def __init__(self,fixed=None,moving=None,transform=None):
self.interval = 20
self.timer = None
# parameter defaults
self.sampleSpacing = 3
self.gradientWindow = 1
self.stepSize = 1
# the parametricTransform
#self.parametricTransform = RegimaticTranslationTransform()
self.parametricTransform = RegimaticTranslateSRotatePATransform()
#self.parametricTransform = RegimaticRigidTransform() #TODO: fix quaternion
# slicer nodes set by the GUI
self.fixed = fixed
self.moving = moving
self.transform = transform
# optimizer state variables
self.iteration = 0
self.metric = 0
# helper objects
self.scratchMatrix = vtk.vtkMatrix4x4()
self.ijkToRAS = vtk.vtkMatrix4x4()
self.rasToIJK = vtk.vtkMatrix4x4()
self.matrixToParent = vtk.vtkMatrix4x4()
self.reslice = vtk.vtkImageReslice()
self.resliceTransform = vtk.vtkTransform()
self.viewer = None
def run(self,referenceNode, inputNode, transformNode, outputNode):
"""
Run the actual algorithm
"""
dimensions = [1,1,1]
referenceNode.GetImageData().GetDimensions(dimensions)
inputIJK2RASMatrix = vtk.vtkMatrix4x4()
inputNode.GetIJKToRASMatrix(inputIJK2RASMatrix)
referenceRAS2IJKMatrix = vtk.vtkMatrix4x4()
referenceNode.GetRASToIJKMatrix(referenceRAS2IJKMatrix)
inputRAS2RASMatrix = transformNode.GetMatrixTransformToParent()
resampleTransform = vtk.vtkTransform()
resampleTransform.Identity()
resampleTransform.PostMultiply()
resampleTransform.SetMatrix(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.CopyOrientation(referenceNode)
outputNode.SetAndObserveImageData(resampler.GetOutput())
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 __init__(self,fixed=None,moving=None,transform=None,fiducial=None,checked = None):
self.interval = 2
self.timer = None
# parameter defaults
self.sampleSpacing = 10
self.gradientWindow = 1
self.stepSize = 1
# slicer nodes set by the GUI
self.fixed = fixed
self.moving = moving
self.transform = transform
self.fiducial = fiducial
self.checked = checked
# optimizer state variables
self.iteration = 0
self.position = [0, 0, 0]
self.paintCoordinates = []
self.x0, self.y0, self.z0 = 0,0,0
self.tx0, self.ty0,self.tz0 = 0,0,0
self.m = vtk.vtkMatrix4x4()
self.r = vtk.vtkTransform()
self.transformNode,self.neutral = None, None
self.before = 0
self.plan = 'plan'
self.actionState = "idle"
self.interactorObserverTags = []
self.styleObserverTags = []
self.sliceWidgetsPerStyle = {}
self.tac=0
self.WMAX = 0
self.L=[]
self.divider = 1
self.step = 1
# helper objects
self.scratchMatrix = vtk.vtkMatrix4x4()
self.ijkToRAS = vtk.vtkMatrix4x4()
self.rasToIJK = vtk.vtkMatrix4x4()
self.reslice = vtk.vtkImageReslice()
self.resliceTransform = vtk.vtkTransform()
self.viewer = None
self.render = None
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 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 resampleInputVolumeNodetoReferenceVolumeNode(self, inputVolumeNode, referenceVolumeNode, outputVolumeNode):
if not inputVolumeNode or not referenceVolumeNode or not outputVolumeNode:
print "Volumes not initialized."
return
inputVolumeIJK2RASMatrix = vtk.vtkMatrix4x4()
inputVolumeNode.GetIJKToRASMatrix(inputVolumeIJK2RASMatrix)
referenceVolumeRAS2IJKMatrix = vtk.vtkMatrix4x4()
referenceVolumeNode.GetRASToIJKMatrix(referenceVolumeRAS2IJKMatrix)
dimensions = referenceVolumeNode.GetImageData().GetDimensions()
outputVolumeResliceTransform = vtk.vtkTransform()
outputVolumeResliceTransform.Identity()
outputVolumeResliceTransform.PostMultiply()
outputVolumeResliceTransform.SetMatrix(inputVolumeIJK2RASMatrix)
if inputVolumeNode.GetTransformNodeID() is not None:
inputVolumeNodeTransformNode = slicer.util.getNode(inputVolumeNode.GetTransformNodeID())
inputVolumeRAS2RASMatrix = vtk.vtkMatrix4x4()
if inputVolumeNodeTransformNode is not None:
inputVolumeNodeTransformNode.GetMatrixTransformToWorld(inputVolumeRAS2RASMatrix)
outputVolumeResliceTransform.Concatenate(inputVolumeRAS2RASMatrix)
outputVolumeResliceTransform.Concatenate(referenceVolumeRAS2IJKMatrix)
outputVolumeResliceTransform.Inverse()
resliceFilter = vtk.vtkImageReslice()
resliceFilter.SetInput(inputVolumeNode.GetImageData())
resliceFilter.SetOutputOrigin(0, 0, 0)
resliceFilter.SetOutputSpacing(1, 1, 1)
resliceFilter.SetOutputExtent(0, dimensions[0]-1, 0, dimensions[1]-1, 0, dimensions[2]-1)
resliceFilter.SetResliceTransform(outputVolumeResliceTransform)
resliceFilter.Update()
outputVolumeNode.CopyOrientation(referenceVolumeNode)
outputVolumeNode.SetAndObserveImageData(resliceFilter.GetOutput())
return
def extractROI(originalVolumeID, newVolumeID, rasCoordinates, diameter):
'''
'''
originalVolume = slicer.mrmlScene.GetNodeByID(originalVolumeID)
newVolume = slicer.mrmlScene.GetNodeByID(newVolumeID)
# code below converted from cropVolume module by A. Fedorov
# optimized after that :)
inputRASToIJK = vtk.vtkMatrix4x4()
inputIJKToRAS = vtk.vtkMatrix4x4()
outputIJKToRAS = vtk.vtkMatrix4x4()
outputRASToIJK = vtk.vtkMatrix4x4()
volumeXform = vtk.vtkMatrix4x4()
T = vtk.vtkMatrix4x4()
originalVolume.GetRASToIJKMatrix(inputRASToIJK)
originalVolume.GetIJKToRASMatrix(inputIJKToRAS)
outputIJKToRAS.Identity()
outputRASToIJK.Identity()
volumeXform.Identity()
T.Identity()
# if the originalVolume is under a transform
volumeTransformNode = originalVolume.GetParentTransformNode()
if volumeTransformNode:
volumeTransformNode.GetMatrixTransformToWorld(volumeXform)
volumeXform.Invert()
maxSpacing = max(originalVolume.GetSpacing())
# build our box
rX = diameter * 4 * maxSpacing
rY = diameter * 4 * maxSpacing
rZ = diameter * 4 * maxSpacing
cX = rasCoordinates[0]
cY = rasCoordinates[1]
cZ = rasCoordinates[2]
inputSpacingX = originalVolume.GetSpacing()[0]
inputSpacingY = originalVolume.GetSpacing()[1]
inputSpacingZ = originalVolume.GetSpacing()[2]
outputExtentX = int(2.0 * rX / inputSpacingX)
outputExtentY = int(2.0 * rY / inputSpacingY)
outputExtentZ = int(2.0 * rZ / inputSpacingZ)
# configure spacing
outputIJKToRAS.SetElement(0, 0, inputSpacingX)
outputIJKToRAS.SetElement(1, 1, inputSpacingY)
outputIJKToRAS.SetElement(2, 2, inputSpacingZ)
# configure origin
outputIJKToRAS.SetElement(0, 3, (cX - rX + inputSpacingX * 0.5))
outputIJKToRAS.SetElement(1, 3, (cY - rY + inputSpacingY * 0.5))
outputIJKToRAS.SetElement(2, 3, (cZ - rZ + inputSpacingZ * 0.5))
outputRASToIJK.DeepCopy(outputIJKToRAS)
outputRASToIJK.Invert()
T.DeepCopy(outputIJKToRAS)
T.Multiply4x4(volumeXform, T, T)
T.Multiply4x4(inputRASToIJK, T, T)
resliceT = vtk.vtkTransform()
resliceT.SetMatrix(T)
reslicer = vtk.vtkImageReslice()
reslicer.SetInterpolationModeToLinear()
reslicer.SetInput(originalVolume.GetImageData())
reslicer.SetOutputExtent(0, int(outputExtentX), 0, int(outputExtentY),
0, int(outputExtentZ))
reslicer.SetOutputOrigin(0, 0, 0)
reslicer.SetOutputSpacing(1, 1, 1)
#reslicer.SetOutputOrigin(image.GetOrigin())
#reslicer.SetOutputSpacing(image.GetSpacing())
reslicer.SetResliceTransform(resliceT)
reslicer.UpdateWholeExtent()
changer = vtk.vtkImageChangeInformation()
changer.SetInput(reslicer.GetOutput())
changer.SetOutputOrigin(0, 0, 0)
changer.SetOutputSpacing(1, 1, 1)
#changer.SetOutputOrigin(image.GetOrigin())
# changer.SetOutputSpacing(image.GetSpacing())
changer.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy(changer.GetOutput())
outImageData.Update()
newVolume.SetAndObserveImageData(outImageData)
newVolume.SetIJKToRASMatrix(outputIJKToRAS)
newVolume.SetRASToIJKMatrix(outputRASToIJK)
newVolume.Modified()
newVolume.SetModifiedSinceRead(1)
def extractROI(originalVolumeID,newVolumeID,rasCoordinates,diameter):
'''
'''
originalVolume = slicer.mrmlScene.GetNodeByID(originalVolumeID)
newVolume = slicer.mrmlScene.GetNodeByID(newVolumeID)
# code below converted from cropVolume module by A. Fedorov
# optimized after that :)
inputRASToIJK = vtk.vtkMatrix4x4()
inputIJKToRAS = vtk.vtkMatrix4x4()
outputIJKToRAS = vtk.vtkMatrix4x4()
outputRASToIJK = vtk.vtkMatrix4x4()
volumeXform = vtk.vtkMatrix4x4()
T = vtk.vtkMatrix4x4()
originalVolume.GetRASToIJKMatrix(inputRASToIJK)
originalVolume.GetIJKToRASMatrix(inputIJKToRAS)
outputIJKToRAS.Identity()
outputRASToIJK.Identity()
volumeXform.Identity()
T.Identity()
# if the originalVolume is under a transform
volumeTransformNode = originalVolume.GetParentTransformNode()
if volumeTransformNode:
volumeTransformNode.GetMatrixTransformToWorld(volumeXform)
volumeXform.Invert()
maxSpacing = max(originalVolume.GetSpacing())
# build our box
rX = diameter*4*maxSpacing
rY = diameter*4*maxSpacing
rZ = diameter*4*maxSpacing
cX = rasCoordinates[0]
cY = rasCoordinates[1]
cZ = rasCoordinates[2]
inputSpacingX = originalVolume.GetSpacing()[0]
inputSpacingY = originalVolume.GetSpacing()[1]
inputSpacingZ = originalVolume.GetSpacing()[2]
outputExtentX = int(2.0*rX/inputSpacingX)
outputExtentY = int(2.0*rY/inputSpacingY)
outputExtentZ = int(2.0*rZ/inputSpacingZ)
# configure spacing
outputIJKToRAS.SetElement(0,0,inputSpacingX)
outputIJKToRAS.SetElement(1,1,inputSpacingY)
outputIJKToRAS.SetElement(2,2,inputSpacingZ)
# configure origin
outputIJKToRAS.SetElement(0,3,(cX-rX+inputSpacingX*0.5))
outputIJKToRAS.SetElement(1,3,(cY-rY+inputSpacingY*0.5))
outputIJKToRAS.SetElement(2,3,(cZ-rZ+inputSpacingZ*0.5))
outputRASToIJK.DeepCopy(outputIJKToRAS)
outputRASToIJK.Invert()
T.DeepCopy(outputIJKToRAS)
T.Multiply4x4(volumeXform,T,T)
T.Multiply4x4(inputRASToIJK,T,T)
resliceT = vtk.vtkTransform()
resliceT.SetMatrix(T)
reslicer = vtk.vtkImageReslice()
reslicer.SetInterpolationModeToLinear()
reslicer.SetInput(originalVolume.GetImageData())
reslicer.SetOutputExtent(0,int(outputExtentX),0,int(outputExtentY),0,int(outputExtentZ))
reslicer.SetOutputOrigin(0,0,0)
reslicer.SetOutputSpacing(1,1,1)
#reslicer.SetOutputOrigin(image.GetOrigin())
#reslicer.SetOutputSpacing(image.GetSpacing())
reslicer.SetResliceTransform(resliceT)
reslicer.UpdateWholeExtent()
changer = vtk.vtkImageChangeInformation()
changer.SetInput(reslicer.GetOutput())
changer.SetOutputOrigin(0,0,0)
changer.SetOutputSpacing(1,1,1)
#changer.SetOutputOrigin(image.GetOrigin())
# changer.SetOutputSpacing(image.GetSpacing())
changer.Update()
outImageData = vtk.vtkImageData()
outImageData.DeepCopy(changer.GetOutput())
outImageData.Update()
newVolume.SetAndObserveImageData(outImageData)
newVolume.SetIJKToRASMatrix(outputIJKToRAS)
newVolume.SetRASToIJKMatrix(outputRASToIJK)
newVolume.Modified()