partial_sim.c

/*
 * partial_sim.c
 *
 * Generate partials for testing scaling
 *
 * (c) 2006-2011 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 <assert.h>

#include "utils.h"
#include "reflist-utils.h"
#include "symmetry.h"
#include "beam-parameters.h"
#include "detector.h"
#include "geometry.h"
#include "stream.h"


static void mess_up_cell(UnitCell *cell)
{
	double ax, ay, az;
	double bx, by, bz;
	double cx, cy, cz;

	/* Cell noise in percent */
	const double cnoise = 0.2;

	//STATUS("Real:\n");
	//cell_print(cell);

	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
	ax = gaussian_noise(ax, cnoise*fabs(ax)/100.0);
	ay = gaussian_noise(ay, cnoise*fabs(ay)/100.0);
	az = gaussian_noise(az, cnoise*fabs(az)/100.0);
	bx = gaussian_noise(bx, cnoise*fabs(bx)/100.0);
	by = gaussian_noise(by, cnoise*fabs(by)/100.0);
	bz = gaussian_noise(bz, cnoise*fabs(bz)/100.0);
	cx = gaussian_noise(cx, cnoise*fabs(cx)/100.0);
	cy = gaussian_noise(cy, cnoise*fabs(cy)/100.0);
	cz = gaussian_noise(cz, cnoise*fabs(cz)/100.0);
	cell_set_reciprocal(cell, ax, ay, az, bx, by, bz, cx, cy, cz);

	//STATUS("Changed:\n");
	//cell_print(cell);
}


/* For each reflection in "partial", fill in what the intensity would be
 * according to "full" */
static void calculate_partials(RefList *partial, double osf,
                               RefList *full, const char *sym,
                               int random_intensities)
{
	Reflection *refl;
	RefListIterator *iter;

	for ( refl = first_refl(partial, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {

		signed int h, k, l;
		Reflection *rfull;
		double p;
		double Ip;
		double If;

		get_indices(refl, &h, &k, &l);
		get_asymm(h, k, l, &h, &k, &l, sym);
		p = get_partiality(refl);

		rfull = find_refl(full, h, k, l);
		if ( rfull == NULL ) {
			if ( random_intensities ) {
				rfull = add_refl(full, h, k, l);
				If = fabs(gaussian_noise(0.0, 1000.0));
				set_int(rfull, If);
				set_redundancy(rfull, 1);
			} else {
				set_redundancy(refl, 0);
				If = 0.0;
			}
		} else {
			If = get_intensity(rfull);
		}

		Ip = osf * p * If;

		Ip = gaussian_noise(Ip, Ip/10.0);

		set_int(refl, Ip);
		set_esd_intensity(refl, Ip/10.0);

	}
}


static void show_help(const char *s)
{
	printf("Syntax: %s [options]\n\n", s);
	printf(
"Generate a stream containing partials from a reflection list.\n"
"\n"
" -h, --help              Display this help message.\n"
"\n"
"You need to provide the following basic options:\n"
" -i, --input=<file>      Read reflections from <file>.\n"
" -o, --output=<file>     Write partials in stream format to <file>.\n"
" -g. --geometry=<file>   Get detector geometry from file.\n"
" -b, --beam=<file>       Get beam parameters from file\n"
" -p, --pdb=<file>        PDB file from which to get the unit cell.\n"
"\n"
" -y, --symmetry=<sym>    Symmetry of the input reflection list.\n"
" -n <n>                  Simulate <n> patterns.  Default: 2.\n"
);
}


int main(int argc, char *argv[])
{
	int c;
	char *input_file = NULL;
	char *output_file = NULL;
	char *beamfile = NULL;
	char *geomfile = NULL;
	char *cellfile = NULL;
	struct detector *det = NULL;
	struct beam_params *beam = NULL;
	RefList *full = NULL;
	char *sym = NULL;
	UnitCell *cell = NULL;
	struct quaternion orientation;
	struct image image;
	FILE *ofh;
	int n = 2;
	int i;
	int random_intensities = 0;

	/* Long options */
	const struct option longopts[] = {
		{"help",               0, NULL,               'h'},
		{"output",             1, NULL,               'o'},
		{"input",              1, NULL,               'i'},
		{"beam",               1, NULL,               'b'},
		{"pdb",                1, NULL,               'p'},
		{"geometry",           1, NULL,               'g'},
		{"symmetry",           1, NULL,               'y'},
		{0, 0, NULL, 0}
	};

	/* Short options */
	while ((c = getopt_long(argc, argv, "hi:o:b:p:g:y:n:",
	                        longopts, NULL)) != -1)
	{
		switch (c) {
		case 'h' :
			show_help(argv[0]);
			return 0;

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

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

		case 'b' :
			beamfile = strdup(optarg);
			break;

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

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

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

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

		case 0 :
			break;

		default :
			return 1;
		}

	}

	/* Load beam */
	if ( beamfile == NULL ) {
		ERROR("You need to provide a beam parameters file.\n");
		return 1;
	}
	beam = get_beam_parameters(beamfile);
	if ( beam == NULL ) {
		ERROR("Failed to load beam parameters from '%s'\n", beamfile);
		return 1;
	}
	free(beamfile);

	/* Load cell */
	if ( cellfile == NULL ) {
		ERROR("You need to give a PDB file with the unit cell.\n");
		return 1;
	}
	cell = load_cell_from_pdb(cellfile);
	if ( cell == NULL ) {
		ERROR("Failed to get cell from '%s'\n", cellfile);
		return 1;
	}
	free(cellfile);

	/* Load geometry */
	if ( geomfile == NULL ) {
		ERROR("You need to give a geometry file.\n");
		return 1;
	}
	det = get_detector_geometry(geomfile);
	if ( det == NULL ) {
		ERROR("Failed to read geometry from '%s'\n", geomfile);
		return 1;
	}
	free(geomfile);

	/* Load (full) reflections */
	if ( input_file != NULL ) {

		full = read_reflections(input_file);
		if ( full == NULL ) {
			ERROR("Failed to read reflections from '%s'\n",
			      input_file);
			return 1;
		}
		free(input_file);
		if ( check_list_symmetry(full, sym) ) {
			ERROR("The input reflection list does not appear to"
			      " have symmetry %s\n", sym);
			return 1;
		}

	} else {
		random_intensities = 1;
	}

	if ( n < 1 ) {
		ERROR("Number of patterns must be at least 1.\n");
		return 1;
	}

	if ( output_file == NULL ) {
		ERROR("You must pgive a filename for the output.\n");
		return 1;
	}
	ofh = fopen(output_file, "w");
	if ( ofh == NULL ) {
		ERROR("Couldn't open output file '%s'\n", output_file);
		return 1;
	}
	free(output_file);
	write_stream_header(ofh, argc, argv);

	image.det = det;
	image.width = det->max_fs;
	image.height = det->max_ss;

	image.lambda = ph_en_to_lambda(eV_to_J(beam->photon_energy));
	image.div = beam->divergence;
	image.bw = beam->bandwidth;
	image.profile_radius = 0.003e9;
	image.i0_available = 0;
	image.filename = malloc(256);

	if ( random_intensities ) {
		full = reflist_new();
	}

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

		double osf;

		if ( random() > RAND_MAX/2 ) {
			osf = 1.0;
		} else {
			osf = 2.0;
		}
		//STATUS("Image %i scale factor %f\n", i, osf);

		/* Set up a random orientation */
		orientation = random_quaternion();
		image.indexed_cell = cell_rotate(cell, orientation);

		snprintf(image.filename, 255, "dummy.h5");
		image.reflections = find_intersections(&image,
		                                       image.indexed_cell);
		calculate_partials(image.reflections, osf, full, sym,
		                   random_intensities);

		/* Give a slightly incorrect cell in the stream */
		mess_up_cell(image.indexed_cell);
		write_chunk(ofh, &image, STREAM_INTEGRATED);

		reflist_free(image.reflections);
		cell_free(image.indexed_cell);

		progress_bar(i+1, n, "Simulating");

	}

	if ( random_intensities ) {
		STATUS("Writing full intensities to partial_sim.hkl\n");
		write_reflist("partial_sim.hkl", full, cell);
	}

	fclose(ofh);
	cell_free(cell);
	free_detector_geometry(det);
	free(beam);
	free(sym);
	reflist_free(full);
	free(image.filename);

	return 0;
}