def Execute(self):
from vmtk import vmtkscripts
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):
print("Compute VC orientation")
self.ctrliner = vmtkscripts.vmtkCenterlines()
self.ctrliner.Surface = self.Surface
self.ctrliner.Execute()
self.Centerlines = self.ctrliner.Centerlines
cc = self.Centerlines
ptCoord = []
for c in xrange(cc.GetNumberOfPoints()):
ptCoord.append(cc.GetPoints().GetPoint(c))
ptCoord = np.array(ptCoord)
datamean = ptCoord.mean(axis=0)
uu, dd, vv = np.linalg.svd(ptCoord - datamean)
# vector of the general direction of the VC
# print(vv[0], datamean, datamean+10*vv[0])
VCvect = vv[0]
if self.ComputeCenterlines:
# print(self.Surface)
self.ctrliner = vmtkscripts.vmtkCenterlines()
self.ctrliner.Surface = self.Surface
# self.ctrliner.SeedSelector = 'openprofiles'
self.ctrliner.Execute()
self.Centerlines = self.ctrliner.Centerlines
# self.Surface = self.Centerlines
else:
self.Centerlines = self.Surface
# if self.Centerlines == None:
# self.PrintError('DUMBASS')
self.vmtkReader = vmtkscripts.vmtkSurfaceReader()
self.vmtkRenderer = vmtkscripts.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.SurfaceViewer = vmtkscripts.vmtkSurfaceViewer()
# self.Surface = self.Centerlines
self.SurfaceViewer.Surface = self.Surface
self.SurfaceViewer.Execute()
self.myattr = vmtkscripts.vmtkCenterlineAttributes()
self.myattr.Centerlines = self.Centerlines
self.myattr.Execute()
self.mybranchextractor = vmtkscripts.vmtkBranchExtractor()
self.mybranchextractor.Centerlines = self.myattr.Centerlines
self.mybranchextractor.RadiusArrayName = self.RadiusArrayName
self.mybranchextractor.Execute()
self.ctrl = self.mybranchextractor.Centerlines
self.mywriter = vmtkscripts.vmtkSurfaceWriter()
self.mywriter.Surface = self.mybranchextractor.Centerlines
self.mywriter.OutputFileName = '/home/florian/liverSim/morpho_analysis/test_surf_open_small_ctrlTESTbranc1.vtp'
self.mywriter.Execute()
self.mybifref = vmtkscripts.vmtkBifurcationReferenceSystems()
self.mybifref.Centerlines = self.ctrl
self.mybifref.RadiusArrayName = self.RadiusArrayName
self.mybifref.BlankingArrayName = self.BlankingArrayName
self.mybifref.GroupIdsArrayName = self.GroupIdsArrayName
self.mybifref.CenterlineIdsArrayName = self.CenterlineIdsArrayName
self.mybifref.TractIdsArrayName = self.TractIdsArrayName
self.mybifref.Execute()
self.myvect = vmtkscripts.vmtkBifurcationVectors()
self.myvect.Centerlines = self.ctrl
self.myvect.ReferenceSystems = self.mybifref.ReferenceSystems
self.myvect.RadiusArrayName = self.RadiusArrayName
self.myvect.BlankingArrayName = self.BlankingArrayName
self.myvect.GroupIdsArrayName = self.GroupIdsArrayName
self.myvect.TractIdsArrayName = self.TractIdsArrayName
self.myvect.CenterlineIdsArrayName = self.CenterlineIdsArrayName
self.myvect.ReferenceSystemsNormalArrayName = self.mybifref.ReferenceSystemsNormalArrayName
self.myvect.ReferenceSystemsUpNormalArrayName = self.mybifref.ReferenceSystemsUpNormalArrayName
self.myvect.Execute()
'''TEMP'''
self.mywriter = vmtkscripts.vmtkSurfaceWriter()
self.mywriter.Surface = self.myvect.BifurcationVectors
self.mywriter.OutputFileName = '/home/florian/liverSim/morpho_analysis/test_surf_open_small_bifvect.vtp'
self.mywriter.Execute()
self.mywriter.Surface = self.ctrl
self.mywriter.OutputFileName = '/home/florian/liverSim/morpho_analysis/test_surf_open_small_ctrl.vtp'
self.mywriter.Execute()
'''/TEMP'''
self.numpytator = vmtksurfacetonumpy.vmtkSurfaceToNumpy()
self.numpytator.Surface = self.myvect.BifurcationVectors
self.numpytator.Execute()
vectData = self.numpytator.ArrayDict.values()
cprint(figlet_format('Results!', font='bubble'))
print('\n InPlaneBifurcationVectors angle:')
print(np.degrees(self.angle_between(vectData[0]["InPlaneBifurcationVectors"][1, :],
vectData[0]["InPlaneBifurcationVectors"][2, :])))
# print('\n OutOfPlaneBifurcationVectors angle:')
# print(np.degrees(self.angle_between(vectData[0]["OutOfPlaneBifurcationVectors"][1, :],
# vectData[0]["OutOfPlaneBifurcationVectors"][2, :])))
print('\n bifurcation angle with the VC:')
print(np.degrees(self.angle_between(vectData[0]["OutOfPlaneBifurcationVectors"][0, :],
VCvect)))
'''
weighted average vector between the vectors pointing from the second
to the first reference point on each centerline
'''
print('\n global direction of the birfurcation:')
print(vectData[0]["BifurcationVectors"][0, :])
'''
the origin of the bifurcation is defined as the barycenter of the four reference points
weighted by the surface of the maximum inscribed sphere defined on the reference points.
The reason of the weighting is that small branches have less impact on the position of
the bifurcation origin
'''
print('\n Origin of the bifurcation:')
print(vectData[1][0])
pass
def Execute(self):
from vmtk import vmtkscripts
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):
from vmtk import vmtkscripts
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):
from vmtk import vmtkscripts
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()