HeartGeometryInformation.hpp

/*

Copyright (c) 2005-2018, University of Oxford.
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This file is part of Chaste.

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 * Redistributions of source code must retain the above copyright notice,
   this list of conditions and the following disclaimer.
 * 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.

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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
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*/
#ifndef HEARTGEOMETRYINFORMATION_HPP_
#define HEARTGEOMETRYINFORMATION_HPP_

#include <vector>
#include <string>
#include <set>
#include "DistanceMapCalculator.hpp"
#include "AbstractTetrahedralMesh.hpp"
#include "ChasteCuboid.hpp"

typedef enum HeartLayerType_
{
    ENDO = 0,
    MID,
    EPI
} HeartLayerType;

typedef unsigned HeartRegionType;


template<unsigned SPACE_DIM>
class HeartGeometryInformation
{
private:

    static const double LEFT_SEPTUM_SIZE;
    static const double RIGHT_SEPTUM_SIZE;

    std::vector<unsigned> mEpiSurface;

    std::vector<unsigned> mEndoSurface;

    std::vector<unsigned> mLVSurface;

    std::vector<unsigned> mRVSurface;

    void GetNodesAtSurface(const std::string& rSurfaceFileName,
                           std::vector<unsigned>& rSurfaceNodes,
                           bool indexFromZero=true) const;

    void ProcessLine(const std::string& rLineFromFile,
                     std::set<unsigned>& rSurfaceNodeIndexSet,
                     unsigned offset) const;

    double GetDistanceToEndo(unsigned nodeIndex);

    double GetDistanceToEpi(unsigned nodeIndex);

    AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>* mpMesh;

    std::vector<double> mDistMapEpicardium;

    std::vector<double> mDistMapEndocardium;

    std::vector<double> mDistMapRightVentricle;

    std::vector<double> mDistMapLeftVentricle;

    unsigned mNumberOfSurfacesProvided;

    std::vector<HeartLayerType> mLayerForEachNode;

    ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfSurface(const std::vector<unsigned>& rSurfaceNodes);

public:

    static const HeartRegionType LEFT_VENTRICLE_WALL=1001;
    static const HeartRegionType RIGHT_VENTRICLE_WALL=1002;
    static const HeartRegionType LEFT_SEPTUM=1003;
    static const HeartRegionType RIGHT_SEPTUM=1004;
    static const HeartRegionType LEFT_VENTRICLE_SURFACE=1005;
    static const HeartRegionType RIGHT_VENTRICLE_SURFACE=1006;
    static const HeartRegionType UNKNOWN=1007;

    HeartGeometryInformation (AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh,
                              const std::string& rEpiFile,
                              const std::string& rEndoFile,
                              bool indexFromZero);


    HeartGeometryInformation (AbstractTetrahedralMesh<SPACE_DIM,SPACE_DIM>& rMesh,
                              const std::string& rEpiFile,
                              const std::string& rLVFile,
                              const std::string& rRVFile,
                              bool indexFromZero);

    HeartGeometryInformation (std::string nodeHeterogeneityFileName);

    HeartRegionType GetHeartRegion (unsigned nodeIndex) const;

    std::vector<double>& rGetDistanceMapEpicardium()
    {
        return mDistMapEpicardium;
    }

    std::vector<double>& rGetDistanceMapEndocardium()
    {
        assert(mNumberOfSurfacesProvided==2);
        return mDistMapEndocardium;
    }

    std::vector<double>& rGetDistanceMapRightVentricle()
    {
        assert(mNumberOfSurfacesProvided==3);
        return mDistMapRightVentricle;
    }

    std::vector<double>& rGetDistanceMapLeftVentricle()
    {
        assert(mNumberOfSurfacesProvided==3);
        return mDistMapLeftVentricle;
    }

    const std::vector<unsigned>& rGetNodesOnEpiSurface()
    {
        return mEpiSurface;
    }


    const std::vector<unsigned>& rGetNodesOnEndoSurface()
    {
        assert(mNumberOfSurfacesProvided==2);
        return mEndoSurface;
    }

    const std::vector<unsigned>& rGetNodesOnLVSurface()
    {
        assert(mNumberOfSurfacesProvided==3);
        return mLVSurface;
    }

    const std::vector<unsigned>& rGetNodesOnRVSurface()
    {
        assert(mNumberOfSurfacesProvided==3);
        return mRVSurface;
    }

    const std::vector<HeartLayerType>& rGetLayerForEachNode()
    {
        assert(mLayerForEachNode.size()>0);
        return mLayerForEachNode;
    }

    double CalculateRelativeWallPosition(unsigned nodeIndex);

    void DetermineLayerForEachNode(double epiFraction, double endoFraction);

    void WriteLayerForEachNode(std::string outputDir, std::string file);

    inline ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfEpi()
    {
        return CalculateBoundingBoxOfSurface(mEpiSurface);
    }
    inline ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfEndo()
    {
        return CalculateBoundingBoxOfSurface(mEndoSurface);
    }
    inline ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfLV()
    {
        return CalculateBoundingBoxOfSurface(mLVSurface);
    }
     inline ChasteCuboid<SPACE_DIM> CalculateBoundingBoxOfRV()
    {
        return CalculateBoundingBoxOfSurface(mRVSurface);
    }
};
#endif //HEARTGEOMETRYINFORMATION_HPP_