//---------------------------------------------------------------------
// SRL algorithm, working version 1.00. 29.12.1997
// (c) Eugene Prosso. WIS, 1997-98
// Scientific supervisor and permanent source of good advices
// Ehud Duchovni, WIS
//---------------------------------------------------------------------

//---------------------------------------------------------------------
// input - input file with format
// "data" file name
// "MC" file name
// output file name 
// id # of sought particle
// flag (1 or 0) 
// number of different numbers of NN
// # of nn_1
// ....
// # of nn_last 
//_____________________________________________________________________


#include <stdlib.h>
#include <stdio.h>

#include <math.h>
#include <iostream.h>
#include <fstream.h>


void ReadInput ( char* InputFileName,
                 char *DataName, char* MCName,
                 char *OutName,  double &RangeMin, double &RangeMax, 
                 double& step, int &idt  ) ;

void CheckInput ( char* DataName, char* MCName,
                  int &ndata, int &nMC, int &d ) ; 

void ReadArrays ( char* DataName, char* MCName,
                  double** &Data, double** &MC, 
                  int ndata, int nMC, int d );

void FindLikelihood ( double** Data,
                      double** MC,
                      char * OutName,
                      int ndata, int nMC,
                      int d, int nnns, int nns[], int flag,
                      int SoughtIdt              ) ; 

inline double EucliDistance ( double *vect1, 
                              double *vect2,
                              int d               ) ; 

inline void CalcProbability ( LinkedList <sosed> &list, 
                              int SoughtIdt, int nnns, int nns[], int flag,
                              double probability[] ) ; 

void panic (char* str) ; 

inline INT (double val) 
{
    return    val < 0 ? (int) (val - 0.5) : int (val + 0.5) ;
}


// ----------------------
//   MAIN
// ----------------------

int main (int  argc, char* argv[])
{
   int     idt;               /* idt being sought */
   int     d;                 /* number of variables */
   int     ndata, nMC ;       /* number of lines in data and MC */

   char*   DataName = new char[30];       // data file name */
   char*   MCName = new char[30];         // MC file name */
   char*   OutName = new char[30];        // output file name */
   double  **Data, **MC; 
   int     nns[20];          // number of neighbours to consider
   int     nnns;             // total number of different nns
   int     flag;             // prob = sqrt(noise)/signal  OR signal/total 

   if (argc < 2) panic ("neighbours <Input File>") ;

   ReadInput ( argv[1],                   // reads command-line arguments
               DataName, MCName, 
               OutName,  nnns, nns, flag,
               idt                    );   
   CheckInput ( DataName, MCName,         // half-checks compatibility 
                ndata, nMC, d   );        // of data & MC files
   ReadArrays ( DataName, MCName,
                Data, MC, ndata, nMC, d );

   FindNeighbours ( Data, MC, OutName,      // finds nns[i] nearest MCnbrs
                    ndata, nMC, d,          // for each pt. in data
                    nnns, nns, flag, idt );   // and prints results in OF[i]
   return 1;
}


/*  Transforms program arguments into corresponding variables
*/

void ReadInput ( char *FileName,
                 char *DataName, char* MCName, 
                 char *OutName,  int &nnns, int nns[],
                 int &flag, int &idt                   )
{
    ifstream   InFile ;
   
    InFile.open (FileName, ios::nocreate);
    if (InFile.fail () ) panic ("No input file" );
  
    InFile >> DataName ;
    InFile >> MCName;
    InFile >> OutName;
    InFile >> idt ;
    InFile >> dx; 
    for (int cnt1 = 0; cnt1 < nnns; cnt1++ )    InFile >> nns[cnt1]; 
    InFile.close(); 
}


/*  1. compares number of columns in MC and data files. 
       (#column(MC) - #coulmn(data) should be 1 )
    2. counts number of variables and number of points in data and MC
*/

void CheckInput ( char* DataName, char* MCName, 
                  int &ndata, int &nMC, int &d )
{
    int      nwords, nlines;
    double   DataNcolumns, MCNcolumns;
    char      *com = (char*) malloc (512);  // command
    ifstream  dummy;
    int       cnt ;  /* counter */

    for (cnt = 0 ; cnt++ <= 1; ) 
    {
            if  (cnt == 1)   sprintf (com, "wc %s > dummyfile", DataName); 
            else             sprintf (com, "wc %s > dummyfile", MCName); 
   	    system (com);    

	    dummy.open ("dummyfile", ios::nocreate);
	    dummy >> nlines >> nwords; 
            if     (cnt == 1)  {
                       DataNcolumns = (double) nwords / nlines ;   
                       ndata = nlines ;
            } else { 
                      MCNcolumns = (double) nwords / nlines ; 
                      nMC = nlines ; 
            }
	    dummy.close();
    }

    if ( fabs ( DataNcolumns - INT (DataNcolumns) > 0.0001 )     ||
         fabs ( MCNcolumns - INT (MCNcolumns + 0.5) > 0.0001 )  ||
         INT (MCNcolumns) - INT (DataNcolumns) != 1  )
             panic ("Bad input files or unmatched number of variables\n") ; 

    d = INT (DataNcolumns) ; 
}


// ------------------------------------------------------------------------
// in the simplest and most naive version of this program 
// this function just reads the data and MC files 
// INTO RAM!!!
// ------------------------------------------------------------------------


void   ReadArrays ( char* DataName, char* MCName,
             double** &Data, double** &MC, 
             int  ndata, int  nMC, int d )
{
      ifstream  DataFile, MCFile; 
      long      cnt1; 

      DataFile.open (DataName, ios::nocreate);
      MCFile.open (MCName, ios::nocreate);

      Data = new double* [ndata]; 

      MC = new double* [nMC];


// reading from data file to data array

      for ( cnt1 = 0 ; cnt1 < ndata; cnt1++ ) 
      { 
          Data[cnt1] = new double [d]; 
          for (int cnt2 = 0; cnt2 < d; cnt2++ ) { 
               DataFile >> Data[cnt1][cnt2]; 
       	       if ( DataFile.eof() )
                  panic ( "Unexpected data EOF in FindNeighbours" );
	  } 
      } 

// reading from MC file to MC array

      for ( cnt1 = 0 ; cnt1 < nMC; cnt1++ ) 
      { 
          MC[cnt1] = new double [d+1]; 
          for (int cnt2 = 0; cnt2 <= d; cnt2++ ) {
              MCFile >> MC[cnt1][cnt2]; 
	      if (MCFile.eof()) 
                    panic( "Unexpected MC EOF in FindNeighbours\n");
          } 
      } 

      DataFile.close (); 
      MCFile.close (); 
}


// ------------------------------------------------------------------------
// The major procedure - finding nn-s for each point &
// printing the results.
// Complexity = O (D * M * d) 
// D - # of data points, M - # of MC points, d - dimensionality  
// ------------------------------------------------------------------------

void FindNeighbours ( double **Data, 
                      double **MC,
                      char *OutName, 
                      int ndata, int nMC, 
                      int d, double dx,
                      int SoughtIdt       )
{
    ofstream   OutputFile;

    int         cnt1, cnt2, cnt, cnt3;           // counters
    double      prob[200];                       // likelihood on each var 
    long        nsig[200], nnoise[200];          // noise and sig on each var 

    if (nnns > 200)  panic (" Too much output nn-s" ) ; 

    OutputFile.open (OutName);

    for (cnt1 = 0 ; cnt1 < ndata; cnt1++ )     // loop on all data point 
    {
        for (cnt2 = 0; cnt2 < nMC; cnt2++)     // loop on all MC points
	{
           for (cnt3 = 0 ; cnt3 < d ; cnt3++ ) 
           { 
               if (fabs (MC[cnt2][cnt3]-D[cnt2][cnt3]) < dx) 
               { 
                  if (MC[cnt2][d] == SoughtIdt) 
                          nsig[cnt3]++; 
                  else    nnoise[cnt3]++; 
               }   
           }
	}

        prob[199] = 1; 
        for (cnt3 = 0 ; cnt3 < d ; cnt3++ ) { 
           prob[cnt3] = (double) nsig / (nsig+nnoise);     
           prob[199] *= prob[cnt3];   
        } 
        OutputFile << prob[199] << endl;   // writing output
    }
    OutputFile.close ();
}


//panic

void panic (char* str)
{
    cerr  << str << endl ; 
    exit (0);
}