VtkMeshReader.cpp

/*

Copyright (C) Fujitsu Laboratories of Europe, 2009

*/

/*

Copyright (c) 2005-2016, University of Oxford.
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 * 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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   software without specific prior written permission.

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*/



#ifdef CHASTE_VTK

#include "VtkMeshReader.hpp"
#include "Exception.hpp"

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::VtkMeshReader(std::string pathBaseName) :
    mIndexFromZero(true),
    mNumNodes(0),
    mNumElements(0),
    mNumFaces(0),
    mNumCableElements(0),
    mNodesRead(0),
    mElementsRead(0),
    mFacesRead(0),
    mBoundaryFacesRead(0),
    mBoundaryFacesSkipped(0),
    mCableElementsRead(0),
    mNumElementAttributes(0),
    mNumFaceAttributes(0),
    mNumCableElementAttributes(0),
    mOrderOfElements(1),
    mNodesPerElement(4),
    mVtkCellType(VTK_TETRA)
{
    vtkXMLUnstructuredGridReader* vtk_xml_unstructured_grid_reader;

    // Check file exists
    mVtuFile.open(pathBaseName.c_str());
    if ( !mVtuFile.is_open() )
    {
        EXCEPTION("Could not open VTU file: " + pathBaseName);
    }
    mVtuFile.close();

    // Load the mesh geometry and data from a file
    vtk_xml_unstructured_grid_reader = vtkXMLUnstructuredGridReader::New();
    vtk_xml_unstructured_grid_reader->SetFileName( pathBaseName.c_str() );
    vtk_xml_unstructured_grid_reader->Update();
    mpVtkUnstructuredGrid = vtk_xml_unstructured_grid_reader->GetOutput();
    CommonConstructor();
    vtk_xml_unstructured_grid_reader->Delete();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::CommonConstructor()
{

    mNumNodes = mpVtkUnstructuredGrid->GetNumberOfPoints();
    unsigned num_cells = mpVtkUnstructuredGrid->GetNumberOfCells();

    if (ELEMENT_DIM == 2u)
    {
        mNodesPerElement = 3;
        mVtkCellType = VTK_TRIANGLE;
    }
    else if (ELEMENT_DIM == 1u)
    {
        mNodesPerElement = 2;
        mVtkCellType = VTK_LINE;
    }

    //Determine if we have multiple cell types - such as cable elements in addition to tets/triangles
    vtkCellTypes* cell_types = vtkCellTypes::New();
    mpVtkUnstructuredGrid->GetCellTypes(cell_types);

    if(cell_types->GetNumberOfTypes() > 1)
    {
        mNumCableElementAttributes = 1;
        for(unsigned cell_id = 0; cell_id < num_cells; ++cell_id)
        {
            if(mpVtkUnstructuredGrid->GetCellType(cell_id) == mVtkCellType)
            {
                ++mNumElements;
                assert(mNumCableElements == 0); //We expect all the simplices first and then the cables at the end of the array
            }
            else if(mpVtkUnstructuredGrid->GetCellType(cell_id) == VTK_LINE)
            {
                ++mNumCableElements;
            }
            else
            {
                NEVER_REACHED;
            }
        }
    }
    else
    {
        //There is only 1 cell type, so all cells are elements
        mNumElements = num_cells;
    }

    cell_types->Delete();


    // Extract the surface faces
    if (ELEMENT_DIM == 2u)
    {
        vtkDataSetSurfaceFilter* p_surface = vtkDataSetSurfaceFilter::New();
        mpVtkFilterEdges = vtkFeatureEdges::New();
#if VTK_MAJOR_VERSION >= 6
        p_surface->SetInputData(mpVtkUnstructuredGrid);
        mpVtkFilterEdges->SetInputConnection(p_surface->GetOutputPort());
#else
        p_surface->SetInput(mpVtkUnstructuredGrid);
        mpVtkFilterEdges->SetInput(p_surface->GetOutput());
#endif
        mpVtkFilterEdges->Update();
        mNumFaces = mpVtkFilterEdges->GetOutput()->GetNumberOfCells();
        p_surface->Delete();
    }
    else if (ELEMENT_DIM == 3u)
    {
        mpVtkGeometryFilter = vtkGeometryFilter::New();
#if VTK_MAJOR_VERSION >= 6
        mpVtkGeometryFilter->SetInputData(mpVtkUnstructuredGrid);
#else
        mpVtkGeometryFilter->SetInput(mpVtkUnstructuredGrid);
#endif
        mpVtkGeometryFilter->Update();

        mNumFaces = mpVtkGeometryFilter->GetOutput()->GetNumberOfCells();
        if (mNumCableElements > 0)
        {
            //The boundary face filter includes the cable elements - get rid of them
            unsigned num_all_cells = mNumFaces;
            for (unsigned i=0; i<num_all_cells; i++)
            {
               if (mpVtkGeometryFilter->GetOutput()->GetCellType(i) == VTK_LINE)
               {
                   mNumFaces--;
               }
            }
        }
    }
    else if (ELEMENT_DIM == 1u)
    {
        mNumFaces = 0;
        vtkSmartPointer<vtkIdList> enclosing_cells = vtkSmartPointer<vtkIdList>::New();
        assert(mNumNodes == (unsigned) mpVtkUnstructuredGrid->GetNumberOfPoints());
        for (unsigned point_index = 0; point_index < mNumNodes; ++point_index)
        {
            mpVtkUnstructuredGrid->GetPointCells(point_index, enclosing_cells);

            if (enclosing_cells->GetNumberOfIds() == 1u)
            {
                mNumFaces++;
            }
        }
    }
    else
    {
        NEVER_REACHED;
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::VtkMeshReader(vtkUnstructuredGrid* p_vtkUnstructuredGrid) :
    mIndexFromZero(true),
    mNumNodes(0),
    mNumElements(0),
    mNumFaces(0),
    mNumCableElements(0),
    mNodesRead(0),
    mElementsRead(0),
    mFacesRead(0),
    mBoundaryFacesRead(0),
    mBoundaryFacesSkipped(0),
    mCableElementsRead(0),
    mNumElementAttributes(0),
    mNumFaceAttributes(0),
    mNumCableElementAttributes(0),
    mOrderOfElements(1),
    mNodesPerElement(4),
    mVtkCellType(VTK_TETRA)
{
    mpVtkUnstructuredGrid = p_vtkUnstructuredGrid;
    CommonConstructor();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::~VtkMeshReader()
{
    if (ELEMENT_DIM == 3u)
    {
        mpVtkGeometryFilter->Delete();
    }
    else if (ELEMENT_DIM == 2u)
    {
        mpVtkFilterEdges->Delete();
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumElements() const
{
    return mNumElements;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumCableElements() const
{
    return mNumCableElements;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumNodes() const
{
    return mNumNodes;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumFaces() const
{
    return mNumFaces;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumEdges() const
{
    return mNumFaces;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumElementAttributes() const
{
    return mNumElementAttributes;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumCableElementAttributes() const
{
    return mNumCableElementAttributes;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNumFaceAttributes() const
{
    return mNumFaceAttributes;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::Reset()
{
    mNodesRead=0;
    mElementsRead=0;
    mFacesRead=0;
    mBoundaryFacesRead=0;
    mBoundaryFacesSkipped=0;
    mCableElementsRead=0;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::Initialize()
{
    mpVtkUnstructuredGrid->Initialize();
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<double> VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNextNode()
{
    if ( mNodesRead >= mNumNodes )
    {
        EXCEPTION( "Trying to read data for a node that doesn't exist" );
    }

    std::vector<double> next_node;

    for (unsigned i = 0; i < 3; i++)
    {
        next_node.push_back( mpVtkUnstructuredGrid->GetPoint(mNodesRead)[i] );
    }

    mNodesRead++;
    return next_node;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNextElementData()
{
    if ( mElementsRead >= mNumElements )
    {
        EXCEPTION( "Trying to read data for an element that doesn't exist" );
    }

    if (mpVtkUnstructuredGrid->GetCellType(mElementsRead)!=  mVtkCellType)
    {
        EXCEPTION("Element is not of expected type (vtkTetra/vtkTriangle)");
    }

    ElementData next_element_data;

    for (unsigned i = 0; i < mNodesPerElement; i++)
    {
        next_element_data.NodeIndices.push_back(mpVtkUnstructuredGrid->GetCell(mElementsRead)->GetPointId(i));
    }

    // \todo implement method to read element data properly (currently returns zero always...)
    next_element_data.AttributeValue = 0;

    mElementsRead++;
    return next_element_data;
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNextCableElementData()
{
    if ( mCableElementsRead >=  mNumCableElements )
    {
        EXCEPTION( "Trying to read data for a cable element that doesn't exist" );
    }

    unsigned next_index = mNumElements + mCableElementsRead;
    assert(mpVtkUnstructuredGrid->GetCellType(next_index)==VTK_LINE);

    ElementData next_element_data;

    for (unsigned i = 0; i < 2; i++)
    {
        next_element_data.NodeIndices.push_back(mpVtkUnstructuredGrid->GetCell(next_index)->GetPointId(i));
    }

    vtkDataArray *p_scalars = mpVtkUnstructuredGrid->GetCellData()->GetArray( "Cable radius" );
    next_element_data.AttributeValue = p_scalars->GetTuple(next_index)[0];

    mCableElementsRead++;
    return next_element_data;
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
ElementData VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetNextFaceData()
{
    if ( mBoundaryFacesRead >= mNumFaces)
    {
        EXCEPTION( "Trying to read data for a boundary element that doesn't exist");
    }

    ElementData next_face_data;

    if (ELEMENT_DIM == 3u)
    {
        while (mpVtkGeometryFilter->GetOutput()->GetCellType(mBoundaryFacesRead + mBoundaryFacesSkipped) == VTK_LINE)
        {
            mBoundaryFacesSkipped++;
        }
        for (unsigned i = 0; i < (mNodesPerElement-1); i++)
        {
            next_face_data.NodeIndices.push_back(mpVtkGeometryFilter->GetOutput()->GetCell(mBoundaryFacesRead + mBoundaryFacesSkipped)->GetPointId(i));
        }
    }
    else if (ELEMENT_DIM == 2u)
    {
        for (unsigned i = 0; i < (mNodesPerElement-1); i++)
        {
            next_face_data.NodeIndices.push_back(mpVtkFilterEdges->GetOutput()->GetCell(mBoundaryFacesRead)->GetPointId(i));
        }
    }
    else if (ELEMENT_DIM == 1u)
    {
        vtkSmartPointer<vtkIdList> enclosing_cells = vtkSmartPointer<vtkIdList>::New();
        assert(mNumNodes == (unsigned) mpVtkUnstructuredGrid->GetNumberOfPoints());
        for (unsigned point_index = mBoundaryFacesSkipped; point_index < mNumNodes; ++point_index)
        {
            mBoundaryFacesSkipped++;
            mpVtkUnstructuredGrid->GetPointCells(point_index, enclosing_cells);

            if (enclosing_cells->GetNumberOfIds() == 1u)
            {
                next_face_data.NodeIndices.push_back(point_index);
                break;
            }
        }
    }
    else
    {
        NEVER_REACHED;
    }

    mBoundaryFacesRead++;
    return next_face_data;
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetCellData(std::string dataName, std::vector<double>& dataPayload)
{
    vtkCellData *p_cell_data = mpVtkUnstructuredGrid->GetCellData();

    if ( !p_cell_data->HasArray(dataName.c_str()) )
    {
        EXCEPTION("No cell data '" + dataName + "'");
    }

    vtkDataArray *p_scalars = p_cell_data->GetArray( dataName.c_str() );
    if (p_scalars->GetNumberOfComponents() != 1)
    {
        EXCEPTION("The cell data '" + dataName + "' is not scalar data.");
    }

    dataPayload.clear();
    for (unsigned i = 0; i < mNumElements; i++)
    {
        dataPayload.push_back( p_scalars->GetTuple(i)[0] );
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetCellData(std::string dataName, std::vector<c_vector<double,SPACE_DIM> >& dataPayload)
{
    vtkCellData *p_cell_data = mpVtkUnstructuredGrid->GetCellData();

    if ( !p_cell_data->HasArray(dataName.c_str()) )
    {
        EXCEPTION("No cell data '" + dataName + "'");
    }

    vtkDataArray *p_scalars = p_cell_data->GetArray( dataName.c_str() );
    if (p_scalars->GetNumberOfComponents() != 3)
    {
        EXCEPTION("The cell data '" + dataName + "' is not 3-vector data.");
    }

    dataPayload.clear();
    for (unsigned i = 0; i < mNumElements; i++)
    {
        c_vector <double, SPACE_DIM> data;
        for (unsigned j = 0; j < SPACE_DIM; j++)
        {
            data[j]=  p_scalars->GetTuple(i)[j];
        }
        dataPayload.push_back(data);
    }
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetPointData(std::string dataName, std::vector<double>& dataPayload)
{
    vtkPointData *p_point_data = mpVtkUnstructuredGrid->GetPointData();

    if ( !p_point_data->HasArray(dataName.c_str()) )
    {
        EXCEPTION("No point data '" + dataName + "'");
    }

    vtkDataArray *p_scalars = p_point_data->GetArray( dataName.c_str() );
    if (p_scalars->GetNumberOfComponents() != 1)
    {
        EXCEPTION("The point data '" + dataName + "' is not scalar data.");
    }

    dataPayload.clear();

    for (unsigned i = 0; i < mNumNodes; i++)
    {
        dataPayload.push_back( p_scalars->GetTuple(i)[0] );
    }
}

template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::GetPointData(std::string dataName, std::vector<c_vector<double,SPACE_DIM> >& dataPayload)
{
   vtkPointData *p_point_data = mpVtkUnstructuredGrid->GetPointData();

    if ( !p_point_data->HasArray(dataName.c_str()) )
    {
        EXCEPTION("No point data '" + dataName + "'");
    }

    vtkDataArray *p_scalars = p_point_data->GetArray( dataName.c_str() );

    if (p_scalars->GetNumberOfComponents() != 3)
    {
        EXCEPTION("The point data '" + dataName + "' is not 3-vector data.");
    }
    dataPayload.clear();
    for (unsigned i = 0; i < mNumNodes; i++)
    {
        c_vector<double, SPACE_DIM> data;
        for (unsigned j = 0; j< SPACE_DIM; j++)
        {
            data[j] = p_scalars->GetTuple(i)[j];
        }
        dataPayload.push_back( data );
    }
}


template <unsigned ELEMENT_DIM, unsigned SPACE_DIM>
vtkUnstructuredGrid* VtkMeshReader<ELEMENT_DIM,SPACE_DIM>::OutputMeshAsVtkUnstructuredGrid()
{
    return mpVtkUnstructuredGrid;
}

// Explicit instantiation

template class VtkMeshReader<1,1>;
template class VtkMeshReader<1,2>;
template class VtkMeshReader<1,3>;
template class VtkMeshReader<2,2>;
template class VtkMeshReader<2,3>;
template class VtkMeshReader<3,3>;
#endif // CHASTE_VTK