VertexMeshWriter.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 "VertexMeshWriter.hpp"
#include "Version.hpp"

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
struct MeshWriterIterators
{
    typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator* pNodeIter;
    typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator* pElemIter;
};

// Implementation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::VertexMeshWriter(const std::string& rDirectory,
                                                           const std::string& rBaseName,
                                                           const bool clearOutputDir)
    : AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>(rDirectory, rBaseName, clearOutputDir),
      mpMesh(NULL),
      mpIters(new MeshWriterIterators<ELEMENT_DIM, SPACE_DIM>),
      mpNodeMap(NULL),
      mNodeMapCurrentIndex(0)
{
    mpIters->pNodeIter = NULL;
    mpIters->pElemIter = NULL;

#ifdef CHASTE_VTK
     // Dubious, since we shouldn't yet know what any details of the mesh are.
     mpVtkUnstructedMesh = vtkUnstructuredGrid::New();
#endif //CHASTE_VTK
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::~VertexMeshWriter()
{
    if (mpIters->pNodeIter)
    {
        delete mpIters->pNodeIter;
        delete mpIters->pElemIter;
    }

    delete mpIters;

    if (mpNodeMap)
    {
        delete mpNodeMap;
    }

#ifdef CHASTE_VTK
     // Dubious, since we shouldn't yet know what any details of the mesh are.
     mpVtkUnstructedMesh->Delete(); // Reference counted
#endif //CHASTE_VTK
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextNode()
{
    if (mpMesh)
    {
        // Sanity check
        assert(this->mNumNodes == mpMesh->GetNumNodes());

        std::vector<double> coordinates(SPACE_DIM+1);

        // Get the node coordinates using the node iterator (thus skipping deleted nodes)
        for (unsigned j=0; j<SPACE_DIM; j++)
        {
            coordinates[j] = (*(mpIters->pNodeIter))->GetPoint()[j];
        }
        coordinates[SPACE_DIM] = (*(mpIters->pNodeIter))->IsBoundaryNode();

        ++(*(mpIters->pNodeIter));

        return coordinates;
    }
    else
    {
        return AbstractMeshWriter<ELEMENT_DIM,SPACE_DIM>::GetNextNode();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VertexElementData VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextElementWithFaces()
{
    // This method should only be called in 3D
    assert(SPACE_DIM == 3);
    assert(mpMesh);
    assert(this->mNumElements == mpMesh->GetNumElements());

    // Create data structure for this element
    VertexElementData elem_data;

    // Store node indices owned by this element
    elem_data.NodeIndices.resize((*(mpIters->pElemIter))->GetNumNodes());
    for (unsigned j=0; j<elem_data.NodeIndices.size(); j++)
    {
        unsigned old_index = (*(mpIters->pElemIter))->GetNodeGlobalIndex(j);
        elem_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
    }

    // Store faces owned by this element
    elem_data.Faces.resize((*(mpIters->pElemIter))->GetNumFaces());
    for (unsigned i=0; i<elem_data.Faces.size(); i++)
    {
        // Get pointer to this face
        VertexElement<ELEMENT_DIM-1, SPACE_DIM>* p_face = (*(mpIters->pElemIter))->GetFace(i);

        // Create data structure for this face
        ElementData face_data;

        // Store this face's index
        face_data.AttributeValue = p_face->GetIndex();

        // Store node indices owned by this face
        face_data.NodeIndices.resize(p_face->GetNumNodes());
        for (unsigned j=0; j<face_data.NodeIndices.size(); j++)
        {
            unsigned old_index = p_face->GetNodeGlobalIndex(j);
            face_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
        }

        // Store this face
        elem_data.Faces[i] = face_data;

    }

    // Set attribute
    elem_data.AttributeValue = (*(mpIters->pElemIter))->GetRegion();
    ++(*(mpIters->pElemIter));

    return elem_data;
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextElement()
{

    if (mpMesh)
    {
        assert(this->mNumElements == mpMesh->GetNumElements());

        ElementData elem_data;
        elem_data.NodeIndices.resize((*(mpIters->pElemIter))->GetNumNodes());
        for (unsigned j=0; j<elem_data.NodeIndices.size(); j++)
        {
            unsigned old_index = (*(mpIters->pElemIter))->GetNodeGlobalIndex(j);
            elem_data.NodeIndices[j] = mpMesh->IsMeshChanging() ? mpNodeMap->GetNewIndex(old_index) : old_index;
        }

        // Set attribute
        elem_data.AttributeValue = (*(mpIters->pElemIter))->GetRegion();
        ++(*(mpIters->pElemIter));

        return elem_data;
    }
    else
    {
        return AbstractMeshWriter<ELEMENT_DIM, SPACE_DIM>::GetNextElement();
    }
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteVtkUsingMesh(VertexMesh<ELEMENT_DIM, SPACE_DIM>& rMesh, std::string stamp)
{
#ifdef CHASTE_VTK
    //Make the Vtk mesh
    assert(SPACE_DIM==3 || SPACE_DIM == 2);
    vtkPoints* p_pts = vtkPoints::New(VTK_DOUBLE);
    p_pts->GetData()->SetName("Vertex positions");
    for (unsigned node_num=0; node_num<rMesh.GetNumNodes(); node_num++)
    {
        c_vector<double, SPACE_DIM> position = rMesh.GetNode(node_num)->rGetLocation();
        if (SPACE_DIM==2)
        {
            p_pts->InsertPoint(node_num, position[0], position[1], 0.0);
        }
        else
        {
            p_pts->InsertPoint(node_num, position[0], position[1], position[2]);
        }
    }

    mpVtkUnstructedMesh->SetPoints(p_pts);
    p_pts->Delete(); // Reference counted
    for (typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator iter = rMesh.GetElementIteratorBegin();
         iter != rMesh.GetElementIteratorEnd();
         ++iter)
    {
        vtkCell* p_cell;
        if (SPACE_DIM == 2)
        {
            p_cell = vtkPolygon::New();
        }
        else
        {
            p_cell = vtkConvexPointSet::New();
        }
        vtkIdList* p_cell_id_list = p_cell->GetPointIds();
        p_cell_id_list->SetNumberOfIds(iter->GetNumNodes());
        for (unsigned j = 0; j < iter->GetNumNodes(); ++j)
        {
            p_cell_id_list->SetId(j, iter->GetNodeGlobalIndex(j));
        }
        mpVtkUnstructedMesh->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
        p_cell->Delete(); //Reference counted
    }

    // Vtk mesh is now made
    assert(mpVtkUnstructedMesh->CheckAttributes() == 0);
    vtkXMLUnstructuredGridWriter* p_writer = vtkXMLUnstructuredGridWriter::New();
    p_writer->SetInput(mpVtkUnstructedMesh);
    // Uninitialised stuff arises (see #1079), but you can remove valgrind problems by removing compression:
    // **** REMOVE WITH CAUTION *****
    p_writer->SetCompressor(NULL);
    // **** REMOVE WITH CAUTION *****

    std::string vtk_file_name = this->mpOutputFileHandler->GetOutputDirectoryFullPath() + this->mBaseName;
    if (stamp != "")
    {
        vtk_file_name += "_" + stamp;
    }
    vtk_file_name += ".vtu";

    p_writer->SetFileName(vtk_file_name.c_str());
    //p_writer->PrintSelf(std::cout, vtkIndent());
    p_writer->Write();
    p_writer->Delete(); // Reference counted
#endif //CHASTE_VTK
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::AddCellData(std::string dataName, std::vector<double> dataPayload)
{
#ifdef CHASTE_VTK
    vtkDoubleArray* p_scalars = vtkDoubleArray::New();
    p_scalars->SetName(dataName.c_str());
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }

    vtkCellData* p_cell_data = mpVtkUnstructedMesh->GetCellData();
    p_cell_data->AddArray(p_scalars);
    p_scalars->Delete(); // Reference counted
#endif //CHASTE_VTK
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::AddPointData(std::string dataName, std::vector<double> dataPayload)
{
#ifdef CHASTE_VTK
    vtkDoubleArray* p_scalars = vtkDoubleArray::New();
    p_scalars->SetName(dataName.c_str());
    for (unsigned i=0; i<dataPayload.size(); i++)
    {
        p_scalars->InsertNextValue(dataPayload[i]);
    }

    vtkPointData* p_point_data = mpVtkUnstructedMesh->GetPointData();
    p_point_data->AddArray(p_scalars);
    p_scalars->Delete(); // Reference counted
#endif //CHASTE_VTK
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFilesUsingMesh(VertexMesh<ELEMENT_DIM,SPACE_DIM>& rMesh)
{

    this->mpMeshReader = NULL;
    mpMesh = &rMesh;

    this->mNumNodes = mpMesh->GetNumNodes();
    this->mNumElements = mpMesh->GetNumElements();

    typedef typename AbstractMesh<ELEMENT_DIM,SPACE_DIM>::NodeIterator NodeIterType;
    mpIters->pNodeIter = new NodeIterType(mpMesh->GetNodeIteratorBegin());

    typedef typename VertexMesh<ELEMENT_DIM,SPACE_DIM>::VertexElementIterator ElemIterType;
    mpIters->pElemIter = new ElemIterType(mpMesh->GetElementIteratorBegin());

    // Set up node map if we might have deleted nodes
    mNodeMapCurrentIndex = 0;
    if (mpMesh->IsMeshChanging())
    {
        mpNodeMap = new NodeMap(mpMesh->GetNumAllNodes());
        for (NodeIterType it = mpMesh->GetNodeIteratorBegin(); it != mpMesh->GetNodeIteratorEnd(); ++it)
        {
            mpNodeMap->SetNewIndex(it->GetIndex(), mNodeMapCurrentIndex++);
        }
    }
    WriteFiles();
}

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VertexMeshWriter<ELEMENT_DIM, SPACE_DIM>::WriteFiles()
{
    std::string comment = "# " + ChasteBuildInfo::GetProvenanceString();

    // Write node file
    std::string node_file_name = this->mBaseName + ".node";
    out_stream p_node_file = this->mpOutputFileHandler->OpenOutputFile(node_file_name);

    // Write the node header
    unsigned num_attr = 0;
    unsigned max_bdy_marker = 1; // as we include boundary node information in the node file
    unsigned num_nodes = this->GetNumNodes();

    *p_node_file << num_nodes << "\t";
    *p_node_file << SPACE_DIM << "\t";
    *p_node_file << num_attr << "\t";
    *p_node_file << max_bdy_marker << "\n";
    *p_node_file << std::setprecision(6);

    // Write each node's data
    for (unsigned item_num=0; item_num<num_nodes; item_num++)
    {
        std::vector<double> current_item = this->GetNextNode();
        *p_node_file << item_num;
        for (unsigned i=0; i<SPACE_DIM+1; i++)
        {
            *p_node_file << "\t" << current_item[i];
        }
        *p_node_file << "\n";
    }
    *p_node_file << comment << "\n";
    p_node_file->close();

    // Write element file
    std::string element_file_name = this->mBaseName + ".cell";
    out_stream p_element_file = this->mpOutputFileHandler->OpenOutputFile(element_file_name);

    // Write the element header
    unsigned num_elements = this->GetNumElements();

    unsigned first_elem_attribute_value = (*(mpIters->pElemIter))->GetRegion();
    if (first_elem_attribute_value != 0)
    {
        num_attr = 1;
    }

    *p_element_file << num_elements << "\t";
    *p_element_file << num_attr << "\n";

    // Write each element's data
    for (unsigned item_num=0; item_num<num_elements; item_num++)
    {
        if (SPACE_DIM == 2) // In 2D, write the node indices owned by this element
        {
            // Get data for this element
            ElementData elem_data = this->GetNextElement();

            // Get the node indices owned by this element
            std::vector<unsigned> node_indices = elem_data.NodeIndices;

            // Write this element's index and the number of nodes owned by it to file
            *p_element_file << item_num <<  "\t" << node_indices.size();

            // Write the node indices owned by this element to file
            for (unsigned i=0; i<node_indices.size(); i++)
            {
                *p_element_file << "\t" << node_indices[i];
            }

            // Write the element attribute
            if (elem_data.AttributeValue != 0)
            {
                *p_element_file << "\t" << elem_data.AttributeValue;
            }

            // New line
            *p_element_file << "\n";
        }
        else // 3D
        {
            assert(SPACE_DIM == 3);

            // Get data for this element
            VertexElementData elem_data_with_faces = this->GetNextElementWithFaces();

            // Get the node indices owned by this element
            std::vector<unsigned> node_indices = elem_data_with_faces.NodeIndices;

            // Write this element's index and the number of nodes owned by it to file
            *p_element_file << item_num <<  "\t" << node_indices.size();

            // Write the node indices owned by this element to file
            for (unsigned i=0; i<node_indices.size(); i++)
            {
                *p_element_file << "\t" << node_indices[i];
            }

            // Get the faces owned by this element (if any)
            std::vector<ElementData> faces = elem_data_with_faces.Faces;

            // Write the number of faces owned by this element to file
            *p_element_file << "\t" << faces.size();

            for (unsigned j=0; j<faces.size(); j++)
            {
                // Get the node indices owned by this face
                std::vector<unsigned> face_node_indices = faces[j].NodeIndices;

                // Write this face's index and the number of nodes owned by it to file
                *p_element_file << "\t" << faces[j].AttributeValue <<  "\t" << face_node_indices.size();

                // Write the node indices owned by this element to file
                for (unsigned i=0; i<face_node_indices.size(); i++)
                {
                    *p_element_file << "\t" << face_node_indices[i];
                }

            }

            // Write the element attribute if necessary
            if (elem_data_with_faces.AttributeValue != 0)
            {
                *p_element_file << "\t" << elem_data_with_faces.AttributeValue;
            }

            // New line
            *p_element_file << "\n";
        }
    }

    *p_element_file << comment << "\n";
    p_element_file->close();
}

// Explicit instantiation

template class VertexMeshWriter<1,1>;
template class VertexMeshWriter<1,2>;
template class VertexMeshWriter<1,3>;
template class VertexMeshWriter<2,2>;
template class VertexMeshWriter<2,3>;
template class VertexMeshWriter<3,3>;