or we can build a pype that does the same thing Vmtkmarchingcubes -ifile foo.vti -ofile foo.vtp o Surface (vtkPolyData,1): the output surface // We can use vmtkmarchingcubes as a stand-alone script by using the built-in I/O functionality ofile SurfaceOutputFileName (str,1): filename for the default Surface writer connectivity Connectivity (bool,1) default=0: only output the largest connected region of the isosurface l Level(float,1) default=0.0: graylevel to generate the isosurface at array ArrayName (str,1): name of the array to work with ![]() ifile ImageInputFileName(str,1): filename for the default Image Reader i Image (vtkImageData,1): the input image disabled Disabled (bool,1) default=0: disable execution and piping Vmtkmarchingcubes : generate an isosurface of given level from a 3D image Take a look into the Basic PypeS tutorial to learn how to effectively pipe vmtk scripts together, the Use PypeS Programmatically tutorial to learn how to interactively work with PypeS objects and into the Advanced PypeS tutorial to learn how to write your own PypeS modules vmtkmarchingcubes -help Vmtkbranchpatching -ifile aorta_clipped_mapping.vtp -groupidsarray GroupIds -longitudinalmappingarray StretchedMapping -circularmappingarray AngularMetric -longitudinalpatchsize 0.5 -circularpatches 12 -ofile aorta_clipped_patching.vtp ![]() Patching of surface mesh and attributes Vmtkbranchmapping -ifile aorta_clipped_metrics.vtp -centerlinesfile aorta_cl.vtp -referencesystemsfile aorta_cl_rs.vtp -normalsarray ParallelTransportNormals -abscissasarray Abscissas -groupidsarray GroupIds -centerlineidsarray CenterlineIds -tractidsarray TractIds -referencesystemsnormalarray Normal -radiusarray MaximumInscribedSphereRadius -blankingarray Blanking -angularmetricarray AngularMetric -abscissametricarray AbscissaMetric -ofile aorta_clipped_mapping.vtp Vmtkbranchmetrics -ifile aorta_clipped.vtp -centerlinesfile aorta_cl.vtp -abscissasarray Abscissas -normalsarray ParallelTransportNormals -groupidsarray GroupIds -centerlineidsarray CenterlineIds -tractidsarray TractIds -blankingarray Blanking -radiusarray MaximumInscribedSphereRadius -ofile aorta_clipped_metrics.vtp Take a look into the Mapping and patching tutorial to learn how to map the surface of a population of vessels onto the same parametric space and enable statistical analyses of surface-based quantities // Longitudinal and circumferential metrics Vmtksurfacereader -ifile foo.vtp -pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles -pipe vmtkdistancetocenterlines -useradius 1 -pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -boundarylayer 1 -ofile foo.vtu Vmtksurfacereader -ifile foo.vtp -pipe vmtkcenterlines -endpoints 1 -seedselector openprofiles -pipe vmtkdistancetocenterlines -useradius 1 -pipe vmtkmeshgenerator -elementsizemode edgelengtharray -edgelengtharray DistanceToCenterlines -edgelengthfactor 0.3 -ofile foo.vtu Generating a radius-adaptive element mesh Vmtkmeshgenerator -ifile foo.vtp -ofile foo.vtu -edgelength 0.5 Louvain // generating a uniform element mesh ![]() Take a look into the Generating a Mesh tutorial to learn how to generate a mesh from a surface and into Meshing based on centerlines (vmtk+gmsh) tutorial to learn how to generate tetrahedral or mixed hexahedral meshes using vmtk coupled to Gmsh.
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