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/*
* alter_stream.c
*
* Do transformations on a stream
*
* (c) 2006-2011 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 <assert.h>
#include "../src/utils.h"
#include "../src/stream.h"
#include "../src/cell.h"
#include "../src/image.h"
#include "../src/beam-parameters.h"
#include "../src/geometry.h"
#include "../src/peaks.h"
static void mess_up_cell(UnitCell *cell)
{
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
/* Cell noise in percent */
const double cnoise = 0.5;
//STATUS("Real:\n");
//cell_print(cell);
cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
ax = gaussian_noise(ax, cnoise*fabs(ax)/100.0);
ay = gaussian_noise(ay, cnoise*fabs(ay)/100.0);
az = gaussian_noise(az, cnoise*fabs(az)/100.0);
bx = gaussian_noise(bx, cnoise*fabs(bx)/100.0);
by = gaussian_noise(by, cnoise*fabs(by)/100.0);
bz = gaussian_noise(bz, cnoise*fabs(bz)/100.0);
cx = gaussian_noise(cx, cnoise*fabs(cx)/100.0);
cy = gaussian_noise(cy, cnoise*fabs(cy)/100.0);
cz = gaussian_noise(cz, cnoise*fabs(cz)/100.0);
cell_set_reciprocal(cell, ax, ay, az, bx, by, bz, cx, cy, cz);
//STATUS("Changed:\n");
//cell_print(cell);
}
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Alter a stream.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
"You need to provide the following basic options:\n"
" -i, --input=<file> Read reflections from <file>.\n"
" -o, --output=<file> Write partials in stream format to <file>.\n"
);
}
int main(int argc, char *argv[])
{
int c;
char *input_file = NULL;
char *output_file = NULL;
struct image image;
struct detector *det = NULL;
struct beam_params *beam = NULL;
char *beamfile = NULL;
char *geomfile = NULL;
FILE *ifh;
FILE *ofh;
int v;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"output", 1, NULL, 'o'},
{"input", 1, NULL, 'i'},
{"beam", 1, NULL, 'b'},
{"geometry", 1, NULL, 'g'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:o:b:g:",
longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'o' :
output_file = strdup(optarg);
break;
case 'i' :
input_file = strdup(optarg);
break;
case 'b' :
beamfile = strdup(optarg);
break;
case 'g' :
geomfile = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( input_file == NULL ) {
ERROR("You must pgive a filename for the output.\n");
return 1;
}
ifh = fopen(input_file, "r");
if ( ifh == NULL ) {
ERROR("Couldn't open input file '%s'\n", input_file);
return 1;
}
free(input_file);
if ( output_file == NULL ) {
ERROR("You must pgive a filename for the output.\n");
return 1;
}
ofh = fopen(output_file, "w");
if ( ofh == NULL ) {
ERROR("Couldn't open output file '%s'\n", output_file);
return 1;
}
free(output_file);
/* Load beam */
if ( beamfile == NULL ) {
ERROR("You need to provide a beam parameters file.\n");
return 1;
}
beam = get_beam_parameters(beamfile);
if ( beam == NULL ) {
ERROR("Failed to load beam parameters from '%s'\n", beamfile);
return 1;
}
free(beamfile);
/* Load geometry */
if ( geomfile == NULL ) {
ERROR("You need to give a geometry file.\n");
return 1;
}
det = get_detector_geometry(geomfile);
if ( det == NULL ) {
ERROR("Failed to read geometry from '%s'\n", geomfile);
return 1;
}
free(geomfile);
write_stream_header(ofh, argc, argv);
image.det = det;
image.width = det->max_fs;
image.height = det->max_ss;
image.lambda = 0.0;
image.div = beam->divergence;
image.bw = beam->bandwidth;
image.profile_radius = 0.0001e9;
image.i0_available = 0;
do {
image.indexed_cell = NULL;
v = read_chunk(ifh, &image);
if ( (v == 0) && (image.indexed_cell != NULL) ) {
mess_up_cell(image.indexed_cell);
image.reflections = find_intersections(&image,
image.indexed_cell);
write_chunk(ofh, &image, NULL, STREAM_INTEGRATED);
}
} while ( v == 0 );
fclose(ofh);
fclose(ifh);
return 0;
}
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