def test_change_spacing(aorta_surface, compare_images):
name = __name__ + '_test_change_spacing.vti'
surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
surfToImage.Surface = aorta_surface
surfToImage.PolyDataToImageDataSpacing = [0.4, 0.4, 0.4]
surfToImage.Execute()
assert compare_images(surfToImage.Image, name) == True
def test_change_spacing(aorta_surface, compare_images):
name = __name__ + '_test_change_spacing.vti'
surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
surfToImage.Surface = aorta_surface
surfToImage.PolyDataToImageDataSpacing = [0.4, 0.4, 0.4]
surfToImage.Execute()
assert compare_images(surfToImage.Image, name) == True
def test_set_inside_outside_values(aorta_surface, compare_images, insidevalue,
outsidevalue, paramid):
name = __name__ + '_test_set_inside_outside_values_' + paramid + '.vti'
surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
surfToImage.Surface = aorta_surface
surfToImage.InsideValue = insidevalue
surfToImage.OutsideValue = outsidevalue
surfToImage.Execute()
assert compare_images(surfToImage.Image, name) == True
def test_set_inside_outside_values(aorta_surface, compare_images,
insidevalue, outsidevalue, paramid):
name = __name__ + '_test_set_inside_outside_values_' + paramid + '.vti'
surfToImage = surfacetobinaryimage.vmtkSurfaceToBinaryImage()
surfToImage.Surface = aorta_surface
surfToImage.InsideValue = insidevalue
surfToImage.OutsideValue = outsidevalue
surfToImage.Execute()
assert compare_images(surfToImage.Image, name) == True
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No Input Surface.')
# Step 0: Check if the surface has any unfilled holes in it. if it does, cap them.
fedges = vtk.vtkFeatureEdges()
fedges.BoundaryEdgesOn()
fedges.FeatureEdgesOff()
fedges.ManifoldEdgesOff()
fedges.SetInputData(self.Surface)
fedges.Update()
ofedges = fedges.GetOutput()
# if the following is not == 0, then the surface contains unfilled holes.
numEdges = ofedges.GetNumberOfPoints()
if numEdges >= 1:
self.PrintLog('Capping unclosed holes in surface.')
tempcapper = vmtksurfacecapper.vmtkSurfaceCapper()
tempcapper.Surface = self.Surface
tempcapper.LogOn = 0
tempcapper.Interactive = 0
tempcapper.Execute()
self.Surface = tempcapper.Surface
# Step 1: Convert the input surface into an image mask of unsigned char type and spacing = PolyDataToImageDataSpacing
# Where voxels lying inside the surface are set to 255 and voxels outside the image are set to value 0.
# since we are creating a new image container from nothing, calculate the origin, extent, and dimensions for the
# vtkImageDataObject from the surface parameters.
self.PrintLog('Converting Surface to Image Mask')
binaryImageFilter = vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage()
binaryImageFilter.Surface = self.Surface
binaryImageFilter.InsideValue = 255
binaryImageFilter.LogOn = 0
binaryImageFilter.OutsideValue = 0
binaryImageFilter.PolyDataToImageDataSpacing = self.PolyDataToImageDataSpacing
binaryImageFilter.Execute()
# Step 2: Feed into the vtkvmtkMedialCurveFilter
# This takes the binary image and computes the average outward flux of the image. This is then
# used to compute the skeleton image. It returns a binary image where values of 1 are skeleton points
# and values of 0 are outside the skeleton. The execution speed of this algorithm is fairly sensetive to
# the extent of the input image.
self.PrintLog('Extracting Centerline Skeleton from Image Mask...')
medialCurveFilter = vtkvmtk.vtkvmtkMedialCurveFilter()
medialCurveFilter.SetInputData(binaryImageFilter.Image)
medialCurveFilter.SetThreshold(self.Threshold)
medialCurveFilter.SetSigma(self.Sigma)
medialCurveFilter.Update()
self.Image = medialCurveFilter.GetOutput()
def Execute(self):
if self.Surface == None:
self.PrintError('Error: No Input Surface.')
# Step 0: Check if the surface has any unfilled holes in it. if it does, cap them.
fedges = vtk.vtkFeatureEdges()
fedges.BoundaryEdgesOn()
fedges.FeatureEdgesOff()
fedges.ManifoldEdgesOff()
fedges.SetInputData(self.Surface)
fedges.Update()
ofedges = fedges.GetOutput()
# if the following is not == 0, then the surface contains unfilled holes.
numEdges = ofedges.GetNumberOfPoints()
if numEdges >= 1:
self.PrintLog('Capping unclosed holes in surface.')
tempcapper = vmtksurfacecapper.vmtkSurfaceCapper()
tempcapper.Surface = self.Surface
tempcapper.LogOn = 0
tempcapper.Interactive = 0
tempcapper.Execute()
self.Surface = tempcapper.Surface
# Step 1: Convert the input surface into an image mask of unsigned char type and spacing = PolyDataToImageDataSpacing
# Where voxels lying inside the surface are set to 255 and voxels outside the image are set to value 0.
# since we are creating a new image container from nothing, calculate the origin, extent, and dimensions for the
# vtkImageDataObject from the surface parameters.
self.PrintLog('Converting Surface to Image Mask')
binaryImageFilter = vmtksurfacetobinaryimage.vmtkSurfaceToBinaryImage()
binaryImageFilter.Surface = self.Surface
binaryImageFilter.InsideValue = 255
binaryImageFilter.LogOn = 0
binaryImageFilter.OutsideValue = 0
binaryImageFilter.PolyDataToImageDataSpacing = self.PolyDataToImageDataSpacing
binaryImageFilter.Execute()
# Step 2: Feed into the vtkvmtkMedialCurveFilter
# This takes the binary image and computes the average outward flux of the image. This is then
# used to compute the skeleton image. It returns a binary image where values of 1 are skeleton points
# and values of 0 are outside the skeleton. The execution speed of this algorithm is fairly sensetive to
# the extent of the input image.
self.PrintLog('Extracting Centerline Skeleton from Image Mask...')
medialCurveFilter = vtkvmtk.vtkvmtkMedialCurveFilter()
medialCurveFilter.SetInputData(binaryImageFilter.Image)
medialCurveFilter.SetThreshold(self.Threshold)
medialCurveFilter.SetSigma(self.Sigma)
medialCurveFilter.Update()
self.Image = medialCurveFilter.GetOutput()
