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SegmentEditorEffect.py
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SegmentEditorEffect.py
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import os
import vtk, qt, slicer
import logging
from SegmentEditorEffects import *
class SegmentEditorEffect(AbstractScriptedSegmentEditorEffect):
"""This effect uses markup fiducials to segment the input volume"""
def __init__(self, scriptedEffect):
scriptedEffect.name = 'Draw tube'
scriptedEffect.perSegment = True # this effect operates on a single selected segment
AbstractScriptedSegmentEditorEffect.__init__(self, scriptedEffect)
self.logic = DrawTubeLogic(scriptedEffect)
# Effect-specific members
self.segmentMarkupNode = None
self.segmentMarkupNodeObservers = []
self.segmentEditorNode = None
self.segmentEditorNodeObserver = None
self.segmentModel = None
self.observedSegmentation = None
self.segmentObserver = None
self.buttonToInterpolationTypeMap = {}
def clone(self):
# It should not be necessary to modify this method
import qSlicerSegmentationsEditorEffectsPythonQt as effects
clonedEffect = effects.qSlicerSegmentEditorScriptedEffect(None)
clonedEffect.setPythonSource(__file__.replace('\\','/'))
return clonedEffect
def icon(self):
# It should not be necessary to modify this method
iconPath = os.path.join(os.path.dirname(__file__), 'SegmentEditorEffect.png')
if os.path.exists(iconPath):
return qt.QIcon(iconPath)
return qt.QIcon()
def helpText(self):
return """<html>Use markup fiducials to create a tube<br>. The tube is generated to connect the placed points.
</html>"""
def setupOptionsFrame(self):
self.interpolationRadioButtons = []
# Fiducial Placement widget
self.fiducialPlacementToggle = slicer.qSlicerMarkupsPlaceWidget()
self.fiducialPlacementToggle.setMRMLScene(slicer.mrmlScene)
self.fiducialPlacementToggle.placeMultipleMarkups = self.fiducialPlacementToggle.ForcePlaceMultipleMarkups
self.fiducialPlacementToggle.buttonsVisible = False
self.fiducialPlacementToggle.show()
self.fiducialPlacementToggle.placeButton().show()
self.fiducialPlacementToggle.deleteButton().show()
# Edit surface button
self.editButton = qt.QPushButton("Edit")
self.editButton.objectName = self.__class__.__name__ + 'Edit'
self.editButton.setToolTip("Edit the previously placed group of fiducials.")
fiducialActionLayout = qt.QHBoxLayout()
fiducialActionLayout.addWidget(self.fiducialPlacementToggle)
fiducialActionLayout.addWidget(self.editButton)
self.scriptedEffect.addLabeledOptionsWidget("Fiducial Placement: ", fiducialActionLayout)
# Radius spinbox
self.radiusSpinBox = slicer.qMRMLSpinBox()
self.radiusSpinBox.value = self.logic.radius
self.radiusSpinBox.quantity = 'length'
self.radiusSpinBox.unitAwareProperties = slicer.qMRMLSpinBox.MaximumValue | slicer.qMRMLSpinBox.Precision | slicer.qMRMLSpinBox.Prefix | slicer.qMRMLSpinBox.Suffix
self.scriptedEffect.addLabeledOptionsWidget("Radius: ", self.radiusSpinBox)
# Interpolation buttons
self.piecewiseLinearButton = qt.QRadioButton("Piecewise linear")
self.interpolationRadioButtons.append(self.piecewiseLinearButton)
self.buttonToInterpolationTypeMap[self.piecewiseLinearButton] = "LINEAR"
self.cardinalSplineButton = qt.QRadioButton("Cardinal spline")
self.interpolationRadioButtons.append(self.cardinalSplineButton)
self.buttonToInterpolationTypeMap[self.cardinalSplineButton] = "CARDINAL_SPLINE"
self.kochanekSplineButton = qt.QRadioButton("Kochanek spline")
self.interpolationRadioButtons.append(self.kochanekSplineButton)
self.buttonToInterpolationTypeMap[self.kochanekSplineButton] = "KOCHANEK_SPLINE"
self.globalPolynomialButton = qt.QRadioButton("Global polynomial")
self.interpolationRadioButtons.append(self.globalPolynomialButton)
self.buttonToInterpolationTypeMap[self.globalPolynomialButton] = "GLOBAL_POLYNOMIAL"
self.movingPolynomialButton = qt.QRadioButton("Moving polynomial")
self.interpolationRadioButtons.append(self.movingPolynomialButton)
self.buttonToInterpolationTypeMap[self.movingPolynomialButton] = "MOVING_POLYNOMIAL"
# Segments per point spinbox
self.numberOfLineSegmentsSpinBox = qt.QSpinBox()
self.numberOfLineSegmentsSpinBox.value = 15
# To keep GUI simple, we do not show numberOfLineSegmentsSpinBox.
# Default value should work for most cases and modules can programmatically change this value, if needed.
# If user feedback confirms that this parameter must be exposed then the next line can be uncommented.
# self.scriptedEffect.addLabeledOptionsWidget("Segments between points: ", self.numberOfLineSegmentsSpinBox)
# Interpolation buttons layout
interpolationLayout = qt.QGridLayout()
interpolationLayout.addWidget(self.piecewiseLinearButton, 0, 0)
interpolationLayout.addWidget(self.cardinalSplineButton, 1, 0)
interpolationLayout.addWidget(self.kochanekSplineButton, 0, 1)
interpolationLayout.addWidget(self.globalPolynomialButton, 1, 1)
interpolationLayout.addWidget(self.movingPolynomialButton, 0, 2)
self.scriptedEffect.addLabeledOptionsWidget("Interpolation:", interpolationLayout)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Generate tube from markup fiducials.")
self.scriptedEffect.addOptionsWidget(self.applyButton)
# Cancel button
self.cancelButton = qt.QPushButton("Cancel")
self.cancelButton.objectName = self.__class__.__name__ + 'Cancel'
self.cancelButton.setToolTip("Clear fiducials and remove from scene.")
# Finish action buttons
finishAction = qt.QHBoxLayout()
finishAction.addWidget(self.cancelButton)
finishAction.addWidget(self.applyButton)
self.scriptedEffect.addOptionsWidget(finishAction)
# Connections
for button in self.interpolationRadioButtons:
button.connect('toggled(bool)',
lambda toggle, widget=self.buttonToInterpolationTypeMap[button]: self.onInterpolationSelectionChanged(widget, toggle))
self.applyButton.connect('clicked()', self.onApply)
self.cancelButton.connect('clicked()', self.onCancel)
self.editButton.connect('clicked()', self.onEdit)
self.fiducialPlacementToggle.placeButton().clicked.connect(self.onFiducialPlacementToggleChanged)
self.radiusSpinBox.connect('valueChanged(double)', self.onRadiusChanged)
self.numberOfLineSegmentsSpinBox.connect('valueChanged(int)', self.onNumberOfLineSegmentsChanged)
def activate(self):
self.scriptedEffect.showEffectCursorInSliceView = False
# Create empty markup fiducial node
if not self.segmentMarkupNode:
self.createNewMarkupNode()
self.fiducialPlacementToggle.setCurrentNode(self.segmentMarkupNode)
self.setAndObserveSegmentMarkupNode(self.segmentMarkupNode)
self.fiducialPlacementToggle.setPlaceModeEnabled(False)
self.setAndObserveSegmentEditorNode(self.scriptedEffect.parameterSetNode())
self.observeSegmentation(True)
self.updateGUIFromMRML()
def deactivate(self):
self.reset()
self.observeSegmentation(False)
self.setAndObserveSegmentEditorNode(None)
def createCursor(self, widget):
# Turn off effect-specific cursor for this effect
return slicer.util.mainWindow().cursor
def setMRMLDefaults(self):
self.scriptedEffect.setParameterDefault("Interpolation", "CARDINAL_SPLINE")
self.scriptedEffect.setParameterDefault("NumberOfLineSegmentsBetweenControlPoints", 15)
def updateGUIFromMRML(self):
if self.segmentMarkupNode:
self.cancelButton.setEnabled(self.segmentMarkupNode.GetNumberOfFiducials() is not 0)
self.applyButton.setEnabled(self.segmentMarkupNode.GetNumberOfFiducials() >= 3)
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
if segmentID and segmentationNode:
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
self.editButton.setVisible(segment.HasTag("DrawTubeEffectMarkupPositions"))
interpolationName = self.scriptedEffect.parameter("Interpolation")
interpolationButton = list(self.buttonToInterpolationTypeMap.keys())[list(self.buttonToInterpolationTypeMap.values()).index(interpolationName)]
interpolationButton.setChecked(True)
self.numberOfLineSegmentsSpinBox.value = self.scriptedEffect.integerParameter("NumberOfLineSegmentsBetweenControlPoints")
#
# Effect specific methods (the above ones are the API methods to override)
#
def onInterpolationSelectionChanged(self, interpolationName, toggle):
if not toggle:
return
self.scriptedEffect.setParameter("Interpolation", interpolationName)
self.updateModelFromSegmentMarkupNode()
def onFiducialPlacementToggleChanged(self):
if self.fiducialPlacementToggle.placeButton().isChecked():
# Create empty model node
if self.segmentModel is None:
self.segmentModel = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelNode")
self.segmentModel.SetName("SegmentEditorDrawTubeModel")
# Create empty markup fiducial node
if self.segmentMarkupNode is None:
self.createNewMarkupNode()
self.fiducialPlacementToggle.setCurrentNode(self.segmentMarkupNode)
def onRadiusChanged(self, radius):
self.logic.radius = radius
self.updateModelFromSegmentMarkupNode()
def onNumberOfLineSegmentsChanged(self, numberOfLineSegments):
self.scriptedEffect.setParameter("NumberOfLineSegmentsBetweenControlPoints", numberOfLineSegments)
self.updateModelFromSegmentMarkupNode()
def onSegmentModified(self, caller, event):
if not self.editButton.isEnabled() and self.segmentMarkupNode.GetNumberOfFiducials() is not 0:
self.reset()
self.createNewMarkupNode()
self.fiducialPlacementToggle.setCurrentNode(self.segmentMarkupNode)
else:
self.updateGUIFromMRML()
if self.segmentModel:
# Get color of edited segment
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
displayNode = segmentationNode.GetDisplayNode()
if displayNode is None:
logging.error("preview: Invalid segmentation display node!")
color = [0.5, 0.5, 0.5]
if self.segmentModel.GetDisplayNode():
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
r, g, b = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
if (r,g,b) != self.segmentModel.GetDisplayNode().GetColor():
self.segmentModel.GetDisplayNode().SetColor(r, g, b) # Edited segment color
def onCancel(self):
self.reset()
self.createNewMarkupNode()
self.fiducialPlacementToggle.setCurrentNode(self.segmentMarkupNode)
def onEdit(self):
# Create empty model node
if self.segmentModel is None:
self.segmentModel = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(self.segmentModel)
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
fPosStr = vtk.mutable("")
segment.GetTag("DrawTubeEffectMarkupPositions", fPosStr)
# convert from space-separated list o fnumbers to 1D array
import numpy
fPos = numpy.fromstring(str(fPosStr), sep=' ')
# convert from 1D array (N*3) to 2D array (N,3)
fPosNum = int(len(fPos)/3)
fPos = fPos.reshape((fPosNum, 3))
for i in range(fPosNum):
self.segmentMarkupNode.AddFiducialFromArray(fPos[i])
self.editButton.setEnabled(False)
self.updateModelFromSegmentMarkupNode()
def reset(self):
if self.fiducialPlacementToggle.placeModeEnabled:
self.fiducialPlacementToggle.setPlaceModeEnabled(False)
if not self.editButton.isEnabled():
self.editButton.setEnabled(True)
if self.segmentModel:
slicer.mrmlScene.RemoveNode(self.segmentModel)
self.segmentModel = None
if self.segmentMarkupNode:
slicer.mrmlScene.RemoveNode(self.segmentMarkupNode)
self.setAndObserveSegmentMarkupNode(None)
def onApply(self):
# Allow users revert to this state by clicking Undo
self.scriptedEffect.saveStateForUndo()
# This can be a long operation - indicate it to the user
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
self.observeSegmentation(False)
self.logic.cutSurfaceWithModel(self.segmentMarkupNode, self.segmentModel)
self.reset()
self.createNewMarkupNode()
self.fiducialPlacementToggle.setCurrentNode(self.segmentMarkupNode)
self.observeSegmentation(True)
qt.QApplication.restoreOverrideCursor()
def observeSegmentation(self, observationEnabled):
import vtkSegmentationCore
if self.scriptedEffect.parameterSetNode().GetSegmentationNode():
segmentation = self.scriptedEffect.parameterSetNode().GetSegmentationNode().GetSegmentation()
else:
segmentation = None
# Remove old observer
if self.observedSegmentation:
self.observedSegmentation.RemoveObserver(self.segmentObserver)
self.segmentObserver = None
# Add new observer
if observationEnabled and segmentation is not None:
self.observedSegmentation = segmentation
self.segmentObserver = self.observedSegmentation.AddObserver(vtkSegmentationCore.vtkSegmentation.SegmentModified,
self.onSegmentModified)
def createNewMarkupNode(self):
# Create empty markup fiducial node
if self.segmentMarkupNode is None:
displayNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsDisplayNode")
displayNode.SetTextScale(0)
self.segmentMarkupNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLMarkupsFiducialNode")
self.segmentMarkupNode.SetName('T')
self.segmentMarkupNode.SetAndObserveDisplayNodeID(displayNode.GetID())
self.setAndObserveSegmentMarkupNode(self.segmentMarkupNode)
self.updateGUIFromMRML()
def setAndObserveSegmentMarkupNode(self, segmentMarkupNode):
if segmentMarkupNode == self.segmentMarkupNode and self.segmentMarkupNodeObservers:
# no change and node is already observed
return
# Remove observer to old parameter node
if self.segmentMarkupNode and self.segmentMarkupNodeObservers:
for observer in self.segmentMarkupNodeObservers:
self.segmentMarkupNode.RemoveObserver(observer)
self.segmentMarkupNodeObservers = []
# Set and observe new parameter node
self.segmentMarkupNode = segmentMarkupNode
if self.segmentMarkupNode:
if (slicer.app.majorVersion >= 5) or (slicer.app.majorVersion >= 4 and slicer.app.minorVersion >= 11):
eventIds = [ vtk.vtkCommand.ModifiedEvent,
slicer.vtkMRMLMarkupsNode.PointModifiedEvent,
slicer.vtkMRMLMarkupsNode.PointAddedEvent,
slicer.vtkMRMLMarkupsNode.PointRemovedEvent ]
else:
eventIds = [ vtk.vtkCommand.ModifiedEvent ]
for eventId in eventIds:
self.segmentMarkupNodeObservers.append(self.segmentMarkupNode.AddObserver(eventId, self.onSegmentMarkupNodeModified))
# Update GUI
self.updateModelFromSegmentMarkupNode()
def onSegmentMarkupNodeModified(self, observer, eventid):
self.updateModelFromSegmentMarkupNode()
self.updateGUIFromMRML()
def setAndObserveSegmentEditorNode(self, segmentEditorNode):
if segmentEditorNode == self.segmentEditorNode and self.segmentEditorNodeObserver:
# no change and node is already observed
return
# Remove observer to old parameter node
if self.segmentEditorNode and self.segmentEditorNodeObserver:
self.segmentEditorNode.RemoveObserver(self.segmentEditorNodeObserver)
self.segmentEditorNodeObserver = None
# Set and observe new parameter node
self.segmentEditorNode = segmentEditorNode
if self.segmentEditorNode:
self.segmentEditorNodeObserver = self.segmentEditorNode.AddObserver(vtk.vtkCommand.ModifiedEvent,
self.onSegmentEditorNodeModified)
def onSegmentEditorNodeModified(self, observer, eventid):
# Get color of edited segment
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
if segmentID and self.segmentModel:
if self.segmentModel.GetDisplayNode():
r, g, b = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
if (r, g, b) != self.segmentModel.GetDisplayNode().GetColor():
self.segmentModel.GetDisplayNode().SetColor(r, g, b) # Edited segment color
self.updateGUIFromMRML()
def updateModelFromSegmentMarkupNode(self):
if not self.segmentMarkupNode or not self.segmentModel:
return
self.logic.updateModelFromMarkup(self.segmentMarkupNode, self.segmentModel)
def interactionNodeModified(self, interactionNode):
# Override default behavior: keep the effect active if markup placement mode is activated
pass
class DrawTubeLogic(object):
def __init__(self, scriptedEffect):
self.scriptedEffect = scriptedEffect
self.radius = 1.0
self.curveGenerator = slicer.vtkCurveGenerator()
def updateModelFromMarkup(self, inputMarkup, outputModel):
"""
Update model to enclose all points in the input markup list
"""
# Create default model display node if does not exist yet
if not outputModel.GetDisplayNode():
modelDisplayNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLModelDisplayNode")
# Get color of edited segment
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
r, g, b = segmentationNode.GetSegmentation().GetSegment(segmentID).GetColor()
modelDisplayNode.SetColor(r, g, b) # Edited segment color
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(2)
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
outputModel.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
outputModel.GetDisplayNode().SliceIntersectionVisibilityOn()
interpolationName = self.scriptedEffect.parameter("Interpolation")
polynomialFitType = slicer.vtkMRMLMarkupsToModelNode.MovingLeastSquares
if interpolationName == "LINEAR":
interpolationType = slicer.vtkMRMLMarkupsToModelNode.Linear
elif interpolationName == "CARDINAL_SPLINE":
interpolationType = slicer.vtkMRMLMarkupsToModelNode.CardinalSpline
elif interpolationName == "KOCHANEK_SPLINE":
interpolationType = slicer.vtkMRMLMarkupsToModelNode.KochanekSpline
elif interpolationName == "GLOBAL_POLYNOMIAL":
interpolationType = slicer.vtkMRMLMarkupsToModelNode.Polynomial
polynomialFitType = slicer.vtkMRMLMarkupsToModelNode.GlobalLeastSquares
elif interpolationName == "MOVING_POLYNOMIAL":
interpolationType = slicer.vtkMRMLMarkupsToModelNode.Polynomial
polynomialFitType = slicer.vtkMRMLMarkupsToModelNode.MovingLeastSquares
NumberOfLineSegmentsBetweenControlPoints = self.scriptedEffect.integerParameter("NumberOfLineSegmentsBetweenControlPoints")
markupsToModel = slicer.modules.markupstomodel.logic()
# Create tube from points
markupsToModel.UpdateOutputCurveModel( inputMarkup, outputModel,
interpolationType, False, self.radius, 8, NumberOfLineSegmentsBetweenControlPoints, True, 3,
slicer.vtkMRMLMarkupsToModelNode.RawIndices, self.curveGenerator,
polynomialFitType )
def cutSurfaceWithModel(self, segmentMarkupNode, segmentModel):
import vtkSegmentationCore
if not segmentMarkupNode:
raise AttributeError("{}: segment markup node not set.".format(self.__class__.__name__))
if not segmentModel:
raise AttributeError("{}: segment model not set.".format(self.__class__.__name__))
if segmentMarkupNode and segmentModel.GetPolyData().GetNumberOfCells() > 0:
segmentationNode = self.scriptedEffect.parameterSetNode().GetSegmentationNode()
if not segmentationNode:
raise AttributeError("{}: Segmentation node not set.".format(self.__class__.__name__))
modifierLabelmap = self.scriptedEffect.defaultModifierLabelmap()
if not modifierLabelmap:
raise AttributeError("{}: ModifierLabelmap not set. This can happen for various reasons:\n"
"No master volume set for segmentation,\n"
"No existing segments for segmentation, or\n"
"No referenceImageGeometry is specified in the segmentation".format(self.__class__.__name__))
WorldToModifierLabelmapIjkTransform = vtk.vtkTransform()
WorldToModifierLabelmapIjkTransformer = vtk.vtkTransformPolyDataFilter()
WorldToModifierLabelmapIjkTransformer.SetTransform(WorldToModifierLabelmapIjkTransform)
WorldToModifierLabelmapIjkTransformer.SetInputConnection(segmentModel.GetPolyDataConnection())
segmentationToSegmentationIjkTransformMatrix = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(segmentationToSegmentationIjkTransformMatrix)
segmentationToSegmentationIjkTransformMatrix.Invert()
WorldToModifierLabelmapIjkTransform.Concatenate(segmentationToSegmentationIjkTransformMatrix)
worldToSegmentationTransformMatrix = vtk.vtkMatrix4x4()
slicer.vtkMRMLTransformNode.GetMatrixTransformBetweenNodes(None, segmentationNode.GetParentTransformNode(),
worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransform.Concatenate(worldToSegmentationTransformMatrix)
WorldToModifierLabelmapIjkTransformer.Update()
polyToStencil = vtk.vtkPolyDataToImageStencil()
polyToStencil.SetOutputSpacing(1.0, 1.0, 1.0)
polyToStencil.SetInputConnection(WorldToModifierLabelmapIjkTransformer.GetOutputPort())
boundsIjk = WorldToModifierLabelmapIjkTransformer.GetOutput().GetBounds()
modifierLabelmapExtent = self.scriptedEffect.modifierLabelmap().GetExtent()
polyToStencil.SetOutputWholeExtent(modifierLabelmapExtent[0], modifierLabelmapExtent[1],
modifierLabelmapExtent[2], modifierLabelmapExtent[3],
int(round(boundsIjk[4])), int(round(boundsIjk[5])))
polyToStencil.Update()
stencilData = polyToStencil.GetOutput()
stencilExtent = [0, -1, 0, -1, 0, -1]
stencilData.SetExtent(stencilExtent)
stencilToImage = vtk.vtkImageStencilToImage()
stencilToImage.SetInputConnection(polyToStencil.GetOutputPort())
stencilToImage.SetInsideValue(1.0)
stencilToImage.SetOutsideValue(0.0)
stencilToImage.SetOutputScalarType(modifierLabelmap.GetScalarType())
stencilPositioner = vtk.vtkImageChangeInformation()
stencilPositioner.SetInputConnection(stencilToImage.GetOutputPort())
stencilPositioner.SetOutputSpacing(modifierLabelmap.GetSpacing())
stencilPositioner.SetOutputOrigin(modifierLabelmap.GetOrigin())
stencilPositioner.Update()
orientedStencilPositionerOutput = vtkSegmentationCore.vtkOrientedImageData()
orientedStencilPositionerOutput.ShallowCopy(stencilToImage.GetOutput())
imageToWorld = vtk.vtkMatrix4x4()
modifierLabelmap.GetImageToWorldMatrix(imageToWorld)
orientedStencilPositionerOutput.SetImageToWorldMatrix(imageToWorld)
vtkSegmentationCore.vtkOrientedImageDataResample.ModifyImage(
modifierLabelmap, orientedStencilPositionerOutput,
vtkSegmentationCore.vtkOrientedImageDataResample.OPERATION_MAXIMUM)
self.scriptedEffect.modifySelectedSegmentByLabelmap(
modifierLabelmap, slicer.qSlicerSegmentEditorAbstractEffect.ModificationModeSet )
# get fiducial positions as space-separated list
import numpy
n = segmentMarkupNode.GetNumberOfFiducials()
fPos = []
for i in range(n):
coord = [0.0, 0.0, 0.0]
segmentMarkupNode.GetNthFiducialPosition(i, coord)
fPos.extend(coord)
fPosString = ' '.join(map(str, fPos))
segmentID = self.scriptedEffect.parameterSetNode().GetSelectedSegmentID()
segment = segmentationNode.GetSegmentation().GetSegment(segmentID)
segment.SetTag("DrawTubeEffectMarkupPositions", fPosString)