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/*
* partial_sim.c
*
* Generate partials for testing scaling
*
* Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
* 2011-2013 Thomas White <taw@physics.org>
*
* 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 <pthread.h>
#include "image.h"
#include "utils.h"
#include "reflist-utils.h"
#include "symmetry.h"
#include "beam-parameters.h"
#include "geometry.h"
#include "stream.h"
#include "thread-pool.h"
#include "cell-utils.h"
/* Number of bins for partiality graph */
#define NBINS 50
static void mess_up_cell(Crystal *cr, double cnoise)
{
double ax, ay, az;
double bx, by, bz;
double cx, cy, cz;
UnitCell *cell = crystal_get_cell(cr);
//STATUS("Real:\n");
//cell_print(cell);
cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
ax = flat_noise(ax, cnoise*fabs(ax)/100.0);
ay = flat_noise(ay, cnoise*fabs(ay)/100.0);
az = flat_noise(az, cnoise*fabs(az)/100.0);
bx = flat_noise(bx, cnoise*fabs(bx)/100.0);
by = flat_noise(by, cnoise*fabs(by)/100.0);
bz = flat_noise(bz, cnoise*fabs(bz)/100.0);
cx = flat_noise(cx, cnoise*fabs(cx)/100.0);
cy = flat_noise(cy, cnoise*fabs(cy)/100.0);
cz = flat_noise(cz, cnoise*fabs(cz)/100.0);
cell_set_reciprocal(cell, ax, ay, az, bx, by, bz, cx, cy, cz);
//STATUS("Changed:\n");
//cell_print(cell);
}
/* For each reflection in "partial", fill in what the intensity would be
* according to "full" */
static void calculate_partials(Crystal *cr,
RefList *full, const SymOpList *sym,
int random_intensities,
pthread_mutex_t *full_lock,
unsigned long int *n_ref, double *p_hist,
double *p_max, double max_q)
{
Reflection *refl;
RefListIterator *iter;
double res;
for ( refl = first_refl(crystal_get_reflections(cr), &iter);
refl != NULL;
refl = next_refl(refl, iter) )
{
signed int h, k, l;
Reflection *rfull;
double L, p, Ip, If;
int bin;
get_indices(refl, &h, &k, &l);
get_asymm(sym, h, k, l, &h, &k, &l);
p = get_partiality(refl);
L = get_lorentz(refl);
pthread_mutex_lock(full_lock);
rfull = find_refl(full, h, k, l);
pthread_mutex_unlock(full_lock);
if ( rfull == NULL ) {
if ( random_intensities ) {
/* The full reflection is immutable (in this
* program) once created, but creating it must
* be an atomic operation. So do the whole
* thing under lock. */
pthread_mutex_lock(full_lock);
rfull = add_refl(full, h, k, l);
If = fabs(gaussian_noise(0.0, 1000.0));
set_intensity(rfull, If);
set_redundancy(rfull, 1);
pthread_mutex_unlock(full_lock);
} else {
set_redundancy(refl, 0);
If = 0.0;
}
} else {
If = get_intensity(rfull);
if ( random_intensities ) {
lock_reflection(rfull);
int red = get_redundancy(rfull);
set_redundancy(rfull, red+1);
unlock_reflection(rfull);
}
}
Ip = crystal_get_osf(cr) * L * p * If;
res = resolution(crystal_get_cell(cr), h, k, l);
bin = NBINS*2.0*res/max_q;
if ( (bin < NBINS) && (bin>=0) ) {
p_hist[bin] += p;
n_ref[bin]++;
if ( p > p_max[bin] ) p_max[bin] = p;
} else {
STATUS("Reflection out of histogram range: %e %i %f\n",
res, bin, p);
}
Ip = gaussian_noise(Ip, 100.0);
set_intensity(refl, Ip);
set_esd_intensity(refl, 100.0);
}
}
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Generate a stream containing partials from a reflection list.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
"You need to provide the following basic options:\n"
" -i, --input=<file> Read reflections from <file>.\n"
" Default: generate random ones instead (see -r).\n"
" -o, --output=<file> Write partials in stream format to <file>.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -b, --beam=<file> Get beam parameters from file\n"
" -p, --pdb=<file> PDB file from which to get the unit cell.\n"
"\n"
" -y, --symmetry=<sym> Symmetry of the input reflection list.\n"
" -n <n> Simulate <n> patterns. Default: 2.\n"
" -r, --save-random=<file> Save randomly generated intensities to file.\n"
" --pgraph=<file> Save a histogram of partiality values to file.\n"
" -c, --cnoise=<val> Add random noise, with a flat distribution, to the\n"
" reciprocal lattice vector components given in the\n"
" stream, with maximum error +/- <val> percent.\n"
" --osf-stddev=<val> Set the standard deviation of the scaling factors.\n"
"\n"
);
}
struct queue_args
{
RefList *full;
pthread_mutex_t full_lock;
int n_done;
int n_started;
int n_to_do;
SymOpList *sym;
int random_intensities;
UnitCell *cell;
double cnoise;
double osf_stddev;
struct image *template_image;
double max_q;
/* The overall histogram */
double p_hist[NBINS];
unsigned long int n_ref[NBINS];
double p_max[NBINS];
Stream *stream;
};
struct worker_args
{
struct queue_args *qargs;
Crystal *crystal;
struct image image;
/* Histogram for this image */
double p_hist[NBINS];
unsigned long int n_ref[NBINS];
double p_max[NBINS];
};
static void *create_job(void *vqargs)
{
struct worker_args *wargs;
struct queue_args *qargs = vqargs;
/* All done already? */
if ( qargs->n_started == qargs->n_to_do ) return NULL;
wargs = malloc(sizeof(struct worker_args));
wargs->qargs = qargs;
wargs->image = *qargs->template_image;
qargs->n_started++;
return wargs;
}
static void run_job(void *vwargs, int cookie)
{
struct quaternion orientation;
struct worker_args *wargs = vwargs;
struct queue_args *qargs = wargs->qargs;
int i;
Crystal *cr;
RefList *reflections;
double osf;
cr = crystal_new();
if ( cr == NULL ) {
ERROR("Failed to create crystal.\n");
return;
}
wargs->crystal = cr;
crystal_set_image(cr, &wargs->image);
do {
osf = gaussian_noise(1.0, qargs->osf_stddev);
} while ( osf <= 0.0 );
crystal_set_osf(cr, osf);
crystal_set_profile_radius(cr, wargs->image.beam->profile_radius);
/* Set up a random orientation */
orientation = random_quaternion();
crystal_set_cell(cr, cell_rotate(qargs->cell, orientation));
snprintf(wargs->image.filename, 255, "dummy.h5");
reflections = find_intersections(&wargs->image, cr);
crystal_set_reflections(cr, reflections);
for ( i=0; i<NBINS; i++ ) {
wargs->n_ref[i] = 0;
wargs->p_hist[i] = 0.0;
wargs->p_max[i] = 0.0;
}
calculate_partials(cr, qargs->full,
qargs->sym, qargs->random_intensities,
&qargs->full_lock,
wargs->n_ref, wargs->p_hist, wargs->p_max,
qargs->max_q);
/* Give a slightly incorrect cell in the stream */
mess_up_cell(cr, qargs->cnoise);
image_add_crystal(&wargs->image, cr);
}
static void finalise_job(void *vqargs, void *vwargs)
{
struct worker_args *wargs = vwargs;
struct queue_args *qargs = vqargs;
int i;
write_chunk(qargs->stream, &wargs->image, NULL, 0, 1);
for ( i=0; i<NBINS; i++ ) {
qargs->n_ref[i] += wargs->n_ref[i];
qargs->p_hist[i] += wargs->p_hist[i];
if ( wargs->p_max[i] > qargs->p_max[i] ) {
qargs->p_max[i] = wargs->p_max[i];
}
}
qargs->n_done++;
progress_bar(qargs->n_done, qargs->n_to_do, "Simulating");
crystal_free(wargs->crystal);
free(wargs);
}
int main(int argc, char *argv[])
{
int c;
char *input_file = NULL;
char *output_file = NULL;
char *beamfile = NULL;
char *geomfile = NULL;
char *cellfile = NULL;
struct detector *det = NULL;
struct beam_params *beam = NULL;
RefList *full = NULL;
char *sym_str = NULL;
SymOpList *sym;
UnitCell *cell = NULL;
Stream *stream;
int n = 2;
int random_intensities = 0;
char *save_file = NULL;
struct queue_args qargs;
struct image image;
int n_threads = 1;
double cnoise = 0.0;
char *rval;
int i;
FILE *fh;
char *phist_file = NULL;
double osf_stddev = 2.0;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"output", 1, NULL, 'o'},
{"input", 1, NULL, 'i'},
{"beam", 1, NULL, 'b'},
{"pdb", 1, NULL, 'p'},
{"geometry", 1, NULL, 'g'},
{"symmetry", 1, NULL, 'y'},
{"save-random", 1, NULL, 'r'},
{"cnoise", 1, NULL, 'c'},
{"pgraph", 1, NULL, 2},
{"osf-stddev", 1, NULL, 3},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:o:b:p:g:y:n:r:j:c:",
longopts, NULL)) != -1)
{
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'o' :
output_file = strdup(optarg);
break;
case 'i' :
input_file = strdup(optarg);
break;
case 'b' :
beamfile = strdup(optarg);
break;
case 'p' :
cellfile = strdup(optarg);
break;
case 'g' :
geomfile = strdup(optarg);
break;
case 'y' :
sym_str = strdup(optarg);
break;
case 'n' :
n = atoi(optarg);
break;
case 'r' :
save_file = strdup(optarg);
break;
case 'j' :
n_threads = atoi(optarg);
break;
case 'c' :
cnoise = strtod(optarg, &rval);
if ( *rval != '\0' ) {
ERROR("Invalid cell noise value.\n");
return 1;
}
break;
case 2 :
phist_file = strdup(optarg);
break;
case 3 :
osf_stddev = strtod(optarg, &rval);
if ( *rval != '\0' ) {
ERROR("Invalid OSF standard deviation.\n");
return 1;
}
if ( osf_stddev <= 0.0 ) {
ERROR("Invalid OSF standard deviation.");
ERROR(" (must be positive).\n");
return 1;
}
break;
case 0 :
break;
case '?' :
break;
default :
ERROR("Unhandled option '%c'\n", c);
break;
}
}
if ( n_threads < 1 ) {
ERROR("Invalid number of threads.\n");
return 1;
}
/* Load beam */
if ( beamfile == NULL ) {
ERROR("You need to provide a beam parameters file.\n");
return 1;
}
beam = get_beam_parameters(beamfile);
if ( beam == NULL ) {
ERROR("Failed to load beam parameters from '%s'\n", beamfile);
return 1;
}
free(beamfile);
/* Load cell */
if ( cellfile == NULL ) {
ERROR("You need to give a PDB file with the unit cell.\n");
return 1;
}
cell = load_cell_from_pdb(cellfile);
if ( cell == NULL ) {
ERROR("Failed to get cell from '%s'\n", cellfile);
return 1;
}
free(cellfile);
if ( !cell_is_sensible(cell) ) {
ERROR("Invalid unit cell parameters:\n");
cell_print(cell);
return 1;
}
/* Load geometry */
if ( geomfile == NULL ) {
ERROR("You need to give a geometry file.\n");
return 1;
}
det = get_detector_geometry(geomfile);
if ( det == NULL ) {
ERROR("Failed to read geometry from '%s'\n", geomfile);
return 1;
}
free(geomfile);
if ( sym_str == NULL ) sym_str = strdup("1");
sym = get_pointgroup(sym_str);
free(sym_str);
if ( save_file == NULL ) save_file = strdup("partial_sim.hkl");
/* Load (full) reflections */
if ( input_file != NULL ) {
full = read_reflections(input_file);
if ( full == NULL ) {
ERROR("Failed to read reflections from '%s'\n",
input_file);
return 1;
}
free(input_file);
if ( check_list_symmetry(full, sym) ) {
ERROR("The input reflection list does not appear to"
" have symmetry %s\n", symmetry_name(sym));
return 1;
}
} else {
random_intensities = 1;
}
if ( n < 1 ) {
ERROR("Number of patterns must be at least 1.\n");
return 1;
}
if ( output_file == NULL ) {
ERROR("You must give a filename for the output.\n");
return 1;
}
stream = open_stream_for_write(output_file);
if ( stream == NULL ) {
ERROR("Couldn't open output file '%s'\n", output_file);
return 1;
}
free(output_file);
image.det = det;
image.width = det->max_fs;
image.height = det->max_ss;
image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy));
image.div = beam->divergence;
image.bw = beam->bandwidth;
image.beam = beam;
image.filename = malloc(256);
image.copyme = NULL;
image.crystals = NULL;
image.n_crystals = 0;
image.indexed_by = INDEXING_NONE;
if ( random_intensities ) {
full = reflist_new();
}
qargs.full = full;
pthread_mutex_init(&qargs.full_lock, NULL);
qargs.n_to_do = n;
qargs.n_done = 0;
qargs.n_started = 0;
qargs.sym = sym;
qargs.random_intensities = random_intensities;
qargs.cell = cell;
qargs.template_image = ℑ
qargs.stream = stream;
qargs.cnoise = cnoise;
qargs.osf_stddev = osf_stddev;
qargs.max_q = largest_q(&image);
for ( i=0; i<NBINS; i++ ) {
qargs.n_ref[i] = 0;
qargs.p_hist[i] = 0.0;
qargs.p_max[i] = 0.0;
}
run_threads(n_threads, run_job, create_job, finalise_job,
&qargs, n, 0, 0, 0);
if ( random_intensities ) {
STATUS("Writing full intensities to %s\n", save_file);
write_reflist(save_file, full);
}
if ( phist_file != NULL ) {
fh = fopen(phist_file, "w");
if ( fh != NULL ) {
for ( i=0; i<NBINS; i++ ) {
double rcen;
rcen = i/(double)NBINS*qargs.max_q
+ qargs.max_q/(2.0*NBINS);
fprintf(fh, "%.2f %7li %.3f %.3f\n", rcen/1.0e9,
qargs.n_ref[i],
qargs.p_hist[i]/qargs.n_ref[i],
qargs.p_max[i]);
}
fclose(fh);
} else {
ERROR("Failed to open file '%s' for writing.\n",
phist_file);
}
}
close_stream(stream);
cell_free(cell);
free_detector_geometry(det);
free(beam);
free_symoplist(sym);
reflist_free(full);
free(image.filename);
return 0;
}
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