def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkImplicitFunctionToImageStencil(), 'Processing.',
(), ('vtkImageStencilData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self,
module_manager,
vtk.vtkImplicitFunctionToImageStencil(),
'Processing.', (), ('vtkImageStencilData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the stencil filter.
# removes all but a sphere.
reader = vtk.vtkPNGReader()
reader.SetDataSpacing(0.8,0.8,1.5)
reader.SetDataOrigin(0.0,0.0,0.0)
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
reader.Update()
sphere = vtk.vtkSphere()
sphere.SetCenter(128,128,0)
sphere.SetRadius(80)
functionToStencil = vtk.vtkImplicitFunctionToImageStencil()
functionToStencil.SetInput(sphere)
functionToStencil.SetInformationInput(reader.GetOutput())
functionToStencil.Update()
# test making a copying of the stencil (for coverage)
stencilOriginal = functionToStencil.GetOutput()
stencilCopy = stencilOriginal.NewInstance()
stencilCopy.DeepCopy(functionToStencil.GetOutput())
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInputConnection(reader.GetOutputPort())
shiftScale.SetScale(0.2)
shiftScale.Update()
stencil = vtk.vtkImageStencil()
stencil.SetInputConnection(reader.GetOutputPort())
stencil.SetBackgroundInputData(shiftScale.GetOutput())
stencil.SetStencilData(stencilCopy)
#!/usr/bin/env python import vtk from vtk.test import Testing from vtk.util.misc import vtkGetDataRoot VTK_DATA_ROOT = vtkGetDataRoot() # A script to test converting a stencil to a binary image sphere = vtk.vtkSphere() sphere.SetCenter(128, 128, 0) sphere.SetRadius(80) functionToStencil = vtk.vtkImplicitFunctionToImageStencil() functionToStencil.SetInput(sphere) functionToStencil.SetOutputOrigin(0, 0, 0) functionToStencil.SetOutputSpacing(1, 1, 1) functionToStencil.SetOutputWholeExtent(0, 255, 0, 255, 0, 0) stencilToImage = vtk.vtkImageStencilToImage() stencilToImage.SetInputConnection(functionToStencil.GetOutputPort()) stencilToImage.SetOutsideValue(0) stencilToImage.SetInsideValue(255) viewer = vtk.vtkImageViewer() viewer.SetInputConnection(stencilToImage.GetOutputPort()) viewer.SetZSlice(0) viewer.SetColorWindow(255) viewer.SetColorLevel(127.5) viewer.Render() # --- end of script --
def getModelROIStencil(self):
import time
_t0 = time.time()
t1 = self.__Transform.GetInverse()
roi_type = self.getModelROIType()
roi_orientation = self.getModelROIOrientation()
# bounds, extent and center
b = self.getModelROIBounds()
# abort early if we haven't been fully set up yet
if b is None:
return None
# determine transformed boundary
_index = [[0, 2, 4], [0, 2, 5], [0, 3, 4], [0, 3, 5], [1, 2, 4], [1, 2, 5], [1, 3, 4], [1, 3, 5]]
b_t = [1e38, -1e38, 1e38, -1e38, 1e38, -1e38]
is_identity = True
# is transform identity?
is_identity = self.__Transform.GetMatrix().Determinant() == 1.0
# is_identity = False
for i in range(8):
i2 = _index[i]
pt = [b[i2[0]], b[i2[1]], b[i2[2]]]
_temp = self.__Transform.TransformPoint(pt[0], pt[1], pt[2])
b_t[0] = min(_temp[0], b_t[0])
b_t[1] = max(_temp[0], b_t[1])
b_t[2] = min(_temp[1], b_t[2])
b_t[3] = max(_temp[1], b_t[3])
b_t[4] = min(_temp[2], b_t[4])
b_t[5] = max(_temp[2], b_t[5])
e_t = self._BoundsToExtent(b_t)
# sanity check - check for inversion (caused by negative spacing)
e_t = list(e_t)
for i in range(3):
if e_t[i * 2] > e_t[i * 2 + 1]:
v = e_t[i * 2]
e_t[i * 2] = e_t[i * 2 + 1]
e_t[i * 2 + 1] = v
# expand stencil extent by one pixel on all sides
e_t = (e_t[0] - 1, e_t[1] + 1, e_t[2] - 1, e_t[3] + 1, e_t[4] - 1, e_t[5] + 1)
# make sure we're dealing with ints
e_t = map(int, e_t)
if is_identity:
# fast, but limited to canonical objects
self._StencilGenerator = vtk.vtkROIStencilSource()
else:
# slow, but more generic
self._StencilGenerator = vtk.vtkImplicitFunctionToImageStencil()
self._StencilGenerator.SetOutputOrigin(self.getImageOrigin())
self._StencilGenerator.SetOutputSpacing(self.getImageSpacing())
# set extent of stencil - taking into account transformation
self._StencilGenerator.SetOutputWholeExtent(e_t)
if is_identity:
# use DG's fast routines
if roi_type == "box":
self._StencilGenerator.SetShapeToBox()
elif roi_type == "cylinder":
if roi_orientation == "X":
self._StencilGenerator.SetShapeToCylinderX()
elif roi_orientation == "Y":
self._StencilGenerator.SetShapeToCylinderY()
elif roi_orientation == "Z":
self._StencilGenerator.SetShapeToCylinderZ()
elif roi_type == "ellipsoid":
self._StencilGenerator.SetShapeToEllipsoid()
self._StencilGenerator.SetBounds(b)
else:
# use JG's slow routines
if roi_type == "box":
obj = vtk.vtkBox()
obj.SetTransform(t1)
obj.SetBounds(b)
elif roi_type == "cylinder":
cyl = vtk.vtkCylinder()
cyl.SetRadius(1.0)
xc, yc, zc = (b[1] + b[0]) * 0.5, (b[3] + b[2]) * 0.5, (b[5] + b[4]) * 0.5
diam_a, diam_b, diam_c = (b[1] - b[0]), (b[3] - b[2]), (b[5] - b[4])
# The cylinder is infinite in extent, so needs to be cropped by using the intersection
# of three implicit functions -- the cylinder, and two cropping
# planes
obj = vtk.vtkImplicitBoolean()
obj.SetOperationTypeToIntersection()
obj.AddFunction(cyl)
clip1 = vtk.vtkPlane()
clip1.SetNormal(0, 1, 0)
obj.AddFunction(clip1)
clip2 = vtk.vtkPlane()
clip2.SetNormal(0, -1, 0)
obj.AddFunction(clip2)
t2 = vtk.vtkTransform()
t2.Translate(xc, yc, zc)
if roi_orientation == "X":
# cylinder is infinite in extent in the y-axis
t2.Scale(1, diam_b / 2.0, diam_c / 2.0)
t2.RotateZ(90)
r = diam_a / 2.0
elif roi_orientation == "Y":
# cylinder is infinite in extent in the y-axis
t2.Scale(diam_a / 2.0, 1, diam_c / 2.0)
r = diam_b / 2.0
elif roi_orientation == "Z":
# cylinder is infinite in extent in the y-axis
t2.Scale(diam_a / 2.0, diam_b / 2.0, 1)
t2.RotateX(90)
r = diam_c / 2.0
clip1.SetOrigin(0, r, 0)
clip2.SetOrigin(0, -r, 0)
# combine transforms
t2.SetInput(self.__Transform)
obj.SetTransform(t2.GetInverse())
elif roi_type == "ellipsoid":
obj = vtk.vtkSphere()
obj.SetRadius(1.0)
xc, yc, zc = (b[1] + b[0]) * 0.5, (b[3] + b[2]) * 0.5, (b[5] + b[4]) * 0.5
diam_a, diam_b, diam_c = (b[1] - b[0]), (b[3] - b[2]), (b[5] - b[4])
t2 = vtk.vtkTransform()
t2.Translate(xc, yc, zc)
t2.Scale(diam_a / 2.0, diam_b / 2.0, diam_c / 2.0)
# combine transforms
t2.SetInput(self.__Transform)
obj.SetTransform(t2.GetInverse())
self._StencilGenerator.SetInput(obj)
_t1 = time.time()
self._StencilGenerator.Update()
_t2 = time.time()
return self._StencilGenerator.GetOutput()
def getModelROIStencil(self):
import time
_t0 = time.time()
t1 = self.__Transform.GetInverse()
roi_type = self.getModelROIType()
roi_orientation = self.getModelROIOrientation()
# bounds, extent and center
b = self.getModelROIBounds()
# abort early if we haven't been fully set up yet
if b is None:
return None
# determine transformed boundary
_index = [
[0, 2, 4], [0, 2, 5], [0, 3, 4], [0, 3, 5],
[1, 2, 4], [1, 2, 5], [1, 3, 4], [1, 3, 5],
]
b_t = [1e38, -1e38, 1e38, -1e38, 1e38, -1e38]
is_identity = True
# is transform identity?
is_identity = self.__Transform.GetMatrix().Determinant() == 1.0
#is_identity = False
for i in range(8):
i2 = _index[i]
pt = [b[i2[0]], b[i2[1]], b[i2[2]]]
_temp = self.__Transform.TransformPoint(pt[0], pt[1], pt[2])
b_t[0] = min(_temp[0], b_t[0])
b_t[1] = max(_temp[0], b_t[1])
b_t[2] = min(_temp[1], b_t[2])
b_t[3] = max(_temp[1], b_t[3])
b_t[4] = min(_temp[2], b_t[4])
b_t[5] = max(_temp[2], b_t[5])
e_t = self._BoundsToExtent(b_t)
# sanity check - check for inversion (caused by negative spacing)
e_t = list(e_t)
for i in range(3):
if e_t[i * 2] > e_t[i * 2 + 1]:
v = e_t[i * 2]
e_t[i * 2] = e_t[i * 2 + 1]
e_t[i * 2 + 1] = v
# expand stencil extent by one pixel on all sides
e_t = (e_t[0] - 1, e_t[1] + 1, e_t[2] - 1,
e_t[3] + 1, e_t[4] - 1, e_t[5] + 1)
# make sure we're dealing with ints
e_t = map(int, e_t)
if is_identity:
# fast, but limited to canonical objects
self._StencilGenerator = vtk.vtkROIStencilSource()
else:
# slow, but more generic
self._StencilGenerator = vtk.vtkImplicitFunctionToImageStencil()
self._StencilGenerator.SetOutputOrigin(self.getImageOrigin())
self._StencilGenerator.SetOutputSpacing(self.getImageSpacing())
# set extent of stencil - taking into account transformation
self._StencilGenerator.SetOutputWholeExtent(e_t)
if is_identity:
# use DG's fast routines
if roi_type == 'box':
self._StencilGenerator.SetShapeToBox()
elif roi_type == 'cylinder':
if roi_orientation == 'X':
self._StencilGenerator.SetShapeToCylinderX()
elif roi_orientation == 'Y':
self._StencilGenerator.SetShapeToCylinderY()
elif roi_orientation == 'Z':
self._StencilGenerator.SetShapeToCylinderZ()
elif roi_type == 'ellipsoid':
self._StencilGenerator.SetShapeToEllipsoid()
self._StencilGenerator.SetBounds(b)
else:
# use JG's slow routines
if roi_type == 'box':
obj = vtk.vtkBox()
obj.SetTransform(t1)
obj.SetBounds(b)
elif roi_type == 'cylinder':
cyl = vtk.vtkCylinder()
cyl.SetRadius(1.0)
xc, yc, zc = (b[1] + b[0]) * \
0.5, (b[3] + b[2]) * 0.5, (b[5] + b[4]) * 0.5
diam_a, diam_b, diam_c = (
b[1] - b[0]), (b[3] - b[2]), (b[5] - b[4])
# The cylinder is infinite in extent, so needs to be cropped by using the intersection
# of three implicit functions -- the cylinder, and two cropping
# planes
obj = vtk.vtkImplicitBoolean()
obj.SetOperationTypeToIntersection()
obj.AddFunction(cyl)
clip1 = vtk.vtkPlane()
clip1.SetNormal(0, 1, 0)
obj.AddFunction(clip1)
clip2 = vtk.vtkPlane()
clip2.SetNormal(0, -1, 0)
obj.AddFunction(clip2)
t2 = vtk.vtkTransform()
t2.Translate(xc, yc, zc)
if roi_orientation == 'X':
# cylinder is infinite in extent in the y-axis
t2.Scale(1, diam_b / 2.0, diam_c / 2.0)
t2.RotateZ(90)
r = diam_a / 2.0
elif roi_orientation == 'Y':
# cylinder is infinite in extent in the y-axis
t2.Scale(diam_a / 2.0, 1, diam_c / 2.0)
r = diam_b / 2.0
elif roi_orientation == 'Z':
# cylinder is infinite in extent in the y-axis
t2.Scale(diam_a / 2.0, diam_b / 2.0, 1)
t2.RotateX(90)
r = diam_c / 2.0
clip1.SetOrigin(0, r, 0)
clip2.SetOrigin(0, -r, 0)
# combine transforms
t2.SetInput(self.__Transform)
obj.SetTransform(t2.GetInverse())
elif roi_type == 'ellipsoid':
obj = vtk.vtkSphere()
obj.SetRadius(1.0)
xc, yc, zc = (b[1] + b[0]) * \
0.5, (b[3] + b[2]) * 0.5, (b[5] + b[4]) * 0.5
diam_a, diam_b, diam_c = (
b[1] - b[0]), (b[3] - b[2]), (b[5] - b[4])
t2 = vtk.vtkTransform()
t2.Translate(xc, yc, zc)
t2.Scale(diam_a / 2.0, diam_b / 2.0, diam_c / 2.0)
# combine transforms
t2.SetInput(self.__Transform)
obj.SetTransform(t2.GetInverse())
self._StencilGenerator.SetInput(obj)
_t1 = time.time()
self._StencilGenerator.Update()
_t2 = time.time()
return self._StencilGenerator.GetOutput()
