get_hkl.c 10.5 KB
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/*
 * get_hkl.c
 *
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 * Small program to manipulate reflection lists
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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>

#include "utils.h"
#include "reflections.h"
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#include "symmetry.h"
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#include "beam-parameters.h"
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static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
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"Manipulate reflection lists.\n"
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"\n"
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"  -h, --help                 Display this help message.\n"
"\n"
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"  -i, --input=<file>         Read reflections from <file>.\n"
"  -y, --symmetry=<sym>       The symmetry of the input reflection list.\n"
"\n"
"You can add noise to the reflections with either of:\n"
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"      --poisson              Simulate Poisson samples.\n"
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"      --noise                Add 10%% random noise.\n"
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"\n"
"To calculate Poisson samples accurately, you must also give:\n"
"  -b, --beam=<file>          Get beam parameters from file.\n"
"\n"
"You can artificially 'twin' the reflections, or expand them out:\n"
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"  -w, --twin=<sym>           Generate twinned data according to the given\n"
"                              point group.\n"
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"  -e, --expand=<sym>         Expand reflections to this point group.\n"
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"\n"
"You can restrict which reflections are written out:\n"
"  -t, --template=<filename>  Only include reflections mentioned in file.\n"
"\n"
"You might sometimes need to do this:\n"
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"      --multiplicity         Multiply intensities by the number of\n"
"                              equivalent reflections.\n"
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"\n"
"Don't forget to specify the output filename:\n"
"  -o, --output=<filename>    Output filename (default: stdout).\n"
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);
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}


/* Apply Poisson noise to all reflections */
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static void poisson_reflections(double *ref, ReflItemList *items,
                                double adu_per_photon)
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{
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	int i;
	const int n = num_items(items);
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	for ( i=0; i<n; i++ ) {
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		struct refl_item *it;
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		double val;
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		int c;
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		it = get_item(items, i);

		val = lookup_intensity(ref, it->h, it->k, it->l);
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		c = adu_per_photon * poisson_noise(val/adu_per_photon);
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		set_intensity(ref, it->h, it->k, it->l, c);

		progress_bar(i, n-1, "Simulating noise");
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	}
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}


/* Apply 10% uniform noise to all reflections */
static void noise_reflections(double *ref, ReflItemList *items)
{
	int i;
	const int n = num_items(items);

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

		struct refl_item *it;
		double val;
		double r;

		it = get_item(items, i);

		val = lookup_intensity(ref, it->h, it->k, it->l);

		r = (double)random()/RAND_MAX;
		val += 0.1 * val * r;

		set_intensity(ref, it->h, it->k, it->l, val);

		progress_bar(i, n-1, "Simulating noise");

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	}
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}


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static ReflItemList *twin_reflections(double *ref, ReflItemList *items,
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                                      const char *holo, const char *mero,
                                      double *esds)
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{
	int i;
	ReflItemList *new;

	new = new_items();

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	if ( num_general_equivs(holo) < num_general_equivs(mero) ) {
		ERROR("%s is not a subgroup of %s!\n", mero, holo);
		return NULL;
	}

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	for ( i=0; i<num_items(items); i++ ) {

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		double total, sigma;
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		struct refl_item *it;
		signed int h, k, l;
		int n, j;
		int skip;

		it = get_item(items, i);

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		/* There is a many-to-one correspondence between reflections
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		 * in the merohedral and holohedral groups.  Do the calculation
		 * only once for each reflection in the holohedral group, which
		 * contains fewer reflections.
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		 */
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		get_asymm(it->h, it->k, it->l, &h, &k, &l, holo);
		if ( find_item(new, h, k, l) ) continue;
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		n = num_equivs(h, k, l, holo);

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		total = 0.0;
		sigma = 0.0;
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		skip = 0;
		for ( j=0; j<n; j++ ) {

			signed int he, ke, le;
			signed int hu, ku, lu;

			get_equiv(h, k, l, &he, &ke, &le, holo, j);

			/* Do we have this reflection?
			 * We might not have the particular (merohedral)
			 * equivalent which belongs to our definition of the
			 * asymmetric unit cell, so check them all.
			 */
			if ( !find_unique_equiv(items, he, ke, le, mero,
			                        &hu, &ku, &lu) ) {
				/* Don't have this reflection, so bail out */
				ERROR("Twinning %i %i %i requires the %i %i %i "
				      "reflection (or an equivalent in %s), "
				      "which I don't have. %i %i %i won't "
				      "appear in the output\n",
				      h, k, l, he, ke, le, mero, h, k, l);
				skip = 1;
				break;
			}

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			total += lookup_intensity(ref, hu, ku, lu);
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			sigma += pow(lookup_sigma(esds, hu, ku, lu), 2.0);
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		}

		if ( !skip ) {

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			set_intensity(ref, h, k, l, total);
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			set_sigma(esds, h, k, l, sqrt(sigma));
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			add_item(new, h, k, l);

		}

	}

	return new;
}


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static ReflItemList *expand_reflections(double *ref, ReflItemList *items,
                                        const char *target, const char *initial)
{
	int i;
	ReflItemList *new;

	new = new_items();

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	if ( num_general_equivs(target) > num_general_equivs(initial) ) {
		ERROR("%s is not a subgroup of %s!\n", initial, target);
		return NULL;
	}

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	for ( i=0; i<num_items(items); i++ ) {

		struct refl_item *it;
		signed int h, k, l;
		signed int hd, kd, ld;
		int n, j;
		double intensity;

		it = get_item(items, i);
		h = it->h;  k = it->k;  l = it->l;

		/* Actually we don't really care what the equivalent is,
		 * we just want to be sure that there is nly be one version of
		 * this reflection. */
		find_unique_equiv(items, h, k, l, initial, &hd, &kd, &ld);

		/* Now find out how many reflections need to be filled in */
		n = num_equivs(h, k, l, initial);
		intensity = lookup_intensity(ref, h, k, l);

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

			signed int he, ke, le;

			/* Get the equivalent */
			get_equiv(h, k, l, &he, &ke, &le, initial, j);

			/* Put it into the asymmetric unit for the target */
			get_asymm(he, ke, le, &he, &ke, &le, target);

			/* Make sure the intensity is in the right place */
			set_intensity(ref, he, ke, le, intensity);

			/* Add the reflection, but only once */
			if ( !find_item(new, he, ke, le) ) {
				add_item(new, he, ke, le);
			}

		}

	}

	return new;
}


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int main(int argc, char *argv[])
{
	int c;
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	double *input_ref;
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	double *phases;
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	double *esds;
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	char *template = NULL;
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	int config_noise = 0;
	int config_poisson = 0;
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	int config_nophase = 0;
	int config_multi = 0;
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	char *holo = NULL;
	char *mero = NULL;
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	char *expand = NULL;
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	char *output = NULL;
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	char *input = NULL;
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	char *filename = NULL;
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	ReflItemList *input_items;
	ReflItemList *write_items;
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	UnitCell *cell = NULL;
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	char *beamfile = NULL;
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	struct beam_params *beam = NULL;
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	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
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		{"template",           1, NULL,               't'},
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		{"poisson",            0, &config_poisson,     1},
		{"noise",              0, &config_noise,       1},
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		{"output",             1, NULL,               'o'},
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		{"symmetry",           1, NULL,               'y'},
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		{"twin",               1, NULL,               'w'},
		{"expand",             1, NULL,               'e'},
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		{"intensities",        1, NULL,               'i'},
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		{"multiplicity",       0, &config_multi,       1},
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		{"beam",               1, NULL,               'b'},
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		{0, 0, NULL, 0}
	};

	/* Short options */
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	while ((c = getopt_long(argc, argv, "ht:o:i:w:y:e:b:",
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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 't' :
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			template = strdup(optarg);
			break;

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

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

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

		case 'w' :
			holo = strdup(optarg);
			break;

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

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		case 'b' :
			beamfile = 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;
		}

	}

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

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	if ( (holo != NULL) && (expand != NULL) ) {
		ERROR("You cannot 'twin' and 'expand' at the same time.\n");
		ERROR("Decide which one you want to do first.\n");
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		return 1;
	}

	if ( beamfile != NULL ) {
		beam = get_beam_parameters(beamfile);
		if ( beam == NULL ) {
			ERROR("Failed to load beam parameters from '%s'\n",
			      beamfile);
			return 1;
		}
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	}

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	cell = load_cell_from_pdb(filename);
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	if ( !config_nophase ) {
		phases = new_list_phase();
	} else {
		phases = NULL;
	}
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	esds = new_list_sigma();
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	input_ref = new_list_intensity();
	input_items = read_reflections(input, input_ref, phases,
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	                               NULL, esds);
	free(input);
	if ( check_symmetry(input_items, mero) ) {
		ERROR("The input reflection list does not appear to"
		      " have symmetry %s\n", mero);
		return 1;
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	}
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	if ( config_poisson ) {
		if ( beam != NULL ) {
			poisson_reflections(input_ref, input_items,
			                    beam->adu_per_photon);
		} else {
			ERROR("You must give a beam parameters file in order"
			      " to calculate Poisson noise.\n");
			return 1;
		}
	}

	if ( config_noise ) noise_reflections(input_ref, input_items);
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	if ( holo != NULL ) {
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		ReflItemList *new;
		STATUS("Twinning from %s into %s\n", mero, holo);
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		new = twin_reflections(input_ref, input_items,
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		                       holo, mero, esds);
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		delete_items(input_items);
		input_items = new;
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	}

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	if ( expand != NULL ) {
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		ReflItemList *new;
		STATUS("Expanding from %s into %s\n", mero, expand);
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		new = expand_reflections(input_ref, input_items, expand, mero);
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		delete_items(input_items);
		input_items = new;
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	}

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	if ( config_multi ) {

		int i;

		for ( i=0; i<num_items(input_items); i++ ) {

			struct refl_item *it;
			double inty;

			it = get_item(input_items, i);
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			inty = lookup_intensity(input_ref, it->h, it->k, it->l);
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			inty *= num_equivs(it->h, it->k, it->l, mero);
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			set_intensity(input_ref, it->h, it->k, it->l, inty);
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			STATUS("%i %i %i %i\n", it->h, it->k, it->l,
			       num_equivs(it->h, it->k, it->l, mero));

		}
	}

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	if ( template ) {
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		/* Write out only reflections which are in the template
		 * (and which we have in the input) */
		ReflItemList *template_items;
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		template_items = read_reflections(template,
		                                  NULL, NULL, NULL, NULL);
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		write_items = intersection_items(input_items, template_items);
		delete_items(template_items);
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	} else {
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		/* Write out all reflections */
		write_items = new_items();
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		/* (quick way of copying a list) */
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		union_items(write_items, input_items);
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	}

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	write_reflections(output, write_items, input_ref, esds, phases,
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	                  NULL, cell);
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	delete_items(input_items);
	delete_items(write_items);
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	return 0;
}