% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) - <i>Downloaded 6.3 MB (100% of 6.3 MB)...</i>
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) - <b>Download finished</b>
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) - <b>Requesting load</b> <i>MRHead</i> from /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/RemoteIO/MR-head.nrrd...
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) -
[INFO][VTK] 17.03.2016 16:34:11 [vtkMRMLVolumeArchetypeStorageNode (0x13c62bcb0)] (/Users/kitware/Dashboards/Package/Slicer-450/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:459) - Loaded volume from file: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/RemoteIO/MR-head.nrrd. Dimensions: 256x256x130. Number of components: 1. Pixel type: short.
[DEBUG][Qt] 17.03.2016 16:34:11 [] (unknown:0) - "Volume" Reader has successfully read the file "/var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/RemoteIO/MR-head.nrrd"
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) - <b>Load finished</b>
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) -
[INFO][Stream] 17.03.2016 16:34:11 [] (unknown:0) - (vtkMRMLScalarVolumeNode)0x1299268f0
[DEBUG][Qt] 17.03.2016 16:34:11 [] (unknown:0) - Python console user input: id = vtk.vtkImageData()
[DEBUG][Qt] 17.03.2016 16:34:11 [] (unknown:0) - Python console user input: id.SetDimensions(1500,1500,1074)
[DEBUG][Qt] 17.03.2016 16:34:11 [] (unknown:0) - Python console user input: id.AllocateScalars(vtk.VTK_FLOAT, 1)
[DEBUG][Qt] 17.03.2016 16:34:11 [] (unknown:0) - Python console user input: head = slicer.util.getNode('MRHead')
[DEBUG][Qt] 17.03.2016 16:34:25 [] (unknown:0) - Python console user input: head.SetAndObserveImageData(id)
[CRITICAL][FD] 17.03.2016 16:37:23 [] (unknown:0) - 2016-03-17 16:37:23.564 Slicer[1947:15597] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[CRITICAL][FD] 17.03.2016 16:37:27 [] (unknown:0) - 2016-03-17 16:37:27.248 Slicer[1947:15597] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[CRITICAL][FD] 17.03.2016 16:37:29 [] (unknown:0) - 2016-03-17 16:37:29.949 Slicer[1947:15597] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[CRITICAL][FD] 17.03.2016 16:37:29 [] (unknown:0) - TIFFReadDirectory: Warning, Unknown field with tag 50838 (0xc696) encountered.
[CRITICAL][FD] 17.03.2016 16:37:29 [] (unknown:0) - TIFFReadDirectory: Warning, Unknown field with tag 50839 (0xc697) encountered.
So so so many of these Tiff errors...
[CRITICAL][FD] 17.03.2016 16:38:10 [] (unknown:0) - TIFFReadDirectory: Warning, Unknown field with tag 50838 (0xc696) encountered.
[CRITICAL][FD] 17.03.2016 16:38:10 [] (unknown:0) - TIFFReadDirectory: Warning, Unknown field with tag 50839 (0xc697) encountered.
[INFO][VTK] 17.03.2016 16:38:12 [vtkMRMLVolumeArchetypeStorageNode (0x1418ea9e0)] (/Users/kitware/Dashboards/Package/Slicer-450/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:459) - Loaded volume from file: /Volumes/Sammy_Tank/CT_Scan_Place/MK84/Slicer_Studies/original_tiffs/subset/ur_0000.tif. Dimensions: 1500x1500x1074. Number of components: 1. Pixel type: float.
[DEBUG][Qt] 17.03.2016 16:38:16 [] (unknown:0) - "Volume" Reader has successfully read the file "/Volumes/Sammy_Tank/CT_Scan_Place/MK84/Slicer_Studies/original_tiffs/subset/ur_0000.tif"
[DEBUG][Qt] 17.03.2016 16:38:23 [] (unknown:0) - Switch to module: "Editor"
[CRITICAL][FD] 17.03.2016 16:38:24 [] (unknown:0) - 2016-03-17 16:38:24.547 Slicer[1947:15597] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
[DEBUG][Qt] 17.03.2016 16:38:44 [] (unknown:0) - Python console user input: import SampleData
[DEBUG][Qt] 17.03.2016 16:38:56 [] (unknown:0) - Python console user input: sdl = SampleData.SampleDataLogic()
[DEBUG][Qt] 17.03.2016 16:39:05 [] (unknown:0) - Python console user input: sl.downloadMRHead()
[CRITICAL][Stream] 17.03.2016 16:39:05 [] (unknown:0) - Traceback (most recent call last):
[CRITICAL][Stream] 17.03.2016 16:39:05 [] (unknown:0) - File "<console>", line 1, in <module>
[CRITICAL][Stream] 17.03.2016 16:39:05 [] (unknown:0) - NameError: name 'sl' is not defined
[DEBUG][Qt] 17.03.2016 16:39:13 [] (unknown:0) - Python console user input: sdl.downloadMRHead()
[INFO][Stream] 17.03.2016 16:39:13 [] (unknown:0) - <b>File already exists in cache - reusing it.</b>
[INFO][Stream] 17.03.2016 16:39:13 [] (unknown:0) - <b>Requesting load</b> <i>MRHead</i> from /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/RemoteIO/MR-head.nrrd...
[INFO][Stream] 17.03.2016 16:39:13 [] (unknown:0) -
[INFO][VTK] 17.03.2016 16:39:13 [vtkMRMLVolumeArchetypeStorageNode (0x13f38b150)] (/Users/kitware/Dashboards/Package/Slicer-450/Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx:459) - Loaded volume from file: /var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/RemoteIO/MR-head.nrrd. Dimensions: 256x256x130. Number of components: 1. Pixel type: short.
[DEBUG][Qt] 17.03.2016 16:39:13 [] (unknown:0) - "Volume" Reader has successfully read the file "/var/folders/dp/pcdkgh614sjfkqjcgscz43zw000s01/T/Slicer/RemoteIO/MR-head.nrrd"
[INFO][Stream] 17.03.2016 16:39:13 [] (unknown:0) - <b>Load finished</b>
[INFO][Stream] 17.03.2016 16:39:13 [] (unknown:0) -
[INFO][Stream] 17.03.2016 16:39:13 [] (unknown:0) - (vtkMRMLScalarVolumeNode)0x129ad04d0
[DEBUG][Qt] 17.03.2016 16:39:30 [] (unknown:0) - Python console user input: id = vtk.vtkImageData()
[DEBUG][Qt] 17.03.2016 16:39:45 [] (unknown:0) - Python console user input: id.SetDimensions(1500,1500,1074)
[DEBUG][Qt] 17.03.2016 16:39:59 [] (unknown:0) - Python console user input: id.AllocateScalars(vtk.VTK_FLOAT,1)
[DEBUG][Qt] 17.03.2016 16:40:11 [] (unknown:0) - Python console user input: head = slicer.util.getNode('MRHead')
[DEBUG][Qt] 17.03.2016 16:40:23 [] (unknown:0) - Python console user input: head = slicer.util.getNode('MRHead')
[DEBUG][Qt] 17.03.2016 16:40:38 [] (unknown:0) - Python console user input: head.SetAndObserveImageData(id)
[CRITICAL][FD] 17.03.2016 16:40:49 [] (unknown:0) - 2016-03-17 16:40:49.076 Slicer[1947:15597] modalSession has been exited prematurely - check for a reentrant call to endModalSession: |
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r24973
This fixes the crash for me. Try tomorrow's nightly build to confirm and close the bug if it is fixed for you.
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=24973
The undo/redo operation will fail silently but that's at least better than a crash for now.
It would make sense to warn the user when undo is not available, but there's a new segmentation module being created and changing the UI of this module doesn't seem worth it. |