partialator: Add --model=

1 files changed, 76 insertions, 25 deletions

diff --git a/src/hrs-scaling.c b/src/hrs-scaling.c
index f60dfe25..3a51e6d9 100644
--- a/src/hrs-scaling.c
+++ b/src/hrs-scaling.c
@@ -60,6 +60,7 @@ struct scale_queue_args
 	Crystal **crystals;
 	int n_started;
 	double max_shift;
+	PartialityModel pmodel;
 };
 
 
@@ -68,6 +69,7 @@ struct scale_worker_args
 	Crystal *crystal;
 	double shift;
 	RefList *reference;
+	PartialityModel pmodel;
 };
 
 
@@ -78,6 +80,7 @@ static void *create_scale_job(void *vqargs)
 
 	wargs = malloc(sizeof(struct scale_worker_args));
 	wargs->reference = qargs->reference;
+	wargs->pmodel = qargs->pmodel;
 
 	wargs->crystal = qargs->crystals[qargs->n_started++];
 
@@ -109,7 +112,7 @@ static void run_scale_job(void *vwargs, int cookie)
 		signed int h, k, l;
 		double Ih, Ihl, esd;
 		Reflection *r;
-		double L, p;
+		double corr;
 
 		if ( !get_scalable(refl) ) continue;
 
@@ -126,11 +129,21 @@ static void run_scale_job(void *vwargs, int cookie)
 			Ih = get_intensity(r);
 		}
 
-		/* If you change this, be sure to change run_merge_job() too */
-		p = get_partiality(refl);
-		L = get_lorentz(refl);
-		Ihl = get_intensity(refl) / (L*p);
-		esd = get_esd_intensity(refl) / (L*p);
+		/* If you change this, be sure to also change
+		 * run_merge_job() and run_esd_job(). */
+		switch ( wargs->pmodel ) {
+
+			case PMODEL_UNITY :
+			corr = 1.0;
+			break;
+
+			case PMODEL_SPHERE :
+			corr = get_partiality(refl) * get_lorentz(refl);
+			break;
+
+		}
+		Ihl = get_intensity(refl) / corr;
+		esd = get_esd_intensity(refl) / corr;
 
 		num += Ih * (Ihl/osf) / pow(esd/osf, 2.0);
 		den += pow(Ih, 2.0)/pow(esd/osf, 2.0);
@@ -160,7 +173,7 @@ static void finalise_scale_job(void *vqargs, void *vwargs)
 
 
 static double iterate_scale(Crystal **crystals, int n, RefList *reference,
-                            int n_threads)
+                            int n_threads, PartialityModel pmodel)
 {
 	struct scale_queue_args qargs;
 
@@ -170,6 +183,7 @@ static double iterate_scale(Crystal **crystals, int n, RefList *reference,
 	qargs.n_started = 0;
 	qargs.crystals = crystals;
 	qargs.max_shift = 0.0;
+	qargs.pmodel = pmodel;
 
 	run_threads(n_threads, run_scale_job, create_scale_job,
 	            finalise_scale_job, &qargs, n, 0, 0, 0);
@@ -184,6 +198,7 @@ struct merge_queue_args
 	pthread_mutex_t full_lock;
 	Crystal **crystals;
 	int n_started;
+	PartialityModel pmodel;
 };
 
 
@@ -192,6 +207,7 @@ struct merge_worker_args
 	Crystal *crystal;
 	RefList *full;
 	pthread_mutex_t *full_lock;
+	PartialityModel pmodel;
 };
 
 
@@ -203,6 +219,7 @@ static void *create_merge_job(void *vqargs)
 	wargs = malloc(sizeof(struct merge_worker_args));
 	wargs->full = qargs->full;
 	wargs->full_lock = &qargs->full_lock;
+	wargs->pmodel = qargs->pmodel;
 
 	wargs->crystal = qargs->crystals[qargs->n_started++];
 
@@ -231,7 +248,7 @@ static void run_merge_job(void *vwargs, int cookie)
 		signed int h, k, l;
 		double num, den;
 		int red;
-		double Ihl, esd, L, p;
+		double Ihl, esd, corr;
 
 		if ( !get_scalable(refl) ) continue;
 
@@ -254,11 +271,22 @@ static void run_merge_job(void *vwargs, int cookie)
 			red = get_redundancy(f);
 		}
 
-		/* If you change this, be sure to change run_scale_job() too */
-		p = get_partiality(refl);
-		L = get_lorentz(refl);
-		Ihl = get_intensity(refl) / (L*p);
-		esd = get_esd_intensity(refl) / (L*p);
+		/* If you change this, be sure to also change
+		 * run_scale_job() and run_esd_job(). */
+		switch ( wargs->pmodel ) {
+
+			case PMODEL_UNITY :
+			corr = 1.0;
+			break;
+
+			case PMODEL_SPHERE :
+			corr = get_partiality(refl) * get_lorentz(refl);
+			break;;
+
+		}
+
+		Ihl = get_intensity(refl) / corr;
+		esd = get_esd_intensity(refl) / corr;
 
 		num += (Ihl/G) / pow(esd/G, 2.0);
 		den += 1.0 / pow(esd/G, 2.0);
@@ -278,7 +306,8 @@ static void finalise_merge_job(void *vqargs, void *vwargs)
 }
 
 
-static RefList *lsq_intensities(Crystal **crystals, int n, int n_threads)
+static RefList *lsq_intensities(Crystal **crystals, int n, int n_threads,
+                                PartialityModel pmodel)
 {
 	RefList *full;
 	struct merge_queue_args qargs;
@@ -290,6 +319,7 @@ static RefList *lsq_intensities(Crystal **crystals, int n, int n_threads)
 	qargs.full = full;
 	qargs.n_started = 0;
 	qargs.crystals = crystals;
+	qargs.pmodel = pmodel;
 	pthread_mutex_init(&qargs.full_lock, NULL);
 
 	run_threads(n_threads, run_merge_job, create_merge_job,
@@ -316,6 +346,7 @@ struct esd_queue_args
 	RefList *full;
 	Crystal **crystals;
 	int n_started;
+	PartialityModel pmodel;
 };
 
 
@@ -323,6 +354,7 @@ struct esd_worker_args
 {
 	Crystal *crystal;
 	RefList *full;
+	PartialityModel pmodel;
 };
 
 
@@ -333,6 +365,7 @@ static void *create_esd_job(void *vqargs)
 
 	wargs = malloc(sizeof(struct esd_worker_args));
 	wargs->full = qargs->full;
+	wargs->pmodel = qargs->pmodel;
 
 	wargs->crystal = qargs->crystals[qargs->n_started++];
 
@@ -360,7 +393,7 @@ static void run_esd_job(void *vwargs, int cookie)
 		Reflection *f;
 		signed int h, k, l;
 		double num;
-		double Ihl, Ih;
+		double Ihl, Ih, corr;
 
 		if ( !get_scalable(refl) ) continue;
 
@@ -372,8 +405,23 @@ static void run_esd_job(void *vwargs, int cookie)
 
 		num = get_temp1(f);
 
+		/* If you change this, be sure to also change
+		 * run_scale_job() and run_merge_job(). */
+		switch ( wargs->pmodel ) {
+
+			case PMODEL_UNITY :
+			corr = 1.0;
+			break;
+
+			case PMODEL_SPHERE :
+			corr = get_partiality(refl) * get_lorentz(refl);
+			break;;
+
+		}
+
+
 		Ih = get_intensity(f);
-		Ihl = get_intensity(refl) / (get_partiality(refl) * G);
+		Ihl = get_intensity(refl) / (corr * G);
 
 		num += pow(Ihl - Ih, 2.0);
 
@@ -390,7 +438,7 @@ static void finalise_esd_job(void *vqargs, void *vwargs)
 
 
 static void calculate_esds(Crystal **crystals, int n, RefList *full,
-                           int n_threads, int min_red)
+                           int n_threads, int min_red, PartialityModel pmodel)
 {
 	struct esd_queue_args qargs;
 	Reflection *refl;
@@ -399,6 +447,7 @@ static void calculate_esds(Crystal **crystals, int n, RefList *full,
 	qargs.full = full;
 	qargs.n_started = 0;
 	qargs.crystals = crystals;
+	qargs.pmodel = pmodel;
 
 	for ( refl = first_refl(full, &iter);
 	      refl != NULL;
@@ -430,7 +479,7 @@ static void calculate_esds(Crystal **crystals, int n, RefList *full,
 
 /* Scale the stack of images */
 RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
-                           int n_threads, int noscale)
+                           int n_threads, int noscale, PartialityModel pmodel)
 {
 	int i;
 	double max_corr;
@@ -440,14 +489,15 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 	for ( i=0; i<n; i++ ) crystal_set_osf(crystals[i], 1.0);
 
 	if ( noscale ) {
-		full = lsq_intensities(crystals, n, n_threads);
-		calculate_esds(crystals, n, full, n_threads, min_redundancy);
+		full = lsq_intensities(crystals, n, n_threads, pmodel);
+		calculate_esds(crystals, n, full, n_threads, min_redundancy,
+		               pmodel);
 		return full;
 	}
 
 	/* No reference -> create an initial list to refine against */
 	if ( gref == NULL ) {
-		full = lsq_intensities(crystals, n, n_threads);
+		full = lsq_intensities(crystals, n, n_threads, pmodel);
 	}
 
 	/* Iterate */
@@ -463,14 +513,15 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 			reference = full;
 		}
 
-		max_corr = iterate_scale(crystals, n, reference, n_threads);
+		max_corr = iterate_scale(crystals, n, reference, n_threads,
+		                         pmodel);
 		//STATUS("Scaling iteration %2i: max correction = %5.2f\n",
 		//       i+1, max_corr);
 
 		/* No reference -> generate list for next iteration */
 		if ( gref == NULL ) {
 			reflist_free(full);
-			full = lsq_intensities(crystals, n, n_threads);
+			full = lsq_intensities(crystals, n, n_threads, pmodel);
 		}
 
 		//show_scale_factors(images, n);
@@ -480,10 +531,10 @@ RefList *scale_intensities(Crystal **crystals, int n, RefList *gref,
 	} while ( (max_corr > 0.01) && (i < MAX_CYCLES) );
 
 	if ( gref != NULL ) {
-		full = lsq_intensities(crystals, n, n_threads);
+		full = lsq_intensities(crystals, n, n_threads, pmodel);
 	} /* else we already did it */
 
-	calculate_esds(crystals, n, full, n_threads, min_redundancy);
+	calculate_esds(crystals, n, full, n_threads, min_redundancy, pmodel);
 
 	return full;
 }