Hdf5ToCmguiConverter.cpp

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#include "Hdf5ToCmguiConverter.hpp"
#include "CmguiMeshWriter.hpp"
#include "UblasCustomFunctions.hpp"
#include "HeartConfig.hpp"
#include "PetscTools.hpp"
#include "Exception.hpp"
#include "ReplicatableVector.hpp"
#include "DistributedVector.hpp"
#include "DistributedVectorFactory.hpp"
#include "Version.hpp"
#include "GenericMeshReader.hpp"
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void Hdf5ToCmguiConverter<ELEMENT_DIM,SPACE_DIM>::Write(std::string type)
{
    out_stream p_file = out_stream(NULL);
 
    unsigned num_nodes = this->mpReader->GetNumberOfRows();
    unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
 
    DistributedVectorFactory factory(num_nodes);
 
    Vec data = factory.CreateVec();//for V
    Vec data_phie = factory.CreateVec();//for phi_e
    Vec data_second_cell = factory.CreateVec();//for the V of the second cell, used in extended bidomain problems.
 
    for (unsigned time_step=0; time_step<num_timesteps; time_step++)
    {
        // Create the file for this time step
        std::stringstream time_step_string;
 
        // unsigned to string
        time_step_string << time_step;
        if (PetscTools::AmMaster())
        {
            p_file = this->mpOutputFileHandler->OpenOutputFile(this->mFileBaseName + "_" + time_step_string.str() + ".exnode");
 
            // Check how many digits are to be output in the solution (0 goes to default value of digits)
            if (this->mPrecision != 0)
            {
               p_file->precision(this->mPrecision);
            }
        }
 
        std::vector<ReplicatableVector*> all_data;
        unsigned num_vars = this->mpReader->GetVariableNames().size();
        for (unsigned var=0; var<num_vars; var++)
        {
            // Read the data for this time step
            this->mpReader->GetVariableOverNodes(data, this->mpReader->GetVariableNames()[var], time_step);
            ReplicatableVector* p_repl_data = new ReplicatableVector(data);
            assert(p_repl_data->GetSize()==num_nodes);
            all_data.push_back(p_repl_data);
        }
 
        if (PetscTools::AmMaster())
        {
            // Write provenance info
            std::string comment = "! " + ChasteBuildInfo::GetProvenanceString();
            *p_file << comment;
            // The header first
            *p_file << "Group name: " << this->mFileBaseName << "\n";
            *p_file << "#Fields=" << num_vars << "\n";
            for (unsigned var=0; var<num_vars; var++)
            {
                *p_file << " " << var+1 << ") " <<this->mpReader->GetVariableNames()[var]<< " , field, rectangular cartesian, #Components=1" << "\n" << "x.  Value index=1, #Derivatives=0, #Versions=1"<<"\n";
                if (var != num_vars-1)
                {
                    *p_file << "\n";
                }
            }
 
            // Write the data
            for (unsigned i=0; i<num_nodes; i++)
            {
                // cmgui counts nodes from 1
                *p_file << "Node: "<< i+1 << "\n";
                for (unsigned var=0; var<num_vars; var++)
                {
                    *p_file  << (*(all_data[var]))[i] << "\n";
                }
            }
        }
 
        for (unsigned var=0; var<num_vars; var++)
        {
           delete all_data[var];
        }
    }
    PetscTools::Destroy(data);
    PetscTools::Destroy(data_phie);
    PetscTools::Destroy(data_second_cell);
 
    if (PetscTools::AmMaster())
    {
        p_file->close();
    }
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Hdf5ToCmguiConverter<ELEMENT_DIM,SPACE_DIM>::Hdf5ToCmguiConverter(const FileFinder& rInputDirectory,
                                                                  const std::string& rFileBaseName,
                                                                  AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>* pMesh,
                                                                  bool hasBath,
                                                                  unsigned precision)
    : AbstractHdf5Converter<ELEMENT_DIM,SPACE_DIM>(rInputDirectory, rFileBaseName, pMesh, "cmgui_output", precision)
{
    while (this->mDatasetNames[this->mOpenDatasetIndex] != "Data")
    {
        bool next_open = this->MoveOntoNextDataset();
        UNUSED_OPT(next_open);
        assert(next_open);
    }
 
    // Write the node data out
    Write("");
 
    // Write mesh in a suitable form for cmgui
    std::string output_directory =  HeartConfig::Instance()->GetOutputDirectory() + "/cmgui_output";
 
    CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM> cmgui_mesh_writer(output_directory, HeartConfig::Instance()->GetOutputFilenamePrefix(), false);
 
    // Used to inform the mesh of the data names
    std::vector<std::string> field_names = this->mpReader->GetVariableNames();
    cmgui_mesh_writer.SetAdditionalFieldNames(field_names);
    if (hasBath)
    {
        std::vector<std::string> names;
        names.push_back("tissue");
        names.push_back("bath");
        cmgui_mesh_writer.SetRegionNames(names);
    }
 
    // Normally the in-memory mesh is converted:
    if (HeartConfig::Instance()->GetOutputUsingOriginalNodeOrdering() == false || !this->mpMesh->IsMeshOnDisk())
    {
        cmgui_mesh_writer.WriteFilesUsingMesh(*(this->mpMesh), false);
    }
    else
    {
        // In this case we expect the mesh to have been read in from file
        // Note that the next line will throw if the mesh has not been read from file
        std::string original_file=this->mpMesh->GetMeshFileBaseName();
        std::shared_ptr<AbstractMeshReader<ELEMENT_DIM, SPACE_DIM> > p_original_mesh_reader
            = GenericMeshReader<ELEMENT_DIM, SPACE_DIM>(original_file);
        cmgui_mesh_writer.WriteFilesUsingMeshReader(*p_original_mesh_reader);
    }
 
    WriteCmguiScript();
    PetscTools::Barrier("Hdf5ToCmguiConverter");
}
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void Hdf5ToCmguiConverter<ELEMENT_DIM,SPACE_DIM>::WriteCmguiScript()
{
    unsigned num_timesteps = this->mpReader->GetUnlimitedDimensionValues().size();
    assert(this->mpReader->GetVariableNames().size() > 0); // seg fault guard
    std::string variable_name = this->mpReader->GetVariableNames()[0];
 
    if (PetscTools::AmMaster())
    {
        out_stream p_script_file = this->mpOutputFileHandler->OpenOutputFile("LoadSolutions.com");
 
        // Write provenance info, note the # instead of ! because this is - essentially - a PERL script that Cmgui interprets
        std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();
        *p_script_file << comment;
 
        *p_script_file << "# Read the mesh \n"
                       << "gfx read node "<<HeartConfig::Instance()->GetOutputFilenamePrefix()<<".exnode \n"
                       << "gfx read elem "<<HeartConfig::Instance()->GetOutputFilenamePrefix()<<".exelem \n" // note the mesh file name is taken from HeartConfig...
                       << "gfx define faces egroup "<<HeartConfig::Instance()->GetOutputFilenamePrefix()<<"\n"
                       << "# Create a window \n"
                       << "gfx cre win 1 \n"
                       << "# Modify the scene (obtained by gfx list g_element XXXX commands) to visualize first var on lines and nodes \n"
                       << "gfx modify g_element "<< HeartConfig::Instance()->GetOutputFilenamePrefix()<<" general clear circle_discretization 6 default_coordinate coordinates element_discretization \"4*4*4\" native_discretization none; \n"
                       << "gfx modify g_element "<< HeartConfig::Instance()->GetOutputFilenamePrefix()<<" lines select_on material default data "<<variable_name<<" spectrum default selected_material default_selected; \n"
                       << "gfx modify g_element "<< HeartConfig::Instance()->GetOutputFilenamePrefix()<<" node_points glyph point general size \"1*1*1\" centre 0,0,0 font default select_on material default data "<<variable_name<<" spectrum default selected_material default_selected; \n"
                       << "# Load the data \n"
                       << "for ($i=0; $i<" << num_timesteps << "; $i++) { \n"
                       << "    gfx read node " << this->mFileBaseName << "_$i.exnode time $i\n" // ...while the data file from mFileBaseName...
                       << "}\n";
        p_script_file->close();
    }
}
 
// Explicit instantiation
template class Hdf5ToCmguiConverter<1,1>;
template class Hdf5ToCmguiConverter<1,2>;
template class Hdf5ToCmguiConverter<2,2>;
template class Hdf5ToCmguiConverter<1,3>;
template class Hdf5ToCmguiConverter<2,3>;
template class Hdf5ToCmguiConverter<3,3>;