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/*
* compare_hkl.c
*
* Compare reflection lists
*
* (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"
#include "statistics.h"
static void show_help(const char *s)
{
printf("Syntax: %s [options] <file1.hkl> <file2.hkl>\n\n", s);
printf(
"Compare intensity lists.\n"
"\n"
" -h, --help Display this help message.\n"
" -o, --output=<filename> Specify output filename for correction factor.\n"
"\n");
}
int main(int argc, char *argv[])
{
int c;
double *ref1;
double *ref2;
double *out;
UnitCell *cell;
char *outfile = NULL;
char *afile = NULL;
char *bfile = NULL;
signed int h, k, l;
double scale, R2, Rmerge, pearson;
unsigned int *c1;
unsigned int *c2;
int i;
int nc1, nc2, ncom;
unsigned int *outcounts;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"output", 1, NULL, 'o'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "ho:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'o' :
outfile = strdup(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
if ( argc != (optind+2) ) {
ERROR("Please provide exactly two HKL files to compare.\n");
return 1;
}
afile = strdup(argv[optind++]);
bfile = strdup(argv[optind]);
cell = load_cell_from_pdb("molecule.pdb");
c1 = new_list_count();
ref1 = read_reflections(afile, c1, NULL);
if ( ref1 == NULL ) {
ERROR("Couldn't open file '%s'\n", afile);
return 1;
}
c2 = new_list_count();
ref2 = read_reflections(bfile, c2, NULL);
if ( ref2 == NULL ) {
ERROR("Couldn't open file '%s'\n", bfile);
return 1;
}
out = new_list_intensity();
outcounts = new_list_count();
/* Knock out the zero beam, in case it's present */
set_count(c1, 0, 0, 0, 0);
set_count(c2, 0, 0, 0, 0);
/* Divide by number of counts, since we're not interested in them */
divide_down(ref1, c1);
divide_down(ref2, c2);
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double i1, i2;
unsigned int c1s, c2s;
c1s = lookup_count(c1, h, k, l);
c2s = lookup_count(c2, h, k, l);
i1 = lookup_intensity(ref1, h, k, l);
i2 = lookup_intensity(ref2, h, k, l);
if ( c1s && c2s ) {
if ( (i1 != 0.0) && (i2 != 0.0) ) {
set_intensity(out, h, k, l,
(i1/(double)c1s)/i2/(double)c2s);
set_count(outcounts, h, k, l, 1);
}
}
}
}
}
nc1 = 0;
nc2 = 0;
ncom = 0;
for ( i=0; i<IDIM*IDIM*IDIM; i++ ) {
nc1 += c1[i];
nc2 += c2[i];
ncom += c1[i] && c2[i];
}
STATUS("%i,%i reflections: %i in common\n", nc1, nc2, ncom);
R2 = stat_r2(ref1, c1, ref2, c2, &scale);
STATUS("R2 = %5.4f %% (scale=%5.2e)\n", R2*100.0, scale);
Rmerge = stat_rmerge(ref1, c1, ref2, c2, &scale);
STATUS("Rmerge = %5.4f %% (scale=%5.2e)\n", Rmerge*100.0, scale);
pearson = stat_pearson(ref1, c1, ref2, c2);
STATUS("Pearson r = %5.4f\n", pearson);
if ( outfile != NULL ) {
write_reflections(outfile, outcounts, out, NULL, 0, cell, 1);
}
return 0;
}
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