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/*
* indexamajig.c
*
* Find hits, index patterns, output hkl+intensity etc.
*
* (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 <hdf5.h>
#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "intensities.h"
#include "ewald.h"
#include "peaks.h"
#include "diffraction.h"
#include "detector.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"
" --no-index Do everything else (including fine peak search and\n"
" writing 'xfel.drx' if DirAx is being used), but\n"
" don't actually index.\n"
" --dirax Use DirAx for indexing.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
" --near-bragg Output a list of reflection intensities to stdout.\n"
" --simulate Simulate the diffraction pattern using the indexed\n"
" unit cell.\n"
"\n");
}
int main(int argc, char *argv[])
{
int c;
char *filename = NULL;
FILE *fh;
char *rval;
int n_images;
int n_hits;
int config_noindex = 0;
int config_dumpfound = 0;
int config_dirax = 0;
int config_nearbragg = 0;
int config_simulate = 0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
{"near-bragg", 0, &config_nearbragg, 1},
{"dirax", 0, &config_dirax, 1},
{"simulate", 0, &config_simulate, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:w", 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;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
image.features = NULL;
image.molecule = NULL;
image.data = NULL;
STATUS("Processing '%s'\n", line);
n_images++;
hdfile = hdfile_open(line);
if ( hdfile == NULL ) {
continue;
} else if ( hdfile_set_first_image(hdfile, "/") ) {
ERROR("Couldn't select path\n");
continue;
}
hdf5_read(hdfile, &image);
/* Perform 'fine' peak search */
search_peaks(&image);
if ( image_feature_count(image.features) > 5 ) {
n_hits++;
if ( config_dumpfound ) dump_peaks(&image);
/* Not indexing? Then there's nothing left to do. */
if ( config_noindex ) goto done;
/* Calculate orientation matrix (by magic) */
index_pattern(&image, config_noindex,
config_dirax);
if ( image.molecule == NULL ) goto done;
if ( config_nearbragg || config_simulate ) {
/* Simulate a diffraction pattern */
image.sfacs = NULL;
image.data = NULL;
image.qvecs = NULL;
image.twotheta = NULL;
image.hdr = NULL;
/* View head-on (unit cell is tilted) */
image.orientation.w = 1.0;
image.orientation.x = 0.0;
image.orientation.y = 0.0;
image.orientation.z = 0.0;
get_ewald(&image);
}
if ( config_nearbragg ) {
/* Read h,k,l,I */
output_intensities(&image);
}
if ( config_simulate ) {
get_diffraction(&image, 8, 8, 8);
if ( image.molecule == NULL ) {
ERROR("Couldn't open molecule.pdb\n");
return 1;
}
record_image(&image, 0, 0, 0);
hdf5_write("simulated.h5", image.data,
image.width, image.height);
}
}
done:
free(image.data);
image_feature_list_free(image.features);
hdfile_close(hdfile);
H5close();
} 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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