indexamajig.c 20.3 KB
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/*
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 * indexamajig.c
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 *
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 * Index patterns, output hkl+intensity etc.
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 *
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 * (c) 2006-2011 Thomas White <taw@physics.org>
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 *
 * 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>
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#include <hdf5.h>
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#include <gsl/gsl_errno.h>
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#include <pthread.h>
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#include <sys/time.h>
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#include "utils.h"
#include "hdf5-file.h"
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#include "index.h"
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#include "peaks.h"
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#include "detector.h"
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#include "sfac.h"
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#include "filters.h"
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#include "reflections.h"
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#include "thread-pool.h"
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#include "beam-parameters.h"
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#include "geometry.h"
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#include "stream.h"
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enum {
	PEAK_ZAEF,
	PEAK_HDF5,
};


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/* Information about the indexing process which is common to all patterns */
struct static_index_args
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{
	UnitCell *cell;
	int config_cmfilter;
	int config_noisefilter;
	int config_verbose;
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	int stream_flags;
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	int config_polar;
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	int config_satcorr;
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	int config_closer;
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	int config_insane;
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	float threshold;
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	float min_gradient;
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	struct detector *det;
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	IndexingMethod *indm;
	IndexingPrivate **ipriv;
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	int peaks;
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	int cellr;
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	struct beam_params *beam;
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	const char *element;
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	/* Output stream */
	pthread_mutex_t *output_mutex;  /* Protects the output stream */
	FILE *ofh;
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};


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/* 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;
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	int config_basename;
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	struct static_index_args static_args;

	int n_indexable;
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	char *use_this_one_instead;
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};


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static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Process and index FEL diffraction images.\n"
"\n"
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" -h, --help               Display this help message.\n"
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"\n"
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" -i, --input=<filename>   Specify file containing list of images to process.\n"
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"                           '-' means stdin, which is the default.\n"
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" -o, --output=<filename>  Write output stream to this file. '-' for stdout.\n"
"                           Default: indexamajig.stream\n"
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"\n"
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"     --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"
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" -g. --geometry=<file>    Get detector geometry from file.\n"
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" -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"
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" -p, --pdb=<file>         PDB file from which to get the unit cell to match.\n"
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"                           Default: 'molecule.pdb'.\n"
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"     --basename           Remove the directory parts of the filenames.\n"
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" -x, --prefix=<p>         Prefix filenames from input file with <p>.\n"
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"     --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"
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"\n\n"
"You can control what information is included in the output stream using\n"
"' --record=<flags>'.  Possible flags are:\n"
"pixels         Include a list of sums of pixel values within the\n"
"                integration domain, correcting for individual pixel\n"
"                solid angles.\n"
"integrated     Include a list of reflection intensities, produced by\n"
"                integrating around predicted peak locations.\n"
"                The flags 'pixels' and 'integrated' are mutually exclusive.\n"
"peaks          Include peak locations and intensities from the peak search.\n"
"peaksifindexed Include peak locations only if the pattern could be indexed.\n"
"\n\n"
"For more control over the process, you might need:\n\n"
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"     --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"
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"     --filter-cm          Perform common-mode noise subtraction on images\n"
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"                           before proceeding.  Intensities will be extracted\n"
"                           from the image as it is after this processing.\n"
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"     --filter-noise       Apply an aggressive noise filter which sets all\n"
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"                           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"
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"     --unpolarized        Don't correct for the polarisation of the X-rays.\n"
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"     --no-sat-corr        Don't correct values of saturated peaks using a\n"
"                           table included in the HDF5 file.\n"
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"     --threshold=<n>      Only accept peaks above <n> ADU.  Default: 800.\n"
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"     --min-gradient=<n>   Minimum gradient for Zaefferer peak search.\n"
"                           Default: 100,000.\n"
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" -e, --image=<element>    Use this image from the HDF5 file.\n"
"                           Example: /data/data0."
"                           Default: The first one found.\n"
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"\n"
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"\nOptions for greater performance or verbosity:\n\n"
"     --verbose            Be verbose about indexing.\n"
" -j <n>                   Run <n> analyses in parallel.  Default 1.\n"
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"\n"
"\nOptions you probably won't need:\n\n"
"     --no-check-prefix    Don't attempt to correct the --prefix.\n"
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"     --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"
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"     --insane             Don't check that the reduced cell accounts for at\n"
"                           least 10%% of the located peaks.\n"
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);
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}


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static void process_image(void *pp, int cookie)
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{
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	struct index_args *pargs = pp;
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	struct hdfile *hdfile;
	struct image image;
	float *data_for_measurement;
	size_t data_size;
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	char *filename = pargs->filename;
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	UnitCell *cell = pargs->static_args.cell;
	int config_cmfilter = pargs->static_args.config_cmfilter;
	int config_noisefilter = pargs->static_args.config_noisefilter;
	int config_verbose = pargs->static_args.config_verbose;
	int config_polar = pargs->static_args.config_polar;
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	IndexingMethod *indm = pargs->static_args.indm;
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	const struct beam_params *beam = pargs->static_args.beam;
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	image.features = NULL;
	image.data = NULL;
	image.indexed_cell = NULL;
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	image.id = cookie;
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	image.filename = filename;
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	image.det = copy_geom(pargs->static_args.det);
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	STATUS("Processing '%s'\n", image.filename);
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	pargs->indexable = 0;
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	hdfile = hdfile_open(filename);
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	if ( hdfile == NULL ) return;

	if ( pargs->static_args.element != NULL ) {

		int r;
		r = hdfile_set_image(hdfile, pargs->static_args.element);
		if ( r ) {
			ERROR("Couldn't select path '%s'\n",
			      pargs->static_args.element);
			hdfile_close(hdfile);
			return;
		}

	} else {

		int r;
		r = hdfile_set_first_image(hdfile, "/");
		if ( r ) {
			ERROR("Couldn't select first path\n");
			hdfile_close(hdfile);
			return;
		}

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	}

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	hdf5_read(hdfile, &image, pargs->static_args.config_satcorr);
	if ( image.lambda < 0.0 ) {
		if ( beam != NULL ) {
			image.lambda = beam->photon_energy;
		} else {
			ERROR("No wavelength in file, so you need to give "
			      "a beam parameters file with -b.\n");
			hdfile_close(hdfile);
			return;
		}
	}
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	fill_in_values(image.det, hdfile);
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	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 {
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		memcpy(data_for_measurement, image.data, data_size);
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	}

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	switch ( pargs->static_args.peaks )
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	{
	case PEAK_HDF5 :
		/* Get peaks from HDF5 */
		if ( get_peaks(&image, hdfile) ) {
			ERROR("Failed to get peaks from HDF5 file.\n");
		}
		break;
	case PEAK_ZAEF :
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		search_peaks(&image, pargs->static_args.threshold,
		             pargs->static_args.min_gradient);
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		break;
	}
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	/* 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;

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	/* Calculate orientation matrix (by magic) */
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	index_pattern(&image, cell, indm, pargs->static_args.cellr,
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		      config_verbose, pargs->static_args.ipriv,
		      pargs->static_args.config_insane);
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	/* No cell at this point?  Then we're done. */
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	if ( image.indexed_cell != NULL ) pargs->indexable = 1;
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	/* Measure intensities if requested */
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	/* Do EITHER: */
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	//image.div = beam->divergence;
	//image.bw = beam->bandwidth;
	//image.profile_radius = 0.0001e9;
	//image.reflections = find_intersections(&image,
	//                                       image.indexed_cell, 0);
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	image.reflections = find_projected_peaks(&image,
	                                         image.indexed_cell,
	                                         0, 0.1);
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	integrate_reflections(&image, config_polar,
	                      pargs->static_args.config_closer);
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	/* OR */
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	//image.reflections = integrate_pixels(&image, 0, 0.1,
	//                                     config_polar);

	pthread_mutex_lock(pargs->static_args.output_mutex);
	write_chunk(pargs->static_args.ofh, &image,
	            pargs->static_args.stream_flags);
	pthread_mutex_unlock(pargs->static_args.output_mutex);
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	/* Only free cell if found */
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	cell_free(image.indexed_cell);
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	free(image.data);
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	free(image.flags);
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	image_feature_list_free(image.features);
	hdfile_close(hdfile);
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	free_detector_geometry(image.det);
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}


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static void *get_image(void *qp)
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{
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	char *line;
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	struct index_args *pargs;
	char *rval;
	struct queue_args *qargs = qp;
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	/* Initialise new task arguments */
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	pargs = malloc(sizeof(struct index_args));
	memcpy(&pargs->static_args, &qargs->static_args,
	       sizeof(struct static_index_args));
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	/* Get the next filename */
	if ( qargs->use_this_one_instead != NULL ) {

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		line = qargs->use_this_one_instead;
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		qargs->use_this_one_instead = NULL;

	} else {

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		line = malloc(1024*sizeof(char));
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		rval = fgets(line, 1023, qargs->fh);
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		if ( rval == NULL ) {
			free(pargs);
			return NULL;
		}
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		chomp(line);

	}
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	if ( qargs->config_basename ) {
		char *tmp;
		tmp = safe_basename(line);
		free(line);
		line = tmp;
	}

	pargs->filename = malloc(strlen(qargs->prefix)+strlen(line)+1);

	snprintf(pargs->filename, 1023, "%s%s", qargs->prefix, line);

	free(line);

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	return pargs;
}
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static void finalise_image(void *qp, void *pp)
{
	struct queue_args *qargs = qp;
	struct index_args *pargs = pp;
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	qargs->n_indexable += pargs->indexable;
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	free(pargs->filename);
	free(pargs);
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}


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int main(int argc, char *argv[])
{
	int c;
	char *filename = NULL;
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	char *outfile = NULL;
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	FILE *fh;
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	FILE *ofh;
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	char *rval = NULL;
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	int n_images;
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	int config_noindex = 0;
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	int config_dumpfound = 0;
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	int config_nearbragg = 0;
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	int config_cmfilter = 0;
	int config_noisefilter = 0;
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	int config_verbose = 0;
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	int config_polar = 1;
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	int config_satcorr = 1;
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	int config_checkprefix = 1;
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	int config_closer = 1;
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	int config_insane = 0;
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	int config_basename = 0;
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	float threshold = 800.0;
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	float min_gradient = 100000.0;
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	struct detector *det;
	char *geometry = NULL;
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	IndexingMethod *indm;
	IndexingPrivate **ipriv;
	int indexer_needs_cell;
	int reduction_needs_cell;
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	char *indm_str = NULL;
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	UnitCell *cell;
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	char *pdb = NULL;
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	char *prefix = NULL;
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	char *speaks = NULL;
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	char *scellr = NULL;
	int cellr;
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	int peaks;
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	int nthreads = 1;
	int i;
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	pthread_mutex_t output_mutex = PTHREAD_MUTEX_INITIALIZER;
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	char *prepare_line;
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	char prepare_filename[1024];
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	struct queue_args qargs;
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	struct beam_params *beam = NULL;
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	char *element = NULL;
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	double nominal_photon_energy;
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	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"input",              1, NULL,               'i'},
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		{"output",             1, NULL,               'o'},
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		{"no-index",           0, &config_noindex,     1},
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		{"dump-peaks",         0, &config_dumpfound,   1},
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		{"peaks",              1, NULL,                2},
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		{"cell-reduction",     1, NULL,                3},
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		{"near-bragg",         0, &config_nearbragg,   1},
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		{"indexing",           1, NULL,               'z'},
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		{"geometry",           1, NULL,               'g'},
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		{"beam",               1, NULL,               'b'},
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		{"filter-cm",          0, &config_cmfilter,    1},
		{"filter-noise",       0, &config_noisefilter, 1},
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		{"verbose",            0, &config_verbose,     1},
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		{"pdb",                1, NULL,               'p'},
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		{"prefix",             1, NULL,               'x'},
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		{"unpolarized",        0, &config_polar,       0},
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		{"no-sat-corr",        0, &config_satcorr,     0},
		{"sat-corr",           0, &config_satcorr,     1}, /* Compat */
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		{"threshold",          1, NULL,               't'},
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		{"min-gradient",       1, NULL,                4},
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		{"no-check-prefix",    0, &config_checkprefix, 0},
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		{"no-closer-peak",     0, &config_closer,      0},
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		{"insane",             0, &config_insane,      1},
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		{"image",              1, NULL,               'e'},
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		{"basename",           0, &config_basename,    1},
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		{0, 0, NULL, 0}
	};

	/* Short options */
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	while ((c = getopt_long(argc, argv, "hi:wp:j:x:g:t:o:b:e:",
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	                        longopts, NULL)) != -1) {
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		switch (c) {
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		case 'h' :
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			show_help(argv[0]);
			return 0;

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		case 'i' :
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			filename = strdup(optarg);
			break;

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		case 'o' :
			outfile = strdup(optarg);
			break;

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		case 'z' :
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			indm_str = strdup(optarg);
			break;

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		case 'p' :
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			pdb = strdup(optarg);
			break;

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		case 'x' :
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			prefix = strdup(optarg);
			break;

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		case 'j' :
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			nthreads = atoi(optarg);
			break;

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		case 'g' :
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			geometry = strdup(optarg);
			break;

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		case 't' :
			threshold = strtof(optarg, NULL);
			break;

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		case 'b' :
			beam = get_beam_parameters(optarg);
			if ( beam == NULL ) {
				ERROR("Failed to load beam parameters"
				      " from '%s'\n", optarg);
				return 1;
			}
			break;

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		case 2 :
			speaks = strdup(optarg);
			break;

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		case 3 :
			scellr = strdup(optarg);
			break;

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		case 4 :
			min_gradient = strtof(optarg, NULL);
			break;

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		case 'e' :
			element = strdup(optarg);
			break;

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		case 0 :
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			break;

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		default :
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			return 1;
		}

	}

	if ( filename == NULL ) {
		filename = strdup("-");
	}
	if ( strcmp(filename, "-") == 0 ) {
		fh = stdin;
	} else {
		fh = fopen(filename, "r");
	}
	if ( fh == NULL ) {
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		ERROR("Failed to open input file '%s'\n", filename);
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		return 1;
	}
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	free(filename);
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	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);

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	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;
	}
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	free(speaks);
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	if ( pdb == NULL ) {
		pdb = strdup("molecule.pdb");
	}

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	if ( prefix == NULL ) {
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		prefix = strdup("");
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	} else {
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		if ( config_checkprefix ) {
			prefix = check_prefix(prefix);
		}
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	}

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	if ( nthreads == 0 ) {
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		ERROR("Invalid number of threads.\n");
		return 1;
	}

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	if ( (indm_str == NULL) ||
	     ((indm_str != NULL) && (strcmp(indm_str, "none") == 0)) ) {
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		STATUS("Not indexing anything.\n");
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		indexer_needs_cell = 0;
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		reduction_needs_cell = 0;
		indm = NULL;
		cellr = CELLR_NONE;
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	} else {
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		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;
			indexer_needs_cell = 0;
		} 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);
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		}
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		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. */
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	}

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	/* No indexing -> no reduction */
	if ( indm == NULL ) reduction_needs_cell = 0;

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	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);

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	if ( reduction_needs_cell || indexer_needs_cell ) {
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		cell = load_cell_from_pdb(pdb);
		if ( cell == NULL ) {
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			ERROR("Couldn't read unit cell (from %s)\n", pdb);
			return 1;
		}
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	} else {
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		STATUS("No cell needed for these choices of indexing"
		       " and reduction.\n");
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		cell = NULL;
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	}
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	free(pdb);
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	/* Start by writing the entire command line to stdout */
	fprintf(ofh, "Command line:");
	for ( i=0; i<argc; i++ ) {
		fprintf(ofh, " %s", argv[i]);
	}
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	fprintf(ofh, "\n");
	fflush(ofh);
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	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;
	}

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	/* Get first filename and use it to set up the indexing */
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	prepare_line = malloc(1024*sizeof(char));
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	rval = fgets(prepare_line, 1023, fh);
	if ( rval == NULL ) {
		ERROR("Failed to get filename to prepare indexing.\n");
		return 1;
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	}
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	chomp(prepare_line);
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	if ( config_basename ) {
		char *tmp;
		tmp = safe_basename(prepare_line);
		free(prepare_line);
		prepare_line = tmp;
	}
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	snprintf(prepare_filename, 1023, "%s%s", prefix, prepare_line);
	qargs.use_this_one_instead = prepare_line;

	/* Prepare the indexer */
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	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;
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	}

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	gsl_set_error_handler_off();
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	qargs.static_args.cell = cell;
	qargs.static_args.config_cmfilter = config_cmfilter;
	qargs.static_args.config_noisefilter = config_noisefilter;
	qargs.static_args.config_verbose = config_verbose;
	qargs.static_args.config_polar = config_polar;
	qargs.static_args.config_satcorr = config_satcorr;
	qargs.static_args.config_closer = config_closer;
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	qargs.static_args.config_insane = config_insane;
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	qargs.static_args.cellr = cellr;
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	qargs.static_args.threshold = threshold;
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	qargs.static_args.min_gradient = min_gradient;
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	qargs.static_args.det = det;
	qargs.static_args.indm = indm;
	qargs.static_args.ipriv = ipriv;
	qargs.static_args.peaks = peaks;
	qargs.static_args.output_mutex = &output_mutex;
	qargs.static_args.ofh = ofh;
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	qargs.static_args.beam = beam;
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	qargs.static_args.element = element;
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	qargs.fh = fh;
	qargs.prefix = prefix;
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	qargs.config_basename = config_basename;
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	qargs.n_indexable = 0;

	n_images = run_threads(nthreads, process_image, get_image,
	                       finalise_image, &qargs, 0);
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	cleanup_indexing(ipriv);

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	free(indm);
	free(ipriv);
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	free(prefix);
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	free(det->panels);
	free(det);
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	free(element);
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	cell_free(cell);
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	if ( fh != stdin ) fclose(fh);
	if ( ofh != stdout ) fclose(ofh);
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	STATUS("There were %i images, of which %i could be indexed.\n",
	        n_images, qargs.n_indexable);
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	return 0;
}