%%cpp -d
#include <iostream> // Stream declarations
#include <vector>
#include <limits>

#include "TChain.h"
#include "TCut.h"
#include "TDirectory.h"
#include "TH1F.h"
#include "TH1.h"
#include "TMath.h"
#include "TFile.h"
#include "TStopwatch.h"
#include "TROOT.h"
#include "TSystem.h"

#include "TMVA/GeneticAlgorithm.h"
#include "TMVA/GeneticFitter.h"
#include "TMVA/IFitterTarget.h"
#include "TMVA/Factory.h"
#include "TMVA/DataLoader.h"//required to load dataset
#include "TMVA/Reader.h"

using std::vector, std::cout, std::endl;

using namespace TMVA;

%%cpp -d

class MyFitness : public IFitterTarget {
public:
   // constructor
   MyFitness( TChain* _chain ) : IFitterTarget() {
      chain = _chain;

      hSignal = new TH1F("hsignal","hsignal",100,-1,1);
      hFP = new TH1F("hfp","hfp",100,-1,1);
      hTP = new TH1F("htp","htp",100,-1,1);

      TString cutsAndWeightSignal  = "weight*(classID==0)";
      nSignal = chain->Draw("Entry$/Entries$>>hsignal",cutsAndWeightSignal,"goff");
      weightsSignal = hSignal->Integral();

   }

   // the output of this function will be minimized
   Double_t EstimatorFunction( std::vector<Double_t> & factors ){

      TString cutsAndWeightTruePositive  = Form("weight*((classID==0) && cls0>%f && cls1>%f && cls2>%f )",factors.at(0), factors.at(1), factors.at(2));
      TString cutsAndWeightFalsePositive = Form("weight*((classID >0) && cls0>%f && cls1>%f && cls2>%f )",factors.at(0), factors.at(1), factors.at(2));

      // Entry$/Entries$ just draws something reasonable. Could in principle anything
      Float_t nTP = chain->Draw("Entry$/Entries$>>htp",cutsAndWeightTruePositive,"goff");
      Float_t nFP = chain->Draw("Entry$/Entries$>>hfp",cutsAndWeightFalsePositive,"goff");

      weightsTruePositive = hTP->Integral();
      weightsFalsePositive = hFP->Integral();

      efficiency = 0;
      if( weightsSignal > 0 )
    efficiency = weightsTruePositive/weightsSignal;

      purity = 0;
      if( weightsTruePositive+weightsFalsePositive > 0 )
    purity = weightsTruePositive/(weightsTruePositive+weightsFalsePositive);

      Float_t effTimesPur = efficiency*purity;

      Float_t toMinimize = std::numeric_limits<float>::max(); // set to the highest existing number
      if( effTimesPur > 0 ) // if larger than 0, take 1/x. This is the value to minimize
    toMinimize = 1./(effTimesPur); // we want to minimize 1/efficiency*purity

      // Print();

      return toMinimize;
   }


   void Print(){
      std::cout << std::endl;
      std::cout << "======================" << std::endl
      << "Efficiency : " << efficiency << std::endl
      << "Purity     : " << purity << std::endl << std::endl
      << "True positive weights : " << weightsTruePositive << std::endl
      << "False positive weights: " << weightsFalsePositive << std::endl
      << "Signal weights        : " << weightsSignal << std::endl;
   }

   Float_t nSignal;

   Float_t efficiency;
   Float_t purity;
   Float_t weightsTruePositive;
   Float_t weightsFalsePositive;
   Float_t weightsSignal;


private:
   TChain* chain;
   TH1F* hSignal;
   TH1F* hFP;
   TH1F* hTP;

};

%%cpp -d
void Training(){
   std::string factoryOptions( "!V:!Silent:Transformations=I;D;P;G,D:AnalysisType=Classification" );
   TString fname = "./tmva_example_multiple_background.root";

   TFile *input(0);
   input = TFile::Open( fname );

   TTree *signal      = (TTree*)input->Get("TreeS");
   TTree *background0 = (TTree*)input->Get("TreeB0");
   TTree *background1 = (TTree*)input->Get("TreeB1");
   TTree *background2 = (TTree*)input->Get("TreeB2");

   / global event weights per tree (see below for setting event-wise weights)
   Double_t signalWeight      = 1.0;
   Double_t background0Weight = 1.0;
   Double_t background1Weight = 1.0;
   Double_t background2Weight = 1.0;

    Create a new root output file.
   TString outfileName( "TMVASignalBackground0.root" );
   TFile* outputFile = TFile::Open( outfileName, "RECREATE" );



    background 0
    ____________
   TMVA::Factory *factory = new TMVA::Factory( "TMVAMultiBkg0", outputFile, factoryOptions );
   TMVA::DataLoader *dataloader=new TMVA::DataLoader("datasetBkg0");

   dataloader->AddVariable( "var1", "Variable 1", "", 'F' );
   dataloader->AddVariable( "var2", "Variable 2", "", 'F' );
   dataloader->AddVariable( "var3", "Variable 3", "units", 'F' );
   dataloader->AddVariable( "var4", "Variable 4", "units", 'F' );

   dataloader->AddSignalTree    ( signal,     signalWeight       );
   dataloader->AddBackgroundTree( background0, background0Weight );

        factory->SetBackgroundWeightExpression("weight");
   TCut mycuts = "";  for example: TCut mycuts = "abs(var1)<0.5 && abs(var2-0.5)<1";
   TCut mycutb = "";  for example: TCut mycutb = "abs(var1)<0.5";

    tell the factory to use all remaining events in the trees after training for testing:
   dataloader->PrepareTrainingAndTestTree( mycuts, mycutb,
                                        "nTrain_Signal=0:nTrain_Background=0:SplitMode=Random:NormMode=NumEvents:!V" );

    Boosted Decision Trees
   factory->BookMethod( dataloader, TMVA::Types::kBDT, "BDTG",
         "!H:!V:NTrees=1000:BoostType=Grad:Shrinkage=0.30:UseBaggedBoost:BaggedSampleFraction=0.6:SeparationType=GiniIndex:nCuts=20:MaxDepth=2" );
   factory->TrainAllMethods();
   factory->TestAllMethods();
   factory->EvaluateAllMethods();

   outputFile->Close();

   delete factory;
   delete dataloader;



    background 1
    ____________

   outfileName = "TMVASignalBackground1.root";
   outputFile = TFile::Open( outfileName, "RECREATE" );
   dataloader=new TMVA::DataLoader("datasetBkg1");

   factory = new TMVA::Factory( "TMVAMultiBkg1", outputFile, factoryOptions );
   dataloader->AddVariable( "var1", "Variable 1", "", 'F' );
   dataloader->AddVariable( "var2", "Variable 2", "", 'F' );
   dataloader->AddVariable( "var3", "Variable 3", "units", 'F' );
   dataloader->AddVariable( "var4", "Variable 4", "units", 'F' );

   dataloader->AddSignalTree    ( signal,     signalWeight       );
   dataloader->AddBackgroundTree( background1, background1Weight );

    dataloader->SetBackgroundWeightExpression("weight");

    tell the factory to use all remaining events in the trees after training for testing:
   dataloader->PrepareTrainingAndTestTree( mycuts, mycutb,
                                        "nTrain_Signal=0:nTrain_Background=0:SplitMode=Random:NormMode=NumEvents:!V" );

    Boosted Decision Trees
   factory->BookMethod( dataloader, TMVA::Types::kBDT, "BDTG",
         "!H:!V:NTrees=1000:BoostType=Grad:Shrinkage=0.30:UseBaggedBoost:BaggedSampleFraction=0.6:SeparationType=GiniIndex:nCuts=20:MaxDepth=2" );
   factory->TrainAllMethods();
   factory->TestAllMethods();
   factory->EvaluateAllMethods();

   outputFile->Close();

   delete factory;
   delete dataloader;


    background 2
    ____________

   outfileName = "TMVASignalBackground2.root";
   outputFile = TFile::Open( outfileName, "RECREATE" );

   factory = new TMVA::Factory( "TMVAMultiBkg2", outputFile, factoryOptions );
   dataloader=new TMVA::DataLoader("datasetBkg2");

   dataloader->AddVariable( "var1", "Variable 1", "", 'F' );
   dataloader->AddVariable( "var2", "Variable 2", "", 'F' );
   dataloader->AddVariable( "var3", "Variable 3", "units", 'F' );
   dataloader->AddVariable( "var4", "Variable 4", "units", 'F' );

   dataloader->AddSignalTree    ( signal,     signalWeight       );
   dataloader->AddBackgroundTree( background2, background2Weight );

        dataloader->SetBackgroundWeightExpression("weight");

    tell the dataloader to use all remaining events in the trees after training for testing:
   dataloader->PrepareTrainingAndTestTree( mycuts, mycutb,
                                        "nTrain_Signal=0:nTrain_Background=0:SplitMode=Random:NormMode=NumEvents:!V" );

    Boosted Decision Trees
   factory->BookMethod( dataloader, TMVA::Types::kBDT, "BDTG",
         "!H:!V:NTrees=1000:BoostType=Grad:Shrinkage=0.30:UseBaggedBoost:BaggedSampleFraction=0.5:SeparationType=GiniIndex:nCuts=20:MaxDepth=2" );
   factory->TrainAllMethods();
   factory->TestAllMethods();
   factory->EvaluateAllMethods();

   outputFile->Close();

   delete factory;
   delete dataloader;

}

%%cpp -d
void ApplicationCreateCombinedTree(){

    Create a new root output file.
   TString outfileName( "tmva_example_multiple_backgrounds__applied.root" );
   TFile* outputFile = TFile::Open( outfileName, "RECREATE" );
   TTree* outputTree = new TTree("multiBkg","multiple backgrounds tree");

   Float_t var1, var2;
   Float_t var3, var4;
   Int_t   classID = 0;
   Float_t weight = 1.f;

   Float_t classifier0, classifier1, classifier2;

   outputTree->Branch("classID", &classID, "classID/I");
   outputTree->Branch("var1", &var1, "var1/F");
   outputTree->Branch("var2", &var2, "var2/F");
   outputTree->Branch("var3", &var3, "var3/F");
   outputTree->Branch("var4", &var4, "var4/F");
   outputTree->Branch("weight", &weight, "weight/F");
   outputTree->Branch("cls0", &classifier0, "cls0/F");
   outputTree->Branch("cls1", &classifier1, "cls1/F");
   outputTree->Branch("cls2", &classifier2, "cls2/F");


    create three readers for the three different signal/background classifications, .. one for each background
   TMVA::Reader *reader0 = new TMVA::Reader( "!Color:!Silent" );
   TMVA::Reader *reader1 = new TMVA::Reader( "!Color:!Silent" );
   TMVA::Reader *reader2 = new TMVA::Reader( "!Color:!Silent" );

   reader0->AddVariable( "var1", &var1 );
   reader0->AddVariable( "var2", &var2 );
   reader0->AddVariable( "var3", &var3 );
   reader0->AddVariable( "var4", &var4 );

   reader1->AddVariable( "var1", &var1 );
   reader1->AddVariable( "var2", &var2 );
   reader1->AddVariable( "var3", &var3 );
   reader1->AddVariable( "var4", &var4 );

   reader2->AddVariable( "var1", &var1 );
   reader2->AddVariable( "var2", &var2 );
   reader2->AddVariable( "var3", &var3 );
   reader2->AddVariable( "var4", &var4 );

    load the weight files for the readers
   TString method =  "BDT method";
   reader0->BookMVA( "BDT method", "datasetBkg0/weights/TMVAMultiBkg0_BDTG.weights.xml" );
   reader1->BookMVA( "BDT method", "datasetBkg1/weights/TMVAMultiBkg1_BDTG.weights.xml" );
   reader2->BookMVA( "BDT method", "datasetBkg2/weights/TMVAMultiBkg2_BDTG.weights.xml" );

    load the input file
   TFile *input(0);
   TString fname = "./tmva_example_multiple_background.root";
   input = TFile::Open( fname );

   TTree* theTree = NULL;

    loop through signal and all background trees
   for( int treeNumber = 0; treeNumber < 4; ++treeNumber ) {
      if( treeNumber == 0 ){
    theTree = (TTree*)input->Get("TreeS");
    std::cout << "--- Select signal sample" << std::endl;
       theTree->SetBranchAddress( "weight", &weight );
    weight = 1;
    classID = 0;
      }else if( treeNumber == 1 ){
    theTree = (TTree*)input->Get("TreeB0");
    std::cout << "--- Select background 0 sample" << std::endl;
       theTree->SetBranchAddress( "weight", &weight );
    weight = 1;
    classID = 1;
      }else if( treeNumber == 2 ){
    theTree = (TTree*)input->Get("TreeB1");
    std::cout << "--- Select background 1 sample" << std::endl;
       theTree->SetBranchAddress( "weight", &weight );
    weight = 1;
    classID = 2;
      }else if( treeNumber == 3 ){
    theTree = (TTree*)input->Get("TreeB2");
    std::cout << "--- Select background 2 sample" << std::endl;
    theTree->SetBranchAddress( "weight", &weight );
    weight = 1;
    classID = 3;
      }


      theTree->SetBranchAddress( "var1", &var1 );
      theTree->SetBranchAddress( "var2", &var2 );
      theTree->SetBranchAddress( "var3", &var3 );
      theTree->SetBranchAddress( "var4", &var4 );


      std::cout << "--- Processing: " << theTree->GetEntries() << " events" << std::endl;
      TStopwatch sw;
      sw.Start();
      Int_t nEvent = theTree->GetEntries();
       Int_t nEvent = 100;
      for (Long64_t ievt=0; ievt<nEvent; ievt++) {

    if (ievt%1000 == 0){
       std::cout << "--- ... Processing event: " << ievt << std::endl;
    }

    theTree->GetEntry(ievt);

     get the classifiers for each of the signal/background classifications
    classifier0 = reader0->EvaluateMVA( method );
    classifier1 = reader1->EvaluateMVA( method );
    classifier2 = reader2->EvaluateMVA( method );

    outputTree->Fill();
      }


       get elapsed time
      sw.Stop();
      std::cout << "--- End of event loop: "; sw.Print();
   }
   input->Close();


    write output tree
/*   outputTree->SetDirectory(outputFile);
     outputTree->Write(); */
   outputFile->Write();

   outputFile->Close();

   std::cout << "--- Created root file: \"" << outfileName.Data() << "\" containing the MVA output histograms" << std::endl;

   delete reader0;
   delete reader1;
   delete reader2;

   std::cout << "==> Application of readers is done! combined tree created" << std::endl << std::endl;

}

%%cpp -d
void MaximizeSignificance(){

         define all the parameters by their minimum and maximum value
         in this example 3 parameters (=cuts on the classifiers) are defined.
        vector<Interval*> ranges;
        ranges.push_back( new Interval(-1,1) );  for some classifiers (especially LD) the ranges have to be taken larger
        ranges.push_back( new Interval(-1,1) );
        ranges.push_back( new Interval(-1,1) );

   std::cout << "Classifier ranges (defined by the user)" << std::endl;
        for( std::vector<Interval*>::iterator it = ranges.begin(); it != ranges.end(); it++ ){
           std::cout << " range: " << (*it)->GetMin() << "   " << (*it)->GetMax() << std::endl;
        }

   TChain* chain = new TChain("multiBkg");
   chain->Add("tmva_example_multiple_backgrounds__applied.root");

        IFitterTarget* myFitness = new MyFitness( chain );

         prepare the genetic algorithm with an initial population size of 20
         mind: big population sizes will help in searching the domain space of the solution
         but you have to weight this out to the number of generations
         the extreme case of 1 generation and populationsize n is equal to
         a Monte Carlo calculation with n tries

        const TString name( "multipleBackgroundGA" );
        const TString opts( "PopSize=100:Steps=30" );

        GeneticFitter mg( *myFitness, name, ranges, opts);
    mg.SetParameters( 4, 30, 200, 10,5, 0.95, 0.001 );

        std::vector<Double_t> result;
        Double_t estimator = mg.Run(result);

   dynamic_cast<MyFitness*>(myFitness)->Print();
   std::cout << std::endl;

   int n = 0;
   for( std::vector<Double_t>::iterator it = result.begin(); it<result.end(); it++ ){
      std::cout << "  cutValue[" << n << "] = " << (*it) << ";"<< std::endl;
      n++;
   }


}

cout << "Start Test TMVAGAexample" << endl
     << "========================" << endl
     << endl;

TString createDataMacro = gROOT->GetTutorialDir() + "/tmva/createData.C";
gROOT->ProcessLine(TString::Format(".L %s",createDataMacro.Data()));
gROOT->ProcessLine("create_MultipleBackground(200)");


cout << endl;
cout << "========================" << endl;
cout << "--- Training" << endl;
Training();

cout << endl;
cout << "========================" << endl;
cout << "--- Application & create combined tree" << endl;
ApplicationCreateCombinedTree();

cout << endl;
cout << "========================" << endl;
cout << "--- maximize significance" << endl;
MaximizeSignificance();