def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
self.Image = cast.GetOutput()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
if not self.ImageSeeder:
self.ImageSeeder = vmtkscripts.vmtkImageSeeder()
self.ImageSeeder.vmtkRenderer = self.vmtkRenderer
self.ImageSeeder.Image = self.Image
self.ImageSeeder.Display = 0
self.ImageSeeder.Execute()
self.ImageSeeder.Display = 1
self.ImageSeeder.BuildView()
if not self.SurfaceViewer:
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
initializationMethods = {
'0': self.CollidingFrontsInitialize,
'1': self.FastMarchingInitialize,
'2': self.ThresholdInitialize,
'3': self.IsosurfaceInitialize,
'4': self.SeedInitialize
}
endInitialization = False
while not endInitialization:
queryString = 'Please choose initialization type: (0: colliding fronts; 1: fast marching; 2: threshold; 3: isosurface, 4: seed): '
initializationType = self.InputText(queryString,self.InitializationTypeValidator)
initializationMethods[initializationType]()
self.DisplayLevelSetSurface(self.InitialLevelSets)
queryString = 'Accept initialization? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
self.MergeLevelSets()
self.DisplayLevelSetSurface(self.MergedInitialLevelSets)
queryString = 'Initialize another branch? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
endInitialization = False
elif inputString == 'n':
endInitialization = True
self.InitialLevelSets = self.MergedInitialLevelSets
self.MergedInitialLevelSets = None
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
cast = vtk.vtkImageCast()
cast.SetInputData(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
self.Image = cast.GetOutput()
if self.NegateImage:
scalarRange = self.Image.GetScalarRange()
negate = vtk.vtkImageMathematics()
negate.SetInputData(self.Image)
negate.SetOperationToMultiplyByK()
negate.SetConstantK(-1.0)
negate.Update()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInputConnection(negate.GetOutputPort())
shiftScale.SetShift(scalarRange[1]+scalarRange[0])
shiftScale.SetOutputScalarTypeToFloat()
shiftScale.Update()
self.Image = shiftScale.GetOutput()
if self.Interactive:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if not self.ImageSeeder:
self.ImageSeeder = vmtkscripts.vmtkImageSeeder()
self.ImageSeeder.vmtkRenderer = self.vmtkRenderer
self.ImageSeeder.Image = self.Image
self.ImageSeeder.Display = 0
self.ImageSeeder.Execute()
##self.ImageSeeder.Display = 1
self.ImageSeeder.BuildView()
if not self.SurfaceViewer:
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
initializationMethods = {
'0': self.CollidingFrontsInitialize,
'1': self.FastMarchingInitialize,
'2': self.ThresholdInitialize,
'3': self.IsosurfaceInitialize,
'4': self.SeedInitialize
}
endInitialization = False
while not endInitialization:
queryString = 'Please choose initialization type: \n 0: colliding fronts;\n 1: fast marching;\n 2: threshold;\n 3: isosurface;\n 4: seed\n '
initializationType = self.InputText(queryString,self.InitializationTypeValidator)
initializationMethods[initializationType]()
self.DisplayLevelSetSurface(self.InitialLevelSets)
queryString = 'Accept initialization? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
self.MergeLevelSets()
self.DisplayLevelSetSurface(self.MergedInitialLevelSets)
queryString = 'Initialize another branch? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
endInitialization = False
elif inputString == 'n':
endInitialization = True
self.InitialLevelSets = self.MergedInitialLevelSets
self.MergedInitialLevelSets = None
else:
if self.Method == "collidingfronts":
self.CollidingFrontsInitialize()
elif self.Method == "fastmarching":
self.FastMarchingInitialize()
elif self.Method == "threshold":
self.ThresholdInitialize()
elif self.Method == "isosurface":
self.IsosurfaceInitialize()
elif self.Method == "seeds":
self.SeedInitialize()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
cast = vtk.vtkImageCast()
cast.SetInputData(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
self.Image = cast.GetOutput()
if not self.InitializationImage:
self.InitializationImage = self.Image
if not self.FeatureImage:
if self.LevelSetsType in ["geodesic", "curves"]:
imageFeatures = vmtkscripts.vmtkImageFeatures()
imageFeatures.Image = self.Image
imageFeatures.FeatureImageType = self.FeatureImageType
imageFeatures.SigmoidRemapping = self.SigmoidRemapping
imageFeatures.DerivativeSigma = self.FeatureDerivativeSigma
imageFeatures.UpwindFactor = self.UpwindFactor
imageFeatures.FWHMRadius = self.FWHMRadius
imageFeatures.FWHMBackgroundValue = self.FWHMBackgroundValue
imageFeatures.Execute()
self.FeatureImage = imageFeatures.FeatureImage
elif self.LevelSetsType in ["threshold", "laplacian"]:
self.FeatureImage = self.Image
else:
self.PrintError('Unsupported LevelSetsType')
if self.NumberOfIterations != 0:
self.LevelSetsInput = self.InitialLevelSets
self.LevelSetEvolution()
self.MergeLevelSet()
return
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.ImageSeeder = vmtkscripts.vmtkImageSeeder()
self.ImageSeeder.vmtkRenderer = self.vmtkRenderer
#self.ImageSeeder.Image = self.Image
self.ImageSeeder.Image = self.InitializationImage
self.ImageSeeder.Display = 0
self.ImageSeeder.Execute()
##self.ImageSeeder.Display = 1
self.ImageSeeder.BuildView()
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
if self.LevelSets != None:
self.DisplayLevelSetSurface(self.LevelSets,0.0)
self.vmtkImageInitialization = vmtkscripts.vmtkImageInitialization()
#self.vmtkImageInitialization.Image = self.Image
self.vmtkImageInitialization.Image = self.InitializationImage
self.vmtkImageInitialization.vmtkRenderer = self.vmtkRenderer
self.vmtkImageInitialization.ImageSeeder = self.ImageSeeder
self.vmtkImageInitialization.SurfaceViewer = self.SurfaceViewer
self.vmtkImageInitialization.NegateImage = self.NegateForInitialization
self.vmtkImageInitialization.OwnRenderer = 0
endSegmentation = 0
while (endSegmentation == 0):
if self.InitialLevelSets == None:
self.vmtkImageInitialization.Execute()
self.LevelSetsInput = self.vmtkImageInitialization.InitialLevelSets
# self.IsoSurfaceValue = self.vmtkImageInitialization.IsoSurfaceValue
self.vmtkImageInitialization.InitialLevelSets = None
# self.vmtkImageInitialization.IsosurfaceValue = 0.0
self.IsoSurfaceValue = 0.0
else:
self.LevelSetsInput = self.InitialLevelSets
self.InitialLevelSets = None
self.DisplayLevelSetSurface(self.LevelSetsInput,self.IsoSurfaceValue)
endEvolution = False
while not endEvolution:
queryString = 'Please input parameters (type return to accept current values, \'e\' to end, \'q\' to quit):\nNumberOfIterations('+str(self.NumberOfIterations)+') [PropagationScaling('+str(self.PropagationScaling)+') CurvatureScaling('+str(self.CurvatureScaling)+') AdvectionScaling('+str(self.AdvectionScaling)+')]: '
inputString = self.InputText(queryString,self.EvolutionParametersValidator)
if inputString == 'q':
return
elif inputString == 'e':
endEvolution = True
elif inputString != '':
splitInputString = inputString.strip().split(' ')
if len(splitInputString) == 1:
self.NumberOfIterations = int(splitInputString[0])
elif len(splitInputString) == 4:
self.NumberOfIterations = int(splitInputString[0])
self.PropagationScaling = float(splitInputString[1])
self.CurvatureScaling = float(splitInputString[2])
self.AdvectionScaling = float(splitInputString[3])
else:
self.PrintLog('Wrong number of parameters.')
continue
if endEvolution:
break
self.LevelSetEvolution()
self.DisplayLevelSetSurface(self.LevelSetsOutput)
queryString = 'Accept result? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
endEvolution = True
elif inputString == 'n':
endEvolution = False
queryString = 'Merge branch? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
self.MergeLevelSet()
elif inputString == 'n':
pass
if self.LevelSets != None:
self.DisplayLevelSetSurface(self.LevelSets)
queryString = 'Segment another branch? (y/n): '
inputString = self.InputText(queryString,self.YesNoValidator)
if inputString == 'y':
endSegmentation = False
elif inputString == 'n':
endSegmentation = True
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
self.Image = cast.GetOutput()
if not self.InitializationImage:
self.InitializationImage = self.Image
if not self.FeatureImage:
if self.LevelSetsType in ["geodesic", "curves"]:
imageFeatures = vmtkscripts.vmtkImageFeatures()
imageFeatures.Image = self.Image
imageFeatures.FeatureImageType = self.FeatureImageType
imageFeatures.SigmoidRemapping = self.SigmoidRemapping
imageFeatures.DerivativeSigma = self.FeatureDerivativeSigma
imageFeatures.UpwindFactor = self.UpwindFactor
imageFeatures.FWHMRadius = self.FWHMRadius
imageFeatures.FWHMBackgroundValue = self.FWHMBackgroundValue
imageFeatures.Execute()
self.FeatureImage = imageFeatures.FeatureImage
elif self.LevelSetsType in ["threshold", "laplacian"]:
self.FeatureImage = self.Image
else:
self.PrintError('Unsupported LevelSetsType')
if self.NumberOfIterations != 0:
self.LevelSetsInput = self.InitialLevelSets
self.LevelSetEvolution()
self.MergeLevelSet()
return
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.ImageSeeder = vmtkscripts.vmtkImageSeeder()
self.ImageSeeder.vmtkRenderer = self.vmtkRenderer
#self.ImageSeeder.Image = self.Image
self.ImageSeeder.Image = self.InitializationImage
self.ImageSeeder.Display = 0
self.ImageSeeder.Execute()
self.ImageSeeder.Display = 1
self.ImageSeeder.BuildView()
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
if self.LevelSets != None:
self.DisplayLevelSetSurface(self.LevelSets, 0.0)
self.vmtkImageInitialization = vmtkscripts.vmtkImageInitialization()
#self.vmtkImageInitialization.Image = self.Image
self.vmtkImageInitialization.Image = self.InitializationImage
self.vmtkImageInitialization.vmtkRenderer = self.vmtkRenderer
self.vmtkImageInitialization.ImageSeeder = self.ImageSeeder
self.vmtkImageInitialization.SurfaceViewer = self.SurfaceViewer
self.vmtkImageInitialization.NegateImage = self.NegateForInitialization
self.vmtkImageInitialization.OwnRenderer = 0
endSegmentation = 0
while (endSegmentation == 0):
if self.InitialLevelSets == None:
self.vmtkImageInitialization.Execute()
self.LevelSetsInput = self.vmtkImageInitialization.InitialLevelSets
# self.IsoSurfaceValue = self.vmtkImageInitialization.IsoSurfaceValue
self.vmtkImageInitialization.InitialLevelSets = None
# self.vmtkImageInitialization.IsosurfaceValue = 0.0
self.IsoSurfaceValue = 0.0
else:
self.LevelSetsInput = self.InitialLevelSets
self.InitialLevelSets = None
self.DisplayLevelSetSurface(self.LevelSetsInput,
self.IsoSurfaceValue)
endEvolution = False
while not endEvolution:
queryString = 'Please input parameters (type return to accept current values, \'e\' to end, \'q\' to quit):\nNumberOfIterations(' + str(
self.NumberOfIterations) + ') [PropagationScaling(' + str(
self.PropagationScaling) + ') CurvatureScaling(' + str(
self.CurvatureScaling
) + ') AdvectionScaling(' + str(
self.AdvectionScaling) + ')]: '
inputString = self.InputText(queryString,
self.EvolutionParametersValidator)
if inputString == 'q':
return
elif inputString == 'e':
endEvolution = True
elif inputString != '':
splitInputString = inputString.strip().split(' ')
if len(splitInputString) == 1:
self.NumberOfIterations = int(splitInputString[0])
elif len(splitInputString) == 4:
self.NumberOfIterations = int(splitInputString[0])
self.PropagationScaling = float(splitInputString[1])
self.CurvatureScaling = float(splitInputString[2])
self.AdvectionScaling = float(splitInputString[3])
else:
self.PrintLog('Wrong number of parameters.')
continue
if endEvolution:
break
self.LevelSetEvolution()
self.DisplayLevelSetSurface(self.LevelSetsOutput)
queryString = 'Accept result? (y/n): '
inputString = self.InputText(queryString, self.YesNoValidator)
if inputString == 'y':
endEvolution = True
elif inputString == 'n':
endEvolution = False
queryString = 'Merge branch? (y/n): '
inputString = self.InputText(queryString, self.YesNoValidator)
if inputString == 'y':
self.MergeLevelSet()
elif inputString == 'n':
pass
if self.LevelSets != None:
self.DisplayLevelSetSurface(self.LevelSets)
queryString = 'Segment another branch? (y/n): '
inputString = self.InputText(queryString, self.YesNoValidator)
if inputString == 'y':
endSegmentation = False
elif inputString == 'n':
endSegmentation = True
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
cast = vtk.vtkImageCast()
cast.SetInput(self.Image)
cast.SetOutputScalarTypeToFloat()
cast.Update()
self.Image = cast.GetOutput()
if self.NegateImage:
scalarRange = self.Image.GetScalarRange()
negate = vtk.vtkImageMathematics()
negate.SetInput(self.Image)
negate.SetOperationToMultiplyByK()
negate.SetConstantK(-1.0)
negate.Update()
shiftScale = vtk.vtkImageShiftScale()
shiftScale.SetInput(negate.GetOutput())
shiftScale.SetShift(scalarRange[1] + scalarRange[0])
shiftScale.SetOutputScalarTypeToFloat()
shiftScale.Update()
self.Image = shiftScale.GetOutput()
if self.Interactive:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if not self.ImageSeeder:
self.ImageSeeder = vmtkscripts.vmtkImageSeeder()
self.ImageSeeder.vmtkRenderer = self.vmtkRenderer
self.ImageSeeder.Image = self.Image
self.ImageSeeder.Display = 0
self.ImageSeeder.Execute()
##self.ImageSeeder.Display = 1
self.ImageSeeder.BuildView()
if not self.SurfaceViewer:
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
self.SurfaceViewer.vmtkRenderer = self.vmtkRenderer
initializationMethods = {
'0': self.CollidingFrontsInitialize,
'1': self.FastMarchingInitialize,
'2': self.ThresholdInitialize,
'3': self.IsosurfaceInitialize,
'4': self.SeedInitialize
}
endInitialization = False
while not endInitialization:
queryString = 'Please choose initialization type: \n 0: colliding fronts;\n 1: fast marching;\n 2: threshold;\n 3: isosurface;\n 4: seed\n '
initializationType = self.InputText(
queryString, self.InitializationTypeValidator)
initializationMethods[initializationType]()
self.DisplayLevelSetSurface(self.InitialLevelSets)
queryString = 'Accept initialization? (y/n): '
inputString = self.InputText(queryString, self.YesNoValidator)
if inputString == 'y':
self.MergeLevelSets()
self.DisplayLevelSetSurface(self.MergedInitialLevelSets)
queryString = 'Initialize another branch? (y/n): '
inputString = self.InputText(queryString, self.YesNoValidator)
if inputString == 'y':
endInitialization = False
elif inputString == 'n':
endInitialization = True
self.InitialLevelSets = self.MergedInitialLevelSets
self.MergedInitialLevelSets = None
else:
if self.Method == "collidingfronts":
self.CollidingFrontsInitialize()
elif self.Method == "fastmarching":
self.FastMarchingInitialize()
elif self.Method == "threshold":
self.ThresholdInitialize()
elif self.Method == "isosurface":
self.IsosurfaceInitialize()
elif self.Method == "seeds":
self.SeedInitialize()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
