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/*
* cubeit.c
*
* "Full integration" of diffraction data
*
* (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 <errno.h>
#include "image.h"
#include "cell.h"
#include "hdf5-file.h"
#define MAX_HITS (1024)
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"'Full integration' of diffraction data.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify the name of the input stream.\n"
" Can be '-' for stdin.\n"
);
}
static UnitCell *read_orientation_matrix(FILE *fh)
{
float u, v, w;
struct rvec as, bs, cs;
UnitCell *cell;
char line[1024];
if ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "astar = %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 ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "bstar = %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 ( fgets(line, 1023, fh) == NULL ) return NULL;
if ( sscanf(line, "cstar = %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);
return cell;
}
static int find_chunk(FILE *fh, UnitCell **cell, char **filename)
{
char line[1024];
char *rval = NULL;
do {
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
if ( strncmp(line, "Reflections from indexing", 25) != 0 ) {
continue;
}
*filename = strdup(line+29);
/* Skip two lines (while checking for errors) */
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
*cell = read_orientation_matrix(fh);
if ( *cell == NULL ) {
STATUS("Got filename but no cell for %s\n", *filename);
continue;
}
return 0;
} while ( rval != NULL );
return 1;
}
int main(int argc, char *argv[])
{
int c;
char *infile = NULL;
FILE *fh;
UnitCell *cell;
char *filename;
unsigned int angles[180];
int i;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'i' :
infile = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( infile == NULL ) infile = strdup("-");
if ( strcmp(infile, "-") == 0 ) {
fh = stdin;
} else {
fh = fopen(infile, "r");
}
if ( fh == NULL ) {
ERROR("Couldn't open input stream '%s'\n", infile);
return ENOENT;
}
/* Initialise histogram */
for ( i=0; i<180; i++ ) angles[i] = 0;
/* Loop over all successfully indexed patterns */
while ( find_chunk(fh, &cell, &filename) == 0 ) {
struct image image;
struct hdfile *hdfile;
double ang;
double asx, asy, asz;
double bsx, bsy, bsz;
double csx, csy, csz;
unsigned int bin;
//STATUS("Processing '%s'\n", filename);
#if 0
hdfile = hdfile_open(filename);
if ( hdfile == NULL ) {
return ENOENT;
} else if ( hdfile_set_image(hdfile, "/data/data0") ) {
ERROR("Couldn't select path\n");
return ENOENT;
}
hdf5_read(hdfile, &image, 0);
#endif
cell_get_reciprocal(cell, &asx, &asy, &asz,
&bsx, &bsy, &bsz,
&csx, &csy, &csz);
ang = angle_between(csx, csy, csz, 0.0, 0.0, 1.0); /* 0->pi */
ang = rad2deg(ang); /* 0->180 deg */
bin = rint(ang);
angles[bin]++;
}
for ( i=0; i<180; i++ ) {
STATUS("%i %i\n", i, angles[i]);
}
return 0;
}
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