static kernel::se3 estimatePose(const KernelCollection &objectEvidence,
const KernelCollection &sceneEvidence,
const int nChains,
const int n)
{
KernelCollection poses;
coord_t objectSize = objectEvidence.moments()->getLocH();
if (!hasOpenMP())
{
NUKLEI_WARN("Nuklei has not been compiled with OpenMP support. "
"Multithreaded execution of this program will not be optimal "
"(sync through POSIX threads, which seems slower than "
"OpenMP's critical.");
}
#pragma omp parallel for
for (int i = 0; i < nChains; ++i)
{
kernel::se3 tmp = mcmc(objectEvidence, sceneEvidence, objectSize, n);
#pragma omp critical(pe_merge_poses)
{
poses.add(tmp);
std::cout << "Finished chain " << i << std::endl;
}
}
return kernel::se3(*poses.sortBegin(1));
}
int main(int ArgI, char* ArgC[])
{
COption op;
CRec geneticmap;
for (int i = 0; i != ArgI-1; ++i)
{
if (strcmp(ArgC[i], "-interval") == 0 && i + 2 < ArgI)
{
op.minpos = atoi(ArgC[i+1]);
op.maxpos = atoi(ArgC[i+2]);
}
if (strcmp(ArgC[i], "-include-variant") == 0) op.fn0 = ArgC[i+1];
if (strcmp(ArgC[i], "-exclude-vatiant") == 0) op.fn1 = ArgC[i+1];
if (strcmp(ArgC[i], "-genetic-map") == 0) geneticmap.Init(ArgC[i+1]);
if (strcmp(ArgC[i], "-buffer") == 0) op.intv = atoi(ArgC[i+1]);
if (strcmp(ArgC[i], "-include-sample") == 0) op.GetIncludedSamples(ArgC[i+1]);
if (strcmp(ArgC[i], "-exclude-sample") == 0) op.GetExcludedSamples(ArgC[i+1]);
if (strcmp(ArgC[i], "-output") == 0) op.fnoutput = ArgC[i+1];
}
op.GetData();
CData dhap (&op);
CData dlk (&op);
for (int i = 0; i != ArgI-1; ++i)
{
if (strcmp(ArgC[i], "-hap") == 0) dhap.GetHaplotype(ArgC[i+1]);
if (strcmp(ArgC[i], "-lk") == 0) dlk.GetLK(ArgC[i+1]);
}
dhap.MatchData(dlk.GetSamples());
dhap.CM_Location(geneticmap);
dlk.CM_Location(geneticmap);
dhap.Estimate_Panel_ID(200);
CMCMC mcmc(&dhap, &op, &geneticmap, &dlk);
dlk.Output(op.GetfnOutput());
return 0;
}
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
//declare variables
mxArray *u_m,*y_m,*theta_m,*theta_0_m;
const mwSize *dims;
long int N;
int order,num_samples;
double elim;
double *u,*y,*theta,*theta_0;
//associate inputs
u_m = mxDuplicateArray(prhs[0]);
y_m = mxDuplicateArray(prhs[1]);
theta_0_m = mxDuplicateArray(prhs[4]);
N = (long int)mxGetScalar(prhs[2]);
order = (int)mxGetScalar(prhs[3]);
elim = (double)mxGetScalar(prhs[5]);
dims = mxGetDimensions(prhs[0]);
num_samples = (int)dims[1];
//associate outputs
theta_m = plhs[0] = mxCreateDoubleMatrix((mwSize)N,2*(order+1),mxREAL);
//associate pointers
u = mxGetPr(u_m);
y = mxGetPr(y_m);
theta = mxGetPr(theta_m);
theta_0 = mxGetPr(theta_0_m);
mcmc(u,y,theta,N,order,num_samples,theta_0,elim);
// mxFree(u_m);
// mxFree(y_m);
// mxFree(theta_m);
// mxFree(theta_0_m);
//
return;
}
int main(int argc, char **argv){
if(argc!=3){
printf("USAGE: %s\n", USAGE);
exit(1);
}
int n_iterations=atoi(argv[1]);
int n_burn=atoi(argv[2]);
int iterMCMC;
int numT;
iterMCMC=n_iterations+n_burn;
double *x,*t;
double *a,*b,*c,*d,*chi;
t=reserva(3000);
x=reserva(3000);//Se usa mucho mas espacio del necesario para no tener problemas con el numero de datos
a=reserva(iterMCMC);
b=reserva(iterMCMC);
c=reserva(iterMCMC);
d=reserva(iterMCMC);
chi=reserva(iterMCMC);
a[0]=0;
b[0]=0;
c[0]=0;
d[0]=1;
numT=importarDatos(t,x,"monthrg.dat");
mcmc(chi,a,b,c,d,x,t,numT,iterMCMC);
imprimirResultados("a",a,n_burn,n_iterations);
imprimirResultados("b",b,n_burn,n_iterations);
imprimirResultados("c",c,n_burn,n_iterations);
imprimirResultados("d",d,n_burn,n_iterations);
guardar(chi,a,b,c,d,n_burn,n_iterations);
guardarLectura(x,t,numT);
}
void
R_mcmc(int *numIterations, int *n, double *theta, double *lambda, int *k, double *b1, double *b2, double *Y)
{
mcmc(numIterations[0], n[0], theta, lambda, k, b1, b2, Y);
}
int main(int argc, char** argv)
{
try {
long seed_from_command_line = 1L;
string params_file; bool error;
po::options_description options("EEMS options from command line");
po::variables_map vm;
options.add_options()
("help", "Produce this help message")
("seed", po::value<long>(&seed_from_command_line)->default_value(time(NULL)), "Set the random seed")
("params", po::value<string>(¶ms_file)->required(), "Specify input parameter file") ;
po::store(po::parse_command_line(argc, argv, options), vm);
po::notify(vm);
if(vm.count("help")) {
cerr << options << endl; return(EXIT_FAILURE);
}
Params params(params_file,seed_from_command_line);
error = params.check_input_params( );
if (error) {
cerr << "[RunEEMS] Error parametrizing EEMS." << endl;
return(EXIT_FAILURE);
}
// Specify the distance metric in the params.ini file
dist_metric = params.distance;
EEMS eems(params);
MCMC mcmc(params);
boost::filesystem::path dir(eems.prevpath().c_str());
if (exists(dir)) {
cerr << "Load final EEMS state from " << eems.prevpath() << endl << endl;
eems.load_final_state();
} else {
cerr << "Initialize EEMS random state" << endl << endl;
eems.initialize_state();
}
error = eems.start_eems(mcmc);
if (error) {
cerr << "[RunEEMS] Error starting EEMS." << endl;
return(EXIT_FAILURE);
}
Proposal proposal;
while (!mcmc.finished) {
switch ( eems.choose_move_type( ) ) {
case Q_VORONOI_BIRTH_DEATH:
eems.propose_birthdeath_qVoronoi(proposal);
break;
case M_VORONOI_BIRTH_DEATH:
eems.propose_birthdeath_mVoronoi(proposal);
break;
case Q_VORONOI_POINT_MOVE:
eems.propose_move_one_qtile(proposal);
break;
case M_VORONOI_POINT_MOVE:
eems.propose_move_one_mtile(proposal);
break;
case Q_VORONOI_RATE_UPDATE:
eems.propose_rate_one_qtile(proposal);
break;
case M_VORONOI_RATE_UPDATE:
eems.propose_rate_one_mtile(proposal);
break;
case M_MEAN_RATE_UPDATE:
eems.propose_overall_mrate(proposal);
break;
case DF_UPDATE:
eems.propose_df(proposal,mcmc);
break;
default:
cerr << "[RunEEMS] Unknown move type" << endl;
return(EXIT_FAILURE);
}
mcmc.add_to_total_moves(proposal.move);
if (eems.accept_proposal(proposal)) { mcmc.add_to_okay_moves(proposal.move); }
if (params.testing) { eems.check_ll_computation( ); }
//eems.update_sigma2( );
eems.update_hyperparams( );
mcmc.end_iteration( );
// Check whether to save the current parameter state,
// as the thinned out iterations are not saved
int iter = mcmc.to_save_iteration( );
if (iter>=0) {
eems.print_iteration(mcmc);
eems.save_iteration(mcmc);
}
}
error = eems.output_results(mcmc);
if (error) { cerr << "[RunEEMS] Error saving eems results to " << eems.mcmcpath() << endl; }
} catch(exception& e) {
cerr << e.what() << endl;
return(EXIT_FAILURE);
}
return(0);
}
