def gridTransformFromCorners(self, volumeNode, sourceCorners,
targetCorners):
"""Create a grid transform that maps between the current and the desired corners.
"""
# sanity check
columns, rows, slices = volumeNode.GetImageData().GetDimensions()
cornerShape = (slices, 2, 2, 3)
if not (sourceCorners.shape == cornerShape
and targetCorners.shape == cornerShape):
raise Exception(
"Corner shapes do not match volume dimensions %s, %s, %s" %
(sourceCorners.shape, targetCorners.shape, cornerShape))
# create the grid transform node
gridTransform = slicer.vtkMRMLGridTransformNode()
gridTransform.SetName(
slicer.mrmlScene.GenerateUniqueName(volumeNode.GetName() +
' acquisition transform'))
slicer.mrmlScene.AddNode(gridTransform)
# place grid transform in the same subject hierarchy folder as the volume node
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(
slicer.mrmlScene)
volumeParentItemId = shNode.GetItemParent(
shNode.GetItemByDataNode(volumeNode))
shNode.SetItemParent(shNode.GetItemByDataNode(gridTransform),
volumeParentItemId)
# create a grid transform with one vector at the corner of each slice
# the transform is in the same space and orientation as the volume node
gridImage = vtk.vtkImageData()
gridImage.SetOrigin(*volumeNode.GetOrigin())
gridImage.SetDimensions(2, 2, slices)
sourceSpacing = volumeNode.GetSpacing()
gridImage.SetSpacing(sourceSpacing[0] * columns,
sourceSpacing[1] * rows, sourceSpacing[2])
gridImage.AllocateScalars(vtk.VTK_DOUBLE, 3)
transform = slicer.vtkOrientedGridTransform()
directionMatrix = vtk.vtkMatrix4x4()
volumeNode.GetIJKToRASDirectionMatrix(directionMatrix)
transform.SetGridDirectionMatrix(directionMatrix)
transform.SetDisplacementGridData(gridImage)
gridTransform.SetAndObserveTransformToParent(transform)
volumeNode.SetAndObserveTransformNodeID(gridTransform.GetID())
# populate the grid so that each corner of each slice
# is mapped from the source corner to the target corner
displacements = slicer.util.arrayFromGridTransform(gridTransform)
for sliceIndex in range(slices):
for row in range(2):
for column in range(2):
displacements[sliceIndex][row][column] = targetCorners[
sliceIndex][row][column] - sourceCorners[
sliceIndex][row][column]
def onExportGrid(self):
"""Converts the current thin plate transform to a grid"""
self.hotUpdateButton = None
state = self.registrationState()
# since the transform is ras-to-ras, we find the extreme points
# in ras space of the fixed (target) volume and fix the unoriented
# box around it. Sample the grid transform at the resolution of
# the fixed volume, which may be a bit overkill but it should aways
# work without too much loss.
rasBounds = [
0,
] * 6
state.fixed.GetRASBounds(rasBounds)
from math import floor, ceil
origin = list(map(int, map(floor, rasBounds[::2])))
maxes = list(map(int, map(ceil, rasBounds[1::2])))
boundSize = [m - o for m, o in zip(maxes, origin)]
spacing = state.fixed.GetSpacing()
samples = [ceil(int(b / s)) for b, s in zip(boundSize, spacing)]
extent = [
0,
] * 6
extent[::2] = [
0,
] * 3
extent[1::2] = samples
extent = list(map(int, extent))
toGrid = vtk.vtkTransformToGrid()
toGrid.SetGridOrigin(origin)
toGrid.SetGridSpacing(state.fixed.GetSpacing())
toGrid.SetGridExtent(extent)
toGrid.SetInput(
state.transform.GetTransformFromParent()) # same in VTKv 5 & 6
toGrid.Update()
gridTransform = slicer.vtkOrientedGridTransform()
if vtk.VTK_MAJOR_VERSION < 6:
gridTransform.SetDisplacementGrid(
toGrid.GetOutput()) # different in VTKv 5 & 6
else:
gridTransform.SetDisplacementGridData(toGrid.GetOutput())
gridNode = slicer.vtkMRMLGridTransformNode()
gridNode.SetAndObserveTransformFromParent(gridTransform)
gridNode.SetName(state.transform.GetName() + "-grid")
slicer.mrmlScene.AddNode(gridNode)
def gridTransformFromCorners(self,volumeNode,sourceCorners,targetCorners):
"""Create a grid transform that maps between the current and the desired corners.
"""
# sanity check
columns, rows, slices = volumeNode.GetImageData().GetDimensions()
cornerShape = (slices, 2, 2, 3)
if not (sourceCorners.shape == cornerShape and targetCorners.shape == cornerShape):
raise Exception("Corner shapes do not match volume dimensions %s, %s, %s" %
(sourceCorners.shape, targetCorners.shape, cornerShape))
# create the grid transform node
gridTransform = slicer.vtkMRMLGridTransformNode()
gridTransform.SetName(slicer.mrmlScene.GenerateUniqueName(volumeNode.GetName()+' acquisition transform'))
slicer.mrmlScene.AddNode(gridTransform)
# place grid transform in the same subject hierarchy folder as the volume node
shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
volumeParentItemId = shNode.GetItemParent(shNode.GetItemByDataNode(volumeNode))
shNode.SetItemParent(shNode.GetItemByDataNode(gridTransform), volumeParentItemId)
# create a grid transform with one vector at the corner of each slice
# the transform is in the same space and orientation as the volume node
gridImage = vtk.vtkImageData()
gridImage.SetOrigin(*volumeNode.GetOrigin())
gridImage.SetDimensions(2, 2, slices)
sourceSpacing = volumeNode.GetSpacing()
gridImage.SetSpacing(sourceSpacing[0] * columns, sourceSpacing[1] * rows, sourceSpacing[2])
gridImage.AllocateScalars(vtk.VTK_DOUBLE, 3)
transform = slicer.vtkOrientedGridTransform()
directionMatrix = vtk.vtkMatrix4x4()
volumeNode.GetIJKToRASDirectionMatrix(directionMatrix)
transform.SetGridDirectionMatrix(directionMatrix)
transform.SetDisplacementGridData(gridImage)
gridTransform.SetAndObserveTransformToParent(transform)
volumeNode.SetAndObserveTransformNodeID(gridTransform.GetID())
# populate the grid so that each corner of each slice
# is mapped from the source corner to the target corner
displacements = slicer.util.arrayFromGridTransform(gridTransform)
for sliceIndex in range(slices):
for row in range(2):
for column in range(2):
displacements[sliceIndex][row][column] = targetCorners[sliceIndex][row][column] - sourceCorners[sliceIndex][row][column]
def onExportGrid(self):
"""Converts the current thin plate transform to a grid"""
state = self.registationState()
# since the transform is ras-to-ras, we find the extreme points
# in ras space of the fixed (target) volume and fix the unoriented
# box around it. Sample the grid transform at the resolution of
# the fixed volume, which may be a bit overkill but it should aways
# work without too much loss.
rasBounds = [0,]*6
state.fixed.GetRASBounds(rasBounds)
from math import floor, ceil
origin = map(int,map(floor,rasBounds[::2]))
maxes = map(int,map(ceil,rasBounds[1::2]))
boundSize = [m - o for m,o in zip(maxes,origin) ]
spacing = state.fixed.GetSpacing()
samples = [ceil(b / s) for b,s in zip(boundSize,spacing)]
extent = [0,]*6
extent[::2] = [0,]*3
extent[1::2] = samples
extent = map(int,extent)
toGrid = vtk.vtkTransformToGrid()
toGrid.SetGridOrigin(origin)
toGrid.SetGridSpacing(state.fixed.GetSpacing())
toGrid.SetGridExtent(extent)
toGrid.SetInput(state.transform.GetTransformFromParent()) # same in VTKv 5 & 6
toGrid.Update()
gridTransform = vtk.vtkGridTransform()
if vtk.VTK_MAJOR_VERSION < 6:
gridTransform.SetDisplacementGrid(toGrid.GetOutput()) # different in VTKv 5 & 6
else:
gridTransform.SetDisplacementGridData(toGrid.GetOutput())
gridNode = slicer.vtkMRMLGridTransformNode()
gridNode.SetAndObserveTransformFromParent(gridTransform)
gridNode.SetName(state.transform.GetName()+"-grid")
slicer.mrmlScene.AddNode(gridNode)
def createAcquisitionTransform(self, volumeNode, metadata):
# Creates transform that applies scan conversion transform
probeRadius = metadata['CurvatureRadiusProbe']
trackRadius = metadata['CurvatureRadiusTrack']
if trackRadius != 0.0:
raise ValueError(f"Curvature Radius (Track) is {trackRadius}. Currently, only volume with zero radius can be imported.")
# Create a sampling grid for the transform
import numpy as np
spacing = np.array(volumeNode.GetSpacing())
averageSpacing = (spacing[0] + spacing[1] + spacing[2]) / 3.0
voxelsPerTransformControlPoint = 20 # the transform is changing smoothly, so we don't need to add too many control points
gridSpacingMm = averageSpacing * voxelsPerTransformControlPoint
gridSpacingVoxel = np.floor(gridSpacingMm / spacing).astype(int)
gridAxesIJK = []
imageData = volumeNode.GetImageData()
extent = imageData.GetExtent()
for axis in range(3):
gridAxesIJK.append(list(range(extent[axis * 2], extent[axis * 2 + 1] + gridSpacingVoxel[axis], gridSpacingVoxel[axis])))
samplingPoints_shape = [len(gridAxesIJK[0]), len(gridAxesIJK[1]), len(gridAxesIJK[2]), 3]
# create a grid transform with one vector at the corner of each slice
# the transform is in the same space and orientation as the volume node
import vtk
gridImage = vtk.vtkImageData()
gridImage.SetOrigin(*volumeNode.GetOrigin())
gridImage.SetDimensions(samplingPoints_shape[:3])
gridImage.SetSpacing(gridSpacingVoxel[0] * spacing[0], gridSpacingVoxel[1] * spacing[1], gridSpacingVoxel[2] * spacing[2])
gridImage.AllocateScalars(vtk.VTK_DOUBLE, 3)
transform = slicer.vtkOrientedGridTransform()
directionMatrix = vtk.vtkMatrix4x4()
volumeNode.GetIJKToRASDirectionMatrix(directionMatrix)
transform.SetGridDirectionMatrix(directionMatrix)
transform.SetDisplacementGridData(gridImage)
# create the grid transform node
gridTransform = slicer.vtkMRMLGridTransformNode()
gridTransform.SetName(slicer.mrmlScene.GenerateUniqueName(volumeNode.GetName() + ' acquisition transform'))
slicer.mrmlScene.AddNode(gridTransform)
gridTransform.SetAndObserveTransformToParent(transform)
# populate the grid so that each corner of each slice
# is mapped from the source corner to the target corner
nshape = tuple(reversed(gridImage.GetDimensions()))
nshape = nshape + (3,)
displacements = vtk.util.numpy_support.vtk_to_numpy(gridImage.GetPointData().GetScalars()).reshape(nshape)
# Get displacements
from math import sin, cos
ijkToRas = vtk.vtkMatrix4x4()
volumeNode.GetIJKToRASMatrix(ijkToRas)
spacing = volumeNode.GetSpacing()
center_IJK = [(extent[0] + extent[1]) / 2.0, extent[2], (extent[4] + extent[5]) / 2.0]
sourcePoints_RAS = numpy.zeros(shape=samplingPoints_shape)
targetPoints_RAS = numpy.zeros(shape=samplingPoints_shape)
for k in range(samplingPoints_shape[2]):
for j in range(samplingPoints_shape[1]):
for i in range(samplingPoints_shape[0]):
samplingPoint_IJK = [gridAxesIJK[0][i], gridAxesIJK[1][j], gridAxesIJK[2][k], 1]
sourcePoint_RAS = np.array(ijkToRas.MultiplyPoint(samplingPoint_IJK)[:3])
radius = probeRadius - (samplingPoint_IJK[1] - center_IJK[1]) * spacing[1]
angleRad = (samplingPoint_IJK[0] - center_IJK[0]) * spacing[0] / probeRadius
targetPoint_RAS = np.array([
-radius * sin(angleRad),
radius * cos(angleRad) - probeRadius,
spacing[2] * (samplingPoint_IJK[2] - center_IJK[2])])
displacements[k][j][i] = targetPoint_RAS - sourcePoint_RAS
return gridTransform
