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/*
* process_hkl.c
*
* Assemble and process FEL Bragg intensities
*
* (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 "statistics.h"
#include "sfac.h"
#include "reflections.h"
/* Number of divisions for R vs |q| graphs */
#define RVQDV (20)
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Assemble and process FEL Bragg intensities.\n"
"\n"
" -h, --help Display this help message.\n"
" -i, --input=<filename> Specify input filename (\"-\" for stdin).\n"
" -o, --output=<filename> Specify output filename for merged intensities\n"
" (don't specify for no output).\n"
"\n"
" --max-only Take the integrated intensity to be equal to the\n"
" maximum intensity measured for that reflection.\n"
" The default is to use the mean value from all\n"
" measurements.\n"
" --sum Sum (rather than average) the intensities for the\n"
" final output list. This is useful for comparing\n"
" results to radially summed powder patterns, but\n"
" will break R-factor analysis.\n"
" --stop-after=<n> Stop after processing n patterns. Zero means\n"
" keep going until the end of the input, and is\n"
" the default.\n"
" -c, --compare-with=<file> Compare with reflection intensities in this file\n"
"\n"
" -e, --output-every=<n> Analyse figures of merit after every n patterns\n"
" Default: 1000. A value of zero means to do the\n"
" analysis only after reading all the patterns.\n"
" -r, --rvsq Output lists of R vs |q| (\"Luzzatti plots\")\n"
" when analysing figures of merit.\n"
" --zone-axis Output an [001] zone axis pattern each time the\n"
" figures of merit are analysed.\n");
}
static void write_RvsQ(const char *name, double *ref, double *trueref,
unsigned int *counts, double scale, UnitCell *cell)
{
FILE *fh;
double smax, sbracket;
signed int h, k, l;
fh = fopen(name, "w");
smax = 0.0;
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double s = 2.0*resolution(cell, h, k, l);
if ( (lookup_count(counts, h, k, l) > 0) && (s > smax) ) {
smax = s;
}
}
}
}
for ( sbracket=0.0; sbracket<smax; sbracket+=smax/RVQDV ) {
double top = 0.0;
double bot = 0.0;
int nhits = 0;
int nrefl = 0;
double R;
double hits_per_refl;
for ( h=-INDMAX; h<INDMAX; h++ ) {
for ( k=-INDMAX; k<INDMAX; k++ ) {
for ( l=-INDMAX; l<INDMAX; l++ ) {
double s;
int c;
if ( (h==0) && (k==0) && (l==0) ) continue;
c = lookup_count(counts, h, k, l);
s = 2.0*resolution(cell, h, k, l);
if ((s>=sbracket) && (s<sbracket+smax/RVQDV) && (c>0)) {
double obs, calc, obsi;
obs = lookup_intensity(ref, h, k, l);
calc = lookup_intensity(trueref, h, k, l);
obsi = obs / (double)c;
top += pow(obsi - scale*calc, 2.0);
bot += pow(obsi, 2.0);
nhits += c;
nrefl++;
}
}
}
}
R = sqrt(top/bot);
hits_per_refl = nrefl ? (double)nhits/nrefl : 0;
fprintf(fh, "%8.5f %8.5f %5.2f\n", sbracket+smax/(2.0*RVQDV),
R, hits_per_refl);
}
fclose(fh);
}
static void process_reflections(double *ref, double *trueref,
unsigned int *counts, unsigned int n_patterns,
UnitCell *cell, int do_rvsq, int do_zoneaxis)
{
int j;
double mean_counts;
int ctot = 0;
int nmeas = 0;
double R, scale;
FILE *fh;
for ( j=0; j<LIST_SIZE; j++ ) {
ctot += counts[j];
if ( counts[j] > 0 ) nmeas++;
}
mean_counts = (double)ctot/nmeas;
R = stat_r2(ref, trueref, counts, LIST_SIZE, &scale);
STATUS("%8u: R=%5.2f%% (sf=%7.4e) mean meas/refl=%5.2f,"
" %i reflections measured\n",
n_patterns, R*100.0, scale, mean_counts, nmeas);
if ( do_rvsq ) {
/* Record graph of R against q for this N */
char name[64];
snprintf(name, 63, "R_vs_q-%u.dat", n_patterns);
write_RvsQ(name, ref, trueref, counts, scale, cell);
}
if ( do_zoneaxis ) {
char name[64];
snprintf(name, 63, "ZA-%u.dat", n_patterns);
write_reflections(name, counts, ref, 1, cell);
}
fh = fopen("results/convergence.dat", "a");
fprintf(fh, "%u %5.2f %5.2f\n", n_patterns, R*100.0, mean_counts);
fclose(fh);
}
int main(int argc, char *argv[])
{
int c;
char *filename = NULL;
char *output = NULL;
FILE *fh;
unsigned int n_patterns;
double *ref, *trueref = NULL;
unsigned int *counts;
char *rval;
UnitCell *cell;
int config_maxonly = 0;
int config_every = 1000;
int config_rvsq = 0;
int config_stopafter = 0;
int config_zoneaxis = 0;
int config_sum = 0;
char *intfile = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
{"max-only", 0, &config_maxonly, 1},
{"output-every", 1, NULL, 'e'},
{"rvsq", 0, NULL, 'r'},
{"stop-after", 1, NULL, 's'},
{"zone-axis", 0, &config_zoneaxis, 1},
{"compare-with", 0, NULL, 'c'},
{"sum", 0, &config_sum, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:e:ro:", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
show_help(argv[0]);
return 0;
}
case 'i' : {
filename = strdup(optarg);
break;
}
case 'o' : {
output = strdup(optarg);
break;
}
case 'r' : {
config_rvsq = 1;
break;
}
case 'e' : {
config_every = atoi(optarg);
break;
}
case 's' : {
config_stopafter = atoi(optarg);
break;
}
case 'c' : {
intfile = strdup(optarg);
break;
}
case 0 : {
break;
}
default : {
return 1;
}
}
}
if ( filename == NULL ) {
ERROR("Please specify filename using the -i option\n");
return 1;
}
if ( intfile != NULL ) {
STATUS("Comparing against '%s'\n", intfile);
trueref = read_reflections(intfile, NULL);
free(intfile);
} else {
trueref = NULL;
}
ref = new_list_intensity();
counts = new_list_count();
cell = load_cell_from_pdb("molecule.pdb");
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
} else {
fh = fopen(filename, "r");
}
free(filename);
if ( fh == NULL ) {
ERROR("Failed to open input file\n");
return 1;
}
n_patterns = 0;
do {
char line[1024];
signed int h, k, l;
float intensity;
int r;
rval = fgets(line, 1023, fh);
if ( strncmp(line, "New pattern", 11) == 0 ) {
if ( n_patterns == 0 ) {
n_patterns++;
continue;
}
if (config_every && (n_patterns % config_every == 0)) {
process_reflections(ref, trueref, counts,
n_patterns, cell,
config_rvsq,
config_zoneaxis);
}
if ( n_patterns == config_stopafter ) break;
n_patterns++;
}
r = sscanf(line, "%i %i %i %f", &h, &k, &l, &intensity);
if ( r != 4 ) continue;
if ( (h==0) && (k==0) && (l==0) ) continue;
if ( !config_maxonly ) {
integrate_intensity(ref, h, k, l, intensity);
if ( config_sum ) {
set_count(counts, h, k, l, 1);
} else {
integrate_count(counts, h, k, l, 1);
}
} else {
if ( intensity > lookup_intensity(ref, h, k, l) ) {
set_intensity(ref, h, k, l, intensity);
}
set_count(counts, h, k, l, 1);
}
} while ( rval != NULL );
fclose(fh);
if ( trueref != NULL ) {
process_reflections(ref, trueref, counts, n_patterns, cell,
config_rvsq, config_zoneaxis);
}
if ( output != NULL ) {
write_reflections(output, counts, ref, 0, cell);
}
if ( config_zoneaxis ) {
char name[64];
snprintf(name, 63, "ZA-%u.dat", n_patterns);
write_reflections(name, counts, ref, 1, cell);
}
STATUS("There were %u patterns.\n", n_patterns);
return 0;
}
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