static void scan_partialities(RefList *reflections, RefList *compare,
                              int *valid, long double *vals[3], int idx,
                              PartialityModel pmodel)
{
	int i;
	Reflection *refl;
	RefListIterator *iter;

	i = 0;
	for ( refl = first_refl(reflections, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int h, k, l;
		Reflection *refl2;
		double rlow, rhigh, p;

		get_indices(refl, &h, &k, &l);
		refl2 = find_refl(compare, h, k, l);
		if ( refl2 == NULL ) {
			valid[i] = 0;
			i++;
			continue;
		}

		get_partial(refl2, &rlow, &rhigh, &p);
		vals[idx][i] = p;
		if ( unlikely(p < 0.0) ) {
			ERROR("Negative partiality! %3i %3i %3i  %f\n",
			      h, k, l, p);
		}

		i++;
	}
}
static void scan_partialities(RefList *reflections, RefList *compare,
                              int *valid, long double *vals[3], int idx)
{
	int i;
	Reflection *refl;
	RefListIterator *iter;

	i = 0;
	for ( refl = first_refl(reflections, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int h, k, l;
		Reflection *refl2;

		get_indices(refl, &h, &k, &l);
		refl2 = find_refl(compare, h, k, l);
		if ( refl2 == NULL ) {
			valid[i] = 0;
			i++;
			continue;
		}

		vals[idx][i] = get_lorentz(refl2);
		i++;
	}
}
Example #3
0
static double guide_dev(Crystal *cr, const RefList *full)
{
	double dev = 0.0;

	/* For each reflection */
	Reflection *refl;
	RefListIterator *iter;

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

		double G, p;
		signed int h, k, l;
		Reflection *full_version;
		double I_full, I_partial;

		if ( (get_intensity(refl) < 3.0*get_esd_intensity(refl))
		  || (get_partiality(refl) < MIN_PART_REFINE) ) continue;

		get_indices(refl, &h, &k, &l);
		assert((h!=0) || (k!=0) || (l!=0));

		full_version = find_refl(full, h, k, l);
		if ( full_version == NULL ) continue;
		/* Some reflections may have recently become scalable, but
		 * scale_intensities() might not yet have been called, so the
		 * full version may not have been calculated yet. */

		G = crystal_get_osf(cr);
		p = get_partiality(refl);
		I_partial = get_intensity(refl);
		I_full = get_intensity(full_version);
		//STATUS("%3i %3i %3i  %5.2f  %5.2f  %5.2f  %5.2f  %5.2f\n",
		//       h, k, l, G, p, I_partial, I_full,
		//       I_partial - p*G*I_full);

		dev += pow(I_partial - p*G*I_full, 2.0);

	}

	return dev;
}
Example #4
0
static struct flist *asymm_and_merge(RefList *in, const SymOpList *sym,
                                     UnitCell *cell, double rmin, double rmax,
                                     SymOpList *amb)
{
	Reflection *refl;
	RefListIterator *iter;
	RefList *asym;
	struct flist *f;
	int n;

	asym = reflist_new();
	if ( asym == NULL ) return NULL;

	for ( refl = first_refl(in, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int h, k, l;
		signed int ha, ka, la;
		Reflection *cr;
		double res;

		get_indices(refl, &h, &k, &l);

		if ( cell == NULL ) {
			ERROR("Can't calculate resolution cutoff - no cell\n");
		} else {
			res = 2.0*resolution(cell, h, k, l);
			if ( res < rmin ) continue;
			if ( res > rmax ) continue;
		}

		get_asymm(sym, h, k, l, &ha, &ka, &la);

		if ( amb != NULL ) {

			signed int hr, kr, lr;
			signed int hra, kra, lra;

			get_equiv(amb, NULL, 0, ha, ka, la, &hr, &kr, &lr);
			get_asymm(sym, hr, kr, lr, &hra, &kra, &lra);

			/* Skip twin-proof reflections */
			if ( (ha==hra) && (ka==kra) && (la==lra) ) {
				//STATUS("%i %i %i is twin proof\n", h, k, l);
				continue;
			}

		}

		cr = find_refl(asym, ha, ka, la);
		if ( cr == NULL ) {
			cr = add_refl(asym, ha, ka, la);
			assert(cr != NULL);
			copy_data(cr, refl);
		} else {
			const double i = get_intensity(cr);
			const int r = get_redundancy(cr);
			set_intensity(cr, (r*i + get_intensity(refl))/(r+1));
			set_redundancy(cr, r+1);
		}
	}

	f = malloc(sizeof(struct flist));
	if ( f == NULL ) {
		ERROR("Failed to allocate flist\n");
		return NULL;
	}

	n = num_reflections(asym);
	f->s = malloc(n*sizeof(unsigned int));
	f->s_reidx = malloc(n*sizeof(unsigned int));
	f->i = malloc(n*sizeof(float));
	f->i_reidx = malloc(n*sizeof(float));
	if ( (f->s == NULL) || (f->i == NULL)
	   || (f->s_reidx == NULL) || (f->i_reidx == NULL) ) {
		ERROR("Failed to allocate flist\n");
		return NULL;
	}

	f->n = 0;
	for ( refl = first_refl(asym, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int h, k, l;

		get_indices(refl, &h, &k, &l);
		f->s[f->n] = SERIAL(h, k, l);

		f->i[f->n] = get_intensity(refl);
		f->n++;
	}
	assert(f->n == n);

	if ( amb != NULL ) {

		RefList *reidx = reflist_new();
		if ( reidx == NULL ) return NULL;

		for ( refl = first_refl(asym, &iter);
		      refl != NULL;
		      refl = next_refl(refl, iter) )
		{
			signed int h, k, l;
			signed int hr, kr, lr;
			signed int hra, kra, lra;
			Reflection *cr;

			get_indices(refl, &h, &k, &l);
			get_equiv(amb, NULL, 0, h, k, l, &hr, &kr, &lr);
			get_asymm(sym, hr, kr, lr, &hra, &kra, &lra);

			cr = add_refl(reidx, hra, kra, lra);
			copy_data(cr, refl);
		}

		n = 0;
		for ( refl = first_refl(reidx, &iter);
		      refl != NULL;
		      refl = next_refl(refl, iter) )
		{
			signed int h, k, l;
			get_indices(refl, &h, &k, &l);
			f->s_reidx[n] = SERIAL(h, k, l);
			f->i_reidx[n++] = get_intensity(refl);
		}

		reflist_free(reidx);
	}

	reflist_free(asym);

	return f;
}
Example #5
0
static int test_lists(int num_items)
{
	struct refltemp *check;
	RefList *list;
	int i;
	signed int h, k, l;
	Reflection *refl;
	RefListIterator *iter;

	check = malloc(num_items * sizeof(struct refltemp));
	list = reflist_new();

	h = RANDOM_INDEX;
	k = RANDOM_INDEX;
	l = RANDOM_INDEX;

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

		int j;
		int num;

		if ( random() > RAND_MAX/2 ) {
			h = RANDOM_INDEX;
			k = RANDOM_INDEX;
			l = RANDOM_INDEX;
		} /* else use the same as last time */

		/* Count the number of times this reflection appeared before */
		num = 1;
		for ( j=0; j<i; j++ ) {
			if ( (check[j].h == h)
			  && (check[j].k == k)
			  && (check[j].l == l) ) {
				num++;
			}
		}

		/* Update all copies with this number */
		for ( j=0; j<i; j++ ) {
			if ( (check[j].h == h)
			  && (check[j].k == k)
			  && (check[j].l == l) ) {
				check[j].num = num;
			}
		}

		add_refl(list, h, k, l);
		check[i].h = h;
		check[i].k = k;
		check[i].l = l;
		check[i].num = num;
		check[i].found = 0;

	}

	printf("Created %i items, num_reflections is %i, tree depth is %i\n",
	       num_items, num_reflections(list), tree_depth(list));

	/* Iterate over the list and check we find everything */
	int count = 0;
	for ( refl = first_refl(list, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) ) {

		signed int h, k, l;

		get_indices(refl, &h, &k, &l);

		for ( i=0; i<num_items; i++ ) {
			if ( (check[i].h == h)
			  && (check[i].k == k)
			  && (check[i].l == l)
			  && (check[i].found == 0) ) {
				check[i].found = 1;
				break;
			}
		}

		count++;

	}
	if ( count != num_reflections(list) ) {
		fprintf(stderr, "num_reflections gave %i, iteration gave %i\n",
		        num_reflections(list), count);
		return 1;
	}

	for ( i=0; i<num_items; i++ ) {
		if ( check[i].found == 0 ) {

			Reflection *test;

			fprintf(stderr, "Iteration didn't find %3i %3i %3i %i\n",
			        check[i].h, check[i].k, check[i].l, i);
			test = find_refl(list, check[i].h, check[i].k,
			                 check[i].l);
			if ( test == NULL ) {
				fprintf(stderr, "Not in list\n");
			} else {
				fprintf(stderr, "But found in list.\n");
			}
			return 1;

		}
	}

	/* Check that all the reflections can be found */
	for ( i=0; i<num_items; i++ ) {

		signed int h, k, l;
		Reflection *refl;

		h = check[i].h;
		k = check[i].k;
		l = check[i].l;

		refl = find_refl(list, h, k, l);
		if ( refl == NULL ) {
			fprintf(stderr, "Couldn't find %3i %3i %3i\n", h, k, l);
			return 1;
		}

	}

	reflist_free(list);
	free(check);

	return 0;
}
Example #6
0
/* Perform one cycle of post refinement on 'image' against 'full' */
static double pr_iterate(Crystal *cr, const RefList *full,
                         PartialityModel pmodel, int *n_filtered)
{
	gsl_matrix *M;
	gsl_vector *v;
	gsl_vector *shifts;
	int param;
	Reflection *refl;
	RefListIterator *iter;
	RefList *reflections;
	double max_shift;
	int nref = 0;
	const int verbose = 0;
	int num_params = 0;
	enum gparam rv[32];

	*n_filtered = 0;

	/* If partiality model is anything other than "unity", refine all the
	 * geometrical parameters */
	if ( pmodel != PMODEL_UNITY ) {
		rv[num_params++] = GPARAM_ASX;
		rv[num_params++] = GPARAM_ASY;
		rv[num_params++] = GPARAM_ASZ;
		rv[num_params++] = GPARAM_BSX;
		rv[num_params++] = GPARAM_BSY;
		rv[num_params++] = GPARAM_BSZ;
		rv[num_params++] = GPARAM_CSX;
		rv[num_params++] = GPARAM_CSY;
		rv[num_params++] = GPARAM_CSZ;
	}

	STATUS("Refining %i parameters.\n", num_params);

	reflections = crystal_get_reflections(cr);

	M = gsl_matrix_calloc(num_params, num_params);
	v = gsl_vector_calloc(num_params);

	/* Construct the equations, one per reflection in this image */
	for ( refl = first_refl(reflections, &iter);
	      refl != NULL;
	      refl = next_refl(refl, iter) )
	{
		signed int ha, ka, la;
		double I_full, delta_I;
		double w;
		double I_partial;
		int k;
		double p, l;
		Reflection *match;
		double gradients[num_params];

		/* Find the full version */
		get_indices(refl, &ha, &ka, &la);
		match = find_refl(full, ha, ka, la);
		if ( match == NULL ) continue;

		if ( (get_intensity(refl) < 3.0*get_esd_intensity(refl))
		  || (get_partiality(refl) < MIN_PART_REFINE)
		  || (get_redundancy(match) < 2) ) continue;

		I_full = get_intensity(match);

		/* Actual measurement of this reflection from this pattern? */
		I_partial = get_intensity(refl) / crystal_get_osf(cr);
		p = get_partiality(refl);
		l = get_lorentz(refl);

		/* Calculate the weight for this reflection */
		w =  pow(get_esd_intensity(refl), 2.0);
		w += l * p * I_full * pow(get_esd_intensity(match), 2.0);
		w = pow(w, -1.0);

		/* Calculate all gradients for this reflection */
		for ( k=0; k<num_params; k++ ) {
			gradients[k] = p_gradient(cr, rv[k], refl, pmodel) * l;
		}

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

			int g;
			double v_c, v_curr;

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

				double M_c, M_curr;

				/* Matrix is symmetric */
				if ( g > k ) continue;

				M_c = gradients[g] * gradients[k];
				M_c *= w * pow(I_full, 2.0);

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

			}

			delta_I = I_partial - (l * p * I_full);
			v_c = w * delta_I * I_full * gradients[k];
			v_curr = gsl_vector_get(v, k);
			gsl_vector_set(v, k, v_curr + v_c);

		}

		nref++;
	}
	if ( verbose ) {
		STATUS("The original equation:\n");
		show_matrix_eqn(M, v);
	}

	//STATUS("%i reflections went into the equations.\n", nref);
	if ( nref == 0 ) {
		crystal_set_user_flag(cr, 2);
		gsl_matrix_free(M);
		gsl_vector_free(v);
		return 0.0;
	}

	max_shift = 0.0;
	shifts = solve_svd(v, M, n_filtered, verbose);
	if ( shifts != NULL ) {

		for ( param=0; param<num_params; param++ ) {
			double shift = gsl_vector_get(shifts, param);
			apply_shift(cr, rv[param], shift);
			//STATUS("Shift %i: %e\n", param, shift);
			if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
		}

	} else {
		crystal_set_user_flag(cr, 3);
	}

	gsl_matrix_free(M);
	gsl_vector_free(v);
	gsl_vector_free(shifts);

	return max_shift;
}