/* ======================================================================== *\
!
! *
! * This file is part of MARS, the MAGIC Analysis and Reconstruction
! * Software. It is distributed to you in the hope that it can be a useful
! * and timesaving tool in analysing Data of imaging Cerenkov telescopes.
! * It is distributed WITHOUT ANY WARRANTY.
! *
! * Permission to use, copy, modify and distribute this software and its
! * documentation for any purpose is hereby granted without fee,
! * provided that the above copyright notice appear in all copies and
! * that both that copyright notice and this permission notice appear
! * in supporting documentation. It is provided "as is" without express
! * or implied warranty.
! *
!
!
!   Author(s): Ester Aliu, 2/2004 <aliu@ifae.es>
|
!   Last Update: 7/2004
!
!
!   Copyright: MAGIC Software Development, 2000-2004
!
!
\* ======================================================================== */

/////////////////////////////////////////////////////////////////////////////
//
//  MIslandCalc
//
// The Island Calc task calculates the some islands parameters for each 
// of the events such as:
// 
//   - fIslNum                 //  number of islands
//   - fIslId[577]             //  island Id
//   - fPixNum[numisl]         //  number of pixels in the island
//   - fSigToNoise[numisl]     //  signal to noise of the island
//   - ftime[numisl][577]      //  mean of the arrival time  
//   - fTimeSpread[numisl]     //  mean arrival time spread of the island
//   - fMeanX[numisl]          //  mean X position of the island
//   - fMeanY[numisl]          //  mean Y position of the island
//   - fDist[numisl]           //  dist between an island and the continent
//   - fLength                 //  major axis of the larger island ellipse
//   - fWidth                  //  minor axis of the larger island ellipse
//   - fDistL[numisl]          //  dist divided by lenght of the larger island
//   - fDistW[numisl]          //  dist divided by width of the larger island
//
// Input Containers:
//   MGeomCam
//   MCerPhotEvt
//   MPedestalCam
//   MArrivalTimeCam
//
// Output Containers:
//   MIslands
//
/////////////////////////////////////////////////////////////////////////////
#include "MIslandCalc.h"

#include <stdlib.h>       // atof					  
#include <fstream>        // ofstream, SavePrimitive

#include "MLog.h"
#include "MLogManip.h"

#include "MIslands.h"

#include "MParList.h"

#include "MGeomPix.h"
#include "MGeomCam.h"

#include "MCerPhotPix.h"
#include "MCerPhotEvt.h"

#include "MPedestalCam.h"
#include "MPedestalPix.h"

#include "MArrivalTimeCam.h"
#include "MArrivalTimePix.h"

ClassImp(MIslandCalc);


using namespace std;

// --------------------------------------------------------------------------
//
// Default constructor.
//
MIslandCalc::MIslandCalc(const char* name, const char* title)    
  : fIsl(NULL)
{
    fName  = name  ? name  : "MIslandCalc";
    fTitle = title ? title : "Calculate island parameters";
}


// --------------------------------------------------------------------------
Int_t MIslandCalc::PreProcess (MParList *pList)
{
    fCam = (MGeomCam*)pList->FindObject(AddSerialNumber("MGeomCam"));
    if (!fCam)
    {
        *fLog << dbginf << "MGeomCam not found (no geometry information available)... aborting." << endl;
        return kFALSE;
    }

    fEvt = (MCerPhotEvt*)pList->FindObject(AddSerialNumber("MCerPhotEvt"));
    if (!fEvt)
    {
        *fLog << dbginf << "MCerPhotEvt not found... aborting." << endl;
        return kFALSE;
    }

    fPed = (MPedestalCam*)pList->FindObject(AddSerialNumber("MPedestalCam"));
    if (!fPed)
      {
        *fLog << dbginf << "MPedestalCam not found... aborting." << endl;
        return kFALSE;
      }

    fTime = (MArrivalTimeCam*)pList->FindObject(AddSerialNumber("MArrivalTimeCam"));
    if (!fTime)
      {
        *fLog << dbginf << "MArrivalTimeCam not found... aborting." << endl;
        return kFALSE;
      }
   
    if (strlen(fIslName) > 0)
      {
	fIsl = (MIslands*)pList->FindCreateObj("MIslands", AddSerialNumber(fIslName));
	//cout << "kk1" << endl;
      }
    else
      {
      fIsl = (MIslands*)pList->FindCreateObj(AddSerialNumber("MIslands"));
      //cout << "kk2" << endl;
      }
    if (!fIsl)
      return kFALSE;
    
    return kTRUE;
}


Int_t MIslandCalc::Process(){
  
  IslandPar();
  
  return kTRUE;  
   
}


Int_t MIslandCalc::IslandPar(){

  //calculates all the island parameters 

  const Int_t nPix=577;
  const Int_t nVect=50;
  Int_t numisl;

  Int_t** vect;
  vect = new Int_t*[nVect];
  for(Int_t i=0;i<nVect;i++)
    vect[i]= new Int_t[nPix];
  
  Int_t num[nVect];
  // num = new Int_t*[nVect];
  
  if (fIslandAlgorithm == 1)
    Calc1(numisl,nVect,nPix,vect,num);
  if (fIslandAlgorithm == 2)
    Calc2(numisl,nVect,nPix,vect,num);
  
  //set the number of islands in one event
  
  fIsl->SetIslNum(numisl);

 
  //examine each island...

  Float_t  noise;
  Float_t  signal;

  /*
  Float_t** ftime;
  ftime = new Float_t*[numisl];

  Int_t pixNumIsl = 0;

  for(Int_t i=0;i<numisl;i++)
    {
      pixNumIsl = num[i+1];
      ftime[i]= new Float_t[pixNumIsl];
    }

  Int_t** fIslId;
  fIslId = new Int_t*[numisl];
  for(Int_t i=0;i<numisl;i++)
    {
      pixNumIsl = num[i+1];
      fIslId[i]= new Int_t[pixNumIsl];
    }
  */
 
  Int_t fPixNum[numisl];
  Float_t fSigToNoise[numisl];
  Float_t time[nPix];
  Float_t timeVariance[numisl];
  Float_t meanX[numisl];
  Float_t meanY[numisl];
  Float_t dist[numisl];
  Float_t distL[numisl];
  Float_t distW[numisl];
  Float_t size, sizeLargeIsl, length, width;


  //reset the "sets" functions
  if (numisl <1)
    fIsl->SetIslNum(0);
  
  for(Int_t i = 0; i<10 ;i++){
    for(Int_t idx = 0; idx<nPix; idx++)
      {
	if (i == 0)
	  fIsl->SetIslId(idx, -1);
	fIsl->SetArrivalTime(i, idx, -1 );
      }
  }
  
  Float_t X = 0;
  Float_t Y = 0;
  sizeLargeIsl = 0;


  for(Int_t i = 1; i<=numisl ; i++)
    {
      Int_t n = 0;
      //Int_t ncore = 0;
      
      Float_t MIN = 10000.;
      Float_t MAX = 0.;
      
      signal = 0;
      noise = 0;

      size = 0;
      meanX[i-1] = 0;
      meanY[i-1] = 0;
      dist[i-1] = 0;

      fPixNum[i-1] = 0;
      timeVariance[i-1] = 0;
      

      for(Int_t idx=0 ; idx<nPix ; idx++)
	{
	  //	  cout << idx << endl;
	  MCerPhotPix *pix = fEvt->GetPixById(idx);
	  if(!pix) continue;
	  const MGeomPix &gpix2 = (*fCam)[pix->GetPixId()];
	  const MPedestalPix &ped  = (*fPed)[idx];
	  const MArrivalTimePix &timepix = (*fTime)[idx];
	  const Float_t nphot = pix->GetNumPhotons();

	  //	  if (pix == NULL) break;
	    
	  if (vect[i][idx]==1){
	    
	    fPixNum[i-1]++;
	    signal += nphot * (fCam->GetPixRatio(idx));
	    noise += pow(ped.GetPedestalRms(),2);
	    
	    size += nphot;
	    if (i == 1)
	      sizeLargeIsl += nphot;

	    meanX[i-1] += nphot * gpix2.GetX();
	    meanY[i-1] += nphot * gpix2.GetY();
	    
	    time[i-1] = timepix.IsLoGainUsed() ? timepix.GetArrivalTimeLoGain() : timepix.GetArrivalTimeHiGain();
	    	  	
	    //	    ftime[i-1][n] = time[i-1];
	    //  fIslId[i-1][n] = idx;

	    //calculates the time spread only for core pixels  
	    if (fEvt->IsPixelCore(idx)){ 
	      
	      if (time[i-1] > MAX)
		MAX = time[i-1];
	      if (time[i-1] < MIN)
		MIN = time[i-1];
	      //  ncore++;
	    }
	    
	    fIsl->SetIslId(idx, i-1);
	    fIsl->SetArrivalTime(i-1, idx, time[n]);

	    n++;
	  }
	  
	}

      meanX[i-1] /= size;
      meanY[i-1] /= size;
  

      if (i == 1){
	X = meanX[i-1];
	Y = meanY[i-1];
      }
  
      dist[i-1] = TMath::Power(meanX[i-1]-X,2) + TMath::Power(meanY[i-1]-Y,2);
      dist[i-1] = TMath::Sqrt(dist[i-1]);
      
      timeVariance[i-1] = MAX-MIN; 
      
      //noise = 0, in the case of MC w/o noise
      if (noise == 0) noise = 1;

      fSigToNoise[i-1]= (Float_t)signal/(Float_t)sqrt(noise);
      
    }

  //fIsl->SetIslId(fIslId);
  //fIsl->SetArrivalTime(ftime);
  fIsl->SetPixNum(fPixNum);
  fIsl->SetSigToNoise(fSigToNoise);
  fIsl->SetTimeSpread(timeVariance);
  fIsl->SetMeanX(meanX);
  fIsl->SetMeanY(meanY);
  fIsl->SetDist(dist);
  

  //Length and Width of the larger island according the definition of the hillas parameters
  
  // calculate 2nd moments
  // ---------------------
  Double_t corrxx=0;                               // [m^2]
  Double_t corrxy=0;                               // [m^2]
  Double_t corryy=0;                               // [m^2]
  
  for(Int_t idx=0 ; idx<nPix ; idx++)
    {
      MCerPhotPix *pix = fEvt->GetPixById(idx);
      if(!pix) continue;
      const MGeomPix &gpix3 = (*fCam)[pix->GetPixId()];
      const Float_t nphot = pix->GetNumPhotons();
      
      //      if (pix == NULL) break;
      
      if (vect[1][idx]==1){
	
	const Float_t dx = gpix3.GetX() - X;     // [mm]
	const Float_t dy = gpix3.GetY() - Y;     // [mm]
	
	
	corrxx += nphot * dx*dx;                     // [mm^2]
	corrxy += nphot * dx*dy;                     // [mm^2]
	corryy += nphot * dy*dy;                     // [mm^2]
	
      }   
    } 
  
  // calculate the hillas parameters Width and Length
  
  const Double_t d0    = corryy - corrxx;
  const Double_t d1    = corrxy*2;
  const Double_t d2    = d0 + TMath::Sqrt(d0*d0 + d1*d1);
  const Double_t tand  = d2 / d1;
  const Double_t tand2 = tand*tand;
  
  const Double_t s2 = tand2+1;
  
  const Double_t axis1 = (tand2*corryy + d2 + corrxx)/s2/sizeLargeIsl;
  const Double_t axis2 = (tand2*corrxx - d2 + corryy)/s2/sizeLargeIsl;
  
  //
  // fLength^2 is the second moment along the major axis of the ellipse
  // fWidth^2  is the second moment along the minor axis of the ellipse
  //
  // From the algorithm we get: fWidth <= fLength is always true
  //
  // very small numbers can get negative by rounding
  //
  length = axis1<0 ? 0 : TMath::Sqrt(axis1);  // [mm]
  width  = axis2<0 ? 0 : TMath::Sqrt(axis2);  // [mm]
  
  fIsl->SetLength(length);
  fIsl->SetWidth(width); 
   
  // for(Int_t i = 1; i<=numisl ; i++){

  // fIsl->SetDistL(fIsl->GetDist(i-1)/length, i-1);
  // fIsl->SetDistW(fIsl->GetDist(i-1)/width, i-1);
  // }

  for(Int_t i = 1; i<=numisl ; i++){
    
    distL[i-1]=dist[i-1]/length;
    distW[i-1]=dist[i-1]/width;
    
  }

  fIsl->SetDistL(distL);
  fIsl->SetDistW(distW);

  fIsl->SetReadyToSave();

 
  for (Int_t i = 0; i< nVect; i++)
    delete [] vect[i]; 

 delete vect;

  return kTRUE;  
}

//------------------------------------------------------------------------------------------
void MIslandCalc::Calc1(Int_t& numisl, const Int_t nv, const Int_t npix, Int_t** vect, Int_t* num){
  
  
  /////////////////////////////
  //
  //        ALGORITHM # 1
  // counts the number of islands as you can see in 
  // the event display after doing the std image cleaning
  //
  /////////////////////////////
  
  Int_t    sflag;
  Int_t    control;
  
  Int_t    nvect = 0;
  
  numisl = 0;

  Int_t    zeros[nv];
  
  for(Int_t m = 0; m < nv ; m++)
    for(Int_t n = 0; n < npix ; n++)
	vect[m][n] = 0;
    
  for(Int_t n = 0; n < nv ; n++)
    zeros[n] = 0;
  
  //cout << "new event" <<endl;
  MCerPhotPix *pix;

  //loop over all pixels
  MCerPhotEvtIter Next(fEvt, kFALSE);
  
  while ((pix=static_cast<MCerPhotPix*>(Next())))
    {
      const Int_t idx = pix->GetPixId();

      const MGeomPix &gpix  = (*fCam)[idx];
      const Int_t    nnmax  = gpix.GetNumNeighbors();

      if( fEvt->IsPixelUsed(idx)) 
     	{
	  //cout << idx <<endl;
	  sflag = 0;
	  
	  for(Int_t j=0; j < nnmax ; j++)
	    {
	      const Int_t idx2 = gpix.GetNeighbor(j);
	      
	      if (idx2 < idx)
		{
		  for(Int_t k = 1; k <= nvect; k++)
		    {
		      if (vect[k][idx2] == 1)
			{
			  sflag = 1;
			  vect[k][idx] = 1;
			}
		    }
		}
	    }
	  
	  if (sflag == 0)
	    {
	      nvect++;
	      // cout << "nvect " << nvect << endl;
	      vect[nvect][idx] = 1;	     
	    }
	  
	}
    }
  
  numisl = nvect;
  
  
  // Repeated Chain Corrections

  
  for(Int_t i = 1; i <= nvect; i++)
    {
      for(Int_t j = i+1; j <= nvect; j++)
	{
	  control = 0;
	  for(Int_t k = 0; k < npix; k++)
	    {
	      if (vect[i][k] == 1 && vect[j][k] == 1)
		{
		  control = 1; 
		  break;
		}
	    }
	  if (control == 1)
	    {
	      for(Int_t k = 0; k < npix; k++)
		{
		  if(vect[j][k] == 1)
		    vect[i][k] = 1;
		  vect[j][k] = 0;
		  zeros[j] = 1;
		}	
	      numisl = numisl-1;	    
	    }
	  
	}
    }
  
  

  Int_t l = 1;
  Int_t numpixels;
  Int_t pixMAX = 0;
  Int_t idMAX = 1;

  for(Int_t i = 1;  i<= nvect ; i++)
    {
      numpixels = 0;

      if (zeros[i] == 0)
	{
	  for(Int_t k = 0; k<npix; k++)
	    {
	      vect[l][k] = vect[i][k];
	      if (vect[l][k] == 1)
		numpixels++;
	      		
	    }
	  if (numpixels>pixMAX)
	    {
	      pixMAX = numpixels;
	      idMAX = l;
	    }
	  l++;
	}
      num[i] = numpixels;

    }
  
  //the larger island will correspond to the 1st component of the vector

  num[nvect +1] = num[1];
  num[1] = num[idMAX];
  num[idMAX]=num[1];

  for(Int_t k = 0; k<npix; k++) 
    {
      vect[nvect+1][k] = vect[1][k];
      vect[1][k] = vect[idMAX][k];
      vect[idMAX][k] = vect[nvect+1][k];
    }
}

//------------------------------------------------------------------------------------------

void MIslandCalc::Calc2(Int_t& numisl, const Int_t nv, const Int_t npix, Int_t** vect, Int_t* num){  

  
  /////////////////////////////
  //
  //        ALGORITHM # 2
  // counts the number of islands considering as the same 
  // islands the ones separated for 2 or less pixels
  //
  /////////////////////////////
  
  Int_t    sflag;
  Int_t    control;
  
  Int_t    nvect = 0;
  numisl = 0;
 
  Int_t    zeros[nv];
  
  Int_t kk[npix];

  for(Int_t m = 0; m < nv ; m++)
    for(Int_t n = 0; n < npix ; n++)
	vect[m][n] = 0;
    
  for(Int_t n = 0; n < nv ; n++)
    zeros[n] = 0;
  
  for(Int_t n = 0; n < npix ; n++)
    kk[n] = 0;
  
  MCerPhotPix *pix;

  //1st loop over all pixels
  MCerPhotEvtIter Next0(fEvt, kFALSE);
 
  while ((pix=static_cast<MCerPhotPix*>(Next0())))
    {
      const Int_t idx = pix->GetPixId();
      
      const MGeomPix &gpix  = (*fCam)[idx]; 
      const Int_t    nnmax  = gpix.GetNumNeighbors();

      if( fEvt->IsPixelUsed(idx))
	{
	  kk[idx] = 1 ;
	  for(Int_t j=0; j< nnmax; j++)
	    {
	      kk[gpix.GetNeighbor(j)] = 1;
	    }
	} 
      
    }
      
  //2nd loop over all pixels
  MCerPhotEvtIter Next(fEvt, kFALSE);
  
  while ((pix=static_cast<MCerPhotPix*>(Next())))
    {
      const Int_t idx = pix->GetPixId();
      
      const MGeomPix &gpix  = (*fCam)[idx];
      const Int_t    nnmax  = gpix.GetNumNeighbors();
      
      if ( kk[idx] > 0)
     	{
	  sflag = 0;
	  
	  for(Int_t j=0; j < nnmax ; j++)
	    {
	      const Int_t idx2 = gpix.GetNeighbor(j);
	      
	      if (idx2 < idx)
		{
		  for(Int_t k = 1; k <= nvect; k++)
		    {
		      if (vect[k][idx2] == 1)
			{
			  sflag = 1;
			  vect[k][idx] = 1;
			}
		    }
		}
	    }
	  
	  if (sflag == 0)
	    {
	      nvect++;
	      vect[nvect][idx] = 1;	     
	    }
	  
	}
    }
  
  numisl = nvect;
  
  
  // Repeated Chain Corrections
  
  for(Int_t i = 1; i <= nvect; i++)
    {
      for(Int_t j = i+1; j <= nvect; j++)
	{
	  control = 0;
	  for(Int_t k = 0; k < npix; k++)
	    {
	      
	      if (vect[i][k] == 1 && vect[j][k] == 1)
		{
		  control = 1; 
		  break;
		}
	    }
	  if (control == 1)
	    {
	      for(Int_t k = 0; k < npix; k++)
		{
		  if(vect[j][k] == 1)
		    vect[i][k] = 1;
		  vect[j][k] = 0;
		  zeros[j] = 1;
		}	
	      numisl = numisl-1;	    
	    }
	  
	}
    }
  
    
  Int_t l = 1;
  Int_t numpixels;
  Int_t pixMAX = 0;
  Int_t idMAX = 1;

  for(Int_t i = 1;  i<= nvect ; i++)
    {
      numpixels = 0;

      if (zeros[i] == 0)
	{
	  for(Int_t k = 0; k<npix; k++)
	    {
	      vect[l][k] = vect[i][k];
	      if (vect[l][k] == 1)
		numpixels++;
	    }
	  if (numpixels>pixMAX)
	    {
	      pixMAX = numpixels;
	      idMAX = l;
	    }
	  l++;
	}
      num[i] = numpixels;
    }
  
  
  //the larger island will correspond to the 1st component of the vector

  num[nvect +1] = num[1];
  num[1] = num[idMAX];
  num[idMAX]=num[1];

  for(Int_t k = 0; k<npix; k++) 
    {
      vect[nvect+1][k] = vect[1][k];
      vect[1][k] = vect[idMAX][k];
      vect[idMAX][k] = vect[nvect+1][k];
    }

}