def __init__(self, sliceWidget):
super(LevelTracingEffectTool, self).__init__(sliceWidget)
# create a logic instance to do the non-gui work
self.logic = LevelTracingEffectLogic(self.sliceWidget.sliceLogic())
# instance variables
self.actionState = ""
# initialization
self.xyPoints = vtk.vtkPoints()
self.rasPoints = vtk.vtkPoints()
self.polyData = vtk.vtkPolyData()
self.tracingFilter = vtkITK.vtkITKLevelTracingImageFilter()
self.ijkToXY = vtk.vtkGeneralTransform()
self.mapper = vtk.vtkPolyDataMapper2D()
self.actor = vtk.vtkActor2D()
property_ = self.actor.GetProperty()
property_.SetColor(107 / 255.0, 190 / 255.0, 99 / 255.0)
property_.SetLineWidth(1)
self.mapper.SetInput(self.polyData)
self.actor.SetMapper(self.mapper)
property_ = self.actor.GetProperty()
property_.SetColor(1, 1, 0)
property_.SetLineWidth(1)
self.renderer.AddActor2D(self.actor)
self.actors.append(self.actor)
def __init__(self, sliceWidget):
super(LevelTracingEffectTool, self).__init__(sliceWidget)
# create a logic instance to do the non-gui work
self.logic = LevelTracingEffectLogic(self.sliceWidget.sliceLogic())
# instance variables
self.actionState = ''
# initialization
self.xyPoints = vtk.vtkPoints()
self.rasPoints = vtk.vtkPoints()
self.polyData = vtk.vtkPolyData()
self.tracingFilter = vtkITK.vtkITKLevelTracingImageFilter()
self.ijkToXY = vtk.vtkGeneralTransform()
self.mapper = vtk.vtkPolyDataMapper2D()
self.actor = vtk.vtkActor2D()
property_ = self.actor.GetProperty()
property_.SetColor(107 / 255., 190 / 255., 99 / 255.)
property_.SetLineWidth(1)
if vtk.VTK_MAJOR_VERSION <= 5:
self.mapper.SetInput(self.polyData)
else:
self.mapper.SetInputData(self.polyData)
self.actor.SetMapper(self.mapper)
property_ = self.actor.GetProperty()
property_.SetColor(1, 1, 0)
property_.SetLineWidth(1)
self.renderer.AddActor2D(self.actor)
self.actors.append(self.actor)
def onReferencePointMarkupPlace(self, fieldIndex, enable):
# Get markup label
field = self.measurementPreset.inputFields[fieldIndex]
# Get valve model from selected valve node
valveId = field[FIELD_VALVE_ID]
if not valveId in self.inputValveModels.keys():
logging.error(
'onReferencePointMarkupPlace failed: no {0} valve node is selected'
.format(valveId))
qt.QTimer.singleShot(
0, self.pointFieldMarkupsNode[fieldIndex].RemoveAllMarkups)
return
valveModel = self.inputValveModels[valveId]
label = field[FIELD_NAME]
if enable:
# Point placement activated - remove old markup
valveModel.removeAnnulusMarkupLabel(label)
self.pointFieldMarkupsNode[fieldIndex].RemoveAllMarkups()
else:
# Point placement completed add new markup on the contour
if self.pointFieldMarkupsNode[fieldIndex].GetNumberOfMarkups(
) == 0:
# duplicate update event
return
# Get point from temporary markup node
pointPositionWorld = [0, 0, 0]
self.pointFieldMarkupsNode[
fieldIndex].GetNthControlPointPositionWorld(
0, pointPositionWorld)
qt.QTimer.singleShot(
0, self.pointFieldMarkupsNode[fieldIndex].RemoveAllMarkups)
# Add label on closest point on contour
worldToProbeTransform = vtk.vtkGeneralTransform()
valveModel.getProbeToRasTransformNode().GetTransformFromWorld(
worldToProbeTransform)
pointPositionAnnulus = worldToProbeTransform.TransformDoublePoint(
pointPositionWorld[0:3])
if field[FIELD_ON_ANNULUS_CONTOUR] is True:
[closestPointOnAnnulusCurve,
_] = valveModel.annulusContourCurve.getClosestPoint(
pointPositionAnnulus)
pointPosition = closestPointOnAnnulusCurve
else:
# NB: no snapping or restriction
pointPosition = pointPositionAnnulus
valveModel.setAnnulusMarkupLabel(label, pointPosition)
self.measurementPreset.onInputFieldChanged(
field[FIELD_ID],
self.inputValveModels,
self.inputFieldValues,
computeDependentValues=True)
def transformPolyData(self, transformNode):
t = vtk.vtkGeneralTransform()
transformNode.GetTransformToWorld(t)
self.transformPolyDataFilter.SetTransform(t)
self.transformPolyDataFilter.SetInputData(self.modelNode.GetPolyData())
self.transformPolyDataFilter.Update()
self.transformedModel.SetAndObservePolyData(self.transformPolyDataFilter.GetOutput())
def run(self, referenceSequenceNode, inputNode, transformSequenceNode,
outputSequenceNode):
"""
Run the actual algorithm
"""
if outputSequenceNode:
outputSequenceNode.RemoveAllDataNodes()
numOfImageNodes = referenceSequenceNode.GetNumberOfDataNodes()
for i in xrange(numOfImageNodes):
referenceNode = referenceSequenceNode.GetNthDataNode(i)
referenceNodeIndexValue = referenceSequenceNode.GetNthIndexValue(i)
dimensions = [1, 1, 1]
referenceNode.GetImageData().GetDimensions(dimensions)
transformNode = transformSequenceNode.GetNthDataNode(i)
inputIJK2RASMatrix = vtk.vtkMatrix4x4()
inputNode.GetIJKToRASMatrix(inputIJK2RASMatrix)
referenceRAS2IJKMatrix = vtk.vtkMatrix4x4()
referenceNode.GetRASToIJKMatrix(referenceRAS2IJKMatrix)
inputRAS2RASMatrix = transformNode.GetTransformToParent()
resampleTransform = vtk.vtkGeneralTransform()
resampleTransform.Identity()
resampleTransform.PostMultiply()
resampleTransform.Concatenate(inputIJK2RASMatrix)
resampleTransform.Concatenate(inputRAS2RASMatrix)
resampleTransform.Concatenate(referenceRAS2IJKMatrix)
resampleTransform.Inverse()
resampler = vtk.vtkImageReslice()
resampler.SetInput(inputNode.GetImageData())
resampler.SetOutputOrigin(0, 0, 0)
resampler.SetOutputSpacing(1, 1, 1)
resampler.SetOutputExtent(0, dimensions[0], 0, dimensions[1], 0,
dimensions[2])
resampler.SetResliceTransform(resampleTransform)
resampler.Update()
outputNode = slicer.vtkMRMLScalarVolumeNode()
outputNode.CopyOrientation(referenceNode)
outputNode.SetAndObserveImageData(resampler.GetOutput())
outputSequenceNode.SetDataNodeAtValue(outputNode,
referenceNodeIndexValue)
return True
def run(self,referenceSequenceNode, inputNode, transformSequenceNode, outputSequenceNode):
"""
Run the actual algorithm
"""
if outputSequenceNode:
outputSequenceNode.RemoveAllDataNodes()
numOfImageNodes = referenceSequenceNode.GetNumberOfDataNodes()
for i in xrange(numOfImageNodes):
referenceNode = referenceSequenceNode.GetNthDataNode(i)
referenceNodeIndexValue = referenceSequenceNode.GetNthIndexValue(i)
dimensions = [1,1,1]
referenceNode.GetImageData().GetDimensions(dimensions)
transformNode = transformSequenceNode.GetNthDataNode(i)
inputIJK2RASMatrix = vtk.vtkMatrix4x4()
inputNode.GetIJKToRASMatrix(inputIJK2RASMatrix)
referenceRAS2IJKMatrix = vtk.vtkMatrix4x4()
referenceNode.GetRASToIJKMatrix(referenceRAS2IJKMatrix)
inputRAS2RASMatrix = transformNode.GetTransformToParent()
resampleTransform = vtk.vtkGeneralTransform()
resampleTransform.Identity()
resampleTransform.PostMultiply()
resampleTransform.Concatenate(inputIJK2RASMatrix)
resampleTransform.Concatenate(inputRAS2RASMatrix)
resampleTransform.Concatenate(referenceRAS2IJKMatrix)
resampleTransform.Inverse()
resampler = vtk.vtkImageReslice()
resampler.SetInput(inputNode.GetImageData())
resampler.SetOutputOrigin(0,0,0)
resampler.SetOutputSpacing(1,1,1)
resampler.SetOutputExtent(0,dimensions[0],0,dimensions[1],0,dimensions[2])
resampler.SetResliceTransform(resampleTransform)
resampler.Update()
outputNode = slicer.vtkMRMLScalarVolumeNode()
outputNode.CopyOrientation(referenceNode)
outputNode.SetAndObserveImageData(resampler.GetOutput())
outputSequenceNode.SetDataNodeAtValue(outputNode, referenceNodeIndexValue)
return True
def updateViewpointCamera(self):
# no logging - it slows Slicer down a *lot*
# Need to set camera attributes according to the concatenated transform
toolCameraToRASTransform = vtk.vtkGeneralTransform()
self.transformNode.GetTransformToWorld(toolCameraToRASTransform)
cameraOriginInRASMm = self.computeCameraOriginInRASMm(toolCameraToRASTransform)
focalPointInRASMm = self.computeCameraFocalPointInRASMm(toolCameraToRASTransform)
upDirectionInRAS = self.computeCameraUpDirectionInRAS(toolCameraToRASTransform,cameraOriginInRASMm,focalPointInRASMm)
self.setCameraParameters(cameraOriginInRASMm,focalPointInRASMm,upDirectionInRAS)
# model visibility
if (self.modelPOVOffNode):
modelPOVOffDisplayNode = self.modelPOVOffNode.GetDisplayNode()
modelPOVOffDisplayNode.SetVisibility(False)
if (self.modelPOVOnNode):
modelPOVOnDisplayNode = self.modelPOVOnNode.GetDisplayNode()
modelPOVOnDisplayNode.SetVisibility(True)
def resliceThroughTransform(sourceNode, transform, referenceNode, targetNode):
"""
Fills the targetNode's vtkImageData with the source after
applying the transform. Uses spacing from referenceNode. Ignores any vtkMRMLTransforms.
sourceNode, referenceNode, targetNode: vtkMRMLScalarVolumeNodes
transform: vtkAbstractTransform
"""
#
# get the transform from RAS back to source pixel space
sourceRASToIJK = vtk.vtkMatrix4x4()
sourceNode.GetRASToIJKMatrix(sourceRASToIJK)
#
# get the transform from target image space to RAS
referenceIJKToRAS = vtk.vtkMatrix4x4()
targetNode.GetIJKToRASMatrix(referenceIJKToRAS)
#
# this is the ijkToRAS concatenated with the passed in (abstract)transform
resliceTransform = vtk.vtkGeneralTransform()
resliceTransform.Concatenate(sourceRASToIJK)
resliceTransform.Concatenate(transform)
resliceTransform.Concatenate(referenceIJKToRAS)
#
# use the matrix to extract the volume and convert it to an array
reslice = vtk.vtkImageReslice()
reslice.SetInterpolationModeToLinear()
reslice.InterpolateOn()
reslice.SetResliceTransform(resliceTransform)
if vtk.VTK_MAJOR_VERSION <= 5:
reslice.SetInput(sourceNode.GetImageData())
else:
reslice.SetInputConnection(sourceNode.GetImageDataConnection())
#
dimensions = referenceNode.GetImageData().GetDimensions()
reslice.SetOutputExtent(0, dimensions[0] - 1, 0, dimensions[1] - 1, 0,
dimensions[2] - 1)
reslice.SetOutputOrigin((0, 0, 0))
reslice.SetOutputSpacing((1, 1, 1))
#
reslice.UpdateWholeExtent()
targetNode.SetAndObserveImageData(reslice.GetOutput())
def resliceThroughTransform(self, sourceNode, transform, referenceNode, targetNode):
"""
Fills the targetNode's vtkImageData with the source after
applying the transform. Uses spacing from referenceNode. Ignores any vtkMRMLTransforms.
sourceNode, referenceNode, targetNode: vtkMRMLScalarVolumeNodes
transform: vtkAbstractTransform
"""
# get the transform from RAS back to source pixel space
sourceRASToIJK = vtk.vtkMatrix4x4()
sourceNode.GetRASToIJKMatrix(sourceRASToIJK)
# get the transform from target image space to RAS
referenceIJKToRAS = vtk.vtkMatrix4x4()
targetNode.GetIJKToRASMatrix(referenceIJKToRAS)
# this is the ijkToRAS concatenated with the passed in (abstract)transform
self.resliceTransform = vtk.vtkGeneralTransform()
self.resliceTransform.Concatenate(sourceRASToIJK)
self.resliceTransform.Concatenate(transform)
self.resliceTransform.Concatenate(referenceIJKToRAS)
# use the matrix to extract the volume and convert it to an array
self.reslice = vtk.vtkImageReslice()
self.reslice.SetInterpolationModeToLinear()
self.reslice.InterpolateOn()
self.reslice.SetResliceTransform(self.resliceTransform)
self.reslice.SetInput( sourceNode.GetImageData() )
dimensions = referenceNode.GetImageData().GetDimensions()
self.reslice.SetOutputExtent(0, dimensions[0]-1, 0, dimensions[1]-1, 0, dimensions[2]-1)
self.reslice.SetOutputOrigin((0,0,0))
self.reslice.SetOutputSpacing((1,1,1))
self.reslice.UpdateWholeExtent()
targetNode.SetAndObserveImageData(self.reslice.GetOutput())
def transformPolyData(self, modelNode, transformNode):
transformedModel = slicer.util.getNode('Transformed Model')
if not transformedModel:
transformedModel = slicer.vtkMRMLModelNode()
transformedModel.SetName('Transformed Model')
transformedModel.SetAndObservePolyData(modelNode.GetPolyData())
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
transformedModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(transformedModel)
transformedModel.SetDisplayVisibility(False)
t = vtk.vtkGeneralTransform()
transformNode.GetTransformToWorld(t)
transformPolyDataFilter = vtk.vtkTransformPolyDataFilter()
transformPolyDataFilter.SetTransform(t)
transformPolyDataFilter.SetInputData(modelNode.GetPolyData())
transformPolyDataFilter.Update()
transformedModel.SetAndObservePolyData(transformPolyDataFilter.GetOutput())
