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/*
* intensities.c
*
* Extract intensities from patterns
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#include <stdlib.h>
#include <math.h>
#include <stdio.h>
#include <assert.h>
#include "image.h"
#include "intensities.h"
#include "cell.h"
#include "sfac.h"
#include "diffraction.h"
#define MAX_HITS (1024)
struct reflhit {
signed int h;
signed int k;
signed int l;
double min_distance;
int x;
int y;
};
static int sum_nearby_points(int16_t *data, int width, int x, int y)
{
int dx, dy;
int intensity = 0;
for ( dx=-3; dx<=3; dx++ ) {
for ( dy=-3; dy<=3; dy++ ) {
intensity += data[(x+dx) + width*(y+dy)];
}
}
return intensity;
}
void output_intensities(struct image *image, UnitCell *cell)
{
int x, y;
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
struct reflhit hits[MAX_HITS];
int n_hits = 0;
int i;
cell_get_cartesian(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
for ( x=0; x<image->width; x++ ) {
for ( y=0; y<image->height; y++ ) {
double hd, kd, ld; /* Indices with decimal places */
double dh, dk, dl; /* Distances in h,k,l directions */
signed int h, k, l;
struct rvec q;
double dist;
int found = 0;
int j;
q = get_q(image, x, y, 1, NULL);
hd = q.u * ax + q.v * ay + q.w * az;
kd = q.u * bx + q.v * by + q.w * bz;
ld = q.u * cx + q.v * cy + q.w * cz;
h = (signed int)rint(hd);
k = (signed int)rint(kd);
l = (signed int)rint(ld);
dh = hd - h;
dk = kd - k;
dl = ld - l;
dist = sqrt(pow(dh, 2.0) + pow(dk, 2.0) + pow(dl, 2.0));
if ( dist > 0.1 ) continue;
for ( j=0; j<n_hits; j++ ) {
if ( (hits[j].h == h) && (hits[j].k == k)
&& (hits[j].l == l) ) {
if ( dist < hits[j].min_distance ) {
hits[j].min_distance = dist;
hits[j].x = x;
hits[j].y = y;
}
found = 1;
}
}
if ( !found ) {
hits[n_hits].min_distance = dist;
hits[n_hits].x = x;
hits[n_hits].y = y;
hits[n_hits].h = h;
hits[n_hits].k = k;
hits[n_hits].l = l;
n_hits++;
assert(n_hits < MAX_HITS);
}
}
}
STATUS("Found %i reflections\n", n_hits);
/* Explicit printf() used here (not normally allowed) because
* we really want to output to stdout */
printf("New pattern: %7.5f %7.5f %7.5f %7.5f\n",
image->orientation.w, image->orientation.x,
image->orientation.y, image->orientation.z);
for ( i=0; i<n_hits; i++ ) {
int intensity;
/* Bounds check */
if ( hits[i].x + 3 >= image->width ) continue;
if ( hits[i].x - 3 < 0 ) continue;
if ( hits[i].y + 3 >= image->height ) continue;
if ( hits[i].y - 3 < 0 ) continue;
intensity = sum_nearby_points(image->data, image->width,
hits[i].x, hits[i].y);
printf("%3i %3i %3i %6i (at %i,%i)\n",
hits[i].h, hits[i].k, hits[i].l, intensity,
hits[i].x, hits[i].y);
}
/* Blank line at end */
printf("\n");
}
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