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|
/*=======================================================================
* All files in the distribution of the DPS system are Copyright
* 1996 by the Computational Biology group in the Department of Biological
* Sciences at Purdue University. All rights reserved.
*
* Redistribution and use in source and binary forms are permitted
* provided that this entire copyright notice is duplicated in all such
* copies, and that any documentation, announcements, and other materials
* related to such distribution and use acknowledge that the software was
* developed by the Computational Biology group in the Department of
* Biological Sciences at Purdue University, W. Lafayette, IN by Ingo
* Steller and Michael G. Rossmann. No charge may be made for copies,
* derivations, or distributions of this material without the express
* written consent of the copyright holder. Neither the name of the
* University nor the names of the authors may be used to endorse or
* promote products derived from this material without specific prior
* written permission.
*
* THIS SOFTWARE IS PROVIDED ``AS IS'' AND WITHOUT ANY EXPRESS OR
* IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR ANY PARTICULAR PURPOSE.
*======================================================================*/
/*=====================================================================*
* *
* Data Processing Suite *
* *
* Utility-Library *
* *
* Written by Ingo Steller *
* *
* File: dps_peaksearch.c *
* *
*=====================================================================*/
/* Modifed 3/24/98 By Andy Arvai to be a subroutine where the data
* is passed as a pointer.
*/
/* Modified 10/24/2015 by H. J. Bernstein to use doubles, rather than
* floats and, reject peaks with background points below half the background
* and clean up the comments to reflect the current subroutinized version
* built on the Chris Neilson, John Skinner version of 2015, which was
* built on the Andy Arvai version. Further extended 10/31/2015 by HJB to allow
* for large fuzzy spots
*/
/* dps_peaksearch
The original standalone program was used as dps_peakssearch frame.file
This version is used as a function call:
#include "dps_peaksearch.h
int dps_peaksearch(unsigned short *data, // The 16 bit data
int nx, int ny, // The dimensions of the data
int npeaks_out, // The maximum number of peaks
double min_isigma, // The minimum I/sigma to accept
int min_spacing, // The minimum spacing in pixels
DPS_Peak *pptr); // The array of peaks
*/
/* This program does a peak search on a given image and returns a list of
R, S coordinates in pixel. It uses the read_frame routine from the util
library and a modified algorithm of Sangsoo Kim. */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include "dps_peaksearch.h"
int xirint(double x) {
if (x == (int)x)
return((int)x);
if (x > 0.0)
return((int)(x+0.5));
else
return((int)(x-0.5));
}
#if defined (__linux__)||defined(sun)
/* Round a double to an integer */
/* Calculate sin() and cos(). */
void
sincos(x, s, c)
double x, *s, *c;
{
*s = sin(x);
*c = cos(x);
}
#endif /* __linux__ */
#if defined(sgi)||defined(Alpha)||defined(hppa)||defined(convex)||defined(rs6000)
/* Calculate sin() and cos(). */
void
sincos(x, s, c)
double x, *s, *c;
{
*s = sin(x);
*c = cos(x);
}
/* Round a double to an integer */
double
rint(x)
register double x;
{
if (x == (int)x)
return(x);
if (x > 0.0)
return((double)((int)(x+0.5)));
else
return((double)((int)(x-0.5)));
}
#endif /* sgi */
int fsign(double x)
{
if (x >= 0.0)
return(1);
else
return(-1);
}
/* Find the "center of mass" around a "spot" centered at x,y in the array
* idata.
*
*/
void
cmass (idata, iwidth, iheight, x, y, cm_x, cm_y, cm_nx, cm_ny)
register unsigned short *idata;
int iwidth, iheight, x, y;
double *cm_x, *cm_y;
int cm_nx, cm_ny;
{
register int i, j, val;
double sum_x=0, sum_y=0, sum_z=0.0;
int prev_x, prev_y;
prev_x = x;
prev_y = y;
for(j= -cm_ny/2;j<=cm_ny/2;j++)
for(i= -cm_nx/2;i<=cm_nx/2;i++) {
if (((j+y) >= iheight) || ((j+y) < 0)
|| ((i+x) >= iwidth) || ((i+x) < 0))
continue;
val = idata[(j+y)*iwidth + (i+x)];
sum_x += ((double)i+x)*val;
sum_y += ((double)j+y)*val;
sum_z += val;
}
if (sum_z == 0.0) {
*cm_x = x;
*cm_y = y;
}
else {
*cm_x = sum_x / sum_z;
*cm_y = sum_y / sum_z;
}
/* Do a second pass to get a better value */
sum_x = sum_y = sum_z = 0;
x = xirint(*cm_x);
y = xirint(*cm_y);
if ((x == prev_x) && (y == prev_y))
return;
for(j= -cm_ny/2;j<=cm_ny/2;j++)
for(i= -cm_nx/2;i<=cm_nx/2;i++) {
if (((j+y) >= iheight) || ((j+y) < 0)
|| ((i+x) >= iwidth) || ((i+x) < 0))
continue;
val = idata[(j+y)*iwidth + (i+x)];
sum_x += ((double)i+x)*val;
sum_y += ((double)j+y)*val;
sum_z += val;
}
if (sum_z == 0.0) {
*cm_x = x;
*cm_y = y;
}
else {
*cm_x = sum_x / sum_z;
*cm_y = sum_y / sum_z;
}
}
static DPS_Peak *dps_peaks = NULL;
static int ccd_image_saturation = 0;
int dps_peaksearch(unsigned short *data, int nx, int ny,
int npeaks_out, double min_isigma,
int min_spacing, DPS_Peak *pptr, int min_value)
{
int stepx;
int stepy;
int small_stepx;
int small_stepy;
double back_count;
double spot_count;
double cm_x, cm_y;
int i, j; /* counter */
int y, dy; /* more counter */
int value; /* variable to store an actual od_value */
int maxval;
int bmax, bmin;
int k, l; /* many more counter... */
int x_max, y_max;
int bma_x, bmi_x, bma_y, bmi_y;
int back, spot;
double noise_thresh = 1.0;
double A, B, I, sigmaI;
int overload = 55000;
int npeaks=0;
int maxpeaks=20480;
int sortfunc();
int nover;
int nunder;
int nxfer;
DPS_Peak dps_temp;
int peakfw, peakfh;
int next_good_y[nx];
int collide;
stepx = (min_spacing+1)/2; /* Initial stepsize for scanning through the image */
if (stepx < 1) stepx = 1;
stepy = stepx;
small_stepx = stepx;
if (small_stepx > 3) small_stepx = 3;
small_stepy = stepy;
if (small_stepy > 3) small_stepy = 3;
back_count = 4*stepx+4*stepy; /* Number of background pixels */
spot_count = (2*stepx-1)*(2*stepy-1); /* Number of spot pixels (see below) */
if (min_isigma > 0)
noise_thresh = min_isigma;
if (ccd_image_saturation > 0)
overload = ccd_image_saturation;
if (dps_peaks != NULL)
free(dps_peaks);
dps_peaks = (DPS_Peak *)malloc(maxpeaks * sizeof(DPS_Peak));
if (dps_peaks == NULL) {
fprintf(stderr,"error: not enough memory for dps_peaksearch.\n");
fflush(stderr);
return 0;
}
/* Initialize the next_good_y array to 0 */
for (i=0; i < nx; i++) next_good_y[i]= 0;
/* The next two loops go over the whole frame with stepsize
* small_stepx and small_stepy, but looking at boxes 2*stepx by 2*stepy.
*/
for(j=2*stepy;j<ny-2*stepy;j=j+small_stepy) {
for(i=2*stepx;i<nx-2*stepx;i=i+small_stepx) {
/* Skip this pixel if too close to prior spots */
collide = 0;
for (l=i-stepx; l<=i+stepx; l++) {
if (next_good_y[l] > j-stepy-1 ) {
collide = 1;
break;
}
}
if (collide) continue;
/* y hold the index of the pixel at i,j */
y = j*nx+i;
/* dx is the difference in index between i,j and
* i, j+stepy */
dy = stepy*nx;
value=data[y];
/* Check if we have a maximum at i,j */
if ((value > data[y+stepx]) &&
(value > data[y-stepx]) &&
(value > data[y+dy]) &&
(value > data[y-dy]) &&
(value > data[y+stepy+dy]) &&
(value > data[y-stepy+dy]) &&
(value > data[y+stepy-dy]) &&
(value > data[y-stepy-dy]) ) {
/* If we have a maximum, try to find the maximum
* in a box around i, j with size 2*stepy x 2*stepx
* and stepsize 1. */
maxval=data[y];
/* x_max, y_max will hold the final maximum */
x_max=j;
y_max=i;
for(k=j-stepy;k<=j+stepy;k++) {
for(l=i-stepx;l<=i+stepx;l++) {
/* Same as above only with stepsize 1 */
y = k*nx+l;
dy = nx;
value=data[y];
if((value >= data[y+1]) &&
(value >= data[y-1]) &&
(value >= data[y+dy]) &&
(value >= data[y-dy]) &&
(value >= maxval) ) {
maxval=value;
x_max=l;
y_max=k;
}
}
}
cmass (data, nx, ny, x_max, y_max, &cm_x, &cm_y, 2*stepx+1, 2*stepy+1);
x_max = cm_x + 0.5;
y_max = cm_y + 0.5;
/* Now we calculate the average background and
* spot values for this position. The box goes
* from i-stepy to i+stepy and j-stepx to
* i+stepx. The background pixels are the pixels
* of a one pixel frame at the border of the box,
* the rest are spot pixels. For stepy=stepy=3 this
* gives 25 spot pixels and 24 background pixels
*/
/* Borders of the box */
bma_y = y_max+stepy;
bmi_y = y_max-stepy;
bma_x = x_max+stepx;
bmi_x = x_max-stepx;
if (bma_y >= ny) bma_y = ny-1;
if (bma_x >= nx) bma_x = nx-1;
if (bmi_y < 0) bmi_y = 0;
if (bmi_x < 0) bmi_x = 0;
back = 0;
bmax = -1;
bmin = 999999;
spot = 0;
nover=0;
nunder=0;
for(k=bmi_y;k<=bma_y;k++) {
for(l=bmi_x;l<=bma_x;l++) {
/* see above */
y = k*nx+l;
value=data[y];
value &= 0xFFFF;
if (value >= overload) {
nover++;
}
if (value < min_value) {
nunder++;
}
/* if counter at border of box, the pixel
* is a background pixel otherwise it is a
* spot pixel */
if ((k == bma_y) ||
(k == bmi_y) ||
(l == bma_x) ||
(l == bmi_x) ) {
back = back + value;
if (value > bmax) bmax = value;
if (value < bmin) bmin = value;
}
else {
spot = spot + value;
}
}
}
/* If the average spot pixel value is larger by a
* certain factor than the average background pixel value
* write the reflection to the output file. Check also
* if the maximum value is an overload value.... */
A = (double)spot;
B = (double)back*spot_count/back_count;
I = A - B;
sigmaI = sqrt(A + B);
if ((sigmaI > 0.0)
&& (I/sigmaI > noise_thresh)
&& (nover <= 4)
&& (nunder < 1)
&&!near_edge(data, nx, ny, x_max, y_max,
((double)back)/((double)(back_count)),
maxval, bmax, bmin, stepx, stepy,
&peakfw, &peakfh, min_value)) {
dps_peaks[npeaks].x = cm_x;
dps_peaks[npeaks].y = cm_y;
dps_peaks[npeaks].isigma = I/sigmaI;
dps_peaks[npeaks].peakfw = peakfw;
dps_peaks[npeaks].peakfh = peakfh;
npeaks++;
/* Update next_good_y for this peak */
for (l=x_max-peakfw/2; l<=x_max+peakfw/2; l++) {
if (next_good_y[l] < y_max+stepy+1 ) {
next_good_y[l] = y_max+stepy+1;
}
}
if (x_max+peakfw/2-small_stepx > i) i = x_max+peakfw/2-small_stepx;
if (npeaks >= maxpeaks) {
maxpeaks *= 2;
dps_peaks = (DPS_Peak *)realloc(dps_peaks, sizeof(DPS_Peak)*maxpeaks);
if (dps_peaks == NULL) {
fprintf(stderr,"error: not enough memory for dps_peaksearch (%d spots).\n",npeaks);
return 0;
}
}
}
}
}
}
if (min_spacing > 0) {
for(i=0;i<npeaks;i++)
for(j=i+1;j<npeaks;j++) {
if ((fabs(dps_peaks[i].x - dps_peaks[j].x) < (dps_peaks[i].peakfw + dps_peaks[j].peakfw)/2) &&
(fabs(dps_peaks[i].y - dps_peaks[j].y) < (dps_peaks[i].peakfh + dps_peaks[j].peakfh)/2)) {
if (dps_peaks[i].isigma > dps_peaks[j].isigma)
dps_peaks[j].isigma = dps_peaks[j].x = dps_peaks[j].y = -9999;
else
dps_peaks[i].isigma = dps_peaks[i].x = dps_peaks[i].y = -9999;
}
}
}
qsort(dps_peaks,npeaks,sizeof(DPS_Peak),sortfunc);
if ((npeaks_out <= 0) || (npeaks < npeaks_out))
npeaks_out = npeaks;
nxfer = 0;
for(i=0;i<npeaks_out;i++)
{
if(dps_peaks[i].x < 0 || dps_peaks[i].y < 0)
continue;
dps_temp.x = dps_peaks[i].x;
dps_temp.y = dps_peaks[i].y;
dps_temp.isigma = dps_peaks[i].isigma;
dps_temp.peakfw = dps_peaks[i].peakfw;
dps_temp.peakfh = dps_peaks[i].peakfh;
*pptr++ = dps_temp;
nxfer++;
}
free(dps_peaks);
return(nxfer);
}
/* Sort pixel value
*/
int
sortfunc(pk1, pk2)
DPS_Peak *pk1, *pk2;
{
if (pk2->isigma > pk1->isigma)
return 1;
else
if (pk2->isigma < pk1->isigma)
return -1;
else
return 0;
}
/* Test if there are more than stepx+stepy pixels within the spot or the spot overlaps the edge
*/
int near_edge(unsigned short *data,
int width, int height,
int xpos, int ypos,
double back, int peak, int bmax, int bmin,
int stepx, int stepy, int* peakfw, int* peakfh, int min_value)
{
int x,y, is, it;
int minstep, maxstep;
int value;
int smin, smax;
double bavg;
x = xpos;
y = ypos;
if (x < stepx)
return 1;
if (x >= width-stepx)
return 1;
if (y < stepy)
return 1;
if (y >= height-stepy)
return 1;
if (bmax >= peak)
return 1;
minstep = maxstep = stepx;
if (stepy > maxstep) maxstep = stepy;
if (stepy < minstep) minstep = stepy;
/* Loop through bounding boxes
When we are is from the peak, we have
2*(2*is+1)+2*(2*is-1) = 8*is points */
for (is = 1; is <= minstep; is++) {
smax = -1;
smin = 999999;
bavg = 0;
for (it = -is; it <= is; it ++) {
value = data[width*(ypos -is)+xpos+it];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value < min_value) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
value = data[width*(ypos +is)+xpos+it];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
}
for (it = -is+1; it <= is-1; it ++) {
value = data[width*(ypos +it)+xpos-is];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
value = data[width*(ypos +it)+xpos+is];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
}
bavg /= (double)(8*is);
if ((double)smin < back/2. && smin < bmin) return 1;
if ((double)bavg >= back*1.1 ) continue;
if (smax <= bmax) {
*peakfw = *peakfh = is*2-1;
return 0;
}
}
for (is = minstep+1; is <= maxstep; is++) {
smax = -1;
smin = 999999;
bavg = 0;
if (stepy > stepx) {
for (it = -minstep; it <= minstep; it ++) {
value = data[width*(ypos -is)+xpos+it];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
value = data[width*(ypos +is)+xpos+it];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
}
for (it = -is+1; it <= is-1; it ++) {
value = data[width*(ypos +it)+xpos-minstep];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
value = data[width*(ypos +it)+xpos+minstep];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
}
} else if (stepx < stepy) {
for (it = -is; it <= is; it ++) {
value = data[width*(ypos -minstep)+xpos+it];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
value = data[width*(ypos +minstep)+xpos+it];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
}
for (it = -minstep+1; it <= minstep-1; it ++) {
value = data[width*(ypos +it)+xpos-is];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
value = data[width*(ypos +it)+xpos+is];
value &= 0xFFFF;
if (value !=0xFFFF && (value & 0XFFFC) == 0xFFFC) return 1;
if (value > smax) smax = value;
if (value < smin) smin = value;
bavg += (double)value;
}
}
bavg /= (double)(4*is+4*minstep);
if ((double)smin < back/2. && smin < bmin) return 1;
if ((double)bavg >= back*1.1 ) continue;
if (smax <= bmax) {
if (stepx < stepy) {
*peakfh = 2*minstep-1;
*peakfw = 2*is-1;
} else {
*peakfw = 2*minstep-1;
*peakfh = 2*is-1;
}
return 0;
}
}
*peakfh = 2*stepy+1;
*peakfw = 2*stepx+1;
return 0;
}
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