BCHistogramFitter.cxx

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/*
 * Copyright (C) 2007-2013, the BAT core developer team
 * All rights reserved.
 *
 * For the licensing terms see doc/COPYING.
 * For documentation see http://mpp.mpg.de/bat
 */

// ---------------------------------------------------------

#include "BCHistogramFitter.h"
#include "BAT/BCLog.h"
#include "BAT/BCDataSet.h"
#include "BAT/BCDataPoint.h"
#include "BAT/BCMath.h"

#include <TH1D.h>
#include <TF1.h>
#include <TGraph.h>
#include <TString.h>
#include <TPad.h>
#include <TRandom3.h>
#include <TLegend.h>
#include <TMath.h>
#include <Math/ProbFuncMathCore.h> //for ROOT::Math namespace
#include <TString.h>

// ---------------------------------------------------------

BCHistogramFitter::BCHistogramFitter()
 : BCFitter()
 , fHistogram(0)
 , fFitFunction(0)
 , fHistogramExpected(0)
{
   // set default options and values
   MCMCSetNIterationsRun(2000);
   SetFillErrorBand();
   fFlagIntegration = true;
   flag_discrete = true;

   // set MCMC for marginalization
   SetMarginalizationMethod(BCIntegrate::kMargMetropolis);
}

// ---------------------------------------------------------

BCHistogramFitter::BCHistogramFitter(const char * name)
 : BCFitter(name)
 , fHistogram(0)
 , fFitFunction(0)
 , fHistogramExpected(0)
{
   // set default options and values
   MCMCSetNIterationsRun(2000);
   SetFillErrorBand();
   fFlagIntegration = true;
   flag_discrete = true;

   // set MCMC for marginalization
   SetMarginalizationMethod(BCIntegrate::kMargMetropolis);
}

// ---------------------------------------------------------

BCHistogramFitter::BCHistogramFitter(TH1D * hist, TF1 * func)
 : BCFitter()
 , fHistogram(0)
 , fFitFunction(0)
 , fHistogramExpected(0)
{
   SetHistogram(hist);
   SetFitFunction(func);

   MCMCSetNIterationsRun(2000);
   SetFillErrorBand();
   fFlagIntegration = true;
   flag_discrete = true;

   // set MCMC for marginalization
   SetMarginalizationMethod(BCIntegrate::kMargMetropolis);
}

// ---------------------------------------------------------

BCHistogramFitter::BCHistogramFitter(const char * name, TH1D * hist, TF1 * func)
 : BCFitter(name)
 , fHistogram(0)
 , fFitFunction(0)
 , fHistogramExpected(0)
{
   SetHistogram(hist);
   SetFitFunction(func);

   MCMCSetNIterationsRun(2000);
   SetFillErrorBand();
   fFlagIntegration = true;
   flag_discrete = true;

   // set MCMC for marginalization
   SetMarginalizationMethod(BCIntegrate::kMargMetropolis);
}

// ---------------------------------------------------------

int BCHistogramFitter::SetHistogram(TH1D * hist)
{
   // check if histogram exists
   if (!hist) {
      BCLog::OutError("BCHistogramFitter::SetHistogram : TH1D not created.");
      return 0;
   }

   // set pointer to histogram
   fHistogram = hist;

   // create a data set. this is necessary in order to calculate the
   // error band. the data set contains as many data points as there
   // are bins.
   BCDataSet * ds = new BCDataSet();

   // create data points and add them to the data set.
   // the x value is the lower edge of the bin, and
   // the y value is the bin count
   int nbins = fHistogram->GetNbinsX();
   for (int i = 0; i < nbins; ++i) {
      BCDataPoint* dp = new BCDataPoint(2);
      dp ->SetValue(0, fHistogram->GetBinLowEdge(i + 1));
      dp ->SetValue(1, fHistogram->GetBinContent(i + 1));
      ds->AddDataPoint(dp);
   }

   // set the new data set.
   SetDataSet(ds);

   // calculate the lower and upper edge in x.
   double xmin = hist->GetBinLowEdge(1);
   double xmax = hist->GetBinLowEdge(nbins + 1);

   // calculate the minimum and maximum range in y.
   double histymin = hist->GetMinimum();
   double histymax = hist->GetMaximum();

   // calculate the minimum and maximum of the function value based on
   // the minimum and maximum value in y.
   double ymin = TMath::Max(0., histymin - 5. * sqrt(histymin));
   double ymax = histymax + 5. * sqrt(histymax);

   // set the data boundaries for x and y values.
   SetDataBoundaries(0, xmin, xmax);
   SetDataBoundaries(1, ymin, ymax);

   // set the indeces for fitting.
   SetFitFunctionIndices(0, 1);

   // no error
   return 1;
}

// ---------------------------------------------------------

int BCHistogramFitter::SetHistogramExpected(const std::vector<double> & parameters)
{
   //clear up previous memory
   if (fHistogramExpected) {
      delete fHistogramExpected;
   }
   //copy all properties from the data histogram
   fHistogramExpected = new TH1D(*fHistogram);

   // get the number of bins
   int nBins = fHistogramExpected->GetNbinsX();

   // get bin width
   double dx = fHistogramExpected->GetBinWidth(1);

   //set the parameters of fit function
   fFitFunction->SetParameters(&parameters[0]);

   // get function value of lower bin edge
   double fedgelow = fFitFunction->Eval(fHistogramExpected->GetBinLowEdge(1));

   // loop over all bins, skip underflow
   for (int ibin = 1; ibin <= nBins; ++ibin) {
      // get upper bin edge
      double xedgehi = fHistogramExpected->GetBinLowEdge(ibin) + dx;

      //expected count
      double yexp = 0.;

      // use ROOT's TH1D::Integral method
      if (fFlagIntegration)
    yexp = fFitFunction->Integral(xedgehi - dx, xedgehi);

      // use linear interpolation
      else {
    // get function value at upper bin edge
    double fedgehi = fFitFunction->Eval(xedgehi);
    yexp = fedgelow * dx + (fedgehi - fedgelow) * dx / 2.;

    // make the upper edge the lower edge for the next iteration
    fedgelow = fedgehi;
      }

      //write the expectation for the bin
      fHistogramExpected->SetBinContent(ibin, yexp);

      //avoid automatic error as sqrt(yexp), used e.g. in Kolmogorov correction factor
      fHistogramExpected->SetBinError(ibin, 0.0);

      // but the data under this model have that sqrt(yexp) uncertainty
      fHistogram->SetBinError(ibin, sqrt(yexp));

   }
   return 1;
}

// ---------------------------------------------------------

int BCHistogramFitter::SetFitFunction(TF1 * func)
{
   // check if function exists
   if (!func) {
      BCLog::OutError("BCHistogramFitter::SetFitFunction : TF1 not created.");
      return 0;
   }

   // set the function
   fFitFunction = func;

   // update the model name to contain the function name
   if(fName=="model")
      SetName(TString::Format("HistogramFitter with %s", fFitFunction->GetName()));

   // reset parameters
   ClearParameters(true);

   // get the new number of parameters
   int n = func->GetNpar();

   // add parameters
   for (int i = 0; i < n; ++i) {
      double xmin;
      double xmax;

      func->GetParLimits(i, xmin, xmax);

      AddParameter(func->GetParName(i), xmin, xmax);
   }

   // set flat prior for all parameters by default
   SetPriorConstantAll();

   return GetNParameters();
}

// ---------------------------------------------------------

BCHistogramFitter::~BCHistogramFitter()
{
   // todo memory leak, many members not removed
   delete fHistogramExpected;
}

// ---------------------------------------------------------

double BCHistogramFitter::LogLikelihood(const std::vector<double> & params)
{
   // initialize probability
   double loglikelihood = 0;

   // set the parameters of the function
   fFitFunction->SetParameters(&params[0]);

   // get the number of bins
   int nbins = fHistogram->GetNbinsX();

   // get bin width
   double dx = fHistogram->GetBinWidth(1);

   // get function value of lower bin edge
   double fedgelow = fFitFunction->Eval(fHistogram->GetBinLowEdge(1));

   // loop over all bins
   for (int ibin = 1; ibin <= nbins; ++ibin) {
      // get upper bin edge
      double xedgehi = fHistogram->GetBinLowEdge(ibin) + dx;

      // get function value at upper bin edge
      double fedgehi = fFitFunction->Eval(xedgehi);

      // get the number of observed events
      double y = fHistogram->GetBinContent(ibin);

      double yexp = 0.;

      // use ROOT's TH1D::Integral method
      if (fFlagIntegration)
    yexp = fFitFunction->Integral(xedgehi - dx, xedgehi);

      // use linear interpolation
      else {
    yexp = fedgelow * dx + (fedgehi - fedgelow) * dx / 2.;

    // make the upper edge the lower edge for the next iteration
    fedgelow = fedgehi;
      }

      // get the value of the Poisson distribution
      loglikelihood += BCMath::LogPoisson(y, yexp);
   }

   return loglikelihood;
}

// ---------------------------------------------------------

double BCHistogramFitter::FitFunction(const std::vector<double> & x, const std::vector<double> & params)
{
   // set the parameters of the function
   fFitFunction->SetParameters(&params[0]);

   return fFitFunction->Eval(x[0]) * fHistogram->GetBinWidth(fHistogram->FindBin(x[0]));
}

// ---------------------------------------------------------

int BCHistogramFitter::Fit(TH1D * hist, TF1 * func)
{
   // set histogram
   if (hist)
      SetHistogram(hist);
   else {
      BCLog::OutError("BCHistogramFitter::Fit : Histogram not defined.");
      return 0;
   }

   // set function
   if (func)
      SetFitFunction(func);
   else {
      BCLog::OutError("BCHistogramFitter::Fit : Fit function not defined.");
      return 0;
   }

   return Fit();
}

// ---------------------------------------------------------

int BCHistogramFitter::Fit()
{
   // set histogram
   if (!fHistogram) {
      BCLog::OutError("BCHistogramFitter::Fit : Histogram not defined.");
      return 0;
   }

   // set function
   if (!fFitFunction) {
      BCLog::OutError("BCHistogramFitter::Fit : Fit function not defined.");
      return 0;
   }

   // perform marginalization
   MarginalizeAll();

   // maximize posterior probability, using the best-fit values close
   // to the global maximum from the MCMC
   BCIntegrate::BCOptimizationMethod method_temp = GetOptimizationMethod();
   SetOptimizationMethod(BCIntegrate::kOptMinuit);
   FindMode( GetBestFitParameters());
   SetOptimizationMethod(method_temp);

   // calculate the p-value using the fast MCMC algorithm
   if( !CalculatePValueFast(GetBestFitParameters()))
      BCLog::OutWarning(
       "BCHistogramFitter::Fit : Could not use the fast p-value evaluation.");

   // print summary to screen
   PrintShortFitSummary();

   // no error
   return 1;
}

// ---------------------------------------------------------

void BCHistogramFitter::DrawFit(const char * options, bool flaglegend)
{
   if (!fHistogram) {
      BCLog::OutError("BCHistogramFitter::DrawFit : Histogram not defined.");
      return;
   }

   if (!fFitFunction) {
      BCLog::OutError("BCHistogramFitter::DrawFit : Fit function not defined.");
      return;
   }

   if (!fErrorBandXY || GetBestFitParameters().empty()) {
      BCLog::OutError("BCHistogramFitter::DrawFit : Fit not performed yet.");
      return;
   }

   // check wheather options contain "same"
   TString opt = options;
   opt.ToLower();

   // if not same, draw the histogram first to get the axes
   if (!opt.Contains("same"))
      fHistogram->Draw(opt.Data());

   // draw the error band as central 68% probability interval
   fErrorBand = GetErrorBandGraph(0.16, 0.84);
   fErrorBand->Draw("f same");

   // now draw the histogram again since it was covered by the band
   fHistogram->Draw(TString::Format("%ssame", opt.Data()));

   // draw the fit function on top
   fGraphFitFunction = GetFitFunctionGraph(GetBestFitParameters());
   fGraphFitFunction->SetLineColor(kRed);
   fGraphFitFunction->SetLineWidth(2);
   fGraphFitFunction->Draw("l same");

   // draw legend
   if (flaglegend) {
      TLegend * legend = new TLegend(0.25, 0.75, 0.55, 0.95);
      legend->SetBorderSize(0);
      legend->SetFillColor(kWhite);
      legend->AddEntry(fHistogram, "Data", "L");
      legend->AddEntry(fGraphFitFunction, "Best fit", "L");
      legend->AddEntry(fErrorBand, "Error band", "F");
      legend->Draw();
   }

   gPad->RedrawAxis();
}

// ---------------------------------------------------------
int BCHistogramFitter::CalculatePValueFast(const std::vector<double> & par, unsigned nIterations)
{
   // check size of parameter vector
   if (par.size() != GetNParameters()) {
      BCLog::OutError(
       "BCHistogramFitter::CalculatePValueFast : Number of parameters is inconsistent.");
      return 0;
   }

   // check if histogram exists
   if (!fHistogram) {
      BCLog::OutError(
       "BCHistogramFitter::CalculatePValueFast : Histogram not defined.");
      return 0;
   }

   //update the expected number of events for all bins
   SetHistogramExpected(par);

   // copy observed and expected values
   std::vector<unsigned> observed(fHistogram->GetNbinsX());
   std::vector<double> expected(fHistogramExpected->GetNbinsX());

   for (int ibin = 0 ; ibin < fHistogram->GetNbinsX(); ++ibin){
      observed[ibin] = (unsigned int) fHistogram->GetBinContent(ibin + 1);
      expected[ibin] = fHistogramExpected->GetBinContent(ibin + 1);
   }

   // create pseudo experiments
   fPValue = BCMath::FastPValue(observed, expected, nIterations, fRandom->GetSeed());

   // correct for fitting bias
   fPValueNDoF = BCMath::CorrectPValue(fPValue, GetNParameters(), fHistogram->GetNbinsX());

   // no error
   return 1;
}

// ---------------------------------------------------------
int BCHistogramFitter::CalculatePValueLikelihood(const std::vector<double> & par)
{
   // initialize test statistic -2*lambda
   double logLambda = 0.0;

   //Calculate expected counts to compare with
   SetHistogramExpected(par);

   for (int ibin = 1; ibin <= fHistogram->GetNbinsX(); ++ibin) {

      // get the number of observed events
      double y = fHistogram->GetBinContent(ibin);

      // get the number of expected events
      double yexp = fHistogramExpected->GetBinContent(ibin);

      // get the contribution from this datapoint
      if (y == 0)
         logLambda += yexp;
      else
         logLambda += yexp - y + y * log(y / yexp);
   }

   // rescale
   logLambda *= 2.0;

   //p value from chi^2 distribution, returns zero if logLambda < 0
   fPValue = TMath::Prob(logLambda, GetNDataPoints());
   fPValueNDoF = TMath::Prob(logLambda, GetNDataPoints() - GetNParameters());

   // no error
   return 1;
}

// ---------------------------------------------------------

int BCHistogramFitter::CalculatePValueLeastSquares(const std::vector<double> & par, bool weightExpect)
{
   // initialize test statistic chi^2
   double chi2 = 0.0;

   //Calculate expected counts to compare with
   SetHistogramExpected(par);

   for (int ibin = 1; ibin <= fHistogram->GetNbinsX(); ++ibin) {

      // get the number of observed events
      double y = fHistogram->GetBinContent(ibin);

      // get the number of expected events
      double yexp = fHistogramExpected->GetBinContent(ibin);

      //convert 1/0.0 into 1 for weighted sum
      double weight;
      if (weightExpect)
         weight = (yexp > 0) ? yexp : 1.0;
      else
         weight = (y > 0) ? y : 1.0;

      // get the contribution from this datapoint
      chi2 += (y - yexp) * (y - yexp) / weight;
   }

   // p value from chi^2 distribution
   fPValue = TMath::Prob(chi2, GetNDataPoints());
   fPValueNDoF = TMath::Prob(chi2, GetNDataPoints() - GetNParameters());

   // no error
   return 1;
}

// ---------------------------------------------------------

int BCHistogramFitter::CalculatePValueKolmogorov(const std::vector<double> & par)
{
   if (!fHistogramExpected || !fHistogram) {
      BCLog::OutError("BCHistogramFitter::CalculatePValueKolmogorov: "
            "Please define the reference distribution by calling \n"
            "BCHistogramFitter::SetHistogramExpected() first!");
      return 0;
   }

   //update expected counts with current parameters
   SetHistogramExpected(par);

   //perform the test
   fPValue = fHistogramExpected->KolmogorovTest(fHistogram);
   fPValue = BCMath::CorrectPValue(fPValue, GetNParameters(), GetNDataPoints());

   // no error
   return 1;
}

// ---------------------------------------------------------

double BCHistogramFitter::CDF(const std::vector<double>& parameters, int index, bool lower)
{

   if (parameters.empty())
      BCLog::OutWarning("BCHistogramFitter::CDF: parameter vector empty!");
   //histogram stores underflow in bin 0, so datapoint 0 is in bin 1
   index++;

   // get the number of observed events (should be integer)
   double yObs = fHistogram->GetBinContent(index);

   // get function value of lower bin edge
   double edgeLow = fHistogram->GetBinLowEdge(index);
   double edgeHigh = edgeLow + fHistogram->GetBinWidth(index);

   // expectation value of this bin
   double yExp = 0.0;

   // use ROOT's TH1D::Integral method
   if (fFlagIntegration)
      yExp = fFitFunction->Integral(edgeLow, edgeHigh, &parameters[0]);

   // use linear interpolation
   else {
      double dx = fHistogram->GetBinWidth(index);
      double fEdgeLow = fFitFunction->Eval(edgeLow);
      double fEdgeHigh = fFitFunction->Eval(edgeHigh);
      yExp = fEdgeLow * dx + (fEdgeHigh - fEdgeLow) * dx / 2.;
   }

   // usually Poisson bins do not agree with fixed probability bins
   // so choose where it should belong

   if (lower) {
      if ((int) yObs >= 1)
    return ROOT::Math::poisson_cdf((unsigned int) (yObs - 1), yExp);
      else
    return 0.0;
   }
   // what if yObs as double doesn't reprepsent a whole number? exception?
   if ((double) (unsigned int) yObs != yObs) {
      BCLog::OutWarning(Form(
       "BCHistogramFitter::CDF: Histogram values should be integer!\n"
          " Bin %d = %f", index, yObs));

      //convert randomly to integer
      // ex. yObs = 9.785 =>
      //      yObs --> 10 with P = 78.5%
      //      yObs --> 9  with P = 21.5%
      double U = fRandom->Rndm();
      double yObsLower = (unsigned int) yObs;
      if (U > (yObs - yObsLower))
    yObs = yObsLower;
      else
    yObs = yObsLower + 1;
   }

   return ROOT::Math::poisson_cdf((unsigned int) yObs, yExp);
}

// ---------------------------------------------------------