From 599f6db02824bfc35ee6915d305a647ce007f914 Mon Sep 17 00:00:00 2001 From: michael Date: Wed, 10 Feb 2021 15:47:24 +0100 Subject: [PATCH] Use the VTK reader from MEDCoupling --- .../tests/swig/BoySurface/BoysSurfaceVTK.py | 7 +- CDMATH/tests/swig/BoySurface/CMakeLists.txt | 4 +- CDMATH/tests/swig/BoySurface/VTKnewReader.py | 325 ------------------ 3 files changed, 5 insertions(+), 331 deletions(-) mode change 100644 => 100755 CDMATH/tests/swig/BoySurface/BoysSurfaceVTK.py delete mode 100644 CDMATH/tests/swig/BoySurface/VTKnewReader.py diff --git a/CDMATH/tests/swig/BoySurface/BoysSurfaceVTK.py b/CDMATH/tests/swig/BoySurface/BoysSurfaceVTK.py old mode 100644 new mode 100755 index 796c844..88b5bf6 --- a/CDMATH/tests/swig/BoySurface/BoysSurfaceVTK.py +++ b/CDMATH/tests/swig/BoySurface/BoysSurfaceVTK.py @@ -2,8 +2,7 @@ # -*- coding: utf-8 -*- import vtk -import VTKnewReader#To generate med file -#import paraview.simple as pvs#to obtain a binary vtu file in append mode +import VTKReader#To generate a med file from a vtk file # ------------------------------------------------------------ # Create Boy's surface @@ -92,7 +91,7 @@ writer.SetFileName("BoySurface"+".vtu") writer.SetInputData(unstructuredGrid) #writer.SetDataModeToBinary() #writer.SetDataModeToAppended() -writer.EncodeAppendedDataOn() +#writer.EncodeAppendedDataOn() writer.Write() #Generate binary vtu file in append mode @@ -100,6 +99,6 @@ writer.Write() #pvs.SaveData('./BoySurface2.vtu', proxy=boySurfaceBisvtu, DataMode='Binary',EncodeAppendedData=1) #Generate med file -vtu = VTKnewReader.VTURawReader('./BoySurface.vtu') +vtu = VTKReader.VTURawReader('./BoySurface.vtu') med = vtu.loadInMEDFileDS() med.write("./BoySurface.med", 2) diff --git a/CDMATH/tests/swig/BoySurface/CMakeLists.txt b/CDMATH/tests/swig/BoySurface/CMakeLists.txt index 7b76770..d17bb9e 100755 --- a/CDMATH/tests/swig/BoySurface/CMakeLists.txt +++ b/CDMATH/tests/swig/BoySurface/CMakeLists.txt @@ -1,7 +1,7 @@ -if (CDMATH_WITH_PYTHON AND CDMATH_WITH_POSTPRO)#The environment is probably too rich for the current test contain +if (CDMATH_WITH_PYTHON AND CDMATH_WITH_POSTPRO) ADD_TEST(Test_Boys_Surface ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/BoysSurfaceVTK.py) endif () -INSTALL(FILES BoysSurfaceVTK.py VTKnewReader.py DESTINATION bin/BoysSurface) +INSTALL(FILES BoysSurfaceVTK.py ${MEDCOUPLING_LIBRARIES}/python${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}/site-packages/VTKReader.py DESTINATION share/examples/BoysSurface) diff --git a/CDMATH/tests/swig/BoySurface/VTKnewReader.py b/CDMATH/tests/swig/BoySurface/VTKnewReader.py deleted file mode 100644 index 74ebdeb..0000000 --- a/CDMATH/tests/swig/BoySurface/VTKnewReader.py +++ /dev/null @@ -1,325 +0,0 @@ -# -*- coding: iso-8859-1 -*- -# Copyright (C) 2007-2016 CEA/DEN, EDF R&D -# -# This library is free software; you can redistribute it and/or -# modify it under the terms of the GNU Lesser General Public -# License as published by the Free Software Foundation; either -# version 2.1 of the License, or (at your option) any later version. -# -# This library is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -# Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public -# License along with this library; if not, write to the Free Software -# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA -# -# See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com -# -# Author : Anthony GEAY (CEA/DEN/DM2S/STMF) - -from MEDLoader import * - -class PVDReader: - @classmethod - def New(cls,fileName): - """ Static constructor. """ - return PVDReader(fileName) - pass - - def __init__(self,fileName): - self._fileName=fileName - pass - - def loadTopInfo(self): - fd=open(self._fileName,"r") - return self.__parseXML(fd) - - def __parseXML(self,fd): - import xml.sax - class PVD_SAX_Reader(xml.sax.ContentHandler): - def __init__(self): - self._tsteps=[] - pass - def startElement(self,name,attrs): - if name=="VTKFile": - if attrs["type"]!="Collection": - raise Exception("Mismatch between reader (PVD) type and file content !") - return - if name=="DataSet": - self._tsteps.append((float(attrs["timestep"]),str(attrs["file"]))) - return - pass - pass - rd=PVD_SAX_Reader() - parser=xml.sax.make_parser() - parser.setContentHandler(rd) - parser.parse(fd) - return rd - pass - -class PVTUReader: - @classmethod - def New(cls,fileName): - """ Static constructor. """ - return PVTUReader(fileName) - pass - - def __init__(self,fileName): - self._fileName=fileName - pass - - def loadParaInfo(self): - fd=open(self._fileName,"r") - return self.__parseXML(fd) - - def __parseXML(self,fd): - import xml.sax - class PVTU_SAX_Reader(xml.sax.ContentHandler): - def __init__(self): - self._data_array={2:self.DAPointData,3:self.DACellData} - self._node_fields=[] - self._cell_fields=[] - self._pfiles=[] - self._tmp=None - pass - def DAPointData(self,attrs): - self._node_fields.append((str(attrs["Name"]),int(attrs["NumberOfComponents"]))) - pass - def DACellData(self,attrs): - self._cell_fields.append((str(attrs["Name"]),int(attrs["NumberOfComponents"]))) - pass - def startElement(self,name,attrs): - if name=="VTKFile": - if attrs["type"]!="PUnstructuredGrid": - raise Exception("Mismatch between reader (PVTU) type and file content !") - return - if name=="Piece": - self._pfiles.append(str(attrs["Source"])) - return - if name=="PPointData": - self._tmp=2 - return - if name=="PCellData": - self._tmp=3 - return - if name=="PDataArray": - if self._tmp in self._data_array: - self._data_array[self._tmp](attrs) - pass - return - pass - pass - rd=PVTU_SAX_Reader() - parser=xml.sax.make_parser() - parser.setContentHandler(rd) - parser.parse(fd) - return rd - pass - -class VTURawReader: - """ Converting a VTU file in raw mode into the MED format. - Warning: VTU file must be write in "Appended" mode, and in "Binary" format. - """ - VTKTypes_2_MC=[-1,0,-1,1,33,NORM_TRI3 ,-1,5,-1,4,14,-1,NORM_HEXA8,16,15,-1,22,-1,-1,-1,-1,2,6,8,20,30,25,23,9,27,-1,-1,-1,-1,7,-1,-1,-1,-1,-1,-1,-1,31] - - class NormalException(Exception): - def __init__(self,lineNb): - Exception.__init__(self) - self._line_nb=lineNb - def getLineNb(self): - return self._line_nb - pass - - class NotRawVTUException(Exception): - pass - - def loadInMEDFileDS(self): - import numpy as np - fd=open(self._fileName,"r") - ref,rd=self.__parseXML(fd) - # - ret=MEDFileData() - ms=MEDFileMeshes() ; ret.setMeshes(ms) - fs=MEDFileFields() ; ret.setFields(fs) - # - types=np.memmap(fd,dtype=rd._type_types,mode='r',offset=ref+rd._off_types,shape=(rd._nb_cells,)) - types=self.__swapIfNecessary(rd._bo,types) - # mesh dimension detection - types2=types.copy() ; types2.sort() ; - types2 =np.unique(types2) - # Get first valid type - meshDim = -1 - for i, typ in enumerate(types2): - if self.VTKTypes_2_MC[typ] != -1: - meshDim=MEDCouplingMesh.GetDimensionOfGeometricType(self.VTKTypes_2_MC[typ]) - if meshDim == -1: - raise Exception("Could not find a valid cell type in the mesh !") - if i > 0: - print("WARNING: some invalid/incompatible cell types were detected - trying to have them as polygons ...") - for typ in types2: - if self.VTKTypes_2_MC[typ] != -1: - md=MEDCouplingMesh.GetDimensionOfGeometricType(self.VTKTypes_2_MC[typ]) - if md!=meshDim: - raise Exception("MultiLevel umeshes not managed yet !") - else: - print("WARNING: invalid/incompatible cell type detected: VTK type number: %d" % typ) - m=MEDCouplingUMesh("mesh",meshDim) - # coordinates - coo=np.memmap(fd,dtype=rd._type_coords,mode='r',offset=ref+rd._off_coords,shape=(rd._nb_nodes*rd._space_dim,)) - coo=self.__swapIfNecessary(rd._bo,coo) ; coo=DataArrayDouble(np.array(coo,dtype='float64')) ; coo.rearrange(rd._space_dim) - m.setCoords(coo) - # connectivity - offsets=np.memmap(fd,dtype=rd._type_off,mode='r',offset=ref+rd._off_off,shape=(rd._nb_cells,)) - offsets=self.__swapIfNecessary(rd._bo,offsets) ; connLgth=offsets[-1] ; offsets2=DataArrayIdType(rd._nb_cells+1) ; offsets2.setIJ(0,0,0) - offsets2[1:]=DataArrayIdType([int(o) for o in offsets]) - offsets3=offsets2.deltaShiftIndex() ; offsets2=offsets3.deepCopy() ; offsets3+=1 ; offsets3.computeOffsetsFull() - offsets=offsets3 - tmp1=DataArrayIdType(len(offsets2),2) ; tmp1[:,0]=1 ; tmp1[:,1]=offsets2 ; tmp1.rearrange(1) ; tmp1.computeOffsetsFull() - tmp1=DataArrayIdType.Range(1,2*len(offsets2),2).buildExplicitArrByRanges(tmp1) - conn=np.memmap(fd,dtype=rd._type_conn,mode='r',offset=ref+rd._off_conn,shape=(connLgth,)) - conn=self.__swapIfNecessary(rd._bo,conn) - types=np.array(types,dtype='int32') ; types=DataArrayIdType(types) ; - types.transformWithIndArr(self.VTKTypes_2_MC) - conn2=DataArrayIdType(offsets.back()) - conn2[offsets[0:-1]]=types - conn2[tmp1]=DataArrayIdType([int(c) for c in conn]) - m.setConnectivity(conn2,offsets,True) - m.checkConsistencyLight() ; mm=MEDFileUMesh() ; mm.setMeshAtLevel(0,m) ; ms.pushMesh(mm) - # Fields on nodes and on cells - for spatialDisc,nbEnt,fields in [(ON_NODES,rd._nb_nodes,rd._node_fields),(ON_CELLS,rd._nb_cells,rd._cell_fields)]: - for name,typ,nbCompo,off in fields: - ff=MEDFileFieldMultiTS() - f=MEDCouplingFieldDouble(spatialDisc,ONE_TIME) - f.setName(name) ; f.setMesh(m) - vals=np.memmap(fd,dtype=typ,mode='r',offset=ref+off,shape=(nbEnt*nbCompo)) - vals=self.__swapIfNecessary(rd._bo,vals) - arr=DataArrayDouble(np.array(vals,dtype='float64')) ; arr.rearrange(nbCompo) - f.setArray(arr) ; f.checkConsistencyLight() - f.setTime(self._time[0],self._time[1],0) - ff.appendFieldNoProfileSBT(f) - fs.pushField(ff) - pass - pass - return ret - - def __parseXML(self,fd): - import xml.sax - class VTU_SAX_Reader(xml.sax.ContentHandler): - def __init__(self): - self._loc=None - self._data_array={0:self.DAPoints,1:self.DACells,2:self.DAPointData,3:self.DACellData} - self._node_fields=[] - self._cell_fields=[] - pass - def setLocator(self,loc): - self._loc=loc - def DAPoints(self,attrs): - self._space_dim=int(attrs["NumberOfComponents"]) - self._type_coords=str(attrs["type"]).lower() - self._off_coords=int(attrs["offset"]) - pass - def DACells(self,attrs): - if attrs["Name"]=="connectivity": - self._type_conn=str(attrs["type"]).lower() - self._off_conn=int(attrs["offset"]) - pass - if attrs["Name"]=="offsets": - self._type_off=str(attrs["type"]).lower() - #self._off_off=int(attrs.get("offset", 0)) - self._off_off=int(attrs["offset"]) - pass - if attrs["Name"]=="types": - self._type_types=str(attrs["type"]).lower() - #self._off_types=int(attrs.get("offset", 0)) - self._off_types=int(attrs["offset"]) - pass - pass - def DAPointData(self,attrs): - numCompo = int(attrs.get("NumberOfComponents", 1)) - offset = int(attrs.get("offset", 0)) - self._node_fields.append((str(attrs["Name"]),str(attrs["type"]).lower(),numCompo,offset)) - pass - def DACellData(self,attrs): - self._cell_fields.append((str(attrs["Name"]),str(attrs["type"]).lower(),int(attrs["NumberOfComponents"]),int(attrs["offset"]))) - pass - def startElement(self,name,attrs): - if name=="VTKFile": - if attrs["type"]!="UnstructuredGrid": - raise Exception("Mismatch between reader (VTU) type and file content !") - self._bo=bool(["LittleEndian","BigEndian"].index(attrs["byte_order"])) - pass - if name=="Piece": - self._nb_cells=int(attrs["NumberOfCells"]) - self._nb_nodes=int(attrs["NumberOfPoints"]) - return - if name=="Points": - self._tmp=0 - return - if name=="Cells": - self._tmp=1 - return - if name=="PointData": - self._tmp=2 - return - if name=="CellData": - self._tmp=3 - return - if name=="DataArray": - self._data_array[self._tmp](attrs) - return - if name=="AppendedData": - if str(attrs["encoding"])=="raw": - raise VTURawReader.NormalException(self._loc.getLineNumber()) - else: - print(attrs["encoding"]) - raise VTURawReader.NotRawVTUException("The file is not a raw VTU ! Change reader !") - pass - pass - rd=VTU_SAX_Reader() - parser=xml.sax.make_parser() - parser.setContentHandler(rd) - locator=xml.sax.expatreader.ExpatLocator(parser) - rd.setLocator(locator) - isOK=False - try: - parser.parse(fd) - except self.NormalException as e: - isOK=True - fd.seek(0) - for i in range(e.getLineNb()): - l = fd.readline() - ref=fd.tell()+12 - pass - if not isOK: - raise Exception("Error in VTURawReader : not a raw format ?") - return ref,rd - - @classmethod - def New(cls,fileName,tim=(0.,0)): - """ Static constructor. """ - return VTURawReader(fileName,tim) - pass - - def __init__(self,fileName,tim=(0.,0)): - msg="The time specified in constructor as 2nd arg should be a tuple containing 2 values 1 float and 1 int !" - if not isinstance(tim, tuple): - raise Exception(msg) - if len(tim)!=2: - raise Exception(msg) - if not isinstance(tim[0], float) or not isinstance(tim[1], int): - raise Exception(msg) - self._fileName=fileName - self._time=tim - pass - - def __swapIfNecessary(self,b,arr): - if b: - ret=arr.copy() - ret.byteswap(True) - return ret - else: - return arr - pass - pass -- 2.39.2