HeartGeometryInformation.hpp

/*

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/>.

*/
#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_