*** simpleaffy2.orig	2004-02-23 20:01:29.000000000 +0100
--- simpleaffy2.c	2004-05-25 15:27:47.000000000 +0200
***************
*** 503,510 ****
  
  // given a spot on a chip, which grid cell is it in?
  void grid(int x, int y, int nrow, int ncol, int gridx, int gridy, int *gx, int *gy) {
!   *gx = (int) ((double) (gridx * x) / (double) nrow);
!   *gy = (int) ((double) (gridy * y) / (double) ncol);
  }
  
  
--- 503,510 ----
  
  // given a spot on a chip, which grid cell is it in?
  void grid(int x, int y, int nrow, int ncol, int gridx, int gridy, int *gx, int *gy) {
!   *gx = (int) ((double) (gridx * x) / (double) ncol);
!   *gy = (int) ((double) (gridy * y) / (double) nrow);
  }
  
  
***************
*** 512,518 ****
  void lookup(int *idx, int no, double *raw, int ncol, int *x, int *y, double *val) {
      *x = idx[no] % ncol;
      *y = idx[no] / ncol;
!     *val = raw[idx[no]];
  }
  
  
--- 512,518 ----
  void lookup(int *idx, int no, double *raw, int ncol, int *x, int *y, double *val) {
      *x = idx[no] % ncol;
      *y = idx[no] / ncol;
!     *val = raw[idx[no]-1];
  }
  
  
***************
*** 522,528 ****
  void bgmas(int *idx, int *nidx,
             double *raw, int *nraw,
             int *rws, int *cls, int *xgridsize, int *ygridsize, double *zonebg, double *zonesd, double *corrected) {
!   int i,j,x,y,gx,gy,gn,pn;
    double tmp;
    double val;
    double w,wsum,bg,nz;
--- 522,528 ----
  void bgmas(int *idx, int *nidx,
             double *raw, int *nraw,
             int *rws, int *cls, int *xgridsize, int *ygridsize, double *zonebg, double *zonesd, double *corrected) {
!   int i,j,x,y,gx,gy,gn,pn,cellsize;
    double tmp;
    double val;
    double w,wsum,bg,nz;
***************
*** 539,550 ****
    double *xc        = (double *)  R_alloc(ngrid,sizeof(double));
    double *yc        = (double *)  R_alloc(ngrid,sizeof(double));
  
    // Initialise the arrays containing the computed backgrounds for each cell
    for(i = 0;i<ngrid; i++) {
      zonebg[i] = 0;
      zonesd[i] = 0;
      ends[i]   = 0;
!     scratches[i] = (double *) R_alloc(ncol*nrow/ngrid,sizeof(double));
    }
    // count the number of spots in each cell and store consecutively in scratch the values from each grid cell
    for(i = 0; i < n; i++) {
--- 539,551 ----
    double *xc        = (double *)  R_alloc(ngrid,sizeof(double));
    double *yc        = (double *)  R_alloc(ngrid,sizeof(double));
  
+   cellsize = ((int) ((double) ncol / (double) gxn) + 1) * ((int) ((double) nrow / (double) gyn) + 1);
    // Initialise the arrays containing the computed backgrounds for each cell
    for(i = 0;i<ngrid; i++) {
      zonebg[i] = 0;
      zonesd[i] = 0;
      ends[i]   = 0;
!     scratches[i] = (double *) R_alloc(cellsize,sizeof(double));
    }
    // count the number of spots in each cell and store consecutively in scratch the values from each grid cell
    for(i = 0; i < n; i++) {
***************
*** 599,605 ****
      if(val < 0.5) val = 0.5;
      tmp = val - bg;
      if(tmp < nfrac * nz) tmp = nfrac * nz;
!     corrected[idx[i]] = tmp;
    }
  }
  
--- 600,606 ----
      if(val < 0.5) val = 0.5;
      tmp = val - bg;
      if(tmp < nfrac * nz) tmp = nfrac * nz;
!     corrected[idx[i]-1] = tmp;
    }
  }