void xy_plots(int first = 5808, int last = 11688)
{
TH1D *h[2][3][2];
int i, j, k;
char str[64];
TCanvas *cv[2];
TPaveStats *st;
float y, dy;
int mask[3] = {2, 4, 8}; // down, middle, up
gROOT->SetStyle("Plain");
gStyle->SetOptStat(1000000);
gStyle->SetOptFit();
TFile *fRoot = new TFile("xy_plots.root", "RECREATE");
HPainter *p[3];
for (i=0; i<3; i++) p[i] = new HPainter(mask[i], first, last);
if (!p[0]->IsOpen() || !p[1]->IsOpen() || !p[2]->IsOpen()) {
printf("Something wrong with data files.\n");
return;
}
for (i=0; i<3; i++) p[i]->SetFile(fRoot);
TCut cVeto("gtFromVeto > 60");
TCut cIso("(gtFromPrevious > 45 && gtToNext > 80 && EventsBetween == 0) || (gtFromPrevious == gtFromVeto)");
TCut cX("PositronX[0] < 0 || (PositronX[0] > 2 && PositronX[0] < 94)");
TCut cY("PositronX[1] < 0 || (PositronX[1] > 2 && PositronX[1] < 94)");
TCut cZ = "PositronX[2] > 3.5 && PositronX[2] < 95.5";
TCut cR("Distance < 100 && DistanceZ > -40 && DistanceZ < 40");
TCut cT20("gtDiff > 2");
TCut cGamma("AnnihilationEnergy < 1.5 && AnnihilationGammas < 9");
TCut cPe("PositronEnergy > 1");
TCut cSig = cIso && cR && cT20 && cGamma && cPe;
fRoot->cd();
for (i=0; i<2; i++) for (j=0; j<3; j++) {
sprintf(str, "hX%d%c", j, (i) ? 'C' : 'S');
h[0][j][i] = new TH1D(str, "Positron vertex X;X, cm;mHz", 25, 0, 100);
sprintf(str, "hY%d%c", j, (i) ? 'C' : 'S');
h[1][j][i] = new TH1D(str, "Positron vertex Y;Y, cm;mHz", 25, 0, 100);
}
printf("Histograms are created\n");
for (i=0; i<3; i++) {
p[i]->Project(h[0][i][0], "PositronX[0]+2", cVeto && cSig && cY && "PositronX[0] >= 0" && cZ);
p[i]->Project(h[0][i][1], "PositronX[0]+2", !cVeto && cSig && cY && "PositronX[0] >= 0" && cZ);
printf("X%d\n", i);
p[i]->Project(h[1][i][0], "PositronX[1]+2", cVeto && cSig && cX && "PositronX[1] >= 0" && cZ);
p[i]->Project(h[1][i][1], "PositronX[1]+2", !cVeto && cSig && cX && "PositronX[1] >= 0" && cZ);
printf("Y%d\n", i);
}
printf("Projections are done\n");
fRoot->cd();
for (i=0; i<2; i++) for (j=0; j<3; j++) for (k=0; k<2; k++) h[i][j][k]->Write();
fRoot->Close();
}
// ----------------------------------------------------------------
// ----------------------------------------------------------------
int wmain(int argc, wchar_t *argv[]) {
// int main(int argc, char **argv) {
int i = 0;
int j = 0;
int k = 0;
bool aTestCti = false;
SAP_UC *aChr;
SAP_cout << TProperties::getInstance()->getVersion(true) << std::endl;
#if 0
for (j = 0; j < 50000; j++) {
SHERLOK_FCT_BEGIN(cR("package1"), cR("aClass1"), cR("aMethod1"), cR("()V"))
SHERLOK_FCT_BEGIN(cR("package2"), cR("aClass2"), cR("aMethod2"), cR("()V"))
aChr = (SAP_UC *)mallocU(1000);
SHERLOK_FCT_END
SHERLOK_FCT_END
}
SLEEP(100000);
#endif
// SAP_cout << TProperties::getInstance()->getVersion(true) << std::endl;
return 0;
}
void stereoCalibThread::stereoCalibRun()
{
imageL=new ImageOf<PixelRgb>;
imageR=new ImageOf<PixelRgb>;
Stamp TSLeft;
Stamp TSRight;
bool initL=false;
bool initR=false;
int count=1;
Size boardSize, imageSize;
boardSize.width=this->boardWidth;
boardSize.height=this->boardHeight;
while (!isStopping()) {
ImageOf<PixelRgb> *tmpL = imagePortInLeft.read(false);
ImageOf<PixelRgb> *tmpR = imagePortInRight.read(false);
if(tmpL!=NULL)
{
*imageL=*tmpL;
imagePortInLeft.getEnvelope(TSLeft);
initL=true;
}
if(tmpR!=NULL)
{
*imageR=*tmpR;
imagePortInRight.getEnvelope(TSRight);
initR=true;
}
if(initL && initR && checkTS(TSLeft.getTime(),TSRight.getTime())){
bool foundL=false;
bool foundR=false;
mutex->wait();
if(startCalibration>0) {
string pathImg=imageDir;
preparePath(pathImg.c_str(), pathL,pathR,count);
string iml(pathL);
string imr(pathR);
imgL= (IplImage*) imageL->getIplImage();
imgR= (IplImage*) imageR->getIplImage();
Mat Left(imgL);
Mat Right(imgR);
std::vector<Point2f> pointbufL;
std::vector<Point2f> pointbufR;
if(boardType == "CIRCLES_GRID") {
foundL = findCirclesGridDefault(Left, boardSize, pointbufL, CALIB_CB_SYMMETRIC_GRID | CALIB_CB_CLUSTERING);
foundR = findCirclesGridDefault(Right, boardSize, pointbufR, CALIB_CB_SYMMETRIC_GRID | CALIB_CB_CLUSTERING);
} else if(boardType == "ASYMMETRIC_CIRCLES_GRID") {
foundL = findCirclesGridDefault(Left, boardSize, pointbufL, CALIB_CB_ASYMMETRIC_GRID | CALIB_CB_CLUSTERING);
foundR = findCirclesGridDefault(Right, boardSize, pointbufR, CALIB_CB_ASYMMETRIC_GRID | CALIB_CB_CLUSTERING);
} else {
foundL = findChessboardCorners( Left, boardSize, pointbufL, CV_CALIB_CB_ADAPTIVE_THRESH | CV_CALIB_CB_FAST_CHECK | CV_CALIB_CB_NORMALIZE_IMAGE);
foundR = findChessboardCorners( Right, boardSize, pointbufR, CV_CALIB_CB_ADAPTIVE_THRESH | CV_CALIB_CB_FAST_CHECK | CV_CALIB_CB_NORMALIZE_IMAGE);
}
if(foundL && foundR) {
cvCvtColor(imgL,imgL,CV_RGB2BGR);
cvCvtColor(imgR,imgR, CV_RGB2BGR);
saveStereoImage(pathImg.c_str(),imgL,imgR,count);
imageListR.push_back(imr);
imageListL.push_back(iml);
imageListLR.push_back(iml);
imageListLR.push_back(imr);
Mat cL(pointbufL);
Mat cR(pointbufR);
drawChessboardCorners(Left, boardSize, cL, foundL);
drawChessboardCorners(Right, boardSize, cR, foundR);
count++;
}
if(count>numOfPairs) {
fprintf(stdout," Running Left Camera Calibration... \n");
monoCalibration(imageListL,this->boardWidth,this->boardHeight,this->Kleft,this->DistL);
fprintf(stdout," Running Right Camera Calibration... \n");
monoCalibration(imageListR,this->boardWidth,this->boardHeight,this->Kright,this->DistR);
stereoCalibration(imageListLR, this->boardWidth,this->boardHeight,this->squareSize);
fprintf(stdout," Saving Calibration Results... \n");
updateIntrinsics(imgL->width,imgL->height,Kright.at<double>(0,0),Kright.at<double>(1,1),Kright.at<double>(0,2),Kright.at<double>(1,2),DistR.at<double>(0,0),DistR.at<double>(0,1),DistR.at<double>(0,2),DistR.at<double>(0,3),"CAMERA_CALIBRATION_RIGHT");
updateIntrinsics(imgL->width,imgL->height,Kleft.at<double>(0,0),Kleft.at<double>(1,1),Kleft.at<double>(0,2),Kleft.at<double>(1,2),DistL.at<double>(0,0),DistL.at<double>(0,1),DistL.at<double>(0,2),DistL.at<double>(0,3),"CAMERA_CALIBRATION_LEFT");
Mat Rot=Mat::eye(3,3,CV_64FC1);
Mat Tr=Mat::zeros(3,1,CV_64FC1);
updateExtrinsics(this->R,this->T,"STEREO_DISPARITY");
fprintf(stdout, "Calibration Results Saved in %s \n", camCalibFile.c_str());
startCalibration=0;
count=1;
imageListR.clear();
imageListL.clear();
imageListLR.clear();
}
}
mutex->post();
ImageOf<PixelRgb>& outimL=outPortLeft.prepare();
outimL=*imageL;
outPortLeft.write();
ImageOf<PixelRgb>& outimR=outPortRight.prepare();
outimR=*imageR;
outPortRight.write();
if(foundL && foundR && startCalibration==1)
Time::delay(2.0);
initL=initR=false;
cout.flush();
}
}
delete imageL;
delete imageR;
}
extern "C" SEXP LC_CoxPH(SEXP R_L, SEXP R_R, SEXP R_x,
SEXP R_b, SEXP R_actInds, SEXP move_X, SEXP AugL, SEXP AugR, SEXP covariates,
SEXP R_LMAXIND, SEXP R_RMININD, SEXP R_MAXUNCENSBETAIND,
SEXP R_MAXUNCENSOBSIND, SEXP R_HASUNCENSORED){
bool c_move_x = LOGICAL(move_X)[0] == TRUE;
int n = LENGTH(R_L);
int k = LENGTH(R_x);
vector<double> x(k);
vector<double> b(k);
for(int i = 0; i < k; i++){
x[i] = REAL(R_x)[i];
b[i] = REAL(R_b)[i];
}
vector<int> cL(n);
vector<int> cR(n);
vector<double> cRepVec(n);
bool leftDone,rightDone;
double leftval, rightval;
for(int i = 0; i < n; i++){
leftval = REAL(R_L)[i];
rightval = REAL(R_R)[i];
leftDone = false;
rightDone = false;
for(int j = 0; j < k; j++){
if(leftDone == false){
if(leftval == x[j]){
cL[i] = j;
leftDone = true;
}
}
if(rightDone == false){
if(rightval == x[j]){
cR[i] = j;
rightDone = true;
}
}
}
if(rightDone == false || leftDone == false){
Rprintf("problem: data does not match x! Quiting\n");
return(R_NilValue);
}
}
SEXP dims = getAttrib(covariates, R_DimSymbol);
PROTECT(dims);
int num_cov = INTEGER(dims)[1];
int cov_n = INTEGER(dims)[0];
UNPROTECT(1);
if(cov_n != n){
Rprintf("Number of covariates does not match number of observations\n");
return(R_NilValue);
}
QuadProgPP::Matrix<double> Covars(cov_n,num_cov);
for(int i = 0; i < cov_n; i++){
for(int j = 0; j < num_cov; j++)
Covars[i][j] = REAL(covariates)[i + j*cov_n];
}
int ak = LENGTH(R_actInds);
vector<int> actInds(ak);
for(int i = 0; i < ak; i++)
actInds[i] = INTEGER(R_actInds)[i] - 1;
double augl = REAL(AugL)[0];
double augr = REAL(AugR)[0];
int LMAXIND = INTEGER(R_LMAXIND)[0] - 1;
int RMININD = INTEGER(R_RMININD)[0] - 1;
double LLAGRMIN = REAL(AugL)[0];
double RLAGRMIN = REAL(AugR)[0];
int MAXUNCENSBETAIND = INTEGER(R_MAXUNCENSBETAIND)[0] - 1;
int MAXUNCENSOBSIND = INTEGER(R_MAXUNCENSOBSIND)[0] - 1;
bool HASUNCENSORED = LOGICAL(R_HASUNCENSORED)[0] == TRUE;
LogConCenPH optObj(0, x, b, cL, cR, actInds, c_move_x, augl, augr, Covars, num_cov,
LMAXIND, RMININD, LLAGRMIN, RLAGRMIN, MAXUNCENSBETAIND, MAXUNCENSOBSIND, HASUNCENSORED);
optObj.updateNu();
optObj.updateRegress();
cout << "starting llk = " <<optObj.llk() << "\n";
optObj.VEMstep();
optObj.ICMstep();
cout << "after VEM and ICM, llk = " << optObj.llk() << "\n";
cout << "k = " << k << " actInds[0] = " << optObj.actIndex[0] << " actInds[getAK()-1] = " << optObj.actIndex[optObj.getAK()-1] << "\n";
// double old_llk = R_NegInf;
// double new_llk = optObj.llk();
int inner_it = 0;
int outer_it = 0;
int max_inner_its = 2;
int max_outer_its = 2;
double outer_tol = pow(10.0, -10);
double inner_tol = pow(10.0, -12);
double outer_error = outer_tol + 1;
double reg_error = outer_tol + 1;
double inner_error;
double inner_llk, outer_llk;
int loopcount = 0;
bool start_move_x = false;
Rprintf("Reminder to Cliff: move_x turned off until updates\n");
while( (outer_it < max_outer_its) && (loopcount < 2)){
outer_it++;
outer_llk = optObj.llk();
cout << "beginning loop llk = " << outer_llk << "\n";
optObj.VEMstep();
cout << "after VEMstep, llk = " << optObj.llk() << "\n";
inner_error = inner_tol + 1;
reg_error = outer_tol + 1;
inner_it = 0;
while(inner_it < max_inner_its && inner_error > inner_tol){
inner_it++;
// if(start_move_x && c_move_x)
// optObj.updateXs();
if(reg_error > outer_tol){
reg_error = optObj.updateRegress();
cout << "after updateRegress step, llk = " << optObj.llk() << "\n";
}
inner_llk = optObj.llk();
optObj.ICMstep();
cout << "after ICM step, llk = " << optObj.llk() << "\n";
inner_error = optObj.llk() - inner_llk;
if(inner_error != inner_error)
break;
}
cout << "k = " << k << " actInds[0] = " << optObj.actIndex[0] << " actInds[getAK()-1] = " << optObj.actIndex[optObj.getAK()-1] << "\n";
cout << "before recenterBeta, llk = " << optObj.llk() <<"\n";
optObj.recenterBeta();
cout << "after recenterBeta, llk = " << optObj.llk() << "\n";
outer_error = optObj.llk() - outer_llk;
if(outer_error != outer_error){
Rprintf("Warning: undefined error. Algorithm terminated at invalid estimate. Please contact Clifford Anderson-Bergman with this dataset!\n");
break;
}
if(outer_error < 0.0001)
start_move_x = true;
if(outer_error < outer_tol){
loopcount++;
}
else
loopcount = 0;
}
optObj.makePropDist();
ak = optObj.getAK();
SEXP output = PROTECT(allocVector(VECSXP, 5) );
SEXP regressP = PROTECT(allocVector(REALSXP, num_cov) );
for(int i = 0; i < num_cov; i++)
REAL(regressP)[i] = optObj.cov_b[i];
SEXP x_out = PROTECT(allocVector(REALSXP, ak) );
SEXP b_out = PROTECT(allocVector(REALSXP, ak) );
SEXP llk_out = PROTECT(allocVector(REALSXP, 1) );
for(int i = 0; i < ak; i++){
REAL(x_out)[i] = optObj.x[optObj.actIndex[i]];
REAL(b_out)[i] = optObj.b[optObj.actIndex[i]];
}
int totValues = num_cov + ak;
SEXP Hess_out = PROTECT(allocMatrix(REALSXP, totValues, totValues));
for(int i = 0; i < totValues; i++){
for(int j = 0; j <= i; j++){
REAL(Hess_out)[i + totValues * j] = optObj.partialDerCovOrBase(i,j);
REAL(Hess_out)[j + totValues * i] = REAL(Hess_out)[i + totValues* j];
}
}
REAL(llk_out)[0] = optObj.llk();
SET_VECTOR_ELT(output, 0, x_out);
SET_VECTOR_ELT(output, 1, b_out);
SET_VECTOR_ELT(output, 2, llk_out);
SET_VECTOR_ELT(output, 3, regressP);
SET_VECTOR_ELT(output, 4, Hess_out);
UNPROTECT(6);
return(output);
}
void many_plots2(int first = 5808, int last = 11688, int mask = 0x801E)
{
TH1D *h[12][2];
int i, j;
char str[64];
TCanvas *cv[2];
TPaveStats *st;
float y, dy;
gROOT->SetStyle("Plain");
gStyle->SetOptStat(1000000);
gStyle->SetOptFit();
TFile *fRoot = new TFile("many_plots.root", "RECREATE");
HPainter *p = new HPainter(mask, first, last);
p->SetFile(fRoot);
if (!p->IsOpen()) {
printf("Something wrong with data files.\n");
return;
}
TCut cVeto("gtFromVeto > 60");
TCut cIso("(gtFromPrevious > 45 && gtToNext > 80 && EventsBetween == 0) || (gtFromPrevious == gtFromVeto)");
TCut cX("PositronX[0] < 0 || (PositronX[0] > 2 && PositronX[0] < 94)");
TCut cY("PositronX[1] < 0 || (PositronX[1] > 2 && PositronX[1] < 94)");
TCut cZ("PositronX[2] > 3.5 && PositronX[2] < 95.5");
TCut cXYZ = cX && cY && cZ;
TCut cR("Distance < 100 && DistanceZ > -40 && DistanceZ < 40");
TCut cT10("gtDiff > 1");
TCut cT20("gtDiff > 2");
TCut cT200("gtDiff < 20"); // strong cut
TCut cGamma("AnnihilationEnergy < 1.5 && AnnihilationGammas < 9");
TCut cPe("PositronEnergy > 1");
TCut cXY("PositronX[0]>=0 && PositronX[1]>=0");
TCut cN4("NeutronEnergy > 4 && NeutronHits >= 5");
for (i=0; i<2; i++) {
sprintf(str, "hR%d", i);
h[0][i] = new TH1D(str, "Distance between positron and neutron;R, cm;mHz", 40, 0, 160);
sprintf(str, "hRZ%d", i);
h[1][i] = new TH1D(str, "Distance between positron and neutron, projection Z;R_{z}, cm;mHz", 100, -100, 100);
sprintf(str, "hT%d", i);
h[2][i] = new TH1D(str, "Time between positron and neutron;T, us;mHz", 50, 0, 50);
sprintf(str, "hX%d", i);
h[3][i] = new TH1D(str, "Positron vertex X;X, cm;mHz", 25, 0, 100);
sprintf(str, "hY%d", i);
h[4][i] = new TH1D(str, "Positron vertex Y;Y, cm;mHz", 25, 0, 100);
sprintf(str, "hZ%d", i);
h[5][i] = new TH1D(str, "Positron vertex Z;Z, cm;mHz", 100, 0, 100);
sprintf(str, "hNE%d", i);
h[6][i] = new TH1D(str, "Energy detected in neutron capture;E_{n}, MeV;mHz", 50, 0, 10);
sprintf(str, "hNN%d", i);
h[7][i] = new TH1D(str, "Number of hits in SiPM for neutron capture;N_{n};mHz", 20, 0, 20);
sprintf(str, "hGE%d", i);
h[8][i] = new TH1D(str, "Energy beyond positron cluster;E_{#gamma}, MeV;mHz", 15, 0, 3);
sprintf(str, "hGN%d", i);
h[9][i] = new TH1D(str, "Number of SiPM hits out of positron cluster;N_{#gamma};mHz", 10, 0, 10);
sprintf(str, "hE%d", i);
h[10][i] = new TH1D(str, "Positorn kinetic energy;E, MeV;mHz", 40, 0, 8);
sprintf(str, "hEC%d", i);
h[11][i] = new TH1D(str, "Positorn kinetic energy, strong background cuts;E, MeV;mHz", 40, 0, 8);
}
printf("Histograms are created\n");
p->Project(h[0][0], "Distance", cVeto && cIso && cT20 && cGamma && cPe && cXYZ);
p->Project(h[0][1], "Distance", !cVeto && cIso && cT20 && cGamma && cPe && cXYZ);
printf("Distance.\n");
p->Project(h[1][0], "DistanceZ", cVeto && cIso && cT20 && cGamma && cPe && cXYZ);
p->Project(h[1][1], "DistanceZ", !cVeto && cIso && cT20 && cGamma && cPe && cXYZ);
printf("DistanceZ.\n");
p->Project(h[2][0], "gtDiff", cVeto && cIso && cT10 && cGamma && cPe && cXYZ && cR);
p->Project(h[2][1], "gtDiff", !cVeto && cIso && cT10 && cGamma && cPe && cXYZ && cR);
printf("gtDiff.\n");
p->Project(h[3][0], "PositronX[0]+2", cVeto && cIso && cT20 && cGamma && cPe && cY && cZ && cR && "PositronX[0] >= 0");
p->Project(h[3][1], "PositronX[0]+2", !cVeto && cIso && cT20 && cGamma && cPe && cY && cZ && cR && "PositronX[0] >= 0");
printf("X.\n");
p->Project(h[4][0], "PositronX[1]+2", cVeto && cIso && cT20 && cGamma && cPe && cX && cZ && cR && "PositronX[1] >= 0");
p->Project(h[4][1], "PositronX[1]+2", !cVeto && cIso && cT20 && cGamma && cPe && cX && cZ && cR && "PositronX[1] >= 0");
printf("Y.\n");
p->Project(h[5][0], "PositronX[2]+0.5", cVeto && cIso && cT20 && cGamma && cPe && cX && cY && cR);
p->Project(h[5][1], "PositronX[2]+0.5", !cVeto && cIso && cT20 && cGamma && cPe && cX && cY && cR);
printf("Z.\n");
p->Project(h[6][0], "NeutronEnergy", cVeto && cIso && cT20 && cGamma && cPe && cY && cZ && cR);
p->Project(h[6][1], "NeutronEnergy", !cVeto && cIso && cT20 && cGamma && cPe && cY && cZ && cR);
printf("NE.\n");
p->Project(h[7][0], "NeutronHits", cVeto && cIso && cT20 && cGamma && cPe && cXYZ && cR);
p->Project(h[7][1], "NeutronHits", !cVeto && cIso && cT20 && cGamma && cPe && cXYZ && cR);
printf("NN.\n");
p->Project(h[8][0], "AnnihilationEnergy", cVeto && cIso && cT20 && cPe && cXYZ && cR);
p->Project(h[8][1], "AnnihilationEnergy", !cVeto && cIso && cT20 && cPe && cXYZ && cR);
printf("AE.\n");
p->Project(h[9][0], "AnnihilationGammas", cVeto && cIso && cT20 && cPe && cXYZ && cR);
p->Project(h[9][1], "AnnihilationGammas", !cVeto && cIso && cT20 && cPe && cXYZ && cR);
printf("AG.\n");
p->Project(h[10][0], "PositronEnergy", cVeto && cIso && cT20 && cGamma && cPe && cXYZ && cR);
p->Project(h[10][1], "PositronEnergy", !cVeto && cIso && cT20 && cGamma && cPe && cXYZ && cR);
p->Project(h[11][0], "PositronEnergy", cVeto && cIso && cT20 && cGamma && cPe && cXYZ && cR && cN4 && cT200);
p->Project(h[11][1], "PositronEnergy", !cVeto && cIso && cT20 && cGamma && cPe && cXYZ && cR && cN4 && cT200);
printf("Projections are done\n");
for (i=0; i<12; i++) {
for (j=0; j<2; j++) h[i][j]->SetLineWidth(4);
h[i][0]->SetLineColor(kGreen);
h[i][1]->SetLineColor(kRed);
h[i][0]->SetMinimum(0);
h[i][1]->SetMinimum(0);
}
// h[1][0]->Fit("gaus", "0");
// h[1][1]->Fit("gaus", "0");
// TF1 *fdec = new TF1("FDEC", "[0]*(exp(-x/[1]) - exp(-x/[2]))", 3);
// fdec->SetParNames("Const", "t_{CAPTURE}", "t_{THERM}");
// fdec->SetParameters(h[2][0]->Integral()/4, 15, 5);
// h[2][0]->Fit("FDEC", "0", "", 2, 50);
for (i=0; i<2; i++) {
sprintf(str, "CV%d", i);
cv[i] = new TCanvas(str, "Plots", 1800, 1200);
cv[i]->Divide(3, 2);
for (j=0; j<6; j++) {
cv[i]->cd(j+1);
h[6*i+j][0]->Draw();
h[6*i+j][1]->Draw("sames");
gPad->Update();
if (i == 0 && j == 1) {
st = (TPaveStats *) h[6*i+j][0]->FindObject("stats");
st->SetOptStat(1100);
st->SetLineColor(kGreen);
st->SetTextColor(kGreen);
y = st->GetY1NDC();
dy = st->GetY2NDC() - y;
st->SetX1NDC(0.72);
st = (TPaveStats *) h[6*i+j][1]->FindObject("stats");
st->SetOptStat(1100);
st->SetLineColor(kRed);
st->SetTextColor(kRed);
st->SetX1NDC(0.72);
st->SetY2NDC(y);
st->SetY1NDC(y - dy);
} else {
st = (TPaveStats *) h[6*i+j][0]->FindObject("stats");
st->SetLineColor(kGreen);
st->SetTextColor(kGreen);
y = st->GetY1NDC();
dy = st->GetY2NDC() - y;
st->SetX1NDC(0.72);
st->SetY1NDC(y + dy/2);
st = (TPaveStats *) h[6*i+j][1]->FindObject("stats");
st->SetLineColor(kRed);
st->SetTextColor(kRed);
st->SetX1NDC(0.72);
st->SetY2NDC(y + dy/2);
}
if (h[6*i+j][0]->GetMaximum() > h[6*i+j][1]->GetMaximum()) {
h[6*i+j][0]->Draw();
h[6*i+j][1]->Draw("sames");
} else {
h[6*i+j][1]->Draw();
h[6*i+j][0]->Draw("sames");
}
gPad->Update();
}
cv[i]->Update();
}
fRoot->cd();
for (i=0; i<12; i++) for (j=0; j<2; j++) h[i][j]->Write();
fRoot->Close();
}
/// <summary>
/// Calculates for each image patch the focus measure value. Result is a vector of Patches (see class Patch).
/// If the image is binary, the relative foreground (foreground pixel / patchSize) and the weight is stored for each Patch.
/// </summary>
/// <param name="fm">The specified focuse measure method fm (e.g. Brenner).</param>
/// <param name="fmImg">The image fmImg to calculate the focus measure on. If empty, the src image is taken.</param>
/// <param name="binary">if set to <c>true</c> [binary] the input image is binary, specifying the foreground image. The foreground area and the weight is saved to the image patch</param>
/// <returns>True if the focus measure could be computed, false otherwise.</returns>
bool FocusEstimation::compute(FocusMeasure fm, cv::Mat fmImg, bool binary)
{
cv::Mat fImg = fmImg;
if (fImg.empty())
fImg = mSrcImg;
if (fImg.empty())
return false;
if (fmImg.channels() != 1 || fImg.depth() != CV_32F)
return false;
BasicFM fmClass;
double f;
mFmPatches.clear();
for (int row = 0; row < fImg.rows; row += (mWindowSize+mSplitSize)) {
for (int col = 0; col < fImg.cols; col += (mWindowSize+mSplitSize)) {
cv::Range rR(row, cv::min(row + mWindowSize, fImg.rows));
cv::Range cR(col, cv::min(col + mWindowSize, fImg.cols));
cv::Mat tile = fImg(rR, cR);
fmClass.setImg(tile);
switch (fm)
{
case dsc::FocusEstimation::BREN:
f = fmClass.computeBREN();
break;
case dsc::FocusEstimation::GLVA:
f = fmClass.computeGLVA();
break;
case dsc::FocusEstimation::GLVN:
f = fmClass.computeGLVN();
break;
case dsc::FocusEstimation::GLLV:
f = fmClass.computeGLLV();
break;
case dsc::FocusEstimation::GRAT:
f = fmClass.computeGRAT();
break;
case dsc::FocusEstimation::GRAS:
f = fmClass.computeGRAS();
break;
case dsc::FocusEstimation::LAPE:
f = fmClass.computeLAPE();
break;
case dsc::FocusEstimation::LAPV:
f = fmClass.computeLAPV();
break;
case dsc::FocusEstimation::ROGR:
f = fmClass.computeROGR();
break;
default:
f = -1;
break;
}
Patch r(cv::Point(col, row), mWindowSize, mWindowSize, f);
if (binary) {
cv::Scalar relArea = cv::sum(tile);
r.setArea(relArea[0]);
relArea[0] = relArea[0] / (double)(mWindowSize * mWindowSize);
//area completely written with text ~ 0.1
//normalize to 1
relArea[0] *= 10.0;
r.setWeight(relArea[0]);
//weight with sigmoid function
//-6: shift sigmoid to the right
//*10: scale normalized Area
//double a = 10.0;
//double b = -6.0;
//double weight = 1.0 / (1 + std::exp(-(relArea[0] * a + b)));
//r.setWeight(weight);
}
mFmPatches.push_back(r);
}
}
return true;
}