void exportHistograms(){
TreeReader reader;
reader.openSeries(257,"D");
reader.openSeries(258,"D");
reader.openSeries(260,"D");
reader.openSeries(261,"D");
reader.openSeries(262,"D");
TH1F hist1("hist1","hist1",100,0,30000);
TH1F hist2("hist2","hist2",100,0,30000);
TH1F hist3("hist3","hist3",100,0,30000);
for(Long64_t i=0;i<reader.tree->GetEntries();i++){
reader.tree->GetEntry(i);
if(fabs(reader.recon.t_gamma[2]-600)<10){
hist1.Fill(reader.recon.E_gamma[2]);
}
if(fabs(reader.recon.t_gamma[6]-600)<10){
hist2.Fill(reader.recon.E_gamma[6]);
}
if(fabs(reader.recon.t_gamma[13]-600)<10){
hist3.Fill(reader.recon.E_gamma[13]);
}
}
ofstream output(Form("%s/output.csv",RDKANAL));
output<<"bin center,det02,det06,det16"<<endl;
for(Long64_t i=1;i<=100;i++){
output<<hist1.GetBinCenter(i)<<","<<hist1.GetBinContent(i)<<",";
output<<hist2.GetBinContent(i)<<","<<hist3.GetBinContent(i)<<endl;
}
output.close();
}
int main3(int argc, const char *argv[])
{
TreeReader tr;
//tr.ParseTree("simple_out.txt", "tes.txt");
tr.ParseTree(argv[1], argv[2]);
//int x;
//std::cin >> x;
return 0;
}
int main(void) {
TreeReader tr;
string test;
test = "((a:2,b:2):3,(c:4,d:4):1):1;";
/*
ifstream infile("../../big_geo/final_ml.tre.cn.rr.pr.nw.pathd8.bgstates.tre");
if (!infile){
cerr << "Could not open file." << endl;
return 1;
}
vector<string> lines;
string line;
while (getline(infile, line)){
lines.push_back(line);
}
infile.close();
test = lines[0];
*/
Tree tree = *tr.readTree(test);
cout << tree.getNodeCount() << endl;
cout << tree.getRoot()->getNewick(true) << ";" << endl;
cout << tree.getRoot()->getNewick(true,"number") << ";" << endl;
string a = "c";
tree.pruneExternalNode(tree.getExternalNode(a));
cout << tree.getRoot()->getNewick(true) << ";" << endl;
StringNodeObject sno("...a node object");
tree.getRoot()->assocObject("test",sno);
cout << tree.getRoot()->getNewick(true,"test") << ";" << endl;
cout << *((StringNodeObject*) (tree.getRoot()->getObject("test"))) << endl;
VectorNodeObject<int> vno;
vno.push_back(1);vno.push_back(2);
tree.getRoot()->assocObject("testvno",vno);
cout << ((VectorNodeObject<int> *) (tree.getRoot()->getObject("testvno")))->at(0) << endl;
a = "b";
tree.setHeightFromRootToNodes();
cout << tree.getExternalNode(a)->getHeight() << endl;
cout << tree.getRoot()->getHeight() << endl;
cout << tree.getInternalNode(0)->getHeight() << endl;
cout << tree.getInternalNode(1)->getHeight() << endl;
//for(int i=0;i<tree.getInternalNodeCount();i++){
//cout << tree.getInternalNode(i).getBL() << endl;
//}
return EXIT_SUCCESS;
}
int main(){
std::vector<MCSample> Samples;
PkPhi.FileName="../PkphiSingle.root";
PkPhi.Description="#Lambda_b -> p K #phi background";
Samples.push_back(PkPhi);
Rare.FileName="../RareMCSingle.root";
Rare.Description="#eta' -> #pi #pi #gamma";
Samples.push_back(Rare);
Rare2.FileName="../Rare2MCSingle.root";
Rare2.Description="#eta' -> #pi #pi #eta";
Samples.push_back(Rare2);
Control.FileName="../CCMCSingle.root";
Control.Description="Control Channel";
Samples.push_back(Control);
for(auto &Sample : Samples){
TreeReader * Reader = new TreeReader("DecayTree");
Reader->AddFile(Sample.FileName.data());
Reader->Initialize();
Long64_t N=Reader->GetEntries();
Sample.CC=new CorrelationCoeff(Sample.Description);
std::string HeadMassName="Lambda_b0_DTF_MF";
Reader->GetEntry(0);
try{
Reader->GetValue("Lambda_b0_DTF_MF");
}catch(...){
HeadMassName="Bu_DTF_MF";
}
for(int i=0;i<N;++i){
Reader->GetEntry(i);
double HeadMass=Reader->GetValue(HeadMassName.data());
double EtaMass=Reader->GetValue("eta_prime_MM");
if(HeadMassName.compare("Lambda_b0_DTF_MF")==0){
if(HeadMass>5200.0&&HeadMass<6000.0&&EtaMass>880.0&&EtaMass<1040.0){
Sample.CC->Fill(HeadMass,EtaMass);
}
}else{
if(HeadMass>5000.0&&HeadMass<5500.0&&EtaMass>880.0&&EtaMass<1040.0){
Sample.CC->Fill(HeadMass,EtaMass);
}
}
}
double NBootStraps=N*10;
std::cout<<"After "<<NBootStraps<<" Boostraps"<<std::endl;
std::cout<<Sample.Description<<" Coefficient = "<<Sample.CC->GetCC()<<" +/- "<<Sample.CC->GetBootstrapError(NBootStraps)<<std::endl;
}
TFile * Output = new TFile("Output.root","RECREATE");
for(auto &Sample : Samples){
Sample.CC->GetBootStrapHist(0)->Write();
Sample.CC->GetCorrelationPlot()->Write();
}
}
void InputReader::readMultipleTreeFile(string filename, vector<Tree *> & ret){
TreeReader tr;
ifstream ifs( filename.c_str() );
string temp;
int count = 1;
while( getline( ifs, temp ) ){
if(temp.size() > 1){
Tree * intree = tr.readTree(temp);
intree->setNewickStr(temp);
cout << "Tree "<< count <<" has " << intree->getExternalNodeCount() << " leaves." << endl;
ret.push_back(intree);
count++;
}
}
}
void listEvents(){
Recon recon;
//TFile f(Form("%s/cal.root",RDKANAL));
//CalibrationList *list=(CalibrationList*)f.Get("CalibrationList");
TString path=Form("%s/calibration/TCfit_511keV_calibration_21Feb11.dat",RDKANAL);
CalibrationList *list=new CalibrationList(path);
TreeReader reader;
reader.reset(kTRUE);
//NData ndata=reader.openList(Form("%s/runlist.csv",RDKANAL));
NData ndata=reader.openSeries(256,"S");
//NData ndata=reader.openSeries(TreeReader::n1400,TreeReader::all1400,"S");
logNdat(ndata);
ofstream log(Form("%s/eventLists/list.csv",RDKANAL));
log<<"Series,Run,EventNum,PeakHeight,Energy,DeltaTime"<<endl;
Int_t series=0,run=0,evnt=0;
for(Long64_t i=0;i<reader.tree->GetEntries();i++){
if(i%10000==0){
cout<<i<<endl;
}
reader.tree->GetEntry(i);
//if(series==reader.entry.nseries && run==reader.entry.nrun){
// reader.entry.nevent=++evnt;
//}else{
// series=reader.entry.nseries;
// run=reader.entry.nrun;
// evnt=0;
//}
recon=list->calibrate(reader.entry,reader.recon);
Int_t delta_t=recon.t_gamma[CH]-recon.t_e-PEAK;
if(recon.E_gamma[CH]>=MIN && recon.E_gamma[CH]<=MAX && recon.t_p-recon.t_e<650
&& delta_t>-ONPEAK && delta_t<=ONPEAK && recon.E_e<30000 && recon.E_p>300 && recon.E_p<1000){
log<<reader.entry.nseries<<","<<reader.entry.nrun<<","<<reader.entry.nevent<<",";
log<<reader.recon.E_gamma[CH]<<","<<recon.E_gamma[CH]<<",";
log<<(recon.t_gamma[CH]-recon.t_e)<<endl;
}
}
log.close();
delete list;
//f.close();
gSystem->ChangeDirectory(WORKDIR);
}
void secondPass(){
TreeReader reader;
reader.openSeries(256,"S");
Int_t i=1,r0,r1;
Long64_t t0,t1;
reader.tree->GetEntry(0);
r0=reader.entry.nrun;
t0=150*reader.entry.timestamp[0];
reader.tree->GetEntry(i);
r1=reader.entry.nrun;
t1=150*reader.entry.timestamp[1];
while(r0==r1){
if(t1-t0<bitError && t0-t1<bitError){
g.SetPoint(i-1,i-1,t1-t0);
}else{
g.SetPoint(i-1,i-1,0);
}
reader.tree->GetEntry(++i);
r0=r1;
t0=t1;
r1=reader.entry.nrun;
t1=150*reader.entry.timestamp[0];
}
}
int main(int argc, char **argv)
{
bool printSw = true;
//TString massModel = "Gauss-m[5622]";
string massModel = "DCB-m[5622]";
TString effbase = "/afs/cern.ch/user/p/pluca/work/Lb/Lmumu/results/";
bool printeff = false;
TString dodata = "data";
bool fitsingle = false;
TString wstr = "physRate_polp006";
TString decayToDo = "Lb2Lmumu";
if(dodata=="genMC") wstr += "_noDecay";
gROOT->ProcessLine(".x lhcbStyle.C");
RooRealVar * cosThetaL = new RooRealVar("cosThetaL","cosThetaL",0.,-1.,1.);
RooRealVar * cosThetaB = new RooRealVar("cosThetaB","cosThetaB",0.,-1.,1.);
RooRealVar * nsig_sw = new RooRealVar("nsig_sw","nsig_sw",1,-1.e6,1.e6);
RooRealVar * MCweight = new RooRealVar(wstr,wstr,1.,-1.e10,1.e10);
RooRealVar * MM = new RooRealVar("Lb_MassConsLambda","Lb_MassConsLambda",5620.,5500.,5900.);
TString datafilename = "/afs/cern.ch/user/p/pluca/work/Lb/Lmumu/candLb.root";
if(dodata=="MC") datafilename = "/afs/cern.ch/user/p/pluca/work/Lb/Lmumu/candLb_MC.root";
if(dodata=="genMC") datafilename = "/afs/cern.ch/work/p/pluca/weighted/Lmumu/"+(string)decayToDo+"_geomMC_Pythia8_NBweighted.root";
TreeReader * data;
if(dodata!="genMC") data = new TreeReader("cand"+decayToDo);
else data = new TreeReader("MCtree");
data->AddFile(datafilename);
TFile * histFile = new TFile("Afb_hist.root","recreate");
RooMsgService::instance().setGlobalKillBelow(RooFit::ERROR);
int nbins = 1;//CutsDef::nq2bins;
double q2min[] = {15.,11.0,15,16,18};//&CutsDef::q2min_highfirst[0];
double q2max[] = {20.,12.5,16,18,20};//&CutsDef::q2max_highfirst[0];
//int nbins = CutsDef::nq2bins
//double *q2min = &CutsDef::q2min[0];
//double *q2max = &CutsDef::q2max[0];
TGraphErrors * Afb_vs_q2 = new TGraphErrors();
TGraphErrors * AfbB_vs_q2 = new TGraphErrors();
TGraphErrors * fL_vs_q2 = new TGraphErrors();
TCanvas * ceff = new TCanvas();
RooCategory * samples = new RooCategory("samples","samples");
samples->defineType("DD");
samples->defineType("LL");
RooRealVar * afb = new RooRealVar("afb","afb",0.,-100,100);
RooRealVar * fL = new RooRealVar("fL","fL",0.7,-1.,10.);
//RooRealVar * afb = new RooRealVar("afb","afb",0.,-1.,1.);
//RooRealVar * fL = new RooRealVar("fL","fL",0.7,0.,1.);
RooRealVar * origafb = new RooRealVar("afb","afb",0.,-1.,1.);
RooRealVar * origfL = new RooRealVar("fL","fL",0.7,-1.,10.);
TString afbLpdf = "((3./8.)*(1.-fL)*(1 + TMath::Power(cosThetaL,2)) + afb*cosThetaL + (3./4.)*fL*(1 - TMath::Power(cosThetaL,2)))";
RooRealVar * afbB = new RooRealVar("afbB","afbB",0.,-100,100);
//RooRealVar * afbB = new RooRealVar("afbB","afbB",0.,-1.,1.);
RooRealVar * origafbB = new RooRealVar("afbB","afbB",0.,-1.,1.);
TString afbBpdf = "(1 + 2*afbB*cosThetaB)";
vector< vector< double > > afb_errs, afbB_errs, fL_errs;
TList * LLlist = new TList, * DDlist = new TList;
TCanvas * cDD = new TCanvas();
TCanvas * cLL = new TCanvas();
TCanvas * cDDB = new TCanvas();
TCanvas * cLLB = new TCanvas();
for(int i = 0; i < nbins; i++)
{
//if(q2min[i] < 8) continue;
TString q2name = ((TString)Form("q2_%4.2f_%4.2f",q2min[i],q2max[i])).ReplaceAll(".","");
TString curq2cut = Form("TMath::Power(J_psi_1S_MM/1000,2) >= %e && TMath::Power(J_psi_1S_MM/1000,2) < %e",q2min[i],q2max[i]);
//TString curq2cut = Form("TMath::Power(J_psi_1S_MM/1000,2) >= %e && TMath::Power(J_psi_1S_MM/1000,2) < %e && (Lb_MassConsLambda > 5680 || Lb_MassConsLambda < 5590)",q2min[i],q2max[i]);
cout << "------------------- q2 bin: " << q2min[i] << " - " << q2max[i] << " -----------------------" << endl;
TFile * effFile = NULL;
TH1F * effDD = NULL, * effLL = NULL, * effLLB = NULL, * effDDB = NULL;
if(q2min[i] == 15 && q2max[i] == 20)
{
effFile = TFile::Open(effbase+"LbeffvscosThetaL_DD.root");
effDD = (TH1F *)effFile->Get("htoteff");
effFile = TFile::Open(effbase+"LbeffvscosThetaL_LL.root");
effLL = (TH1F *)effFile->Get("htoteff");
effFile = TFile::Open(effbase+"LbeffvscosThetaB_DD.root");
effDDB = (TH1F *)effFile->Get("htot_nodet_eff");
effFile = TFile::Open(effbase+"LbeffvscosThetaB_LL.root");
effLLB = (TH1F *)effFile->Get("htot_nodet_eff");
}
else
{
effFile = TFile::Open(effbase+"Lbeff2D_cosThetaL_vs_q2_DD.root");
TH2F * effDD2D = (TH2F *)effFile->Get("htot_eff");
effDD = (TH1F*)GetSliceX(effDD2D,(q2max[i]+q2min[i])/2.);
effFile = TFile::Open(effbase+"Lbeff2D_cosThetaL_vs_q2_LL.root");
TH2F * effLL2D = (TH2F *)effFile->Get("htot_eff");
effLL = (TH1F*)GetSliceX(effLL2D,(q2max[i]+q2min[i])/2.);
effFile = TFile::Open(effbase+"Lbeff2D_cosThetaB_vs_q2_DD.root");
TH2F * effDDB2D = (TH2F *)effFile->Get("hupper_eff");
effDDB = (TH1F*)GetSliceX(effDDB2D,(q2max[i]+q2min[i])/2.);
effFile = TFile::Open(effbase+"Lbeff2D_cosThetaB_vs_q2_LL.root");
TH2F * effLLB2D = (TH2F *)effFile->Get("hupper_eff");
effLLB = (TH1F*)GetSliceX(effLLB2D,(q2max[i]+q2min[i])/2.);
}
ceff->cd();
/** FIT EFFICIENCY **/
RooDataHist * hLL = new RooDataHist("hLL","hLL",*cosThetaL,effLL);
RooDataHist * hDD = new RooDataHist("hDD","hDD",*cosThetaL,effDD);
RooRealVar * c1LL = new RooRealVar("c1LL","",0.,-1.,1);
RooRealVar * c1DD = new RooRealVar("c1DD","",0.,-1.,1);
RooRealVar * c2LL = new RooRealVar("c2LL","",0.,-1.,1);
RooRealVar * c2DD = new RooRealVar("c2DD","",0.,-1.,1);
TString effLLstr = "(1 + c1LL*cosThetaL + c2LL*TMath::Power(cosThetaL,2))";
TString effDDstr = "(1 + c1DD*cosThetaL + c2DD*TMath::Power(cosThetaL,2))";
RooAbsPdf * effLLpdf = new RooGenericPdf("effLLpdf", "", effLLstr, RooArgSet(*cosThetaL, *c1LL, *c2LL));
RooAbsPdf * effDDpdf = new RooGenericPdf("effDDpdf", "", effDDstr, RooArgSet(*cosThetaL, *c1DD, *c2DD));
effLLpdf->fitTo(*hLL,PrintLevel(-1));
effDDpdf->fitTo(*hDD,PrintLevel(-1));
fixParams(effLLpdf,cosThetaL);
fixParams(effDDpdf,cosThetaL);
RooDataHist * hLLB = new RooDataHist("hLLB","hLLB",*cosThetaB,effLLB);
RooDataHist * hDDB = new RooDataHist("hDDB","hDDB",*cosThetaB,effDDB);
RooRealVar * cB1LL = new RooRealVar("cB1LL","",0,-1.,1);
RooRealVar * cB1DD = new RooRealVar("cB1DD","",0,-1.,1);
RooRealVar * cB2LL = new RooRealVar("cB2LL","",0,-1.,1);
RooRealVar * cB2DD = new RooRealVar("cB2DD","",0,-1.,1);
TString effLLBstr = "(1 + cB1LL*cosThetaB + cB2LL*TMath::Power(cosThetaB,2))";
TString effDDBstr = "(1 + cB1DD*cosThetaB + cB2DD*TMath::Power(cosThetaB,2))";
RooAbsPdf * effLLpdfB = new RooGenericPdf("effLLpdfB", "", effLLBstr, RooArgSet(*cosThetaB, *cB1LL, *cB2LL));
RooAbsPdf * effDDpdfB = new RooGenericPdf("effDDpdfB", "", effDDBstr, RooArgSet(*cosThetaB, *cB1DD, *cB2DD));
effLLpdfB->fitTo(*hLLB,PrintLevel(-1));
effDDpdfB->fitTo(*hDDB,PrintLevel(-1));
fixParams(effLLpdfB,cosThetaB);
fixParams(effDDpdfB,cosThetaB);
//cout << q2min[i] << " - " << q2max[i] << " LL cosThetaL -> " << c1LL->getVal() << " " << c2LL->getVal() << endl;
//cout << q2min[i] << " - " << q2max[i] << " DD cosThetaL -> " << c1DD->getVal() << " " << c2DD->getVal() << endl;
//cout << q2min[i] << " - " << q2max[i] << " LL cosThetaB -> " << cB1LL->getVal() << " " << cB2LL->getVal() << endl;
//cout << q2min[i] << " - " << q2max[i] << " DD cosThetaB -> " << cB1DD->getVal() << " " << cB2DD->getVal() << endl;
if(printeff) {
GetFrame(cosThetaL, hLL,effLLpdf,"-nochi2",0,NULL,0,"cos#theta_{l}","Tot. eff.")->Draw();
ceff->Print("DDeffFit"+q2name+".pdf");
GetFrame(cosThetaL, hDD,effDDpdf,"-nochi2",0,NULL,0,"cos#theta_{l}","Tot. eff.")->Draw();
ceff->Print("LLeffFit"+q2name+".pdf");
GetFrame(cosThetaB, hLLB,effLLpdfB,"-nochi2",0,NULL,0,"cos#theta_{#Lambda}","Tot. eff.")->Draw();
ceff->Print("DDeffFitB"+q2name+".pdf");
GetFrame(cosThetaB, hDDB,effDDpdfB,"-nochi2",0,NULL,0,"cos#theta_{#Lambda}","Tot. eff.")->Draw();
ceff->Print("LLeffFitB"+q2name+".pdf"); }
/** FIT AFB **/
afb->setVal(0);
afbB->setVal(0);
fL->setVal(0.7);
TString LLnorm = "1./( 1. + (2./3.)*afb*c1LL + (2./5.)*c2LL - (1./5.)*c2LL*fL )*"+effLLstr;
TString DDnorm = "1./( 1. + (2./3.)*afb*c1DD + (2./5.)*c2DD - (1./5.)*c2DD*fL )*"+effDDstr;
RooAbsPdf * corrPdfLL = new RooGenericPdf(Form("corrPdfLL_%i",i),LLnorm+"*"+afbLpdf,RooArgSet(*cosThetaL, *afb, *fL, *c1LL, *c2LL) );
RooAbsPdf * corrPdfDD = new RooGenericPdf(Form("corrPdfDD_%i",i),DDnorm+"*"+afbLpdf,RooArgSet(*cosThetaL, *afb, *fL, *c1DD, *c2DD) );
TString LLnormB = "1./( (2./3.)*( 2*afbB*cB1LL + cB2LL + 3.) )*"+effLLBstr;
TString DDnormB = "1./( (2./3.)*( 2*afbB*cB1DD + cB2DD + 3.) )*"+effDDBstr;
RooAbsPdf * corrPdfLLB = new RooGenericPdf(Form("corrPdfLLB_%i",i),LLnormB+"*"+afbBpdf,RooArgSet(*cosThetaB, *afbB, *cB1LL, *cB2LL) );
RooAbsPdf * corrPdfDDB = new RooGenericPdf(Form("corrPdfDDB_%i",i),DDnormB+"*"+afbBpdf,RooArgSet(*cosThetaB, *afbB, *cB1DD, *cB2DD) );
TCut cutLL = CutsDef::LLcut + (TCut)curq2cut;
TCut cutDD = CutsDef::DDcut + (TCut)curq2cut;
if(dodata=="genMC")
{
corrPdfLLB = new RooGenericPdf("corrPdfLL",afbBpdf,RooArgSet(*cosThetaB, *afbB, *cB1LL, *cB2LL) );
corrPdfDDB = new RooGenericPdf("corrPdfDD",afbBpdf,RooArgSet(*cosThetaB, *afbB, *cB1DD, *cB2DD) );
corrPdfLL = new RooGenericPdf("corrPdfLL",afbLpdf,RooArgSet(*cosThetaL, *afb, *fL, *c1LL, *c2LL) );
corrPdfDD = new RooGenericPdf("corrPdfDD",afbLpdf,RooArgSet(*cosThetaL, *afb, *fL, *c1DD, *c2DD) );
cutLL = (TCut)curq2cut;
cutDD = (TCut)curq2cut;
}
Analysis * anaLL = new Analysis(Form("LL_mass_%i",i),"Lb",data,&cutLL,MM);
anaLL->AddVariable(cosThetaL);
anaLL->AddVariable(cosThetaB);
anaLL->AddVariable("J_psi_1S_MM");
if(dodata!="data") anaLL->SetWeight(wstr);
RooDataSet * dataLL = anaLL->GetDataSet("-recalc-docuts");
Analysis * anaDD = new Analysis(Form("DD_mass_%i",i),"Lb",data,&cutDD,MM);
anaDD->AddVariable(cosThetaL);
anaDD->AddVariable(cosThetaB);
anaDD->AddVariable("J_psi_1S_MM");
if(dodata!="data") anaDD->SetWeight(wstr);
RooDataSet * dataDD = anaDD->GetDataSet("-recalc-docuts");
RooDataSet * sdataDD, * sdataLL;
if(dodata=="data")
{
sdataLL = anaLL->CalcSweight("",massModel.c_str(),"Exp");
if(printSw) {
GetFrame(MM,NULL,sdataLL,"-nochi2",30,NULL,0,"M(#Lambda#mu#mu) (MeV/c^{2})")->Draw();
ceff->Print("Mass_LL_sWeighted"+q2name+".pdf");
GetFrame(cosThetaL,NULL,sdataLL,"-nochi2",6,NULL,0,"cos#theta_{l}")->Draw();
ceff->Print("cosThetaL_LL_sWeighted"+q2name+".pdf");
GetFrame(cosThetaL,NULL,dataLL,"-nochi2",6,NULL,0,"cos#theta_{l}")->Draw();
ceff->Print("cosThetaL_LL_"+q2name+".pdf");
}
sdataDD = anaDD->CalcSweight("",massModel.c_str(),"Exp");
if(printSw) {
GetFrame(MM,NULL,sdataDD,"-nochi2",30,NULL,0,"M(#Lambda#mu#mu) (MeV/c^{2})")->Draw();
ceff->Print("Mass_DD_sWeighted"+q2name+".pdf");
GetFrame(cosThetaL,NULL,sdataDD,"-nochi2",10,NULL,0,"cos#theta_{l}")->Draw();
ceff->Print("cosThetaL_DD_sWeighted"+q2name+".pdf");
GetFrame(cosThetaL,NULL,dataDD,"-nochi2",10,NULL,0,"cos#theta_{l}")->Draw();
ceff->Print("cosThetaL_DD_"+q2name+".pdf");
}
}
else { sdataLL = dataLL; sdataDD = dataDD; }
histFile->cd();
TTree * LLTree = (TTree*)sdataLL->tree();
LLTree->SetName(Form("treeLL_%i",i));
LLlist->Add(LLTree);
TTree * DDTree = (TTree*)sdataDD->tree();
DDTree->SetName(Form("treeDD_%i",i));
DDlist->Add(DDTree);
// CREATE COMBINED DATASET
RooDataSet * combData;
if(dodata=="data") combData = new RooDataSet(Form("combData_%i",i),"combined data",RooArgSet(*cosThetaL,*cosThetaB,*nsig_sw),Index(*samples),Import("DD",*sdataDD),Import("LL",*sdataLL),WeightVar("nsig_sw"));
else combData = new RooDataSet(Form("combData_%i",i),"combined data",RooArgSet(*cosThetaL,*cosThetaB,*MCweight),Index(*samples),Import("DD",*sdataDD),Import("LL",*sdataLL),WeightVar(wstr));
// FIT COS LEPTON
RooSimultaneous * combModel = new RooSimultaneous(Form("combModel_%i",i),"",*samples);
combModel->addPdf(*corrPdfLL,"LL");
combModel->addPdf(*corrPdfDD,"DD");
combModel->fitTo(*combData,PrintLevel(-1),Verbose(kFALSE),SumW2Error(kTRUE));
if(fitsingle) corrPdfLL->fitTo(*sdataLL,PrintLevel(-1),Verbose(kFALSE),SumW2Error(kTRUE));
GetFrame(cosThetaL,corrPdfLL,sdataLL,"-sumW2err-nochi2-noCost",6,NULL,0,"cos#theta_{l}")->Draw();
ceff->Print("Afb_LL_"+q2name+".pdf");
if(fitsingle) corrPdfDD->fitTo(*sdataDD,PrintLevel(-1),Verbose(kFALSE),SumW2Error(kTRUE));
GetFrame(cosThetaL,corrPdfDD,sdataDD,"-sumW2err-nochi2-noCost",10,NULL,0,"cos#theta_{l}")->Draw();
ceff->Print("Afb_DD_"+q2name+".pdf");
Afb_vs_q2->SetPoint(i,(q2max[i] + q2min[i])/2.,afb->getVal());
Afb_vs_q2->SetPointError(i,(q2max[i] - q2min[i])/2.,afb->getError());
fL_vs_q2->SetPoint(i,(q2max[i] + q2min[i])/2.,fL->getVal());
fL_vs_q2->SetPointError(i,(q2max[i] - q2min[i])/2.,fL->getError());
// FIT COS HADRON
RooSimultaneous * combModelB = new RooSimultaneous(Form("combModelB_%i",i),"",*samples);
combModelB->addPdf(*corrPdfLLB,"LL");
combModelB->addPdf(*corrPdfDDB,"DD");
combModelB->fitTo(*combData,PrintLevel(-1),Verbose(kFALSE),SumW2Error(kTRUE));
if(fitsingle) corrPdfLLB->fitTo(*sdataLL,PrintLevel(-1),Verbose(kFALSE),SumW2Error(kTRUE));
GetFrame(cosThetaB,corrPdfLLB,sdataLL,"-sumW2err-nochi2-noCost",6,NULL,0,"cos#theta_{#Lambda}")->Draw();
ceff->Print("AfbB_LL_"+q2name+".pdf");
if(fitsingle) corrPdfDDB->fitTo(*sdataDD,PrintLevel(-1),Verbose(kFALSE),SumW2Error(kTRUE));
GetFrame(cosThetaB,corrPdfDDB,sdataDD,"-sumW2err-nochi2-noCost",10,NULL,0,"cos#theta_{#Lambda}")->Draw();
ceff->Print("AfbB_DD_"+q2name+".pdf");
AfbB_vs_q2->SetPoint(i,(q2max[i] + q2min[i])/2.,afbB->getVal());
AfbB_vs_q2->SetPointError(i,(q2max[i] - q2min[i])/2.,afbB->getError());
cout << endl << fixed << setprecision(6) << "AfbB = " << afbB->getVal() << " +/- " << afbB->getError() << endl;
cout << "Afb = " << afb->getVal() << " +/- " << afb->getError() << endl;
cout << "fL = " << fL->getVal() << " +/- " << fL->getError() << endl;
cout << endl;
cout << "------------------------ FELDMAN AND COUSINS ------------------------" << endl;
vector < RooDataSet * > datas;
vector < RooAbsPdf * > pdfs, pdfsB;
vector < TString > cat;
cat.push_back("LL");
cat.push_back("DD");
datas.push_back(sdataLL);
datas.push_back(sdataDD);
RooArgSet * origPars = new RooArgSet();
origPars->add(*origafb);
origPars->add(*origfL);
pdfs.push_back(corrPdfLL);
pdfs.push_back(corrPdfDD);
vector< double > afb_err, afbB_err, fL_err;
/*
double fLval = fL->getVal(), fLerr = fL->getError();
FeldmanCousins * FC = new FeldmanCousins(q2name,cat,datas,pdfs,cosThetaL,afb,"nsig_sw");
//FC->SetNPointsToScan(20);
//FC->SetNExp(1000);
if(q2min[i]==18) afb_err = FC->ExtractLimits(origPars,-0.3,0.3);
else if( (afb->getVal()-1.4*afb->getError()) > -1 && (afb->getVal()+1.4*afb->getError()) < 1 )
afb_err = FC->ExtractLimits(origPars,afb->getVal()-1.4*afb->getError(),afb->getVal()+1.4*afb->getError());
else afb_err = FC->ExtractLimits(origPars,-0.4,0.4);
//FeldmanCousins * FCfL = new FeldmanCousins(q2name,cat,datas,pdfs,cosThetaL,fL,"nsig_sw");
//if(q2min[i]==11) fL_err = FCfL->ExtractLimits(origPars,0.,0.6);
//else if (q2min[i]==18) fL_err = FCfL->ExtractLimits(origPars,0.75,0.992);
//( (fLval-1.3*fLerr) > 0 && (fLval+1.3*fLerr) <= 1 )
//else fL_err = FCfL->ExtractLimits(origPars,fLval-1.3*fLerr,fLval+1.3*fLerr);
afb_errs.push_back(afb_err);
//fL_errs.push_back(fL_err);
RooArgSet * origParsB = new RooArgSet();
origParsB->add(*origafbB);
pdfsB.push_back(corrPdfLLB);
pdfsB.push_back(corrPdfDDB);
FeldmanCousins * FCB = new FeldmanCousins(q2name,cat,datas,pdfsB,cosThetaB,afbB,"nsig_sw");
if( (afbB->getVal()-1.5*afbB->getError()) > -1 && (afbB->getVal()+1.5*afbB->getError()) < 1 )
afbB_err = FCB->ExtractLimits(origParsB,afbB->getVal()-1.5*afbB->getError(),afbB->getVal()+1.5*afbB->getError());
else afbB_err = FCB->ExtractLimits(origParsB,-0.4,0.4);
afbB_errs.push_back(afbB_err);
*/
delete effDD;
delete effLL;
delete effLLB;
delete effDDB;
}
cDD->Print("DDeff.pdf");
cLL->Print("LLeff.pdf");
cDDB->Print("DDBeff.pdf");
cLLB->Print("LLBeff.pdf");
Afb_vs_q2->GetXaxis()->SetTitle("q^{2}");
Afb_vs_q2->GetYaxis()->SetTitle("Afb");
Afb_vs_q2->SetMaximum(1);
Afb_vs_q2->SetMinimum(-1);
Afb_vs_q2->Draw("AP");
ceff->Print("Afb_vs_q2.pdf");
AfbB_vs_q2->GetXaxis()->SetTitle("q^{2}");
AfbB_vs_q2->GetYaxis()->SetTitle("AfbB");
AfbB_vs_q2->SetMaximum(1);
AfbB_vs_q2->SetMinimum(-1);
AfbB_vs_q2->Draw("AP");
ceff->Print("AfbB_vs_q2.pdf");
fL_vs_q2->GetXaxis()->SetTitle("q^{2}");
fL_vs_q2->GetYaxis()->SetTitle("fL");
fL_vs_q2->Draw("AP");
ceff->Print("fL_vs_q2.pdf");
for(int bb = 0; bb < Afb_vs_q2->GetN(); bb++)
{
double qq, qqerr, afbv, afbBv, fLv;
Afb_vs_q2->GetPoint(bb,qq,afbv);
qqerr = Afb_vs_q2->GetErrorX(bb);
AfbB_vs_q2->GetPoint(bb,qq,afbBv);
fL_vs_q2->GetPoint(bb,qq,fLv);
cout << fixed << setprecision(1) << qq-qqerr << " - " << qq+qqerr;
cout << fixed << setprecision(4);
//cout << " & $" << afbv << "_{-" << TMath::Abs(afb_errs[bb][0] - afbv) << "}^{+" << TMath::Abs(afb_errs[bb][1] - afbv) << "} \\text{(stat)} \\pm \\text{(sys)}$ ";
//cout << " & $" << afbBv << "_{-" << TMath::Abs(afbB_errs[bb][0] - afbBv) << "}^{+" << TMath::Abs(afbB_errs[bb][1]-afbBv) << "} \\text{(stat)} \\pm \\text{(sys)}$ " ;
//cout << " & $" << fLv << "_{-" << TMath::Abs(fL_errs[bb][0] - fLv) << "}^{+" << TMath::Abs(fL_errs[bb][1] - fLv) << "} \\text{(stat)} \\pm \\text{(sys)}$ ";
cout << " \\\\ " << endl;
}
histFile->cd();
TTree * finalLLtree = (TTree*)TTree::MergeTrees(LLlist);
TTree * finalDDtree = (TTree*)TTree::MergeTrees(DDlist);
finalLLtree->SetName("LL_data");
finalDDtree->SetName("DD_data");
finalLLtree->Write();
finalDDtree->Write();
delete ceff;
histFile->Write();
delete histFile;
}
int main(int argc, char **argv)
{
bool printeff = true;
string fc = "none";
gROOT->ProcessLine(".x lhcbStyle.C");
if(argc > 1)
{
for(int a = 1; a < argc; a++)
{
string arg = argv[a];
string str = arg.substr(2,arg.length()-2);
if(arg.find("-E")!=string::npos) fc = str;
if(arg=="-peff") printeff = true;
}
}
int nexp = 100;
int nbins = 6;
double q2min[] = {8.,15.,11.0,15,16,18};
double q2max[] = {11.,20.,12.5,16,18,20};
TString datafilename = "/afs/cern.ch/work/p/pluca/weighted/Lmumu/candLb.root";
TreeReader * data = new TreeReader("candLb2Lmumu");
data->AddFile(datafilename);
TreeReader * datajpsi = new TreeReader("candLb2JpsiL");
datajpsi->AddFile(datafilename);
TFile * histFile = new TFile("Afb_bkgSys.root","recreate");
string options = "-quiet-noPlot-lin-stdAxis-XM(#Lambda#mu#mu) (MeV/c^{2})-noCost-noParams";
Analysis::SetPrintLevel("s");
RooRealVar * cosThetaL = new RooRealVar("cosThetaL","cosThetaL",0.,-1.,1.);
RooRealVar * cosThetaB = new RooRealVar("cosThetaB","cosThetaB",0.,-1.,1.);
RooRealVar * MM = new RooRealVar("Lb_MassConsLambda","Lb_MassConsLambda",5621.,5400.,6000.);
MM->setRange("Signal",5600,5640);
RooMsgService::instance().setGlobalKillBelow(RooFit::ERROR);
//TGraphAsymmErrors * fL_vs_q2 = new TGraphAsymmErrors();
//TCanvas * ceff = new TCanvas();
RooCategory * samples = new RooCategory("samples","samples");
samples->defineType("DD");
samples->defineType("LL");
RooRealVar * afb = new RooRealVar("afb","afb",0.,-0.75,0.75);
RooRealVar * fL = new RooRealVar("fL","fL",0.6,0.,1.);
TString afbLpdf = "((3./8.)*(1.-fL)*(1 + TMath::Power(cosThetaL,2)) + afb*cosThetaL + (3./4.)*fL*(1 - TMath::Power(cosThetaL,2)))";
RooRealVar * afbB = new RooRealVar("afbB","afbB",0.,-0.5,0.5);
TString afbBpdf = "(1 + 2*afbB*cosThetaB)";
RooAbsPdf * teoPdf = new RooGenericPdf("teoPdf",afbLpdf,RooArgSet(*cosThetaL,*afb,*fL));
RooAbsPdf * teoPdfB = new RooGenericPdf("teoPdfB",afbBpdf,RooArgSet(*cosThetaB,*afbB));
TreeReader * mydata = datajpsi;
Str2VarMap jpsiParsLL = getJpsiPars("LL", CutsDef::LLcut, histFile);
Str2VarMap jpsiParsDD = getJpsiPars("DD", CutsDef::DDcut, histFile);
vector<TH1 *> fLsysh, afbsysh, afbBsysh, fLsysh_frac, afbsysh_frac, afbBsysh_frac;
for(int i = 0; i < nbins; i++)
{
TString q2name = ((TString)Form("q2_%4.2f_%4.2f",q2min[i],q2max[i])).ReplaceAll(".","");
if(i>0) { mydata = data; MM->setRange(5400,6000); }
else { q2name = "jpsi"; MM->setRange(5500,5850); }
TString curq2cut = Form("TMath::Power(J_psi_1S_MM/1000,2) >= %e && TMath::Power(J_psi_1S_MM/1000,2) < %e",q2min[i],q2max[i]);
cout << "------------------- q2 bin: " << q2min[i] << " - " << q2max[i] << " -----------------------" << endl;
/** GET AND FIT EFFICIENCIES **/
RooAbsPdf * effDDpdf = NULL, * effLLpdf = NULL, * effLLBpdf = NULL, * effDDBpdf = NULL;
getEfficiencies(q2min[i],q2max[i],&effLLpdf,&effDDpdf,&effLLBpdf,&effDDBpdf,printeff);
cout << "Efficiencies extracted" << endl;
histFile->cd();
/** FIT AFB **/
afb->setVal(0);
afbB->setVal(-0.37);
fL->setVal(0.6);
RooAbsPdf * corrPdfLL = new RooProdPdf("sigPdfLL"+q2name,"corrPdfLL",*teoPdf,*effLLpdf);
RooAbsPdf * corrPdfDD = new RooProdPdf("sigPdfDD"+q2name,"corrPdfDD",*teoPdf,*effDDpdf);
RooAbsPdf * corrPdfLLB = new RooProdPdf("sigPdfLLB"+q2name,"corrPdfLLB",*teoPdfB,*effLLBpdf);
RooAbsPdf * corrPdfDDB = new RooProdPdf("sigPdfDDB"+q2name,"corrPdfDDB",*teoPdfB,*effDDBpdf);
TCut baseCut = "";
TCut cutLL = CutsDef::LLcut + (TCut)curq2cut + baseCut;
TCut cutDD = CutsDef::DDcut + (TCut)curq2cut + baseCut;
histFile->cd();
double fracDDv[2], fracLLv[2];
double nsigDD, nsigLL;
RooDataSet * dataLL = getDataAndFrac("LL",q2name,mydata,cutLL,MM,&fracLLv[0],jpsiParsLL,&nsigLL);
RooDataSet * dataDD = getDataAndFrac("DD",q2name,mydata,cutDD,MM,&fracDDv[0],jpsiParsDD,&nsigDD);
double nevts = nsigDD+nsigLL;
cout << fixed << setprecision(3) << fracDDv[0] << " " << fracDDv[1] << endl;
RooRealVar * fracLL = new RooRealVar("fracLL","fracLL",fracLLv[0]);
RooRealVar * fracDD = new RooRealVar("fracDD","fracDD",fracDDv[0]);
RooAbsPdf * bkgLL = NULL, * bkgLLB = NULL, * bkgDD = NULL, * bkgDDB = NULL;
buildBkgPdfs(q2min[i],q2max[i],"LL",CutsDef::LLcut,&bkgLL,&bkgLLB);
buildBkgPdfs(q2min[i],q2max[i],"DD",CutsDef::DDcut,&bkgDD,&bkgDDB);
cout << "Backgrounds extracted" << endl;
RooAbsPdf * modelLL = new RooAddPdf("modelLL","modelLL",RooArgSet(*corrPdfLL,*bkgLL),*fracLL);
RooAbsPdf * modelDD = new RooAddPdf("modelDD","modelDD",RooArgSet(*corrPdfDD,*bkgDD),*fracDD);
RooAbsPdf * modelLLB = new RooAddPdf("modelLLB","modelLLB",RooArgSet(*corrPdfLLB,*bkgLLB),*fracLL);
RooAbsPdf * modelDDB = new RooAddPdf("modelDDB","modelDDB",RooArgSet(*corrPdfDDB,*bkgDDB),*fracDD);
// CREATE COMBINED DATASET
RooDataSet * combData = new RooDataSet(Form("combData_%i",i),"combined data",RooArgSet(*MM,*cosThetaL,*cosThetaB),Index(*samples),Import("DD",*dataDD),Import("LL",*dataLL));
Str2VarMap params;
params["fL"] = fL;
params["afb"] = afb;
Str2VarMap paramsB;
paramsB["afbB"] = afbB;
// FIT COS LEPTON
RooSimultaneous * combModel = new RooSimultaneous(Form("combModel_%i",i),"",*samples);
combModel->addPdf(*modelLL,"LL");
combModel->addPdf(*modelDD,"DD");
RooFitResult * res = safeFit(combModel,combData,params,&isInAllowedArea);
// FIT COS HADRON
RooSimultaneous * combModelB = new RooSimultaneous(Form("combModelB_%i",i),"",*samples);
combModelB->addPdf(*modelLLB,"LL");
combModelB->addPdf(*modelDDB,"DD");
RooFitResult * resB = safeFit(combModelB,combData,paramsB,&isInAllowedAreaB);
cout << endl << fixed << setprecision(6) << "AfbB = " << afbB->getVal() << " +/- " << afbB->getError() << endl;
cout << "Afb = " << afb->getVal() << " +/- " << afb->getError() << endl;
cout << "fL = " << fL->getVal() << " +/- " << fL->getError() << endl;
cout << endl;
cout << "lepton: " << res->edm() << " " << res->covQual() << endl;
cout << "baryon: " << resB->edm() << " " << resB->covQual() << endl;
cout << endl;
TH1F * fLsys = new TH1F(Form("fLsys_%i",i),"fLsys",40,-1,1);
TH1F * afbsys = new TH1F(Form("afbsys_%i",i),"afbsys",40,-1,1);
TH1F * afbBsys = new TH1F(Form("afbBsys_%i",i),"afbBsys",40,-1,1);
TH1F * fLsys_frac = new TH1F(Form("fLsys_frac%i",i),"fLsys",40,-1,1);
TH1F * afbsys_frac = new TH1F(Form("afbsys_frac%i",i),"afbsys",40,-1,1);
TH1F * afbBsys_frac = new TH1F(Form("afbBsys_frac%i",i),"afbBsys",40,-1,1);
RooAbsPdf * mybkgDD_2 = NULL, * mybkgDDB_2 = NULL;
buildBkgPdfs(q2min[i],q2max[i],"DD",CutsDef::DDcut,&mybkgDD_2,&mybkgDDB_2,"RooKeyPdf");
//cout << nevts << endl;
//TRandom3 r(0);
for(int e = 0; e < nexp; e++)
{
histFile->cd();
RooAbsPdf * toypdf = (RooAbsPdf *)modelDD->Clone();
Analysis * toy = new Analysis("toy",cosThetaL,modelDD,nevts);
RooAbsPdf * toypdfB = (RooAbsPdf *)modelDDB->Clone();
Analysis * toyB = new Analysis("toyB",cosThetaB,modelDDB,nevts);
afb->setVal(0);
afbB->setVal(-0.37);
fL->setVal(0.6);
safeFit(toypdf,toy->GetDataSet("-recalc"),params,&isInAllowedArea);
safeFit(toypdfB,toyB->GetDataSet("-recalc"),paramsB,&isInAllowedAreaB);
double def_afb = afb->getVal();
double def_fL = fL->getVal();
double def_afbB = afbB->getVal();
afb->setVal(0);
afbB->setVal(-0.37);
fL->setVal(0.6);
RooAbsPdf * modelDD_2 = new RooAddPdf("modelDD_2","modelDD",RooArgSet(*corrPdfDD,*mybkgDD_2),*fracDD);
RooAbsPdf * modelDDB_2 = new RooAddPdf("modelDDB_2","modelDDB",RooArgSet(*corrPdfDDB,*mybkgDDB_2),*fracDD);
safeFit(modelDD_2,toy->GetDataSet("-recalc"),params,&isInAllowedArea);
safeFit(modelDDB_2,toyB->GetDataSet("-recalc"),paramsB,&isInAllowedAreaB);
double oth_afb = afb->getVal();
double oth_fL = fL->getVal();
double oth_afbB = afbB->getVal();
fLsys->Fill(oth_fL-def_fL);
afbsys->Fill(oth_afb-def_afb);
afbBsys->Fill(oth_afbB-def_afbB);
afb->setVal(0.);
afbB->setVal(-0.37);
fL->setVal(0.6);
//double rdm_frac = r.Gaus(fracDDv[0],fracDDv[1]);
double rdm_frac = fracDDv[0] + fracDDv[1];
RooRealVar * fracDD_2 = new RooRealVar("fracDD_2","fracDD_2",rdm_frac);
RooAbsPdf * modelDD_3 = new RooAddPdf("modelDD_3","modelDD",RooArgSet(*corrPdfDD,*bkgDD),*fracDD_2);
RooAbsPdf * modelDDB_3 = new RooAddPdf("modelDDB_3","modelDDB",RooArgSet(*corrPdfDDB,*bkgDDB),*fracDD_2);
safeFit(modelDD_3,toy->GetDataSet("-recalc"),params,&isInAllowedArea);
safeFit(modelDDB_3,toyB->GetDataSet("-recalc"),paramsB,&isInAllowedAreaB);
double frc_afb = afb->getVal();
double frc_fL = fL->getVal();
double frc_afbB = afbB->getVal();
fLsys_frac->Fill(frc_fL-def_fL);
afbsys_frac->Fill(frc_afb-def_afb);
afbBsys_frac->Fill(frc_afbB-def_afbB);
}
afbsysh.push_back(afbsys);
afbBsysh.push_back(afbBsys);
fLsysh.push_back(fLsys);
afbsysh_frac.push_back(afbsys_frac);
afbBsysh_frac.push_back(afbBsys_frac);
fLsysh_frac.push_back(fLsys_frac);
}
for(int q = 0; q < nbins; q++)
{
cout << fixed << setprecision(2) << "-------- Bin " << q2min[q] << "-" << q2max[q] << endl;
cout << fixed << setprecision(5) << "fL sys = " << fLsysh[q]->GetMean() << " +/- " << fLsysh[q]->GetMeanError() << endl;
cout << "Afb sys = " << afbsysh[q]->GetMean() << " +/- " << afbsysh[q]->GetMeanError() << endl;
cout << "AfbB sys = " << afbBsysh[q]->GetMean() << " +/- " << afbBsysh[q]->GetMeanError() << endl;
}
cout << "#################################################################" << endl;
for(int q = 0; q < nbins; q++)
{
cout << fixed << setprecision(2) << "-------- Bin " << q2min[q] << "-" << q2max[q] << endl;
cout << fixed << setprecision(5) << "fL sys = " << fLsysh_frac[q]->GetMean() << " +/- " << fLsysh_frac[q]->GetMeanError() << endl;
cout << "Afb sys = " << afbsysh_frac[q]->GetMean() << " +/- " << afbsysh_frac[q]->GetMeanError() << endl;
cout << "AfbB sys = " << afbBsysh_frac[q]->GetMean() << " +/- " << afbBsysh_frac[q]->GetMeanError() << endl;
}
cout << "#################################################################" << endl;
for(int q = 0; q < nbins; q++)
{
cout << fixed << setprecision(2) << "-------- Bin " << q2min[q] << "-" << q2max[q] << endl;
cout << fixed << setprecision(5) << "fL sys = " << TMath::Sqrt(TMath::Power(fLsysh_frac[q]->GetMean(),2) + TMath::Power(fLsysh[q]->GetMean(),2) ) << endl;
cout << "Afb sys = " << TMath::Sqrt(TMath::Power(afbsysh_frac[q]->GetMean(),2) + TMath::Power(afbsysh[q]->GetMean(),2) ) << endl;
cout << "AfbB sys = " << TMath::Sqrt(TMath::Power(afbBsysh_frac[q]->GetMean(),2) + TMath::Power(afbBsysh[q]->GetMean(),2) ) << endl;
}
}
int main() {
bool recutdata=false;
bool recutmc=false;
bool remakedatasets=false;
std::vector<std::string> VariablesToCompare= {"gamma_CL","nSPDHits","Bu_DIRA_OWNPV","Bu_M01"};
auto BranchesToKeepMC = ControlCuts::BranchesToKeep;
for(auto branch : VariablesToCompare) {
if (std::find(BranchesToKeepMC.begin(),BranchesToKeepMC.end(),branch)==std::end(BranchesToKeepMC)) {
BranchesToKeepMC.push_back(std::move(branch));
}
}
auto BranchesToKeep = ControlCuts::BranchesToKeep;
for(auto branch : VariablesToCompare) {
if (std::find(BranchesToKeep.begin(),BranchesToKeep.end(),branch)==std::end(BranchesToKeep)) {
BranchesToKeep.push_back(std::move(branch));
}
}
if(recutdata) {
DataFile TwelA(std::getenv("BUKETAPDATAROOT"),Data,Twel,MagAll,buketap,"TriggerCut_SampleA");
DataFile TwelB(std::getenv("BUKETAPDATAROOT"),Data,Twel,MagAll,buketap,"TriggerCut_SampleB");
DataFile ElevA(std::getenv("BUKETAPDATAROOT"),Data,Elev,MagAll,buketap,"TriggerCut_SampleA");
DataFile ElevB(std::getenv("BUKETAPDATAROOT"),Data,Elev,MagAll,buketap,"TriggerCut_SampleB");
TreeReader* TwelReader = new TreeReader("DecayTree");
TwelReader->AddFile(TwelA);
TwelReader->AddFile(TwelB);
TreeReader* ElevReader = new TreeReader("DecayTree");
ElevReader->AddFile(ElevA);
ElevReader->AddFile(ElevB);
TwelReader->Initialize(BranchesToKeep,"names");
ElevReader->Initialize(BranchesToKeep,"names");
auto TwelMinimalFile=std::make_unique<TFile>("TwelMinimalFile.root","RECREATE");
TTree* TwelMinimalTree=TwelReader->CopyTree("gamma_CL>0.1",-1,"DecayTree");
TwelMinimalTree->Write();
auto ElevMinimalFile=std::make_unique<TFile>("ElevMinimalFile.root","RECREATE");
TTree* ElevMinimalTree=ElevReader->CopyTree("gamma_CL>0.1",-1,"DecayTree");
ElevMinimalTree->Write();
}
if(recutmc) {
DataFile MCTwel(std::getenv("BUKETAPMCROOT"),MC,Twel,MagAll,buketap,"TriggerCut");
DataFile MCElev(std::getenv("BUKETAPMCROOT"),MC,Elev,MagAll,buketap,"TriggerCut");
TreeReader* TwelReaderMC = new TreeReader("DecayTree");
TwelReaderMC->AddFile(MCTwel);
TreeReader* ElevReaderMC = new TreeReader("DecayTree");
ElevReaderMC->AddFile(MCElev);
TwelReaderMC->Initialize(BranchesToKeepMC,"names");
ElevReaderMC->Initialize(BranchesToKeepMC,"names");
auto TwelMinimalFileMC=std::make_unique<TFile>("TwelMinimalFileMC.root","RECREATE");
TTree* TwelMinimalTreeMC=TwelReaderMC->CopyTree("gamma_CL>0.1",-1,"DecayTree");
TwelMinimalTreeMC->Write();
auto ElevMinimalFileMC=std::make_unique<TFile>("ElevMinimalFileMC.root","RECREATE");
TTree* ElevMinimalTreeMC=ElevReaderMC->CopyTree("gamma_CL>0.1",-1,"DecayTree");
ElevMinimalTreeMC->Write();
}
if(remakedatasets||recutmc||recutdata) {
RooArgSet* MCVars= new RooArgSet("MCVars");
RooArgSet* Vars= new RooArgSet("Vars");
for(auto & Branch : BranchesToKeep) {
Vars->add(*(HandyFunctions::CreateRealVar(Branch)));
}
for(auto & MCBranch: BranchesToKeepMC) {
MCVars->add(*(HandyFunctions::CreateRealVar(MCBranch)));
std::cout<<MCBranch<<std::endl;
}
auto TwelMinimalFile = std::make_unique<TFile>("TwelMinimalFile.root");
TTree* TwelMinimalTree=(TTree*)TwelMinimalFile->Get("DecayTree");
std::cout<<"Tree Entreies = "<<TwelMinimalTree->GetEntries()<<std::endl;
RooDataSet* TwelData= new RooDataSet("TwelData","TwelData",*Vars,Import(*TwelMinimalTree));
std::cout<<"Events in Dataset= "<<TwelData->sumEntries()<<std::endl;
auto ElevMinimalFile = std::make_unique<TFile>("ElevMinimalFile.root");
TTree* ElevMinimalTree=(TTree*)ElevMinimalFile->Get("DecayTree");
std::cout<<"Tree Entreies = "<<ElevMinimalTree->GetEntries()<<std::endl;
RooDataSet* ElevData= new RooDataSet("ElevData","ElevData",*Vars,Import(*ElevMinimalTree));
std::cout<<"Events in Dataset= "<<ElevData->sumEntries()<<std::endl;
auto TwelMinimalFileMC = std::make_unique<TFile>("TwelMinimalFileMC.root");
TTree* TwelMinimalTreeMC=(TTree*)TwelMinimalFileMC->Get("DecayTree");
std::cout<<"Tree Entreies = "<<TwelMinimalTreeMC->GetEntries()<<std::endl;
RooDataSet* TwelDataMC= new RooDataSet("TwelDataMC","TwelDataMC",*Vars,Import(*TwelMinimalTreeMC));
std::cout<<"Events in Dataset= "<<TwelDataMC->sumEntries()<<std::endl;
auto ElevMinimalFileMC = std::make_unique<TFile>("ElevMinimalFileMC.root");
TTree* ElevMinimalTreeMC=(TTree*)ElevMinimalFileMC->Get("DecayTree");
std::cout<<"Tree Entreies = "<<ElevMinimalTreeMC->GetEntries()<<std::endl;
RooDataSet* ElevDataMC= new RooDataSet("ElevDataMC","ElevDataMC",*Vars,Import(*ElevMinimalTreeMC));
std::cout<<"Events in Dataset= "<<ElevDataMC->sumEntries()<<std::endl;
TwelMinimalFile->Close();
ElevMinimalFile->Close();
TwelMinimalFileMC->Close();
ElevMinimalFileMC->Close();
auto DataSetCache=std::make_unique<TFile>("DataSetCache.root","RECREATE");
gDirectory->pwd();
TwelData->Write();
ElevData->Write();
TwelDataMC->Write();
ElevDataMC->Write();
}
TFile* DataSetCache= new TFile("DataSetCache.root");
RooDataSet* Data12=SafeGetDataSet(DataSetCache,"TwelData");
RooDataSet* Data11=SafeGetDataSet(DataSetCache,"ElevData");
RooDataSet* MC12=SafeGetDataSet(DataSetCache,"TwelDataMC");
RooDataSet* MC11=SafeGetDataSet(DataSetCache,"ElevDataMC");
RooRealVar * BuMass= new RooRealVar("Bu_DTF_MF","Bu_DTF_MF",5000.0,5500.0);
RooRealVar* BkgP1= new RooRealVar("BkgP1","BkgP1",-1.0,-10.0,10.0);
RooRealVar* BkgP2= new RooRealVar("BkgP2","BkgP2",1.0,-10.0,10.0);
RooChebychev* BkgPdf= new RooChebychev("BkgPdf","BkgPdf",*BuMass,RooArgList(*BkgP1,*BkgP2));
BkgPdf->fitTo(*Data12,Range(5000.0,5200.));
RooPlot* BFrame = BuMass->frame(Bins(50));
Data12->plotOn(BFrame);
BkgPdf->plotOn(BFrame);
BkgPdf->paramOn(BFrame);
TCanvas C;
BFrame->Draw();
C.SaveAs("BFrame.pdf");
}
int main(int argc, char * argv[]) {
log_call(argc, argv);
bool datafileset = false; // not used
bool treefileset = false; // not used
bool conffileset = false;
bool logfileset = false;
bool outancfileset = false;
bool outstochtimefileset = false;
bool outstochnumfileset = false;
bool outstochnumanyfileset = false;
bool datawide = false;
bool periodsset = false;
bool dataz = false; //the datafile will have probabilities
char * conff = NULL;
char * treef = NULL;
char * dataf = NULL;
char * logf = NULL;
char * outanc = NULL;
char * outnum = NULL;
char * outnumany = NULL;
char * outtime = NULL;
string periodstring;
vector<string> ptokens;
vector<double> period_times;
while (1) {
int oi = -1;
int c = getopt_long(argc, argv, "d:t:c:o:n:m:a:l:p:hVwz", long_options, &oi);
if (c == -1) {
break;
}
switch(c) {
case 'd':
datafileset = true;
dataf = strdup(optarg);
check_file_exists(dataf);
break;
case 'z':
dataz = true;
datawide = true;
break;
case 'w':
datawide = true;
break;
case 't':
treefileset = true;
treef = strdup(optarg);
check_file_exists(treef);
break;
case 'c':
conffileset = true;
conff = strdup(optarg);
check_file_exists(conff);
break;
case 'o':
outancfileset = true;
outanc = strdup(optarg);
break;
case 'n':
outstochnumfileset = true;
outnum = strdup(optarg);
break;
case 'm':
outstochtimefileset = true;
outtime = strdup(optarg);
break;
case 'a':
outstochnumanyfileset = true;
outnumany = strdup(optarg);
break;
case 'p':
periodsset = true;
periodstring = (strdup(optarg));
parse_comma_list(periodstring, period_times);
break;
case 'l':
logfileset = true;
logf = strdup(optarg);
break;
case 'h':
print_help();
exit(0);
case 'V':
cout << versionline << endl;
exit(0);
default:
print_error(argv[0], (char)c);
exit(0);
}
}
ofstream * logout = NULL;
ostream * loos = NULL;
if (logfileset == true) {
logout = new ofstream(logf);
loos = logout;
} else {
loos = &cout;
}
if (conffileset == false) {
cerr << "right now, you need to have a conf file. to change soon." << endl;
print_help();
exit(0);
}
bool verbose = true;
string outfile_stochnum_any ="";
string ratematrixfile = "";
vector<vector<double> > ratematrix;
bool estimate = true;
map<string,vector<string> > mrcas;
vector<string> stochtime;
vector<string> stochnumber;
vector<string> stochnumber_any;
vector<string> ancstates;
string freeparams = "_one_"; //right now, just _all_ or _one_
/*************
* read the configuration file
**************/
ifstream ifs(conff);
string line;
while (getline(ifs, line)) {
if (line.size() > 1) {
if (strcmp( (&line[0]), "#") != 0) {
//if ((&line[0]) != "#") {
vector<string> tokens;
string del("=");
tokens.clear();
tokenize(line, tokens, del);
for (unsigned int j=0; j < tokens.size(); j++) {
trim_spaces(tokens[j]);
}
if (!strcmp(tokens[0].c_str(), "freeparams")) {
freeparams = tokens[1];
} else if (!strcmp(tokens[0].c_str(), "outstnum_any")) {
outfile_stochnum_any = tokens[1];
} else if (!strcmp(tokens[0].c_str(), "ratematrix")) {
ratematrixfile = tokens[1];
if (ratematrixfile == "d" || ratematrixfile == "D") {
ratematrixfile = "";
}
estimate =false;
} else if (!strcmp(tokens[0].c_str(), "mrca")) {
/*
* need to make sure that the mrca exist in the tree,
* that the names are correct
*/
vector<string> searchtokens;
tokenize(tokens[1], searchtokens, ", ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
}
vector<string> mrc;
for (unsigned int j=1; j < searchtokens.size(); j++) {
mrc.push_back(searchtokens[j]);
}
mrcas[searchtokens[0]] = mrc;
} else if (!strcmp(tokens[0].c_str(), "stochtime")) {
vector<string> searchtokens;
tokenize(tokens[1], searchtokens, ", ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
stochtime.push_back(searchtokens[j]);
}
} else if (!strcmp(tokens[0].c_str(), "stochnumber")) {
vector<string> searchtokens;
tokenize(tokens[1], searchtokens, ", ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
stochnumber.push_back(searchtokens[j]);
}
} else if (!strcmp(tokens[0].c_str(), "stochnumber_any")) {
vector<string> searchtokens;
tokenize(tokens[1], searchtokens, ", ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
stochnumber_any.push_back(searchtokens[j]);
}
} else if (!strcmp(tokens[0].c_str(), "ancstates")) {
vector<string> searchtokens;
tokenize(tokens[1], searchtokens, ", ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
ancstates.push_back(searchtokens[j]);
}
}
}
}
}
if (verbose) {
(*loos) << "finished reading config file" << endl;
}
/**
* read the data file
*/
vector<Sequence> seqs;
Sequence seq;
ifstream * fstr = new ifstream(dataf);
istream * pios = fstr;
line = "";
int ft = test_seq_filetype_stream(*pios,line);
while (read_next_seq_from_stream(*pios,ft,line,seq)) {
//(*loos) << seq.get_sequence() << endl;
seqs.push_back(seq);
}
//fasta has a trailing one
if (ft == 2) {
seqs.push_back(seq);
}
if (verbose) {
(*loos) << "taxa: " << seqs.size() << endl;
}
/**
* read the tree file
*/
TreeReader tr;
vector<Tree *> trees;
ifstream infile2(treef);
if (!infile2) {
cerr << "Could not open treefile." << endl;
return 1;
}
line = "";
while (getline(infile2, line)) {
if (line.length() > 5) {
trees.push_back(tr.readTree(line));
}
}
infile2.close();
if (verbose) {
(*loos) << "trees: "<< trees.size() << endl;
}
/**
* process the data
* datawide means
*
* NOT datawide means
*/
int nstates;
int nsites;
if (datawide) {
if (dataz == false) {
nstates = seqs[0].get_sequence().length();
} else {
vector<string> searchtokens;
tokenize(seqs[0].get_sequence(), searchtokens, ",");
nstates = searchtokens.size();
}
nsites = 1;
} else {
int maxstate=1;
vector<string> searchtokens;
tokenize(seqs[0].get_sequence(), searchtokens, " ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
}
nsites = searchtokens.size();
if (verbose) {
(*loos) << "nsites: " << nsites << endl;
}
for (unsigned int se = 0;se<seqs.size();se++) {
searchtokens = vector<string> ();
tokenize(seqs[se].get_sequence(), searchtokens, " ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
int pos = atoi(searchtokens[j].c_str());
if (pos > maxstate) {
maxstate = pos;
}
}
}
nstates = maxstate+1;//TODO this can be determined by largest number +1
}
if (verbose) {
(*loos) << "total number of states in dataset: " << nstates << endl;
}
//reading ratematrixfile
if (ratematrixfile.size() > 1) {
ratematrix = processRateMatrixConfigFile(ratematrixfile,nstates);
}
//end ratematrixfile
ofstream ancout;
ofstream stnumout;
ofstream sttimeout;
ofstream sttnumout_any;
if (ancstates.size() > 0 && outancfileset == true) {
ancout.open(outanc,ios::out);
ancout << "site\ttree\tMRCA\tlnL";
for (int i=0; i < nstates; i++) {
ancout << "\tstate_" << i+1;
}
ancout << endl;
}
if (stochnumber.size() > 0 && outstochnumfileset == true) {
stnumout.open(outnum,ios::out);
stnumout << "site\ttree\tMRCA\tlnL";
for (int i=0; i < nstates; i++) {
for (int j=0; j < nstates; j++) {
if (i != j) {
stnumout << "\tstate_" << i+1 << "->state_" << j+1;
}
}
}
stnumout << endl;
}
if (stochtime.size() > 0 && outstochtimefileset == true ) {
sttimeout.open(outtime,ios::out);
sttimeout << "site\ttree\tMRCA\tlnL";
for (int i=0; i < nstates; i++) {
sttimeout << "\tstate_" << i+1;
}
sttimeout << endl;
}
if (stochnumber_any.size() > 0 && outstochnumanyfileset == true) {
sttnumout_any.open(outnumany,ios::out);
sttnumout_any << "site\ttree\tMRCA\tlnL";
sttnumout_any << "\tanystate";
sttnumout_any << endl;
}
for (int n = 0; n < nsites; n++) {
(*loos) << "site: " << n+1 << endl;
/*
* this converts the data and is a little long to accomodate datasets
* with sites that don't have all the states but the results can still
* be printed to the same outfile for analysis after
*/
//need to put the data into a wide view
vector<Sequence> runseqs;
int nstates_site_n;
vector<int> existing_states(nstates,0);
if (datawide == false) {
for (unsigned int se = 0;se<seqs.size();se++) {
vector<string> searchtokens;
tokenize(seqs[se].get_sequence(), searchtokens, " ");
for (unsigned int j=0; j < searchtokens.size(); j++) {
trim_spaces(searchtokens[j]);
}
string tseqs(nstates,'0');
if (searchtokens[n]=="?") {
for (int mse = 0; mse < nstates; mse++) {
tseqs.replace(mse,1,"1");
}
} else {
int pos = atoi(searchtokens[n].c_str());
tseqs.replace(pos,1,"1");
}
for (int i=0; i < nstates; i++) {
if (tseqs.at(i) =='1') {
existing_states[i] = 1;
}
}
Sequence tse =Sequence(seqs[se].get_id(),tseqs,true);
runseqs.push_back(tse);
}
nstates_site_n = sum(existing_states);
} else {
runseqs = seqs;
if (dataz == false) {
for (unsigned int se=0; se < seqs.size(); se++) {
for (int i=0; i < nstates; i++) {
if (seqs[se].get_sequence().at(i) =='1') {
existing_states[i] = 1;
}
}
}
nstates_site_n = sum(existing_states);
} else {
for (int i=0; i < nstates; i++) {
existing_states[i] = 1;
}
nstates_site_n = nstates;
}
}
//mapping the existing states to the full states
//int statecnt = 0; // not used
for (int i=nstates-1; i >= 0; i--) {
if (existing_states[i] == 1) {
continue;
} else {
for (unsigned int se=0; se < runseqs.size(); se++) {
runseqs[se].set_sequence(runseqs[se].get_sequence().erase(i,1));
}
}
}
if (verbose) {
(*loos) <<"states: " << nstates_site_n << endl;
(*loos) << "trees: ";
}
for (unsigned int i=0; i < trees.size(); i++) {
if (verbose) {
(*loos) << i << endl;
}
vector<RateModel> rms;
RateModel rm(nstates_site_n);
StateReconstructor sr(rm,rms);
rm.setup_P(0.1,false);
if (periodsset == true) {
rms.push_back(rm);
for (unsigned int p=1; p < period_times.size(); p++) {
RateModel rm2(nstates_site_n);
rm2.setup_P(0.1,false);
rms.push_back(rm2);
}
sr.set_periods(period_times,rms);
}
sr.set_store_p_matrices(false);
Tree * tree = trees[i];
if (verbose) {
(*loos) << "tips: "<< tree->getExternalNodeCount() << endl;
}
sr.set_tree(tree);
if (periodsset == true) {
sr.set_periods_model();
}
//checking that the data and the tree have the same names
if (checkdata(tree,runseqs) == 0) {
exit(0);
}
bool same;
if (dataz == false) {
same = sr.set_tip_conditionals(runseqs);
} else {
same = sr.set_tip_conditionals_already_given(runseqs);
}
if (same == true) {
(*loos) << "skipping calculation" <<endl;
continue;
}
double finallike; Superdouble totlike_sd;
if (periodsset == false) {
mat free_var(nstates_site_n,nstates_site_n);
free_var.fill(0);
int ct = 0;
if (freeparams == "_one_") {
ct = 1;
} else if (freeparams == "_all_") {
ct = 0;
for (int k=0; k < nstates_site_n; k++) {
for (int j=0; j < nstates_site_n; j++) {
if (k != j) {
free_var(k,j) = ct;
ct += 1;
}
}
}
}
if (verbose) {
(*loos) << free_var << endl;
(*loos) << ct << endl;
}
rm.neg_p = false;
cout << "likelihood: " << sr.eval_likelihood() << endl;
//estimating the optimal rates
if (estimate) {//optimize
optimize_sr_nlopt(&rm,&sr,&free_var,ct);
} else { // requires that the ratematrix is available
for (int i=0; i < nstates_site_n; i++) {
for (int j=0; j < nstates_site_n; j++) {
free_var(i,j) = ratematrix[i][j];
}
}
}
//end estimating
if (verbose) {
(*loos) << free_var << endl;
}
rm.setup_Q(free_var);
sr.set_store_p_matrices(true);
finallike = sr.eval_likelihood();
if (verbose) {
(*loos) << "final_likelihood: " << finallike << endl;
}
} else { //optimize with periods
vector<mat> periods_free_var(period_times.size());
int ct = 0;
if (freeparams == "_one_") {
ct = 1;
for (unsigned int s=0; s < period_times.size(); s++) {
mat free_var(nstates_site_n,nstates_site_n);free_var.fill(0);
periods_free_var[s] = free_var;
}
} else if (freeparams == "_all_") {
ct = 0;
for (unsigned int s=0; s < period_times.size(); s++) {
mat free_var(nstates_site_n,nstates_site_n);free_var.fill(0);
for (int k=0; k < nstates_site_n; k++) {
for (int j=0; j < nstates_site_n; j++) {
if (k != j) {
free_var(k, j) = ct;
ct += 1;
}
}
}
periods_free_var[s] = free_var;
}
}
if (verbose) {
for (unsigned int s=0; s < period_times.size(); s++) {
(*loos) << periods_free_var[s] << endl;
}
(*loos) << ct << endl;
}
rm.neg_p = false;
cout << "likelihood: " << sr.eval_likelihood() << endl;
optimize_sr_periods_nlopt(&rms,&sr,&periods_free_var,ct);
if (verbose) {
for (unsigned int s=0; s < period_times.size(); s++) {
(*loos) << periods_free_var[s] << endl;
}
(*loos) << ct << endl;
cout << "////////////////////////" << endl;
}
for (unsigned int s=0; s < period_times.size(); s++) {
rms[s].setup_Q(periods_free_var[s]);
}
sr.set_store_p_matrices(true);
finallike = sr.eval_likelihood();
if (verbose) {
(*loos) << "final_likelihood: " << finallike << endl;
}
cout << "period set and so no ancestral states just yet" << endl;
continue;
}
if (verbose) {
(*loos) << "ancestral states" <<endl;
}
sr.prepare_ancstate_reverse();
for (unsigned int j=0; j < ancstates.size(); j++) {
if (ancstates[j] == "_all_") {
vector<Superdouble> lhoods;
for (int l=0; l < tree->getInternalNodeCount(); l++) {
lhoods = sr.calculate_ancstate_reverse_sd(*tree->getInternalNode(l));
totlike_sd = calculate_vector_Superdouble_sum(lhoods);
//bool neg = false; // not used
int excount = 0;
double highest = 0;
int high = 0;
for (int k=0; k < nstates; k++) {
if (existing_states[k] == 1) {
if (double(lhoods[excount]/totlike_sd) > highest) {
highest= double(lhoods[excount]/totlike_sd);
high = k;
}
excount += 1;
}
}
std::string s;
std::stringstream out;
out << high;
tree->getInternalNode(l)->setName(out.str());
}
ancout << getNewickString(tree) << endl;
} else {
vector<Superdouble> lhoods;
if (verbose) {
(*loos) <<"node: " << tree->getMRCA(mrcas[ancstates[j]])->getName() << "\tmrca: " << ancstates[j] << endl;
}
ancout << n+1 << "\t" << i+1 << "\t" << ancstates[j] << "\t" << finallike;
lhoods = sr.calculate_ancstate_reverse_sd(*tree->getMRCA(mrcas[ancstates[j]]));
totlike_sd = calculate_vector_Superdouble_sum(lhoods);
bool neg = false;
int excount = 0;
for (int k=0; k < nstates; k++) {
if (existing_states[k] == 1) {
if (verbose) {
(*loos) << double(lhoods[excount]/totlike_sd) << " ";//"(" << lhoods[excount] << ") ";
}
ancout << "\t" << double(lhoods[excount]/totlike_sd);
if (double(lhoods[excount]/totlike_sd) < 0)
neg = true;
excount += 1;
} else {
if (verbose) {
(*loos) << "NA" << " ";
ancout << "\t" << "NA";
}
}
}
if (neg == true) {
exit(0);
}
ancout <<endl;
if (verbose) {
(*loos) << endl;
}
}
}
if (verbose) {
(*loos) << endl;
(*loos) << "stochastic time" << endl;
}
for (unsigned int j=0; j < stochtime.size(); j++) {
if (tree->getMRCA(mrcas[stochtime[j]])->isRoot() == false) {
vector<double> lhoods;
if (verbose) {
(*loos) << "mrca: " << stochtime[j] << endl;
}
sttimeout << n+1 << "\t" << i+1 << "\t" << stochtime[j]<< "\t" << finallike;
bool neg = false;
int excount = 0;
for (int k=0; k < nstates; k++) {
if (existing_states[k]==1) {
sr.prepare_stochmap_reverse_all_nodes(excount,excount);
sr.prepare_ancstate_reverse();
vector<double> stoch = sr.calculate_reverse_stochmap(*tree->getMRCA(mrcas[stochtime[j]]),true);
double tnum = sum(stoch)/double(totlike_sd);
double bl = tree->getMRCA(mrcas[stochtime[j]])->getBL();
if (verbose) {
(*loos) << tnum << " ";
}
sttimeout << "\t" << tnum/bl;
if (tnum < 0) {
neg = true;
}
excount += 1;
} else {
if (verbose) {
(*loos) << "NA" << " ";
}
sttimeout << "\t" << "NA";
}
}
sttimeout << endl;
if (verbose) {
(*loos) << endl;
}
if (neg == true) {
exit(0);
}
}
}
if (verbose) {
(*loos) << endl;
(*loos) << "stochastic number" << endl;
}
for (unsigned int j=0; j < stochnumber.size(); j++) {
if (tree->getMRCA(mrcas[stochnumber[j]])->isRoot() == false) {
vector<double> lhoods;
if (verbose) {
(*loos) << "mrca: " << stochnumber[j] << endl;
}
stnumout << n+1 << "\t" << i+1 << "\t" << stochnumber[j]<< "\t" << finallike;
bool neg = false;
int excount = 0;
for (int k=0; k < nstates; k++) {
if (existing_states[k]==1) {
int excount2 = 0;
for (int l=0; l < nstates; l++) {
if (existing_states[l] == 1) {
if (k == l) {
if (verbose) {
(*loos) << " - ";
}
} else {
sr.prepare_stochmap_reverse_all_nodes(excount,excount2);
sr.prepare_ancstate_reverse();
vector<double> stoch = sr.calculate_reverse_stochmap(*tree->getMRCA(mrcas[stochnumber[j]]),false);
double tnum = sum(stoch)/totlike_sd;
if (verbose) {
(*loos) << tnum << " ";
}
stnumout << "\t" << tnum;
if (tnum < 0) {
neg = true;
}
}
excount2 += 1;
} else {
if (verbose) {
(*loos) << "NA" << " ";
}
stnumout << "\t" << "NA";
}
}
if (verbose) {
(*loos) << endl;
}
excount += 1;
} else {
for (int l=0; l < nstates; l++) {
if (k == l) {
if (verbose) {
(*loos) << " - ";
}
} else {
if (verbose) {
(*loos) << "NA" << " ";
}
stnumout << "\t" << "NA";
}
}
if (verbose) {
(*loos) << endl;
}
}
}
stnumout << endl;
if (verbose) {
(*loos) << endl;
}
if (neg == true) {
exit(0);
}
}
}
if (verbose) {
(*loos) << endl;
}
if (verbose) {
(*loos) << "stochastic number (any)" << endl;
}
if (stochnumber_any.size() > 0) {
sr.prepare_stochmap_reverse_all_nodes_all_matrices();
sr.prepare_ancstate_reverse();
}
for (unsigned int j=0; j < stochnumber_any.size(); j++) {
if (tree->getMRCA(mrcas[stochnumber_any[j]])->isRoot() == false) {
vector<double> lhoods;
if (verbose) {
(*loos) <<"node: " << tree->getMRCA(mrcas[stochnumber_any[j]])->getName() << " mrca: " << stochnumber_any[j] << endl;
}
sttnumout_any << n+1 << "\t" << i+1 << "\t" << stochnumber_any[j]<< "\t" << finallike;
vector<double> stoch = sr.calculate_reverse_stochmap(*tree->getMRCA(mrcas[stochnumber_any[j]]),false);
double tnum = sum(stoch)/totlike_sd;
//(*loos) << sum(stoch)<< " "<<totlike << endl;
if (verbose) {
(*loos) << tnum << " " ;
}
sttnumout_any << "\t" << tnum;
sttnumout_any << endl;
if (verbose) {
(*loos) << endl;
}
}
}
//delete tree;
}
}
if (ancstates.size() > 0 && outancfileset == true) {
ancout.close();
}
if (stochnumber.size() > 0) {
stnumout.close();
}
if (stochtime.size() > 0) {
sttimeout.close();
}
if (logfileset) {
logout->close();
delete loos;
}
return EXIT_SUCCESS;
}
int main(int argc, char** argv)
{
string dataType = "12";
//if(argc > 1) if((string)argv[1] == "11") dataType = "11";
NeuroBayesTeacher* nb = NeuroBayesTeacher::Instance();
nb->NB_DEF_TASK("CLASSIFICATION");
//setup network topology
int nvar = 20; // Set this to number of inputs to your NN
char ** varnames = new char*[nvar];
varnames[0] = "chi2_DTF";
varnames[1] = "Lb_TAU";
varnames[2] = "Lb_DIRA_OWNPV";
varnames[3] = "Lb_IPCHI2_OWNPV";
varnames[4] = "max_mu_IPCHI2_OWNPV";
varnames[5] = "min_mu_TRACKCHI2";
varnames[6] = "min_mu_PID";
varnames[7] = "min_mu_PID";
varnames[8] = "LL_Lambda0_IPCHI2_OWNPV";
varnames[9] = "LL_Lambda0_FDCHI2_OWNPV";
varnames[10] = "LL_Lambda0_PT";
varnames[11] = "DD_Lambda0_IPCHI2_OWNPV";
varnames[12] = "DD_Lambda0_FDCHI2_OWNPV";
varnames[13] = "DD_Lambda0_PT";
varnames[14] = "DD_pplus_IPCHI2_OWNPV";
varnames[15] = "DD_piminus_IPCHI2_OWNPV";
varnames[16] = "DD_piminus_PT";
varnames[17] = "LL_pplus_IPCHI2_OWNPV";
varnames[18] = "LL_piminus_IPCHI2_OWNPV";
varnames[19] = "LL_piminus_PT";
nb->NB_DEF_NODE1(nvar+1);
nb->NB_DEF_NODE2(nvar); // nodes in hidden layer
nb->NB_DEF_NODE3(1); // nodes in output layer
nb->NB_DEF_TASK("CLA"); // binominal classification
nb->NB_DEF_PRE(822);
// nb->NB_DEF_PRE(812);
nb->NB_DEF_REG("REG"); // 'OFF','REG' (def) ,'ARD','ASR','ALL'
nb->NB_DEF_LOSS("ENTROPY"); // 'ENTROPY'(def),'QUADRATIC'
nb->NB_DEF_METHOD("BFGS");
nb->NB_DEF_SHAPE("DIAG");
nb->NB_DEF_LEARNDIAG(1);
nb->NB_DEF_RTRAIN(1.0); // use 70% of events for training
// nb->NB_DEF_EPOCH(200); // weight update after n events
nb->NB_DEF_SPEED(2.0); // multiplicative factor to enhance global learning speed
nb->NB_DEF_MAXLEARN(1.0); // multiplicative factor to limit the global learning speed in any direction, this number should be smaller than NB_DEF_SPEED
nb->NB_DEF_ITER(100); // number of training iteration
//nb->NB_DEF_ITER(0); // number of training iteration
//int i = 4701;
//int j = 29;
//nb->NB_RANVIN(i,j,2); // random number seed initialisation, i has to be an odd number, the third argument is a debugging flag
nb->SetOutputFile(("expert_"+dataType+".nb").c_str()); // expert file
SetupNNPrepro(nb);
// MC
TreeReader* reader = new TreeReader("tree");
reader->AddFile("/afs/cern.ch/work/p/pluca/Lmumu/weighted/Lb2Lmumu_MC_Pythia8_NBweighted_new.root");
reader->Initialize();
// We take all signal and 20% of background
nb->SetTarget(1);
int ntot = reader->GetEntries();
int npassedMC = 0;
cout << "Read in " << ntot << " events" << endl;
int nstepMC = 5;
//if(dataType=="11") nstepMC = 5;
TFile ofile("/afs/cern.ch/work/p/pluca/Lmumu/weighted/samplesMVA_"+(TString)dataType+".root","recreate");
TTree * sigTrainSample = new TTree("sigTrainSample","");
reader->BranchNewTree(sigTrainSample);
TTree * sigTestSample = new TTree("sigTestSample","");
reader->BranchNewTree(sigTestSample);
for(int event = 0; event < ntot; event++)
{
reader->GetEntry(event);
if( TrueID(reader) && TriggerPassed(reader))
{
if( event%nstepMC==0 && npassedMC <= 4e4 )
{
npassedMC++;
float InputArray[nvar+1];
fillInputArray(reader,InputArray);
if(isnan(InputArray[0])) continue;
nb->SetWeight(reader->GetValue("Lb_weight"));
nb->SetNextInput(nvar,InputArray);
sigTrainSample->Fill();
}
else sigTestSample->Fill();
}
}
// Data
TreeReader* reader2 = new TreeReader("tree");
reader2->AddFile("/afs/cern.ch/work/p/pluca/Lmumu/weighted/Lb2Lmumu_CL_NBweighted.root");
reader2->Initialize();
TTree * bkgTrainSample = new TTree("bkgTrainSample","");
reader2->BranchNewTree(bkgTrainSample);
TTree * bkgTestSample = new TTree("bkgTestSample","");
reader2->BranchNewTree(bkgTestSample);
nb->SetTarget(0);
int ntot2 = reader2->GetEntries();
int npassed = 0;
cout << "Read in " << ntot2 << " events" << endl;
int nstep = 2;
//if(dataType=="11") nstep = 2;
for(int event = 0; event < ntot2; event++)
{
reader2->GetEntry(event);
double massLb = reader2->GetValue("Lb_MassConsLambda_M",0);
double massJpsi = reader2->GetValue("J_psi_1S_MM");
if(massLb > 6000 && TMath::Abs(massJpsi - 3096) > 100 && TMath::Abs(massJpsi - 3686) > 90 && TriggerPassed(reader2))
{
if(event%nstep==0 && npassed <=4e4)
{
float InputArray[100];
npassed++;
fillInputArray(reader2,InputArray);
if(isnan(InputArray[0])) continue;
nb->SetWeight(1.);
nb->SetNextInput(nvar,InputArray);
bkgTrainSample->Fill();
}
else bkgTestSample->Fill();
}
}
bkgTrainSample->Write();
bkgTestSample->Write();
sigTestSample->Write();
sigTrainSample->Write();
ofile.Close();
cout << "\nData used = " << npassed << ", MC used = " << npassedMC << endl;
cout << "Train the Network\n" << endl;
nb->TrainNet();
nb->nb_correl_signi(varnames,"correl_signi.txt","correl_signi.html");
cout << "\nData used = " << npassed << ", MC used = " << npassedMC << endl;
return 0;
}
int ParsimonyCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//randomtree will tell us if user had their own treefile or if they just want the random distribution
//user has entered their own tree
if (randomtree == "") {
m->setTreeFile(treefile);
TreeReader* reader;
if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); }
else { reader = new TreeReader(treefile, countfile); }
T = reader->getTrees();
ct = T[0]->getCountTable();
delete reader;
if(outputDir == "") { outputDir += m->hasPath(treefile); }
map<string, string> variables;
variables["[filename]"] = outputDir + m->getSimpleName(treefile) + ".";
output = new ColumnFile(getOutputFileName("parsimony",variables), itersString);
outputNames.push_back(getOutputFileName("parsimony",variables));
outputTypes["parsimony"].push_back(getOutputFileName("parsimony",variables));
sumFile = getOutputFileName("psummary",variables);
m->openOutputFile(sumFile, outSum);
outputNames.push_back(sumFile);
outputTypes["psummary"].push_back(sumFile);
}else { //user wants random distribution
getUserInput();
if(outputDir == "") { outputDir += m->hasPath(randomtree); }
output = new ColumnFile(outputDir+ m->getSimpleName(randomtree), itersString);
outputNames.push_back(outputDir+ m->getSimpleName(randomtree));
outputTypes["parsimony"].push_back(outputDir+ m->getSimpleName(randomtree));
}
//set users groups to analyze
SharedUtil util;
vector<string> mGroups = m->getGroups();
vector<string> tGroups = ct->getNamesOfGroups();
util.setGroups(mGroups, tGroups, allGroups, numGroups, "parsimony"); //sets the groups the user wants to analyze
util.getCombos(groupComb, mGroups, numComp);
m->setGroups(mGroups);
if (numGroups == 1) { numComp++; groupComb.push_back(allGroups); }
Parsimony pars;
counter = 0;
Progress* reading;
reading = new Progress("Comparing to random:", iters);
if (m->control_pressed) {
delete reading; delete output;
delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
m->clearGroups();
return 0;
}
//get pscore for users tree
userData.resize(numComp,0); //data = AB, AC, BC, ABC.
randomData.resize(numComp,0); //data = AB, AC, BC, ABC.
rscoreFreq.resize(numComp);
uscoreFreq.resize(numComp);
rCumul.resize(numComp);
uCumul.resize(numComp);
userTreeScores.resize(numComp);
UScoreSig.resize(numComp);
if (randomtree == "") {
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
userData = pars.getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
if (m->control_pressed) {
delete reading; delete output;
delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
m->clearGroups();
return 0;
}
//output scores for each combination
for(int k = 0; k < numComp; k++) {
//update uscoreFreq
map<int,double>::iterator it = uscoreFreq[k].find(userData[k]);
if (it == uscoreFreq[k].end()) {//new score
uscoreFreq[k][userData[k]] = 1;
}else{ uscoreFreq[k][userData[k]]++; }
//add users score to valid scores
validScores[userData[k]] = userData[k];
//save score for summary file
userTreeScores[k].push_back(userData[k]);
}
}
//get pscores for random trees
for (int j = 0; j < iters; j++) {
//create new tree with same num nodes and leaves as users
randT = new Tree(ct);
//create random relationships between nodes
randT->assembleRandomTree();
//get pscore of random tree
randomData = pars.getValues(randT, processors, outputDir);
if (m->control_pressed) {
delete reading; delete output; delete randT;
if (randomtree == "") { outSum.close(); }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
m->clearGroups();
return 0;
}
for(int r = 0; r < numComp; r++) {
//add trees pscore to map of scores
map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
if (it != rscoreFreq[r].end()) {//already have that score
rscoreFreq[r][randomData[r]]++;
}else{//first time we have seen this score
rscoreFreq[r][randomData[r]] = 1;
}
//add randoms score to validscores
validScores[randomData[r]] = randomData[r];
}
//update progress bar
reading->update(j);
delete randT;
}
}else {
//get pscores for random trees
for (int j = 0; j < iters; j++) {
//create new tree with same num nodes and leaves as users
randT = new Tree(ct);
//create random relationships between nodes
randT->assembleRandomTree();
if (m->control_pressed) {
delete reading; delete output; delete randT; delete ct;
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
}
//get pscore of random tree
randomData = pars.getValues(randT, processors, outputDir);
if (m->control_pressed) {
delete reading; delete output; delete randT; delete ct;
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;
}
for(int r = 0; r < numComp; r++) {
//add trees pscore to map of scores
map<int,double>::iterator it = rscoreFreq[r].find(randomData[r]);
if (it != rscoreFreq[r].end()) {//already have that score
rscoreFreq[r][randomData[r]]++;
}else{//first time we have seen this score
rscoreFreq[r][randomData[r]] = 1;
}
//add randoms score to validscores
validScores[randomData[r]] = randomData[r];
}
//update progress bar
reading->update(j);
delete randT;
}
}
for(int a = 0; a < numComp; a++) {
float rcumul = 0.0000;
float ucumul = 0.0000;
//this loop fills the cumulative maps and put 0.0000 in the score freq map to make it easier to print.
for (map<int,double>::iterator it = validScores.begin(); it != validScores.end(); it++) {
if (randomtree == "") {
map<int,double>::iterator it2 = uscoreFreq[a].find(it->first);
//user data has that score
if (it2 != uscoreFreq[a].end()) { uscoreFreq[a][it->first] /= T.size(); ucumul+= it2->second; }
else { uscoreFreq[a][it->first] = 0.0000; } //no user trees with that score
//make uCumul map
uCumul[a][it->first] = ucumul;
}
//make rscoreFreq map and rCumul
map<int,double>::iterator it2 = rscoreFreq[a].find(it->first);
//get percentage of random trees with that info
if (it2 != rscoreFreq[a].end()) { rscoreFreq[a][it->first] /= iters; rcumul+= it2->second; }
else { rscoreFreq[a][it->first] = 0.0000; } //no random trees with that score
rCumul[a][it->first] = rcumul;
}
//find the signifigance of each user trees score when compared to the random trees and save for printing the summary file
for (int h = 0; h < userTreeScores[a].size(); h++) {
UScoreSig[a].push_back(rCumul[a][userTreeScores[a][h]]);
}
}
if (m->control_pressed) {
delete reading; delete output;
delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (randomtree == "") { outSum.close(); }
for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
return 0;
}
//finish progress bar
reading->finish();
delete reading;
printParsimonyFile();
if (randomtree == "") { printUSummaryFile(); }
delete output; delete ct; for (int i = 0; i < T.size(); i++) { delete T[i]; }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "ParsimonyCommand", "execute");
exit(1);
}
}
int main(int argc, char **argv)
{
TString analysis = "Lb2Lmumu";
bool MC = false;
TString base = "/afs/cern.ch/work/p/pluca/weighted/Lmumu/";
if(argc > 1)
{
string arg = argv[1];
if(arg == "MC") MC = true;
}
vector< string > novar;
novar.push_back("Lb_MassCons");
novar.push_back("Lb_MassConsLambda");
novar.push_back("Lb_MassConsJpsiLambda");
novar.push_back("cosTheta");
novar.push_back("cosThetaL");
novar.push_back("cosThetaB");
novar.push_back("phiL");
novar.push_back("phiB");
novar.push_back("dphi");
novar.push_back("cosTheta_TRUE");
novar.push_back("cosThetaL_TRUE");
novar.push_back("cosThetaB_TRUE");
novar.push_back("phiL_TRUE");
novar.push_back("phiB_TRUE");
novar.push_back("dphi_TRUE");
TCut cutJpsi = CutsDef::cutJpsi;
TCut cutMuMu = CutsDef::cutMuMu_veto;
TreeReader* treeReader = new TreeReader("tree");
TString namefile = base + "candLb";
if(MC) namefile += "_MC";
namefile += ".root";
TFile * candFile = new TFile(namefile,"recreate");
if(!MC) treeReader->AddFile(base+analysis+"_CL_NBweighted.root");
else treeReader->AddFile(base+analysis+"_MC_Pythia8_NBweighted.root");
treeReader->Initialize(novar,"except");
Analysis * anaLbMuMu = new Analysis("Lb2Lmumu","Lb",treeReader,&cutMuMu);
candFile->cd();
TTree * candLbMuMu = anaLbMuMu->applyCuts(&addVariables);
candLbMuMu->Write();
string tnameMuMu = candLbMuMu->GetName();
candFile->Close();
candFile = TFile::Open(namefile,"update");
TTree * singleCand_LbMuMu = anaLbMuMu->checkMultiple("weight",namefile,tnameMuMu,&randomKill);
singleCand_LbMuMu->Write();
if(MC)
{
treeReader = new TreeReader("tree");
treeReader->AddFile(base+"Lb2JpsiL_MC_Pythia8_NBweighted.root");
treeReader->Initialize(novar,"except");
}
Analysis * anaLbJpsi = new Analysis("Lb2JpsiL","Lb",treeReader,&cutJpsi);
candFile->cd();
TTree * candLbJpsi = anaLbJpsi->applyCuts(&addVariables);
candLbJpsi->Write();
string tnameJpsi = candLbJpsi->GetName();
candFile->Close();
candFile = TFile::Open(namefile,"update");
TTree * singleCand_LbJpsi = anaLbJpsi->checkMultiple("weight",namefile,tnameJpsi,&randomKill);
singleCand_LbJpsi->Write();
candFile->cd();
TTree * candLbJpsi_reduced = anaLbJpsi->applyCuts(&addVariables,300);
candLbJpsi_reduced->SetName("candLb2JpsiL_reduced");
candLbJpsi_reduced->Write();
if(MC)
{
candFile->cd();
TCut jpsiSwap = cutJpsi + CutsDef::jpsiSwapID;
TCut mumuSwap = cutMuMu + CutsDef::mumuSwapID;
TTree * mumuSwapTree = anaLbMuMu->applyCuts(&mumuSwap, false,&addVariables);
mumuSwapTree->SetName("candLmumuSwap");
mumuSwapTree->Write();
TTree * jpsiSwapTree = anaLbJpsi->applyCuts(&jpsiSwap, false, &addVariables);
jpsiSwapTree->SetName("candJpsiLSwap");
jpsiSwapTree->Write();
TreeReader * KSReader = new TreeReader("tree");
KSReader->AddFile(base+"Bd2JpsiKS_MC12_NBweighted.root");
KSReader->Initialize(novar,"except");
TCut cutBdLL = cutJpsi + CutsDef::LLcut;
TCut cutBdDD = cutJpsi + CutsDef::DDcut;
Analysis * KSAnalysis_LL = new Analysis("BdJpsiKS_LL","B0",KSReader,&cutBdLL);
TTree *KSTree_LL = KSAnalysis_LL->applyCuts(&addVariables);
KSTree_LL->Write();
Analysis * KSAnalysis_DD = new Analysis("BdJpsiKS_DD","B0",KSReader,&cutBdDD);
TTree *KSTree_DD = KSAnalysis_DD->applyCuts(&addVariables);
KSTree_DD->Write();
Analysis * KSAnalysis_all = new Analysis("BdJpsiKS","B0",KSReader,&cutJpsi);
TTree *KSTree = KSAnalysis_all->applyCuts(&addVariables);
KSTree->Write();
candFile->cd();
TreeReader * KstmumuReader = new TreeReader("tree");
KstmumuReader->AddFile(base+"Bu2Kstmumu_MC12_NBweighted.root");
KstmumuReader->Initialize(novar,"except");
Analysis * KstmumuAnalysis = new Analysis("BuKstmumu","B0",KstmumuReader,&cutMuMu);
TTree *KstmumuTree = KstmumuAnalysis->applyCuts(&addVariables);
KstmumuTree->Write();
candFile->cd();
TreeReader * KSmumuReader = new TreeReader("tree");
KSmumuReader->AddFile(base+"Bd2KSmumu_MC12_NBweighted.root");
KSmumuReader->Initialize(novar,"except");
Analysis * KSmumuAnalysis = new Analysis("BdKSmumu","B0",KSmumuReader,&cutMuMu);
TTree *KSmumuTree = KSmumuAnalysis->applyCuts(&addVariables);
KSmumuTree->Write();
candFile->cd();
TreeReader * JpsiGenReader = new TreeReader("tree");
JpsiGenReader->AddFile("/afs/cern.ch/work/k/kreps/public/LbLMuMuAna/generatorLevel/LbJpsiLGenOnlyDaughInAccForRadiativeTail.root");
JpsiGenReader->Initialize();
TCut JpsiTailCut = "TMath::Power(J_psi_1S_MASS/1000,2) < 8 && Lb_MASS > 5300 && Lambda0_MASS > 1105 && Lambda0_MASS < 1125";
Analysis * JpsiTailAnalysis = new Analysis("JpsiTail","Lb",JpsiGenReader,&JpsiTailCut);
TTree *JpsiTailTree = JpsiTailAnalysis->applyCuts(&RenameMass, 0.1);
JpsiTailTree->Write();
}
candFile->Close();
delete candFile;
return 0;
}
void ROC_Occupancy() {
gStyle->SetPalette(1);
TH2D* l1 = new TH2D("l1","Layer 1;Modules along Z;Ladders",72, -4.5, 4.5, 42, -10.5, 10.5);
TH2D* l2 = new TH2D("l2","Layer 2;Modules along Z;Ladders",72, -4.5, 4.5, 66, -16.5, 16.5);
TH2D* l3 = new TH2D("l3","Layer 3;Modules along Z;Ladders",72, -4.5, 4.5, 90, -22.5, 22.5);
TH2D* fpixI = new TH2D("fpixI","FPix Inner Shells (+x);;Blades", 72, -4.5, 4.5, 144, 0.5, 12.5);
TH2D* fpixO = new TH2D("fpixO","FPix Outer Shells (-X);;Blades", 72, -4.5, 4.5, 144, -12.5, -0.5);
fpixI->GetXaxis()->SetBinLabel(1, "Disk-2 Pnl2");
fpixI->GetXaxis()->SetBinLabel(9, "Disk-2 Pnl1");
fpixI->GetXaxis()->SetBinLabel(19, "Disk-1 Pnl2");
fpixI->GetXaxis()->SetBinLabel(27, "Disk-1 Pnl1");
fpixI->GetXaxis()->SetBinLabel(41, "Disk+1 Pnl1");
fpixI->GetXaxis()->SetBinLabel(49, "Disk+1 Pnl2");
fpixI->GetXaxis()->SetBinLabel(59, "Disk+2 Pnl1");
fpixI->GetXaxis()->SetBinLabel(67, "Disk+2 Pnl2");
fpixI->GetXaxis()->LabelsOption("d");
fpixO->GetXaxis()->SetBinLabel(1, "Disk-2 Pnl2");
fpixO->GetXaxis()->SetBinLabel(9, "Disk-2 Pnl1");
fpixO->GetXaxis()->SetBinLabel(19, "Disk-1 Pnl2");
fpixO->GetXaxis()->SetBinLabel(27, "Disk-1 Pnl1");
fpixO->GetXaxis()->SetBinLabel(41, "Disk+1 Pnl1");
fpixO->GetXaxis()->SetBinLabel(49, "Disk+1 Pnl2");
fpixO->GetXaxis()->SetBinLabel(59, "Disk+2 Pnl1");
fpixO->GetXaxis()->SetBinLabel(67, "Disk+2 Pnl2");
fpixO->GetXaxis()->LabelsOption("d");
TreeReader tr;
TChain *filechain = new TChain("filechain");
filechain->Add("Ntuple.root");
gROOT->SetStyle("Plain");
gStyle->SetOptStat(0);
TCanvas c("c","c",1200,800);
c.Divide(3,2);
TObjArray* files=filechain->GetListOfFiles();
for (int nf=0; nf<files->GetEntries(); ++nf) {
TFile* file = TFile::Open(files->At(nf)->GetTitle());
tr.readtrees(*file);
for (Long64_t i=0; i<tr.nclu(); i++) {
tr.clu_read(i);
Cluster clu = tr.clu();
EventData e = tr.clu_evt();
int clu_sdpx = ((clu.mod_on.disk>0) ? 1 : -1) * (2 * (abs(clu.mod_on.disk) - 1) + clu.mod_on.panel);
// Roc BinX number for ROC map plots (clust branch)
int clu_roc_binx = NOVAL_I;
if (clu.mod_on.det==0) {
for (int j=1;j<=8;j++) if (clu.y>=((8-j)*52.0)&&clu.y<((9-j)*52.0))
clu_roc_binx = (clu.mod_on.module+4)*8 + j;
} else if (clu.mod_on.det==1) {
// Roc is left (0) or right (1) on the ROC map plot (+Z side)
int binselx = (clu.mod_on.panel==1&&(clu.mod_on.module==1||clu.mod_on.module==4)) ? (clu.mod_on.module==1)
: ((clu.mod_on.panel==1&&clu.x<80.0)||(clu.mod_on.panel==2&&clu.x>=80.0));
// Gives the Roc location inside a panel (0 to 5 on +Z side)
int nperpan = 2 * clu.mod_on.module + clu.mod_on.panel - 1 + binselx;
clu_roc_binx = ((clu.mod_on.disk>0) ? nperpan : 9 - nperpan) + (clu_sdpx + 4) * 8
- 2 * ((abs(clu.mod_on.disk)==1) ? clu.mod_on.disk : 0);
}
// Roc BinY number for ROC map plots (c branch)
int clu_roc_biny = NOVAL_I;
if (clu.mod_on.det==0) {
// Roc is in bottom (0) or top bin (1) inside a ladder on th ROC map plot
int binsely = ((clu.mod_on.half==1&&((clu.mod_on.ladder<0&&clu.mod_on.ladder%2==0)||clu.mod_on.ladder%2==1))
||(clu.mod_on.half==0&&((clu.mod_on.ladder<0 &&((clu.mod_on.ladder%2==-1&&clu.x<80.0)
||(clu.mod_on.ladder%2==0&&clu.x>=80.0)))
||(clu.mod_on.ladder>0 &&((clu.mod_on.ladder%2==0&&clu.x<80.0)
||(clu.mod_on.ladder%2==1&&clu.x>=80.0))))));
clu_roc_biny = (clu.mod_on.layer * 6 + clu.mod_on.ladder + 4) * 2 + 1 + binsely;
} else if (clu.mod_on.det==1) {
// Gives the number of ROCs along ly
int nrocly = clu.mod_on.module + clu.mod_on.panel;
for (int j=0; j<nrocly; j++) {
// ROC number = nrocly - 1 - j for + LX and nrocly + j for -LX.
int k = (clu.mod_on.disk<0) ? j : nrocly - 1 - j;
if (clu.y>=(k*52.0)&&clu.y<((k+1)*52.0))
clu_roc_biny = 6 - nrocly + 2 * j + ((clu.mod_on.blade>0) ? clu.mod_on.blade-1 : clu.mod_on.blade + 12)*12 + 1;
}
}
if (clu.mod_on.layer==1) l1->SetBinContent(clu_roc_binx,clu_roc_biny, l1->GetBinContent(clu_roc_binx,clu_roc_biny)+1);
else if (clu.mod_on.layer==2) l2->SetBinContent(clu_roc_binx,clu_roc_biny, l2->GetBinContent(clu_roc_binx,clu_roc_biny)+1);
else if (clu.mod_on.layer==3) l3->SetBinContent(clu_roc_binx,clu_roc_biny, l3->GetBinContent(clu_roc_binx,clu_roc_biny)+1);
else if (clu.mod_on.blade>0) {
fpixI->SetBinContent(clu_roc_binx,clu_roc_biny, fpixI->GetBinContent(clu_roc_binx,clu_roc_biny)+1);
fpixI->SetBinContent(clu_roc_binx,clu_roc_biny+1, fpixI->GetBinContent(clu_roc_binx,clu_roc_biny+1)+1);
} else if (clu.mod_on.blade<0) {
fpixO->SetBinContent(clu_roc_binx,clu_roc_biny, fpixO->GetBinContent(clu_roc_binx,clu_roc_biny)+1);
fpixO->SetBinContent(clu_roc_binx,clu_roc_biny+1, fpixO->GetBinContent(clu_roc_binx,clu_roc_biny+1)+1);
}
if (i%500000==0) {
c.cd(1);
l1->Draw("COLZ");
c.cd(2);
l2->Draw("COLZ");
c.cd(3);
l3->Draw("COLZ");
c.cd(4);
fpixI->Draw("COLZ");
c.cd(5);
fpixO->Draw("COLZ");
gPad->Update();
}
}
c.SaveAs("output.root");
} std::cout<<"Done."<<std::endl;
}
int main(int argc, char * argv[]) {
log_call(argc, argv);
bool cfileset = false;
bool tfileset = false;
bool outfileset = false;
char * treef = NULL;
char * charf = NULL;
char * outf = NULL;
int analysis = 0;
while (1) {
int oi = -1;
int c = getopt_long(argc, argv, "c:t:o:hV", long_options, &oi);
if (c == -1) {
break;
}
switch(c) {
case 'c':
cfileset = true;
charf = strdup(optarg);
check_file_exists(charf);
break;
case 't':
tfileset = true;
treef = strdup(optarg);
check_file_exists(treef);
break;
case 'o':
outfileset = true;
outf = strdup(optarg);
break;
case 'h':
print_help();
exit(0);
case 'V':
cout << versionline << endl;
exit(0);
default:
print_error(argv[0], (char)c);
exit(0);
}
}
istream * pios = NULL;
istream * poos = NULL;
ifstream * cfstr = NULL;
ifstream * tfstr = NULL;
ostream * poouts = NULL;
ofstream * ofstr = NULL;
if (tfileset == true) {
tfstr = new ifstream(treef);
poos = tfstr;
} else {
poos = &cin;
}
if (cfileset == true) {
cfstr = new ifstream(charf);
pios = cfstr;
} else {
cout << "you have to set a character file. Only a tree file can be read in through the stream;" << endl;
}
//out file
//
if (outfileset == true){
ofstr = new ofstream(outf);
poouts = ofstr;
} else{
poouts = &cout;
}
//
string retstring;
int ft = test_char_filetype_stream(*pios, retstring);
if (ft != 1 && ft != 2) {
cout << "only fasta and phylip (with spaces) supported so far" << endl;
exit(0);
}
Sequence seq;
vector <Sequence> seqs;
map <string, int> seq_map;
int y = 0;
int nchars = 0 ;
while (read_next_seq_char_from_stream(*pios, ft, retstring, seq)) {
seqs.push_back(seq);
nchars = seq.get_num_cont_char();
seq_map[seq.get_id()] = y;
seq.clear_cont_char();
y++;
}
cout << "nchars: " << nchars << endl;
if (ft == 2) {
seqs.push_back(seq);
seq_map[seq.get_id()] = y;
seq.clear_cont_char();
}
//read trees
TreeReader tr;
vector<Tree *> trees;
while (getline(*poos,retstring)) {
if (retstring.size()<4){
continue;
}
trees.push_back(tr.readTree(retstring));
}
int x = 0;
//conduct analyses for each character
for (int i=0; i < trees[x]->getExternalNodeCount(); i++) {
vector<Superdouble> tv (nchars);
for (int c=0; c < nchars; c++) {
tv[c] = seqs[seq_map[trees[x]->getExternalNode(i)->getName()]].get_cont_char(c);
}
trees[x]->getExternalNode(i)->assocDoubleVector("val",tv);
}
for (int i=0; i < trees[x]->getInternalNodeCount(); i++) {
vector<Superdouble> tv (nchars);
for (int c=0; c < nchars; c++) {
tv[c] = 0;
}
trees[x]->getInternalNode(i)->assocDoubleVector("val",tv);
}
float sigma = 1;
cout << calc_bm_prune(trees[x], sigma) << endl;
optimize_single_rate_bm_bl(trees[x]);
(*poouts) << trees[x]->getRoot()->getNewick(true) << ";" << endl;
cout << calc_bm_prune(trees[x], sigma) << endl;
if (cfileset) {
cfstr->close();
delete pios;
}
if (tfileset) {
tfstr->close();
delete poos;
}
if (outfileset) {
ofstr->close();
delete poouts;
}
return EXIT_SUCCESS;
}
TTree* cudaFitTest(){
//find/record test signals
TreeReader reader;
reader.openFile(258,0);
int index[512],channel[512];
float energy[512],time[512];
int i=0,j=0;
while(i<512 && j<reader.tree->GetEntries()){
reader.tree->GetEntry(j);
for(int k=0;k<11;k++){
int t=reader.recon.t_gamma[CH[k]];
float E=reader.recon.E_gamma[CH[k]];
if(t>0 && t<NPOINTS && E>3000 && E<6000 && i<512){
index[i]=j;
channel[i]=CH[k];
time[i]=t;
energy[i]=E;
i++;
}
}
j++;
}
reader.reset();
//copy signals to data;
RawFileReader rawReader(258,0);
Entry entry;
RawData rdata;
data=new float[512];
i=0;
rawReader.initialize();
for(i=0;i<512;i++){
data[i]=new float[2048];
j=index[i];
int k=channel[i];
rawReader.seek(j);
rawReader.readNext(entry,rdata);
for(int x=0;x<2048;x++){
data[i][x]=rdata.ch[k][x];
}
}
rawReader.close();
//fit
fitter=new cudaFit(512);
fitter->setData(data);
float *initParam=new float[8];
initParam[0]=100;
initParam[1]=0;
initParam[2]=15000;
initParam[3]=1.1e-3;
initParam[4]=1.3e-3;
initParam[5]=625;
initParam[6]=0;
initParam[7]=0;
fitter->fit(initParam,0);
float **param=new float[512];
for(i=0;i<512;i++){
param[i]=new float[8];
}
float fitE[512],fitT[512];
fitter->getParameters(param);
for(int evnt=0;evnt<512;evnt++){
fitE[evnt]=peakHeight(param[evnt]);
fitT[evnt]=param[evnt][5];
}
//compare
deltaT=new TH1F("deltaT","deltaT",250,-250,0);
deltaE=new TH1F("deltaE","deltaE",200,0,2);
paramB=new TH1F("paramB","paramB",500,10000,30000);
for(int evnt=0;evnt<512;evnt++){
deltaT->Fill(time[evnt]-fitT[evnt]);
deltaE->Fill(fitE[evnt]/energy[evnt]);
paramB->Fill(param[evnt][2]);
}
delete[] param;
delete[] initParam;
}