CreateTpsWithFiducials.py

# Copy and paste into Slicer Python interactor
# Drag visible fiducials to deform transform

# Scale defines how large cube will be created
# numPerEdge defines how many fiducials to put on each edge of the cube

scale = 30.0
numPerEdge = 3

# Create the FROM fiducial list, and hide it so it doesn't change with mouse interactions

fromFids = slicer.vtkMRMLMarkupsFiducialNode()
fromFids.SetName('FromFids')
slicer.mrmlScene.AddNode(fromFids)
for x in range(numPerEdge):
  for y in range(numPerEdge):
    for z in range(numPerEdge):
      cx = (x-float(numPerEdge-1)/2.0)*scale
      cy = (y-float(numPerEdge-1)/2.0)*scale
      cz = (z-float(numPerEdge-1)/2.0)*scale
      fromFids.AddFiducial(cx, cy, cz)

fromFids.GetDisplayNode().SetVisibility(False)

# Create the TO fiducial list, and make its label text invisibly small

toFids = slicer.vtkMRMLMarkupsFiducialNode()
toFids.SetName('T')
slicer.mrmlScene.AddNode(toFids)
for x in range(numPerEdge):
  for y in range(numPerEdge):
    for z in range(numPerEdge):
      cx = (x-float(numPerEdge-1)/2.0)*scale
      cy = (y-float(numPerEdge-1)/2.0)*scale
      cz = (z-float(numPerEdge-1)/2.0)*scale
      toFids.AddFiducial(cx, cy, cz)

toFids.GetDisplayNode().SetTextScale(0)

# Create the transform node to hold the deformable transformation later

tNode = slicer.vtkMRMLTransformNode()
tNode.SetName( 'TpsTransform' )
slicer.mrmlScene.AddNode( tNode )

# Function that will be called whenever a TO fiducial moves and the transform needs an update

def updateTpsTransform(caller, eventid):
  numPerEdge = fromFids.GetNumberOfFiducials()
  if numPerEdge != toFids.GetNumberOfFiducials():
    print('Error: Fiducial numbers are not equal!')
    return
  
  fp = vtk.vtkPoints()
  tp = vtk.vtkPoints()
  f = [0, 0, 0]
  t = [0, 0, 0]
  
  for i in range(numPerEdge):
    fromFids.GetNthFiducialPosition(i, f)
    toFids.GetNthFiducialPosition(i, t)
    fp.InsertNextPoint(f)
    tp.InsertNextPoint(t)
  
  tps = vtk.vtkThinPlateSplineTransform()
  tps.SetSourceLandmarks( fp )
  tps.SetTargetLandmarks( tp )
  tps.SetBasisToR()
  tNode.SetAndObserveTransformToParent( tps )

toFids.AddObserver(vtk.vtkCommand.ModifiedEvent, updateTpsTransform)

# A ROI annotation defines the region where the transform will be visualized

roi = slicer.vtkMRMLAnnotationROINode()
roi.SetName( 'RoiNode' )
slicer.mrmlScene.AddNode( roi )
roi.SetDisplayVisibility(False)
roi.SetXYZ(0, 0, 0)
roi.SetRadiusXYZ(scale, scale, scale)

# Set up transform visualization as gridlines

tNode.CreateDefaultDisplayNodes()
d = tNode.GetDisplayNode()
d.SetAndObserveRegionNode(roi)
d.SetVisualizationMode( slicer.vtkMRMLTransformDisplayNode.VIS_MODE_GRID)
d.SetVisibility(True)

tps.SetBasisToR()