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/*
* get_hkl.c
*
* Small program to write out a list of h,k,l,I values given a structure
*
* (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 "sfac.h"
#include "reflections.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Write idealised intensity lists.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -t, --template=<filename> Only include reflections mentioned in file.\n"
" --poisson Simulate Poisson samples.\n"
" --twin Generate twinned data.\n"
" -o, --output=<filename> Output filename (default: stdout).\n"
" --zone-axis Generate hk0 intensities only (and add\n"
" Synth2D-style header.\n"
" -i, --intensities=<file> Read intensities from file instead of\n"
" calculating them from scratch. You might use\n"
" this if you need to apply noise or twinning.\n"
" -p, --pdb=<file> PDB file from which to get the structure.\n"
);
}
static int template_reflections(const char *filename, unsigned int *counts)
{
char *rval;
FILE *fh;
fh = fopen(filename, "r");
if ( fh == NULL ) {
return 1;
}
do {
char line[1024];
int r;
signed int h, k, l;
rval = fgets(line, 1023, fh);
r = sscanf(line, "%i %i %i", &h, &k, &l);
if ( r != 3 ) continue;
set_count(counts, h, k, l, 1);
} while ( rval != NULL );
fclose(fh);
return 0;
}
/* Apply Poisson noise to all reflections */
static void noisify_reflections(double *ref)
{
signed int h, k, l;
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double val;
int c;
val = lookup_intensity(ref, h, k, l);
c = poisson_noise(val);
set_intensity(ref, h, k, l, c);
}
}
progress_bar(h+INDMAX, 2*INDMAX, "Simulating noise");
}
}
int main(int argc, char *argv[])
{
int c;
double *ideal_ref;
double *phases;
struct molecule *mol;
char *template = NULL;
int config_noisify = 0;
int config_twin = 0;
int config_za = 0;
char *output = NULL;
unsigned int *counts;
unsigned int *cts;
char *input = NULL;
signed int h, k, l;
char *filename = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"template", 1, NULL, 't'},
{"poisson", 0, &config_noisify, 1},
{"output", 1, NULL, 'o'},
{"twin", 0, &config_twin, 1},
{"zone-axis", 0, &config_za, 1},
{"intensities", 1, NULL, 'i'},
{"pdb", 1, NULL, 'p'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "ht:o:i:p:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 't' :
template = strdup(optarg);
break;
case 'o' :
output = strdup(optarg);
break;
case 'i' :
input = strdup(optarg);
break;
case 'p' :
filename = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( filename == NULL ) {
filename = strdup("molecule.pdb");
}
mol = load_molecule(filename);
cts = new_list_count();
phases = new_list_intensity(); /* "intensity" type used for phases */
if ( input == NULL ) {
ideal_ref = get_reflections(mol, eV_to_J(1790.0), 1/(0.05e-9),
cts, phases);
} else {
ideal_ref = read_reflections(input, cts, phases);
free(input);
}
counts = new_list_count();
if ( template != NULL ) {
if ( template_reflections(template, counts) != 0 ) {
ERROR("Failed to template reflections.\n");
return 1;
}
} else {
/* No template? Then only mark reflections which were
* calculated. */
for ( h=-INDMAX; h<=INDMAX; h++ ) {
for ( k=-INDMAX; k<=INDMAX; k++ ) {
for ( l=-INDMAX; l<=INDMAX; l++ ) {
unsigned int c;
c = lookup_count(cts, h, k, l);
set_count(counts, h, k, l, c);
}
}
}
}
if ( config_noisify ) noisify_reflections(ideal_ref);
if ( config_twin ) {
for ( h=-INDMAX; h<=INDMAX; h++ ) {
for ( k=-INDMAX; k<=INDMAX; k++ ) {
for ( l=-INDMAX; l<=INDMAX; l++ ) {
double a, b, c, d;
double t;
if ( abs(h+k) > INDMAX ) {
set_intensity(ideal_ref, h, k, l, 0.0);
continue;
}
a = lookup_intensity(ideal_ref, h, k, l);
b = lookup_intensity(ideal_ref, k, h, -l);
c = lookup_intensity(ideal_ref, -(h+k), k, -l);
d = lookup_intensity(ideal_ref, -(h+k), h, l);
t = (a+b+c+d)/4.0;
set_intensity(ideal_ref, h, k, l, t);
set_intensity(ideal_ref, k, h, -l, t);
set_intensity(ideal_ref, -(h+k), h, l, t);
set_intensity(ideal_ref, -(h+k), k, -l, t);
}
}
}
}
write_reflections(output, counts, ideal_ref, phases,
config_za, mol->cell, 1);
return 0;
}
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