void uv_orb::fillDeltagrids(const std::string& file){
E_delta.clear();L_delta.clear();Delta.clear();
E_delta = create_range(E0,Emax,NE);
L_delta = std::vector<VecDoub>(NE,VecDoub(NL,0.));
Delta = std::vector<VecDoub>(NE,VecDoub(NL,0.));
#pragma omp parallel for schedule (dynamic)
for(int i=0; i<NE;i++){
double R = Pot->R_E(E_delta[i]);
for(double j=0;j<NL;j++){
L_delta[i][j] = Pot->L_circ(R)*(j*0.8/(double)(NL-1)+0.001);
find_best_delta DD(Pot, E_delta[i], L_delta[i][j]);
Delta[i][j]=DD.delta(R*.9);
if(Delta[i][j]<0. or Delta[i][j]!=Delta[i][j])
Delta[i][j]=R/5.;
std::cerr<<"DeltaGrid: "
<<OUTPUT(E_delta[i])
<<OUTPUT(L_delta[i][j])
<<OUTPUT(R)
<<OUTPUTE(Delta[i][j]);
}
}
std::cerr<<"DeltaGrid calculated: NE = "<<NE<<", NL = "<<NL<<std::endl;
std::ofstream outfile; outfile.open(file);
for(int i=0;i<NE;++i)
for(int j=0;j<NL;++j)
outfile<<E_delta[i]<<" "<<L_delta[i][j]<<" "<<Delta[i][j]<<std::endl;
outfile.close();
}
void uv_orb::readDeltagrids(const std::string& file){
std::ifstream infile; infile.open(file);
if(!infile.is_open())std::cerr<<"Problem: "<<file<<" doesn't exist."<<std::endl;
E_delta = VecDoub(NE,0.);
L_delta = std::vector<VecDoub>(NE,VecDoub(NL,0.));
Delta = L_delta;
for(int i=0;i<NE;++i) infile>>E_delta[i];
for(int i=0;i<NE;++i)for(int j=0;j<NL;++j) infile>>L_delta[i][j];
for(int i=0;i<NE;++i)for(int j=0;j<NL;++j) infile>>Delta[i][j];
infile.close();
}
MultipoleExpansion::MultipoleExpansion(Density *rho,int NR, int NA, int LMAX1, int MMAX1, double a0, double rmin, double rmax,
bool axisymmetric, bool triaxial, bool flip, double err)
:rho(rho), NR(NR), NA(NA), a0(a0),rmin(rmin),rmax(rmax),
axisymmetric(axisymmetric), triaxial(triaxial), flip(flip), err(err){
NA_phi = axisymmetric?1:NA;
NA_theta = NA;
if(LMAX1>0) LMAX = LMAX1;
else{
if(flip)LMAX = NA_theta*8.;
else LMAX = NA_theta*4.;
}
if(MMAX1>0) MMAX = MMAX1;
else MMAX = LMAX;
if(axisymmetric) MMAX = 0;
GLtheta = std::unique_ptr<GaussLegendreIntegrator>
(new GaussLegendreIntegrator(2.*NA_theta-1));
GLphi = std::unique_ptr<GaussLegendreIntegrator>
(new GaussLegendreIntegrator(2.*NA_phi-1));
fill_radial_grid(a0,rmin,rmax);
rho_grid=std::vector<std::vector<VecDoub>>(2*NA_theta-1,std::vector<VecDoub>(2*NA_phi-1,VecDoub(NR,0.)));
fill_density_grid();
Phi_grid=std::vector<std::vector<VecDoub>>(LMAX+1,std::vector<VecDoub>(2.*LMAX+1,VecDoub(NR,0.)));
dPhi_grid=Phi_grid;
fillPhigrid();
}
ModelParameters::ModelParameters ()
{
// init parameter values
mf_NumSpecies = 2 ;
mf_NumReacs = 4 ;
mf_ReacRates = VecDoub ( mf_NumReacs , 0. ) ;
mf_ReacRates[0] = 0.0 ; //mrna_prod
mf_ReacRates[1] = 0.0 ; //mrna_degrad
mf_ReacRates[2] = 0.0 ; //protein_prod
mf_ReacRates[3] = 0.0 ; //protein_degrad
}
MultipoleExpansion::MultipoleExpansion(const std::string& inFile):err(0.){
std::ifstream infile; infile.open(inFile);
if(!infile.is_open())std::cerr<<"Can't open "<<inFile<<std::endl;
infile >>NR>>NA>>LMAX>>MMAX>>a0>>rmin>>rmax>>axisymmetric>>triaxial>>flip;
NA_phi = axisymmetric?1:NA;
NA_theta = NA;
GLtheta = std::unique_ptr<GaussLegendreIntegrator>
(new GaussLegendreIntegrator(2.*NA_theta-1));
GLphi = std::unique_ptr<GaussLegendreIntegrator>
(new GaussLegendreIntegrator(2.*NA_phi-1));
fill_radial_grid(a0,rmin,rmax);
rho_grid=std::vector<std::vector<VecDoub>>(2.*NA_theta-1,std::vector<VecDoub>(2.*NA_phi-1,VecDoub(NR,0.)));
for(unsigned int i=0;i<rho_grid.size();i++)
for(unsigned int j=0;j<rho_grid[0].size();j++)
for(unsigned int k=0;k<rho_grid[0][0].size();k++){
infile>>rho_grid[i][j][k];
}
if(axisymmetric) MMAX = 0;
Phi_grid=std::vector<std::vector<VecDoub>>(LMAX+1,std::vector<VecDoub>(2.*LMAX+1,VecDoub(NR,0.)));
dPhi_grid=Phi_grid;
for(unsigned int i=0;i<Phi_grid.size();i++)
for(unsigned int j=0;j<Phi_grid[0].size();j++)
for(unsigned int k=0;k<Phi_grid[0][0].size();k++){
infile>>Phi_grid[i][j][k];
}
for(unsigned int i=0;i<dPhi_grid.size();i++)
for(unsigned int j=0;j<dPhi_grid[0].size();j++)
for(unsigned int k=0;k<dPhi_grid[0][0].size();k++){
infile>>dPhi_grid[i][j][k];
}
infile.close();
}
Actions_AxisymmetricFudge_InterpTables::Actions_AxisymmetricFudge_InterpTables(Potential_JS *Pot, std::string name, bool tab, double Rm, double Rn,int NR, int NGRID,int NED,int NEL)
:Pot(Pot),name(name)
,Rmin(Rm),Rmax(Rn),NR(NR),NGRID(NGRID),UV(new uv_orb(Pot,Rm,Rn,NED,NEL)){
no_table=false;
Rgrid = VecDoub(NR); Lzgrid = VecDoub(NR); Vmax = VecDoub(NR);
Lcgrid = VecDoub(NR);
E0grid = VecDoub(NR); Unigrid = VecDoub(NGRID+1);
Iu0 = VecDoub(NR); Iv0 = VecDoub(NR);
kappagrid = VecDoub(NR); nugrid = VecDoub(NR); Omegacgrid = VecDoub(NR);
Jr_LzEIu=std::vector<std::vector<VecDoub>>(NR,std::vector<VecDoub>(NGRID,VecDoub(NGRID)));
Iugrid=Jr_LzEIu; Jz_LzEIv=Jr_LzEIu; Ivgrid=Jr_LzEIu;
Iumin=std::vector<VecDoub>(NR,VecDoub(NGRID)); Iumax=Iumin;
Ivmin=std::vector<VecDoub>(NR,VecDoub(NGRID)); Ivmax=Ivmin;
for(int i=0; i<=NGRID; i++)
Unigrid[i]=((double)i/(double)(NGRID));// standard grid
for(int i=0; i<NR; i++)
Rgrid[i]=Rmin+i*(Rmax-Rmin)/((double)(NR-1));
if(tab) tab_acts();
else get_acts();
}
void MiaMarkerStatistics::readKeyValues(MiaMarker* marker, A* inData)
{
MiaPoint4D lastpt;
VecDoub x = VecDoub( marker->getKeyPointNumber() ); //this data structure is specific from numerical recipes
VecDoub y = VecDoub( marker->getKeyPointNumber() );
double curr_dist = 0;
marker->keyValueList.clear();
if ( marker->getKeyPointNumber() > 0 )
{
lastpt = inputImage->convertPatientCoordinateToVoxel(marker->getKeyPointAt(0));
}
else
{
return;
}
// qDebug()<<"Before fitting";
for (int i = 0; i < marker->getKeyPointNumber(); i++)
{
MiaPoint4D pt = marker->getKeyPointAt(i);
pt = inputImage->convertPatientCoordinateToVoxel(pt);
float value = inputImage->getValueAt(pt.pos);
value = -value-1.0;
if(value>0)
value = 0;
curr_dist = curr_dist + lastpt.distance(pt);
x[i] = curr_dist;
y[i] = value;
lastpt = pt;
// qDebug()<<x[i]<<y[i];
}
//robust regression from numerical recipes
float last_a = 10.0, last_b = 0.0;
// if(soomthingWindow>100)
// {
// MiaMarker3DPolygon* centerline = (MiaMarker3DPolygon*)marker;
// if(centerline->bifurcationNodeList.size()<2)
// {
// qDebug()<<"Single Segment Robust fitting";
// Fitmed f(x, y);
// qDebug()<<f.b<<f.a;
// if(f.b<0)
// {
// f.a = f.a + f.b * curr_dist/2.0;
// f.b = 0;
// qDebug()<<f.b<<f.a;
// }
// //modify the kewValueList with the values obtained from the regression
// for (int i = 0; i < marker->getKeyPointNumber(); i++)
// {
// Point4D v;
// v.pos[3] = f.a + f.b * x[i];
// if(v.pos[3]>-1.0)
// v.pos[3] = -1.0;
// marker->keyValueList.append(v);
// // qDebug()<<x[i]<<v.pos[3];
// }
// }
// else
// {
// qDebug()<<"Multipele Segment Robust fitting";
// for(int seg = 0; seg < centerline->bifurcationNodeList.size() -1; seg++)
// {
// int start = centerline->bifurcationNodeList.at(seg);
// int end = centerline->bifurcationNodeList.at(seg+1);
// VecDoub sx = VecDoub( end - start );
// VecDoub sy = VecDoub( end - start );
// for(int i = start; i <end ; i ++)
// {
// sx[i-start] = x[i];
// sy[i-start] = y[i];
// }
// Fitmed f(sx, sy);
// qDebug()<<f.b<<f.a;
// if(f.b<0)
// {
// f.a = f.a + f.b * x[(start+end)/2]/2.0;
// f.b = 0;
// qDebug()<<f.b<<f.a;
// }
// //modify the kewValueList with the values obtained from the regression
// for(int i = start; i <end ; i ++)
// {
// Point4D v;
// v.pos[3] = f.a + f.b * x[i];
// if(v.pos[3]>-1.0)
// v.pos[3] = -1.0;
// marker->keyValueList.append(v);
//// qDebug()<<x[i]<<v.pos[3];
// }
// if(end == marker->getKeyPointNumber()-1)
// {
// Point4D v;
// v.pos[3] = f.a + f.b * x[end];
// if(v.pos[3]>-1.0)
// v.pos[3] = -1.0;
// marker->keyValueList.append(v);
// }
// }
// qDebug()<<marker->keyPointList.size();
// qDebug()<<marker->keyValueList.size();
// }
// return;
// }
int local_n = soomthingWindow;
for(int i = 0; i < marker->getKeyPointNumber(); i++)
{
int pre_n,next_n;
float localmean = 0.0;
pre_n = max(0,i-local_n);
next_n = min(marker->getKeyPointNumber(), i+local_n);
for(int j = pre_n; j < next_n; j++)
{
localmean += y[j];
}
localmean = localmean/(float)(next_n - pre_n);
MiaPoint4D v;
v.pos[3] = localmean - 0.5; //0.5 is a bias field if too large the cylinder will grow forever, if too small the cynlinder will disappear
//apperantly using cubic of the distance function will help to stablize this behavior
if(v.pos[3]>-1.0)
v.pos[3] = -1.0;
marker->keyValueList.append(v);
// qDebug()<<y[i]<<v.pos[3];
}
}