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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"
#include "symmetry.h"
/* Number of bins for plot of resolution shells */
#define NBINS (10)
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"
" -y, --symmetry=<sym> The symmetry of both the input files.\n"
" -p, --pdb=<filename> PDB file to use (default: molecule.pdb).\n"
" --shells Plot the figures of merit by resolution.\n"
" --rmin=<res> Fix lower resolution limit for --shells (m^-1).\n"
" --rmax=<res> Fix upper resolution limit for --shells (m^-1).\n"
"\n");
}
static void plot_shells(const double *ref1, const double *ref2,
ReflItemList *items, double scale, UnitCell *cell,
const char *sym, double rmin_fix, double rmax_fix)
{
double num[NBINS];
int cts[NBINS];
int possible[NBINS];
unsigned int *counted;
unsigned int measurements[NBINS];
unsigned int measured[NBINS];
double total_vol, vol_per_shell;
double rmins[NBINS];
double rmaxs[NBINS];
double snr[NBINS];
double den;
double rmin, rmax;
signed int h, k, l;
int i;
int ctot;
FILE *fh;
int nout = 0;
if ( cell == NULL ) {
ERROR("Need the unit cell to plot resolution shells.\n");
return;
}
fh = fopen("shells.dat", "w");
if ( fh == NULL ) {
ERROR("Couldn't open 'shells.dat'\n");
return;
}
for ( i=0; i<NBINS; i++ ) {
num[i] = 0.0;
cts[i] = 0;
possible[i] = 0;
measured[i] = 0;
measurements[i] = 0;
snr[i] = 0;
}
rmin = +INFINITY;
rmax = 0.0;
for ( i=0; i<num_items(items); i++ ) {
struct refl_item *it;
signed int h, k, l;
double d;
it = get_item(items, i);
h = it->h; k = it->k; l = it->l;
d = resolution(cell, h, k, l) * 2.0;
if ( d > rmax ) rmax = d;
if ( d < rmin ) rmin = d;
}
STATUS("1/d goes from %f to %f nm^-1\n", rmin/1e9, rmax/1e9);
/* Widen the range just a little bit */
rmin -= 0.001e9;
rmax += 0.001e9;
/* Fixed resolution shells if needed */
if ( rmin_fix > 0.0 ) rmin = rmin_fix;
if ( rmax_fix > 0.0 ) rmax = rmax_fix;
total_vol = pow(rmax, 3.0) - pow(rmin, 3.0);
vol_per_shell = total_vol / NBINS;
rmins[0] = rmin;
for ( i=1; i<NBINS; i++ ) {
double r;
r = vol_per_shell + pow(rmins[i-1], 3.0);
r = pow(r, 1.0/3.0);
/* Shells of constant volume */
rmaxs[i-1] = r;
rmins[i] = r;
/* Shells of constant thickness */
//rmins[i] = rmins[i-1] + (rmax-rmin)/NBINS;
//rmaxs[i-1] = rmins[i-1] + (rmax-rmin)/NBINS;
STATUS("Shell %i: %f to %f\n", i-1,
rmins[i-1]/1e9, rmaxs[i-1]/1e9);
}
rmaxs[NBINS-1] = rmax;
STATUS("Shell %i: %f to %f\n", NBINS-1,
rmins[NBINS-1]/1e9, rmaxs[NBINS-1]/1e9);
/* Count the number of reflections possible in each shell */
counted = new_list_count();
for ( h=-50; h<=+50; h++ ) {
for ( k=-50; k<=+50; k++ ) {
for ( l=-50; l<=+50; l++ ) {
double d;
signed int hs, ks, ls;
int bin;
get_asymm(h, k, l, &hs, &ks, &ls, sym);
if ( lookup_count(counted, hs, ks, ls) ) continue;
set_count(counted, hs, ks, ls, 1);
d = resolution(cell, h, k, l) * 2.0;
bin = -1;
for ( i=0; i<NBINS; i++ ) {
if ( (d>rmins[i]) && (d<=rmaxs[i]) ) {
bin = i;
break;
}
}
if ( bin == -1 ) continue;
possible[bin]++;
}
}
}
free(counted);
den = 0.0;
ctot = 0;
nout = 0;
for ( i=0; i<num_items(items); i++ ) {
struct refl_item *it;
signed int h, k, l;
double d;
int bin;
double i1, i2;
int j;
it = get_item(items, i);
h = it->h; k = it->k; l = it->l;
d = resolution(cell, h, k, l) * 2.0;
bin = -1;
for ( j=0; j<NBINS; j++ ) {
if ( (d>rmins[j]) && (d<=rmaxs[j]) ) {
bin = j;
break;
}
}
/* Outside resolution range? */
if ( bin == -1 ) {
nout++;
continue;
}
i1 = lookup_intensity(ref1, h, k, l);
i2 = lookup_intensity(ref2, h, k, l);
i2 *= scale;
num[bin] += fabs(i1 - i2);
den += i1;
ctot++;
cts[bin]++;
}
if ( nout ) {
STATUS("Warning; %i reflections outside resolution range.\n",
nout);
}
for ( i=0; i<NBINS; i++ ) {
double r, cen;
cen = rmins[i] + (rmaxs[i] - rmins[i])/2.0;
r = (num[i]/den)*((double)ctot/cts[i]);
fprintf(fh, "%f %f\n", cen*1.0e-9, r*100.0);
}
fclose(fh);
}
int main(int argc, char *argv[])
{
int c;
double *ref1;
double *ref2;
double *ref2_transformed;
double *out;
UnitCell *cell;
char *outfile = NULL;
char *afile = NULL;
char *bfile = NULL;
char *sym = NULL;
double scale, scale_r2, scale_rdig, R1, R2, R1i, Rdiff, pearson;
double scale_rintint, scale_r1i, scale_r1, scale_r1fi;
int i, ncom;
ReflItemList *i1, *i2, *icommon;
int config_shells = 0;
char *pdb = NULL;
double *esd1;
double *esd2;
int rej1 = 0;
int rej2 = 0;
unsigned int *cts1;
float rmin_fix = -1.0;
float rmax_fix = -1.0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"output", 1, NULL, 'o'},
{"symmetry", 1, NULL, 'y'},
{"shells", 0, &config_shells, 1},
{"pdb", 1, NULL, 'p'},
{"rmin", 1, NULL, 2},
{"rmax", 1, NULL, 3},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "ho:y:p:", longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'o' :
outfile = strdup(optarg);
break;
case 'y' :
sym = strdup(optarg);
break;
case 'p' :
pdb = strdup(optarg);
break;
case 0 :
break;
case 2 :
if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
ERROR("Invalid value for --rmin\n");
return 1;
}
break;
case 3 :
if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
ERROR("Invalid value for --rmax\n");
return 1;
}
break;
default :
return 1;
}
}
if ( argc != (optind+2) ) {
ERROR("Please provide exactly two HKL files to compare.\n");
return 1;
}
if ( sym == NULL ) {
sym = strdup("1");
}
afile = strdup(argv[optind++]);
bfile = strdup(argv[optind]);
if ( pdb == NULL ) {
pdb = strdup("molecule.pdb");
}
cell = load_cell_from_pdb(pdb);
free(pdb);
ref1 = new_list_intensity();
esd1 = new_list_sigma();
cts1 = new_list_count();
i1 = read_reflections(afile, ref1, NULL, cts1, esd1);
if ( i1 == NULL ) {
ERROR("Couldn't open file '%s'\n", afile);
return 1;
}
ref2 = new_list_intensity();
esd2 = new_list_sigma();
i2 = read_reflections(bfile, ref2, NULL, NULL, esd2);
if ( i2 == NULL ) {
ERROR("Couldn't open file '%s'\n", bfile);
return 1;
}
/* Check that the intensities have the correct symmetry */
if ( check_symmetry(i1, sym) ) {
ERROR("The first input reflection list does not appear to"
" have symmetry %s\n", sym);
return 1;
}
if ( check_symmetry(i2, sym) ) {
ERROR("The second input reflection list does not appear to"
" have symmetry %s\n", sym);
return 1;
}
/* List for output scale factor map */
out = new_list_intensity();
/* Find common reflections (taking symmetry into account) */
icommon = new_items();
ref2_transformed = new_list_intensity();
for ( i=0; i<num_items(i1); i++ ) {
struct refl_item *it;
signed int h, k, l;
signed int he, ke, le;
double val1, val2;
double sig1, sig2;
int ig = 0;
double d;
it = get_item(i1, i);
h = it->h; k = it->k; l = it->l;
if ( !find_unique_equiv(i2, h, k, l, sym, &he, &ke, &le) ) {
//STATUS("%i %i %i not matched (%f nm).\n", h, k, l,
// 1.0/(2.0*resolution(cell, h, k, l)/1e9));
continue;
}
val1 = lookup_intensity(ref1, h, k, l);
val2 = lookup_intensity(ref2, he, ke, le);
sig1 = lookup_sigma(esd1, h, k, l);
sig2 = lookup_sigma(esd2, he, ke, le);
if ( val1 < 3.0 * sig1 ) {
rej1++;
ig = 1;
}
if ( val2 < 3.0 * sig2 ) {
rej2++;
ig = 1;
}
d = 0.5/resolution(cell, h, k, l);
if ( d > 55.0e-10 ) ig = 1;
//if ( d < 15.0e-10 ) ig = 1;
//if ( ig ) continue;
set_intensity(ref2_transformed, h, k, l, val2);
set_intensity(out, h, k, l, val1/val2);
add_item(icommon, h, k, l);
}
ncom = num_items(icommon);
STATUS("%i reflections in '%s' had I < 3.0*sigma(I)\n", afile, rej1);
STATUS("%i reflections in '%s' had I < 3.0*sigma(I)\n", bfile, rej2);
STATUS("%i,%i reflections: %i in common\n",
num_items(i1), num_items(i2), ncom);
R1 = stat_r1_ignore(ref1, ref2_transformed, icommon, &scale_r1fi);
STATUS("R1(F) = %5.4f %% (scale=%5.2e) (ignoring negative intensities)\n",
R1*100.0, scale_r1fi);
R1 = stat_r1_zero(ref1, ref2_transformed, icommon, &scale_r1);
STATUS("R1(F) = %5.4f %% (scale=%5.2e) (zeroing negative intensities)\n",
R1*100.0, scale_r1);
R2 = stat_r2(ref1, ref2_transformed, icommon, &scale_r2);
STATUS("R2(I) = %5.4f %% (scale=%5.2e)\n", R2*100.0, scale_r2);
R1i = stat_r1_i(ref1, ref2_transformed, icommon, &scale_r1i);
STATUS("R1(I) = %5.4f %% (scale=%5.2e)\n", R1i*100.0, scale_r1i);
Rdiff = stat_rdiff_ignore(ref1, ref2_transformed, icommon, &scale_rdig);
STATUS("Rint(F) = %5.4f %% (scale=%5.2e) (ignoring negative intensities)\n",
Rdiff*100.0, scale_rdig);
Rdiff = stat_rdiff_zero(ref1, ref2_transformed, icommon, &scale);
STATUS("Rint(F) = %5.4f %% (scale=%5.2e) (zeroing negative intensities)\n",
Rdiff*100.0, scale);
Rdiff = stat_rdiff_intensity(ref1, ref2_transformed, icommon,
&scale_rintint);
STATUS("Rint(I) = %5.4f %% (scale=%5.2e)\n",
Rdiff*100.0, scale_rintint);
pearson = stat_pearson_i(ref1, ref2_transformed, icommon);
STATUS("Pearson r(I) = %5.4f\n", pearson);
pearson = stat_pearson_f_ignore(ref1, ref2_transformed, icommon);
STATUS("Pearson r(F) = %5.4f (ignoring negative intensities)\n",
pearson);
pearson = stat_pearson_f_zero(ref1, ref2_transformed, icommon);
STATUS("Pearson r(F) = %5.4f (zeroing negative intensities)\n",
pearson);
if ( config_shells ) {
plot_shells(ref1, ref2_transformed, icommon, scale_r1fi,
cell, sym, rmin_fix, rmax_fix);
}
if ( outfile != NULL ) {
write_reflections(outfile, icommon, out, NULL,
NULL, NULL, cell);
STATUS("Sigma(I) values in output file are not meaningful.\n");
}
return 0;
}
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