void Tgam::computeNextState(const int time, GrGrid& grid, Stats& stats, bool tnfrDynamics, bool, bool, bool tgammatransition)
{
// check if it is time to die
if (timeToDie(time)) {
_nextState = TGAM_DEAD;
}
// Always pass in false for nfkbDynamics for T cell apoptosis since they DO NOT have NFkB dynamics
else if (TNFinducedApoptosis(grid, tnfrDynamics, false)) {
++stats.getTcellApoptosisTNF();
_nextState = TGAM_DEAD;
grid.incKillings(_pos);
}
else {
switch (_state) {
case TGAM_DEAD:
// if dead, stay dead
_nextState = TGAM_DEAD;
break;
case TGAM_ACTIVE:
handleActive(time, grid, stats, tgammatransition);
break;
case TGAM_DOWN_REGULATED:
handleDownRegulated(time, grid, stats);
break;
case TGAM_ACTIVE_DOUBLE:
handleActiveDouble(time, grid, stats);
break;
case TGAM_INDUCED_REG:
handleInducedReg(time, grid, stats);
break;
default:
throw std::runtime_error("Unknown Tgam state");
}
}
}
void Snapshot::takeSnapshot(const int time, const Stats& stats)
{
_outFile << time;
_outFile << (stats.getNrOfMacs()) << ',';
for(size_t i=0; i<Mac::NSTATES; i++)
_outFile << (stats.getNrOfMacs(Mac::State(i))) << ',';
_outFile << (stats.getNrOfTgams()) << ',';
for(size_t i=0; i<Tgam::NSTATES; i++)
_outFile << (stats.getNrOfTgams(Tgam::State(i))) << ',';
_outFile << (stats.getNrOfTcyts()) << ',';
for(size_t i=0; i<Tcyt::NSTATES; i++)
_outFile << (stats.getNrOfTcyts(Tcyt::State(i))) << ',';
_outFile << (stats.getNrOfTregs()) << ',';
for(size_t i=0; i<Treg::NSTATES; i++)
_outFile << (stats.getNrOfTregs(Treg::State(i))) << ',';
_outFile
<< stats.getTotIntMtb() << ','
<< stats.getTotExtMtb() << ','
<< stats.getTotNonRepExtMtb() << ','
<< (stats.getTotIntMtb() + stats.getTotExtMtb()) << ','
<< stats.getTotTNF() << ','
<< stats.getTotCCL2() << ','
<< stats.getTotCCL5() << ','
<< stats.getTotCXCL9() << ','
<< stats.getAreaTNF() << ','
<< stats.getAreaCellDensity() << ','
<< stats.getMDC() << ','
<< stats.getN4() << ','
<< stats.getTH0() << ','
<< stats.getTH1() << ','
<< stats.getN8() << ','
<< stats.getT80() << ','
<< stats.getT8() << ','
<< stats.getTC() << ','
<< stats.getTH0lung() << ','
<< stats.getTH1lung() << ','
<< stats.getT80lung() << ','
<< stats.getT8lung() << ','
<< stats.getTClung();
int startState = 1; // Skip the dead state: apoptosis doesn't occur for an already dead mac.
static int totMacApoptosisTNF[Mac::NSTATES] = {0}; //Just temporary for Mohammed Fallahi
int sumMacApoptosisTNF = 0;
for(int i=startState; i<Mac::NSTATES; i++) //Keep a running sum of deaths
{
totMacApoptosisTNF[i]+=(stats.getMacApoptosisTNF((Mac::State)i));
sumMacApoptosisTNF+=totMacApoptosisTNF[i];
}
_outFile << (stats.getTotNrSources()) << ',';
for(size_t i=0; i<NAGENTS; i++)
_outFile << (stats.getNrSources((AgentType)i)) << ',';
_outFile << stats.getNrCaseated()
<< ','
<< sumMacApoptosisTNF
<< ',';
for(int i=startState; i<Mac::NSTATES; i++)
_outFile<<totMacApoptosisTNF[i]<<',';
_outFile
<< stats.getTcellApoptosisTNF();
_outFile << std::endl;
}