//#include "sls/ansi.h"
#include <iostream>
#define CORR

#define C_GHOST 0.0004

#define CM_ROWS 50

//#define VERSION_V1

//#include "moench03T1ZmqData.h"
#ifdef NEWRECEIVER
#ifndef RECT
#include "moench03T1ReceiverDataNew.h"
#endif

#ifdef RECT
#include "moench03T1ReceiverDataNewRect.h"
#endif

#endif


#ifdef CSAXS_FP
#include "moench03T1ReceiverData.h"
#endif 
#ifdef OLDDATA
#include "moench03Ctb10GbT1Data.h"
#endif 

// #include "interpolatingDetector.h"
//#include "etaInterpolationPosXY.h"
// #include "linearInterpolation.h"
// #include "noInterpolation.h"
#include "multiThreadedCountingDetector.h"
//#include "multiThreadedAnalogDetector.h"
#include "singlePhotonDetector.h"
#include "moench03GhostSummation.h"
#include "moench03CommonMode.h"
//#include "interpolatingDetector.h"

#include <stdio.h>
#include <map>
#include <fstream>
#include <sys/stat.h>

#include <ctime>
using namespace std;


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


  if (argc<4) {
    cout << "Usage is " << argv[0] << "indir outdir fname [runmin] [runmax] [pedfile] [threshold] [nframes] [xmin xmax ymin ymax] [gainmap]" << endl;
    cout << "threshold <0 means analog; threshold=0 means cluster finder; threshold>0 means photon counting" << endl;
    cout << "nframes <0 means sum everything; nframes=0 means one file per run; nframes>0 means one file every nframes" << endl;
    return 1;
  }

  int p=10000;
  int fifosize=1000;
  int nthreads=10;
  int nsubpix=25;
  int etabins=nsubpix*10;
  double etamin=-1, etamax=2;
  int csize=3;
  int save=1;
  int nsigma=5;
  int nped=10000;
  int ndark=100;
  int ok;
  int iprog=0;

  int cf=0;

#ifdef NEWRECEIVER
#ifdef RECT
  cout << "Should be rectangular!" <<endl;
#endif
  moench03T1ReceiverDataNew *decoder=new  moench03T1ReceiverDataNew();
  cout << "RECEIVER DATA WITH ONE HEADER!"<<endl;
#endif

#ifdef CSAXS_FP
  moench03T1ReceiverData *decoder=new  moench03T1ReceiverData();
  cout << "RECEIVER DATA WITH ALL HEADERS!"<<endl;
#endif

#ifdef OLDDATA
  moench03Ctb10GbT1Data *decoder=new  moench03Ctb10GbT1Data();
  cout << "OLD RECEIVER DATA!"<<endl;
#endif

  int nx=400, ny=400;

  decoder->getDetectorSize(nx,ny);

  int ncol_cm=CM_ROWS;
  double xt_ghost=C_GHOST;
  moench03CommonMode *cm=NULL;
  moench03GhostSummation *gs;
  double *gainmap=NULL;
  float *gm;



  int size = 327680;////atoi(argv[3]);
  
  int* image;
	//int* image =new int[327680/sizeof(int)];

  int ff, np;
  //cout << " data size is " << dsize;
  


  ifstream filebin;
  char *indir=argv[1];
  char *outdir=argv[2];
  char *fformat=argv[3];
  int runmin=0;
  
  // cout << "argc is " << argc << endl;
 if (argc>=5) {
   runmin=atoi(argv[4]);
  }

 int runmax=runmin;

 if (argc>=6) {
   runmax=atoi(argv[5]);
  }

  char *pedfile=NULL;
  if (argc>=7) {
    pedfile=argv[6];
  }
  double thr=0;
  double thr1=1;

  if (argc>=8) {
    thr=atof(argv[7]);
  }
  

  int nframes=0;
  
  if (argc>=9) {
    nframes=atoi(argv[8]);
  }

  int xmin=0, xmax=nx, ymin=0, ymax=ny;
  if (argc>=13) {
    xmin=atoi(argv[9]);
    xmax=atoi(argv[10]);
    ymin=atoi(argv[11]);
    ymax=atoi(argv[12]);
  }

  
  char *gainfname=NULL;
  if (argc>13) {
    gainfname=argv[13];
    cout << "Gain map file name is: " << gainfname << endl;
  }

  


  char ffname[10000];
  char fname[10000];
  char imgfname[10000];
  char cfname[10000];
  char fn[10000];
  
  std::time_t end_time;

  FILE *of=NULL;
  cout << "input directory is " << indir << endl;
  cout << "output directory is " << outdir << endl;
  cout << "input file is " << fformat << endl;
  cout << "runmin is " << runmin << endl;
  cout << "runmax is " << runmax << endl;
  if (pedfile)
    cout << "pedestal file is " << pedfile << endl;
 if (thr>0) 
    cout << "threshold is " << thr << endl;
 cout << "Nframes is " << nframes << endl;
 
 uint32 nnx, nny;
 double *gmap;

  // if (gainfname) {
  //   gm=ReadFromTiff(gainfname, nny, nnx);
  //   if (gm && nnx==nx && nny==ny) {
  //     gmap=new double[nx*ny];
  //     for (int i=0; i<nx*ny; i++) {
  // 	gmap[i]=gm[i];
  //     }
  //     delete gm;
  //   } else
  //     cout << "Could not open gain map " << gainfname << endl;
  // }

#ifdef CORR
 cout << "Applying common mode  " << ncol_cm << endl;
  cm=new moench03CommonMode(ncol_cm);
  

  cout << "Applying ghost corrections " << xt_ghost << endl;
  gs=new moench03GhostSummation(decoder, xt_ghost);
#endif

  singlePhotonDetector *filter=new singlePhotonDetector(decoder,csize, nsigma, 1, cm, nped, 200, -1, -1, gainmap, gs);

  if (gainfname) {

    if (filter->readGainMap(gainfname))
      cout << "using gain map " << gainfname << endl;
    else
      cout << "Could not open gain map " << gainfname << endl;
  } else
    thr=0.15*thr;
  filter->newDataSet();
  int dsize=decoder->getDataSize();


  char data[dsize];





  //#ifndef ANALOG
  if (thr>0) {
    cout << "threshold is " << thr << endl;
    //#ifndef ANALOG
    filter->setThreshold(thr);
    //#endif
      cf=0;

  } else
    cf=1;
  //#endif


  filter->setROI(xmin,xmax,ymin,ymax);
  std::time(&end_time);
  cout << std::ctime(&end_time) <<   endl;

  char* buff;

  // multiThreadedAnalogDetector *mt=new multiThreadedAnalogDetector(filter,nthreads,fifosize);
 multiThreadedCountingDetector *mt=new multiThreadedCountingDetector(filter,nthreads,fifosize);
#ifndef ANALOG
    mt->setDetectorMode(ePhotonCounting);
    cout << "Counting!" << endl;
  if (thr>0) {
    cf=0;
  } 
#endif
//{
#ifdef ANALOG
      mt->setDetectorMode(eAnalog);
      cout << "Analog!" << endl;
      cf=0;
      //thr1=thr;
#endif  
      //  }
  
  mt->StartThreads();
  mt->popFree(buff);


  //  cout << "mt " << endl;

  int ifr=0;

  double ped[nx*ny], *ped1;


  if (pedfile) {

    cout << "PEDESTAL " << endl;
    sprintf(imgfname,"%s/pedestals.tiff",outdir);

    if (string(pedfile).find(".tif")==std::string::npos){
      sprintf(fname,"%s.raw",pedfile);
      cout << fname << endl ;
      std::time(&end_time);
      cout << "aaa" << std::ctime(&end_time) <<   endl;
      
      
      mt->setFrameMode(ePedestal);
      // sprintf(fn,fformat,irun);
      filebin.open((const char *)(fname), ios::in | ios::binary);
      //      //open file
      if (filebin.is_open()){
	ff=-1;
	while (decoder->readNextFrame(filebin, ff, np,buff)) {
	  if (np==40) {
	    mt->pushData(buff);
	    mt->nextThread();
	    mt->popFree(buff);
	    ifr++;
	    if (ifr%100==0) 
	      cout << ifr << " " << ff << " " << np << endl;
	  } else
	    cout << ifr << " " << ff << " " << np << endl;
	  ff=-1;
	}
	filebin.close();	 
	while (mt->isBusy()) {;}
	
      } else 
	cout << "Could not open pedestal file "<< fname << " for reading " << endl;
    } else {
      float *pp=ReadFromTiff(pedfile, nny, nnx);
      if (pp && nnx==nx && nny==ny) {
	for (int i=0; i<nx*ny; i++) {
	  ped[i]=pp[i];
	}
	delete [] pp;
	mt->setPedestal(ped);
	// ped1=mt->getPedestal();
	
	// for (int i=0; i<nx*ny; i++) {

	//   cout << ped[i]<<"/"<<ped1[i] << " " ;
	// }
	cout << "Pedestal set from tiff file " << pedfile << endl;
      } else {
	cout << "Could not open pedestal tiff file "<< pedfile << " for reading " << endl;
      }
    }
    mt->writePedestal(imgfname);
    std::time(&end_time);
    cout << std::ctime(&end_time) <<   endl;
  }
  


  ifr=0;
  int ifile=0;
  
  mt->setFrameMode(eFrame);

  for (int irun=runmin; irun<=runmax; irun++) {
    cout << "DATA " ;
    // sprintf(fn,fformat,irun);
    sprintf(ffname,"%s/%s.raw",indir,fformat);
    sprintf(fname,ffname,irun);
    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
    sprintf(imgfname,ffname,irun);
    sprintf(ffname,"%s/%s.clust",outdir,fformat);
    sprintf(cfname,ffname,irun);
    cout << fname << " " ;
    cout << imgfname << endl;
    std::time(&end_time);
    cout << std::ctime(&end_time) <<    endl;
    //  cout <<  fname << " " << outfname << " " << imgfname <<  endl;
    filebin.open((const char *)(fname), ios::in | ios::binary);
    //      //open file
    ifile=0;
    if (filebin.is_open()){
      if (thr<=0 && cf!=0) { //cluster finder
	  if (of==NULL) {
	    of=fopen(cfname,"w");
	    if (of) {
	    mt->setFilePointer(of);
	    cout << "file pointer set " << endl;
	    } else {
	      cout << "Could not open "<< cfname << " for writing " << endl;
	      mt->setFilePointer(NULL);
	      return 1;
	    }
	  }
      }
      //     //while read frame 
      ff=-1;
      ifr=0;
      while (decoder->readNextFrame(filebin, ff, np,buff)) {
	if (np==40) {
	//	cout << "*"<<ifr++<<"*"<<ff<< endl;
	//	cout << ff << " " << np << endl;
  	//         //push
	  mt->pushData(buff);
	  // 	//         //pop
	  mt->nextThread();
	  // // 		//	cout << " " << (void*)buff;
	  mt->popFree(buff);




	  ifr++;
	  if (ifr%100==0) cout << ifr << " " << ff << endl;
	  if (nframes>0) {
	    if (ifr%nframes==0) {
	      //The name has an additional "_fXXXXX" at the end, where "XXXXX" is the initial frame number of the image (0,1000,2000...)
	      
	      sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
	      sprintf(imgfname,ffname,irun);
	      //cout << "Writing tiff to " << imgfname << " " << thr1 << endl;
	      mt->writeImage(imgfname, thr1);
	      mt->clearImage();
	      ifile++;
	    }
	  }
	} else
	  cout << ifr << " " << ff << " " << np << endl;
	ff=-1;
      }
      cout << "--" << endl;
      filebin.close();	 
      //      //close file 
      //     //join threads
      while (mt->isBusy()) {;}
      if (nframes>=0) {
	if (nframes>0) {
	    sprintf(ffname,"%s/%s_f%05d.tiff",outdir,fformat,ifile);
	    sprintf(imgfname,ffname,irun);
	} else {
	  sprintf(ffname,"%s/%s.tiff",outdir,fformat);
	  sprintf(imgfname,ffname,irun);
	}
	cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
	mt->writeImage(imgfname, thr1);
	mt->clearImage();
	if (of) {
	  fclose(of);
	  of=NULL;
	  mt->setFilePointer(NULL);
	}
      }	
      std::time(&end_time);
      cout << std::ctime(&end_time) <<   endl;
    } else 
      cout << "Could not open "<< fname << " for reading " << endl;
  }
  if (nframes<0){
    sprintf(ffname,"%s/%s.tiff",outdir,fformat);
    strcpy(imgfname,ffname);
    cout << "Writing tiff to " << imgfname << " " << thr1 <<endl;
    mt->writeImage(imgfname, thr1);
  }
    


  return 0;
}