I’m fairly new to using slicer so I might have made a mistake somewhere but I keep getting an error while running my script and I can not figure out why. I have written a script to automate part of the segmentation process based on CT scans. As I have a lot of scans to go through I have put several segment editor functions in a double loop that goes over the different scans and segments in python. I have run the program before without any problems but the last few days I keep getting an error without having changed anything. What I don’t understand is that I get an error for a function that doesn’t give a problem the first time(s) it is executed by the script but then it suddenly doesn’t seem to work anymore (sometimes it does go over the loops once or twice before giving the error). I call all segment editor functions in a similar fashion but the part calling the closing function seems to be the only one giving problems.
This is part of the script I wrote, the last line of the ‘Closing gaps’ part is the line that gives the error. After this part it runs a few more segment editor functions and it assigns names to the different segments, but I left that out for now.
Islands min_size_islands = 20000 # Closing cl_kernel_size_mm = 8 # Set range of required images for segmentation Numbers = list(range(21,42)) # List of segments for segmentation Segments = ["Bone", "Bone_2", "Bone_3", "Bone_4", "Bone_5", "Bone_6"] # PROCESSING for i in Numbers: # Open mrb file slicer.util.loadScene(filepath + "SlicerSegmentation_" + str(i) + ".mrb") masterVolumeNode = getNode("vtkMRMLScalarVolumeNode" + str(i-20)) # Create segment editor to get access to effects segmentEditorWidget = slicer.qMRMLSegmentEditorWidget() segmentEditorWidget.setMRMLScene(slicer.mrmlScene) segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentEditorNode") segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode) segmentEditorWidget.setSegmentationNode(getNode("vtkMRMLSegmentationNode" + str(i-20))) segmentEditorWidget.setMasterVolumeNode(masterVolumeNode) # Split islands segmentEditorWidget.setActiveEffectByName("Islands") effect = segmentEditorWidget.activeEffect() effect.setParameter("Operation", "SPLIT_ISLANDS_TO_SEGMENTS") effect.setParameter("MinimumSize", min_size_islands) effect.self().onApply() # Set Masking segmentEditorNode.SetMaskMode(0) segmentEditorNode.SetOverwriteMode(2) for x in Segments: # Closing gaps segmentEditorWidget.setCurrentSegmentID(x) segmentEditorWidget.setActiveEffectByName("Smoothing") effect = segmentEditorWidget.activeEffect() effect.setParameter("SmoothingMethod", "CLOSING") effect.setParameter("KernelSizeMm", cl_kernel_size_mm) effect.self().onApply() # Cleaning up segmentEditorWidget = None slicer.mrmlScene.RemoveNode(segmentEditorNode) slicer.mrmlScene.RemoveNode(getNode("vtkMRMLSubjectHierarchyNode" + str(i-20))) slicer.mrmlScene.RemoveNode(getNode("vtkMRMLScalarVolumeNode" + str(i-20))) slicer.mrmlScene.RemoveNode(getNode("vtkMRMLSegmentationNode" + str(i-20)))
And the error I keep getting is the following:
Traceback (most recent call last): File "<console>", line 1, in <module> File "<string>", line 71, in <module> File "/Applications/Slicer.app/Contents/lib/Slicer-5.0/qt-scripted-modules/SegmentEditorEffects/SegmentEditorSmoothingEffect.py", line 235, in onApply self.smoothSelectedSegment(maskImage, maskExtent) File "/Applications/Slicer.app/Contents/lib/Slicer-5.0/qt-scripted-modules/SegmentEditorEffects/SegmentEditorSmoothingEffect.py", line 348, in smoothSelectedSegment thresh.SetOutputScalarType(clippedSelectedSegmentLabelmap.GetScalarType()) AttributeError: 'NoneType' object has no attribute 'GetScalarType'
I can’t figure out what the problem is as it was running smoothly before and still does sometimes. I have tried to change “CLOSING” to “MORPHOLOGICAL_CLOSING” (as it is called here) but that did not seem to solve the problem.
Another thing I noticed is that slicer sometimes skips a number when naming the nodes automatically. As you can see my script relies on the numbering of the different nodes, which causes an error when a number is skipped. I can fix this by just running the script again but it seems there should be a better solution to this?
Thanks in advance!