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/*
* peaks.c
*
* Peak search and other image analysis
*
* (c) 2006-2009 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#include <string.h>
#include <assert.h>
#include "image.h"
#include "utils.h"
#define PEAK_WINDOW_SIZE (10)
static int in_streak(int x, int y)
{
if ( (y>512) && (y<768) && (abs(x-493)<15) ) return 1;
if ( (y>768) && (abs(x-480)<15) ) return 1;
return 0;
}
struct peak {
int x;
int y;
int i;
int invalid;
};
int image_fom(struct image *image)
{
int x, y;
int integr, n;
float fintegr, mean, sd, th;
struct peak peaks[1024];
int i, n_peaks, n_nearby, n_valid;
/* Measure mean */
integr = 0;
n = 0;
for ( x=0; x<1024; x++ ) {
for ( y=600; y<1024; y++ ) {
int val;
if ( (x>400) && (x<600) ) continue;
val = image->data[x+image->height*y];
if ( val < 0 ) continue;
integr += val;
n++;
}
}
mean = (float)integr / n; /* As integer to keep maths fast */
/* Standard deviation */
fintegr = 0;
for ( x=0; x<1024; x++ ) {
for ( y=600; y<1024; y++ ) {
float val;
if ( (x>400) && (x<600) ) continue;
val = (float)image->data[x+image->height*y];
if ( val < 0 ) continue;
val -= mean;
val = powf(val, 2.0);
fintegr += val;
}
}
sd = sqrtf(fintegr / n);
/* Threshold */
th = mean + 5*sd;
STATUS("mean=%f ,sd=%f, th=%f\n", mean, sd, th);
/* Find pixels above threshold */
n_peaks = 0;
for ( x=0; x<1024; x++ ) {
for ( y=600; y<1024; y++ ) {
int val;
/* Chop out streaky region */
if ( (x>400) && (x<600) ) continue;
val = image->data[x+image->height*y];
if ( val > th ) {
peaks[n_peaks].x = x;
peaks[n_peaks].y = y;
peaks[n_peaks].i = val;
peaks[n_peaks].invalid = 0;
n_peaks++;
}
}
}
do {
int max, max_i = -1;
int adjacent;
n_nearby = 0;
/* Find brightest peak */
max = 0;
for ( i=0; i<n_peaks; i++ ) {
if ( peaks[i].i > max ) {
max = peaks[i].i;
max_i = i;
}
}
/* Must be at least one adjacent bright pixel */
adjacent = 0;
for ( i=0; i<n_peaks; i++ ) {
int td;
td = abs(peaks[i].x - peaks[max_i].x) +
abs(peaks[i].y - peaks[max_i].y);
if ( td == 1 ) {
adjacent++;
break; /* One is enough */
}
}
if ( adjacent < 1 ) {
peaks[i].invalid = 1;
continue;
}
/* Remove nearby (non-invalidated) peaks from list */
n_nearby = 0;
for ( i=0; i<n_peaks; i++ ) {
int dx, dy, ds;
if ( peaks[i].invalid ) continue;
dx = abs(peaks[i].x - peaks[max_i].x);
dy = abs(peaks[i].y - peaks[max_i].y);
ds = dx*dx + dy*dy;
if ( ds < 36 ) {
n_nearby++;
peaks[i].invalid = 1;
}
}
} while ( n_nearby );
n_valid = 0;
for ( i=0; i<n_peaks; i++ ) {
if ( peaks[i].invalid ) continue;
//printf("%i %i\n", peaks[i].x, peaks[i].y);
n_valid++;
}
return n_valid;
}
void search_peaks(struct image *image, int dump_peaks)
{
int x, y, width, height;
int16_t *data;
data = image->data;
width = image->width;
height = image->height;
if ( image->features != NULL ) {
image_feature_list_free(image->features);
}
image->features = image_feature_list_new();
for ( x=1; x<image->width-1; x++ ) {
for ( y=1; y<image->height-1; y++ ) {
double dx1, dx2, dy1, dy2;
double dxs, dys;
double grad;
int mask_x, mask_y;
int sx, sy;
double max;
unsigned int did_something = 1;
/* Overall threshold */
if ( data[x+width*y] < 800 ) continue;
/* Ignore streak */
if ( in_streak(x, y) ) continue;
/* Get gradients */
dx1 = data[x+width*y] - data[(x+1)+width*y];
dx2 = data[(x-1)+width*y] - data[x+width*y];
dy1 = data[x+width*y] - data[(x+1)+width*(y+1)];
dy2 = data[x+width*(y-1)] - data[x+width*y];
/* Average gradient measurements from both sides */
dxs = ((dx1*dx1) + (dx2*dx2)) / 2;
dys = ((dy1*dy1) + (dy2*dy2)) / 2;
/* Calculate overall gradient */
grad = dxs + dys;
if ( grad < 2000000 ) continue;
mask_x = x;
mask_y = y;
while ( (did_something)
&& (distance(mask_x, mask_y, x, y)<50) ) {
max = data[mask_x+width*mask_y];
did_something = 0;
for ( sy=biggest(mask_y-PEAK_WINDOW_SIZE/2, 0);
sy<smallest(mask_y+PEAK_WINDOW_SIZE/2, height);
sy++ ) {
for ( sx=biggest(mask_x-PEAK_WINDOW_SIZE/2, 0);
sx<smallest(mask_x+PEAK_WINDOW_SIZE/2, width);
sx++ ) {
if ( data[sx+width*sy] > max ) {
max = data[sx+width*sy];
mask_x = sx;
mask_y = sy;
did_something = 1;
}
}
}
}
if ( !did_something ) {
double d;
int idx;
assert(mask_x<image->width);
assert(mask_y<image->height);
assert(mask_x>=0);
assert(mask_y>=0);
/* Too far from foot point? */
if ( distance(mask_x, mask_y, x, y) > 50.0 ) continue;
/* Check for a feature at exactly the
* same coordinates */
image_feature_closest(image->features, mask_x, mask_y,
&d, &idx);
if ( d > 1.0 ) {
/* Map and record reflection */
if ( dump_peaks ) {
printf("%i %i\n", x, y);
}
image_add_feature(image->features,
mask_x, mask_y, image, 1.0);
}
}
}
}
}
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