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/*
* facetron.c
*
* Profile fitting for coherent nanocrystallography
*
* (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 <pthread.h>
#include <sys/time.h>
#include <assert.h>
#include "utils.h"
#include "hdf5-file.h"
#include "symmetry.h"
#include "reflections.h"
#include "stream.h"
#include "geometry.h"
#define MAX_THREADS (256)
struct process_args
{
struct image *image;
/* Thread control */
pthread_mutex_t control_mutex; /* Protects the scary stuff below */
int start;
int finish;
int done;
/* Analysis parameters */
const char *sym;
ReflItemList *obs;
double *i_full;
};
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Post-refinement and profile fitting for coherent nanocrystallography.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify the name of the input 'stream'.\n"
" (must be a file, not e.g. stdin)\n"
" -o, --output=<filename> Output filename. Default: facetron.hkl.\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
" --basename Remove the directory parts of the filenames.\n"
" --no-check-prefix Don't attempt to correct the --prefix.\n"
" -y, --symmetry=<sym> Merge according to symmetry <sym>.\n"
" -n, --iterations=<n> Run <n> cycles of post-refinement.\n"
"\n"
" -j <n> Run <n> analyses in parallel.\n");
}
static void refine_image(struct image *image, ReflItemList *obs, double *i_full)
{
//struct hdfile *hdfile;
image->features = NULL;
image->data = NULL;
image->flags = NULL;
image->hits = NULL;
image->n_hits = 0;
/* View head-on (unit cell is tilted) */
image->orientation.w = 1.0;
image->orientation.x = 0.0;
image->orientation.y = 0.0;
image->orientation.z = 0.0;
//hdfile = hdfile_open(pargs->filename);
//if ( hdfile == NULL ) {
// return;
//} else if ( hdfile_set_first_image(hdfile, "/") ) {
// ERROR("Couldn't select path\n");
// hdfile_close(hdfile);
// return;
//}
//hdf5_read(hdfile, &image, 1);
free(image->data);
if ( image->flags != NULL ) free(image->flags);
//hdfile_close(hdfile);
}
static void *worker_thread(void *pargsv)
{
struct process_args *pargs = pargsv;
int finish;
do {
int wakeup;
refine_image(pargs->image, pargs->obs, pargs->i_full);
pthread_mutex_lock(&pargs->control_mutex);
pargs->done = 1;
pthread_mutex_unlock(&pargs->control_mutex);
/* Go to sleep until told to exit or process next image */
do {
pthread_mutex_lock(&pargs->control_mutex);
/* Either of these can result in the thread waking up */
wakeup = pargs->start || pargs->finish;
finish = pargs->finish;
pthread_mutex_unlock(&pargs->control_mutex);
usleep(20000);
} while ( !wakeup );
} while ( !pargs->finish );
return NULL;
}
static void refine_all(struct image *images, int n_total_patterns,
struct detector *det, const char *sym,
ReflItemList *obs, double *i_full, int nthreads)
{
pthread_t workers[MAX_THREADS];
struct process_args *worker_args[MAX_THREADS];
int worker_active[MAX_THREADS];
int i;
int n_done = 0;
int n_started = 0;
/* Initialise worker arguments with the unchanging data */
for ( i=0; i<nthreads; i++ ) {
worker_args[i] = malloc(sizeof(struct process_args));
worker_active[i] = 0;
pthread_mutex_init(&worker_args[i]->control_mutex, NULL);
worker_args[i]->sym = sym;
}
/* Start threads off */
for ( i=0; i<nthreads; i++ ) {
struct process_args *pargs;
int r;
pargs = worker_args[i];
pargs->image = &images[n_started++];
pthread_mutex_lock(&pargs->control_mutex);
pargs->done = 0;
pargs->start = 1;
pargs->finish = 0;
pthread_mutex_unlock(&pargs->control_mutex);
worker_active[i] = 1;
r = pthread_create(&workers[i], NULL, worker_thread, pargs);
if ( r != 0 ) {
worker_active[i] = 0;
ERROR("Couldn't start thread %i\n", i);
}
}
/* Keep threads busy until the end of the data */
do {
int i;
for ( i=0; i<nthreads; i++ ) {
struct process_args *pargs;
int done;
/* Spend time working, not managing threads */
usleep(100000);
/* Are we using this thread record at all? */
if ( !worker_active[i] ) continue;
/* Has the thread finished yet? */
pargs = worker_args[i];
pthread_mutex_lock(&pargs->control_mutex);
done = pargs->done;
pthread_mutex_unlock(&pargs->control_mutex);
if ( !done ) continue;
/* Reset "done" flag */
pargs->done = 0;
n_done++;
progress_bar(n_done, n_total_patterns, "Refining");
/* If there are no more patterns, "done" will remain
* zero, so the last pattern will not be re-counted. */
if ( n_started == n_total_patterns ) break;
/* Start work on the next pattern */
pargs->image = &images[n_started++];
pthread_mutex_lock(&pargs->control_mutex);
pargs->start = 1;
pthread_mutex_unlock(&pargs->control_mutex);
}
} while ( n_started < n_total_patterns );
/* Join threads */
for ( i=0; i<nthreads; i++ ) {
if ( !worker_active[i] ) continue;
/* Tell the thread to exit */
struct process_args *pargs = worker_args[i];
pthread_mutex_lock(&pargs->control_mutex);
pargs->finish = 1;
pthread_mutex_unlock(&pargs->control_mutex);
/* Wait for it to join */
pthread_join(workers[i], NULL);
if ( pargs->done ) {
n_done++;
progress_bar(n_done, n_total_patterns, "Refining");
} /* else this thread was not busy */
}
}
static double partiality(struct image *image, double x, double y)
{
return 1.0;
}
static void estimate_full(struct image *images, int n_total_patterns,
struct detector *det, const char *sym,
ReflItemList *obs, double *i_full)
{
int i;
for ( i=0; i<n_total_patterns; i++ ) {
struct reflhit *spots;
struct image *image = &images[i];
int j, n;
/* Get the "spots" appearing in this pattern */
spots = find_intersections(image, image->indexed_cell,
image->div, image->bw, &n, 0);
/* For each spot, estimate the partiality */
for ( j=0; j<n; j++ ) {
double p = partiality(image, spots[j].x, spots[j].y);
}
progress_bar(i, n_total_patterns-1, "Integrating");
}
}
int main(int argc, char *argv[])
{
int c;
char *infile = NULL;
char *outfile = NULL;
char *geomfile = NULL;
char *prefix = NULL;
char *sym = NULL;
FILE *fh;
int nthreads = 1;
int config_basename = 0;
int config_checkprefix = 1;
struct detector *det;
double *i_full;
ReflItemList *obs;
int i;
int n_total_patterns;
struct image *images;
int n_iter = 10;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
{"geometry", 1, NULL, 'g'},
{"prefix", 1, NULL, 'x'},
{"basename", 0, &config_basename, 1},
{"no-check-prefix", 0, &config_checkprefix, 0},
{"symmetry", 1, NULL, 'y'},
{"iterations", 1, NULL, 'n'},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:g:x:j:y:o:",
longopts, NULL)) != -1)
{
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'i' :
infile = strdup(optarg);
break;
case 'g' :
geomfile = strdup(optarg);
break;
case 'x' :
prefix = strdup(optarg);
break;
case 'j' :
nthreads = atoi(optarg);
break;
case 'y' :
sym = strdup(optarg);
break;
case 'o' :
outfile = strdup(optarg);
break;
case 'n' :
n_iter = atoi(optarg);
break;
case 0 :
break;
default :
return 1;
}
}
/* Sanitise input filename and open */
if ( infile == NULL ) {
infile = strdup("-");
}
if ( strcmp(infile, "-") == 0 ) {
fh = stdin;
} else {
fh = fopen(infile, "r");
}
if ( fh == NULL ) {
ERROR("Failed to open input file '%s'\n", infile);
return 1;
}
free(infile);
/* Sanitise output filename */
if ( outfile == NULL ) {
outfile = strdup("facetron.hkl");
}
/* Sanitise prefix */
if ( prefix == NULL ) {
prefix = strdup("");
} else {
if ( config_checkprefix ) {
prefix = check_prefix(prefix);
}
}
/* Get detector geometry */
det = get_detector_geometry(geomfile);
if ( det == NULL ) {
ERROR("Failed to read detector geometry from '%s'\n", geomfile);
return 1;
}
free(geomfile);
/* Prepare for iteration */
i_full = new_list_intensity();
obs = new_items();
n_total_patterns = count_patterns(fh);
STATUS("There are %i patterns to process\n", n_total_patterns);
images = malloc(n_total_patterns * sizeof(struct image));
if ( images == NULL ) {
ERROR("Couldn't allocate memory for images.\n");
return 1;
}
/* Fill in what we know about the images so far */
rewind(fh);
for ( i=0; i<n_total_patterns; i++ ) {
UnitCell *cell;
char *filename;
char fnamereal[1024];
if ( find_chunk(fh, &cell, &filename) == 1 ) {
ERROR("Couldn't get all of the filenames and cells"
" from the input stream.\n");
return 1;
}
images[i].indexed_cell = cell;
/* Mangle the filename now */
if ( config_basename ) {
char *tmp;
tmp = strdup(basename(filename));
free(filename);
filename = tmp;
}
snprintf(fnamereal, 1023, "%s%s", prefix, filename);
images[i].filename = fnamereal;
images[i].div = 0.5e-3;
images[i].bw = 0.001;
free(filename);
progress_bar(i, n_total_patterns-1, "Loading pattern data");
}
fclose(fh);
free(prefix);
/* Make initial estimates */
estimate_full(images, n_total_patterns, det, sym, obs, i_full);
/* Iterate */
for ( i=0; i<n_iter; i++ ) {
STATUS("Post refinement iteration %i of %i\n", i+1, n_iter);
/* Refine the geometry of all patterns to get the best fit */
refine_all(images, n_total_patterns, det, sym, obs, i_full,
nthreads);
/* Re-estimate all the full intensities */
estimate_full(images, n_total_patterns, det, sym, obs, i_full);
}
/* Output results */
write_reflections(outfile, obs, i_full, NULL, NULL, NULL);
/* Clean up */
free(i_full);
delete_items(obs);
free(sym);
free(outfile);
return 0;
}
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