def vmtkcenterlinegeometry(centerlines, smoothing=0, iterations=100):
"""Compute the local geometry of centerlines.
Args:
centerlines: Centerlines.
smoothing (bool): Laplacian smooth centerlines before computing
geometric variables.
iterations: Number of smoothing iterations.
Returns:
Centerlines with geometric variables defined at each point.
Pointdata (selection):
Curvature: Local curvature.
Torsion: Local torsion.
Celldata (selection):
Tortuosity: Tortuosity of each centerline.
Length: Length of each centerline.
Note:
Since the computation of the geometric variables depends on first,
second and third derivatives of the line coordinates, and since such
derivatives are approximated using a simple finite difference scheme
along the line, it is very likely that such derivatives will be affected
by noise that is not appreciable when looking at the line itself. For
this reason, it might be necessary to run the Laplacian smoothing filter
before computing the derivatives and the related quantities.
"""
clgeometry = vmtkscripts.vmtkCenterlineGeometry()
clgeometry.Centerlines = centerlines
clgeometry.LineSmoothing = smoothing
clgeometry.NumberOfSmoothingIterations = iterations
clgeometry.Execute()
return clgeometry.Centerlines
def vmtkcenterlinegeometry(centerlines, smoothing=0, iterations=100):
"""Compute the local geometry of centerlines.
Args:
centerlines: Centerlines.
smoothing (bool): Laplacian smooth centerlines before computing
geometric variables.
iterations: Number of smoothing iterations.
Returns:
Centerlines with geometric variables defined at each point.
Pointdata (selection):
Curvature: Local curvature.
Torsion: Local torsion.
Celldata (selection):
Tortuosity: Tortuosity of each centerline.
Length: Length of each centerline.
Note:
Since the computation of the geometric variables depends on first,
second and third derivatives of the line coordinates, and since such
derivatives are approximated using a simple finite difference scheme
along the line, it is very likely that such derivatives will be affected
by noise that is not appreciable when looking at the line itself. For
this reason, it might be necessary to run the Laplacian smoothing filter
before computing the derivatives and the related quantities.
"""
clgeometry = vmtkscripts.vmtkCenterlineGeometry()
clgeometry.Centerlines = centerlines
clgeometry.LineSmoothing = smoothing
clgeometry.NumberOfSmoothingIterations = iterations
clgeometry.Execute()
return clgeometry.Centerlines
def vmtk_compute_geometric_features(centerlines,
smooth,
outputsmoothed=False,
factor=1.0,
iterations=100):
"""Wrapper for vmtk centerline geometry.
Args:
centerlines (vtkPolyData): Line to compute centerline geometry from.
smooth (bool): Turn on and off smoothing before computing the geometric features.
outputsmoothed (bool): Turn on and off the smoothed centerline.
factor (float): Smoothing factor.
iterations (int): Number of iterations.
Returns:
line (vtkPolyData): Line with geometry.
"""
geometry = vmtkscripts.vmtkCenterlineGeometry()
geometry.Centerlines = centerlines
if smooth:
geometry.LineSmoothing = 1
geometry.OutputSmoothedLines = outputsmoothed
geometry.SmoothingFactor = factor
geometry.NumberOfSmoothingIterations = iterations
geometry.FernetTangentArrayName = "FernetTangent"
geometry.FernetNormalArrayName = "FernetNormal"
geometry.FrenetBinormalArrayName = "FernetBiNormal"
geometry.CurvatureArrayName = "Curvature"
geometry.TorsionArrayName = "Torsion"
geometry.TortuosityArrayName = "Tortuosity"
geometry.Execute()
return geometry.Centerlines
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 vmtkcenterlinegeometry(centerline):
computer = vmtkscripts.vmtkCenterlineGeometry()
computer.Centerlines = centerline
computer.Execute()
return computer.Centerlines
poly_data = read_polydata(infile)
x_list = []
y_list = []
z_list = []
for i in range(poly_data.GetNumberOfPoints()):
x_list.append(float(poly_data.GetPoints().GetPoint(i)[0]))
y_list.append(float(poly_data.GetPoints().GetPoint(i)[1]))
z_list.append(float(poly_data.GetPoints().GetPoint(i)[2]))
return [np.mean(x_list), np.mean(y_list), np.mean(z_list)]
################################################################################
centerline_data = read_polydata(centerline_file)
#calculate Frenet tangential vector
centergeometry = vmtkscripts.vmtkCenterlineGeometry()
centergeometry.Centerlines = centerline_data
centergeometry.Execute()
centerline_data = centergeometry.Centerlines
write_polydata(centerline_data, centerline_file)
num_pts = centerline_data.GetNumberOfPoints()
print "Number of Points:", centerline_data.GetNumberOfPoints()
print "Number of arrays:", centerline_data.GetCellData().GetNumberOfArrays()
num_cells = centerline_data.GetNumberOfCells()
print "Number of Cells:", centerline_data.GetNumberOfCells()
###read cell data, for each cell (line), the lists record its centerline id (n lines starting from the inlet to outlets), blanking (0 non bifurcation, 1 bifurcation),
###group ids (vessels are splitted into single segments/branches and a bifurcation region,
centerlineDistance.Centerlines = centerline.Centerlines
centerlineDistance.DistanceToCenterlinesArrayName = 'DistanceToCenterlines'
centerlineDistance.UseRadiusInformation = 1
centerlineDistance.Execute()
surface = centerlineDistance.Surface
# VTP writer - centerline distance
vtp_writer.SetFileName(path.join(ofile_mesh + "_centerline-distance.vtp"))
vtp_writer.SetInputData(surface)
vtp_writer.Update()
vtp_writer.Write()
if CenterlineMesh:
### Centerline geometry data ###
centerline_geo = vmtkscripts.vmtkCenterlineGeometry()
centerline_geo.Centerlines = centerline.Centerlines
# if NonConstThickness:
# centerline_geo.Centerlines = centerline2.Centerlines
centerline_geo.CenterlinesOutputFileName = path.join(ofile_mesh +
"_centerline_geo.vtp")
centerline_geo.Execute()
# Convert to numpy array(s)
centerline_geo_vmtktoNumpy = vmtkscripts.vmtkCenterlinesToNumpy()
centerline_geo_vmtktoNumpy.Centerlines = centerline_geo.Centerlines
centerline_geo_vmtktoNumpy.Execute()
# Centerline points coords
centerline_points = centerline_geo_vmtktoNumpy.ArrayDict["Points"]
np.save(path.join(ofile_mesh + "_centerline_points.npy"),