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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkmeshaddexternallayer.py,v $
## Language: Python
## Date: $$
## Version: $$
## Copyright (c) Luca Antiga, David Steinman. All rights reserved.
## See LICENCE file for details.
## This software is distributed WITHOUT ANY WARRANTY; without even
## the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
## PURPOSE. See the above copyright notices for more information.
## Note: this class was contributed by
## Tangui Morvan
## Kalkulo AS
## Simula Research Laboratory
## This class builds an external layer around a mesh.
import vtk
import vtkvmtk
import sys
import vmtkscripts
import vmtkcontribscripts
import pypes
vmtkmeshaddexternallayer = 'vmtkMeshAddExternalLayer'
class vmtkMeshAddExternalLayer(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Mesh = None
self.CellEntityIdsArrayName = 'CellEntityIds'
#Id of the first wall (mesh surface)
self.SurfaceCellEntityId = 1
#Id of the first openprofile in the walls
self.InletOutletCellEntityId = 2
#Id of the surface cells to extrude
self.ExtrudeCellEntityId = 1
self.ThicknessArrayName = ''
self.Thickness = 1.0
self.ThicknessRatio = 0.1
self.MaximumThickness = 1E10
self.NumberOfSubLayers = 1
self.SubLayerRatio = 1.0
self.ConstantThickness = 1;
self.IncludeSurfaceCells = 0
self.NegateWarpVectors = 0
self.IncludeExtrudedOpenProfilesCells = 1
self.IncludeExtrudedSurfaceCells = 1
self.IncludeOriginalSurfaceCells = 0
self.SetScriptName('vmtkmeshaddexternallayer')
self.SetScriptDoc('create an external prismatic layer from the wall of a mesh and the normals on the wall.')
self.SetInputMembers([
['Mesh','i','vtkUnstructuredGrid',1,'','the input mesh','vmtkmeshreader'],
['CellEntityIdsArrayName','entityidsarray','str',1,''],
['SurfaceCellEntityId','surfacecellentityid','int',1,'','id of the first surface cells in the entityids list'],
['InletOutletCellEntityId','inletoutletcellentityid','int',1],
['ExtrudeCellEntityId','extrudecellentityid','int',1,'','id of the surface cells to extrude'],
['ThicknessArrayName','thicknessarray','str',1,'','name of the array where scalars defining boundary layer thickness are stored'],
['Thickness','thickness','float',1,'','value of constant boundary layer thickness'],
['ThicknessRatio','thicknessratio','float',1,'(0.0,)','multiplying factor for boundary layer thickness'],
['MaximumThickness','maximumthickness','float',1,'','maximum allowed value for boundary layer thickness'],
['NumberOfSubLayers','numberofsublayers','int',1,'(0,)','number of sublayers which the boundary layer has to be made of'],
['SubLayerRatio','sublayerratio','float',1,'(0.0,)','ratio between the thickness of two successive boundary layers'],
['ConstantThickness','constantthickness','bool',1,'','toggle constant boundary layer thickness'],
['IncludeSurfaceCells','includesurfacecells','bool',0,'','include all surface cells in output mesh'],
['IncludeExtrudedOpenProfilesCells','includeextrudedopenprofilescells','bool',1,'','include the cells from the open profiles extruded surface in output mesh'],
['IncludeExtrudedSurfaceCells','includeextrudedsurfacecells','bool',1,'','include the cells from the extruded surface in output mesh'],
['IncludeOriginalSurfaceCells','includeoriginalsurfacecells','bool',1,'','include the cells from the original surfacein output mesh']
])
self.SetOutputMembers([
['Mesh','o','vtkUnstructuredGrid',1,'','the output mesh','vmtkmeshwriter'],
])
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: No input mesh.')
if not self.CellEntityIdsArrayName:
self.PrintError('Error: No input CellEntityIdsArrayName.')
return
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName)
#cut off the volumetric elements
wallThreshold = vtk.vtkThreshold()
wallThreshold.SetInput(self.Mesh)
wallThreshold.ThresholdByUpper(self.SurfaceCellEntityId-0.5)
wallThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
wallThreshold.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = wallThreshold.GetOutput()
meshToSurface.Execute()
#Compute the normals for this surface, orientation should be right because the surface is closed
#TODO: Add option for cell normals in vmtksurfacenormals
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInput(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOff()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normalsFilter.GetOutput()
surfaceToMesh.Execute()
#Save the current normals
wallWithBoundariesMesh = surfaceToMesh.Mesh
savedNormals = vtk.vtkDoubleArray()
savedNormals.DeepCopy(wallWithBoundariesMesh.GetCellData().GetNormals())
savedNormals.SetName('SavedNormals')
wallWithBoundariesMesh.GetCellData().AddArray(savedNormals)
#cut off the boundaries and other surfaces
extrudeThresholdLower = vtk.vtkThreshold()
extrudeThresholdLower.SetInput(wallWithBoundariesMesh)
extrudeThresholdLower.ThresholdByLower(self.ExtrudeCellEntityId+0.5)
extrudeThresholdLower.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdLower.Update()
extrudeThresholdUpper = vtk.vtkThreshold()
extrudeThresholdUpper.SetInput(extrudeThresholdLower.GetOutput())
extrudeThresholdUpper.ThresholdByUpper(self.ExtrudeCellEntityId-0.5)
extrudeThresholdUpper.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdUpper.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = extrudeThresholdUpper.GetOutput()
meshToSurface.Execute()
#Compute cell normals without boundaries
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInput(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
normals = wallWithoutBoundariesSurface.GetCellData().GetNormals()
savedNormals = wallWithoutBoundariesSurface.GetCellData().GetArray('SavedNormals')
math = vtk.vtkMath()
#If the normal are inverted, recompute the normals with flipping on
if normals.GetNumberOfTuples() > 0 and math.Dot(normals.GetTuple3(0),savedNormals.GetTuple3(0)) < 0:
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInput(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(1)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
wallWithoutBoundariesSurface.GetPointData().GetNormals().SetName('Normals')
wallWithoutBoundariesSurface.GetCellData().RemoveArray('SavedNormals')
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = wallWithoutBoundariesSurface
surfaceToMesh.Execute()
#Offset to apply to the array
wallOffset = 0
if self.IncludeSurfaceCells or self.IncludeOriginalSurfaceCells:
wallOffset += 1
if self.IncludeSurfaceCells or self.IncludeExtrudedSurfaceCells:
wallOffset+=1
boundaryLayer = vmtkcontribscripts.vmtkBoundaryLayer2()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = False
boundaryLayer.ThicknessArrayName = self.ThicknessArrayName
boundaryLayer.ConstantThickness = self.ConstantThickness
boundaryLayer.IncludeSurfaceCells = self.IncludeSurfaceCells
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.Thickness
boundaryLayer.ThicknessRatio = self.Thickness
boundaryLayer.MaximumThickness = self.MaximumThickness
boundaryLayer.CellEntityIdsArrayName = self.CellEntityIdsArrayName
boundaryLayer.IncludeExtrudedOpenProfilesCells = self.IncludeExtrudedOpenProfilesCells
boundaryLayer.IncludeExtrudedSurfaceCells = self.IncludeExtrudedSurfaceCells
boundaryLayer.IncludeOriginalSurfaceCells = self.IncludeOriginalSurfaceCells
boundaryLayer.LayerEntityId = self.SurfaceCellEntityId
boundaryLayer.SurfaceEntityId = self.InletOutletCellEntityId + 1
if cellEntityIdsArray != None:
#Append the new surface ids
idRange = cellEntityIdsArray.GetRange()
boundaryLayer.OpenProfilesEntityId = idRange[1] + wallOffset + 2
boundaryLayer.Execute()
if cellEntityIdsArray != None:
#offset the previous cellentityids to make room for the new ones
arrayCalculator = vtk.vtkArrayCalculator()
arrayCalculator.SetInput(self.Mesh)
arrayCalculator.SetAttributeModeToUseCellData()
arrayCalculator.AddScalarVariable("entityid",self.CellEntityIdsArrayName,0)
arrayCalculator.SetFunction("if( entityid > " + str(self.InletOutletCellEntityId-1) +", entityid + " + str(wallOffset) + ", entityid)")
arrayCalculator.SetResultArrayName('CalculatorResult')
arrayCalculator.Update()
#This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
arrayCalculator.SetFunction("if( entityid > " + str(self.SurfaceCellEntityId-1) +", entityid + 1, entityid)")
arrayCalculator.Update()
##This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(self.Mesh)
appendFilter.AddInput(boundaryLayer.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
if self.Mesh.GetSource():
self.Mesh.GetSource().UnRegisterAllOutputs()
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
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