TissueConfig.cpp

/*

Copyright (C) University of Oxford, 2005-2010

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/>.

*/
#include "TissueConfig.hpp"

TissueConfig* TissueConfig::mpInstance = NULL;

TissueConfig* TissueConfig::Instance()
{
    if (mpInstance == NULL)
    {
        mpInstance = new TissueConfig;
    }
    return mpInstance;
}

TissueConfig::TissueConfig()
{
    // Make sure there's only one instance - enforces correct serialization
    assert(mpInstance == NULL);

    Reset();
}

void TissueConfig::Reset()
{
    // Default parameter values
    mStemCellG1Duration = 14.0;
    mTransitCellG1Duration = 2.0;
    mHepaOneCellG1Duration = 8.0;   // taken from Owen et al, 2004 (doi:10.1016/j.jtbi.2003.09.004)
    mMinimumGapDuration = 0.01;     // educated guess
    mSDuration = 5.0;               // apparently between 5-6 hours normally
    mG2Duration = 4.0;              // apparently 3-4 hours normally
    mMDuration = 1.0;               // taken from Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)

    mMaxTransitGenerations = 3u;    // taken from Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
    mCryptWidth = 10.0;
    mCryptLength = 22.0;            // this is MOUSE (small intestine)
    mSpringStiffness = 15.0;        // denoted by mu in Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
    mMechanicsCutOffLength = DBL_MAX; // This needs to be set by a caller
    mDampingConstantNormal = 1.0;   // denoted by nu in Meineke et al, 2001 (doi:10.1046/j.0960-7722.2001.00216.x)
    mDampingConstantMutant = 1.0;
    mBetaCatSpringScaler = 18.14 / 6.0; // this scales the spring constant with the amount of beta-catenin
                                        // (divided by 6 as a cell normally is a hexagon)
    mApoptosisTime = 0.25;          // cell takes 15 min to fully undergo apoptosis
    mDivisionRestingSpringLength = 0.5;
    mDivisionSeparation = 0.3;
    mHepaOneCellHypoxicConcentration = 0.4;
    mHepaOneCellQuiescentConcentration = 1.0;
    mWntStemThreshold = 0.8;
    mWntTransitThreshold = 0.65;
    mWntLabelledThreshold = 0.65;
    mWntConcentrationParameter = 1.0;
    mCriticalHypoxicDuration = 2.0;
    mCryptProjectionParameterA = 0.5;
    mCryptProjectionParameterB = 2.0;

    mApoptoticSpringTensionStiffness = 0.25*mSpringStiffness;
    mApoptoticSpringCompressionStiffness = 0.75*mSpringStiffness;

    mWntChemotaxisStrength = 100.0;
    mSymmetricDivisionProbability = 0.0;

    mAreaBasedDampingConstantParameter = 0.1;

    mMatureCellTargetArea = 1.0; //0.785398163;//pi/4.0; used to be 1

    /*
     * The following four parameters are used in vertex-based tissue simulations
     * based on the mechanical model proposed by T. Nagai and H. Honda ("A dynamic
     * cell model for the formation of epithelial tissues", Philosophical Magazine
     * Part B 81:699-719). They are rescaled such that mDampingConstantNormal takes
     * the default value 1, whereas Nagai and Honda (who denote the parameter by nu)
     * take the value 0.01.
     */
    mDeformationEnergyParameter = 100.0; // This is 1.0 in the Nagai & Honda paper
    mMembraneSurfaceEnergyParameter = 10.0;  // This is 0.1 the Nagai & Honda paper
    mCellCellAdhesionEnergyParameter = 1.0; // This is 0.01 the Nagai & Honda paper
    mCellBoundaryAdhesionEnergyParameter = 1.0; // This is 0.01 the Nagai & Honda paper

    mWelikyOsterAreaParameter = 1.0;
    mWelikyOsterPerimeterParameter = 1.0;

    mOutputCellIdData = false;
    mOutputCellMutationStates = false;
    mOutputCellAncestors = false;
    mOutputCellProliferativeTypes = false;
    mOutputCellVariables = false;
    mOutputCellCyclePhases = false;
    mOutputCellAges = false;
    mOutputCellAreas = false;
    mOutputVoronoiData = false;
    mOutputTissueAreas = false;
    mOutputNodeVelocities = false;
}

// Getter methods

double TissueConfig::GetStemCellG1Duration()
{
    return mStemCellG1Duration;
}
double TissueConfig::GetTransitCellG1Duration()
{
    return mTransitCellG1Duration;
}
double TissueConfig::GetHepaOneCellG1Duration()
{
    return mHepaOneCellG1Duration;
}
double TissueConfig::GetMinimumGapDuration()
{
    return mMinimumGapDuration;
}
double TissueConfig::GetSG2MDuration()
{
    return mSDuration + mG2Duration + mMDuration;
}
double TissueConfig::GetSDuration()
{
    return mSDuration;
}
double TissueConfig::GetG2Duration()
{
    return mG2Duration;
}
double TissueConfig::GetMDuration()
{
    return mMDuration;
}
unsigned TissueConfig::GetMaxTransitGenerations()
{
    return mMaxTransitGenerations;
}
double TissueConfig::GetCryptLength()
{
    return mCryptLength;
}
double TissueConfig::GetCryptWidth()
{
    return mCryptWidth;
}
double TissueConfig::GetSpringStiffness()
{
    return mSpringStiffness;
}
double TissueConfig::GetMechanicsCutOffLength()
{
    return mMechanicsCutOffLength;
}
double TissueConfig::GetDampingConstantNormal()
{
    return mDampingConstantNormal;
}
double TissueConfig::GetDampingConstantMutant()
{
    return mDampingConstantMutant;
}
double TissueConfig::GetBetaCatSpringScaler()
{
    return mBetaCatSpringScaler;
}
double TissueConfig::GetApoptosisTime()
{
    return mApoptosisTime;
}
double TissueConfig::GetDivisionRestingSpringLength()
{
    return mDivisionRestingSpringLength;
}
double TissueConfig::GetDivisionSeparation()
{
    return mDivisionSeparation;
}
double TissueConfig::GetHepaOneCellHypoxicConcentration()
{
    return mHepaOneCellHypoxicConcentration;
}
double TissueConfig::GetHepaOneCellQuiescentConcentration()
{
    return mHepaOneCellQuiescentConcentration;
}
double TissueConfig::GetWntTransitThreshold()
{
    return mWntTransitThreshold;
}
double TissueConfig::GetWntStemThreshold()
{
    return mWntStemThreshold;
}
double TissueConfig::GetWntLabelledThreshold()
{
    return mWntLabelledThreshold;
}
double TissueConfig::GetWntConcentrationParameter()
{
    return mWntConcentrationParameter;
}
double TissueConfig::GetCriticalHypoxicDuration()
{
    return mCriticalHypoxicDuration;
}
double TissueConfig::GetCryptProjectionParameterA()
{
    return mCryptProjectionParameterA;
}
double TissueConfig::GetCryptProjectionParameterB()
{
    return mCryptProjectionParameterB;
}
double TissueConfig::GetApoptoticSpringTensionStiffness()
{
    return mApoptoticSpringTensionStiffness;
}
double TissueConfig::GetApoptoticSpringCompressionStiffness()
{
    return mApoptoticSpringCompressionStiffness;
}
double TissueConfig::GetWntChemotaxisStrength()
{
    return mWntChemotaxisStrength;
}
double TissueConfig::GetSymmetricDivisionProbability()
{
    return mSymmetricDivisionProbability;
}
double TissueConfig::GetAreaBasedDampingConstantParameter()
{
    return mAreaBasedDampingConstantParameter;
}
double TissueConfig::GetMatureCellTargetArea()
{
    return mMatureCellTargetArea;
}
double TissueConfig::GetDeformationEnergyParameter()
{
    return mDeformationEnergyParameter;
}
double TissueConfig::GetMembraneSurfaceEnergyParameter()
{
    return mMembraneSurfaceEnergyParameter;
}
double TissueConfig::GetCellCellAdhesionEnergyParameter()
{
    return mCellCellAdhesionEnergyParameter;
}
double TissueConfig::GetCellBoundaryAdhesionEnergyParameter()
{
    return mCellBoundaryAdhesionEnergyParameter;
}
double TissueConfig::GetWelikyOsterAreaParameter()
{
    return mWelikyOsterAreaParameter;
}
double TissueConfig::GetWelikyOsterPerimeterParameter()
{
    return mWelikyOsterPerimeterParameter;
}
bool TissueConfig::GetOutputCellIdData()
{
    return mOutputCellIdData;
}
bool TissueConfig::GetOutputCellMutationStates()
{
    return mOutputCellMutationStates;
}
bool TissueConfig::GetOutputCellAncestors()
{
    return mOutputCellAncestors;
}
bool TissueConfig::GetOutputCellProliferativeTypes()
{
    return mOutputCellProliferativeTypes;
}
bool TissueConfig::GetOutputCellVariables()
{
    return mOutputCellVariables;
}
bool TissueConfig::GetOutputCellCyclePhases()
{
    return mOutputCellCyclePhases;
}
bool TissueConfig::GetOutputCellAges()
{
    return mOutputCellAges;
}
bool TissueConfig::GetOutputCellAreas()
{
    return mOutputCellAreas;
}
bool TissueConfig::GetOutputVoronoiData()
{
    return mOutputVoronoiData;
}
bool TissueConfig::GetOutputTissueAreas()
{
    return mOutputTissueAreas;
}
bool TissueConfig::GetOutputNodeVelocities()
{
    return mOutputNodeVelocities;
}

// Setter methods

void TissueConfig::SetStemCellG1Duration(double stemCellG1Duration)
{
    assert(stemCellG1Duration > 0.0);
    mStemCellG1Duration = stemCellG1Duration;
}
void TissueConfig::SetTransitCellG1Duration(double transitCellG1Duration)
{
    assert(transitCellG1Duration > 0.0);
    mTransitCellG1Duration = transitCellG1Duration;
}
void TissueConfig::SetHepaOneCellG1Duration(double hepaOneCellG1Duration)
{
    assert(hepaOneCellG1Duration > 0.0);
    mHepaOneCellG1Duration = hepaOneCellG1Duration;
}
void TissueConfig::SetMinimumGapDuration(double minimumGapDuration)
{
    assert(minimumGapDuration > 0.0);
    mMinimumGapDuration = minimumGapDuration;
}
void TissueConfig::SetSDuration(double SDuration)
{
    assert(SDuration > 0.0);
    mSDuration = SDuration;
}
void TissueConfig::SetG2Duration(double G2Duration)
{
    assert(G2Duration > 0.0);
    mG2Duration = G2Duration;
}
void TissueConfig::SetMDuration(double MDuration)
{
    assert(MDuration > 0.0);
    mMDuration = MDuration;
}
void TissueConfig::SetMaxTransitGenerations(unsigned maxTransitGens)
{
    mMaxTransitGenerations = maxTransitGens;
}
void TissueConfig::SetCryptLength(double cryptLength)
{
    assert(cryptLength > 0.0);
    mCryptLength = cryptLength;
}
void TissueConfig::SetCryptWidth(double cryptWidth)
{
    assert(cryptWidth > 0.0);
    mCryptWidth = cryptWidth;
}
void TissueConfig::SetSpringStiffness(double springStiffness)
{
    assert(springStiffness > 0.0);
    mSpringStiffness = springStiffness;
}
void TissueConfig::SetMechanicsCutOffLength(double mechanicsCutOffLength)
{
    assert(mechanicsCutOffLength > 0.0);
    mMechanicsCutOffLength = mechanicsCutOffLength;
}

void TissueConfig::SetDampingConstantNormal(double dampingConstantNormal)
{
    assert(dampingConstantNormal > 0.0);
    mDampingConstantNormal = dampingConstantNormal;
}
void TissueConfig::SetDampingConstantMutant(double dampingConstantMutant)
{
    assert(dampingConstantMutant > 0.0);
    mDampingConstantMutant = dampingConstantMutant;
}
void TissueConfig::SetBetaCatSpringScaler(double betaCatSpringScaler)
{
    assert(betaCatSpringScaler > 0.0);
    mBetaCatSpringScaler = betaCatSpringScaler;
}
void TissueConfig::SetApoptosisTime(double apoptosisTime)
{
    assert(apoptosisTime > 0.0);
    mApoptosisTime = apoptosisTime;
}
void TissueConfig::SetDivisionRestingSpringLength(double divisionRestingSpringLength)
{
    assert(divisionRestingSpringLength<=1.0);
    assert(divisionRestingSpringLength>=0.0);

    mDivisionRestingSpringLength = divisionRestingSpringLength;
}
void TissueConfig::SetDivisionSeparation(double divisionSeparation)
{
    assert(divisionSeparation<=1.0);
    assert(divisionSeparation>=0.0);
    mDivisionSeparation = divisionSeparation;
}
void TissueConfig::SetHepaOneCellHypoxicConcentration(double hepaOneCellHypoxicConcentration)
{
    assert(hepaOneCellHypoxicConcentration<=1.0);
    assert(hepaOneCellHypoxicConcentration>=0.0);
    mHepaOneCellHypoxicConcentration = hepaOneCellHypoxicConcentration;
}
void TissueConfig::SetHepaOneCellQuiescentConcentration(double hepaOneCellQuiescentConcentration)
{
    assert(hepaOneCellQuiescentConcentration<=1.0);
    assert(hepaOneCellQuiescentConcentration>=0.0);
    mHepaOneCellQuiescentConcentration = hepaOneCellQuiescentConcentration;
}
void TissueConfig::SetWntTransitThreshold(double wntThreshold)
{
    assert(wntThreshold<=1.0);
    assert(wntThreshold>=0.0);
    mWntTransitThreshold = wntThreshold;
}
void TissueConfig::SetWntStemThreshold(double wntThreshold)
{
    assert(wntThreshold<=1.0);
    assert(wntThreshold>=0.0);
    mWntStemThreshold = wntThreshold;
}
void TissueConfig::SetWntLabelledThreshold(double wntThreshold)
{
    assert(wntThreshold<=1.0);
    assert(wntThreshold>=0.0);
    mWntLabelledThreshold = wntThreshold;
}
void TissueConfig::SetWntConcentrationParameter(double top)
{
    assert(top > 0.0);
    //assert(top <= 1.0); This doesn't apply for exponential Wnt gradients.
    mWntConcentrationParameter = top;
}
void TissueConfig::SetCriticalHypoxicDuration(double criticalHypoxicDuration)
{
    assert(criticalHypoxicDuration>=0.0);
    mCriticalHypoxicDuration = criticalHypoxicDuration;
}
void TissueConfig::SetHepaOneParameters()
{
    mStemCellG1Duration = mHepaOneCellG1Duration;
}
void TissueConfig::SetCryptProjectionParameterA(double cryptProjectionParameterA)
{
    assert(cryptProjectionParameterA>=0.0);
    mCryptProjectionParameterA = cryptProjectionParameterA;
}
void TissueConfig::SetCryptProjectionParameterB(double cryptProjectionParameterB)
{
    assert(cryptProjectionParameterB>=0.0);
    mCryptProjectionParameterB = cryptProjectionParameterB;
}
void TissueConfig::SetApoptoticSpringTensionStiffness(double apoptoticSpringTensionStiffness)
{
    assert(apoptoticSpringTensionStiffness>=0.0);
    mApoptoticSpringTensionStiffness = apoptoticSpringTensionStiffness;
}
void TissueConfig::SetApoptoticSpringCompressionStiffness(double apoptoticSpringCompressionStiffness)
{
    assert(apoptoticSpringCompressionStiffness>=0.0);
    mApoptoticSpringCompressionStiffness = apoptoticSpringCompressionStiffness;
}
void TissueConfig::SetWntChemotaxisStrength(double wntChemotaxisStrength)
{
    assert(wntChemotaxisStrength>=0.0);
    mWntChemotaxisStrength = wntChemotaxisStrength;
}
void TissueConfig::SetSymmetricDivisionProbability(double symmetricDivisionProbability)
{
    assert(symmetricDivisionProbability<=1.0);
    assert(symmetricDivisionProbability>=0.0);
    mSymmetricDivisionProbability = symmetricDivisionProbability;
}
void TissueConfig::SetAreaBasedDampingConstantParameter(double areaBasedDampingConstantParameter)
{
    assert(areaBasedDampingConstantParameter>=0.0);
    mAreaBasedDampingConstantParameter = areaBasedDampingConstantParameter;
}
void TissueConfig::SetMatureCellTargetArea(double matureCellTargetArea)
{
    assert(matureCellTargetArea>=0.0);
    mMatureCellTargetArea = matureCellTargetArea;
}
void TissueConfig::SetDeformationEnergyParameter(double deformationEnergyParameter)
{
    mDeformationEnergyParameter = deformationEnergyParameter;
}
void TissueConfig::SetMembraneSurfaceEnergyParameter(double membraneSurfaceEnergyParameter)
{
    mMembraneSurfaceEnergyParameter = membraneSurfaceEnergyParameter;
}
void TissueConfig::SetCellCellAdhesionEnergyParameter(double cellCellAdhesionEnergyParameter)
{
    mCellCellAdhesionEnergyParameter = cellCellAdhesionEnergyParameter;
}
void TissueConfig::SetCellBoundaryAdhesionEnergyParameter(double cellBoundaryAdhesionEnergyParameter)
{
    mCellBoundaryAdhesionEnergyParameter = cellBoundaryAdhesionEnergyParameter;
}
void TissueConfig::SetWelikyOsterAreaParameter(double welikyOsterAreaParameter)
{
    mWelikyOsterAreaParameter = welikyOsterAreaParameter;
}
void TissueConfig::SetWelikyOsterPerimeterParameter(double welikyOsterPerimeterParameter)
{
    mWelikyOsterPerimeterParameter = welikyOsterPerimeterParameter;
}
void TissueConfig::SetOutputCellIdData(bool writeCellIdData)
{
    mOutputCellIdData = writeCellIdData;
}
void TissueConfig::SetOutputCellMutationStates(bool outputCellMutationStates)
{
    mOutputCellMutationStates = outputCellMutationStates;
}
void TissueConfig::SetOutputCellAncestors(bool outputCellAncestors)
{
    mOutputCellAncestors = outputCellAncestors;
}
void TissueConfig::SetOutputCellProliferativeTypes(bool outputCellProliferativeTypes)
{
    mOutputCellProliferativeTypes = outputCellProliferativeTypes;
}
void TissueConfig::SetOutputCellVariables(bool outputCellVariables)
{
    mOutputCellVariables = outputCellVariables;
}
void TissueConfig::SetOutputCellCyclePhases(bool outputCellCyclePhases)
{
    mOutputCellCyclePhases = outputCellCyclePhases;
}
void TissueConfig::SetOutputCellAges(bool outputCellAges)
{
    mOutputCellAges = outputCellAges;
}
void TissueConfig::SetOutputCellAreas(bool outputCellAreas)
{
    mOutputCellAreas = outputCellAreas;
}
void TissueConfig::SetOutputVoronoiData(bool outputVoronoiData)
{
    mOutputVoronoiData = outputVoronoiData;
}
void TissueConfig::SetOutputTissueAreas(bool outputTissueAreas)
{
    mOutputTissueAreas = outputTissueAreas;
}
void TissueConfig::SetOutputNodeVelocities(bool outputNodeVelocities)
{
    mOutputNodeVelocities = outputNodeVelocities;
}