I'm trying to get into Extension programming in 3DSlicer using Python. There is a tutorial online. Unfortunately there is a problem with the third example script "HelloSharpen". I did the exact same thing they did but I get this error:
Traceback (most recent call last):
File "C:/Users/johan/Desktop/HelloPythonSlicer4/helloPython/code/HelloSharpen.py", line 105, in onApply
laplacian.SetInput(inputVolume.GetImageData())
AttributeError: 'vtkImagingGeneralPython.vtkImageLaplacian' object has no attribute 'SetInput'
I solved this by changing laplacian.SetInput(inputVolume.GetImageData()) to laplacian.SetInputData(inputVolume.GetImageData()) because I read that they changed this in the newer versions of VTK.
However when I try to run this a new error comes up:
Traceback (most recent call last):
File "C:/Users/johan/Desktop/HelloPythonSlicer4/helloPython/code/HelloSharpen.py", line 107, in onApply
laplacian.GetOutput().Update()
AttributeError: 'vtkCommonDataModelPython.vtkImageData' object has no attribute 'Update'
It seems that laplacian.GetOutput().Update() is causing problems so
I tried to find something on the Internet if they also changed this in the newer versions of VTK but I couldn't find anything. I tried to change this into "UpdateData" but this doesn't work.
Do you know if they also changed this and if yes, do you know what I should replace this with?
Here is the full code for "HelloSharpen":
from __main__ import vtk, qt, ctk, slicer
#
# HelloSharpen
#
class HelloSharpen:
def __init__(self, parent):
parent.title = "Hello Python Part D - Sharpen"
parent.categories = ["Examples"]
parent.dependencies = []
parent.contributors = ["Jean-Christophe Fillion-Robin (Kitware)",
"Steve Pieper (Isomics)",
"Sonia Pujol (BWH)"] # replace with "Firstname Lastname (Org)"
parent.helpText = """
Example of scripted loadable extension for the HelloSharpen tutorial.
"""
parent.acknowledgementText = """
This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.,
Steve Pieper, Isomics, Inc., and Sonia Pujol, Brigham and Women's Hospital and was
partially funded by NIH grant 3P41RR013218-12S1 (NAC) and is part of the National Alliance
for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the
NIH Roadmap for Medical Research, Grant U54 EB005149.""" # replace with organization, grant and thanks.
self.parent = parent
#
# qHelloPythonWidget
#
class HelloSharpenWidget:
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def setup(self):
# Collapsible button
self.laplaceCollapsibleButton = ctk.ctkCollapsibleButton()
self.laplaceCollapsibleButton.text = "Sharpen Operator"
self.layout.addWidget(self.laplaceCollapsibleButton)
# Layout within the laplace collapsible button
self.laplaceFormLayout = qt.QFormLayout(self.laplaceCollapsibleButton)
#
# the volume selectors
#
self.inputFrame = qt.QFrame(self.laplaceCollapsibleButton)
self.inputFrame.setLayout(qt.QHBoxLayout())
self.laplaceFormLayout.addWidget(self.inputFrame)
self.inputSelector = qt.QLabel("Input Volume: ", self.inputFrame)
self.inputFrame.layout().addWidget(self.inputSelector)
self.inputSelector = slicer.qMRMLNodeComboBox(self.inputFrame)
self.inputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.setMRMLScene( slicer.mrmlScene )
self.inputFrame.layout().addWidget(self.inputSelector)
self.outputFrame = qt.QFrame(self.laplaceCollapsibleButton)
self.outputFrame.setLayout(qt.QHBoxLayout())
self.laplaceFormLayout.addWidget(self.outputFrame)
self.outputSelector = qt.QLabel("Output Volume: ", self.outputFrame)
self.outputFrame.layout().addWidget(self.outputSelector)
self.outputSelector = slicer.qMRMLNodeComboBox(self.outputFrame)
self.outputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.outputSelector.setMRMLScene( slicer.mrmlScene )
self.outputFrame.layout().addWidget(self.outputSelector)
self.sharpen = qt.QCheckBox("Sharpen", self.laplaceCollapsibleButton)
self.sharpen.toolTip = "When checked, subtract laplacian from input volume"
self.sharpen.checked = True
self.laplaceFormLayout.addWidget(self.sharpen)
# Apply button
laplaceButton = qt.QPushButton("Apply")
laplaceButton.toolTip = "Run the Laplace or Sharpen Operator."
self.laplaceFormLayout.addWidget(laplaceButton)
laplaceButton.connect('clicked(bool)', self.onApply)
# Add vertical spacer
self.layout.addStretch(1)
# Set local var as instance attribute
self.laplaceButton = laplaceButton
def onApply(self):
inputVolume = self.inputSelector.currentNode()
outputVolume = self.outputSelector.currentNode()
if not (inputVolume and outputVolume):
qt.QMessageBox.critical(
slicer.util.mainWindow(),
'Sharpen', 'Input and output volumes are required for Laplacian')
return
# run the filter
laplacian = vtk.vtkImageLaplacian()
laplacian.SetInputData(inputVolume.GetImageData())
laplacian.SetDimensionality(3)
laplacian.GetOutput().Update()
ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputVolume.SetIJKToRASMatrix(ijkToRAS)
outputVolume.SetAndObserveImageData(laplacian.GetOutput())
# optionally subtract laplacian from original image
if self.sharpen.checked:
parameters = {}
parameters['inputVolume1'] = inputVolume.GetID()
parameters['inputVolume2'] = outputVolume.GetID()
parameters['outputVolume'] = outputVolume.GetID()
slicer.cli.run( slicer.modules.subtractscalarvolumes, None, parameters, wait_for_completion=True )
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
selectionNode.SetReferenceActiveVolumeID(outputVolume.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection(0)
