def Read_and_Smooth(path_reader,
path_writer,
coeff_smooth=0.001,
nb_iterations=50):
#READ THE SURFACE
print(" ---> Reading Marching-Cube surface")
myReader = vmtkscripts.vmtkSurfaceReader()
myReader.InputFileName = path_reader
myReader.Format = 'stl'
myReader.Execute()
#SMOOTH THE SURFACE
print(" ---> Smoothing surface with coeff {} and {} ierations".format(
coeff_smooth, nb_iterations))
mySmoother = vmtkscripts.vmtkSurfaceSmoothing()
mySmoother.Surface = myReader.Surface
mySmoother.PassBand = coeff_smooth
mySmoother.NumberOfIterations = nb_iterations
mySmoother.Execute()
#WRITE TO STL FILE
print(" ---> Writing results to STL file ")
myWriter = vmtkscripts.vmtkSurfaceWriter()
myWriter.Surface = mySmoother.Surface
myWriter.OutputFileName = path_writer
myWriter.Format = 'stl'
myWriter.Execute()
def vmtksurfacesmoothing(surface, iterations=100, method='taubin'):
smoother = vmtkscripts.vmtkSurfaceSmoothing()
smoother.Surface = surface
smoother.Method = method
smoother.NumberOfIterations = iterations
smoother.PassBand = 0.1
smoother.Execute()
return smoother.Surface
def Add_extension(path_reader,
path_writer,
extension_ratio=10,
target_edge_length=0.7,
nb_iterations=5):
myReader = vmtkscripts.vmtkSurfaceReader()
myReader.InputFileName = path_reader
myReader.Format = 'stl'
myReader.Execute()
myCenterline = vmtkscripts.vmtkCenterlines()
myCenterline.Surface = myReader.Surface
myCenterline.SeedSelectorName = 'openprofiles'
myCenterline.Execute()
myExtension = vmtkscripts.vmtkFlowExtensions()
myExtension.Surface = myReader.Surface
myExtension.Centerlines = myCenterline.Centerlines
myExtension.AdaptiveExtensionLength = 1
myExtension.AdaptiveExtensionRadius = 1
myExtension.ExtensionMode = "boundarynormal"
myExtension.ExtensionRatio = extension_ratio
myExtension.Interactive = 0
myExtension.Execute()
mySmoother = vmtkscripts.vmtkSurfaceSmoothing()
mySmoother.Surface = myExtension.Surface
mySmoother.PassBand = 0.3
mySmoother.NumberOfIterations = 5
mySmoother.Execute()
myRemesh = vmtkscripts.vmtkSurfaceRemeshing()
myRemesh.Surface = mySmoother.Surface
myRemesh.ElementSizeMode = 'edgelength'
myRemesh.TargetEdgeLength = target_edge_length
myRemesh.NumberOfIterations = nb_iterations
myRemesh.Execute()
myWriter = vmtkscripts.vmtkSurfaceWriter()
myWriter.Surface = myRemesh.Surface
myWriter.OutputFileName = path_writer
myWriter.Format = 'stl'
myWriter.Execute()
def vmtk_smooth_surface(surface,
method,
iterations=800,
passband=1.0,
relaxation=0.01,
normalize_coordinates=True,
smooth_boundary=True):
"""Wrapper for a vmtksurfacesmoothing.
Args:
smooth_boundary (bool): Toggle allow change of position of boundary points
normalize_coordinates (bool): Normalization of coordinates prior to filtering,
minimize spurious translation effects (Taubin only)
surface (vtkPolyData): Input surface to be smoothed.
method (str): Smoothing method.
iterations (int): Number of iterations.
passband (float): The passband for Taubin smoothing.
relaxation (float): The relaxation for laplace smoothing.
Returns:
surface (vtkPolyData): The smoothed surface.
"""
smoother = vmtkscripts.vmtkSurfaceSmoothing()
smoother.Surface = surface
smoother.NumberOfIterations = iterations
if method == "laplace":
smoother.RelaxationFactor = relaxation
elif method == "taubin":
smoother.PassBand = passband
if not normalize_coordinates:
smoother.NormalizeCoordinates = 0
if not smooth_boundary:
smoother.BoundarySmoothing = 0
smoother.Method = method
smoother.Execute()
surface = smoother.Surface
return surface
def vmtksurfacesmoothing(surface, iterations=100, method='taubin'):
"""Smooth a surface.
Args:
surface: Surface mesh.
iterations: Number of smoothing iterations.
method ('taubin', 'laplace'): Taubin's volume-preserving or a Laplacian
smoothing filter.
Returns:
Smoothed surface.
"""
smoother = vmtkscripts.vmtkSurfaceSmoothing()
smoother.Surface = surface
smoother.Method = method
smoother.NumberOfIterations = iterations
smoother.PassBand = 0.1
smoother.Execute()
return smoother.Surface
def vmtksurfacesmoothing(surface, iterations=100, method='taubin'):
"""Smooth a surface.
Args:
surface: Surface mesh.
iterations: Number of smoothing iterations.
method ('taubin', 'laplace'): Taubin's volume-preserving or a Laplacian
smoothing filter.
Returns:
Smoothed surface.
"""
smoother = vmtkscripts.vmtkSurfaceSmoothing()
smoother.Surface = surface
smoother.Method = method
smoother.NumberOfIterations = iterations
smoother.PassBand = 0.1
smoother.Execute()
return smoother.Surface
def Execute(self):
# Error handling
if self.Surface == None:
self.PrintError(
'Error: no input surface was supplied, ensure file exists, ensure correct environment'
)
# Allocate a renderer and label own renderer in use to prevent multiple renderers from being used
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
# Render and build view of the input surface
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.BuildView()
# Test question in render window
#queryStr = 'Is this the question you wanted to see? '
#inputStr = self.YesNoInput(queryStr, self.YesNoValidator)
# Surface smoothing, try defaults first then take user input if not adequate
acceptableResult = 0
response = 0
while acceptableResult == 0:
if response == 0:
self.SurfaceSmoothing = vmtkscripts.vmtkSurfaceSmoothing()
self.SurfaceSmoothing.NumberOfIterations = 100
self.PassBand = 0.001
elif response == 1:
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.BuildView()
self.SurfaceSmoothing = vmtkscripts.vmtkSurfaceSmoothing()
#Take passband from user
queryStr = 'Please enter value for pass band (0.001 - 0.1): '
self.SurfaceSmoothing.PassBand = float(
self.InputText(queryStr, self.PassBandValidator))
#Take number of iterations from user
queryStr = 'Please enter number of iterations (1-999): '
self.SurfaceSmoothing.NumberOfIterations = int(
self.InputText(queryStr, self.IterationValidator))
self.SurfaceSmoothing.Surface = self.Surface
self.SurfaceSmoothing.Execute()
self.SurfaceViewer.Surface = self.SurfaceSmoothing.Surface
self.SurfaceViewer.BuildView()
# Accept or reject result of smoothing surface
queryStr = 'Accept result of smoothing?(y/n): '
if (self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
self.Surface = self.SurfaceSmoothing.Surface
else:
acceptableResult = 0
response = 1
# Surface clipping
# The only issue here is that 2 renderers get built 2/2 the structure of vmtkSurfaceClipper
# Issue to be revisited later
acceptableResult = 0
while acceptableResult == 0:
self.SurfaceClipper = vmtkscripts.vmtkSurfaceClipper()
self.SurfaceClipper.Surface = self.Surface
self.SurfaceClipper.Execute()
self.SurfaceViewer.Surface = self.SurfaceClipper.Surface
self.SurfaceViewer.BuildView()
queryStr = 'Accept result of clipping?(y/n): '
if (self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
self.Surface = self.SurfaceClipper.Surface
else:
acceptableResult = 0
self.SurfaceViewer.Surface = self.SurfaceClipper.Surface
self.SurfaceViewer.BuildView()
# Create centerlines based off the acceptable clipped surface
centerliner = vmtkscripts.vmtkCenterlines()
centerliner.Surface = self.Surface
centerliner.SeedSelectorName = 'openprofiles'
centerliner.Execute()
self.Centerlines = centerliner.Centerlines
# Add flow extensions until user has acceptable result
acceptableResult = 0
response = 0
while (acceptableResult == 0):
self.FlowExtensions = vmtkscripts.vmtkFlowExtensions()
self.FlowExtensions.Surface = self.Surface
self.FlowExtensions.Centerlines = self.Centerlines
self.FlowExtensions.AdaptiveExtensionLength = 1
#self.FlowExtensions.CenterlineNormalEstimationDistanceRatio = 1
self.FlowExtensions.Interactive = 0
# Take user extension ratio if response to acceptable outcome question
# Default extension ratio is 10
if (response == 0):
self.FlowExtensions.ExtensionRatio = 10
elif (response == 1):
#Take extension ratio from user
queryStr = 'Please enter value for pass band; default is 20 (min/max 1-50): '
self.FlowExtensions.ExtensionRatio = float(
self.InputText(queryStr, self.ExtensionRatioValidator))
self.FlowExtensions.Execute()
self.SurfaceViewer.Surface = self.FlowExtensions.Surface
self.SurfaceViewer.BuildView()
queryStr = 'Accept flow extensions?(y/n): '
if (self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
self.Surface = self.FlowExtensions.Surface
else:
acceptableResult = 0
response = 1
# self.SurfaceViewer.BuildView()
# Deallocate renderer
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.BuildView()
queryStr = 'Accept results of level set and marching cubes? (y/n): '
if(self.YesNoInput(queryStr, self.YesNoValidator)):
acceptableResult = 1
else:
acceptableResult = 0
# Surface smoothing, try defaults first then take user input if not adequate
acceptableResult = 0
response = 0
while acceptableResult == 0:
if response == 0:
self.SurfaceSmoothing = vmtkscripts.vmtkSurfaceSmoothing()
self.SurfaceSmoothing.NumberOfIterations = 50
self.PassBand = 0.01
elif response == 1:
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.BuildView()
self.SurfaceSmoothing = vmtkscripts.vmtkSurfaceSmoothing()
#Take passband from user
queryStr = 'Please enter value for pass band [default = 0.01] (0.001 - 0.1): '
self.SurfaceSmoothing.PassBand = float(self.InputText(queryStr, self.PassBandValidator))
#Take number of iterations from user
queryStr = 'Please enter number of iterations [default = 50] (1-999): '
self.SurfaceSmoothing.NumberOfIterations = int(self.InputText(queryStr, self.IterationValidator))