HeartGeometryInformation.hpp

/*

Copyright (c) 2005-2012, University of Oxford.
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This file is part of Chaste.

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modification, are permitted provided that the following conditions are met:
 * 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,
   this list of conditions and the following disclaimer in the documentation
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 * Neither the name of the University of Oxford nor the names of its
   contributors may be used to endorse or promote products derived from this
   software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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& surfaceFile, std::vector<unsigned>& rSurfaceNodes, bool indexFromZero=true) const;

    void ProcessLine(const std::string& line, 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_