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/*
* facetron.c
*
* Profile fitting for coherent nanocrystallography
*
* (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 "image.h"
#include "cell.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Profile fitting for coherent nanocrystallography.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify the name of the image to work on.\n"
" -m, --matrix=<filename> Specify the file which contains the initial\n"
" orientation matrix. Can be '-' for stdin,\n"
" which is the default. Units are nm^-1.\n"
);
}
static UnitCell *read_orientation_matrix(const char *filename)
{
FILE *mfh;
float u, v, w;
struct rvec as, bs, cs;
UnitCell *cell;
if ( (filename == NULL) || (strcmp(filename, "-") == 0) ) {
mfh = stdin;
} else {
mfh = fopen(filename, "r");
}
if ( mfh == NULL ) {
ERROR("Failed to open matrix file '%s'\n", filename);
return NULL;
}
if ( fscanf(mfh, "%f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read a-star\n");
return NULL;
}
as.u = u*1e9; as.v = v*1e9; as.w = w*1e9;
if ( fscanf(mfh, "%f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read b-star\n");
return NULL;
}
bs.u = u*1e9; bs.v = v*1e9; bs.w = w*1e9;
if ( fscanf(mfh, "%f %f %f", &u, &v, &w) != 3 ) {
ERROR("Couldn't read c-star\n");
return NULL;
}
cs.u = u*1e9; cs.v = v*1e9; cs.w = w*1e9;
cell = cell_new_from_axes(as, bs, cs);
fclose(mfh);
return cell;
}
int main(int argc, char *argv[])
{
int c;
char *infile = NULL;
char *matrix = NULL;
UnitCell *cell;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"matrix", 1, NULL, 'm'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:m:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'i' :
infile = strdup(optarg);
break;
case 'm' :
matrix = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
cell = read_orientation_matrix(matrix);
free(matrix);
if ( cell == NULL ) {
ERROR("Couldn't read initial orientation matrix.\n");
return 1;
}
cell_print(cell);
return 0;
}
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