Dear all,
I just checked Python_scripting and ScriptRepository pages and couldn’t find an example for cropping an image, I wrote this simple example. It runs without problem inside a module or extension but when I run it in an external python script it also runs and produces the correct output cropped image but there are error messages I don’t understand. Here is the mentioned complete script code:
Despite the correct output cropped image, I get this output in the terminal:
~/sw/Slicer-4.8.1/Slicer --no-main-window --python-script ./myScript.py
Qt: Cannot set locale modifiers:
Number of registered modules: 150
Number of instantiated modules: 150
Number of loaded modules: 150
myScript
Loaded volume from file: ./myVolume.nrrd. Dimensions: 485x485x121. Number of components: 1. Pixel type: short.
"Volume" Reader has successfully read the file "./myVolume.nrrd" "[0.56s]"
vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file ./_DUMMY_DOES_NOT_EXIST__ does not exist.
Algorithm vtkITKArchetypeDiffusionTensorImageReaderFile(0x4a977b0) returned failure for request:
vtkInformation (0x4a9aea0)
Debug: Off
Modified Time: 827149
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file ./_DUMMY_DOES_NOT_EXIST__ does not exist.
Algorithm vtkITKArchetypeImageSeriesVectorReaderSeries(0x48edfb0) returned failure for request: vtkInformation (0x4a978f0)
Debug: Off
Modified Time: 828705
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
vtkITKArchetypeImageSeriesReader::ExecuteInformation: Archetype file /_DUMMY_DOES_NOT_EXIST__
does not exist.
Algorithm vtkITKArchetypeImageSeriesScalarReader(0x4a6be60) returned failure for request: vtkInformation (0x4a8c600)
Debug: Off
Modified Time: 829510
Reference Count: 1
Registered Events: (none)
Request: REQUEST_INFORMATION
ALGORITHM_AFTER_FORWARD: 1
FORWARD_DIRECTION: 0
ReadData: This is not a nrrd file
ReadData: Cannot read file as a volume of type DiffusionTensorVolume[fullName
/_DUMMY_DOES_NOT_EXIST__]
Number of files listed in the node = 0.
File reader says it was able to read 0 files.
File reader used the archetype file name of //_DUMMY_DOES_NOT_EXIST__ []
FileNotFoundError
ReadData: This is not a nrrd file
ReadData: Failed to instantiate a file reader
ReadData: Cannot read file as a volume of type Volume[fullName = /_DUMMY_DOES_NOT_EXIST__]
Number of files listed in the node = 0.
File reader says it was able to read 0 files.
File reader used the archetype file name of /_DUMMY_DOES_NOT_EXIST__ []
FileNotFoundError
Generic Warning: In /home/kitware/Dashboards/Package/Slicer-
481/Libs/MRML/Core/vtkDataFileFormatHelper.cxx, line 237
vtkDataFileFormatHelper::GetFileExtensionFromFormatString: please update deprecated extension-only
format specifier to 'File format name (.ext)' format! Current format string: .nrrd
All tasks are done!
Hello @brhoom, I saw your post here and thought you might be familiar with cropping volume in Python. I am wondering if you know of a way to crop a volume using ROI in 3D slicer in Python, modify the cropped volume and put it back into the original volume (at the same position). Essentially, what I am trying to do is like this
Drag some ROI in 3D slicer
croppedVolumeNode = some_internal_cropping_function(volumeNode, roiNode)
modify the cropped volume
volumeNode.update(croppedVolumeNode) # to put it back to the original location
Sorry for the late reply. I do the cropping using only one point, the center of the cropping. So to get the croppingBounds in my code above from a defined point:
spacing = inputVolume.GetSpacing()
imgData = inputVolume.GetImageData()
dimensions = imgData.GetDimensions()
size = [lengthX,lengthY,lengthZ] # defined volume dimensions
# Calculate lower and upper cropping bounds
lower = [0,0,0]
for i in range(0,3):
lower[i] = point[i] - int((size[i]/spacing[i])/2)
upper = [0,0,0]
for i in range(0,3):
upper[i] = dimensions[i] - (point[i]+int((size[i]/spacing[i])/2))
croppingBounds = [lower,upper]
I think in your case, I will do the following
create a copy of the original volume.
do the cropping
process the cropped volume.
convert the copied volume and the cropped volume to np arrays and replace the voxels in the first volume with the cropped one.
Probably there is a better way. I am not the Slicer expert here. Also, I think it is not a good idea to ask different question in different post. I would open a new post with the new question to keep the forum organized.
