HeartGeometryInformation.cpp

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*/
 
#include "HeartGeometryInformation.hpp"
 
#include <cmath>
#include <fstream>
#include <sstream>
#include "OutputFileHandler.hpp"
#include "Exception.hpp"
#include "PetscTools.hpp"
 
// Area of the septum considered to belong to the each ventricle (relative to 1)
template<unsigned SPACE_DIM>
const double HeartGeometryInformation<SPACE_DIM>::LEFT_SEPTUM_SIZE = 2.0/3.0;
 
template<unsigned SPACE_DIM>
const double HeartGeometryInformation<SPACE_DIM>::RIGHT_SEPTUM_SIZE = 1.0/3.0;
 
template<unsigned SPACE_DIM>
HeartGeometryInformation<SPACE_DIM>::HeartGeometryInformation(AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh,
                                                              const std::string& rEpiFile,
                                                              const std::string& rEndoFile,
                                                              bool indexFromZero)
   : mpMesh(&rMesh)
{
    DistanceMapCalculator<SPACE_DIM, SPACE_DIM> distance_calculator(*mpMesh);
 
    // Get nodes defining each surface
    GetNodesAtSurface(rEpiFile, mEpiSurface, indexFromZero);
    GetNodesAtSurface(rEndoFile, mEndoSurface, indexFromZero);
 
    // Compute the distance map of each surface
    distance_calculator.ComputeDistanceMap(mEpiSurface, mDistMapEpicardium);
    distance_calculator.ComputeDistanceMap(mEndoSurface, mDistMapEndocardium);
    mNumberOfSurfacesProvided = 2;
}
 
template<unsigned SPACE_DIM>
HeartGeometryInformation<SPACE_DIM>::HeartGeometryInformation (AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh,
                                                               const std::string& rEpiFile,
                                                               const std::string& rLVFile,
                                                               const std::string& rRVFile,
                                                               bool indexFromZero)
    : mpMesh(&rMesh)
{
    DistanceMapCalculator<SPACE_DIM, SPACE_DIM> distance_calculator(*mpMesh);
 
    // Get nodes defining each surface and compute the distance map of each surface
 
    GetNodesAtSurface(rEpiFile, mEpiSurface, indexFromZero);
 
    if (rLVFile != "")
    {
        GetNodesAtSurface(rLVFile, mLVSurface, indexFromZero);
    }
    else
    {
        if (rRVFile == "")
        {
            EXCEPTION("At least one of left ventricle or right ventricle files is required");
        }
    }
    if (rRVFile != "")
    {
        GetNodesAtSurface(rRVFile, mRVSurface, indexFromZero);
    }
    distance_calculator.ComputeDistanceMap(mEpiSurface, mDistMapEpicardium);
    distance_calculator.ComputeDistanceMap(mLVSurface, mDistMapLeftVentricle);
    distance_calculator.ComputeDistanceMap(mRVSurface, mDistMapRightVentricle);
 
    mNumberOfSurfacesProvided = 3;
}
 
template<unsigned SPACE_DIM>
HeartGeometryInformation<SPACE_DIM>::HeartGeometryInformation (std::string nodeHeterogeneityFileName)
{
    mpMesh = NULL;
    std::ifstream heterogeneity_file;
    heterogeneity_file.open(nodeHeterogeneityFileName.c_str());
 
    if (!(heterogeneity_file.is_open()))
    {
        heterogeneity_file.close();
        EXCEPTION("Could not open heterogeneities file (" << nodeHeterogeneityFileName << ")");
    }
 
    while (!heterogeneity_file.eof())
    {
        int value;
 
        heterogeneity_file >> value;
 
        // Format error (for example read a double), or value not equal to 0, 1, or 2.
        if ((heterogeneity_file.fail() && !heterogeneity_file.eof()) || value < 0 || value > 2)
        {
            heterogeneity_file.close();
            EXCEPTION("A value in the heterogeneities file (" << nodeHeterogeneityFileName
               << ") is out of range (or not an integer). It should be epi = 0, mid = 1, endo = 2");
        }
 
        if (!heterogeneity_file.eof())
        {
            if (value==0)
            {
                mLayerForEachNode.push_back(EPI);
            }
            else if (value==1)
            {
                mLayerForEachNode.push_back(MID);
            }
            else
            {
                assert(value==2);
                mLayerForEachNode.push_back(ENDO);
            }
        }
    }
 
    heterogeneity_file.close();
}
 
template<unsigned SPACE_DIM>
void HeartGeometryInformation<SPACE_DIM>::ProcessLine(
        const std::string& rLineFromFile,
        std::set<unsigned>& rSurfaceNodeIndexSet,
        unsigned offset) const
{
    std::stringstream line_stream(rLineFromFile);
    while (!line_stream.eof())
    {
        unsigned item;
        line_stream >> item;
        // If offset==1 then shift the nodes, since we are assuming MEMFEM format (numbered from 1 on)
        if (item == 0 && offset != 0)
        {
            EXCEPTION("Error when reading surface file.  It was assumed not to be indexed from zero, but zero appeared in the list.");
        }
        rSurfaceNodeIndexSet.insert(item-offset);
    }
}
 
template<unsigned SPACE_DIM>
void HeartGeometryInformation<SPACE_DIM>::GetNodesAtSurface(
        const std::string& rSurfaceFileName,
        std::vector<unsigned>& rSurfaceNodes,
        bool indexFromZero) const
{
    // Open the file defining the surface
    std::ifstream file_stream;
    unsigned offset=0;
    if (indexFromZero == false)
    {
        offset=1;
    }
 
    file_stream.open(rSurfaceFileName.c_str());
    if (!file_stream.is_open())
    {
        EXCEPTION("Wrong surface definition file name " + rSurfaceFileName);
    }
 
    // Temporary storage for the nodes, helps discarding repeated values
    std::set<unsigned> surface_original_node_index_set;
 
    // Loop over all the triangles and add node indexes to the set
    std::string line;
    getline(file_stream, line);
    do
    {
        ProcessLine(line, surface_original_node_index_set, offset);
 
        getline(file_stream, line);
    }
    while (!file_stream.eof());
    file_stream.close();
 
    // Make vector big enough
    rSurfaceNodes.reserve(surface_original_node_index_set.size());
 
    if (mpMesh->rGetNodePermutation().empty())
    {
        // Copy the node indexes from the set to the vector as they are
        for (std::set<unsigned>::iterator node_index_it=surface_original_node_index_set.begin();
            node_index_it != surface_original_node_index_set.end();
            node_index_it++)
        {
            rSurfaceNodes.push_back(*node_index_it);
        }
    }
    else
    {
        // Copy the original node indices from the set to the vector applying the permutation
        for (std::set<unsigned>::iterator node_index_it=surface_original_node_index_set.begin();
            node_index_it != surface_original_node_index_set.end();
            node_index_it++)
        {
            rSurfaceNodes.push_back(mpMesh->rGetNodePermutation()[*node_index_it]);
        }
    }
}
 
template<unsigned SPACE_DIM>
HeartRegionType HeartGeometryInformation<SPACE_DIM>::GetHeartRegion(unsigned nodeIndex) const
{
 
    if (mDistMapRightVentricle[nodeIndex] >= mDistMapEpicardium[nodeIndex] &&
        mDistMapRightVentricle[nodeIndex] >= mDistMapLeftVentricle[nodeIndex])
    {
        return LEFT_VENTRICLE_WALL;
    }
 
    if (mDistMapLeftVentricle[nodeIndex] >= mDistMapEpicardium[nodeIndex] &&
        mDistMapLeftVentricle[nodeIndex] >= mDistMapRightVentricle[nodeIndex])
    {
        return RIGHT_VENTRICLE_WALL;
    }
 
    if (mDistMapEpicardium[nodeIndex] >= mDistMapLeftVentricle[nodeIndex] &&
        mDistMapEpicardium[nodeIndex] >= mDistMapRightVentricle[nodeIndex])
    {
        if (mDistMapLeftVentricle[nodeIndex]
            < LEFT_SEPTUM_SIZE*(mDistMapLeftVentricle[nodeIndex] + mDistMapRightVentricle[nodeIndex]))
        {
            return LEFT_SEPTUM;
        }
        else
        {
            return RIGHT_SEPTUM;
        }
    }
 
    NEVER_REACHED;
    return UNKNOWN; // LCOV_EXCL_LINE
}
 
template<unsigned SPACE_DIM>
double HeartGeometryInformation<SPACE_DIM>::GetDistanceToEndo(unsigned nodeIndex)
{
    // General case where you provide 3 surfaces: LV, RV, epicardium
    if (mNumberOfSurfacesProvided == 3)
    {
        HeartRegionType node_region = GetHeartRegion(nodeIndex);
        switch(node_region)
        {
            case LEFT_VENTRICLE_WALL:
            case LEFT_VENTRICLE_SURFACE:
                return mDistMapLeftVentricle[nodeIndex];
                break;
 
            case RIGHT_VENTRICLE_WALL:
            case RIGHT_VENTRICLE_SURFACE:
                return mDistMapRightVentricle[nodeIndex];
                break;
 
            case LEFT_SEPTUM:
                return mDistMapLeftVentricle[nodeIndex];
                break;
 
            case RIGHT_SEPTUM:
                return mDistMapRightVentricle[nodeIndex] ;
                break;
 
            // LCOV_EXCL_START
            case UNKNOWN:
                std::cerr << "Wrong distances node: " << nodeIndex << "\t"
                          << "Epi " << mDistMapEpicardium[nodeIndex] << "\t"
                          << "RV " << mDistMapRightVentricle[nodeIndex] << "\t"
                          << "LV " << mDistMapLeftVentricle[nodeIndex]
                          << std::endl;
 
                // Make wall_thickness=0 as in Martin's code
                return 0.0;
                break;
            // LCOV_EXCL_STOP
 
            default:
                NEVER_REACHED;
        }
    }
    // Simplified case where you only provide epi and endo surface definitions
    else
    {
        return mDistMapEndocardium[nodeIndex];
    }
 
    // gcc wants to see a return statement at the end of the method.
    NEVER_REACHED;
    return 0.0; // LCOV_EXCL_LINE
}
 
template<unsigned SPACE_DIM>
double HeartGeometryInformation<SPACE_DIM>::GetDistanceToEpi(unsigned nodeIndex)
{
    return mDistMapEpicardium[nodeIndex];
}
 
template<unsigned SPACE_DIM>
double HeartGeometryInformation<SPACE_DIM>::CalculateRelativeWallPosition(unsigned nodeIndex)
{
 
    double dist_endo = GetDistanceToEndo(nodeIndex);
    double dist_epi = GetDistanceToEpi(nodeIndex);
    assert( (dist_endo + dist_epi) != 0 );
    /*
     *  A node contained on both epicardium and lv (or rv) surfaces has wall thickness 0/0.
     *  By setting its value to 0 we consider it contained only on the lv (or rv) surface.
     */
    double relative_position = dist_endo / (dist_endo + dist_epi);
    return relative_position;
}
 
template<unsigned SPACE_DIM>
void HeartGeometryInformation<SPACE_DIM>::DetermineLayerForEachNode(double epiFraction, double endoFraction)
{
    if (epiFraction+endoFraction>1)
    {
        EXCEPTION("The sum of fractions of epicardial and endocardial layers must be lesser than 1");
    }
 
    if ((endoFraction<0) || (epiFraction<0))
    {
        EXCEPTION("A fraction of a layer must be positive");
    }
 
    mLayerForEachNode.resize(mpMesh->GetNumNodes());
    for (unsigned i=0; i<mpMesh->GetNumNodes(); i++)
    {
        double position = CalculateRelativeWallPosition(i);
        if (position<endoFraction)
        {
            mLayerForEachNode[i] = ENDO;
        }
        else if (position<(1-epiFraction))
        {
            mLayerForEachNode[i] = MID;
        }
        else
        {
            mLayerForEachNode[i] = EPI;
        }
    }
}
 
template<unsigned SPACE_DIM>
void HeartGeometryInformation<SPACE_DIM>::WriteLayerForEachNode(std::string outputDir, std::string file)
{
    OutputFileHandler handler(outputDir,false);
    if (PetscTools::AmMaster())
    {
        out_stream p_file = handler.OpenOutputFile(file);
 
        assert(mLayerForEachNode.size()>0);
        for (unsigned i=0; i<mpMesh->GetNumNodes(); i++)
        {
            if (mLayerForEachNode[i]==EPI)
            {
                *p_file << "0\n";
            }
            else if (mLayerForEachNode[i]==MID)
            {
                *p_file << "1\n";
            }
            else // endo
            {
                *p_file << "2\n";
            }
        }
 
        p_file->close();
    }
    PetscTools::Barrier("HeartGeometryInformation::WriteLayerForEachNode"); // Make other processes wait until we're done
}
 
template<unsigned SPACE_DIM>
ChasteCuboid<SPACE_DIM> HeartGeometryInformation<SPACE_DIM>::CalculateBoundingBoxOfSurface(
        const std::vector<unsigned>& rSurfaceNodes)
{
 
    assert(rSurfaceNodes.size()>0);
    //Set min to DBL_MAX etc.
    c_vector<double, SPACE_DIM> my_minimum_point = scalar_vector<double>(SPACE_DIM, DBL_MAX);
    //Set max to -DBL_MAX etc.
    c_vector<double, SPACE_DIM> my_maximum_point=-my_minimum_point;
 
    //Iterate through the set of points on the surface
    for (unsigned surface_index=0; surface_index<rSurfaceNodes.size(); surface_index++)
    {
        unsigned global_index=rSurfaceNodes[surface_index];
        if (mpMesh->GetDistributedVectorFactory()->IsGlobalIndexLocal(global_index) )
        {
            const c_vector<double, SPACE_DIM>& r_position = mpMesh->GetNode(global_index)->rGetLocation();
            //Update max/min
            for (unsigned i=0; i<SPACE_DIM; i++)
            {
                if (r_position[i] < my_minimum_point[i])
                {
                    my_minimum_point[i] = r_position[i];
                }
                if (r_position[i] > my_maximum_point[i])
                {
                    my_maximum_point[i] = r_position[i];
                }
            }
        }
    }
 
    //Share the local data and reduce over all processes
    c_vector<double, SPACE_DIM> global_minimum_point;
    c_vector<double, SPACE_DIM> global_maximum_point;
    MPI_Allreduce(&my_minimum_point[0], &global_minimum_point[0], SPACE_DIM, MPI_DOUBLE, MPI_MIN, PETSC_COMM_WORLD);
    MPI_Allreduce(&my_maximum_point[0], &global_maximum_point[0], SPACE_DIM, MPI_DOUBLE, MPI_MAX, PETSC_COMM_WORLD);
 
    ChastePoint<SPACE_DIM> min(global_minimum_point);
    ChastePoint<SPACE_DIM> max(global_maximum_point);
 
    return ChasteCuboid<SPACE_DIM>(min, max);
}
 
// Explicit instantiation
template class HeartGeometryInformation<2>;
template class HeartGeometryInformation<3>;