// file to fit fluo spectrum per pixel
// and save peak position and uncertainty

#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/jungfrauCommonHeader.h"
#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/jungfrauCommonFunctions.h"

#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/jungfrauFile.C"
#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/jungfrauPixelMask.C"
#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/jungfrauPedestal.C"

#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/energyCalibration.h"
#include "/afs/psi.ch/project/mythen/sophie/sls_detector_calibration/energyCalibration.cpp"

#include "TGraph.h"
#include "TGraphErrors.h"
#include "TF1.h"
#include "TFile.h"
#include "TPaveStats.h"
#include "TLegend.h"
#include "TPaveText.h"

int main(int argc, char* argv[]) {
  jungfrauStyle();
  gStyle->SetOptFit(11);

  if (argc != 2) {
    cout << "Correct usage:" << endl;
    cout << "arg 1: specify module number" << endl;
    cout << "eg: ./JFMC_FluoCalibFit 006" << endl;
    cout << " " << endl;
    exit(1);
  }

  string module_str = argv[1];

  char histoname[128];
  char savename[128];
  TCanvas* c1 = new TCanvas("c1","");

  sprintf(savename,"/mnt/pcmoench_jungfrau_data/jungfrau_ana_sophie/M%s_CalibAna/Fluo_comb.root", module_str.c_str());
  TFile* comb_file = new TFile((const char *)(savename),"READ");

  jungfrauPixelMask *pixelMaskObject = new jungfrauPixelMask();
  static int pixel_mask [NCH];
  pixelMaskObject->initialisePixelMask(pixel_mask);

  TH1F* peak_fit_pos = new TH1F("peak_fit_pos","",100,250,400);
  TH1F* peak_fit_poserr = new TH1F("peak_fit_poserr","",100,0,2);
  TH2F* peak_fit_pos_2d = new TH2F("peak_fit_pos_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* peak_fit_poserr_2d = new TH2F("peak_fit_poserr_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);

  TH1F* noise_fit_pos = new TH1F("noise_fit_pos","",100,-30,30);
  TH1F* noise_fit_poserr = new TH1F("noise_fit_poserr","",100,0,0.1);
  TH2F* noise_fit_pos_2d = new TH2F("noise_fit_pos_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* noise_fit_poserr_2d = new TH2F("noise_fit_poserr_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);

  TH1F* gain_fit = new TH1F("gain_fit","",100,250,400);
  TH1F* gain_fiterr = new TH1F("gain_fiterr","",100,0,2);
  TH2F* gain_fit_2d = new TH2F("gain_fit_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* gain_fiterr_2d = new TH2F("gain_fiterr_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);

  TH1F* gain_fit_isEdge = new TH1F("gain_fit_isEdge","",100,250,400);
  TH1F* gain_fit_isInnerEdge = new TH1F("gain_fit_isInnerEdge","",100,250,400);
  TH1F* gain_fit_isDouble = new TH1F("gain_fit_isDouble","",100,250,400);
  TH1F* gain_fit_isNextToDouble = new TH1F("gain_fit_isNextToDouble","",100,250,400);
  TH1F* gain_fit_isQuad = new TH1F("gain_fit_isQuad","",100,250,400);
  TH1F* gain_fit_isBulk = new TH1F("gain_fit_isBulk","",100,250,400);

  TH2F* gain_ADUper1keV_2d = new TH2F("gain_ADUper1keV_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* gainerr_ADUper1keV_2d = new TH2F("gainerr_ADUper1keV_2d","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);

  int low_bin_noise = 101;
  int high_bin_noise = 301;
  int low_bin_peak = 301;
  int high_bin_peak = 601;

  for (int j=1; j<9; j++) {
    cout << "slice " << j << endl;
    sprintf(histoname,"adc2d_%i",j);
    TH2I* adc2d_j = (TH2I*)(comb_file->Get((const char *)(histoname)));
    cout << adc2d_j->GetEntries() << endl;
    adc2d_j->Draw("colz");
    c1->Update();

    for (int i=(65536*(j-1)); i<(65536*(j)); i++) {
      if (i%10000==0){cout << "another 10k" << endl;}

      TH1D* proj = adc2d_j->ProjectionX("bin1",i-(65536*(j-1))+1,i-(65536*(j-1))+1);

      if (proj->Integral(low_bin_noise,high_bin_noise)!=0 && proj->Integral(low_bin_peak,high_bin_peak)!=0) {

	// noise
	TH1D *proj_noise = dynamic_cast<TH1D*>(proj->Rebin(4,"proj_noise"));
	proj_noise->SetStats(kTRUE);
	proj_noise->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_noise),proj->GetBinLowEdge(high_bin_noise+1));
	proj_noise->Fit("gaus","Q","",-50,50);
	TF1 *fit = proj_noise->GetFunction("gaus");

	noise_fit_pos->Fill(fit->GetParameter(1));
	noise_fit_pos_2d->Fill(i%NC,i/NC,fit->GetParameter(1));
	noise_fit_poserr->Fill(fit->GetParError(1));
	noise_fit_poserr_2d->Fill(i%NC,i/NC,fit->GetParError(1));

	// peak
	TH1D *proj_peak = dynamic_cast<TH1D*>(proj->Rebin(4,"proj_peak"));
	proj_peak->SetStats(kTRUE);
	proj_peak->GetXaxis()->SetRangeUser(proj->GetBinLowEdge(low_bin_peak),proj->GetBinLowEdge(high_bin_peak+1));

	Double_t mypar[6];
	mypar[0] = 0.0;
	mypar[1] = 0.0;
	mypar[2] = proj_peak->GetBinCenter(proj_peak->GetMaximumBin());
	mypar[3] = 19.;
	mypar[4] = 60.;
	mypar[5] = 0.18;
	  
	Double_t emypar[6];
	energyCalibration *thiscalibration = new energyCalibration();
	thiscalibration->setScanSign(1);
	thiscalibration->setStartParametersKb(mypar);
	thiscalibration->fixParameter(0,0.); // no background
	thiscalibration->fixParameter(1,0.);
	TF1* fittedfun = thiscalibration->fitSpectrum(proj_peak,mypar,emypar);

	peak_fit_pos->Fill(mypar[2]);
	peak_fit_poserr->Fill(emypar[2]);
	peak_fit_pos_2d->Fill(i%NC,i/NC,mypar[2]);
	peak_fit_poserr_2d->Fill(i%NC,i/NC,emypar[2]);

	if ((i >= 58000 && i < 58000+10) || // bulk
	    (i >= 10 && i < 10+10) || // edge
	    (i >= 1024+10 && i < 1024+10+10) || // inner edge
	    (i >= (256*1024)+10 && i < (256*1024)+10+10) || // double
	    (i >= (257*1024)+10 && i < (257*1024)+10+10) || // next to double
	    (i == (255*1024)+255) // quad
	    ) {

	  string pixel_type = "x";
	  if (i >= 58000 && i < 58000+10) {
	    pixel_type = "b";
	  } else if (i >= 10 && i < 10+10) {
	    pixel_type = "e";
	  } else if (i >= 1024+10 && i < 1024+10+10) {
	    pixel_type = "ie";
	  } else if (i >= (256*1024)+10 && i < (256*1024)+10+10) {
	    pixel_type = "d";
	  } else if (i >= (257*1024)+10 && i < (257*1024)+10+10) {
	    pixel_type = "ntd";
	  } else if (i == (255*1024)+255) {
	    pixel_type = "q";
	  }
	    
	  proj_noise->Draw();
	  c1->Update();
	  proj_noise->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
	  TPaveStats *st0 = (TPaveStats*)proj_noise->FindObject("stats");
	  st0->SetX1NDC(0.65);
	  st0->SetX2NDC(0.94);
	  st0->SetY1NDC(0.75);
	  st0->SetY2NDC(0.94);
	  st0->SetBorderSize(0);
	  sprintf(savename,"plots/M%s/CuFluo/proj_noise_%s_%d.png", module_str.c_str(), pixel_type.c_str(), i);
	  c1->SaveAs((const char *)(savename));

	  proj_peak->Draw();
	  fittedfun->Draw("same");
	  c1->Update();
	  proj_peak->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
	  TPaveStats *st = (TPaveStats*)proj_peak->FindObject("stats");
	  st->SetX1NDC(0.22);
	  st->SetX2NDC(0.55);
	  st->SetY1NDC(0.55);
	  st->SetY2NDC(0.94);
	  st->SetBorderSize(0);
	  sprintf(savename,"plots/M%s/CuFluo/proj_peak_%s_%d.png", module_str.c_str(), pixel_type.c_str(), i);
	  c1->SaveAs((const char *)(savename));
	}

	// gain
	gain_fit->Fill(mypar[2] - fit->GetParameter(1));
	gain_fiterr->Fill(sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)));
	gain_fit_2d->Fill(i%NC,i/NC,mypar[2] - fit->GetParameter(1));
	gain_fiterr_2d->Fill(i%NC,i/NC,sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)));
	gain_ADUper1keV_2d->Fill(i%NC,i/NC,(mypar[2] - fit->GetParameter(1)) / 8.0);
	gainerr_ADUper1keV_2d->Fill(i%NC,i/NC,sqrt(pow(emypar[2],2) + pow(fit->GetParError(1),2)) / 8.0);

	if (isEdge(i)) {
	  gain_fit_isEdge->Fill(mypar[2] - fit->GetParameter(1));
	}
	if (isInnerEdge(i)) {
	  gain_fit_isInnerEdge->Fill(mypar[2] - fit->GetParameter(1));
	}
	if (isDouble(i)) {
	  gain_fit_isDouble->Fill(mypar[2] - fit->GetParameter(1));
	}
	if (isNextToDouble(i)) {
	  gain_fit_isNextToDouble->Fill(mypar[2] - fit->GetParameter(1));
	}
	if (isQuad(i)) {
	  gain_fit_isQuad->Fill(mypar[2] - fit->GetParameter(1));
	}
	if (isBulk(i)) {
	  gain_fit_isBulk->Fill(mypar[2] - fit->GetParameter(1));
	}
	  
	delete thiscalibration;
	delete proj_noise;
	delete proj_peak;
	delete proj;

      } else {
	pixel_mask[i] = 0;
      }
    }
  }

  sprintf(savename,"plots/M%s/CuFluo/pixelmask_afterfit.png", module_str.c_str());
  pixelMaskObject->plotPixelMask(pixel_mask,savename);

  TCanvas *mapcanvas = new TCanvas("mapcanvas","",150,10,800,400);
  mapcanvas->SetLeftMargin(0.1);
  mapcanvas->SetRightMargin(0.13);
  mapcanvas->SetTopMargin(0.08);
  mapcanvas->SetBottomMargin(0.15);

  TPaveText *pave = new TPaveText(0.86,0.95,0.91,0.98,"blNDC");
  pave->SetBorderSize(0);
  pave->SetFillStyle(0);
  pave->SetTextSize(0.06);
  pave->SetTextAlign(32);

  peak_fit_pos_2d->GetXaxis()->SetTitle("Column");
  peak_fit_pos_2d->GetYaxis()->SetTitle("Row");
  peak_fit_pos_2d->GetYaxis()->SetTitleOffset(0.7);
  peak_fit_pos_2d->Draw("colz");
  peak_fit_pos_2d->GetZaxis()->SetRangeUser(250,400);
  sprintf(savename,"plots/M%s/CuFluo/peak_fit_pos_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  peak_fit_poserr_2d->GetXaxis()->SetTitle("Column");
  peak_fit_poserr_2d->GetYaxis()->SetTitle("Row");
  peak_fit_poserr_2d->GetYaxis()->SetTitleOffset(0.7);
  peak_fit_poserr_2d->Draw("colz");
  peak_fit_poserr_2d->GetZaxis()->SetRangeUser(0,2);
  sprintf(savename,"plots/M%s/CuFluo/peak_fit_poserr_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  noise_fit_pos_2d->GetXaxis()->SetTitle("Column");
  noise_fit_pos_2d->GetYaxis()->SetTitle("Row");
  noise_fit_pos_2d->GetYaxis()->SetTitleOffset(0.7);
  noise_fit_pos_2d->Draw("colz");
  noise_fit_pos_2d->GetZaxis()->SetRangeUser(-30,30);
  sprintf(savename,"plots/M%s/CuFluo/noise_fit_pos_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  noise_fit_poserr_2d->GetXaxis()->SetTitle("Column");
  noise_fit_poserr_2d->GetYaxis()->SetTitle("Row");
  noise_fit_poserr_2d->GetYaxis()->SetTitleOffset(0.7);
  noise_fit_poserr_2d->Draw("colz");
  noise_fit_poserr_2d->GetZaxis()->SetRangeUser(0,0.05);
  sprintf(savename,"plots/M%s/CuFluo/noise_fit_poserr_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  gain_fit_2d->GetXaxis()->SetTitle("Column");
  gain_fit_2d->GetYaxis()->SetTitle("Row");
  gain_fit_2d->GetYaxis()->SetTitleOffset(0.7);
  gain_fit_2d->Draw("colz");
  pave->AddText("G0 [ADU/8 keV]");
  pave->Draw();
  gain_fit_2d->GetZaxis()->SetRangeUser(250,400);
  sprintf(savename,"plots/M%s/CuFluo/gain_fit_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  gain_fiterr_2d->GetXaxis()->SetTitle("Column");
  gain_fiterr_2d->GetYaxis()->SetTitle("Row");
  gain_fiterr_2d->GetYaxis()->SetTitleOffset(0.7);
  gain_fiterr_2d->Draw("colz");
  gain_fiterr_2d->GetZaxis()->SetRangeUser(0,2);
  sprintf(savename,"plots/M%s/CuFluo/gain_fiterr_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  gain_ADUper1keV_2d->GetXaxis()->SetTitle("Column");
  gain_ADUper1keV_2d->GetYaxis()->SetTitle("Row");
  gain_ADUper1keV_2d->GetYaxis()->SetTitleOffset(0.7);
  gain_ADUper1keV_2d->Draw("colz");
  gain_ADUper1keV_2d->GetZaxis()->SetRangeUser(35,50);
  sprintf(savename,"plots/M%s/CuFluo/gain_ADUper1keV_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  gainerr_ADUper1keV_2d->GetXaxis()->SetTitle("Column");
  gainerr_ADUper1keV_2d->GetYaxis()->SetTitle("Row");
  gainerr_ADUper1keV_2d->GetYaxis()->SetTitleOffset(0.7);
  gainerr_ADUper1keV_2d->Draw("colz");
  gainerr_ADUper1keV_2d->GetZaxis()->SetRangeUser(0,0.25);
  sprintf(savename,"plots/M%s/CuFluo/gainerr_ADUper1keV_2d.png",module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  c1->cd();
  peak_fit_pos->GetXaxis()->SetTitle("Peak position [ADU]");
  peak_fit_pos->Draw();
  sprintf(savename,"plots/M%s/CuFluo/peak_fit_pos.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  peak_fit_poserr->GetXaxis()->SetTitle("Peak position uncert [ADU]");
  peak_fit_poserr->Draw();
  sprintf(savename,"plots/M%s/CuFluo/peak_fit_poserr.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  noise_fit_pos->GetXaxis()->SetTitle("Noise position [ADU]");
  noise_fit_pos->Draw();
  sprintf(savename,"plots/M%s/CuFluo/noise_fit_pos.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  noise_fit_poserr->GetXaxis()->SetTitle("Noise position uncert [ADU]");
  noise_fit_poserr->Draw();
  sprintf(savename,"plots/M%s/CuFluo/noise_fit_poserr.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  gain_fit->GetXaxis()->SetTitle("Gain G0 [ADU / 8 keV]");
  gain_fit->Draw();
  sprintf(savename,"plots/M%s/CuFluo/gain_fit.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  gain_fit->Fit("gaus");
  gain_fit->Draw();
  sprintf(savename,"plots/M%s/CuFluo/gain_fit_fit.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  gain_fiterr->GetXaxis()->SetTitle("Gain uncert [ADU / 8 keV]");
  gain_fiterr->Draw();
  sprintf(savename,"plots/M%s/CuFluo/gain_fiterr.png",module_str.c_str());
  c1->SaveAs((const char *)(savename));

  gain_fit_isEdge->SetLineColor(kBlue);
  gain_fit_isInnerEdge->SetLineColor(kCyan);
  gain_fit_isDouble->SetLineColor(kGreen+2);
  gain_fit_isNextToDouble->SetLineColor(kRed);
  gain_fit_isQuad->SetLineColor(kOrange);

  gain_fit_isEdge->Scale(1./gain_fit_isEdge->GetEntries());
  gain_fit_isInnerEdge->Scale(1./gain_fit_isInnerEdge->GetEntries());
  gain_fit_isDouble->Scale(1./gain_fit_isDouble->GetEntries());
  gain_fit_isNextToDouble->Scale(1./gain_fit_isNextToDouble->GetEntries());
  gain_fit_isQuad->Scale(1./gain_fit_isQuad->GetEntries());
  gain_fit_isBulk->Scale(1./gain_fit_isBulk->GetEntries());

  TLegend *leg = new TLegend(0.62,0.6,0.93,0.93);
  leg->AddEntry(gain_fit_isBulk, "Normal", "l");
  leg->AddEntry(gain_fit_isDouble, "Double", "l");
  leg->AddEntry(gain_fit_isNextToDouble, "Next to D", "l");
  leg->AddEntry(gain_fit_isEdge, "Edge", "l");
  leg->AddEntry(gain_fit_isInnerEdge, "Inner E", "l");

  gain_fit_isDouble->GetXaxis()->SetTitle("Gain G0 [ADU / 8 keV]");
  gain_fit_isDouble->GetYaxis()->SetTitle("Normalised");
  gain_fit_isDouble->GetYaxis()->SetTitleOffset(1.3);
  gain_fit_isDouble->SetMinimum(0.0);
  gain_fit_isDouble->SetMaximum(0.16);
  gain_fit_isDouble->Draw();
  gain_fit_isEdge->Draw("same");
  gain_fit_isInnerEdge->Draw("same");
  gain_fit_isNextToDouble->Draw("same");
  gain_fit_isBulk->Draw("same");
  leg->Draw("same");
  sprintf(savename,"plots/M%s/CuFluo/gain_fit_perType.png", module_str.c_str());
  c1->SaveAs((const char *)(savename));

  sprintf(savename,"data/M%s/CuF_gain_M%s.root", module_str.c_str(), module_str.c_str());
  TFile* saved_file = new TFile((const char *)(savename),"RECREATE");
  gain_ADUper1keV_2d->Write();
  gainerr_ADUper1keV_2d->Write();
  saved_file->Close();
  
}