// file to calculate pedestal correction of fluo data
// make correction and save spectrum per pixel

#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 "TGraph.h"
#include "TGraphErrors.h"
#include "TF1.h"
#include "TFile.h"


int main(int argc, char* argv[]) {
  jungfrauStyle();

  if (argc != 5) {
    cout << "Correct usage:" << endl;
    cout << "arg 1: specify module number" << endl;
    cout << "arg 2: specify data location" << endl;
    cout << "arg 3: specify pede file" << endl;
    cout << "arg 4: specify data file" << endl;
    cout << "eg: ./JFMC_FluoCalibFit 006 /data_pool/Module_006_161116 10us_500Hz_QS_allgain_pede 10us_500Hz_QS_G0_Cu" << endl;
    cout << " " << endl;
    exit(1);
  }

  string module_str = argv[1];
  string data_loc = argv[2];
  string pede_file = argv[3];
  string data_file = argv[4];

  jungfrauFile *thisfile = new jungfrauFile();

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

  jungfrauPedestal *pedestalObject = new jungfrauPedestal();
  pedestalObject->pedestalSetNFrames(1000); // using 1000 frames, rolling window
  static uint16_t pedestals16_G0[NCH];

  TH2F* pedestalsG0 = new TH2F("pedestalsG0","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* pedestalsG1 = new TH2F("pedestalsG1","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* pedestalsG2 = new TH2F("pedestalsG2","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);

  TH2F* pedeRMSG0 = new TH2F("pedeRMSG0","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* pedeRMSG1 = new TH2F("pedeRMSG1","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);
  TH2F* pedeRMSG2 = new TH2F("pedeRMSG2","",NC,-0.5,NC-0.5,NR,-0.5,NR-0.5);

  TH1D* adcpc_spec = new TH1D("adcpc_spec","",300,0,3000);

  TH2I* adc2d_1 = new TH2I("adc2d_1","",1000,-200-0.5,800-0.5,65536,(65536*0-0.5),(65536*1-0.5));
  TH2I* adc2d_2 = new TH2I("adc2d_2","",1000,-200-0.5,800-0.5,65536,(65536*1-0.5),(65536*2-0.5));
  TH2I* adc2d_3 = new TH2I("adc2d_3","",1000,-200-0.5,800-0.5,65536,(65536*2-0.5),(65536*3-0.5));
  TH2I* adc2d_4 = new TH2I("adc2d_4","",1000,-200-0.5,800-0.5,65536,(65536*3-0.5),(65536*4-0.5));
  TH2I* adc2d_5 = new TH2I("adc2d_5","",1000,-200-0.5,800-0.5,65536,(65536*4-0.5),(65536*5-0.5));
  TH2I* adc2d_6 = new TH2I("adc2d_6","",1000,-200-0.5,800-0.5,65536,(65536*5-0.5),(65536*6-0.5));
  TH2I* adc2d_7 = new TH2I("adc2d_7","",1000,-200-0.5,800-0.5,65536,(65536*6-0.5),(65536*7-0.5));
  TH2I* adc2d_8 = new TH2I("adc2d_8","",1000,-200-0.5,800-0.5,65536,(65536*7-0.5),(65536*8-0.5));

  char savename[128];

  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);

  // open pede file
  sprintf(savename,"%s/%s_%%6.6d.dat", data_loc.c_str(), pede_file.c_str());
  thisfile->open((char*)savename, 0);

  // calculate pixel mask
  pixelMaskObject->initialisePixelMask(pixel_mask);
  if (module_str == "006") {
    pixelMaskObject->maskChip(6, pixel_mask);
    pixelMaskObject->maskSupercolumn(4,1, pixel_mask);
    pixelMaskObject->maskSupercolumn(4,2, pixel_mask);
  } else if (module_str == "040") {
    pixelMaskObject->maskSupercolumn(4,2, pixel_mask);
  }

  int nevents = 0;
  while (thisfile->readNextFrame()) {
    nevents++;
  }
  thisfile->rewind();
  cout << "read " << nevents << " events" << endl;

  if (nevents == 2999) {

    for (int i = 0; i < 1000; i++) {
      thisfile->readNextFrame();
      pixelMaskObject->maskIfGainNot(0, thisfile->getFrameDataHandle(), (int*)(&pixel_mask));
    }
    for (int i = 0; i < 1000; i++) {
      thisfile->readNextFrame();
      pixelMaskObject->maskIfGainNot(1, thisfile->getFrameDataHandle(), (int*)(&pixel_mask));
    }
    for (int i = 0; i < 999; i++) {
      thisfile->readNextFrame();
      pixelMaskObject->maskIfGainNot(3, thisfile->getFrameDataHandle(), (int*)(&pixel_mask));
    }

  } else {

    while (thisfile->readNextFrame()) {
      pixelMaskObject->maskIfGainNot(0, thisfile->getFrameDataHandle(), (int*)(&pixel_mask));
    }
  }

  thisfile->rewind();
  
  sprintf(savename,"plots/M%s/CuFluo/pixelmask.png", module_str.c_str());
  pixelMaskObject->plotPixelMask(pixel_mask,savename);
  cout << "after chip mask, n masked pixels is " << pixelMaskObject->getNMasked(pixel_mask) << endl;
  
  // caluclate pedestals
  if (nevents == 2999) {
    
    for (int i = 0; i < 1000; i++) {
      thisfile->readNextFrame();
      pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
    }
    for (int i = 0; i < NCH; i++) {
      if (pixel_mask[i] == 1) {
	pedestalsG0->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
	pedeRMSG0->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
      }
    }
    pedestalObject->pedestalData((uint16_t*)(&pedestals16_G0));
    pedestalObject->pedestalClear();
    
    for (int i = 0; i < 1000; i++) {
      thisfile->readNextFrame();
      pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
    }
    for (int i = 0; i < NCH; i++) {
      if (pixel_mask[i] == 1) {
	pedestalsG1->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
	pedeRMSG1->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
      }
    }
    pedestalObject->pedestalClear();
    
    for (int i = 0; i < 999; i++) {
      thisfile->readNextFrame();
      pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
    }
    for (int i = 0; i < NCH; i++) {
      if (pixel_mask[i] == 1) {
	pedestalsG2->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
	pedeRMSG2->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
      }
    }
    pedestalObject->pedestalClear();

  } else {
    
    while (thisfile->readNextFrame()) {
      pedestalObject->addFrameToPedestalCalculation(thisfile->getFrameDataHandle());
    }
    for (int i = 0; i < NCH; i++) {
      if (pixel_mask[i] == 1) {
	pedestalsG0->Fill(i%NC,i/NC,pedestalObject->pedestalOfChannel(i));
	pedeRMSG0->Fill(i%NC,i/NC,pedestalObject->rmsOfChannel(i));
      }
    }
    pedestalObject->pedestalData((uint16_t*)(&pedestals16_G0));
    pedestalObject->pedestalClear();
  }
  
  thisfile->close();
  
  pedestalsG0->GetXaxis()->SetTitle("Column");
  pedestalsG0->GetYaxis()->SetTitle("Row");
  pedestalsG0->GetYaxis()->SetTitleOffset(0.7);
  pedestalsG0->Draw("colz");
  sprintf(savename,"plots/M%s/CuFluo/pedeG0.png", module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));
  
  pedestalsG1->GetXaxis()->SetTitle("Column");
  pedestalsG1->GetYaxis()->SetTitle("Row");
  pedestalsG1->GetYaxis()->SetTitleOffset(0.7);
  pedestalsG1->Draw("colz");
  sprintf(savename,"plots/M%s/CuFluo/pedeG1.png", module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));
  
  pedestalsG2->GetXaxis()->SetTitle("Column");
  pedestalsG2->GetYaxis()->SetTitle("Row");
  pedestalsG2->GetYaxis()->SetTitleOffset(0.7);
  pedestalsG2->Draw("colz");
  sprintf(savename,"plots/M%s/CuFluo/pedeG2.png", module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));
  
  pedeRMSG0->GetXaxis()->SetTitle("Column");
  pedeRMSG0->GetYaxis()->SetTitle("Row");
  pedeRMSG0->GetYaxis()->SetTitleOffset(0.7);
  pedeRMSG0->GetZaxis()->SetRangeUser(0,30);
  pedeRMSG0->Draw("colz");
  sprintf(savename,"plots/M%s/CuFluo/pedeRMSG0.png", module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));
    
  pedeRMSG1->GetXaxis()->SetTitle("Column");
  pedeRMSG1->GetYaxis()->SetTitle("Row");
  pedeRMSG1->GetYaxis()->SetTitleOffset(0.7);
  pedeRMSG1->GetZaxis()->SetRangeUser(0,100);
  pedeRMSG1->Draw("colz");
  sprintf(savename,"plots/M%s/CuFluo/pedeRMSG1.png", module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));
    
  pedeRMSG2->GetXaxis()->SetTitle("Column");
  pedeRMSG2->GetYaxis()->SetTitle("Row");
  pedeRMSG2->GetYaxis()->SetTitleOffset(0.7);
  pedeRMSG2->GetZaxis()->SetRangeUser(0,300);
  pedeRMSG2->Draw("colz");
  sprintf(savename,"plots/M%s/CuFluo/pedeRMSG2.png", module_str.c_str());
  mapcanvas->SaveAs((const char *)(savename));

  pedestalsG0->Reset();
  pedestalsG1->Reset();
  pedestalsG2->Reset();
  pedeRMSG0->Reset();
  pedeRMSG1->Reset();
  pedeRMSG2->Reset();
    
  for (int filen = 0; filen < 20; filen++) {

    // open data file
    sprintf(savename,"%s/%s_%%6.6d.dat", data_loc.c_str(), data_file.c_str());
    thisfile->open((char*)savename, filen);

    while (thisfile->readNextFrame()) {
      
      uint16_t* imagedptr = thisfile->getFrameDataHandle();
	
      for (int i = 0; i < NCH; i++) {
	if (pixel_mask[i] == 1) {

	  uint16_t gain = (imagedptr[i]&0xc000) >> 14;

	  if (gain == 0) {

	    int adcpc = (imagedptr[i]&0x3fff) - pedestals16_G0[i];
	    adcpc_spec->Fill(adcpc);

	    if (i < (65536*1)) {
	      adc2d_1->Fill(adcpc,i);
	    } else if (i < (65536*2)) {
	      adc2d_2->Fill(adcpc,i);
	    } else if (i < (65536*3)) {
	      adc2d_3->Fill(adcpc,i);
	    } else if (i < (65536*4)) {
	      adc2d_4->Fill(adcpc,i);
	    } else if (i < (65536*5)) {
	      adc2d_5->Fill(adcpc,i);
	    } else if (i < (65536*6)) {
	      adc2d_6->Fill(adcpc,i);
	    } else if (i < (65536*7)) {
	      adc2d_7->Fill(adcpc,i);
	    } else if (i < (65536*8)) {
	      adc2d_8->Fill(adcpc,i);
	    }
	  }
	}
      }
    }
    thisfile->close();

    sprintf(savename,"/mnt/pcmoench_jungfrau_data/jungfrau_ana_sophie/M%s_CalibAna/Fluo_file%d.root", module_str.c_str(), filen);
    TFile* saved_file = new TFile((const char *)(savename),"RECREATE");
    adc2d_1->Write();
    adc2d_2->Write();
    adc2d_3->Write();
    adc2d_4->Write();
    adc2d_5->Write();
    adc2d_6->Write();
    adc2d_7->Write();
    adc2d_8->Write();
    saved_file->Close();

    adcpc_spec->GetXaxis()->SetTitle("Pedestal corrected ADC [ADU]");
    adcpc_spec->Draw();
    mapcanvas->SetLogy();
    sprintf(savename,"plots/M%s/CuFluo/adcpc_spec_file%d.png",module_str.c_str(), filen);
    mapcanvas->SaveAs((const char *)(savename));
    mapcanvas->SetLogy(0);

    adc2d_1->Reset();
    adc2d_2->Reset();
    adc2d_3->Reset();
    adc2d_4->Reset();
    adc2d_5->Reset();
    adc2d_6->Reset();
    adc2d_7->Reset();
    adc2d_8->Reset();
    adcpc_spec->Reset();

  } // end of file loop

}