CompuCell/DOXYGEN/core/CompuCell3D/steppables/Dicty/DictyChemotaxisSteppable.cpp

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#include <CompuCell3D/Simulator.h>

#include <CompuCell3D/Field3D/Point3D.h>
#include <CompuCell3D/Automaton/Automaton.h>
#include <CompuCell3D/Potts3D/Potts3D.h>
#include <CompuCell3D/Potts3D/CellInventory.h>
#include <CompuCell3D/plugins/SimpleClock/SimpleClockPlugin.h>
#include <BasicUtils/BasicClassAccessor.h>
#include <CompuCell3D/steppables/PDESolvers/DiffusableVector.h>
#include <CompuCell3D/Field3D/Field3D.h>
#include <CompuCell3D/Field3D/WatchableField3D.h>

#include <CompuCell3D/ClassRegistry.h>
#include <CompuCell3D/Field3D/Field3D.h>



using namespace CompuCell3D;
using namespace std;

#define EXP_STL
#include "DictyChemotaxisSteppable.h"


DictyChemotaxisSteppable::DictyChemotaxisSteppable():potts(0),cellInventoryPtr(0)
{

        clockReloadValue=0;
        chemotactUntil=0;
        chetmotaxisActivationThreshold=0.0;
        chemotactingCellsCounter=0;
        ignoreFirstSteps=0;


}

void DictyChemotaxisSteppable::update(CC3DXMLElement *_xmlData, bool _fullInitFlag){

        if(_xmlData->findElement("ClockReloadValue"))
                clockReloadValue=_xmlData->getFirstElement("ClockReloadValue")->getUInt();

        if(_xmlData->findElement("ChemotactUntil"))
                chemotactUntil=_xmlData->getFirstElement("ChemotactUntil")->getUInt();

        if(_xmlData->findElement("ChemotactUntil"))
                chemotactUntil=_xmlData->getFirstElement("ChemotactUntil")->getUInt();

        if(_xmlData->findElement("ChetmotaxisActivationThreshold"))
                chetmotaxisActivationThreshold=_xmlData->getFirstElement("ChetmotaxisActivationThreshold")->getDouble();

        if(_xmlData->findElement("IgnoreFirstSteps"))
                ignoreFirstSteps=_xmlData->getFirstElement("IgnoreFirstSteps")->getUInt();

        if(_xmlData->findElement("ChemicalField")){
                chemicalFieldName=_xmlData->getFirstElement("ChemicalField")->getText();
                chemicalFieldSource=_xmlData->getFirstElement("ChemicalField")->getAttribute("Source");
        }

        ASSERT_OR_THROW("ChemotactUntil has to be smaller than Clock Reload Value!",chemotactUntil<clockReloadValue);

}

void DictyChemotaxisSteppable::init(Simulator *_simulator, CC3DXMLElement *_xmlData){

        update(_xmlData,true);

        simulator=_simulator;
        potts = simulator->getPotts();
        cellFieldG = (WatchableField3D<CellG*>*)potts->getCellFieldG();

        cellInventoryPtr=& potts->getCellInventory();

        bool pluginAlreadyRegisteredFlag;
        SimpleClockPlugin * simpleClockPlugin = (SimpleClockPlugin *) Simulator::pluginManager.get("SimpleClock",&pluginAlreadyRegisteredFlag); //this will load PlasticityTracker plugin if it is not already loaded  
        if(!pluginAlreadyRegisteredFlag)
                simpleClockPlugin->init(simulator);

        simpleClockAccessorPtr = simpleClockPlugin->getSimpleClockAccessorPtr();

        simulator->registerSteerableObject(this);
}



void DictyChemotaxisSteppable::extraInit(Simulator *_simulator){

        ClassRegistry *classRegistry=simulator->getClassRegistry();
        Steppable * steppable=classRegistry->getStepper(chemicalFieldSource);

        field=((DiffusableVector<float> *) steppable)->getConcentrationField(chemicalFieldName);

        ASSERT_OR_THROW("No chemical field has been loaded!", field);
        cerr<<"GOT FIELD INTO CHEMOTAXIS STEPPABLE: "<<field<<endl;

        fieldDim=field->getDim();

}

void DictyChemotaxisSteppable::start(){
}

void DictyChemotaxisSteppable::step(const unsigned int currentStep){

        cerr<<"ignoreFirstSteps="<<ignoreFirstSteps<<endl;

        if(currentStep < ignoreFirstSteps)
                return;

        Point3D pt;
        CellG * currentCellPtr;
        int * currentClockPtr;
        char * clockFlagPtr;
        float currentConcentration;

        for (pt.z = 0; pt.z < fieldDim.z; ++pt.z)
                for (pt.y = 0; pt.y < fieldDim.y; ++pt.y)
                        for (pt.x = 0; pt.x < fieldDim.x; ++pt.x){

                                currentCellPtr=cellFieldG->get(pt);
                                /*cerr<<"currentCellPtr="<<currentCellPtr<<endl;*/
                                if(!currentCellPtr) continue;
                                //cerr<<"1 currentCellPtr="<<currentCellPtr<<endl;
                                //cerr<<"Type currentCellPtr="<<(int)currentCellPtr->type<<endl;

                                currentClockPtr = &(simpleClockAccessorPtr->get(currentCellPtr->extraAttribPtr)->clock);
                                clockFlagPtr = &(simpleClockAccessorPtr->get(currentCellPtr->extraAttribPtr)->flag);
                                currentConcentration=field->get(pt);

                                if(currentConcentration > chetmotaxisActivationThreshold && *currentClockPtr==0){
                                        //simpleClockAccessorPtr->get(currentCellPtr->extraAttribPtr)->clock = clockReloadValue;
                                        *currentClockPtr=clockReloadValue; 
                                        *clockFlagPtr = 1;
                                        cerr<<endl<<endl;
                                        //cerr<<"\t\treloading clock and activating chemotaxis"<<endl;
                                        cerr<<endl<<endl;
                                        ++chemotactingCellsCounter;
                                }

                        }

                        CellInventory::cellInventoryIterator cInvItr;
                        for(cInvItr=cellInventoryPtr->cellInventoryBegin() ; cInvItr !=cellInventoryPtr->cellInventoryEnd() ;++cInvItr ){

                                currentCellPtr=*cInvItr;
                                currentClockPtr = &(simpleClockAccessorPtr->get(currentCellPtr->extraAttribPtr)->clock);
                                clockFlagPtr = &simpleClockAccessorPtr->get(currentCellPtr->extraAttribPtr)->flag;

                                if(*currentClockPtr>=1){
                                        --(*currentClockPtr);
                                }

                                if( *currentClockPtr < chemotactUntil && *clockFlagPtr){
                                        *clockFlagPtr=0;
                                        //cerr<<"Deactivating chemotaxis"<<endl;
                                        --chemotactingCellsCounter;
                                }

                        }

                        //          cerr<<"\n\n \t\t THERE ARE "<<chemotactingCellsCounter<<" CELLS CHEMOTACTING\n"<<endl;
}

std::string DictyChemotaxisSteppable::toString(){
        return "DictyChemotaxisSteppable";
}


std::string DictyChemotaxisSteppable::steerableName(){
        return toString();
}

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