CmguiMeshWriter.cpp

/*

Copyright (C) University of Oxford, 2005-2011

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste 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.

Chaste 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. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#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->GetRegion() < mRegionNames.size());//segfault guard

            *elem_files[iter->GetRegion()] << "Element:\t" << iter->GetIndex()+1 << " 0 0 Nodes:\t";
            for (unsigned i=0; i<this->mNodesPerElement; i++)
            {
                *elem_files[iter->GetRegion()]  << iter->GetNodeGlobalIndex(i)+1 << "\t";
            }

            *elem_files[iter->GetRegion()] << "\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;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool CmguiMeshWriter<ELEMENT_DIM,SPACE_DIM>::CompareCmguiFiles(std::string& rPath1, std::string& rPath2)
{
    std::string compare_command = "diff --ignore-matching-lines=\"! \" ";
    compare_command += rPath1;
    compare_command += " ";
    compare_command += rPath2;

    // Compare the new test file with one from the repository
    if (system(compare_command.c_str()) == 0)
    {
        return true;
    }
    else
    {
        return false;
    }
}

// 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>;