def onLandmarkMoved_NOT(self,state):
"""Perform the linear transform using the vtkLandmarkTransform class"""
if state.transformed.GetTransformNodeID() != state.linearTransform.GetID():
state.transformed.SetAndObserveTransformNodeID(state.linearTransform.GetID())
self.linearMode = "Rigid"
# try to use user selection, but fall back if not enough points are available
landmarkTransform = vtk.vtkLandmarkTransform()
if self.linearMode == 'Rigid':
landmarkTransform.SetModeToRigidBody()
if self.linearMode == 'Similarity':
landmarkTransform.SetModeToSimilarity()
if self.linearMode == 'Affine':
landmarkTransform.SetModeToAffine()
if state.fixedFiducials.GetNumberOfFiducials() < 3:
landmarkTransform.SetModeToRigidBody()
points = {}
point = [0,]*3
for volumeNode in (state.fixed,state.moving):
points[volumeNode] = vtk.vtkPoints()
indices = range(state.fixedFiducials.GetNumberOfFiducials())
fiducialLists = (state.fixedFiducials,state.movingFiducials)
volumeNodes = (state.fixed,state.moving)
for fiducials,volumeNode in zip(fiducialLists,volumeNodes):
for index in indices:
fiducials.GetNthFiducialPosition(index,point)
points[volumeNode].InsertNextPoint(point)
landmarkTransform.SetSourceLandmarks(points[state.moving])
landmarkTransform.SetTargetLandmarks(points[state.fixed])
landmarkTransform.Update()
t = state.linearTransform
t.SetAndObserveMatrixTransformToParent(landmarkTransform.GetMatrix())
def onLandmarkMoved(self,state):
"""Perform the linear transform using the vtkLandmarkTransform class"""
if state.transformed.GetTransformNodeID() != state.linearTransform.GetID():
state.transformed.SetAndObserveTransformNodeID(state.linearTransform.GetID())
self.linearMode = "Rigid"
# try to use user selection, but fall back if not enough points are available
landmarkTransform = vtk.vtkLandmarkTransform()
if self.linearMode == 'Rigid':
landmarkTransform.SetModeToRigidBody()
if self.linearMode == 'Similarity':
landmarkTransform.SetModeToSimilarity()
if self.linearMode == 'Affine':
landmarkTransform.SetModeToAffine()
if state.fixedFiducials.GetNumberOfFiducials() < 3:
landmarkTransform.SetModeToRigidBody()
volumeNodes = (state.fixed, state.moving)
fiducialNodes = (state.fixedFiducials,state.movingFiducials)
points = state.logic.vtkPointForVolumes( volumeNodes, fiducialNodes )
landmarkTransform.SetSourceLandmarks(points[state.moving])
landmarkTransform.SetTargetLandmarks(points[state.fixed])
landmarkTransform.Update()
t = state.linearTransform
t.SetAndObserveMatrixTransformToParent(landmarkTransform.GetMatrix())
def performLinearRegistration(self,fixed,moving,landmarks,transform,transformed):
"""Perform the linear transform using the vtkLandmarkTransform class"""
print('performing registration')
transformed.SetAndObserveTransformNodeID(transform.GetID())
# try to use user selection, but fall back if not enough points are available
landmarkTransform = vtk.vtkLandmarkTransform()
if self.linearMode == 'Rigid':
landmarkTransform.SetModeToRigidBody()
if self.linearMode == 'Similarity':
landmarkTransform.SetModeToSimilarity()
if self.linearMode == 'Affine':
landmarkTransform.SetModeToAffine()
if len(landmarks.values()) < 3:
landmarkTransform.SetModeToRigidBody()
points = {}
point = [0,]*3
for volumeNode in (fixed,moving):
points[volumeNode] = vtk.vtkPoints()
for fiducials in landmarks.values():
for volumeNode,fid in zip((fixed,moving),fiducials):
fid.GetFiducialCoordinates(point)
points[volumeNode].InsertNextPoint(point)
print("%s: %s" % (volumeNode.GetName(), str(point)))
landmarkTransform.SetSourceLandmarks(points[moving])
landmarkTransform.SetTargetLandmarks(points[fixed])
landmarkTransform.Update()
transform.SetAndObserveMatrixTransformToParent(landmarkTransform.GetMatrix())
def onLandmarkMoved(self, state):
"""Perform the linear transform using the vtkLandmarkTransform class"""
if state.transformed:
if state.transformed.GetTransformNodeID() != state.transform.GetID(
):
state.transformed.SetAndObserveTransformNodeID(
state.transform.GetID())
if not state.fixedFiducials or not state.movingFiducials:
return
# try to use user selection, but fall back if not enough points are available
landmarkTransform = vtk.vtkLandmarkTransform()
if self.linearMode == 'Rigid':
landmarkTransform.SetModeToRigidBody()
if self.linearMode == 'Similarity':
landmarkTransform.SetModeToSimilarity()
if self.linearMode == 'Affine':
landmarkTransform.SetModeToAffine()
if state.fixedFiducials.GetNumberOfFiducials() < 3:
landmarkTransform.SetModeToRigidBody()
volumeNodes = (state.fixed, state.moving)
fiducialNodes = (state.fixedFiducials, state.movingFiducials)
points = state.logic.vtkPointsForVolumes(volumeNodes, fiducialNodes)
landmarkTransform.SetSourceLandmarks(points[state.moving])
landmarkTransform.SetTargetLandmarks(points[state.fixed])
landmarkTransform.Update()
state.transform.SetAndObserveTransformToParent(landmarkTransform)
def performLinearRegistration(self,fixed,moving,landmarks,transform,transformed):
transformed.SetAndObserveTransformNodeID(transform.GetID())
landmarkTransform = vtk.vtkLandmarkTransform()
if self.linearMode == 'Rigid':
landmarkTransform.SetModeToRigidBody()
if self.linearMode == 'Similarity':
landmarkTransform.SetModeToSimilarity()
if self.linearMode == 'Affine':
landmarkTransform.SetModeToAffine()
points = {}
point = [0,]*3
for volumeNode in (fixed,moving):
points[volumeNode] = vtk.vtkPoints()
for fiducials in landmarks.values():
for volumeNode,fid in zip((fixed,moving),fiducials):
fid.GetFiducialCoordinates(point)
points[volumeNode].InsertNextPoint(point)
print("%s: %s" % (volumeNode.GetName(), str(point)))
landmarkTransform.SetSourceLandmarks(points[moving])
landmarkTransform.SetTargetLandmarks(points[fixed])
landmarkTransform.Update()
transform.SetAndObserveMatrixTransformToParent(landmarkTransform.GetMatrix())
def GetDiffusingLaserTransform(self):
fiducialsNode = self.inputFiducialsNodeSelector.currentNode();
print fiducialsNode.GetClassName()
if fiducialsNode.GetClassName() == "vtkMRMLMarkupsFiducialNode":
# slicer4 Markups node
NumFid = fiducialsNode.GetNumberOfFiducials()
if NumFid < 2:
print("Two Fiducials Needed ")
return None
# get fiducial positions
else:
# slicer Points
pointtip = [0.0, 0.0, 0.0]
fiducialsNode.GetNthFiducialPosition(0, pointtip )
pointentry = [0.0, 0.0, 0.0]
fiducialsNode.GetNthFiducialPosition(1, pointentry)
else:
print("Unknown Class ")
return None
# diffusing applicator center at coordinate (0, 0., 0. ) mm
# template laser distal ends at coordinates (0, +/- DiffusingTipLength/2., 0. ) mm
originalOrientation = vtk.vtkPoints()
originalOrientation.SetNumberOfPoints(3)
originalOrientation.SetPoint(0, 0., 0.,0.)
originalOrientation.SetPoint(1, 0.,self.DiffusingTipLength/2.,0.)
originalOrientation.SetPoint(2,self.DiffusingTipLength/10., 0.,0.)
# compute target landmarks
slicerLength = numpy.linalg.norm( numpy.array(pointentry) - numpy.array(pointtip) )
unitdirection = 1./slicerLength * (numpy.array(pointentry) - numpy.array(pointtip) )
pointtip = pointtip - self.PullBackValueSliderWidget.value * unitdirection
pointscaled = pointtip - self.PullBackValueSliderWidget.value * unitdirection + self.DiffusingTipLength/2. * unitdirection
# compute cross product for other direction
appcross = numpy.cross(pointtip ,pointscaled )
normcross = numpy.linalg.norm( appcross )
appcross = pointtip + 1./normcross * appcross
print "points", pointentry, pointtip, pointscaled, slicerLength, numpy.linalg.norm( unitdirection ), numpy.linalg.norm( pointscaled - pointtip ) ,appcross
slicerOrientation = vtk.vtkPoints()
slicerOrientation.SetNumberOfPoints(3)
slicerOrientation.SetPoint(0,pointtip[ 0],pointtip[ 1],pointtip[ 2] )
slicerOrientation.SetPoint(1,pointscaled[0],pointscaled[1],pointscaled[2] )
slicerOrientation.SetPoint(2,appcross[ 0],appcross[ 1],appcross[ 2] )
LaserLineTransform = vtk.vtkLandmarkTransform()
LaserLineTransform.SetSourceLandmarks(originalOrientation)
LaserLineTransform.SetTargetLandmarks(slicerOrientation )
LaserLineTransform.SetModeToRigidBody()
LaserLineTransform.Update()
print LaserLineTransform.GetMatrix()
## # Get RAS transformation
## rasToXY = vtk.vtkMatrix4x4()
## layoutManager = slicer.app.layoutManager()
## sliceWidget = layoutManager.sliceWidget('Red')
## sliceLogic = sliceWidget.sliceLogic()
## layerLogic = sliceLogic.GetBackgroundLayer()
## xyToIJK = layerLogic.GetXYToIJKTransform().GetMatrix()
## rasToXY.DeepCopy( xyToIJK )
## #rasToXY.Invert()
## outnode = self.outputSelector.currentNode()
## ras2ijk = vtk.vtkMatrix4x4()
## ijk2ras = vtk.vtkMatrix4x4()
## outnode.GetRASToIJKMatrix(ras2ijk)
## outnode.GetIJKToRASMatrix(ijk2ras)
## print ras2ijk
## print ijk2ras
## print rasToXY
## print pointtip
## print rasToXY.MultiplyPoint( (pointtip[0],pointtip[1],pointtip[2],1.) )
## print ras2ijk.MultiplyPoint( (pointtip[0],pointtip[1],pointtip[2],1.) )
return LaserLineTransform