import vtk.util.colors points = vtk.vtkPoints() points.InsertNextPoint(0, 0, 0) points.InsertNextPoint(0, 1, 0) points.InsertNextPoint(1, 0, 0) points.InsertNextPoint(0, 0, 1) pointsPolyData = vtk.vtkPolyData() pointsPolyData.SetPoints(points) pointsImageData = vtk.vtkImageData() pointsImageData.GetPointData().ShallowCopy(pointsPolyData.GetPointData()) pointsImageData.GetCellData().ShallowCopy(pointsPolyData.GetCellData()) bsplineCoeff = vtk.vtkImageBSplineCoefficients() bsplineCoeff.SetInputData(pointsImageData) bsplineCoeff.SetSplineDegree(3) bsplineCoeff.SetBorderModeToClamp() bsplineCoeff.Update() bsplineInter = vtk.vtkImageBSplineInterpolator() bsplineInter.SetSplineDegree(3) bsplineInter.SetBorderModeToClamp() bsplineInter.Initialize(bsplineCoeff.GetOutput()) bsplineInter.Update() #TO FINISH vertexFilter = vtk.vtkVertexGlyphFilter() vertexFilter.SetInputData(pointsPolyData)
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetDataSpacing(3.2,3.2,1.5)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
transform = vtk.vtkTransform()
# rotate about the center of the image
transform.Translate(+100.8,+100.8,+69.0)
transform.RotateWXYZ(10,1,1,0)
transform.Translate(-100.8,-100.8,-69.0)
bspline3 = vtk.vtkImageBSplineInterpolator()
bspline3.SetSplineDegree(3)
bspline9 = vtk.vtkImageBSplineInterpolator()
bspline9.SetSplineDegree(9)
coeffs1 = vtk.vtkImageBSplineCoefficients()
coeffs1.SetInputConnection(reader.GetOutputPort())
coeffs1.SetSplineDegree(3)
coeffs2 = vtk.vtkImageBSplineCoefficients()
coeffs2.SetInputConnection(reader.GetOutputPort())
coeffs2.SetSplineDegree(9)
reslice1 = vtk.vtkImageReslice()
reslice1.SetInputConnection(coeffs1.GetOutputPort())
reslice1.SetResliceTransform(transform)
reslice1.SetInterpolator(bspline3)
reslice1.SetOutputSpacing(2.0,2.0,1.5)
reslice1.SetOutputOrigin(-32,-32,40)
reslice1.SetOutputExtent(0,127,0,127,0,0)
reslice2 = vtk.vtkImageReslice()
reslice2.SetInputConnection(coeffs1.GetOutputPort())
reslice2.SetInterpolator(bspline3)
reader.ReleaseDataFlagOff()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0, 63, 0, 63, 1, 93)
reader.SetDataSpacing(3.2, 3.2, 1.5)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/headsq/quarter")
reader.SetDataMask(0x7fff)
transform = vtk.vtkTransform()
# rotate about the center of the image
transform.Translate(+100.8, +100.8, +69.0)
transform.RotateWXYZ(10, 1, 1, 0)
transform.Translate(-100.8, -100.8, -69.0)
bspline3 = vtk.vtkImageBSplineInterpolator()
bspline3.SetSplineDegree(3)
bspline9 = vtk.vtkImageBSplineInterpolator()
bspline9.SetSplineDegree(9)
coeffs1 = vtk.vtkImageBSplineCoefficients()
coeffs1.SetInputConnection(reader.GetOutputPort())
coeffs1.SetSplineDegree(3)
coeffs2 = vtk.vtkImageBSplineCoefficients()
coeffs2.SetInputConnection(reader.GetOutputPort())
coeffs2.SetSplineDegree(9)
reslice1 = vtk.vtkImageReslice()
reslice1.SetInputConnection(coeffs1.GetOutputPort())
reslice1.SetResliceTransform(transform)
reslice1.SetInterpolator(bspline3)
reslice1.SetOutputSpacing(2.0, 2.0, 1.5)
reslice1.SetOutputOrigin(-32, -32, 40)
reslice1.SetOutputExtent(0, 127, 0, 127, 0, 0)
reslice2 = vtk.vtkImageReslice()
reslice2.SetInputConnection(coeffs1.GetOutputPort())
reslice2.SetInterpolator(bspline3)
def convert_transform_to_vtk(transform):
"""Produce an output vtkBSplineTransform corresponding to the
registration results. Input is a numpy array corresponding to the displacement field.
"""
displacement_field_vtk = vtk.util.numpy_support.numpy_to_vtk(
num_array=transform, deep=True, array_type=vtk.VTK_FLOAT)
displacement_field_vtk.SetNumberOfComponents(3)
displacement_field_vtk.SetName('DisplacementField')
grid_image = vtk.vtkImageData()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
grid_image.AllocateScalars(vtk.VTK_FLOAT, 3)
grid_image.GetPointData().SetScalars(displacement_field_vtk)
else:
grid_image.SetScalarTypeToFloat()
grid_image.SetNumberOfScalarComponents(3)
grid_image.GetPointData().SetScalars(displacement_field_vtk)
grid_image.Update()
#print "CONVERT TXFORM 1:", grid_image.GetExtent(), displacement_field_vtk.GetSize()
# this is a hard-coded assumption about where the polydata is located in space.
# other code should check that it is centered.
# This code uses a grid of 240mm x 240mm x 240mm
#spacing origin extent
num_vectors = len(transform) / 3
dims = round(numpy.power(num_vectors, 1.0 / 3.0))
# This MUST correspond to the size used in congeal_multisubject update_nonrigid_grid
#size_mm = 240.0
size_mm = 200.0
origin = -size_mm / 2.0
# assume 240mm x 240mm x 240mm grid
spacing = size_mm / (dims - 1)
grid_image.SetOrigin(origin, origin, origin)
grid_image.SetSpacing(spacing, spacing, spacing)
#grid_image.SetExtent(0, dims-1.0, 0, dims-1.0, 0, dims-1.0)
grid_image.SetDimensions(int(dims), int(dims), int(dims))
#print "CONVERT TXFORM:", num_vectors, dims, int(dims), dims-1.0, grid_image.GetExtent(),
#print "GRID:", grid_image
coeff = vtk.vtkImageBSplineCoefficients()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
coeff.SetInputData(grid_image)
else:
coeff.SetInput(grid_image)
coeff.Update()
# this was in the test code.
coeff.UpdateWholeExtent()
#print "TX:", transform.shape, transform, displacement_field_vtk, grid_image.GetExtent(), coeff.GetOutput().GetExtent()
vtktrans = vtk.vtkBSplineTransform()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
vtktrans.SetCoefficientData(coeff.GetOutput())
else:
vtktrans.SetCoefficients(coeff.GetOutput())
vtktrans.SetBorderModeToZero()
## print "~~~~~~~~~~~~~~~~~~~~~~~~"
## print "COEFF:", coeff.GetOutput()
## print "*********"
## print "COEFF2:", vtktrans.GetCoefficients()
## print "======="
return vtktrans
def convert_transform_to_vtk(transform):
"""Produce an output vtkBSplineTransform corresponding to the
registration results. Input is a numpy array corresponding to the displacement field.
"""
displacement_field_vtk = vtk.util.numpy_support.numpy_to_vtk(num_array=transform, deep=True, array_type=vtk.VTK_FLOAT)
displacement_field_vtk.SetNumberOfComponents(3)
displacement_field_vtk.SetName('DisplacementField')
grid_image = vtk.vtkImageData()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
grid_image.AllocateScalars(vtk.VTK_FLOAT, 3)
grid_image.GetPointData().SetScalars(displacement_field_vtk)
else:
grid_image.SetScalarTypeToFloat()
grid_image.SetNumberOfScalarComponents(3)
grid_image.GetPointData().SetScalars(displacement_field_vtk)
grid_image.Update()
#print "CONVERT TXFORM 1:", grid_image.GetExtent(), displacement_field_vtk.GetSize()
# this is a hard-coded assumption about where the polydata is located in space.
# other code should check that it is centered.
# This code uses a grid of 240mm x 240mm x 240mm
#spacing origin extent
num_vectors = len(transform) / 3
dims = round(numpy.power(num_vectors, 1.0/3.0))
# This MUST correspond to the size used in congeal_multisubject update_nonrigid_grid
#size_mm = 240.0
size_mm = 200.0
origin = -size_mm / 2.0
# assume 240mm x 240mm x 240mm grid
spacing = size_mm / (dims - 1)
grid_image.SetOrigin(origin, origin, origin)
grid_image.SetSpacing(spacing, spacing, spacing)
#grid_image.SetExtent(0, dims-1.0, 0, dims-1.0, 0, dims-1.0)
grid_image.SetDimensions(int(dims), int(dims), int(dims))
#print "CONVERT TXFORM:", num_vectors, dims, int(dims), dims-1.0, grid_image.GetExtent(),
#print "GRID:", grid_image
coeff = vtk.vtkImageBSplineCoefficients()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
coeff.SetInputData(grid_image)
else:
coeff.SetInput(grid_image)
coeff.Update()
# this was in the test code.
coeff.UpdateWholeExtent()
#print "TX:", transform.shape, transform, displacement_field_vtk, grid_image.GetExtent(), coeff.GetOutput().GetExtent()
vtktrans = vtk.vtkBSplineTransform()
if (vtk.vtkVersion().GetVTKMajorVersion() >= 6.0):
vtktrans.SetCoefficientData(coeff.GetOutput())
else:
vtktrans.SetCoefficients(coeff.GetOutput())
vtktrans.SetBorderModeToZero()
## print "~~~~~~~~~~~~~~~~~~~~~~~~"
## print "COEFF:", coeff.GetOutput()
## print "*********"
## print "COEFF2:", vtktrans.GetCoefficients()
## print "======="
return vtktrans
