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/*
* estimate-background.c
*
* Like 'process_hkl', but for signal/noise ratios
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include "utils.h"
#include "statistics.h"
#include "sfac.h"
#include "reflections.h"
#include "symmetry.h"
#include "stream.h"
/* Number of bins for plot of resolution shells */
#define NBINS (10)
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Estimate peak SNR from FEL Bragg intensities.\n"
"\n"
" -h, --help Display this help message.\n"
" -i, --input=<filename> Specify input filename (\"-\" for stdin).\n"
);
}
int main(int argc, char *argv[])
{
int c;
char *filename = NULL;
FILE *fh;
int rval;
double total_vol, vol_per_shell;
double rmin, rmax;
double rmins[NBINS];
double rmaxs[NBINS];
double snrs[NBINS];
unsigned int counts[NBINS];
UnitCell *real_cell;
double overall_snr;
unsigned int overall_counts;
int i;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:e:ro:p:y:g:f:a:r:",
longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'i' :
filename = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( filename == NULL ) {
ERROR("Please specify filename using the -i option\n");
return 1;
}
/* Open the data stream */
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
} else {
fh = fopen(filename, "r");
}
free(filename);
if ( fh == NULL ) {
ERROR("Failed to open input file\n");
return 1;
}
/* FIXME: Fixed resolution shells */
rmin = 0.120e9;
rmax = 1.172e9;
for ( i=0; i<NBINS; i++ ) {
counts[i] = 0;
snrs[i] = 0.0;
}
total_vol = pow(rmax, 3.0) - pow(rmin, 3.0);
vol_per_shell = total_vol / NBINS;
rmins[0] = rmin;
for ( i=1; i<NBINS; i++ ) {
double r;
r = vol_per_shell + pow(rmins[i-1], 3.0);
r = pow(r, 1.0/3.0);
/* Shells of constant volume */
rmaxs[i-1] = r;
rmins[i] = r;
/* Shells of constant thickness */
//rmins[i] = rmins[i-1] + (rmax-rmin)/NBINS;
//rmaxs[i-1] = rmins[i-1] + (rmax-rmin)/NBINS;
STATUS("Shell %i: %f to %f\n", i-1,
rmins[i-1]/1e9, rmaxs[i-1]/1e9);
}
rmaxs[NBINS-1] = rmax;
STATUS("Shell %i: %f to %f\n", NBINS-1,
rmins[NBINS-1]/1e9, rmaxs[NBINS-1]/1e9);
real_cell = load_cell_from_pdb("../../1JB0.pdb");
do {
char *rval2;
UnitCell *cell;
char *filename;
char line[1024];
int done = 0;
rval = find_chunk(fh, &cell, &filename);
if ( rval != 0 ) break;
do {
signed int h, k, l;
float intensity, x, y, max, bg;
int r, j;
double d, snr;
int bin;
rval2 = fgets(line, 1024, fh);
if ( strncmp(line, "Peak statistics:", 16) == 0 ) {
done = 1;
}
r = sscanf(line, "%i %i %i %f (at %f,%f) max=%f bg=%f",
&h, &k, &l, &intensity, &x, &y, &max, &bg);
if ( r != 8 ) {
continue;
}
d = resolution(real_cell, h, k, l) * 2.0;
//STATUS("'%s'", line);
//STATUS("-> %i %i %i %f\n", h, k, l, d/1e9);
bin = -1;
for ( j=0; j<NBINS; j++ ) {
if ( (d>rmins[j]) && (d<=rmaxs[j]) ) {
bin = j;
break;
}
}
if ( bin == -1 ) {
ERROR("Warnung! %i %i %i %f\n", h, k, l, d/1e9);
continue;
}
snr = max/bg;
snrs[bin] += snr;
counts[bin]++;
} while ( !done );
} while ( !rval );
/* Print out results */
overall_snr = 0.0;
overall_counts = 0;
for ( i=0; i<NBINS; i++ ) {
double snr, cen;
cen = rmins[i] + (rmaxs[i] - rmins[i])/2.0;
snr = snrs[i] / (double)counts[i];
printf("%f %f (%f / %i)\n", cen*1.0e-9, snr, snrs[i], counts[i]);
if ( i>0 ) {
overall_snr += snrs[i];
overall_counts += counts[i];
}
}
printf("Overall: %f (%f / %i)\n", overall_snr/(double)overall_counts,
overall_snr, overall_counts);
fclose(fh);
return 0;
}
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