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#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkmeshwriter2.py,v $
## Language: Python
## Date: $Date: 2006/07/27 08:27:40 $
## Version: $Revision: 1.13 $
## 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 is a slightly modified version of vmtkmeshwriter.
## An option has been added to write ascii files.
## The Dolphin writer has been modified (see vtkvmtkDolfinWriter2)
import sys
import vtk
import vtkvmtk
import vtkvmtkcontrib
import pypes
vmtkmeshwriter2 = 'vmtkMeshWriter2'
class vmtkMeshWriter2(pypes.pypeScript):
def __init__(self):
pypes.pypeScript.__init__(self)
self.Format = ''
self.GuessFormat = 1
self.OutputFileName = ''
self.Mesh = None
self.Input = None
self.Ascii = False
self.Compressed = 1
self.CellEntityIdsOffset = 0
self.CellEntityIdsArrayName = ''
self.SetScriptName('vmtkmeshwriter')
self.SetScriptDoc('write a mesh to disk')
self.SetInputMembers([
['Mesh','i','vtkUnstructuredGrid',1,'','the input mesh','vmtkmeshreader'],
['Format','f','str',1,'["vtkxml","vtk","xda","fdneut","tecplot","lifev","dolfin","fluent","pointdata"]','file format (xda - libmesh ASCII format, fdneut - FIDAP neutral format)'],
['GuessFormat','guessformat','bool',1,'','guess file format from extension'],
['Compressed','compressed','bool',1,'','output gz compressed file (dolfin only)'],
['OutputFileName','ofile','str',1,'','output file name'],
['Mesh','o','vtkUnstructuredGrid',1,'','the output mesh'],
['CellEntityIdsArrayName','entityidsarray','str',1,'','name of the array where entity ids are stored'],
['CellEntityIdsOffset','entityidsoffset','int',1,'','add this number to entity ids in output (dolfin only)'],
['Ascii','ascii','boolean',1,'','write the data as ascii']
])
self.SetOutputMembers([])
def WriteVTKMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing VTK mesh file.')
writer = vtk.vtkUnstructuredGridWriter()
if self.Ascii:
writer.SetDataModeToAscii()
writer.SetInput(self.Mesh)
writer.SetFileName(self.OutputFileName)
writer.Write()
def WriteVTKXMLMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing VTK XML mesh file.')
writer = vtk.vtkXMLUnstructuredGridWriter()
if self.Ascii:
writer.SetDataModeToAscii()
writer.SetInput(self.Mesh)
writer.SetFileName(self.OutputFileName)
writer.Write()
def WriteXdaMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing Xda mesh file.')
writer = vtkvmtk.vtkvmtkXdaWriter()
writer.SetInput(self.Mesh)
writer.SetFileName(self.OutputFileName)
if self.CellEntityIdsArrayName != '':
writer.SetBoundaryDataArrayName(self.CellEntityIdsArrayName)
writer.Write()
def WriteFDNEUTMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing FDNEUT mesh file.')
writer = vtkvmtk.vtkvmtkFDNEUTWriter()
writer.SetInput(self.Mesh)
writer.SetFileName(self.OutputFileName)
writer.Write()
def WriteTecplotMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing Tecplot file.')
triangleFilter = vtk.vtkDataSetTriangleFilter()
triangleFilter.SetInput(self.Mesh)
triangleFilter.Update()
self.Mesh = triangleFilter.GetOutput()
f=open(self.OutputFileName, 'w')
line = "VARIABLES = X,Y,Z"
arrayNames = []
for i in range(self.Mesh.GetPointData().GetNumberOfArrays()):
array = self.Mesh.GetPointData().GetArray(i)
arrayName = array.GetName()
if arrayName == None:
continue
if (arrayName[-1]=='_'):
continue
arrayNames.append(arrayName)
if (array.GetNumberOfComponents() == 1):
line = line + ',' + arrayName
else:
for j in range(array.GetNumberOfComponents()):
line = line + ',' + arrayName + str(j)
line = line + '\n'
f.write(line)
tetraCellIdArray = vtk.vtkIdTypeArray()
tetraCellType = 10
self.Mesh.GetIdsOfCellsOfType(tetraCellType,tetraCellIdArray)
numberOfTetras = tetraCellIdArray.GetNumberOfTuples()
line = "ZONE " + "N=" + str(self.Mesh.GetNumberOfPoints()) + ',' + "E=" + str(numberOfTetras) + ',' + "F=FEPOINT" + ',' + "ET=TETRAHEDRON" + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = self.Mesh.GetPoint(i)
line = str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2])
for arrayName in arrayNames:
array = self.Mesh.GetPointData().GetArray(arrayName)
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + str(array.GetComponent(i,j))
line = line + '\n'
f.write(line)
for i in range(numberOfTetras):
cellPointIds = self.Mesh.GetCell(tetraCellIdArray.GetValue(i)).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if (j>0):
line = line + ' '
line = line + str(cellPointIds.GetId(j)+1)
line = line + '\n'
f.write(line)
def WriteLifeVMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing LifeV file.')
self.Mesh.BuildLinks()
cellEntityIdsArray = vtk.vtkIntArray()
cellEntityIdsArray.DeepCopy(self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName))
tetraCellType = 10
triangleCellType = 5
f=open(self.OutputFileName, 'w')
line = "MeshVersionFormatted 1\n\n"
line += "Dimension\n"
line += "3\n\n"
line += "Vertices\n"
line += "%d\n" % self.Mesh.GetNumberOfPoints()
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = self.Mesh.GetPoint(i)
pointCells = vtk.vtkIdList()
self.Mesh.GetPointCells(i,pointCells)
minTriangleCellEntityId = -1
tetraCellEntityId = -1
for j in range(pointCells.GetNumberOfIds()):
cellId = pointCells.GetId(j)
if self.Mesh.GetCellType(cellId) == triangleCellType:
cellEntityId = cellEntityIdsArray.GetValue(cellId)
if cellEntityId < minTriangleCellEntityId or minTriangleCellEntityId == -1:
minTriangleCellEntityId = cellEntityId
else:
tetraCellEntityId = cellEntityIdsArray.GetValue(cellId)
cellEntityId = tetraCellEntityId
if minTriangleCellEntityId != -1:
cellEntityId = minTriangleCellEntityId
line = "%f %f %f %d\n" % (point[0], point[1], point[2], cellEntityId)
f.write(line)
line = "\n"
tetraCellIdArray = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(tetraCellType,tetraCellIdArray)
numberOfTetras = tetraCellIdArray.GetNumberOfTuples()
line += "Tetrahedra\n"
line += "%d\n" % numberOfTetras
f.write(line)
for i in range(numberOfTetras):
tetraCellId = tetraCellIdArray.GetValue(i)
cellPointIds = self.Mesh.GetCell(tetraCellId).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if j>0:
line += ' '
line += "%d" % (cellPointIds.GetId(j)+1)
line += ' %d\n' % 1
f.write(line)
line = "\n"
triangleCellIdArray = vtk.vtkIdTypeArray()
self.Mesh.GetIdsOfCellsOfType(triangleCellType,triangleCellIdArray)
numberOfTriangles = triangleCellIdArray.GetNumberOfTuples()
line += "Triangles\n"
line += "%d\n" % numberOfTriangles
f.write(line)
for i in range(numberOfTriangles):
triangleCellId = triangleCellIdArray.GetValue(i)
cellPointIds = self.Mesh.GetCell(triangleCellId).GetPointIds()
line = ''
for j in range(cellPointIds.GetNumberOfIds()):
if j>0:
line += ' '
line += "%d" % (cellPointIds.GetId(j)+1)
cellEntityId = cellEntityIdsArray.GetValue(triangleCellId)
line += ' %d\n' % cellEntityId
f.write(line)
def WriteDolfinMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing Dolfin file.')
if self.Compressed:
self.OutputFileName += '.gz'
writer = vtkvmtkcontrib.vtkvmtkDolfinWriter2()
writer.SetInput(self.Mesh)
writer.SetFileName(self.OutputFileName)
if self.CellEntityIdsArrayName != '':
writer.SetCellEntityIdsArrayName(self.CellEntityIdsArrayName)
writer.SetCellEntityIdsOffset(self.CellEntityIdsOffset)
writer.Write()
if self.Compressed:
file = open(self.OutputFileName,'r')
xml = file.read()
file.close()
import gzip
gzfile = gzip.open(self.OutputFileName,'w')
gzfile.write(xml)
gzfile.close()
def WriteFluentMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
# self.PrintError('Error: Fluent writer not implemented yet.')
# return
self.PrintLog('Writing Fluent file.')
writer = vtkvmtk.vtkvmtkFluentWriter()
writer.SetInput(self.Mesh)
writer.SetFileName(self.OutputFileName)
if self.CellEntityIdsArrayName != '':
writer.SetBoundaryDataArrayName(self.CellEntityIdsArrayName)
writer.Write()
def WritePointDataMeshFile(self):
if (self.OutputFileName == ''):
self.PrintError('Error: no OutputFileName.')
self.PrintLog('Writing PointData file.')
f=open(self.OutputFileName, 'w')
line = "X Y Z"
arrayNames = []
for i in range(self.Mesh.GetPointData().GetNumberOfArrays()):
array = self.Mesh.GetPointData().GetArray(i)
arrayName = array.GetName()
if arrayName == None:
continue
if (arrayName[-1]=='_'):
continue
arrayNames.append(arrayName)
if (array.GetNumberOfComponents() == 1):
line = line + ' ' + arrayName
else:
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + arrayName + str(j)
line = line + '\n'
f.write(line)
for i in range(self.Mesh.GetNumberOfPoints()):
point = self.Mesh.GetPoint(i)
line = str(point[0]) + ' ' + str(point[1]) + ' ' + str(point[2])
for arrayName in arrayNames:
array = self.Mesh.GetPointData().GetArray(arrayName)
for j in range(array.GetNumberOfComponents()):
line = line + ' ' + str(array.GetComponent(i,j))
line = line + '\n'
f.write(line)
def Execute(self):
if self.Mesh == None:
if self.Input == None:
self.PrintError('Error: no Mesh.')
self.Mesh = self.Input
extensionFormats = {'vtu':'vtkxml',
'vtkxml':'vtkxml',
'vtk':'vtk',
'xda':'xda',
'FDNEUT':'fdneut',
'lifev':'lifev',
'xml':'dolfin',
'msh':'fluent',
'tec':'tecplot',
'dat':'pointdata'}
if self.OutputFileName == 'BROWSER':
import tkFileDialog
initialDir = '.'
self.OutputFileName = tkFileDialog.asksaveasfilename(title="Output mesh",initialdir=initialDir)
if not self.OutputFileName:
self.PrintError('Error: no OutputFileName.')
if self.GuessFormat and self.OutputFileName and not self.Format:
import os.path
extension = os.path.splitext(self.OutputFileName)[1]
if extension:
extension = extension[1:]
if extension in extensionFormats.keys():
self.Format = extensionFormats[extension]
if (self.Format == 'vtk'):
self.WriteVTKMeshFile()
elif (self.Format == 'vtkxml'):
self.WriteVTKXMLMeshFile()
elif (self.Format == 'xda'):
self.WriteXdaMeshFile()
elif (self.Format == 'fdneut'):
self.WriteFDNEUTMeshFile()
elif (self.Format == 'lifev'):
self.WriteLifeVMeshFile()
elif (self.Format == 'dolfin'):
self.WriteDolfinMeshFile()
elif (self.Format == 'fluent'):
self.WriteFluentMeshFile()
elif (self.Format == 'tecplot'):
self.WriteTecplotMeshFile()
elif (self.Format == 'pointdata'):
self.WritePointDataMeshFile()
else:
self.PrintError('Error: unsupported format '+ self.Format + '.')
if __name__=='__main__':
main = pypes.pypeMain()
main.Arguments = sys.argv
main.Execute()
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