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/*
* process_images.c
*
* Find hits, index patterns, output hkl+intensity etc.
*
* (c) 2006-2009 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 "hdf5-file.h"
#include "dirax.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Process and index FEL diffraction images.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify file containing list of images to process.\n"
" '-' means stdin, which is the default.\n"
"\n");
}
static int sum_of_peaks(struct image *image)
{
int x, y;
int integr = 0;
for ( x=0; x<400; x++ ) {
for ( y=600; y<1024; y++ ) {
int val;
val = image->data[x+image->height*y];
if ( val > 1000 ) integr+=val;
}
}
for ( x=700; x<1023; x++ ) {
for ( y=600; y<1024; y++ ) {
int val;
val = image->data[x+image->height*y];
if ( val > 1000 ) integr+=val;
}
}
return integr;
}
int main(int argc, char *argv[])
{
int c;
char *filename = NULL;
FILE *fh;
char *rval;
int n_images;
int n_hits;
/* 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:", 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 ) {
filename = strdup("-");
}
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;
}
n_images = 0;
n_hits = 0;
do {
char line[1024];
struct hdfile *hdfile;
struct image image;
int integr;
rval = fgets(line, 1023, fh);
chomp(line);
STATUS("Processing '%s'\n", line);
hdfile = hdfile_open(line);
if ( hdfile == NULL ) {
ERROR("Couldn't open file '%s'\n", filename);
} else if ( hdfile_set_first_image(hdfile, "/") ) {
ERROR("Couldn't select path\n");
}
hdf5_read(hdfile, &image);
integr = sum_of_peaks(&image);
printf("%6i %i\n", n_images, integr);
if ( integr > 200000 ) {
STATUS("Hit: %s\n", line);
index_pattern(&image);
n_hits++;
}
n_images++;
} while ( rval != NULL );
fclose(fh);
STATUS("There were %i images.\n", n_images);
STATUS("%i hits were found.\n", n_hits);
return 0;
}
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