CmguiMeshWriter.cpp

/*
 
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*/
 
#include "CmguiMeshWriter.hpp"
 
#include <string>
 
#include <boost/shared_ptr.hpp>
 
#include "AbstractTetrahedralMesh.hpp"
#include "DistributedTetrahedralMesh.hpp"
#include "Exception.hpp"
#include "FilesystemPermissions.hpp"
#include "Version.hpp"
 
template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::CmguiMeshWriter(const std::string& rDirectory,
                                                         const std::string& rBaseName,
                                                         bool cleanDirectory)
        : AbstractTetrahedralMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, cleanDirectory)
{
    this->mIndexFromZero = false;
    mGroupName = this->mBaseName;
 
    switch (ELEMENT_DIM)
    {
        case 1:
        {
            mElementFileHeader = CmguiElementFileHeader1D;
            mCoordinatesFileHeader = CmguiCoordinatesFileHeader1D;
            mAdditionalFieldHeader = CmguiAdditionalFieldHeader1D;
            break;
        }
        case 2:
        {
            mElementFileHeader = CmguiElementFileHeader2D;
            mCoordinatesFileHeader = CmguiCoordinatesFileHeader2D;
            mAdditionalFieldHeader = CmguiAdditionalFieldHeader2D;
            break;
        }
        case 3:
        {
            mElementFileHeader = CmguiElementFileHeader3D;
            mCoordinatesFileHeader = CmguiCoordinatesFileHeader3D;
            mAdditionalFieldHeader = CmguiAdditionalFieldHeader3D;
            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }
 
 
    mNumNodesPerElement = ELEMENT_DIM+1;
    mReordering.resize(mNumNodesPerElement);
    for (unsigned i=0; i<mNumNodesPerElement; i++)
    {
        mReordering[i] = i;
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM>::WriteFiles()
{
    // Write the exnode file
    out_stream p_node_file = OpenNodeFile();
    WriteNodeFileHeader(p_node_file);
 
    // Write each node's data
    for (unsigned item_num=0; item_num<this->GetNumNodes(); item_num++)
    {
        std::vector<double> current_item = this->GetNextNode();
 
        *p_node_file << "Node:\t" << item_num+1 << "\t";
        for (unsigned i=0; i<SPACE_DIM; i++)
        {
            *p_node_file << current_item[i] << "\t";
        }
 
        *p_node_file << "\n";
    }
    p_node_file->close();
 
    // Write the exlem file
 
    std::vector<boost::shared_ptr<std::ofstream> > elem_files = OpenElementFiles();
    WriteElementsFileHeader(elem_files);
 
    // Write each elements's data
    for (unsigned item_num=0; item_num<this->GetNumElements(); item_num++)
    {
        ElementData elem =this->GetNextElement();
        std::vector<unsigned> current_element = elem.NodeIndices;
 
        assert(elem.AttributeValue < mRegionNames.size());
 
        *elem_files[elem.AttributeValue] << "Element:\t" << item_num+1 << " 0 0 Nodes:\t";
        for (unsigned i=0; i<mNumNodesPerElement; i++)
        {
            *elem_files[elem.AttributeValue] << current_element[mReordering[i]]+1 << "\t";
        }
 
        *elem_files[elem.AttributeValue] << "\n";
 
    }
 
    for (unsigned region_index=0; region_index<mRegionNames.size(); region_index++)
    {
        elem_files[region_index]->close();
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM>::SetAdditionalFieldNames(std::vector<std::string>& rFieldNames)
{
    mAdditionalFieldNames = rFieldNames;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM>::SetRegionNames(std::vector<std::string>& rRegionNames)
{
    mRegionNames = rRegionNames;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
out_stream CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::OpenNodeFile(bool append)
{
    std::string node_file_name = this->mBaseName + ".exnode";
    return this->mpOutputFileHandler->OpenOutputFile(node_file_name, GetOpenMode(append));
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<boost::shared_ptr<std::ofstream> > CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::OpenElementFiles(bool append)
{
 
    std::vector<boost::shared_ptr<std::ofstream> > elem_files;
    // If nobody defined region names we default to the same name as the file name.
    if (mRegionNames.size() == 0)
    {
       mRegionNames.push_back(this->mBaseName);
    }
    elem_files.resize(mRegionNames.size());
 
    std::string directory = this->mpOutputFileHandler->GetOutputDirectoryFullPath();
    for (unsigned region_index=0; region_index<mRegionNames.size(); region_index++)
    {
        std::string elem_file_name = mRegionNames[region_index] + ".exelem";
        fs::path elem_file_path(directory);
        elem_file_path /= elem_file_name;
 
        boost::shared_ptr<std::ofstream> p_output_file(new std::ofstream(elem_file_path, GetOpenMode(append)));
// LCOV_EXCL_START
        if (!p_output_file->is_open())
        {
            EXCEPTION("Could not open file \"" + elem_file_name + "\" in " + directory);
        }
// LCOV_EXCL_STOP
        FilesystemPermissions::SetFilePermissions(elem_file_path);
 
        // NOTE THAT one could simply do:
        //
        // elem_files[region_index]  = this->mpOutputFileHandler->OpenOutputFile(elem_file_name, GetOpenMode(append));
        //
        // but that implies automatic conversion between std::shared_ptr to boost::shared_ptr.
        // That is OK with most compilers, but the combination of gcc 4.1 and boost 1.33 complains about that
        elem_files[region_index]  = p_output_file;
    }
    return elem_files;
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM>::WriteNodeFileHeader(out_stream& rpNodeFile)
{
    // Write provenance info
    std::string comment = "! " + ChasteBuildInfo::GetProvenanceString();
    *rpNodeFile << comment;
 
    // Write the node header
    *rpNodeFile << "Group name: " << this->mGroupName << "\n";
    switch (SPACE_DIM)
    {
        case 1:
        {
            *rpNodeFile << CmguiNodeFileHeader1D;
            break;
        }
        case 2:
        {
            *rpNodeFile << CmguiNodeFileHeader2D;
            break;
        }
        case 3:
        {
            *rpNodeFile << CmguiNodeFileHeader3D;
            break;
        }
        default:
        {
            NEVER_REACHED;
        }
    }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM>::WriteElementsFileHeader(std::vector<boost::shared_ptr<std::ofstream> >& rElemFiles)
{
 
       for (unsigned region_index=0; region_index<mRegionNames.size(); region_index++)
       {
           // Write the elem header
 
           //write provenance info
           std::string comment = "! " + ChasteBuildInfo::GetProvenanceString();
           *rElemFiles[region_index] << comment;
 
           *rElemFiles[region_index] << "Group name: " << mGroupName << "\n";
           *rElemFiles[region_index] << mElementFileHeader;
 
           // Now we need to figure out how many additional fields we have
           unsigned number_of_fields = mAdditionalFieldNames.size();
           std::stringstream string_of_number_of_fields;
 
           // We write the number of additional fields + 1 because the coordinates field gets written anyway...
           string_of_number_of_fields << number_of_fields+1;
 
           // ...and write accordingly the total number of fields
           *rElemFiles[region_index] << " #Fields="<<string_of_number_of_fields.str()<<"\n";
 
           // First field (the coordinates field is fixed and alwys there)
           *rElemFiles[region_index] << mCoordinatesFileHeader;
 
           // Now write the specification for each additional field
           for (unsigned i = 0; i <  number_of_fields; i++)
           {
               //unsigned to string
               std::stringstream i_string;
               i_string << i+2;
               *rElemFiles[region_index]<<i_string.str()<<")  "<<mAdditionalFieldNames[i]<<" ,";
               *rElemFiles[region_index] << mAdditionalFieldHeader;
           }
       }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::CreateFilesWithHeaders()
{
    /*
     *  Node file
     */
    out_stream p_node_file = OpenNodeFile();
    WriteNodeFileHeader(p_node_file);
    p_node_file->close();
 
    /*
     *  Element files
     */
     // Array with file descriptors for each of regions
     std::vector<boost::shared_ptr<std::ofstream> > elem_files = OpenElementFiles();
     WriteElementsFileHeader(elem_files);
     for (unsigned i = 0; i < elem_files.size(); i++)
     {
         elem_files[i]->close();
     }
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::AppendLocalDataToFiles()
{
    //Nodes first
    out_stream p_node_file = OpenNodeFile(true);
 
    typedef typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator NodeIterType;
 
    for (NodeIterType iter = this->mpDistributedMesh->GetNodeIteratorBegin();
         iter != this->mpDistributedMesh->GetNodeIteratorEnd();
         ++iter)
    {
        const c_vector<double, SPACE_DIM>& r_current_item = iter->rGetLocation();
        *p_node_file << "Node:\t" << iter->GetIndex()+1 << "\t";
 
        for (unsigned i=0; i<SPACE_DIM; i++)
        {
            *p_node_file << r_current_item[i] << "\t";
        }
 
        *p_node_file << "\n";
    }
    p_node_file->close();
 
    //Now Element files
 
    std::vector<boost::shared_ptr<std::ofstream> > elem_files = OpenElementFiles(true);
    typedef typename AbstractTetrahedralMesh<ELEMENT_DIM,SPACE_DIM>::ElementIterator ElemIterType;
 
    for (ElemIterType iter = this->mpDistributedMesh->GetElementIteratorBegin();
         iter != this->mpDistributedMesh->GetElementIteratorEnd();
         ++iter)
    {
        if (this->mpDistributedMesh->CalculateDesignatedOwnershipOfElement(iter->GetIndex()))
        {
            assert(iter->GetUnsignedAttribute() < mRegionNames.size());//segfault guard
 
            *elem_files[iter->GetUnsignedAttribute()] << "Element:\t" << iter->GetIndex()+1 << " 0 0 Nodes:\t";
            for (unsigned i=0; i<this->mNodesPerElement; i++)
            {
                *elem_files[iter->GetUnsignedAttribute()]  << iter->GetNodeGlobalIndex(i)+1 << "\t";
            }
 
            *elem_files[iter->GetUnsignedAttribute()] << "\n";
        }
    }
 
    for (unsigned region_index=0; region_index<mRegionNames.size(); region_index++)
    {
        elem_files[region_index]->close();
    }
 
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesFooter()
{
    //No need of footers here, but void implementation is needed
}
 
template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::ios_base::openmode CmguiMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetOpenMode(bool append)
{
    std::ios_base::openmode mode = std::ios::out;
    if (append)
    {
        mode |= std::ios::app; // Note: bitwise OR operation
    }
    else
    {
        mode |= std::ios::trunc;
    }
    return mode;
}
 
// Explicit instantiation
template class CmguiMeshWriter<1,1>;
template class CmguiMeshWriter<1,2>;
template class CmguiMeshWriter<1,3>;
template class CmguiMeshWriter<2,2>;
template class CmguiMeshWriter<2,3>;
template class CmguiMeshWriter<3,3>;