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tismod/src/signalAndMechanicalForces.cpp
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signalAndMechanicalForces.cpp
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#include "signalAndMechanicalForces.hpp"
#include <limits>
using namespace std;
template<class Interactor>
void SignalAndMechanicalForces<Interactor>::initParameters(){ //TODO
we_min= 0.01;
we_r = 10.0;
hill_co = 4.0;
h_pressure = 2;
HC_pressure = 10;
k_sig=0.3;
k_pressure=0.0;
k_tension=0.2;
max_pert = 0.001;
small_cell=false;
hfdp = 3;
#ifdef REAL_LATTICE
h_we = 15;//220;//200
small_cell_thresh= 0.3;//0.3;
tau_sig= 0;//20;
small_bound_thresh = 1.0;
#else
h_we = 600;//220;//200
small_cell_thresh= 0.1;//0.25;
tau_sig= 10;
small_bound_thresh = 0.2;
#endif
tau_mech=0.05;
k_pressure*=tau_mech;
k_tension*=tau_mech;
}
template<class Interactor>
void SignalAndMechanicalForces<Interactor>::operator()(const state_type &y,state_type &dydt,const double t){
fill(dydt.begin(), dydt.end(), 0); //necessary
// cout<<"signaling..."<<endl;
MechanicalForces::fromState(y);
signaling(y,dydt,t);
double n2= norm2(dydt);
// cout<<t<<" - "<<n2<<endl;
// updatePressure(y);
uint nbcells = lattice->getNbCells();
// cout<<"computing forces"<<endl;
for (uint c=0;c<nbcells;c++){
Cell& ce = lattice->getCell(c);
if(!ce.isEmpty() && ! ce.isFrozen()){
dTensionAndPressure(&ce,y,dydt);
}
}
n2= norm2(dydt);
// cout<<t<<" "<<n2<<endl;
addPerturbations(dydt);
// cout<<"pert"<<endl;
checkIntegrity(y,dydt);
// cout<<"OK"<<endl;
//#endif
}
template<class Interactor>
void SignalAndMechanicalForces<Interactor>::initState(state_type &s, double *delta){
s.resize(state_dim);
uint idx = MechanicalForces::initState(s,false);
signaling.initState(s,delta);
// int n= lattice->getNbCells();
// uint m = cellStateDim();
// std::cout<<"filling in..."<<m<<" "<<n<<std::endl;
// for (int c=0;c<n;c++){
// // std::cout<<c<<std::endl;
// uint idx = lattice->getCell(c).stateVectorIndex();
// for (uint i=0;i<m;i++){
// s[idx++] = delta[c*m+i];
// }
// }
}
template<class Interactor>
void SignalAndMechanicalForces<Interactor>::updateState(state_type &s){
s.resize(state_dim);
cout<<"base init"<<endl;
MechanicalForces::initState(s,false);
cout<<"signal init"<<endl;
signaling.updateDeadCellState(s);
cout<<"signal done"<<endl;
}
template<class Interactor>
void SignalAndMechanicalForces<Interactor>::setLattice(Lattice *lat){
lattice = lat;
signaling.setLattice(lat);
// signaling.setMechanics(this);
uint n= lat->getNbCells();
m_pressure.resize(n);
// m_signal.resize(n);
m_area.resize(n);
m_perimeter.resize(n);
uint m = setStateVectorIndex();
state_dim= m;
// observer.resize(m);
}
template<class Interactor>
uint SignalAndMechanicalForces<Interactor>::setStateVectorIndex(){
uint n = MechanicalForces::setStateVectorIndex();
return signaling.setStateVectorIndex(n);
}
template<class Interactor>
float SignalAndMechanicalForces<Interactor>::getWeight(Boundary *b, const state_type &y){
return signaling.getWeight(b,y);
}
template<class Interactor>
void SignalAndMechanicalForces<Interactor>::delaminate(int c){
vector<Boundary *> mem;
Cell& ce = lattice->getCell(c);
while(ce.getNbBoundaries()>3){
double min_score=std::numeric_limits<double>::max();
Boundary *min_b=NULL;
BoundaryIterator it(&ce);
for(Boundary *b=it.first();!it.isLast();b=it.next()){
double score = signaling.delaminationScore(b);
// double ori = abs(rpos.sinAngle(Vec2(1,0)));//TODO find something smarter
if(score<min_score){
min_score=score;
min_b = b;
}
// cout<< "checking "<<b->oppositeCell()->id()<<" "<<ori<<endl;
}
if(min_b){
cout<<"T1 trans "<<min_b->oppositeCell()->id()<<endl;
min_b->doT1Transition();
mem.push_back(min_b);
}
}
cout<<"handing over"<<endl;
ce.doT2Transition();
}
// void SignalAndMechanicalForces::checkT1Transition(Boundary *b){
// // std::cout<<"check"<<std::endl;
// if(isHC(b->cell()) && isHC(b->oppositeCell())){
// double len = b->scaledLength(Vec2(getScaleX(),getScaleY()));
// if(len < 0.2){
// // cout<<"correcting between "<<b->cell()->id()<<" "<< b->oppositeCell()->id()<<endl;
// b->doT1Transition();
// }
// }
// }
// template void checkT1TransitionWrapper<SignalAndMechanicalForces>(Boundary *b, void *arg);
// void myWrapper(Boundary *b, void *args){
// checkT1TransitionWrapper<SignalAndMechanicalForces>(b,args);
// }
// void SignalAndMechanicalForces::findT1Transitions(){
// // lattice->forAllBoundaries(MechanicalForces::checkT1TransitionWrapper,(void *)this);
// lattice->forAllBoundaries(myWrapper,(void *)this);
// }
// void SignalAndMechanicalForces::checkT1TransitionWrapper(Boundary *b, void *arg){
// MechanicalForces *forces = (MechanicalForces *)arg;
// if(!b->isGhost()){
// forces->checkT1Transition(b);
// }
// }
// void MechanicalForces::checkT1Transition(Boundary *b){
// if(isHC(b->cell()) && isHC(b->oppositeCell())){
// double len = b->scaledLength(Vec2(getScaleX(),getScaleY()));
// if(len < 0.2){
// // cout<<"correcting between "<<b->cell()->id()<<" "<< b->oppositeCell()->id()<<endl;
// b->doT1Transition();
// }
// }
// }
// void SignalAndMechanicalForces::findT1Transitions(){
// lattice->forAllBoundaries(SignalAndMechanicalForces::checkT1TransitionWrapper,(void *)this);
// }
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