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|
/*
* indexamajig.c
*
* Find hits, index patterns, output hkl+intensity etc.
*
* (c) 2006-2010 Thomas White <taw@physics.org>
*
* Part of CrystFEL - crystallography with a FEL
*
*/
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#define _GNU_SOURCE 1
#include <stdarg.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <getopt.h>
#include <hdf5.h>
#include <gsl/gsl_errno.h>
#include <pthread.h>
#include <sys/time.h>
#include "utils.h"
#include "hdf5-file.h"
#include "index.h"
#include "peaks.h"
#include "diffraction.h"
#include "diffraction-gpu.h"
#include "detector.h"
#include "sfac.h"
#include "filters.h"
#include "reflections.h"
#define MAX_THREADS (96)
struct process_args
{
char *filename;
int id;
pthread_mutex_t *output_mutex; /* Protects stdout */
pthread_mutex_t *gpu_mutex; /* Protects "gctx" */
UnitCell *cell;
int config_cmfilter;
int config_noisefilter;
int config_writedrx;
int config_dumpfound;
int config_verbose;
int config_alternate;
int config_nearbragg;
int config_gpu;
int config_simulate;
int config_nomatch;
int config_unpolar;
IndexingMethod indm;
const double *intensities;
const unsigned int *counts;
struct gpu_context *gctx;
};
struct process_result
{
int hit;
int peaks_sane;
};
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
printf(
"Process and index FEL diffraction images.\n"
"\n"
" -h, --help Display this help message.\n"
"\n"
" -i, --input=<filename> Specify file containing list of images to process.\n"
" '-' means stdin, which is the default.\n"
"\n"
" --indexing=<method> Use 'method' for indexing. Choose from:\n"
" none : no indexing\n"
" dirax : invoke DirAx\n"
"\n\nWith just the above options, this program does not do much of practical "
"use.\nYou should also enable some of the following:\n\n"
" --near-bragg Output a list of reflection intensities to stdout.\n"
" When pixels with fractional indices within 0.1 of\n"
" integer values (the Bragg condition) are found,\n"
" the integral of pixels within a ten pixel radius\n"
" of the nearest-to-Bragg pixel will be reported as\n"
" the intensity. The centroid of the pixels will\n"
" be given as the coordinates, as well as the h,k,l\n"
" (integer) indices of the reflection. If a peak\n"
" was located by the initial peak search close to\n"
" the \"near Bragg\" location, its coordinates will\n"
" be taken as the centre instead.\n"
" --simulate Simulate the diffraction pattern using the indexed\n"
" unit cell. The simulated pattern will be saved\n"
" as \"simulated.h5\". You can TRY to combine this\n"
" with \"-j <n>\" with n greater than 1, but it's\n"
" not a good idea.\n"
" --filter-cm Perform common-mode noise subtraction on images\n"
" before proceeding. Intensities will be extracted\n"
" from the image as it is after this processing.\n"
" --filter-noise Apply an aggressive noise filter which sets all\n"
" pixels in each 3x3 region to zero if any of them\n"
" have negative values. Intensity measurement will\n"
" be performed on the image as it was before this.\n"
" --write-drx Write 'xfel.drx' for visualisation of reciprocal\n"
" space. Implied by any indexing method other than\n"
" 'none'. Beware: the units in this file are\n"
" reciprocal Angstroms.\n"
" --dump-peaks Write the results of the peak search to stdout.\n"
" The intensities in this list are from the\n"
" centroid/integration procedure.\n"
" --no-match Don't attempt to match the indexed cell to the\n"
" model, just proceed with the one generated by the\n"
" auto-indexing procedure.\n"
" --unpolarized Don't correct for the polarisation of the X-rays.\n"
"\n\nOptions for greater performance or verbosity:\n\n"
" --verbose Be verbose about indexing.\n"
" --gpu Use the GPU to speed up the simulation.\n"
" -j <n> Run <n> analyses in parallel. Default 1.\n"
"\n\nControl of model and data input:\n\n"
" --intensities=<file> Specify file containing reflection intensities\n"
" to use when simulating.\n"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.\n"
" -x, --prefix=<p> Prefix filenames from input file with 'p'.\n"
);
}
static struct image *get_simage(struct image *template, int alternate)
{
struct image *image;
struct panel panels[2];
image = malloc(sizeof(*image));
/* Simulate a diffraction pattern */
image->twotheta = NULL;
image->data = NULL;
image->det = template->det;
/* 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;
/* Detector geometry for the simulation
* - not necessarily the same as the original. */
image->width = 1024;
image->height = 1024;
image->det.n_panels = 2;
if ( alternate ) {
/* Upper */
panels[0].min_x = 0;
panels[0].max_x = 1023;
panels[0].min_y = 512;
panels[0].max_y = 1023;
panels[0].cx = 523.6;
panels[0].cy = 502.5;
panels[0].clen = 56.4e-2; /* 56.4 cm */
panels[0].res = 13333.3; /* 75 microns/pixel */
/* Lower */
panels[1].min_x = 0;
panels[1].max_x = 1023;
panels[1].min_y = 0;
panels[1].max_y = 511;
panels[1].cx = 520.8;
panels[1].cy = 525.0;
panels[1].clen = 56.7e-2; /* 56.7 cm */
panels[1].res = 13333.3; /* 75 microns/pixel */
image->det.panels = panels;
} else {
/* Copy pointer to old geometry */
image->det.panels = template->det.panels;
}
image->lambda = ph_en_to_lambda(eV_to_J(1.8e3));
image->features = template->features;
image->filename = template->filename;
image->indexed_cell = template->indexed_cell;
image->f0 = template->f0;
/* Prevent muppetry */
image->hits = NULL;
image->n_hits = 0;
return image;
}
static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
const double *intensities,
const unsigned int *counts, UnitCell *cell)
{
/* Set up GPU if necessary */
if ( (gctx != NULL) && (*gctx == NULL) ) {
*gctx = setup_gpu(0, simage, intensities, counts);
}
if ( (gctx != NULL) && (*gctx != NULL) ) {
get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell);
} else {
get_diffraction(simage, 24, 24, 40,
intensities, counts, cell, 0, GRADIENT_MOSAIC);
}
record_image(simage, 0);
hdf5_write("simulated.h5", simage->data, simage->width, simage->height,
H5T_NATIVE_FLOAT);
}
static void *process_image(void *pargsv)
{
struct process_args *pargs = pargsv;
struct hdfile *hdfile;
struct image image;
struct image *simage;
float *data_for_measurement;
size_t data_size;
const char *filename = pargs->filename;
UnitCell *cell = pargs->cell;
int config_cmfilter = pargs->config_cmfilter;
int config_noisefilter = pargs->config_noisefilter;
int config_writedrx = pargs->config_writedrx;
int config_dumpfound = pargs->config_dumpfound;
int config_verbose = pargs->config_verbose;
int config_alternate = pargs->config_alternate;
int config_nearbragg = pargs->config_nearbragg;
int config_gpu = pargs->config_gpu;
int config_simulate = pargs->config_simulate;
int config_nomatch = pargs->config_nomatch;
int config_unpolar = pargs->config_unpolar;
IndexingMethod indm = pargs->indm;
const double *intensities = pargs->intensities;
const unsigned int *counts = pargs->counts;
struct gpu_context *gctx = pargs->gctx;
struct process_result *result;
image.features = NULL;
image.data = NULL;
image.indexed_cell = NULL;
image.id = pargs->id;
image.filename = filename;
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;
STATUS("Processing '%s'\n", image.filename);
result = malloc(sizeof(*result));
if ( result == NULL ) return NULL;
hdfile = hdfile_open(filename);
if ( hdfile == NULL ) {
result->hit = 0;
return result;
} else if ( hdfile_set_first_image(hdfile, "/") ) {
ERROR("Couldn't select path\n");
result->hit = 0;
return result;
}
#include "geometry-lcls.tmp"
hdf5_read(hdfile, &image);
if ( config_cmfilter ) {
filter_cm(&image);
}
/* Take snapshot of image after CM subtraction but before
* the aggressive noise filter. */
data_size = image.width*image.height*sizeof(float);
data_for_measurement = malloc(data_size);
if ( config_noisefilter ) {
filter_noise(&image, data_for_measurement);
} else {
memcpy(data_for_measurement, image.data, data_size);
}
/* Perform 'fine' peak search */
search_peaks(&image);
/* Get rid of noise-filtered version at this point
* - it was strictly for the purposes of peak detection. */
free(image.data);
image.data = data_for_measurement;
if ( image_feature_count(image.features) < 5 ) goto done;
if ( config_dumpfound ) dump_peaks(&image, pargs->output_mutex);
/* Not indexing nor writing xfel.drx?
* Then there's nothing left to do. */
if ( (!config_writedrx) && (indm == INDEXING_NONE) ) {
goto done;
}
/* Calculate orientation matrix (by magic) */
if ( config_writedrx || (indm != INDEXING_NONE) ) {
index_pattern(&image, cell, indm, config_nomatch,
config_verbose);
}
/* No cell at this point? Then we're done. */
result->peaks_sane = 0;
if ( image.indexed_cell == NULL ) goto done;
/* Sanity check */
if ( !peak_sanity_check(&image, image.indexed_cell) ) {
STATUS("Failed peak sanity check.\n");
result->peaks_sane = 0;
goto done;
} else {
result->peaks_sane = 1;
}
/* Measure intensities if requested */
if ( config_nearbragg ) {
output_intensities(&image, image.indexed_cell,
pargs->output_mutex, config_unpolar);
}
simage = get_simage(&image, config_alternate);
/* Simulate if requested */
if ( config_simulate ) {
if ( config_gpu ) {
pthread_mutex_lock(pargs->gpu_mutex);
simulate_and_write(simage, &gctx, intensities,
counts, image.indexed_cell);
pthread_mutex_unlock(pargs->gpu_mutex);
} else {
simulate_and_write(simage, NULL, intensities,
counts, image.indexed_cell);
}
}
/* Finished with alternate image */
if ( simage->twotheta != NULL ) free(simage->twotheta);
if ( simage->data != NULL ) free(simage->data);
free(simage);
/* Only free cell if found */
free(image.indexed_cell);
done:
free(image.data);
free(image.det.panels);
image_feature_list_free(image.features);
free(image.hits);
hdfile_close(hdfile);
if ( image.indexed_cell == NULL ) {
result->hit = 0;
} else {
result->hit = 1;
}
return result;
}
int main(int argc, char *argv[])
{
int c;
struct gpu_context *gctx = NULL;
char *filename = NULL;
FILE *fh;
char *rval = NULL;
int n_images;
int n_hits;
int n_sane;
int config_noindex = 0;
int config_dumpfound = 0;
int config_nearbragg = 0;
int config_writedrx = 0;
int config_simulate = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
int config_nomatch = 0;
int config_gpu = 0;
int config_verbose = 0;
int config_alternate = 0;
int config_unpolar = 0;
IndexingMethod indm;
char *indm_str = NULL;
UnitCell *cell;
double *intensities = NULL;
char *intfile = NULL;
unsigned int *counts;
char *pdb = NULL;
char *prefix = NULL;
int nthreads = 1;
pthread_t workers[MAX_THREADS];
struct process_args *worker_args[MAX_THREADS];
int worker_active[MAX_THREADS];
int i;
pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"gpu", 0, &config_gpu, 1},
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
{"near-bragg", 0, &config_nearbragg, 1},
{"write-drx", 0, &config_writedrx, 1},
{"indexing", 1, NULL, 'z'},
{"simulate", 0, &config_simulate, 1},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
{"no-match", 0, &config_nomatch, 1},
{"verbose", 0, &config_verbose, 1},
{"alternate", 0, &config_alternate, 1},
{"intensities", 1, NULL, 'q'},
{"pdb", 1, NULL, 'p'},
{"prefix", 1, NULL, 'x'},
{"unpolarized", 0, &config_unpolar, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:wp:j:x:", longopts, NULL)) != -1) {
switch (c) {
case 'h' : {
show_help(argv[0]);
return 0;
}
case 'i' : {
filename = strdup(optarg);
break;
}
case 'z' : {
indm_str = strdup(optarg);
break;
}
case 'q' : {
intfile = strdup(optarg);
break;
}
case 'p' : {
pdb = strdup(optarg);
break;
}
case 'x' : {
prefix = strdup(optarg);
break;
}
case 'j' : {
nthreads = atoi(optarg);
break;
}
case 0 : {
break;
}
default : {
return 1;
}
}
}
if ( filename == NULL ) {
filename = strdup("-");
}
if ( strcmp(filename, "-") == 0 ) {
fh = stdin;
} else {
fh = fopen(filename, "r");
}
if ( fh == NULL ) {
ERROR("Failed to open input file '%s'\n", filename);
return 1;
}
free(filename);
if ( intfile != NULL ) {
counts = new_list_count();
intensities = read_reflections(intfile, counts);
} else {
intensities = NULL;
counts = NULL;
}
if ( pdb == NULL ) {
pdb = strdup("molecule.pdb");
}
if ( prefix == NULL ) {
prefix = strdup("");
}
if ( (nthreads == 0) || (nthreads > MAX_THREADS) ) {
ERROR("Invalid number of threads.\n");
return 1;
}
if ( indm_str == NULL ) {
STATUS("You didn't specify an indexing method, so I won't"
" try to index anything.\n"
"If that isn't what you wanted, re-run with"
" --indexing=<method>.\n");
indm = INDEXING_NONE;
} else if ( strcmp(indm_str, "none") == 0 ) {
indm = INDEXING_NONE;
} else if ( strcmp(indm_str, "dirax") == 0) {
indm = INDEXING_DIRAX;
} else {
ERROR("Unrecognised indexing method '%s'\n", indm_str);
return 1;
}
free(indm_str);
cell = load_cell_from_pdb(pdb);
if ( cell == NULL ) {
if ( pdb == NULL ) {
ERROR("Couldn't read unit cell (from molecule.pdb)\n");
} else {
ERROR("Couldn't read unit cell (from %s)\n", pdb);
}
return 1;
}
free(pdb);
gsl_set_error_handler_off();
n_images = 0;
n_hits = 0;
n_sane = 0;
for ( i=0; i<nthreads; i++ ) {
worker_args[i] = malloc(sizeof(struct process_args));
worker_args[i]->filename = malloc(1024);
worker_active[i] = 0;
}
/* Initially, fire off the full number of threads */
for ( i=0; i<nthreads; i++ ) {
char line[1024];
struct process_args *pargs;
int r;
pargs = worker_args[i];
rval = fgets(line, 1023, fh);
if ( rval == NULL ) continue;
chomp(line);
snprintf(pargs->filename, 1023, "%s%s", prefix, line);
n_images++;
pargs->output_mutex = &output_mutex;
pargs->gpu_mutex = &gpu_mutex;
pargs->config_cmfilter = config_cmfilter;
pargs->config_noisefilter = config_noisefilter;
pargs->config_writedrx = config_writedrx;
pargs->config_dumpfound = config_dumpfound;
pargs->config_verbose = config_verbose;
pargs->config_alternate = config_alternate;
pargs->config_nearbragg = config_nearbragg;
pargs->config_gpu = config_gpu;
pargs->config_simulate = config_simulate;
pargs->config_nomatch = config_nomatch;
pargs->config_unpolar = config_unpolar;
pargs->cell = cell;
pargs->indm = indm;
pargs->intensities = intensities;
pargs->counts = counts;
pargs->gctx = gctx;
pargs->id = i;
worker_active[i] = 1;
r = pthread_create(&workers[i], NULL, process_image, pargs);
if ( r != 0 ) {
worker_active[i] = 0;
ERROR("Couldn't start thread %i\n", i);
}
}
/* Start new threads as old ones finish */
do {
int i;
for ( i=0; i<nthreads; i++ ) {
char line[1024];
int r;
struct process_result *result = NULL;
struct timespec t;
struct timeval tv;
struct process_args *pargs;
if ( !worker_active[i] ) continue;
pargs = worker_args[i];
gettimeofday(&tv, NULL);
t.tv_sec = tv.tv_sec;
t.tv_nsec = tv.tv_usec * 1000 + 20000;
r = pthread_timedjoin_np(workers[i], (void *)&result,
&t);
if ( r != 0 ) continue; /* Not ready yet */
worker_active[i] = 0;
if ( result != NULL ) {
n_hits += result->hit;
n_sane += result->peaks_sane;
free(result);
}
rval = fgets(line, 1023, fh);
if ( rval == NULL ) break;
chomp(line);
snprintf(pargs->filename, 1023, "%s%s", prefix, line);
worker_active[i] = 1;
r = pthread_create(&workers[i], NULL, process_image,
pargs);
if ( r != 0 ) {
worker_active[i] = 0;
ERROR("Couldn't start thread %i\n", i);
}
n_images++;
}
} while ( rval != NULL );
/* Catch all remaining threads */
for ( i=0; i<nthreads; i++ ) {
struct process_result *result = NULL;
if ( !worker_active[i] ) goto free;
pthread_join(workers[i], (void *)&result);
worker_active[i] = 0;
if ( result != NULL ) {
n_hits += result->hit;
free(result);
}
free:
if ( worker_args[i]->filename != NULL ) {
free(worker_args[i]->filename);
}
free(worker_args[i]);
}
free(prefix);
free(cell);
fclose(fh);
STATUS("There were %i images.\n", n_images);
STATUS("%i hits were found, of which %i were sane.\n", n_hits, n_sane);
if ( gctx != NULL ) {
cleanup_gpu(gctx);
}
return 0;
}
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