facetron.c 15 KB
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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>
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#include <assert.h>
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#include <pthread.h>
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#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_linalg.h>
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#include "utils.h"
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#include "hdf5-file.h"
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#include "symmetry.h"
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#include "reflections.h"
#include "stream.h"
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#include "geometry.h"
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#include "peaks.h"
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#include "thread-pool.h"
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#include "beam-parameters.h"
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/* Refineable parameters */
enum {
	REF_SCALE,
	NUM_PARAMS
};


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static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
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"Post-refinement and profile fitting for coherent nanocrystallography.\n"
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"\n"
"  -h, --help                 Display this help message.\n"
"\n"
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"  -i, --input=<filename>     Specify the name of the input 'stream'.\n"
"                              (must be a file, not e.g. stdin)\n"
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"  -o, --output=<filename>    Output filename.  Default: facetron.hkl.\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 initial\n"
"                              values for parameters, and nominal wavelengths\n"
"                              if no per-shot value is found in an HDF5 file.\n"
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"  -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"
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"  -y, --symmetry=<sym>       Merge according to symmetry <sym>.\n"
"  -n, --iterations=<n>       Run <n> cycles of post-refinement.\n"
"\n"
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"  -j <n>                     Run <n> analyses in parallel.\n");
}


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struct refine_args
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{
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	const char *sym;
	ReflItemList *obs;
	double *i_full;
	struct image *image;
};


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/* Return the gradient of parameter 'k' given the current status of 'image'. */
static double gradient(struct image *image, int k,
                       struct cpeak spot, double I_partial)
{
	switch ( k ) {

	case REF_SCALE :
		return I_partial;

	}

	ERROR("No gradient defined for parameter %i\n", k);
	abort();
}


/* Apply the given shift to the 'k'th parameter of 'image'. */
static void apply_shift(struct image *image, int k, double shift)
{
	switch ( k ) {

	case REF_SCALE :
		image->osf += shift;
		break;

	default :
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		ERROR("No shift defined for parameter %i\n", k);
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		abort();

	}
}


static double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
                               const char *sym, double *i_full)
{
	int h;
	double delta_I;

	for ( h=0; h<n; h++ ) {

		signed int hind, kind, lind;
		signed int ha, ka, la;
		double I_full;
		float I_partial;
		float xc, yc;

		hind = spots[h].h;
		kind = spots[h].k;
		lind = spots[h].l;

		/* Don't attempt to use spots with very small
		 * partialities, since it won't be accurate. */
		if ( spots[h].p < 0.1 ) continue;

		/* Actual measurement of this reflection from this
		 * pattern? */
		/* FIXME: Coordinates aren't whole numbers */
		if ( integrate_peak(image, spots[h].x, spots[h].y,
		                    &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
			continue;
		}

		get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
		I_full = lookup_intensity(i_full, ha, ka, la);
		delta_I += I_partial - spots[h].p * I_full;

	}

	return delta_I / (double)n;
}


static double iterate(struct image *image, double *i_full, const char *sym,
                      struct cpeak *spots, int n)
{
	gsl_matrix *M;
	gsl_vector *v;
	gsl_vector *shifts;
	int h, shift;

	M = gsl_matrix_alloc(NUM_PARAMS, NUM_PARAMS);
	v = gsl_vector_alloc(NUM_PARAMS);

	/* Construct the equations, one per reflection in this image */
	for ( h=0; h<n; h++ ) {

		signed int hind, kind, lind;
		signed int ha, ka, la;
		double I_full, delta_I;
		float I_partial;
		float xc, yc;
		int k;

		hind = spots[h].h;
		kind = spots[h].k;
		lind = spots[h].l;

		/* Don't attempt to use spots with very small
		 * partialities, since it won't be accurate. */
		if ( spots[h].p < 0.1 ) continue;

		/* Actual measurement of this reflection from this
		 * pattern? */
		/* FIXME: Coordinates aren't whole numbers */
		if ( integrate_peak(image, spots[h].x, spots[h].y,
		                    &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
			continue;
		}

		get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
		I_full = lookup_intensity(i_full, ha, ka, la);
		delta_I = I_partial - spots[h].p * I_full;

		for ( k=0; k<NUM_PARAMS; k++ ) {

			int g;
			double v_c;

			for ( g=0; g<NUM_PARAMS; g++ ) {

				double M_curr, M_c;

				M_curr = gsl_matrix_get(M, g, k);

				M_c = gradient(image, g, spots[h], I_partial)
				    * gradient(image, k, spots[h], I_partial);
				M_c *= pow(I_full, 2.0);

				gsl_matrix_set(M, g, k, M_curr + M_c);

			}

			v_c = delta_I * I_full * gradient(image, k, spots[h],
			                                  I_partial);
			gsl_vector_set(v, k, v_c);

		}

	}

	shifts = gsl_vector_alloc(NUM_PARAMS);
	gsl_linalg_HH_solve(M, v, shifts);
	for ( shift=0; shift<NUM_PARAMS; shift++ ) {
		apply_shift(image, shift, gsl_vector_get(shifts, shift));
	}

	free(spots);
	spots = find_intersections(image, image->indexed_cell, &n, 0);
	return mean_partial_dev(image, spots, n, sym, i_full);
}


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static void refine_image(int mytask, void *tasks)
{
	struct refine_args *all_args = tasks;
	struct refine_args *pargs = &all_args[mytask];
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	struct image *image = pargs->image;
	double nominal_photon_energy = pargs->image->beam->photon_energy;
	struct hdfile *hdfile;
	struct cpeak *spots;
	int n;
	double dev;

	hdfile = hdfile_open(image->filename);
	if ( hdfile == NULL ) {
		ERROR("Couldn't open '%s'\n", image->filename);
		return;
	} else if ( hdfile_set_image(hdfile, "/data/data0") ) {
		ERROR("Couldn't select path\n");
		hdfile_close(hdfile);
		return;
	}

	if ( hdf5_read(hdfile, pargs->image, 0, nominal_photon_energy) ) {
		ERROR("Couldn't read '%s'\n", image->filename);
		hdfile_close(hdfile);
		return;
	}

	spots = find_intersections(image, image->indexed_cell, &n, 0);
	dev = iterate(image, pargs->i_full, pargs->sym, spots, n);
	STATUS("Iteration %2i: mean dev = %5.2f\n", 0, dev);

	free(image->data);
	if ( image->flags != NULL ) free(image->flags);
	hdfile_close(hdfile);

	/* Muppet proofing */
	image->data = NULL;
	image->flags = NULL;
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}


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struct integrate_args
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{
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	const char *sym;
	ReflItemList *obs;
	double *i_full;
	unsigned int *cts;
	pthread_mutex_t *list_lock;
	struct image *image;
};


static void integrate_image(int mytask, void *tasks)
{
	struct integrate_args *all_args = tasks;
	struct integrate_args *pargs = &all_args[mytask];
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	struct cpeak *spots;
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	int j, n;
	struct hdfile *hdfile;
	struct image *image = pargs->image;
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	double nominal_photon_energy = pargs->image->beam->photon_energy;
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	hdfile = hdfile_open(image->filename);
	if ( hdfile == NULL ) {
		ERROR("Couldn't open '%s'\n", image->filename);
		return;
	} else if ( hdfile_set_image(hdfile, "/data/data0") ) {
		ERROR("Couldn't select path\n");
		hdfile_close(hdfile);
		return;
	}

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	if ( hdf5_read(hdfile, pargs->image, 0, nominal_photon_energy) ) {
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		ERROR("Couldn't read '%s'\n", image->filename);
		hdfile_close(hdfile);
		return;
	}

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	/* Figure out which spots should appear in this pattern */
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	spots = find_intersections(image, image->indexed_cell, &n, 1);
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	/* For each reflection, estimate the partiality */
	for ( j=0; j<n; j++ ) {

		signed int h, k, l;
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		signed int ha, ka, la;
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		float i_partial;
		float xc, yc;
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		float i_full_est;
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		h = spots[j].h;
		k = spots[j].k;
		l = spots[j].l;

		/* Don't attempt to use spots with very small
		 * partialities, since it won't be accurate. */
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		if ( spots[j].p < 0.1 ) continue;
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		/* Actual measurement of this reflection from this
		 * pattern? */
		/* FIXME: Coordinates aren't whole numbers */
		if ( integrate_peak(image, spots[j].x, spots[j].y,
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		                    &xc, &yc, &i_partial, NULL, NULL, 1, 1) ) {
			continue;
		}
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		i_full_est = i_partial / spots[j].p;
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		get_asymm(h, k, l, &ha, &ka, &la, pargs->sym);

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		pthread_mutex_lock(pargs->list_lock);
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		integrate_intensity(pargs->i_full, ha, ka, la, i_full_est);
		integrate_count(pargs->cts, ha, ka, la, 1);
		if ( !find_item(pargs->obs, ha, ka, la) ) {
			add_item(pargs->obs, ha, ka, la);
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		}
		pthread_mutex_unlock(pargs->list_lock);

	}

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	free(image->data);
	if ( image->flags != NULL ) free(image->flags);
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	hdfile_close(hdfile);
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	free(spots);

	/* Muppet proofing */
	image->data = NULL;
	image->flags = NULL;
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}


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static void refine_all(struct image *images, int n_total_patterns,
                       struct detector *det, const char *sym,
                       ReflItemList *obs, double *i_full, int nthreads)
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{
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	struct refine_args *tasks;
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	int i;
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	tasks = malloc(n_total_patterns * sizeof(struct refine_args));
	for ( i=0; i<n_total_patterns; i++ ) {
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		tasks[i].sym = sym;
		tasks[i].obs = obs;
		tasks[i].i_full = i_full;
		tasks[i].image = &images[i];
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	}

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	run_thread_range(n_total_patterns, nthreads, "Refining",
	                 refine_image, tasks);
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	free(tasks);
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}


static void estimate_full(struct image *images, int n_total_patterns,
                          struct detector *det, const char *sym,
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                          ReflItemList *obs, double *i_full, unsigned int *cts,
                          int nthreads)
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{
	int i;
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	struct integrate_args *tasks;
	pthread_mutex_t list_lock = PTHREAD_MUTEX_INITIALIZER;
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	clear_items(obs);
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	tasks = malloc(n_total_patterns * sizeof(struct integrate_args));
	for ( i=0; i<n_total_patterns; i++ ) {

		tasks[i].sym = sym;
		tasks[i].obs = obs;
		tasks[i].i_full = i_full;
		tasks[i].cts = cts;
		tasks[i].list_lock = &list_lock;
		tasks[i].image = &images[i];

	}

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	run_thread_range(n_total_patterns, nthreads, "Integrating",
	                 integrate_image, tasks);
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	free(tasks);
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	/* Divide the totals to get the means */
	for ( i=0; i<num_items(obs); i++ ) {
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		struct refl_item *it;
		double total;
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		it = get_item(obs, i);
		total = lookup_intensity(i_full, it->h, it->k, it->l);
		total /= lookup_count(cts, it->h, it->k, it->l);
		set_intensity(i_full, it->h, it->k, it->l, total);
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	}
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}
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int main(int argc, char *argv[])
{
	int c;
	char *infile = NULL;
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	char *outfile = NULL;
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	char *geomfile = NULL;
	char *prefix = NULL;
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	char *sym = NULL;
	FILE *fh;
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	int nthreads = 1;
	int config_basename = 0;
	int config_checkprefix = 1;
	struct detector *det;
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	double *i_full;
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	unsigned int *cts;
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	ReflItemList *obs;
	int i;
	int n_total_patterns;
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	struct image *images;
	int n_iter = 10;
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	struct beam_params *beam = NULL;
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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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		{"geometry",           1, NULL,               'g'},
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		{"beam",               1, NULL,               'b'},
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		{"prefix",             1, NULL,               'x'},
		{"basename",           0, &config_basename,    1},
		{"no-check-prefix",    0, &config_checkprefix, 0},
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		{"symmetry",           1, NULL,               'y'},
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		{"iterations",         1, NULL,               'n'},
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		{0, 0, NULL, 0}
	};

	/* Short options */
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	while ((c = getopt_long(argc, argv, "hi:g:x:j:y:o:b:",
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	                        longopts, NULL)) != -1)
	{
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		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;

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		case 'y' :
			sym = strdup(optarg);
			break;

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

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		case 'n' :
			n_iter = atoi(optarg);
			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 0 :
			break;

		default :
			return 1;
		}

	}

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	/* Sanitise input filename and open */
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	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);

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	/* Sanitise output filename */
	if ( outfile == NULL ) {
		outfile = strdup("facetron.hkl");
	}

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

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	if ( sym == NULL ) sym = strdup("1");

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	/* Get detector geometry */
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	det = get_detector_geometry(geomfile);
	if ( det == NULL ) {
		ERROR("Failed to read detector geometry from '%s'\n", geomfile);
		return 1;
	}
	free(geomfile);

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	if ( beam == NULL ) {
		ERROR("You must provide a beam parameters file.\n");
		return 1;
	}

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	/* 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);

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	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;
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		char *fnamereal;
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		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;
		}
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		fnamereal = malloc(1024);
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		snprintf(fnamereal, 1023, "%s%s", prefix, filename);

		images[i].filename = fnamereal;
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		images[i].div = beam->divergence;
		images[i].bw = beam->bandwidth;
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		images[i].det = det;
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		images[i].beam = beam;
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		images[i].osf = 1.0;
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		/* Muppet proofing */
		images[i].data = NULL;
		images[i].flags = NULL;

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		free(filename);

		progress_bar(i, n_total_patterns-1, "Loading pattern data");

	}
	fclose(fh);
	free(prefix);

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	cts = new_list_count();

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	/* Make initial estimates */
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	estimate_full(images, n_total_patterns, det, sym, obs, i_full, cts,
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	              nthreads);
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	/* Iterate */
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	for ( i=0; i<n_iter; i++ ) {
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		STATUS("Post refinement iteration %i of %i\n", i+1, n_iter);
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		/* Refine the geometry of all patterns to get the best fit */
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		refine_all(images, n_total_patterns, det, sym, obs, i_full,
		           nthreads);
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		/* Re-estimate all the full intensities */
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		estimate_full(images, n_total_patterns, det, sym, obs, i_full,
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		              cts, nthreads);
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	}

	/* Output results */
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	write_reflections(outfile, obs, i_full, NULL, NULL, cts, NULL);
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	/* Clean up */
	free(i_full);
	delete_items(obs);
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	free(sym);
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	free(outfile);
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	free(det->panels);
	free(det);
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	free(beam);
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	free(cts);
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	for ( i=0; i<n_total_patterns; i++ ) {
		cell_free(images[i].indexed_cell);
		free(images[i].filename);
	}
	free(images);
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	return 0;
}