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|
/*
* indexamajig.c
*
* 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
#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"
#include "thread-pool.h"
#include "beam-parameters.h"
#include "symmetry.h"
enum {
PEAK_ZAEF,
PEAK_HDF5,
};
/* Information about the indexing process which is common to all patterns */
struct static_index_args
{
pthread_mutex_t *gpu_mutex; /* Protects "gctx" */
UnitCell *cell;
int config_cmfilter;
int config_noisefilter;
int config_dumpfound;
int config_verbose;
int config_alternate;
int config_nearbragg;
int config_gpu;
int config_simulate;
int config_polar;
int config_satcorr;
int config_closer;
int config_insane;
float threshold;
float min_gradient;
struct detector *det;
IndexingMethod *indm;
IndexingPrivate **ipriv;
const double *intensities;
const unsigned char *flags;
const char *sym; /* Symmetry of "intensities" and "flags" */
struct gpu_context *gctx;
int gpu_dev;
int peaks;
int cellr;
double nominal_photon_energy;
/* Output stream */
pthread_mutex_t *output_mutex; /* Protects the output stream */
FILE *ofh;
};
/* Information about the indexing process for one pattern */
struct index_args
{
/* "Input" */
char *filename;
struct static_index_args static_args;
/* "Output" */
int indexable;
};
/* Information needed to choose the next task and dispatch it */
struct queue_args
{
FILE *fh;
char *prefix;
struct static_index_args static_args;
int n_indexable;
char *use_this_one_instead;
};
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"
" -o, --output=<filename> Write indexed stream to this file. '-' for stdout.\n"
"\n"
" --indexing=<methods> Use 'methods' for indexing. Provide one or more\n"
" methods separated by commas. Choose from:\n"
" none : no indexing (default)\n"
" dirax : invoke DirAx\n"
" mosflm : invoke MOSFLM (DPS)\n"
" template : index by template matching\n"
" -g. --geometry=<file> Get detector geometry from file.\n"
" -b, --beam=<file> Get beam parameters from file (provides nominal\n"
" wavelength value if no per-shot value is found in\n"
" the HDF5 files.\n"
" -p, --pdb=<file> PDB file from which to get the unit cell to match.\n"
" Default: 'molecule.pdb'.\n"
" -x, --prefix=<p> Prefix filenames from input file with <p>.\n"
" --peaks=<method> Use 'method' for finding peaks. Choose from:\n"
" zaef : Use Zaefferer (2000) gradient detection.\n"
" This is the default method.\n"
" hdf5 : Get from /processing/hitfinder/peakinfo\n"
" in the HDF5 file.\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"
" --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"
"\n"
"\nFor more control over the process, you might need:\n\n"
" --cell-reduction=<m> Use <m> as the cell reduction method. Choose from:\n"
" none : no matching, just use the raw cell.\n"
" reduce : full cell reduction.\n"
" compare : match by at most changing the order of\n"
" the indices.\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"
" --unpolarized Don't correct for the polarisation of the X-rays.\n"
" --no-sat-corr Don't correct values of saturated peaks using a\n"
" table included in the HDF5 file.\n"
" --threshold=<n> Only accept peaks above <n> ADU. Default: 800.\n"
" --min-gradient=<n> Minimum gradient for Zaefferer peak search.\n"
" Default: 100,000.\n"
"\n"
"\nIf you used --simulate, you may also want:\n\n"
" --intensities=<file> Specify file containing reflection intensities\n"
" to use when simulating.\n"
" -y, --symmetry=<sym> The symmetry of the intensities file.\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"
" --gpu-dev=<n> Use GPU device <n>. Omit this option to see the\n"
" available devices.\n"
" -j <n> Run <n> analyses in parallel. Default 1.\n"
"\n"
"\nOptions you probably won't need:\n\n"
" --no-check-prefix Don't attempt to correct the --prefix.\n"
" --no-closer-peak Don't integrate from the location of a nearby peak\n"
" instead of the position closest to the reciprocal\n"
" lattice point.\n"
" --insane Don't check that the reduced cell accounts for at\n"
" least 10%% of the located peaks.\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;
image->flags = NULL;
image->f0_available = 0;
image->f0 = 1.0;
/* 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->cpeaks = NULL;
image->n_cpeaks = 0;
return image;
}
static void simulate_and_write(struct image *simage, struct gpu_context **gctx,
const double *intensities,
const unsigned char *flags, UnitCell *cell,
int gpu_dev, const char *sym)
{
/* Set up GPU if necessary.
* Unfortunately, setup has to go here since until now we don't know
* enough about the situation. */
if ( (gctx != NULL) && (*gctx == NULL) ) {
*gctx = setup_gpu(0, simage, intensities, flags, sym, gpu_dev);
}
if ( (gctx != NULL) && (*gctx != NULL) ) {
get_diffraction_gpu(*gctx, simage, 24, 24, 40, cell);
} else {
get_diffraction(simage, 24, 24, 40,
intensities, NULL, flags, cell, 0,
GRADIENT_MOSAIC, sym);
}
record_image(simage, 0);
hdf5_write("simulated.h5", simage->data, simage->width, simage->height,
H5T_NATIVE_FLOAT);
}
static void process_image(void *pp, int cookie)
{
struct index_args *pargs = pp;
struct hdfile *hdfile;
struct image image;
struct image *simage;
float *data_for_measurement;
size_t data_size;
char *filename = pargs->filename;
UnitCell *cell = pargs->static_args.cell;
int config_cmfilter = pargs->static_args.config_cmfilter;
int config_noisefilter = pargs->static_args.config_noisefilter;
int config_dumpfound = pargs->static_args.config_dumpfound;
int config_verbose = pargs->static_args.config_verbose;
int config_alternate = pargs->static_args.config_alternate;
int config_nearbragg = pargs->static_args.config_nearbragg;
int config_gpu = pargs->static_args.config_gpu;
int config_simulate = pargs->static_args.config_simulate;
int config_polar = pargs->static_args.config_polar;
IndexingMethod *indm = pargs->static_args.indm;
const double *intensities = pargs->static_args.intensities;
const unsigned char *flags = pargs->static_args.flags;
struct gpu_context *gctx = pargs->static_args.gctx;
const char *sym = pargs->static_args.sym;
image.features = NULL;
image.data = NULL;
image.indexed_cell = NULL;
image.id = cookie;
image.filename = filename;
image.cpeaks = NULL;
image.n_cpeaks = 0;
image.det = pargs->static_args.det;
STATUS("Processing '%s'\n", image.filename);
pargs->indexable = 0;
hdfile = hdfile_open(filename);
if ( hdfile == NULL ) {
return;
} else if ( hdfile_set_first_image(hdfile, "/") ) {
ERROR("Couldn't select path\n");
return;
}
hdf5_read(hdfile, &image, pargs->static_args.config_satcorr,
pargs->static_args.nominal_photon_energy);
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);
}
switch ( pargs->static_args.peaks )
{
case PEAK_HDF5 :
/* Get peaks from HDF5 */
if ( get_peaks(&image, hdfile) ) {
ERROR("Failed to get peaks from HDF5 file.\n");
return;
}
break;
case PEAK_ZAEF :
search_peaks(&image, pargs->static_args.threshold,
pargs->static_args.min_gradient);
break;
}
/* 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 ( config_dumpfound ) {
dump_peaks(&image, pargs->static_args.ofh,
pargs->static_args.output_mutex);
}
/* Not indexing? Then there's nothing left to do. */
if ( indm == NULL ) goto done;
/* Calculate orientation matrix (by magic) */
index_pattern(&image, cell, indm, pargs->static_args.cellr,
config_verbose, pargs->static_args.ipriv,
pargs->static_args.config_insane);
/* No cell at this point? Then we're done. */
if ( image.indexed_cell == NULL ) goto done;
pargs->indexable = 1;
/* Measure intensities if requested */
if ( config_nearbragg ) {
output_intensities(&image, image.indexed_cell,
pargs->static_args.output_mutex,
config_polar,
pargs->static_args.config_closer,
pargs->static_args.ofh, 0, 0.1);
}
simage = get_simage(&image, config_alternate);
/* Simulate if requested */
if ( config_simulate ) {
if ( config_gpu ) {
pthread_mutex_lock(pargs->static_args.gpu_mutex);
simulate_and_write(simage, &gctx, intensities, flags,
image.indexed_cell,
pargs->static_args.gpu_dev, sym);
pthread_mutex_unlock(pargs->static_args.gpu_mutex);
} else {
simulate_and_write(simage, NULL, intensities, flags,
image.indexed_cell, 0, sym);
}
}
/* 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 */
cell_free(image.indexed_cell);
done:
free(image.data);
free(image.flags);
image_feature_list_free(image.features);
free(image.cpeaks);
hdfile_close(hdfile);
}
static void *get_image(void *qp)
{
char line[1024];
struct index_args *pargs;
char *rval;
struct queue_args *qargs = qp;
/* Initialise new task arguments */
pargs = malloc(sizeof(struct index_args));
memcpy(&pargs->static_args, &qargs->static_args,
sizeof(struct static_index_args));
/* Get the next filename */
if ( qargs->use_this_one_instead != NULL ) {
pargs->filename = malloc(strlen(qargs->prefix) +
strlen(qargs->use_this_one_instead) + 1);
snprintf(pargs->filename, 1023, "%s%s", qargs->prefix,
qargs->use_this_one_instead);
qargs->use_this_one_instead = NULL;
} else {
rval = fgets(line, 1023, qargs->fh);
if ( rval == NULL ) {
free(pargs);
return NULL;
}
chomp(line);
pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);
snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);
}
return pargs;
}
static void finalise_image(void *qp, void *pp)
{
struct queue_args *qargs = qp;
struct index_args *pargs = pp;
qargs->n_indexable += pargs->indexable;
free(pargs->filename);
free(pargs);
}
int main(int argc, char *argv[])
{
int c;
struct gpu_context *gctx = NULL;
char *filename = NULL;
char *outfile = NULL;
FILE *fh;
FILE *ofh;
char *rval = NULL;
int n_images;
int config_noindex = 0;
int config_dumpfound = 0;
int config_nearbragg = 0;
int config_simulate = 0;
int config_cmfilter = 0;
int config_noisefilter = 0;
int config_gpu = 0;
int config_verbose = 0;
int config_alternate = 0;
int config_polar = 1;
int config_satcorr = 1;
int config_checkprefix = 1;
int config_closer = 1;
int config_insane = 0;
float threshold = 800.0;
float min_gradient = 100000.0;
struct detector *det;
char *geometry = NULL;
IndexingMethod *indm;
IndexingPrivate **ipriv;
int indexer_needs_cell;
int reduction_needs_cell;
char *indm_str = NULL;
UnitCell *cell;
double *intensities = NULL;
unsigned char *flags;
char *intfile = NULL;
char *pdb = NULL;
char *prefix = NULL;
char *speaks = NULL;
char *scellr = NULL;
int cellr;
int peaks;
int nthreads = 1;
int i;
pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
pthread_mutex_t gpu_mutex = PTHREAD_MUTEX_INITIALIZER;
char prepare_line[1024];
char prepare_filename[1024];
struct queue_args qargs;
struct beam_params *beam = NULL;
double nominal_photon_energy;
int gpu_dev = -1;
char *sym = NULL;
/* Long options */
const struct option longopts[] = {
{"help", 0, NULL, 'h'},
{"input", 1, NULL, 'i'},
{"output", 1, NULL, 'o'},
{"gpu", 0, &config_gpu, 1},
{"no-index", 0, &config_noindex, 1},
{"dump-peaks", 0, &config_dumpfound, 1},
{"peaks", 1, NULL, 2},
{"cell-reduction", 1, NULL, 3},
{"near-bragg", 0, &config_nearbragg, 1},
{"indexing", 1, NULL, 'z'},
{"geometry", 1, NULL, 'g'},
{"beam", 1, NULL, 'b'},
{"simulate", 0, &config_simulate, 1},
{"filter-cm", 0, &config_cmfilter, 1},
{"filter-noise", 0, &config_noisefilter, 1},
{"verbose", 0, &config_verbose, 1},
{"alternate", 0, &config_alternate, 1},
{"intensities", 1, NULL, 'q'},
{"symmetry", 1, NULL, 'y'},
{"pdb", 1, NULL, 'p'},
{"prefix", 1, NULL, 'x'},
{"unpolarized", 0, &config_polar, 0},
{"no-sat-corr", 0, &config_satcorr, 0},
{"sat-corr", 0, &config_satcorr, 1}, /* Compat */
{"threshold", 1, NULL, 't'},
{"min-gradient", 1, NULL, 4},
{"no-check-prefix", 0, &config_checkprefix, 0},
{"no-closer-peak", 0, &config_closer, 0},
{"gpu-dev", 1, NULL, 5},
{"insane", 1, &config_insane, 1},
{0, 0, NULL, 0}
};
/* Short options */
while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:y:",
longopts, NULL)) != -1) {
switch (c) {
case 'h' :
show_help(argv[0]);
return 0;
case 'i' :
filename = strdup(optarg);
break;
case 'o' :
outfile = 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 'g' :
geometry = strdup(optarg);
break;
case 't' :
threshold = strtof(optarg, NULL);
break;
case 'y' :
sym = strdup(optarg);
break;
case 'b' :
beam = get_beam_parameters(optarg);
if ( beam == NULL ) {
ERROR("Failed to load beam parameters"
" from '%s'\n", optarg);
return 1;
}
break;
case 2 :
speaks = strdup(optarg);
break;
case 3 :
scellr = strdup(optarg);
break;
case 4 :
min_gradient = strtof(optarg, NULL);
break;
case 5 :
gpu_dev = 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 ( outfile == NULL ) {
outfile = strdup("-");
}
if ( strcmp(outfile, "-") == 0 ) {
ofh = stdout;
} else {
ofh = fopen(outfile, "w");
}
if ( ofh == NULL ) {
ERROR("Failed to open output file '%s'\n", outfile);
return 1;
}
free(outfile);
if ( sym == NULL ) sym = strdup("1");
if ( speaks == NULL ) {
speaks = strdup("zaef");
STATUS("You didn't specify a peak detection method.\n");
STATUS("I'm using 'zaef' for you.\n");
}
if ( strcmp(speaks, "zaef") == 0 ) {
peaks = PEAK_ZAEF;
} else if ( strcmp(speaks, "hdf5") == 0 ) {
peaks = PEAK_HDF5;
} else {
ERROR("Unrecognised peak detection method '%s'\n", speaks);
return 1;
}
free(speaks);
if ( intfile != NULL ) {
ReflItemList *items;
int i;
items = read_reflections(intfile, intensities,
NULL, NULL, NULL);
flags = new_list_flag();
for ( i=0; i<num_items(items); i++ ) {
struct refl_item *it = get_item(items, i);
set_flag(flags, it->h, it->k, it->l, 1);
}
if ( check_symmetry(items, sym) ) {
ERROR("The input reflection list does not appear to"
" have symmetry %s\n", sym);
return 1;
}
delete_items(items);
} else {
intensities = NULL;
flags = NULL;
}
if ( pdb == NULL ) {
pdb = strdup("molecule.pdb");
}
if ( prefix == NULL ) {
prefix = strdup("");
} else {
if ( config_checkprefix ) {
prefix = check_prefix(prefix);
}
}
if ( nthreads == 0 ) {
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 = NULL;
} else {
indm = build_indexer_list(indm_str, &indexer_needs_cell);
if ( indm == NULL ) {
ERROR("Invalid indexer list '%s'\n", indm_str);
return 1;
}
free(indm_str);
}
reduction_needs_cell = 0;
if ( scellr == NULL ) {
STATUS("You didn't specify a cell reduction method, so I'm"
" going to use 'reduce'.\n");
cellr = CELLR_REDUCE;
reduction_needs_cell = 1;
} else if ( strcmp(scellr, "none") == 0 ) {
cellr = CELLR_NONE;
} else if ( strcmp(scellr, "reduce") == 0) {
cellr = CELLR_REDUCE;
reduction_needs_cell = 1;
} else if ( strcmp(scellr, "compare") == 0) {
cellr = CELLR_COMPARE;
reduction_needs_cell = 1;
} else {
ERROR("Unrecognised cell reduction method '%s'\n", scellr);
return 1;
}
free(scellr); /* free(NULL) is OK. */
if ( geometry == NULL ) {
ERROR("You need to specify a geometry file with --geometry\n");
return 1;
}
det = get_detector_geometry(geometry);
if ( det == NULL ) {
ERROR("Failed to read detector geometry from '%s'\n", geometry);
return 1;
}
free(geometry);
if ( reduction_needs_cell || indexer_needs_cell ) {
cell = load_cell_from_pdb(pdb);
if ( cell == NULL ) {
ERROR("Couldn't read unit cell (from %s)\n", pdb);
return 1;
}
} else {
STATUS("No cell needed for these choices of indexing"
" and reduction.\n");
cell = NULL;
}
free(pdb);
/* Start by writing the entire command line to stdout */
fprintf(ofh, "Command line:");
for ( i=0; i<argc; i++ ) {
fprintf(ofh, " %s", argv[i]);
}
fprintf(ofh, "\n");
fflush(ofh);
if ( beam != NULL ) {
nominal_photon_energy = beam->photon_energy;
} else {
STATUS("No beam parameters file was given, so I'm taking the"
" nominal photon energy to be 2 keV.\n");
nominal_photon_energy = 2000.0;
}
/* Get first filename and use it to set up the indexing */
rval = fgets(prepare_line, 1023, fh);
if ( rval == NULL ) {
ERROR("Failed to get filename to prepare indexing.\n");
return 1;
}
chomp(prepare_line);
snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
qargs.use_this_one_instead = prepare_line;
/* Prepare the indexer */
if ( indm != NULL ) {
ipriv = prepare_indexing(indm, cell, prepare_filename, det,
nominal_photon_energy);
if ( ipriv == NULL ) {
ERROR("Failed to prepare indexing.\n");
return 1;
}
} else {
ipriv = NULL;
}
gsl_set_error_handler_off();
qargs.static_args.gpu_mutex = &gpu_mutex;
qargs.static_args.cell = cell;
qargs.static_args.config_cmfilter = config_cmfilter;
qargs.static_args.config_noisefilter = config_noisefilter;
qargs.static_args.config_dumpfound = config_dumpfound;
qargs.static_args.config_verbose = config_verbose;
qargs.static_args.config_alternate = config_alternate;
qargs.static_args.config_nearbragg = config_nearbragg;
qargs.static_args.config_gpu = config_gpu;
qargs.static_args.config_simulate = config_simulate;
qargs.static_args.config_polar = config_polar;
qargs.static_args.config_satcorr = config_satcorr;
qargs.static_args.config_closer = config_closer;
qargs.static_args.config_insane = config_insane;
qargs.static_args.cellr = cellr;
qargs.static_args.threshold = threshold;
qargs.static_args.min_gradient = min_gradient;
qargs.static_args.det = det;
qargs.static_args.indm = indm;
qargs.static_args.ipriv = ipriv;
qargs.static_args.intensities = intensities;
qargs.static_args.flags = flags;
qargs.static_args.sym = sym;
qargs.static_args.gctx = gctx;
qargs.static_args.gpu_dev = gpu_dev;
qargs.static_args.peaks = peaks;
qargs.static_args.output_mutex = &output_mutex;
qargs.static_args.ofh = ofh;
qargs.static_args.nominal_photon_energy = nominal_photon_energy;
qargs.fh = fh;
qargs.prefix = prefix;
qargs.n_indexable = 0;
n_images = run_threads(nthreads, process_image, get_image,
finalise_image, &qargs, 0);
cleanup_indexing(ipriv);
free(indm);
free(ipriv);
free(prefix);
free(det->panels);
free(det);
cell_free(cell);
if ( fh != stdin ) fclose(fh);
if ( ofh != stdout ) fclose(ofh);
free(sym);
STATUS("There were %i images, of which %i could be indexed.\n",
n_images, qargs.n_indexable);
if ( gctx != NULL ) {
cleanup_gpu(gctx);
}
return 0;
}
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