#ifndef ANALYSIS_LIB_H
#define ANALYSIS_LIB_H

#include <cstdio>
#include <vector>
#include <fstream>
#include <string>
#include <iostream>

#include <TMacro.h>
#include <TList.h>
#include <TFile.h>
#include <TMath.h>
#include <TObjArray.h>
#include <TCutG.h>
#include <TGraph.h>

namespace AnalysisLib {

//*######################################### Execute Python Script
std::vector<std::string> executePythonScript(std::string command) {
  std::vector<std::string> result;
  printf("Python : %s \n", command.c_str());
  FILE* pipe = popen(command.c_str(), "r");
  if (!pipe) {
      std::cerr << "Failed to open pipe for command: " << command << std::endl;
      return result;
  }

  constexpr int buffer_size = 256;
  char buffer[buffer_size];

  while (fgets(buffer, buffer_size, pipe) != nullptr) {
      result.emplace_back(buffer);
  }

  pclose(pipe);
  return result;
}

//*######################################### TRAPEZOID 
TGraph * TrapezoidFilter(TGraph * trace, int baseLineEnd = 80, int riseTime = 10, int flatTop = 20, float decayTime = 2000){
  ///Trapezoid filter https://doi.org/10.1016/0168-9002(94)91652-7
  
  TGraph *  trapezoid = new TGraph();
  trapezoid->Clear();
  
  ///find baseline;
  double baseline = 0;
  for( int i = 0; i < baseLineEnd; i++){
    baseline += trace->Eval(i);
  }
  baseline = baseline*1./baseLineEnd;
  
  int length = trace->GetN();
  
  double pn = 0.;
  double sn = 0.;
  for( int i = 0; i < length ; i++){
  
    double dlk = trace->Eval(i) - baseline;
    if( i - riseTime >= 0            ) dlk -= trace->Eval(i - riseTime)             - baseline;
    if( i - flatTop - riseTime >= 0  ) dlk -= trace->Eval(i - flatTop - riseTime)   - baseline;
    if( i - flatTop - 2*riseTime >= 0) dlk += trace->Eval(i - flatTop - 2*riseTime) - baseline;
    
    if( i == 0 ){
        pn = dlk;
        sn = pn + dlk*decayTime;
    }else{
        pn = pn + dlk;
        sn = sn + pn + dlk*decayTime;
    }      
    trapezoid->SetPoint(i, i, sn / decayTime / riseTime);
  }
  return trapezoid;
}

bool isEmptyOrSpaces(const std::string& str) {
  if (str.empty()) {
    return true;
  }
  for (char c : str) {
    if (!std::isspace(c)) {
      return false;
    }
  }
  return true;
}

std::vector<std::string> SplitStr(std::string tempLine, std::string splitter, int shift = 0){

  std::vector<std::string> output;

  size_t pos;
  do{
    pos = tempLine.find(splitter); /// fine splitter
    if( pos == 0 ){ ///check if it is splitter again
      tempLine = tempLine.substr(pos+1);
      continue;
    }

    std::string secStr;
    if( pos == std::string::npos ){
      secStr = tempLine;
    }else{
      secStr = tempLine.substr(0, pos+shift);
      tempLine = tempLine.substr(pos+shift);
    }

    ///check if secStr is begin with space
    while( secStr.substr(0, 1) == " ") secStr = secStr.substr(1);
    
    ///check if secStr is end with space
    while( secStr.back() == ' ') secStr = secStr.substr(0, secStr.size()-1);

    output.push_back(secStr);
    ///printf(" |%s---\n", secStr.c_str());
    
  }while(pos != std::string::npos );

  return output;
};

//************************************** TCutG

TObjArray * LoadListOfTCut(TString fileName, TString cutName = "cutList"){

  if( fileName == "" ) return nullptr;

  TObjArray * cutList = nullptr;

  TFile * fCut = new TFile(fileName);
  bool isCutFileOpen = fCut->IsOpen();
  if(!isCutFileOpen) {
    printf( "Failed to open rdt-cutfile 1 : %s\n" , fileName.Data());
  }else{
    cutList = (TObjArray *) fCut->FindObjectAny(cutName);

    if( cutList ){
      int numCut = cutList->GetEntries();
      printf("=========== found %d cutG in %s \n", numCut, fCut->GetName());

      for(int i = 0; i < numCut ; i++){
        printf("cut name : %s , VarX: %s, VarY: %s, numPoints: %d \n",
          cutList->At(i)->GetName(),
          ((TCutG*)cutList->At(i))->GetVarX(),
          ((TCutG*)cutList->At(i))->GetVarY(),
          ((TCutG*)cutList->At(i))->GetN()
        );
      }
    }
  }

  return cutList;
}

TCutG * LoadSingleTCut( TString fileName, TString cutName = "cutEZ"){
  
  if( fileName == "" ) return nullptr;
  TCutG * cut = nullptr;
  
  TFile * fCut = new TFile(fileName);
  bool isCutFileOpen = fCut->IsOpen(); 
  if( !isCutFileOpen)  {
    printf( "Failed to open E-Z cutfile : %s\n" , fileName.Data());
  }else{
    cut = (TCutG *) fCut->FindObjectAny(cutName);
    if( cut != NULL ) {
        printf("Found EZ cut| name : %s, VarX: %s, VarY: %s, numPoints: %d \n", 
          cut->GetName(),
          cut->GetVarX(),
          cut->GetVarY(),
          cut->GetN()
        );
    }
  }

  return cut;
}


//************************************** Others
std::vector<std::vector<double>> combination(std::vector<double> arr, int r){
  
  std::vector<std::vector<double>> output;
  
  int n = arr.size();
  std::vector<int> v(n);
  std::fill(v.begin(), v.begin()+r, 1);
  do {
    //for( int i = 0; i < n; i++) { printf("%d ", v[i]); }; printf("\n");
    
    std::vector<double> temp;
    for (int i = 0; i < n; ++i) { 
      if (v[i]) {
        //printf("%.1f, ", arr[i]); 
        temp.push_back(arr[i]);
      }
    }
    //printf("\n");
    
    output.push_back(temp);
    
  } while (std::prev_permutation(v.begin(), v.end()));
  
  return output;
}

double* sumMeanVar(std::vector<double> data){
  
  int n = data.size();
  double sum = 0;
  for( int k = 0; k < n; k++) sum += data[k];
  double mean = sum/n;
  double var = 0;
  for( int k = 0; k < n; k++) var += pow(data[k] - mean,2);
  
  static double output[3];
  output[0] = sum;
  output[1] = mean;
  output[2] = var;
  
  return output;
}

double*  fitSlopeIntercept(std::vector<double> dataX, std::vector<double> dataY){
  
  double * smvY = sumMeanVar(dataY);
  double sumY = smvY[0];
  double meanY = smvY[1];

  double * smvX = sumMeanVar(dataX);
  double sumX = smvX[0];
  double meanX = smvX[1];
  double varX = smvX[2];
  
  int n = dataX.size();
  double sumXY = 0;
  for( int j = 0; j < n; j++) sumXY += dataX[j] * dataY[j];

  double slope = ( sumXY - sumX * sumY/n ) / varX;
  double intercept = meanY - slope * meanX;
  
  static double output[2];
  output[0] = slope;
  output[1] = intercept;
  
  return output;
  
}

std::vector<std::vector<double>> FindMatchingPair(std::vector<double> enX, std::vector<double> enY){

   //output[0] = fitEnergy;
   //output[1] = refEnergy;

   int nX = enX.size();
   int nY = enY.size();
   
   std::vector<double> fitEnergy;
   std::vector<double> refEnergy;
   
   if( nX > nY ){
      
      std::vector<std::vector<double>> output = combination(enX, nY);
      
      double * smvY = sumMeanVar(enY);
      double sumY = smvY[0];
      double meanY = smvY[1];
      double varY = smvY[2];
      
      double optRSquared = 0;
      double absRSqMinusOne = 1;
      int maxID = 0;
      
      for( int k = 0; k < (int) output.size(); k++){
        
        double * smvX = sumMeanVar(output[k]);
        double sumX = smvX[0];
        double meanX = smvX[1];
        double varX = smvX[2];
        
        double sumXY = 0;
        for( int j = 0; j < nY; j++) sumXY += output[k][j] * enY[j];
        
        double rSq = abs(sumXY - sumX*sumY/nY)/sqrt(varX*varY);
        
        //for( int j = 0; j < nY ; j++){ printf("%.1f, ", output[k][j]); }; printf("| %.10f\n", rSq);
        
        if( abs(rSq-1) < absRSqMinusOne ) {
          absRSqMinusOne = abs(rSq-1);
          optRSquared = rSq;
          maxID = k;
        }
      }
      
      fitEnergy = output[maxID];
      refEnergy = enY;
      
      printf(" R^2 : %.20f\n", optRSquared);      
      
      //calculation fitting coefficient
      //double * si = fitSlopeIntercept(fitEnergy, refEnergy);
      //printf( " y = %.4f x + %.4f\n", si[0], si[1]);
      
    }else if( nX < nY ){
    
      std::vector<std::vector<double>> output = combination(enY, nX);
      
      
      double * smvX = sumMeanVar(enX);
      double sumX = smvX[0];
      double meanX = smvX[1];
      double varX = smvX[2];
      
      double optRSquared = 0;
      double absRSqMinusOne = 1;
      int maxID = 0;
      
      for( int k = 0; k < (int) output.size(); k++){
        
        double * smvY = sumMeanVar(output[k]);
        double sumY = smvY[0];
        double meanY = smvY[1];
        double varY = smvY[2];
        
        double sumXY = 0;
        for( int j = 0; j < nX; j++) sumXY += output[k][j] * enX[j];
        
        double rSq = abs(sumXY - sumX*sumY/nX)/sqrt(varX*varY);
        
        //for( int j = 0; j < nX ; j++){ printf("%.1f, ", output[k][j]); }; printf("| %.10f\n", rSq);
        
        if( abs(rSq-1) < absRSqMinusOne ) {
          absRSqMinusOne = abs(rSq-1);
          optRSquared = rSq;
          maxID = k;
        }
      }
      
      fitEnergy = enX;
      refEnergy = output[maxID];
      printf(" R^2 : %.20f\n", optRSquared);   
    
    }else{
      fitEnergy = enX;
      refEnergy = enY;
      
      //if nX == nY, ther could be cases that only partial enX and enY are matched. 
      
    }
    
    printf("fitEnergy = ");for( int k = 0; k < (int) fitEnergy.size() ; k++){ printf("%7.2f, ", fitEnergy[k]); }; printf("\n");
    printf("refEnergy = ");for( int k = 0; k < (int) refEnergy.size() ; k++){ printf("%7.2f, ", refEnergy[k]); }; printf("\n");
    
    std::vector<std::vector<double>> haha;
    haha.push_back(fitEnergy);
    haha.push_back(refEnergy);
    
    return haha;
   
}

std::string create_range_string(const std::vector<int>& nums) {
  std::string range_str;
  int lastNum = nums[0];
  int rangeStart = lastNum;
  for (int i = 1; i < (int) nums.size(); i++) {
    if (nums[i] == lastNum + 1) {
      lastNum = nums[i];
    } else {
      if (rangeStart == lastNum) {
        range_str += std::to_string(rangeStart) + "_";
      } else {
          range_str += std::to_string(rangeStart) + "-" + std::to_string(lastNum) + "_";
      }
      rangeStart = lastNum = nums[i];
    }
  }
  // Add the last range
  if (rangeStart == lastNum) {
    range_str += std::to_string(rangeStart);
  } else {
    range_str += std::to_string(rangeStart) + "-" + std::to_string(lastNum);
  }
  return range_str;
}


}

#endif