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|
/*
* compare_hkl.c
*
* Compare reflection lists
*
* Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2010-2017 Thomas White <taw@physics.org>
* 2013 Lorenzo Galli <lorenzo.galli@desy.de>
*
* This file is part of CrystFEL.
*
* CrystFEL is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* CrystFEL is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with CrystFEL. If not, see <http://www.gnu.org/licenses/>.
*
*/
#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 <assert.h>
#include <utils.h>
#include <symmetry.h>
#include <reflist-utils.h>
#include <cell-utils.h>
#include <fom.h>
#include "version.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"
" -y, --symmetry=<sym> The symmetry of both the input files.\n"
" -p, --pdb=<filename> Unit cell file to use.\n"
" --fom=<FoM> Calculate this figure of merit Choose from:\n"
" R1I, R1F, R2, Rsplit, CC, CCstar,\n"
" CCano, CRDano, Rano, Rano/Rsplit, d1sig,\n"
" d2sig\n"
" --nshells=<n> Use <n> resolution shells.\n"
" -u Force scale factor to 1.\n"
" --shell-file=<file> Write resolution shells to <file>.\n"
"\n"
"You can control which reflections are included in the calculation:\n"
"\n"
" --ignore-negs Ignore reflections with negative intensities.\n"
" --zero-negs Set negative intensities to zero.\n"
" --sigma-cutoff=<n> Discard reflections with I/sigma(I) < n.\n"
" --rmin=<res> Low resolution cutoff (1/d in m^-1).\n"
" --rmax=<res> High resolution cutoff (1/d in m^-1).\n"
" --lowres=<n> Low resolution cutoff in (d in A).\n"
" --highres=<n> High resolution cutoff in (d in A).\n"
"\n"
" -h, --help Display this help message.\n"
" --version Print CrystFEL version number and exit.\n"
);
}
static void do_fom(RefList *list1, RefList *list2, UnitCell *cell,
double rmin, double rmax, enum fom_type fom,
int config_unity, int nshells, const char *filename,
SymOpList *sym)
{
struct fom_shells *shells;
struct fom_context *fctx;
FILE *fh;
int i;
const char *t1, *t2;
/* Calculate the bins */
shells = fom_make_resolution_shells(rmin, rmax, nshells);
if ( shells == NULL ) {
ERROR("Failed to set up shells.\n");
return;
}
fctx = fom_calculate(list1, list2, cell, shells, fom,
config_unity, sym);
switch ( fom ) {
case FOM_R1I :
STATUS("Overall R1(I) = %.2f %%\n", 100.0*fom_overall(fctx));
break;
case FOM_R1F :
STATUS("Overall R1(F) = %.2f %%\n", 100.0*fom_overall(fctx));
break;
case FOM_R2 :
STATUS("Overall R(2) = %.2f %%\n", 100.0*fom_overall(fctx));
break;
case FOM_RSPLIT :
STATUS("Overall Rsplit = %.2f %%\n", 100.0*fom_overall(fctx));
break;
case FOM_CC :
STATUS("Overall CC = %.7f\n", fom_overall(fctx));
break;
case FOM_CCSTAR :
STATUS("Overall CC* = %.7f\n", fom_overall(fctx));
break;
case FOM_CCANO :
STATUS("Overall CCano = %.7f\n", fom_overall(fctx));
break;
case FOM_CRDANO :
STATUS("Overall CRDano = %.7f\n", fom_overall(fctx));
break;
case FOM_RANO :
STATUS("Overall Rano = %.2f %%\n", 100.0*fom_overall(fctx));
break;
case FOM_RANORSPLIT :
STATUS("Overall Rano/Rsplit = %.7f\n", fom_overall(fctx));
break;
case FOM_D1SIG :
STATUS("Fraction of differences less than 1 sigma = %.7f %%\n",
100.0*fom_overall(fctx));
break;
case FOM_D2SIG :
STATUS("Fraction of differences less than 2 sigma = %.7f %%\n",
100.0*fom_overall(fctx));
break;
}
fh = fopen(filename, "w");
if ( fh == NULL ) {
ERROR("Couldn't open '%s'\n", filename);
return;
}
t1 = " 1/d centre";
t2 = " d / A Min 1/nm Max 1/nm";
switch ( fom ) {
case FOM_R1I :
fprintf(fh, "%s R1(I)/%% nref%s\n", t1, t2);
break;
case FOM_R1F :
fprintf(fh, "%s R1(F)/%% nref%s\n", t1, t2);
break;
case FOM_R2 :
fprintf(fh, "%s R2/%% nref%s\n", t1, t2);
break;
case FOM_RSPLIT :
fprintf(fh, "%s Rsplit/%% nref%s\n", t1, t2);
break;
case FOM_CC :
fprintf(fh, "%s CC nref%s\n", t1, t2);
break;
case FOM_CCSTAR :
fprintf(fh, "%s CC* nref%s\n", t1, t2);
break;
case FOM_CCANO :
fprintf(fh, "%s CCano nref%s\n", t1, t2);
break;
case FOM_CRDANO :
fprintf(fh, "%s CRDano nref%s\n", t1, t2);
break;
case FOM_RANO :
fprintf(fh, "%s Rano/%% nref%s\n", t1, t2);
break;
case FOM_RANORSPLIT :
fprintf(fh, "%s Rano/Rsplit nref%s\n", t1, t2);
break;
case FOM_D1SIG :
fprintf(fh, "%s D<1sigma/%% nref%s\n", t1, t2);
break;
case FOM_D2SIG :
fprintf(fh, "%s D<2sigma/%% nref%s\n", t1, t2);
break;
}
for ( i=0; i<nshells; i++ ) {
double r, cen;
cen = fom_shell_label(shells, i);
r = fom_shell(fctx, i);
switch ( fom ) {
case FOM_R1I :
case FOM_R1F :
case FOM_R2 :
case FOM_RSPLIT :
case FOM_RANO :
fprintf(fh, "%10.3f %10.2f %10i %10.2f "
"%10.3f %10.3f\n",
cen*1.0e-9, r*100.0, fctx->cts[i],
(1.0/cen)*1e10,
shells->rmins[i]*1.0e-9,
shells->rmaxs[i]*1.0e-9);
break;
case FOM_CC :
case FOM_CCSTAR :
case FOM_CCANO :
case FOM_CRDANO :
fprintf(fh, "%10.3f %10.7f %10i %10.2f "
"%10.3f %10.3f\n",
cen*1.0e-9, r, fctx->cts[i], (1.0/cen)*1e10,
shells->rmins[i]*1.0e-9,
shells->rmaxs[i]*1.0e-9);
break;
case FOM_RANORSPLIT :
fprintf(fh, "%10.3f %10.7f %10i %10.2f "
"%10.3f %10.3f\n",
cen*1.0e-9, r, fctx->cts[i], (1.0/cen)*1e10,
shells->rmins[i]*1.0e-9,
shells->rmaxs[i]*1.0e-9);
break;
case FOM_D1SIG :
case FOM_D2SIG :
fprintf(fh, "%10.3f %10.2f %10i %10.2f "
"%10.3f %10.3f\n",
cen*1.0e-9, r*100.0, fctx->cts[i],
(1.0/cen)*1e10,
shells->rmins[i]*1.0e-9,
shells->rmaxs[i]*1.0e-9);
break;
}
}
fclose(fh);
}
static void check_highres()
{
static int have = 0;
if ( have ) {
ERROR("You cannot use --rmax and --highres at the same time.\n");
exit(1);
}
have = 1;
}
static void check_lowres()
{
static int have = 0;
if ( have ) {
ERROR("You cannot use --rmin and --lowres at the same time.\n");
exit(1);
}
have = 1;
}
int main(int argc, char *argv[])
{
int c;
UnitCell *cell;
char *afile = NULL;
char *bfile = NULL;
char *sym_str = NULL;
char *sym_str_fromfile = NULL;
char *sym_str_fromfile1 = NULL;
char *sym_str_fromfile2 = NULL;
SymOpList *sym;
int ncom;
RefList *list1_acc;
RefList *list2_acc;
RefList *list1;
RefList *list2;
RefList *list1_raw;
RefList *list2_raw;
enum fom_type fom = FOM_R1I;
char *cellfile = NULL;
float rmin_fix = -1.0;
float rmax_fix = -1.0;
double rmin, rmax;
float sigma_cutoff = -INFINITY;
int config_ignorenegs = 0;
int config_zeronegs = 0;
int config_unity = 0;
int nshells = 10;
char *shell_file = NULL;
float highres, lowres;
int mul_cutoff = 0;
int anom;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"version", 0, NULL, 10 },
{"symmetry", 1, NULL, 'y'},
{"pdb", 1, NULL, 'p'},
{"rmin", 1, NULL, 2},
{"rmax", 1, NULL, 3},
{"fom", 1, NULL, 4},
{"sigma-cutoff", 1, NULL, 5},
{"nshells", 1, NULL, 6},
{"shell-file", 1, NULL, 7},
{"highres", 1, NULL, 8},
{"lowres", 1, NULL, 9},
{"min-measurements", 1, NULL, 11},
{"ignore-negs", 0, &config_ignorenegs, 1},
{"zero-negs", 0, &config_zeronegs, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hy:p:u",
longopts, NULL)) != -1)
{
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 10 :
printf("CrystFEL: %s\n",
crystfel_version_string());
printf("%s\n",
crystfel_licence_string());
return 0;
case 'y' :
sym_str = strdup(optarg);
break;
case 'p' :
cellfile = strdup(optarg);
break;
case 'u' :
config_unity = 1;
break;
case 0 :
break;
case 2 :
check_lowres();
if ( sscanf(optarg, "%e", &rmin_fix) != 1 ) {
ERROR("Invalid value for --rmin\n");
return 1;
}
break;
case 3 :
check_highres();
if ( sscanf(optarg, "%e", &rmax_fix) != 1 ) {
ERROR("Invalid value for --rmax\n");
return 1;
}
break;
case 4 :
fom = fom_type_from_string(optarg);
break;
case 5 :
if ( sscanf(optarg, "%f", &sigma_cutoff) != 1 ) {
ERROR("Invalid value for --sigma-cutoff\n");
return 1;
}
STATUS("WARNING: You are using --sigma-cutoff. "
"Be aware that the figures of merit will not "
"reflect the entire data set!\n");
break;
case 6 :
if ( sscanf(optarg, "%i", &nshells) != 1 ) {
ERROR("Invalid value for --nshells\n");
return 1;
}
break;
case 7 :
shell_file = strdup(optarg);
break;
case 8 :
check_highres();
if ( sscanf(optarg, "%e", &highres) != 1 ) {
ERROR("Invalid value for --highres\n");
return 1;
}
rmax_fix = 1.0 / (highres/1e10);
break;
case 9 :
check_lowres();
if ( sscanf(optarg, "%e", &lowres) != 1 ) {
ERROR("Invalid value for --lowres\n");
return 1;
}
rmin_fix = 1.0 / (lowres/1e10);
break;
case 11 :
if ( sscanf(optarg, "%i", &mul_cutoff) != 1 ) {
ERROR("Invalid value for --min-measurements\n");
return 1;
}
break;
case '?' :
break;
default :
ERROR("Unhandled option '%c'\n", c);
break;
}
}
if ( argc != (optind+2) ) {
ERROR("Please provide exactly two HKL files to compare.\n");
return 1;
}
if ( !config_ignorenegs && !config_zeronegs ) {
switch ( fom )
{
case FOM_R1F :
ERROR("Your chosen figure of merit involves converting"
" intensities to structure factors, but you have"
" not specified how to handle negative"
" intensities.\n");
ERROR("Please try again with --ignore-negs or"
" --zero-negs.\n");
exit(1);
case FOM_R2 :
case FOM_R1I :
case FOM_RSPLIT :
case FOM_CC :
case FOM_CCSTAR :
case FOM_CCANO :
case FOM_CRDANO :
case FOM_RANO :
case FOM_RANORSPLIT :
case FOM_D1SIG :
case FOM_D2SIG :
break;
}
}
if ( (fom != FOM_R1F) && (config_ignorenegs || config_zeronegs) ) {
ERROR("WARNING: You are using --zero-negs or --ignore-negs "
"even though your chosen figure of merit does not "
"require it.\n");
ERROR("The figures of merit will not reflect the entire data "
"set!\n");
}
afile = strdup(argv[optind++]);
bfile = strdup(argv[optind]);
if ( shell_file == NULL ) shell_file = strdup("shells.dat");
cell = load_cell_from_file(cellfile);
if ( cellfile == NULL ) {
ERROR("You must provide a unit cell.\n");
exit(1);
}
if ( cell == NULL ) {
ERROR("Failed to load cell.\n");
return 1;
}
free(cellfile);
list1_raw = read_reflections_2(afile, &sym_str_fromfile1);
if ( list1_raw == NULL ) {
ERROR("Couldn't read file '%s'\n", afile);
return 1;
}
list2_raw = read_reflections_2(bfile, &sym_str_fromfile2);
if ( list2_raw == NULL ) {
ERROR("Couldn't read file '%s'\n", bfile);
return 1;
}
if ( (sym_str_fromfile1 != NULL) && (sym_str_fromfile2 != NULL) ) {
if ( strcmp(sym_str_fromfile1, sym_str_fromfile2) != 0 ) {
ERROR("The symmetries of the two list do not match:\n");
ERROR(" %s: %s\n", afile, sym_str_fromfile1);
ERROR(" %s: %s\n", bfile, sym_str_fromfile2);
return 1;
}
sym_str_fromfile = sym_str_fromfile1;
free(sym_str_fromfile2);
}
if ( sym_str == NULL ) {
if ( sym_str_fromfile != NULL ) {
STATUS("Using symmetry from reflection files: %s\n",
sym_str_fromfile);
sym_str = sym_str_fromfile;
} else {
sym_str = strdup("1");
}
}
sym = get_pointgroup(sym_str);
free(sym_str);
if ( is_centrosymmetric(sym) ) {
switch ( fom )
{
case FOM_R1F :
case FOM_R2 :
case FOM_R1I :
case FOM_RSPLIT :
case FOM_CC :
case FOM_CCSTAR :
case FOM_D1SIG :
case FOM_D2SIG :
break;
case FOM_CCANO :
case FOM_CRDANO :
case FOM_RANO :
case FOM_RANORSPLIT :
ERROR("You are trying to measure an anomalous signal in"
" a centrosymmetric point group.\n");
ERROR("This is a silly thing to do, and I'm refusing to"
" help you do it.\n");
ERROR("Please review your earlier processing steps and"
" try again using a non-centrosymmetric point"
" group for '-y'.\n");
return 1;
}
}
/* Check that the intensities have the correct symmetry */
if ( check_list_symmetry(list1_raw, sym) ) {
ERROR("The first input reflection list does not appear to"
" have symmetry %s\n", symmetry_name(sym));
if ( cell_get_lattice_type(cell) == L_MONOCLINIC ) {
ERROR("You may need to specify the unique axis in your "
"point group. The default is unique axis c.\n");
ERROR("See 'man crystfel' for more details.\n");
}
return 1;
}
if ( check_list_symmetry(list2_raw, sym) ) {
ERROR("The second input reflection list does not appear to"
" have symmetry %s\n", symmetry_name(sym));
if ( cell_get_lattice_type(cell) == L_MONOCLINIC ) {
ERROR("You may need to specify the unique axis in your "
"point group. The default is unique axis c.\n");
ERROR("See 'man crystfel' for more details.\n");
}
return 1;
}
resolution_limits(list1_raw, cell, &rmin, &rmax);
STATUS("%s: %i reflections, resolution range %.2f to %.2f Angstroms"
" (%.5f to %.5f nm^-1).\n", afile,
num_reflections(list1_raw),
1e10/rmin, 1e10/rmax, rmin/1e9, rmax/1e9);
resolution_limits(list2_raw, cell, &rmin, &rmax);
STATUS("%s: %i reflections, resolution range %.2f to %.2f Angstroms"
" (%.5f to %.5f nm^-1).\n", bfile,
num_reflections(list2_raw),
1e10/rmin, 1e10/rmax, rmin/1e9, rmax/1e9);
list1 = asymmetric_indices(list1_raw, sym);
list2 = asymmetric_indices(list2_raw, sym);
reflist_free(list1_raw);
reflist_free(list2_raw);
list1_acc = reflist_new();
list2_acc = reflist_new();
anom = ( (fom == FOM_CCANO) || (fom == FOM_CRDANO)
|| (fom == FOM_RANO) || (fom == FOM_RANORSPLIT) );
ncom = fom_select_reflections(list1, list2, list1_acc, list2_acc,
cell, sym,
anom, rmin_fix, rmax_fix, sigma_cutoff,
config_ignorenegs, config_zeronegs,
mul_cutoff);
reflist_free(list1);
reflist_free(list2);
gsl_set_error_handler_off();
STATUS("%i reflection pairs accepted.\n", ncom);
resolution_limits(list1_acc, cell, &rmin, &rmax);
resolution_limits(list2_acc, cell, &rmin, &rmax);
STATUS("Accepted resolution range: %f to %f nm^-1"
" (%.2f to %.2f Angstroms).\n",
rmin/1e9, rmax/1e9, 1e10/rmin, 1e10/rmax);
if ( rmin_fix >= 0.0 ) {
rmin = rmin_fix;
}
if ( rmax_fix >= 0.0 ) {
rmax = rmax_fix;
}
if ( (rmin_fix>=0.0) || (rmax_fix>=0.0) ) {
STATUS("Fixed resolution range: %f to %f nm^-1"
" (%.2f to %.2f Angstroms).\n",
rmin/1e9, rmax/1e9, 1e10/rmin, 1e10/rmax);
}
do_fom(list1_acc, list2_acc, cell, rmin, rmax, fom, config_unity,
nshells, shell_file, sym);
free(shell_file);
reflist_free(list1_acc);
reflist_free(list2_acc);
return 0;
}
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