CmguiMeshWriter.cpp

/*

Copyright (c) 2005-2012, University of Oxford.
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This file is part of Chaste.

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modification, are permitted provided that the following conditions are met:
 * Redistributions of source code must retain the above copyright notice,
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 * Redistributions in binary form must reproduce the above copyright notice,
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   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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*/
#include "Exception.hpp"
#include "CmguiMeshWriter.hpp"
#include "Version.hpp"
#include <boost/shared_ptr.hpp>

#include "AbstractTetrahedralMesh.hpp"
#include "DistributedTetrahedralMesh.hpp"

// Implementation

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<ELEMENT_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";

        boost::shared_ptr<std::ofstream> p_output_file(new std::ofstream((directory+elem_file_name).c_str(), GetOpenMode(append)));
#define COVERAGE_IGNORE
        if (!p_output_file->is_open())
        {
            EXCEPTION("Could not open file \"" + elem_file_name + "\" in " + directory);
        }
#undef COVERAGE_IGNORE

        // 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::auto_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<ELEMENT_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>;