def ExtractGeometry(centerlines):
#centerlines=EquispacedSpline(centerlines.Centerlines,0.05) # every 0.5mm
centerlineResampling = vmtkscripts.vmtkCenterlineResampling()
centerlineResampling.Centerlines = centerlines.Centerlines
centerlineResampling.Length = 0.05
centerlineResampling.Execute()
centerlineGeometry = vmtkscripts.vmtkCenterlineGeometry()
centerlineGeometry.Centerlines = centerlineResampling.Centerlines
centerlineGeometry.SmoothingFactor = 0.4
centerlineGeometry.FrenetTangentArrayName = 'FrenetTangent'
centerlineGeometry.FrenetNormalArrayName = 'FrenetNormal'
centerlineGeometry.FrenetBinormalArrayName = 'FrenetBinormal'
centerlineGeometry.Execute()
centerlineAttributes = vmtkscripts.vmtkCenterlineAttributes()
centerlineAttributes.Centerlines = centerlineGeometry.Centerlines
centerlineAttributes.Execute()
branchExtractor = vmtkscripts.vmtkBranchExtractor()
branchExtractor.Centerlines = centerlineAttributes.Centerlines
branchExtractor.GroupIdsArrayName = 'GroupIds'
branchExtractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
branchExtractor.CenterlineIdsArrayName = 'CenterlineIds'
branchExtractor.BlankingArrayName = 'Blanking'
branchExtractor.Execute()
return branchExtractor
def vmtk_compute_centerline_attributes(centerlines):
""" Wrapper for centerline attributes.
Args:
centerlines (vtkPolyData): Line to investigate.
Returns:
line (vtkPolyData): Line with centerline atributes.
"""
attributes = vmtkscripts.vmtkCenterlineAttributes()
attributes.Centerlines = centerlines
attributes.NormalsArrayName = parallelTransportNormalsArrayName
attributes.AbscissaArrayName = abscissasArrayName
attributes.Execute()
centerlines = attributes.Centerlines
return centerlines
def vmtkcenterlineattributes(centerlines):
"""Compute centerline attributes.
Args:
centerlines: Centerlines.
Returns:
Centerlines with attributes.
Pointdata:
MaximumInscribedSphereRadius: If the point on the centerline is the
center of a sphere, this is the radius of the largest possible
sphere that does not intersect the surface.
Abscissas: Position along the centerlines. By default, the abscissa
is measured from the start of the centerlines.
ParallelTransportNormals: 'Normal' of the centerlines (perpendicular
to centerline direction).
"""
clattributes = vmtkscripts.vmtkCenterlineAttributes()
clattributes.Centerlines = centerlines
clattributes.Execute()
return clattributes.Centerlines
def vmtkcenterlineattributes(centerlines):
"""Compute centerline attributes.
Args:
centerlines: Centerlines.
Returns:
Centerlines with attributes.
Pointdata:
MaximumInscribedSphereRadius: If the point on the centerline is the
center of a sphere, this is the radius of the largest possible
sphere that does not intersect the surface.
Abscissas: Position along the centerlines. By default, the abscissa
is measured from the start of the centerlines.
ParallelTransportNormals: 'Normal' of the centerlines (perpendicular
to centerline direction).
"""
clattributes = vmtkscripts.vmtkCenterlineAttributes()
clattributes.Centerlines = centerlines
clattributes.Execute()
return clattributes.Centerlines
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
time.asctime(time.localtime(time.time())))
exit()
start_time = time()
args = "vmtksurfacereader -ifile " + surfaceFile
myPype = pypes.PypeRun(args)
mySurface = myPype.GetScriptObject('vmtksurfacereader', '0').Surface
myctrl = vmtkscripts.vmtkCenterlines()
myctrl.Surface = mySurface
myctrl.SeedSelectorName = 'openprofiles'
# myctrl.Centerlines = centerlinesFile
myctrl.Execute()
myattr = vmtkscripts.vmtkCenterlineAttributes()
myattr.Centerlines = myctrl.Centerlines
myattr.Execute()
mybranchextractor = vmtkscripts.vmtkBranchExtractor()
mybranchextractor.Centerlines = myattr.Centerlines
mybranchextractor.RadiusArrayName = 'MaximumInscribedSphereRadius'
mybranchextractor.Execute()
# mywriter = vmtkscripts.vmtkSurfaceWriter()
# mywriter.Surface = mybranchextractor.Centerlines
# mywriter.OutputFileName = centerlinesFileName
# mywriter.Execute()
mybifref = vmtkscripts.vmtkBoundaryReferenceSystems()
mybifref.Surface = mybranchextractor.Centerlines
def vmtkcenterlineattributes(centerline):
computer = vmtkscripts.vmtkCenterlineAttributes()
computer.Centerlines = centerline
computer.Execute()
return computer.Centerlines
def vmtkcenterlineattributes(centerline):
computer = vmtkscripts.vmtkCenterlineAttributes()
computer.Centerlines = centerline
computer.Execute()
return computer.Centerlines