Hdf5ToMeshalyzerConverter.cpp

00001 /*
00002 
00003 Copyright (C) University of Oxford, 2005-2011
00004 
00005 University of Oxford means the Chancellor, Masters and Scholars of the
00006 University of Oxford, having an administrative office at Wellington
00007 Square, Oxford OX1 2JD, UK.
00008 
00009 This file is part of Chaste.
00010 
00011 Chaste is free software: you can redistribute it and/or modify it
00012 under the terms of the GNU Lesser General Public License as published
00013 by the Free Software Foundation, either version 2.1 of the License, or
00014 (at your option) any later version.
00015 
00016 Chaste is distributed in the hope that it will be useful, but WITHOUT
00017 ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
00018 FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
00019 License for more details. The offer of Chaste under the terms of the
00020 License is subject to the License being interpreted in accordance with
00021 English Law and subject to any action against the University of Oxford
00022 being under the jurisdiction of the English Courts.
00023 
00024 You should have received a copy of the GNU Lesser General Public License
00025 along with Chaste. If not, see <http://www.gnu.org/licenses/>.
00026 
00027 */
00028 
00029 #include "Hdf5ToMeshalyzerConverter.hpp"
00030 #include "MeshalyzerMeshWriter.hpp"
00031 #include "GenericMeshReader.hpp"
00032 #include "UblasCustomFunctions.hpp"
00033 #include "HeartConfig.hpp"
00034 #include "PetscTools.hpp"
00035 #include "Exception.hpp"
00036 #include "ReplicatableVector.hpp"
00037 #include "DistributedVector.hpp"
00038 #include "DistributedVectorFactory.hpp"
00039 #include "Version.hpp"
00040 
00041 template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00042 void Hdf5ToMeshalyzerConverter<ELEMENT_DIM,SPACE_DIM>::Write(std::string type)
00043 {
00044     out_stream p_file=out_stream(NULL);
00045     if (PetscTools::AmMaster())
00046     {
00047         p_file = this->mpOutputFileHandler->OpenOutputFile(this->mFileBaseName + "_" + type + ".dat");
00048     }
00049 
00050     unsigned num_nodes = this->mpReader->GetNumberOfRows();
00051     unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
00052 
00053     DistributedVectorFactory factory(num_nodes);
00054 
00055     Vec data = factory.CreateVec();
00056     ReplicatableVector repl_data(num_nodes);
00057     for (unsigned time_step=0; time_step<num_timesteps; time_step++)
00058     {
00059         this->mpReader->GetVariableOverNodes(data, type, time_step);
00060         repl_data.ReplicatePetscVector(data);
00061         
00062         assert(repl_data.GetSize()==num_nodes);
00063 
00064         if(PetscTools::AmMaster())
00065         {
00066             for(unsigned i=0; i<num_nodes; i++)
00067             {
00068                 *p_file << repl_data[i] << "\n";
00069             }
00070         }
00071     }
00072     VecDestroy(data);
00073     if(PetscTools::AmMaster())
00074     {
00075         std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
00076         *p_file << comment;
00077         p_file->close();
00078     }
00079 }
00080 
00081 
00082 template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
00083 Hdf5ToMeshalyzerConverter<ELEMENT_DIM,SPACE_DIM>::Hdf5ToMeshalyzerConverter(std::string inputDirectory,
00084                           std::string fileBaseName,
00085                           AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM> *pMesh) :
00086                      AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(inputDirectory, fileBaseName, pMesh, "output")
00087 {
00088     std::vector<std::string> variable_names = this->mpReader->GetVariableNames();
00089     for (unsigned i=0; i<variable_names.size(); i++)
00090     {
00091         Write(variable_names[i]);
00092     }
00093 
00094     //Write mesh in a suitable form for meshalyzer
00095     std::string output_directory =  HeartConfig::Instance()->GetOutputDirectory() + "/output";
00096     MeshalyzerMeshWriter<ELEMENT_DIM,SPACE_DIM> mesh_writer(output_directory, HeartConfig::Instance()->GetOutputFilenamePrefix()+"_mesh", false);
00097     //Normal case is that the in-memory mesh is converted
00098     if (HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering() == false )
00099     {
00100         // The second argument tells the writer to not follow original element ordering for performance reasons.
00101         mesh_writer.WriteFilesUsingMesh(*(this->mpMesh), false);
00102     }
00103     else
00104     {
00105         //In this case we expect the mesh to have been read in from file
00107         //Note that the next line will throw if the mesh has not been read from file
00108         std::string original_file=this->mpMesh->GetMeshFileBaseName();
00109         GenericMeshReader<ELEMENT_DIM, SPACE_DIM> original_mesh_reader(original_file);
00110         mesh_writer.WriteFilesUsingMeshReader(original_mesh_reader);
00111     }
00112     PetscTools::Barrier("Hdf5ToMeshalyzerConverter");
00113 }
00114 
00115 
00117 // Explicit instantiation
00119 
00120 template class Hdf5ToMeshalyzerConverter<1,1>;
00121 template class Hdf5ToMeshalyzerConverter<1,2>;
00122 template class Hdf5ToMeshalyzerConverter<2,2>;
00123 template class Hdf5ToMeshalyzerConverter<1,3>;
00124 template class Hdf5ToMeshalyzerConverter<2,3>;
00125 template class Hdf5ToMeshalyzerConverter<3,3>;

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