partialator: Scale (strictly) using strong reflections only

1 files changed, 6 insertions, 328 deletions

diff --git a/src/post-refinement.c b/src/post-refinement.c
index cf3108db..487ce872 100644
--- a/src/post-refinement.c
+++ b/src/post-refinement.c
@@ -216,21 +216,9 @@ double gradient(Crystal *cr, int k, Reflection *refl, PartialityModel pmodel)
 	struct image *image = crystal_get_image(cr);
 	double R = crystal_get_profile_radius(cr);
 	double gr;
-	signed int hi, ki, li;
-	double s;
 
-	get_indices(refl, &hi, &ki, &li);
-	s = resolution(crystal_get_cell(cr), hi, ki, li);
 	get_partial(refl, &rlow, &rhigh, &p);
 
-	if ( k == GPARAM_OSF ) {
-		return 1.0;
-	}
-
-	if ( k == GPARAM_BFAC ) {
-		return -s*s;
-	}
-
 	if ( k == GPARAM_R ) {
 
 		double Rglow, Rghigh;
@@ -347,18 +335,6 @@ static void apply_shift(Crystal *cr, int k, double shift)
 		crystal_set_profile_radius(cr, t);
 		break;
 
-		case GPARAM_BFAC :
-		t = crystal_get_Bfac(cr);
-		t += shift;
-		crystal_set_Bfac(cr, t);
-		break;
-
-		case GPARAM_OSF :
-		t = crystal_get_osf(cr);
-		t += shift;
-		crystal_set_osf(cr, t);
-		break;
-
 		case GPARAM_ASX :
 		case GPARAM_ASY :
 		case GPARAM_ASZ :
@@ -379,141 +355,6 @@ static void apply_shift(Crystal *cr, int k, double shift)
 }
 
 
-/* Perform one cycle of scaling of 'cr' against 'full' */
-static double scale_iterate(Crystal *cr, const RefList *full,
-                            PartialityModel pmodel)
-{
-	gsl_matrix *M;
-	gsl_vector *v;
-	gsl_vector *shifts;
-	int param;
-	Reflection *refl;
-	RefListIterator *iter;
-	RefList *reflections;
-	double max_shift;
-	int nref = 0;
-	int num_params = 0;
-	enum gparam rv[32];
-	double G, B;
-
-	rv[num_params++] = GPARAM_OSF;
-	rv[num_params++] = GPARAM_BFAC;
-
-	M = gsl_matrix_calloc(num_params, num_params);
-	v = gsl_vector_calloc(num_params);
-
-	reflections = crystal_get_reflections(cr);
-	G = crystal_get_osf(cr);
-	B = crystal_get_Bfac(cr);
-
-	/* Scaling terms */
-	for ( refl = first_refl(reflections, &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) )
-	{
-		signed int ha, ka, la;
-		double I_full, delta_I, esd;
-		double w;
-		double I_partial;
-		int k;
-		double p, L, s;
-		double fx;
-		Reflection *match;
-		double gradients[num_params];
-
-		/* If reflection is free-flagged, don't use it here */
-		if ( get_flag(refl) ) continue;
-
-		/* Find the full version */
-		get_indices(refl, &ha, &ka, &la);
-		match = find_refl(full, ha, ka, la);
-		if ( match == NULL ) continue;
-
-		/* Merged intensitty */
-		I_full = get_intensity(match);
-
-		/* Actual measurement of this reflection from this pattern */
-		I_partial = get_intensity(refl);
-		esd = get_esd_intensity(refl);
-		p = get_partiality(refl);
-
-		/* Scale only using strong reflections */
-		if ( I_partial <= 3.0*esd ) continue; /* Also because of log */
-		if ( get_redundancy(match) < 2 ) continue;
-		if ( I_full <= 0 ) continue;  /* Because log */
-		if ( p <= 0.0 ) continue; /* Because of log */
-
-		L = get_lorentz(refl);
-		s = resolution(crystal_get_cell(cr), ha, ka, la);
-
-		/* Calculate the weight for this reflection */
-		w = 1.0;
-
-		/* Calculate all gradients for this reflection */
-		for ( k=0; k<num_params; k++ ) {
-			gradients[k] = gradient(cr, rv[k], refl, pmodel);
-		}
-
-		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 = w * gradients[g] * gradients[k];
-
-				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);
-
-			}
-
-			fx = G + log(p) - log(L) - B*s*s + log(I_full);
-			delta_I = log(I_partial) - fx;
-			v_c = w * delta_I * gradients[k];
-			v_curr = gsl_vector_get(v, k);
-			gsl_vector_set(v, k, v_curr + v_c);
-
-		}
-
-		nref++;
-	}
-
-	if ( nref < num_params ) {
-		crystal_set_user_flag(cr, PRFLAG_FEWREFL);
-		gsl_matrix_free(M);
-		gsl_vector_free(v);
-		return 0.0;
-	}
-
-	max_shift = 0.0;
-	shifts = solve_svd(v, M, NULL, 0);
-	if ( shifts != NULL ) {
-
-		for ( param=0; param<num_params; param++ ) {
-			double shift = gsl_vector_get(shifts, param);
-			apply_shift(cr, rv[param], shift);
-			if ( fabs(shift) > max_shift ) max_shift = fabs(shift);
-		}
-
-	} else {
-		crystal_set_user_flag(cr, PRFLAG_SOLVEFAIL);
-	}
-
-	gsl_matrix_free(M);
-	gsl_vector_free(v);
-	gsl_vector_free(shifts);
-
-	return max_shift;
-}
-
-
 /* Perform one cycle of post refinement on 'image' against 'full' */
 static double pr_iterate(Crystal *cr, const RefList *full,
                          PartialityModel pmodel,
@@ -667,74 +508,8 @@ static double pr_iterate(Crystal *cr, const RefList *full,
 }
 
 
-static double log_residual(Crystal *cr, const RefList *full, int free,
-                           int *pn_used, const char *filename)
-{
-	double dev = 0.0;
-	double G, B;
-	Reflection *refl;
-	RefListIterator *iter;
-	int n_used = 0;
-	FILE *fh = NULL;
-
-	G = crystal_get_osf(cr);
-	B = crystal_get_Bfac(cr);
-	if ( filename != NULL ) {
-		fh = fopen(filename, "a");
-		if ( fh == NULL ) {
-			ERROR("Failed to open '%s'\n", filename);
-		}
-	}
-
-	for ( refl = first_refl(crystal_get_reflections(cr), &iter);
-	      refl != NULL;
-	      refl = next_refl(refl, iter) )
-	{
-		double p, L, s, w;
-		signed int h, k, l;
-		Reflection *match;
-		double esd, I_full, I_partial;
-		double fx, dc;
-
-		if ( free && !get_flag(refl) ) continue;
-
-		get_indices(refl, &h, &k, &l);
-		match = find_refl(full, h, k, l);
-		if ( match == NULL ) continue;
-
-		p = get_partiality(refl);
-		L = get_lorentz(refl);
-		I_partial = get_intensity(refl);
-		I_full = get_intensity(match);
-		esd = get_esd_intensity(refl);
-		s = resolution(crystal_get_cell(cr), h, k, l);
-
-		if ( I_partial <= 3.0*esd ) continue; /* Also because of log */
-		if ( get_redundancy(match) < 2 ) continue;
-		if ( I_full <= 0 ) continue;  /* Because log */
-		if ( p <= 0.0 ) continue; /* Because of log */
-
-		fx = G + log(p) - log(L) - B*s*s + log(I_full);
-		dc = log(I_partial) - fx;
-		w = 1.0;
-		dev += w*dc*dc;
-
-		if ( fh != NULL ) {
-			fprintf(fh, "%4i %4i %4i %e %e\n",
-			        h, k, l, s, dev);
-		}
-
-	}
-
-	if ( fh != NULL ) fclose(fh);
-
-	if ( pn_used != NULL ) *pn_used = n_used;
-	return dev;
-}
-
-
-static double residual(Crystal *cr, const RefList *full, int free,
-                       int *pn_used, const char *filename)
+double residual(Crystal *cr, const RefList *full, int free,
+                int *pn_used, const char *filename)
 {
 	double dev = 0.0;
 	double G, B;
@@ -799,39 +574,6 @@ static double residual(Crystal *cr, const RefList *full, int free,
 }
 
 
-void all_residuals(Crystal **crystals, int n_crystals, RefList *full,
-                   double *presidual, double *pfree_residual,
-                   double *plog_residual, double *pfree_log_residual)
-{
-	int i;
-
-	*presidual = 0.0;
-	*pfree_residual = 0.0;
-	*plog_residual = 0.0;
-	*pfree_log_residual = 0.0;
-
-	for ( i=0; i<n_crystals; i++ ) {
-
-		double r, free_r, log_r, free_log_r;
-
-		if ( crystal_get_user_flag(crystals[i]) ) continue;
-
-		r = residual(crystals[i], full, 0, NULL, NULL);
-		free_r = residual(crystals[i], full, 1, NULL, NULL);
-		log_r = log_residual(crystals[i], full, 0, NULL, NULL);
-		free_log_r = log_residual(crystals[i], full, 1, NULL, NULL);
-
-		if ( isnan(r) || isnan(free_r)
-		  || isnan(log_r) || isnan(free_log_r) ) continue;
-
-		*presidual += r;
-		*pfree_residual += free_r;
-		*plog_residual += log_r;
-		*pfree_log_residual += free_log_r;
-	}
-}
-
-
 static void write_residual_graph(Crystal *cr, const RefList *full)
 {
 	int i;
@@ -877,49 +619,6 @@ static void write_residual_graph(Crystal *cr, const RefList *full)
 }
 
 
-static void do_scale_refine(Crystal *cr, const RefList *full,
-                            PartialityModel pmodel, int verbose)
-{
-	int i, done;
-	double old_dev;
-
-	old_dev = log_residual(cr, full, 0, NULL, NULL);
-
-	if ( verbose ) {
-		STATUS("Initial G=%.2f, B=%e\n",
-		       crystal_get_osf(cr), crystal_get_Bfac(cr));
-		STATUS("Scaling initial  dev =  %10.5e, free dev = %10.5e\n",
-		       old_dev, log_residual(cr, full, 1, NULL, NULL));
-	}
-
-	i = 0;
-	done = 0;
-	do {
-
-		double dev;
-
-		scale_iterate(cr, full, pmodel);
-
-		dev = log_residual(cr, full, 0, 0, NULL);
-		if ( fabs(dev - old_dev) < dev*0.01 ) done = 1;
-
-		if ( verbose ) {
-			STATUS("Scaling %2i: dev = %10.5e, free dev = %10.5e\n",
-			       i+1, dev, log_residual(cr, full, 0, 0, NULL));
-		}
-
-		i++;
-		old_dev = dev;
-
-	} while ( i < MAX_CYCLES && !done );
-
-	if ( verbose ) {
-		STATUS("Final G=%.2f, B=%e\n", crystal_get_osf(cr),
-		       crystal_get_Bfac(cr));
-	}
-}
-
-
 static void do_pr_refine(Crystal *cr, const RefList *full,
                          PartialityModel pmodel, int verbose)
 {
@@ -977,8 +676,7 @@ static void do_pr_refine(Crystal *cr, const RefList *full,
 
 
 static struct prdata pr_refine(Crystal *cr, const RefList *full,
-                               PartialityModel pmodel, int no_scale, int no_pr,
-                               double max_B)
+                               PartialityModel pmodel)
 {
 	int verbose = 0;
 	struct prdata prdata;
@@ -986,23 +684,11 @@ static struct prdata pr_refine(Crystal *cr, const RefList *full,
 	prdata.refined = 0;
 	prdata.n_filtered = 0;
 
-	if ( !no_scale ) {
-		do_scale_refine(cr, full, pmodel, verbose);
-	}
-
-	/* Reject if B factor modulus is very large */
-	if ( fabs(crystal_get_Bfac(cr)) > max_B ) {
-		crystal_set_user_flag(cr, PRFLAG_BIGB);
-		return prdata;
-	}
-
 	if ( verbose ) {
 		write_residual_graph(cr, full);
 	}
 
-	if ( !no_pr ) {
-		do_pr_refine(cr, full, pmodel, verbose);
-	}
+	do_pr_refine(cr, full, pmodel, verbose);
 
 	if ( crystal_get_user_flag(cr) == 0 ) {
 		prdata.refined = 1;
@@ -1017,9 +703,6 @@ struct refine_args
 	RefList *full;
 	Crystal *crystal;
 	PartialityModel pmodel;
-	int no_scale;
-	int no_pr;
-	double max_B;
 	struct prdata prdata;
 };
 
@@ -1039,8 +722,7 @@ static void refine_image(void *task, int id)
 	struct refine_args *pargs = task;
 	Crystal *cr = pargs->crystal;
 
-	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel,
-	                          pargs->no_scale, pargs->no_pr, pargs->max_B);
+	pargs->prdata = pr_refine(cr, pargs->full, pargs->pmodel);
 }
 
 
@@ -1072,8 +754,7 @@ static void done_image(void *vqargs, void *task)
 
 
 void refine_all(Crystal **crystals, int n_crystals,
-                RefList *full, int nthreads, PartialityModel pmodel,
-                int no_scale, int no_pr, double max_B)
+                RefList *full, int nthreads, PartialityModel pmodel)
 {
 	struct refine_args task_defaults;
 	struct queue_args qargs;
@@ -1083,9 +764,6 @@ void refine_all(Crystal **crystals, int n_crystals,
 	task_defaults.pmodel = pmodel;
 	task_defaults.prdata.refined = 0;
 	task_defaults.prdata.n_filtered = 0;
-	task_defaults.no_scale = no_scale;
-	task_defaults.no_pr = no_pr;
-	task_defaults.max_B = max_B;
 
 	qargs.task_defaults = task_defaults;
 	qargs.n_started = 0;