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CCM.cpp
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/*
list of throw exceptions:
1 = vectors fed to the constructor are not the same size
2 = normalization of sample vector error = its field of zeroes
3 = vectors in dot product are not the same size
*/
#include <algorithm> // copy
#include <atomic>
#include <bits/stdc++.h>
#include <fstream> //open file
#include <fstream>
#include <iomanip>
#include <iostream>
#include <mutex>
#include <sstream>
#include <stdexcept> // std::out_of_range
#include <stdio.h> //strcat
#include <string>
#include <sys/stat.h>
#include <sys/types.h>
#include <thread>
#include <vector>
// Root
#include "TAxis.h"
#include "TCanvas.h"
#include "TFile.h"
#include "TGraph.h"
#include "TH1D.h"
#include "TH2D.h"
#include "TROOT.h"
#include "TTree.h"
#include "CCM.h"
// #include "CheckCCM.h"
#include "Cross_correlation.h"
#include "variables.h"
double useless_function(double *x, double *par)
{
return x[0];
}
CCM::CCM(const TH2D &matrix, const std::vector<Region_of_interest> &_ROIs, const double reference_time_low,
const double reference_time_high)
: CCM(matrix, _ROIs)
{
// create sample_vector
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
this->CreateReferenceVector(ROI_index, reference_time_low, reference_time_high);
}
}
CCM::CCM(const TH2D &matrix, const std::vector<Region_of_interest> &_ROIs)
{
V.TEMAT = dynamic_cast<TH2D *>(matrix.Clone(Form("%s_clone", matrix.GetName())));
fXbins = matrix.GetXaxis()->GetNbins();
fYbins = matrix.GetYaxis()->GetNbins();
for (const auto &roi : _ROIs)
{
V.ROIs.emplace_back(roi);
}
// V.ROIs = _ROIs;
V.number_of_ROIs = _ROIs.size();
V.total_tasks = fXbins * V.number_of_ROIs;
V.time_bins = fXbins;
// reserve space for result container structure
ResVec = new ResCont *[V.number_of_ROIs];
for (int ROI = 0; ROI < V.number_of_ROIs; ROI++)
{
ResVec[ROI] = new ResCont[V.time_bins];
}
// reserve space for fit container - fit results and other variables
FitVec = new FitCont[V.time_bins];
this->CopyMatrixContent(V.TEMAT);
}
CCM::~CCM()
{
if (fFixedTEMAT)
delete fFixedTEMAT;
for (int ROI = 0; ROI < V.number_of_ROIs; ROI++)
{
delete[] ResVec[ROI];
}
delete[] ResVec;
delete[] FitVec;
for (auto i = 0; i < V.number_of_ROIs; i++)
{
for (auto j = 0; j < fXbins; j++)
{
delete[] V.TEMATarr[i][j];
}
delete[] V.TEMATarr[i];
}
delete[] V.TEMATarr;
delete V.TEMAT;
for (auto &f : fCorrectionFunctions)
{
delete f.first;
f.first = nullptr;
}
}
void CCM::SetCorrectionFunction(const TF1 &fcn, const std::string &fit_options)
{
if (!fcn.GetFormula())
{
throw std::runtime_error("Error! Function must be created using TFormula, e.i. using the text string, "
"otherwise it cannot be saved in a ROOT file and used in the CCM object!");
}
if (fCorrectionFunctions.size() > 0)
{
throw std::runtime_error("Error! Primary function needs to be set first, only one primary function can be set");
}
TF1 *fclone = (TF1 *)fcn.Clone();
// TF1 *fclone = new TF1("gain_fcn", "[0]*x", 0, 4000);
fclone->SetNpx(V.TEMAT->GetYaxis()->GetNbins() * 100);
fclone->SetRange(V.TEMAT->GetYaxis()->GetBinLowEdge(1),
V.TEMAT->GetYaxis()->GetBinUpEdge(V.TEMAT->GetYaxis()->GetNbins()));
fclone->Update();
fCorrectionFunctions.emplace_back(std::make_pair(fclone, fit_options + "NQ"));
// add empty function for cases when no ROI is valid - this eseential does nothing
TF1 *empty_function = new TF1("empty_function", "x", V.TEMAT->GetYaxis()->GetBinLowEdge(1),
V.TEMAT->GetYaxis()->GetBinUpEdge(V.TEMAT->GetYaxis()->GetNbins()));
fCorrectionFunctions.emplace_back(std::make_pair(empty_function, "NQ"));
}
void CCM::SetFallbackCorrectionFunction(const TF1 &fcn, const std::string &fit_options)
{
if (!fcn.GetFormula())
{
throw std::runtime_error("Error! Function must be created using TFormula, e.i. using the text string, "
"otherwise it cannot be saved in a ROOT file and used in the CCM object!");
}
if (fCorrectionFunctions.size() == 0)
{
throw std::runtime_error("Error! Primary function not set, it needs to be set first!");
}
auto it = std::find_if(fCorrectionFunctions.begin(), fCorrectionFunctions.end(),
[&fcn](const auto &f) { return fcn.GetNpar() == f.first->GetNpar(); });
if (it != fCorrectionFunctions.end())
{
throw std::runtime_error("Error! Function with the same number of parameters already exists!");
}
for (const auto &f : fCorrectionFunctions)
{
if (strcmp(f.first->GetName(), fcn.GetName()) == 0)
{
throw std::runtime_error("Error! You are trying to add function with same name of an existing function!");
}
}
TF1 *fclone = (TF1 *)fcn.Clone();
fclone->SetNpx(V.TEMAT->GetYaxis()->GetNbins() * 100);
fclone->SetRange(V.TEMAT->GetYaxis()->GetBinLowEdge(1),
V.TEMAT->GetYaxis()->GetBinUpEdge(V.TEMAT->GetYaxis()->GetNbins()));
fCorrectionFunctions.emplace_back(std::make_pair(fclone, fit_options + "NQ"));
std::sort(fCorrectionFunctions.begin(), fCorrectionFunctions.end(),
[](const auto &a, const auto &b) { return a.first->GetNpar() > b.first->GetNpar(); });
}
TGraph *CCM::GetROIShifts(const int roi_index, const bool valid_only)
{
TGraph *gr = new TGraph();
gr->SetBit(TGraph::kIsSortedX);
gr->SetName(Form("shift_ROI_%i", roi_index));
for (int time = 0; time < V.time_bins; time++)
{
if (valid_only && !ResVec[roi_index][time].isValid)
{
continue;
}
gr->AddPoint(GetMatrixTime(time), ResVec[roi_index][time].bin_shift);
}
return gr;
}
TGraph *CCM::GetShiftProfile(const int time_bin, const bool valid_only)
{
TGraph *gr = new TGraph();
gr->SetBit(TGraph::kIsSortedX);
gr->SetTitle(Form("%i", time_bin));
for (int roi_index = 0; roi_index < V.number_of_ROIs; roi_index++)
{
if (ResVec[roi_index][time_bin].isValid)
{
if (valid_only && !ResVec[roi_index][time_bin].isValid)
{
continue;
}
gr->AddPoint(V.ROIs[roi_index].desired_energy, ResVec[roi_index][time_bin].bin_shift);
}
}
gr->SetMarkerColor(kRed);
gr->SetMarkerStyle(20);
return gr;
}
void CCM::CopyMatrixContent(TH2D *matrix)
{
// V.TEMAT = matrix;
// fXbins = V.TEMAT->GetXaxis()->GetNbins();
// V.time_bins = fXbins;
V.TEMATarr = new double **[V.number_of_ROIs];
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
V.TEMATarr[ROI_index] = new double *[fXbins];
for (uint j = 0; j < fXbins; j++)
{
V.TEMATarr[ROI_index][j] = new double[V.ROIs[ROI_index].displacement_range];
}
}
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
for (int x = 0; x < fXbins; x++)
{
for (int y = 0; y < V.ROIs[ROI_index].displacement_range; y++)
{
V.TEMATarr[ROI_index][x][y] =
V.TEMAT->GetBinContent(x + 1, y + V.ROIs[ROI_index].bin_window_low +
V.ROIs[ROI_index].bin_displacement_low); // y+ 1?? - check
}
}
}
}
void CCM::CreateReferenceVector(const int ROI_index, const double sample_time_low, const double sample_time_high)
{
std::vector<double> vec(V.ROIs[ROI_index].vector_dimension);
int vector_iterator{0};
// loop over energy
int tbin_start = V.TEMAT->GetXaxis()->FindBin(sample_time_low);
int tbin_end = V.TEMAT->GetXaxis()->FindBin(sample_time_high);
for (int e_bin = V.ROIs[ROI_index].bin_window_low; e_bin < V.ROIs[ROI_index].bin_window_high;
e_bin++, vector_iterator++)
{
vec[vector_iterator] = 0;
// loop over time, since sample vector should be formed of more than 1 time-bin width of TEMAT
for (int t_bin = tbin_start; t_bin <= tbin_end; t_bin++)
{
vec[vector_iterator] += V.TEMAT->GetBinContent(t_bin, e_bin);
}
}
this->Normalize(vec);
V.sample_vector.emplace_back(std::move(vec));
}
void CCM::Normalize(std::vector<double> &v)
{
double norm = std::inner_product(v.begin(), v.end(), v.begin(), 0.0);
if (norm <= 0)
{
throw std::runtime_error("Normalization ERROR, sample vector cannot consist of zeros!");
}
norm = sqrt(norm);
std::transform(v.begin(), v.end(), v.begin(), [norm](double &x) { return x / norm; });
}
void CCM::CalculateEnergyShifts(const unsigned int threads)
{
this->CheckReferenceVectors();
fNthreads = threads;
std::vector<std::thread> t;
t.reserve(fNthreads);
std::cout << "***** Starting calculations of Cross-correlation corrections *****" << std::endl;
fThreadTask = -1; // so that the first job start at zero
CrossCorrel *starting_class[fNthreads];
for (int i = 0; i < fNthreads; i++)
{
starting_class[i] = new CrossCorrel(&V, ResVec);
}
std::mutex mtx_task;
std::mutex mtx_fit;
// start threads
if (fNthreads > V.total_tasks)
{
for (int i = 0; i < V.total_tasks; i++)
{
// pass thread task, VarManger variable, mutex and ResVec as reference
t.push_back(std::thread(&CrossCorrel::Process, starting_class[i], i + 1, &fThreadTask, std::ref(mtx_task),
std::ref(mtx_fit)));
}
}
else
{
for (int i = 0; i < fNthreads; i++)
{
// pass thread task, VarManger variable, mutex and ResVec as reference
t.push_back(std::thread(&CrossCorrel::Process, starting_class[i], i + 1, &fThreadTask, std::ref(mtx_task),
std::ref(mtx_fit)));
}
}
for (auto &th : t)
th.join();
std::cout << std::endl;
std::cout << "Done" << std::endl;
}
void CCM::SaveToRootFile(const std::string &outroot_file)
{
TFile file(outroot_file.c_str(), "RECREATE");
{
TH2D *mat = dynamic_cast<TH2D *>(V.TEMAT->Clone("CCM_matrix"));
mat->Write();
if (fFixedTEMAT)
fFixedTEMAT->Write();
}
for (int roi = 0; roi < V.number_of_ROIs; roi++)
{
ResCont results;
double time;
// TTree *t = new TTree(Form("ROI_%i", roi), Form("CCM tree of ROI %i", roi));
TTree *t = new TTree(Form("ROI_%i", roi), Form("CCM tree of ROI %i", roi));
t->Branch("fit_valid", &results.isValid);
t->Branch("bin_shift", &results.bin_shift);
t->Branch("energy_shift", &results.energy_shift);
t->Branch("dot_product", &results.dp);
t->Branch("dp_vector", &results.dp_vec);
t->Branch("gfit_chi2", &results.gfit_chi2);
t->Branch("gfit_sigma", &results.gfit_sigma);
t->Branch("gfit_mu", &results.gfit_sigma);
t->Branch("time", &time);
for (int time_bin = 0; time_bin < V.time_bins; time_bin++)
{
time = this->GetMatrixTime(time_bin);
results = ResVec[roi][time_bin];
t->Fill();
}
file.cd();
t->Write();
}
{
std::string fcn_name;
std::vector<double> fcn_coefs;
double time;
TTree *t = new TTree("fit_coef", "Fit coefficients for given time, parameters = 0.");
t->Branch("time", &time);
t->Branch("fcn_name", &fcn_name);
t->Branch("fcn_coef", &fcn_coefs);
for (int time_bin = 0; time_bin < V.time_bins; time_bin++)
{
time = this->GetMatrixTime(time_bin);
// first zero out params
fcn_name = FitVec[time_bin].functionUsed;
fcn_coefs = FitVec[time_bin].coef;
t->Fill();
}
file.cd();
t->Write();
}
file.mkdir("fit_fcns");
file.cd("fit_fcns");
for (unsigned int i = 0; i < fCorrectionFunctions.size(); i++)
{
fCorrectionFunctions[i].first->Write();
}
// save coefficients to file
file.Close();
}
void CCM::SaveShiftTable(const std::string &table_filename)
{
std::ofstream output;
output.open(table_filename);
// table head
output << "# number of ROIs (regions of interest) in the matrix \n";
output << V.number_of_ROIs << '\n';
output << "# desired energies for each ROI \n";
for (const auto &r : V.ROIs)
{
output << std::setprecision(15) << r.desired_energy << " ";
}
output << '\n';
output << "################ \n";
output << "# time_bin time_start time_end ";
for (int roi = 0; roi < V.number_of_ROIs; roi++)
{
output << "ROI" << roi << "_ok(bool) "
<< "ROI" << roi << "_shift(double) ";
}
output << "\n";
for (int time_slice_index = 0; time_slice_index < V.time_bins; time_slice_index++)
{
output << time_slice_index + 1 << std::setprecision(15) << '\t';
output << std::setprecision(15) << V.TEMAT->GetXaxis()->GetBinLowEdge(time_slice_index + 1) << '\t';
output << std::setprecision(15) << V.TEMAT->GetXaxis()->GetBinUpEdge(time_slice_index + 1) << '\t';
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
// check if shift is converted to energy units
output << '\t' << ResVec[ROI_index][time_slice_index].isValid << '\t'
<< ResVec[ROI_index][time_slice_index].energy_shift;
}
output << '\n';
}
}
// void CCM::BuildInterpolators(const bool valid_only)
// {
// for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
// {
// bool graph_defined = std::find(fInterpolator.begin(), fInterpolator.end(),
// [&](const CCMInterpolator &x) { return x.GetROI() == ROI_index; }
// ) == fInterpolator.end();
// if (graph_defined)
// continue;
// fInterpolator.emplace_back(ROI_index);
// for (int time_index = 0; time_index < V.time_bins; time_index++)
// {
// if (valid_only)
// {
// fInterpolator.back().AddPoint(V.TEMAT->GetXaxis()->GetBinCenter(time_index + 1),
// ResVec[ROI_index][time_index].energy_shift,
// ResVec[ROI_index][time_index].isValid);
// }
// else
// {
// fInterpolator.back().AddPoint(V.TEMAT->GetXaxis()->GetBinCenter(time_index + 1),
// ResVec[ROI_index][time_index].energy_shift, true);
// }
// }
// }
// }
// void CCM::PerformFits(const bool valid_only, const bool use_spline)
// {
// if (V.number_of_ROIs == 0)
// {
// throw std::runtime_error("No ROIs added to the CCM object");
// }
// int nrois;
// double x[V.number_of_ROIs];
// double y[V.number_of_ROIs];
// std::vector<TGraph> roi_graphs;
// std::vector<TSpline3> roi_splines;
// // prepare splines if needed
// if (use_spline)
// {
// for (int time_index = 0; time_index < V.time_bins; time_index++)
// {
// roi_graphs.emplace_back();
// roi_graphs.back().SetName(Form("ROI_%i", roi_graphs.size() - 1));
// roi_graphs.back().SetTitle(
// Form("ROI_%i; time slice index; energy shift [energy units]", roi_graphs.size() - 1));
// for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
// {
// if (valid_only && !ResVec[ROI_index][time_index].isValid)
// continue;
// roi_graphs.back().AddPoint(time_index, V.ROIs[ROI_index].desired_energy +
// ResVec[ROI_index][time_index].energy_shift);
// }
// }
// for (auto &gr : roi_graphs)
// {
// roi_splines.emplace_back(Form("spline_%s", gr.GetName()), &gr);
// }
// }
// for (int time_index = 0; time_index < V.time_bins; time_index++)
// {
// nrois = 0;
// for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
// {
// // ResVec[ROI_index][time_index].print();
// if (valid_only && ResVec[ROI_index][time_index].isValid)
// {
// x[nrois] = V.ROIs[ROI_index].desired_energy;
// y[nrois] = V.ROIs[ROI_index].desired_energy - ResVec[ROI_index][time_index].energy_shift;
// nrois++; // get number of good points
// }
// else if (use_spline)
// {
// x[nrois] = V.ROIs[ROI_index].desired_energy;
// y[nrois] = V.ROIs[ROI_index].desired_energy - roi_splines[ROI_index].Eval(time_index);
// nrois++;
// }
// }
// std::pair<TF1 *, std::string> *fcn = nullptr; // TF1 *fcn{nullptr};
// for (auto &f : fCorrectionFunctions)
// {
// if (nrois >= f.first->GetNpar())
// {
// fcn = &f;
// break;
// }
// }
// // if (fcn->first == nullptr)
// // {
// // auto min =
// // std::min_element(fCorrectionFunctions.begin(), fCorrectionFunctions.end(),
// // [](const auto &a, const auto &b) { return a.first->GetNpar() <
// b.first->GetNpar();
// // });
// // std::cerr
// // << "No suitable function found for time slice " << time_index << ", this slice has in total " <<
// // nrois
// // << " valid ROIs available to fit, but smallest minimum degree of freedom from provided functions
// is "
// // << (*min).first->GetNpar() << std::endl;
// // std::cerr << "skipping slice" << std::endl;
// // continue;
// // }
// if (strcmp(fcn->first->GetName(), "empty_function") == 0)
// {
// FitVec[time_index].functionUsed = "empty_function";
// continue;
// }
// TGraph gr(nrois, x, y);
// gr.Fit(fcn->first, fcn->second.c_str());
// FitVec[time_index].functionUsed = fcn->first->GetName();
// for (int i = 0; i < fcn->first->GetNpar(); i++)
// {
// // std::cout << std::setprecision(6) << "par[" << i << "] = " << fcn->first->GetParameter(i) <<
// std::endl; FitVec[time_index].coef.emplace_back(fcn->first->GetParameter(i));
// }
// }
// // SaveFitTable(&V, FitVec);
// fFitDone = true;
// }
void CCM::PerformFits(const bool valid_only, const bool use_spline)
{
if (V.number_of_ROIs == 0)
{
throw std::runtime_error("No ROIs added to the CCM object");
}
int nrois;
double x[V.number_of_ROIs];
double y[V.number_of_ROIs];
std::vector<TGraph> roi_graphs;
std::vector<TSpline3> roi_splines;
// prepare splines if needed
if (use_spline)
{
for (int time_index = 0; time_index < V.time_bins; time_index++)
{
roi_graphs.emplace_back();
roi_graphs.back().SetName(Form("ROI_%i", roi_graphs.size() - 1));
roi_graphs.back().SetTitle(
Form("ROI_%i; time slice index; energy shift [energy units]", roi_graphs.size() - 1));
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
if (valid_only && !ResVec[ROI_index][time_index].isValid)
continue;
roi_graphs.back().AddPoint(time_index, V.ROIs[ROI_index].desired_energy +
ResVec[ROI_index][time_index].energy_shift);
}
}
for (auto &gr : roi_graphs)
{
roi_splines.emplace_back(Form("spline_%s", gr.GetName()), &gr);
}
}
for (int time_index = 0; time_index < V.time_bins; time_index++)
{
nrois = 0;
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
// ResVec[ROI_index][time_index].print();
if (valid_only && ResVec[ROI_index][time_index].isValid)
{
x[nrois] = V.ROIs[ROI_index].desired_energy;
y[nrois] = V.ROIs[ROI_index].desired_energy - ResVec[ROI_index][time_index].energy_shift;
nrois++; // get number of good points
}
else if (use_spline)
{
x[nrois] = V.ROIs[ROI_index].desired_energy;
y[nrois] = V.ROIs[ROI_index].desired_energy - roi_splines[ROI_index].Eval(time_index);
nrois++;
}
}
std::pair<TF1 *, std::string> *fcn = nullptr; // TF1 *fcn{nullptr};
for (auto &f : fCorrectionFunctions)
{
if (nrois >= f.first->GetNpar())
{
fcn = &f;
break;
}
}
// if (fcn->first == nullptr)
// {
// auto min =
// std::min_element(fCorrectionFunctions.begin(), fCorrectionFunctions.end(),
// [](const auto &a, const auto &b) { return a.first->GetNpar() < b.first->GetNpar();
// });
// std::cerr
// << "No suitable function found for time slice " << time_index << ", this slice has in total " <<
// nrois
// << " valid ROIs available to fit, but smallest minimum degree of freedom from provided functions is "
// << (*min).first->GetNpar() << std::endl;
// std::cerr << "skipping slice" << std::endl;
// continue;
// }
if (strcmp(fcn->first->GetName(), "empty_function") == 0)
{
FitVec[time_index].functionUsed = "empty_function";
continue;
}
TGraph gr(nrois, x, y);
gr.Fit(fcn->first, fcn->second.c_str());
FitVec[time_index].functionUsed = fcn->first->GetName();
for (int i = 0; i < fcn->first->GetNpar(); i++)
{
// std::cout << std::setprecision(6) << "par[" << i << "] = " << fcn->first->GetParameter(i) << std::endl;
FitVec[time_index].coef.emplace_back(fcn->first->GetParameter(i));
}
}
// SaveFitTable(&V, FitVec);
fFitDone = true;
}
void CCM::SaveFitTable(const std::string &data_filename, const std::string &detector_name)
{
if (!fFitDone)
{
std::cerr << "Warning! PerformFits() function was not yet called, it will be called with default parameters "
"(valid only, no spline)"
<< std::endl;
this->PerformFits();
}
std::ofstream output;
output.open(data_filename);
output << "# detector_name\n" << detector_name << '\n';
output << "# Timestamp range covered by this file\n";
output << std::setprecision(20) << V.TEMAT->GetXaxis()->GetBinLowEdge(1) << " " << std::setprecision(20)
<< V.TEMAT->GetXaxis()->GetBinUpEdge(V.time_bins) << '\n';
output << "# number of functions used \n";
output << fCorrectionFunctions.size() << '\n';
output << "# fcn_name number_of_parameters function_equation\n";
for (const auto &f : fCorrectionFunctions)
{
output << f.first->GetName() << "\t" << f.first->GetNpar() << "\t" << f.first->GetExpFormula() << '\n';
}
output << "#############################################################" << '\n';
output << "# TS_start TS_stop fcn_name par0 par1 ..." << '\n';
for (int time_index = 0; time_index < V.time_bins; time_index++)
{
output << V.TEMAT->GetXaxis()->GetBinLowEdge(time_index + 1) << '\t'
<< V.TEMAT->GetXaxis()->GetBinUpEdge(time_index + 1) << '\t';
output << FitVec[time_index].functionUsed << '\t' << FitVec[time_index].coef.size() << '\t';
for (int i = 0; i < FitVec[time_index].coef.size(); i++)
{
output << FitVec[time_index].coef[i] << '\t';
}
output << '\n';
}
}
TH2D *CCM::FixMatrix()
{
if (!fFitDone)
{
std::cerr << "Warning! PerformFits() function was not yet called, it will be called with default parameters "
"(valid only, no spline)"
<< std::endl;
this->PerformFits();
}
fFixedTEMAT = dynamic_cast<TH2D *>(V.TEMAT->Clone(Form("%s_corrected", V.TEMAT->GetName())));
fFixedTEMAT->Reset();
Double_t bin_cont;
Double_t total_ratio, en_low_edge, en_up_edge, new_en_low_edge, new_en_up_edge;
Int_t global_bin, bin_start, bin_end;
const Double_t bin_width = V.TEMAT->GetYaxis()->GetBinWidth(1);
const TAxis *axis = V.TEMAT->GetYaxis();
for (int time_bin = 1; time_bin <= V.TEMAT->GetXaxis()->GetNbins(); time_bin++)
{
// load function with parameters
TF1 *fcn{nullptr};
for (int i = 0; i < fCorrectionFunctions.size(); i++)
{
if (FitVec[time_bin - 1].functionUsed == std::string(fCorrectionFunctions[i].first->GetName()))
{
fcn = fCorrectionFunctions[i].first;
break;
}
}
if (fcn == nullptr)
{
throw std::runtime_error("No function found for time slice " + std::to_string(time_bin) + " with name " +
FitVec[time_bin - 1].functionUsed);
}
for (unsigned int i = 0; i < FitVec[time_bin - 1].coef.size(); i++)
{
fcn->SetParameter(i, FitVec[time_bin - 1].coef[i]);
}
if (strcmp(fcn->GetName(), "useless_function") == 0)
continue;
// set bins
for (int en_bin = 1; en_bin <= axis->GetNbins(); en_bin++)
{
bin_cont = V.TEMAT->GetBinContent(V.TEMAT->GetBin(time_bin, en_bin));
if (bin_cont == 0)
continue;
// we need to get the new corrected energies that are matching low and up edges of the old bin
en_low_edge = axis->GetBinLowEdge(en_bin);
en_up_edge = axis->GetBinUpEdge(en_bin);
new_en_low_edge = fcn->Eval(en_low_edge);
new_en_up_edge = fcn->Eval(en_up_edge);
// the new_en will not cover range that might be multiple bins in width, and there is also a difference in
// coverage - new low edge will cover only partially the new bin, same for up edge so we need to get ratios
// on how to distribute the content of the old bin to the new bins
bin_start = axis->FindBin(new_en_low_edge);
bin_end = axis->FindBin(new_en_up_edge);
// in case we are covering just 1 bin, put the content in
if (bin_start == bin_end)
{
global_bin = fFixedTEMAT->GetBin(time_bin, bin_start);
fFixedTEMAT->AddBinContent(global_bin, bin_cont);
continue;
}
// get to total ratio of "bin equivalent widths" we are covering with the new energy
total_ratio = static_cast<double>(bin_end - bin_start - 1);
// std::cout << std::setprecision(6) << "total ratio " << total_ratio << " ";
total_ratio += (double)(axis->GetBinUpEdge(bin_start) - new_en_low_edge) / (double)bin_width;
// std::cout << std::setprecision(6) << total_ratio << " ";
total_ratio += (new_en_up_edge - axis->GetBinLowEdge(bin_end)) / bin_width;
// std::cout << std::setprecision(6) << total_ratio << std::endl;
// set manually to new lower bin content
{
global_bin = fFixedTEMAT->GetBin(time_bin, bin_start);
fFixedTEMAT->AddBinContent(global_bin,
(bin_cont * (axis->GetBinUpEdge(bin_start) - new_en_low_edge) / bin_width) /
total_ratio);
}
// set manually to new upper bin content
{
global_bin = fFixedTEMAT->GetBin(time_bin, bin_end);
fFixedTEMAT->AddBinContent(
global_bin, (bin_cont * (new_en_up_edge - axis->GetBinLowEdge(bin_end)) / bin_width) / total_ratio);
}
// in case there are more bins in between, fill them here (skipping first already bin_start and bin_end)
for (int ybin = bin_start + 1; ybin < bin_end; ybin++)
{
global_bin = fFixedTEMAT->GetBin(time_bin, ybin);
fFixedTEMAT->AddBinContent(global_bin, bin_cont / total_ratio);
}
}
}
fFixedTEMAT->SetEntries(V.TEMAT->GetEntries());
fFixedTEMAT->ResetStats();
return fFixedTEMAT;
}
TH2D *CCM::FixMatrix(const TH2D *input_mat, const bool valid_only)
{
if (!fFitDone)
{
std::cerr << "Warning! PerformFits() function was not yet called, it will be called with default parameters "
"(valid only, no spline)"
<< std::endl;
this->PerformFits();
}
TH2D *fixed_mat = dynamic_cast<TH2D *>(input_mat->Clone(Form("%s_corrected", input_mat->GetName())));
fixed_mat->Reset();
fixed_mat->SetDirectory(0);
Double_t bin_cont;
Double_t total_ratio, en_low_edge, en_up_edge, new_en_low_edge, new_en_up_edge;
Int_t global_bin, bin_start, bin_end;
const Double_t bin_width = fixed_mat->GetYaxis()->GetBinWidth(1);
const TAxis *axis = fixed_mat->GetYaxis();
std::vector<TGraph> roi_graphs;
std::vector<TSpline3> roi_splines;
// replace missing poi
for (int ROI_index = 0; ROI_index < V.number_of_ROIs; ROI_index++)
{
roi_graphs.emplace_back();
roi_graphs.back().SetName(Form("graph_ROI_%i", ROI_index));
roi_graphs.back().SetTitle(Form("graph of ROI %i; time slice index; energy shift [energy units]", ROI_index));
for (int time_index = 0; time_index < V.time_bins; time_index++)
{
if (valid_only && !ResVec[ROI_index][time_index].isValid)
continue;
roi_graphs.back().AddPoint(this->GetMatrixTime(time_index),
V.ROIs[ROI_index].desired_energy - ResVec[ROI_index][time_index].energy_shift);
}
}
for (auto &gr : roi_graphs)
{
roi_splines.emplace_back(Form("spline_%s", gr.GetName()), &gr);
}
double timestamp;
TF1 *fcn{nullptr};
std::pair<TF1 *, std::string> *correction_fcn{nullptr};
for (int time_bin = 1; time_bin <= fixed_mat->GetXaxis()->GetNbins(); time_bin++)
{
timestamp = input_mat->GetXaxis()->GetBinCenter(time_bin);
// load function with parameters
{
TGraph gr;
int roi_index = 0;
for (const TSpline3 &spline : roi_splines)
{
if (timestamp < spline.GetXmin())
{
gr.AddPoint(V.ROIs[roi_index].desired_energy, spline.Eval(spline.GetXmin()));
continue;
}
if (timestamp > spline.GetXmax())
{
gr.AddPoint(V.ROIs[roi_index].desired_energy, spline.Eval(spline.GetXmax()));
continue;
}
gr.AddPoint(V.ROIs[roi_index].desired_energy, spline.Eval(timestamp));
roi_index++;
}
if (gr.GetN() == 0)
{
correction_fcn = this->FindCorrectionFunction(0);
}
else
{
correction_fcn = this->FindCorrectionFunction(gr.GetN());
gr.Fit(correction_fcn->first, correction_fcn->second.c_str());
}
}
// set bins
for (int en_bin = 1; en_bin <= axis->GetNbins(); en_bin++)
{
bin_cont = input_mat->GetBinContent(input_mat->GetBin(time_bin, en_bin));
if (bin_cont == 0)
continue;
// we need to get the new corrected energies that are matching low and up edges of the old bin
en_low_edge = axis->GetBinLowEdge(en_bin);
en_up_edge = axis->GetBinUpEdge(en_bin);
new_en_low_edge = correction_fcn->first->Eval(en_low_edge);
new_en_up_edge = correction_fcn->first->Eval(en_up_edge);
// the new_en will not cover range that might be multiple bins in width, and there is also a difference in
// coverage - new low edge will cover only partially the new bin, same for up edge so we need to get ratios
// on how to distribute the content of the old bin to the new bins
bin_start = axis->FindBin(new_en_low_edge);
bin_end = axis->FindBin(new_en_up_edge);
// in case we are covering just 1 bin, put the content in
if (bin_start == bin_end)
{
global_bin = fixed_mat->GetBin(time_bin, bin_start);
fixed_mat->AddBinContent(global_bin, bin_cont);
continue;
}
// get to total ratio of "bin equivalent widths" we are covering with the new energy
total_ratio = static_cast<double>(bin_end - bin_start - 1);
// std::cout << std::setprecision(6) << "total ratio " << total_ratio << " ";
total_ratio += (double)(axis->GetBinUpEdge(bin_start) - new_en_low_edge) / (double)bin_width;
// std::cout << std::setprecision(6) << total_ratio << " ";
total_ratio += (new_en_up_edge - axis->GetBinLowEdge(bin_end)) / bin_width;
// std::cout << std::setprecision(6) << total_ratio << std::endl;
// set manually to new lower bin content
{
global_bin = fixed_mat->GetBin(time_bin, bin_start);
fixed_mat->AddBinContent(global_bin,
(bin_cont * (axis->GetBinUpEdge(bin_start) - new_en_low_edge) / bin_width) /
total_ratio);
}
// set manually to new upper bin content
{
global_bin = fixed_mat->GetBin(time_bin, bin_end);
fixed_mat->AddBinContent(
global_bin, (bin_cont * (new_en_up_edge - axis->GetBinLowEdge(bin_end)) / bin_width) / total_ratio);
}
// in case there are more bins in between, fill them here (skipping first already bin_start and bin_end)
for (int ybin = bin_start + 1; ybin < bin_end; ybin++)
{
global_bin = fixed_mat->GetBin(time_bin, ybin);
fixed_mat->AddBinContent(global_bin, bin_cont / total_ratio);
}
}
}
fixed_mat->SetEntries(input_mat->GetEntries());
fixed_mat->ResetStats();
return fixed_mat;
}
void CCM::FixTree(const std::string &tfilename, const std::string &treename, const std::string &e_branchname,
const std::string &ts_branchname, const bool valid_only, const int time_subdivision)
{
// input checks
TFile *old_file = TFile::Open(tfilename.c_str(), "READ");
if (!old_file || old_file->IsZombie())
{
std::cerr << "Error opening file\n";
return;
}
TTree *old_tree = (TTree *)old_file->Get(treename.c_str());
if (!old_tree)
{
std::cerr << "Error getting tree\n";
return;
}
TBranch *branch_e = old_tree->GetBranch(e_branchname.c_str());
TBranch *branch_t = old_tree->GetBranch(ts_branchname.c_str());
if (!branch_e || !branch_t)
{
std::cerr << "Branch does not exist\n";
return;
}
// if (!fFitDone)
// {
// std::cerr << "Warning! PerformFits() function was not yet called, it will be called with default parameters "
// "(valid only, no spline)"
// << std::endl;
// this->PerformFits();
// }
// prepare new root file
// copy all branches but the corrected ones
old_tree->SetBranchStatus("*", 1);
old_tree->SetBranchStatus(e_branchname.c_str(), 0);
// create new file and clone the tree
std::string new_file = "corrected_" + tfilename.substr(tfilename.find_last_of('/') + 1);
TFile *new_tfile = new TFile(new_file.c_str(), "RECREATE");
TTree *new_tree = old_tree->CloneTree();
// add missing branches in the new tree
double new_e, old_e;
Long64_t timestamp;
TBranch *new_branch_e = new_tree->Branch(e_branchname.c_str(), &new_e);
// now we need to iterate through the old tree to get the original energy and timestamp, and store corrected values
// in a new tree
old_tree->SetBranchStatus("*", 0);
old_tree->SetBranchStatus(e_branchname.c_str(), 1);