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/*
* calibrate_detector.c
*
* Attempt to refine detector geometry
*
* (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 "utils.h"
#include "image.h"
#include "detector.h"
#include "index.h"
#include "hdf5-file.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options] -i <file.h5>\n\n", s);
printf(
"Optimise detector geometry.\n"
"\n"
" -h, --help Display this help message.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -i, --input=<file> Input filename.\n"
" --split Break up input file into panels according to\n"
" the detector geometry description.\n"
"\n");
}
static void split_image(struct image *image)
{
int i;
const struct detector *det = image->det;
for ( i=0; i<det->n_panels; i++ ) {
int x, y;
struct panel *p;
float *data;
int width, height;
char filename[1024];
p = &det->panels[i];
width = 1 + p->max_fs - p->min_fs;
height = 1 + p->max_ss - p->min_ss;
data = malloc(width*height*sizeof(float));
snprintf(filename, 1023, "%s-%i.h5", image->filename, i);
STATUS("Panel %i, %i by %i pixels -> %s\n", i, width, height,
filename);
for ( x=0; x<width; x++ ) {
for ( y=0; y<height; y++ ) {
int im_x, im_y;
im_x = x+p->min_fs;
im_y = y+p->min_ss;
data[x+width*y] = image->data[im_x+image->width*im_y];
}
}
hdf5_write(filename, data, width, height, H5T_NATIVE_FLOAT);
free(data);
}
}
int main(int argc, char *argv[])
{
int c;
struct image image;
int x, y;
struct hdfile *hdfile;
char *filename = NULL;
char *geometry = NULL;
int split = 0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"geometry", 1, NULL, 'g'},
{"split", 0, &split, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:g:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 0 :
break;
case 'i' :
filename = strdup(optarg);
break;
case 'g' :
geometry = strdup(optarg);
break;
default :
return 1;
}
}
if ( filename == NULL ) {
ERROR("You must specify the input filename with -i\n");
return 1;
}
image.filename = filename;
if ( geometry == NULL ) {
ERROR("You need to specify a geometry file with --geometry\n");
return 1;
}
image.det = get_detector_geometry(geometry);
if ( image.det == NULL ) {
ERROR("Failed to read detector geometry from '%s'\n", geometry);
return 1;
}
free(geometry);
hdfile = hdfile_open(filename);
hdfile_set_image(hdfile, "/data/data");
hdf5_read(hdfile, &image, 1);
if ( split ) {
split_image(&image);
exit(0);
}
for ( x=0; x<image.width; x++ ) {
for ( y=0; y<image.height; y++ ) {
double q;
int intensity;
struct rvec r;
r = get_q(&image, x, y, NULL, 1.0/image.lambda);
q = modulus(r.u, r.v, r.w);
intensity = image.data[x + image.width*y];
printf("%5i\t%5i\t%7.3f\t%7i\n", x, y, q/1.0e9, intensity);
}
}
return 0;
}
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