check_hkl: Move "single-list" FoMs into API

Reasons for differences:

1. Resolution shells slightly different
The binning calculation needs to take into account small rounding errors
in the resolution calculation, when not using an explicit resolution
range (--highres).  The old version did this by taking a min/max
resolution range slightly larger than the resolution of the data.  The
new version handles the rounding errors explicitly, so does not need
this.

2. Number of reflections with infinite/invalid I/sigI values halved
The number reported for this count was twice what it should have been,
due to a bug in the old check_hkl.

3. Overall SNR is different
When the above warning message applies, the old version still allowed
the reflections with invalid I/sigI values to contribute to the
denominator of the mean SNR calculation.  The new version does not
include them in the SNR calculation at all.  Note that the reflections
contribute to the other figures of merit unless otherwise stated.

4. Standard deviation of intensity is not calculated
It would've been a lot of work to include this in the new version, and
it's a totally useless number.  If you disagree, please get in touch!

1 files changed, 502 insertions, 110 deletions

diff --git a/libcrystfel/src/fom.c b/libcrystfel/src/fom.c
index 19f35a86..c2de704a 100644
--- a/libcrystfel/src/fom.c
+++ b/libcrystfel/src/fom.c
@@ -43,6 +43,33 @@
 #include "reflist.h"
 #include "reflist-utils.h"
 
+struct fom_context
+{
+	enum fom_type fom;
+	int nshells;
+	int *cts;
+
+	/* For R-factors */
+	double *num;
+	double *den;
+
+	/* For "double" R-factors */
+	double *num2;
+	double *den2;
+
+	/* For CCs */
+	double **vec1;
+	double **vec2;
+	int *n;
+	int nmax;
+
+	/* For "counting" things e.g. d1sig or d2sig */
+	int *n_within;
+
+	long int *n_meas;
+	long int *possible;
+};
+
 enum fom_type fom_type_from_string(const char *s)
 {
 	if ( strcasecmp(s, "r1i") == 0 ) return FOM_R1I;
@@ -78,6 +105,12 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		fctx->cts[i] = 0;
 	}
 
+	fctx->num = NULL;
+	fctx->den = NULL;
+	fctx->num2 = NULL;
+	fctx->den2 = NULL;
+	fctx->possible = NULL;
+
 	switch ( fctx->fom ) {
 
 		case FOM_RANORSPLIT :
@@ -95,6 +128,10 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		case FOM_R2 :
 		case FOM_RSPLIT :
 		case FOM_RANO :
+		case FOM_MEAN_INTENSITY :
+		case FOM_STDDEV_INTENSITY :
+		case FOM_SNR :
+		case FOM_REDUNDANCY :
 		fctx->num = malloc(nshells*sizeof(double));
 		fctx->den = malloc(nshells*sizeof(double));
 		if ( (fctx->num == NULL) || (fctx->den == NULL) ) return NULL;
@@ -104,6 +141,15 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 		}
 		break;
 
+		case FOM_COMPLETENESS :
+		/* Uses 'cts' and 'possible' only */
+		break;
+
+		case FOM_NUM_MEASUREMENTS :
+		fctx->n_meas = calloc(nshells, sizeof(long int));
+		if ( fctx->n_meas == NULL ) return NULL;
+		break;
+
 		case FOM_CC :
 		case FOM_CCSTAR :
 		case FOM_CCANO :
@@ -140,37 +186,45 @@ static struct fom_context *init_fom(enum fom_type fom, int nmax, int nshells)
 }
 
 
-static void add_to_fom(struct fom_context *fctx, double i1, double i2,
-                       double i1bij, double i2bij, double sig1, double sig2,
-                       int bin)
+static int add_to_fom(struct fom_context *fctx,
+                      Reflection *refl1,
+                      Reflection *refl2,
+                      Reflection *refl1bij,
+                      Reflection *refl2bij,
+                      int bin)
 {
-	double f1, f2;
+	double i1, i2, i1bij, i2bij, sig1, sig2;
 	double im, imbij;
+	int bad = 0;
 
 	fctx->cts[bin]++;
 
-	/* Negative intensities have already been weeded out. */
-	f1 = sqrt(i1);
-	f2 = sqrt(i2);
-
 	switch ( fctx->fom ) {
 
 		case FOM_R1I :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
 		fctx->num[bin] += fabs(i1 - i2);
 		fctx->den[bin] += i1;
 		break;
 
 		case FOM_R1F :
-		fctx->num[bin] += fabs(f1 - f2);
-		fctx->den[bin] += f1;
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
+		fctx->num[bin] += fabs(sqrt(i1) - sqrt(i2));
+		fctx->den[bin] += sqrt(i1);
 		break;
 
 		case FOM_R2 :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
 		fctx->num[bin] += pow(i1 - i2, 2.0);
 		fctx->den[bin] += pow(i1, 2.0);
 		break;
 
 		case FOM_RSPLIT :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
 		fctx->num[bin] += fabs(i1 - i2);
 		fctx->den[bin] += i1 + i2;
 		break;
@@ -178,6 +232,8 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
 		case FOM_CC :
 		case FOM_CCSTAR :
 		assert(fctx->n[bin] < fctx->nmax);
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
 		fctx->vec1[bin][fctx->n[bin]] = i1;
 		fctx->vec2[bin][fctx->n[bin]] = i2;
 		fctx->n[bin]++;
@@ -186,17 +242,27 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
 		case FOM_CCANO :
 		case FOM_CRDANO :
 		assert(fctx->n[bin] < fctx->nmax);
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
+		i1bij = get_intensity(refl1bij);
+		i2bij = get_intensity(refl2bij);
 		fctx->vec1[bin][fctx->n[bin]] = i1 - i1bij;
 		fctx->vec2[bin][fctx->n[bin]] = i2 - i2bij;
 		fctx->n[bin]++;
 		break;
 
 		case FOM_RANORSPLIT :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
 		fctx->num2[bin] += fabs(i1 - i2);
 		fctx->den2[bin] += i1 + i2;
 		/* Intentional fall-through (no break) */
 
 		case FOM_RANO :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
+		i1bij = get_intensity(refl1bij);
+		i2bij = get_intensity(refl2bij);
 		im = (i1 + i2)/2.0;
 		imbij = (i1bij + i2bij)/2.0;
 		fctx->num[bin] += fabs(im - imbij);
@@ -204,22 +270,69 @@ static void add_to_fom(struct fom_context *fctx, double i1, double i2,
 		break;
 
 		case FOM_D1SIG :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
+		sig1 = get_esd_intensity(refl1);
+		sig2 = get_esd_intensity(refl2);
 		if ( fabs(i1-i2) < sqrt(sig1*sig1 + sig2*sig2) ) {
 			fctx->n_within[bin]++;
 		}
 		break;
 
 		case FOM_D2SIG :
+		i1 = get_intensity(refl1);
+		i2 = get_intensity(refl2);
+		sig1 = get_esd_intensity(refl1);
+		sig2 = get_esd_intensity(refl2);
 		if ( fabs(i1-i2) < 2.0*sqrt(sig1*sig1 + sig2*sig2) ) {
 			fctx->n_within[bin]++;
 		}
 		break;
 
+		case FOM_NUM_MEASUREMENTS :
+		fctx->n_meas[bin] += get_redundancy(refl1);
+		break;
+
+		case FOM_REDUNDANCY :
+		fctx->num[bin] += get_redundancy(refl1);
+		fctx->den[bin] += 1.0;
+		break;
+
+		case FOM_SNR :
+		i1 = get_intensity(refl1);
+		sig1 = get_esd_intensity(refl1);
+		if ( isfinite(i1/sig1) ) {
+			fctx->num[bin] += i1/sig1;
+			fctx->den[bin] += 1.0;
+		} else {
+			bad = 1;
+		}
+		break;
+
+		case FOM_MEAN_INTENSITY :
+		i1 = get_intensity(refl1);
+		fctx->num[bin] += i1;
+		fctx->den[bin] += 1.0;
+		break;
+
+		/* FIXME: Delete this FoM? */
+		case FOM_STDDEV_INTENSITY :
+		fctx->num[bin] += 1.0;
+		fctx->den[bin] += 1.0;
+		break;
+
+		case FOM_COMPLETENESS :
+		/* fctx->cts already incremented, as needed.
+		 * Will calculate possible reflections later */
+		break;
+
 	}
+
+	return bad;
 }
 
 
-double fom_overall(struct fom_context *fctx)
+double fom_overall_value(struct fom_context *fctx)
 {
 	double overall_num = INFINITY;
 	double overall_den = 0.0;
@@ -234,6 +347,9 @@ double fom_overall(struct fom_context *fctx)
 	double variance_signal;
 	double variance_error;
 	double cc = INFINITY;
+	long int total_meas = 0;
+	long int overall_cts = 0;
+	long int overall_possible = 0;
 
 	switch ( fctx->fom ) {
 
@@ -242,6 +358,10 @@ double fom_overall(struct fom_context *fctx)
 		case FOM_R2 :
 		case FOM_RSPLIT :
 		case FOM_RANO :
+		case FOM_REDUNDANCY :
+		case FOM_SNR :
+		case FOM_MEAN_INTENSITY :
+		case FOM_STDDEV_INTENSITY :
 		overall_num = 0.0;
 		overall_den = 0.0;
 		for ( i=0; i<fctx->nshells; i++ ) {
@@ -321,14 +441,38 @@ double fom_overall(struct fom_context *fctx)
 		}
 		break;
 
+		case FOM_NUM_MEASUREMENTS :
+		total_meas = 0;
+		for ( i=0; i<fctx->nshells; i++ ) {
+			total_meas += fctx->n_meas[i];
+		}
+		break;
+
+		case FOM_COMPLETENESS :
+		for ( i=0; i<fctx->nshells; i++ ) {
+			overall_cts += fctx->cts[i];
+			overall_possible += fctx->possible[i];
+		}
+		break;
+
 	}
 
 	switch ( fctx->fom ) {
 
 		case FOM_R1I :
 		case FOM_R1F :
+		case FOM_REDUNDANCY :
+		case FOM_SNR :
+		case FOM_MEAN_INTENSITY :
+		case FOM_STDDEV_INTENSITY :
 		return overall_num/overall_den;
 
+		case FOM_COMPLETENESS :
+		return (double)overall_cts / overall_possible;
+
+		case FOM_NUM_MEASUREMENTS :
+		return total_meas;
+
 		case FOM_R2 :
 		return sqrt(overall_num/overall_den);
 
@@ -361,7 +505,7 @@ double fom_overall(struct fom_context *fctx)
 }
 
 
-double fom_shell(struct fom_context *fctx, int i)
+double fom_shell_value(struct fom_context *fctx, int i)
 {
 	double cc;
 	int j;
@@ -374,6 +518,10 @@ double fom_shell(struct fom_context *fctx, int i)
 
 		case FOM_R1I :
 		case FOM_R1F :
+		case FOM_REDUNDANCY :
+		case FOM_SNR :
+		case FOM_MEAN_INTENSITY :
+		case FOM_STDDEV_INTENSITY :
 		return fctx->num[i]/fctx->den[i];
 
 		case FOM_R2 :
@@ -420,6 +568,12 @@ double fom_shell(struct fom_context *fctx, int i)
 		case FOM_D2SIG :
 		return (double)fctx->n_within[i] / fctx->cts[i];
 
+		case FOM_NUM_MEASUREMENTS :
+		return fctx->n_meas[i];
+
+		case FOM_COMPLETENESS :
+		return (double)fctx->cts[i] / fctx->possible[i];
+
 	}
 
 	ERROR("This point is never reached.\n");
@@ -469,7 +623,7 @@ struct fom_shells *fom_make_resolution_shells(double rmin, double rmax,
 }
 
 
-double fom_shell_label(struct fom_shells *s, int i)
+double fom_shell_centre(struct fom_shells *s, int i)
 {
 	return s->rmins[i] + (s->rmaxs[i] - s->rmins[i])/2.0;
 }
@@ -605,15 +759,143 @@ static int wilson_scale(RefList *list1, RefList *list2, UnitCell *cell)
 }
 
 
+static int calculate_possible(struct fom_context *fctx,
+                              struct fom_shells *shells,
+                              UnitCell *cell,
+                              const SymOpList *sym)
+{
+	RefList *counted;
+	int hmax, kmax, lmax;
+	double ax, ay, az;
+	double bx, by, bz;
+	double cx, cy, cz;
+	signed int h, k, l;
+
+	fctx->possible = calloc(fctx->nshells, sizeof(long int));
+	if ( fctx->possible == NULL ) return 1;
+
+	counted = reflist_new();
+	if ( counted == NULL ) {
+		free(fctx->possible);
+		return 1;
+	}
+
+	cell_get_cartesian(cell, &ax, &ay, &az,
+	                         &bx, &by, &bz,
+	                         &cx, &cy, &cz);
+	hmax = shells->rmaxs[fctx->nshells-1] * modulus(ax, ay, az);
+	kmax = shells->rmaxs[fctx->nshells-1] * modulus(bx, by, bz);
+	lmax = shells->rmaxs[fctx->nshells-1] * modulus(cx, cy, cz);
+	for ( h=-hmax; h<=hmax; h++ ) {
+	for ( k=-kmax; k<=kmax; k++ ) {
+	for ( l=-lmax; l<=lmax; l++ ) {
+
+		double d;
+		signed int hs, ks, ls;
+		int bin;
+		int i;
+
+		get_asymm(sym, h, k, l, &hs, &ks, &ls);
+		d = 2.0 * resolution(cell, hs, ks, ls);
+
+		if ( forbidden_reflection(cell, h, k, l) ) continue;
+
+		bin = -1;
+		for ( i=0; i<fctx->nshells; i++ ) {
+			if ( (d>shells->rmins[i]) && (d<=shells->rmaxs[i]) ) {
+				bin = i;
+				break;
+			}
+		}
+		if ( bin == -1 ) continue;
+
+		if ( find_refl(counted, hs, ks, ls) != NULL ) continue;
+		add_refl(counted, hs, ks, ls);
+
+		fctx->possible[bin]++;
+
+	}
+	}
+	}
+	reflist_free(counted);
+
+	return 0;
+}
+
+
+static int is_anomalous(enum fom_type fom)
+{
+	switch ( fom ) {
+
+		case FOM_CCANO:
+		case FOM_RANO:
+		case FOM_CRDANO:
+		case FOM_RANORSPLIT:
+		return 1;
+
+		case FOM_R1I:
+		case FOM_R1F:
+		case FOM_R2:
+		case FOM_RSPLIT:
+		case FOM_CC:
+		case FOM_CCSTAR:
+		case FOM_D1SIG:
+		case FOM_D2SIG:
+		case FOM_NUM_MEASUREMENTS:
+		case FOM_REDUNDANCY:
+		case FOM_SNR:
+		case FOM_MEAN_INTENSITY:
+		case FOM_STDDEV_INTENSITY:
+		case FOM_COMPLETENESS:
+		return 0;
+	}
+
+	ERROR("This point never reached\n");
+	abort();
+}
+
+
+static int is_single_list(enum fom_type fom)
+{
+	switch ( fom ) {
+
+		case FOM_CCANO:
+		case FOM_RANO:
+		case FOM_CRDANO:
+		case FOM_RANORSPLIT:
+		case FOM_R1I:
+		case FOM_R1F:
+		case FOM_R2:
+		case FOM_RSPLIT:
+		case FOM_CC:
+		case FOM_CCSTAR:
+		case FOM_D1SIG:
+		case FOM_D2SIG:
+		return 0;
+
+		case FOM_NUM_MEASUREMENTS:
+		case FOM_REDUNDANCY:
+		case FOM_SNR:
+		case FOM_MEAN_INTENSITY:
+		case FOM_STDDEV_INTENSITY:
+		case FOM_COMPLETENESS:
+		return 1;
+	}
+
+	ERROR("This point never reached\n");
+	abort();
+}
+
 
 struct fom_context *fom_calculate(RefList *list1, RefList *list2, UnitCell *cell,
                                   struct fom_shells *shells, enum fom_type fom,
-                                  int noscale, SymOpList *sym)
+                                  int noscale, const SymOpList *sym)
 {
 	Reflection *refl1;
 	RefListIterator *iter;
 	struct fom_context *fctx;
-	int n_out;
+	long int n_out = 0;
+	long int n_rej = 0;
 
 	fctx = init_fom(fom, num_reflections(list1), shells->nshells);
 
@@ -622,40 +904,44 @@ struct fom_context *fom_calculate(RefList *list1, RefList *list2, UnitCell *cell
 		return NULL;
 	}
 
-	if ( !noscale && wilson_scale(list1, list2, cell) ) {
-		ERROR("Error with scaling.\n");
-		return NULL;
-	}
+	if ( !is_single_list(fom) ) {
+		if ( !noscale && wilson_scale(list1, list2, cell) ) {
+			ERROR("Error with scaling.\n");
+			return NULL;
+		}
 
-	for ( refl1 = first_refl(list1, &iter);
-	      refl1 != NULL;
-	      refl1 = next_refl(refl1, iter) )
-	{
-		Reflection *refl2;
-		signed int h, k, l;
-		set_flag(refl1, 0);
-		get_indices(refl1, &h, &k, &l);
-		refl2 = find_refl(list2, h, k, l);
-		assert(refl2 != NULL);
-		set_flag(refl2, 0);
+		for ( refl1 = first_refl(list1, &iter);
+		      refl1 != NULL;
+		      refl1 = next_refl(refl1, iter) )
+		{
+			Reflection *refl2;
+			signed int h, k, l;
+			set_flag(refl1, 0);
+			get_indices(refl1, &h, &k, &l);
+			refl2 = find_refl(list2, h, k, l);
+			assert(refl2 != NULL);
+			set_flag(refl2, 0);
+		}
 	}
 
-	n_out = 0;
 	for ( refl1 = first_refl(list1, &iter);
 	      refl1 != NULL;
 	      refl1 = next_refl(refl1, iter) )
 	{
 		signed int h, k, l;
 		int bin;
-		double i1, i2;
-		double i1bij, i2bij;
-		double sig1, sig2;
 		Reflection *refl2;
+		Reflection *refl1_bij = NULL;
+		Reflection *refl2_bij = NULL;
 
 		get_indices(refl1, &h, &k, &l);
 
-		refl2 = find_refl(list2, h, k, l);
-		if ( refl2 == NULL ) continue;
+		if ( is_single_list(fom) ) {
+			refl2 = NULL;
+		} else {
+			refl2 = find_refl(list2, h, k, l);
+			if ( refl2 == NULL ) continue;
+		}
 
 		bin = get_bin(shells, refl1, cell);
 		if ( bin == -1 ) {
@@ -663,17 +949,8 @@ struct fom_context *fom_calculate(RefList *list1, RefList *list2, UnitCell *cell
 			continue;
 		}
 
-		i1 = get_intensity(refl1);
-		i2 = get_intensity(refl2);
-		sig1 = get_esd_intensity(refl1);
-		sig2 = get_esd_intensity(refl2);
+		if ( is_anomalous(fom) ) {
 
-		if ( (fom == FOM_CCANO) || (fom == FOM_CRDANO)
-		  || (fom == FOM_RANO) || (fom == FOM_RANORSPLIT) )
-		{
-
-			Reflection *refl1_bij = NULL;
-			Reflection *refl2_bij = NULL;
 			signed int hb, kb, lb;
 
 			if ( find_equiv_in_list(list1, -h, -k, -l, sym,
@@ -700,46 +977,59 @@ struct fom_context *fom_calculate(RefList *list1, RefList *list2, UnitCell *cell
 			assert(refl1_bij != NULL);
 			assert(refl2_bij != NULL);
 
-			i1bij = get_intensity(refl1_bij);
-			i2bij = get_intensity(refl2_bij);
-
-		} else {
-
-			/* Make it obvious if these get used by mistake */
-			i1bij = +INFINITY;
-			i2bij = +INFINITY;
-
 		}
 
-		add_to_fom(fctx, i1, i2, i1bij, i2bij, sig1, sig2, bin);
+		n_rej += add_to_fom(fctx, refl1, refl2, refl1_bij, refl2_bij, bin);
+
 	}
-	if ( n_out)  {
+	if ( n_out )  {
 		ERROR("WARNING: %i reflection pairs outside range.\n", n_out);
 	}
+	if ( n_rej ) {
+		if ( fom == FOM_SNR ) {
+			ERROR("WARNING: %li reflections had infinite or "
+			      "invalid values of I/sigma(I).\n", n_rej);
+		} else {
+			ERROR("WARNING: %li reflections rejected by add_to_fom\n",
+			      n_rej);
+		}
+	}
+
+	if ( fom == FOM_COMPLETENESS ) {
+		calculate_possible(fctx, shells, cell, sym);
+	}
 
 	return fctx;
 }
 
 
-int fom_select_reflections(RefList *list1, RefList *list2,
-                           RefList *list1_acc, RefList *list2_acc,
-                           UnitCell *cell, SymOpList *sym,
-                           int anom, double rmin_fix, double rmax_fix,
-                           double sigma_cutoff, int ignore_negs,
-                           int zero_negs, int mul_cutoff)
+struct fom_rejections fom_select_reflection_pairs(RefList *list1, RefList *list2,
+                                                  RefList **plist1_acc,
+                                                  RefList **plist2_acc,
+                                                  UnitCell *cell, SymOpList *sym,
+                                                  int anom, double rmin_fix, double rmax_fix,
+                                                  double sigma_cutoff, int ignore_negs,
+                                                  int zero_negs, int mul_cutoff)
 {
 	Reflection *refl1;
 	RefListIterator *iter;
-	int ncom, nrej, nmul, nneg, nres, nbij, ncen;
-
-	/* Select reflections to be used */
-	ncom = 0;
-	nrej = 0;
-	nmul = 0;
-	nneg = 0;
-	nres = 0;
-	nbij = 0;
-	ncen = 0;
+	struct fom_rejections rej;
+	RefList *list1_acc;
+	RefList *list2_acc;
+
+	rej.common = 0;
+	rej.low_snr = 0;
+	rej.negative_deleted = 0;
+	rej.negative_zeroed = 0;
+	rej.few_measurements = 0;
+	rej.outside_resolution_range = 0;
+	rej.no_bijvoet = 0;
+	rej.centric = 0;
+	rej.nan_inf_value = 0;
+
+	list1_acc = reflist_new();
+	list2_acc = reflist_new();
+
 	for ( refl1 = first_refl(list1, &iter);
 	      refl1 != NULL;
 	      refl1 = next_refl(refl1, iter) )
@@ -766,20 +1056,27 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 		mul1 = get_redundancy(refl1);
 		mul2 = get_redundancy(refl2);
 
+		if ( !isfinite(val1) || !isfinite(val2)
+		  || !isfinite(esd1) || !isfinite(esd2) )
+		{
+			rej.nan_inf_value++;
+			continue;
+		}
+
 		if ( (val1 < sigma_cutoff * esd1)
 		  || (val2 < sigma_cutoff * esd2) )
 		{
-			nrej++;
+			rej.low_snr++;
 			continue;
 		}
 
 		if ( ignore_negs && ((val1 < 0.0) || (val2 < 0.0)) ) {
-			nneg++;
+			rej.negative_deleted++;
 			continue;
 		}
 
 		if ( (mul1 < mul_cutoff) || (mul2 < mul_cutoff) ) {
-			nmul++;
+			rej.few_measurements++;
 			continue;
 		}
 
@@ -793,13 +1090,14 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 				val2 = 0.0;
 				d = 1;
 			}
-			if ( d ) nneg++;
+			if ( d ) rej.negative_zeroed++;
+			continue;
 		}
 
 		if ( rmin_fix > 0.0 ) {
 			double res = 2.0*resolution(cell, h, k, l);
 			if ( res < rmin_fix ) {
-				nres++;
+				rej.outside_resolution_range++;
 				continue;
 			}
 		}
@@ -807,7 +1105,7 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 		if ( rmax_fix > 0.0 ) {
 			double res = 2.0*resolution(cell, h, k, l);
 			if ( res > rmax_fix ) {
-				nres++;
+				rej.outside_resolution_range++;
 				continue;
 			}
 		}
@@ -820,7 +1118,7 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 		copy_data(refl2_acc, refl2);
 		set_intensity(refl2_acc, val2);
 
-		ncom++;
+		rej.common++;
 
 	}
 
@@ -833,7 +1131,7 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 		list1_acc = reflist_new();
 		list2_acc = reflist_new();
 
-		ncom = 0;
+		rej.common = 0;
 
 		for ( refl1 = first_refl(list1, &iter);
 		      refl1 != NULL;
@@ -857,7 +1155,7 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 			val2 = get_intensity(refl2);
 
 			if ( is_centric(h, k, l, sym) ) {
-				ncen++;
+				rej.centric++;
 				continue;
 			}
 
@@ -874,7 +1172,7 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 			}
 
 			if ( (refl1_bij == NULL) || (refl2_bij == NULL) ) {
-				nbij++;
+				rej.no_bijvoet++;
 				continue;
 			}
 
@@ -886,44 +1184,138 @@ int fom_select_reflections(RefList *list1, RefList *list2,
 			copy_data(refl2_acc, refl2);
 			set_intensity(refl2_acc, val2);
 
-			ncom++;
+			rej.common++;
 		}
 	}
 
-	if ( nrej > 0 ) {
-		STATUS("Discarded %i reflection pairs because either or both"
-		       " versions had I/sigma(I) < %f.\n", nrej, sigma_cutoff);
-	}
+	*plist1_acc = list1_acc;
+	*plist2_acc = list2_acc;
+	return rej;
+}
 
-	if ( ignore_negs && (nneg > 0) ) {
-		STATUS("Discarded %i reflection pairs because either or both"
-		       " versions had negative intensities.\n", nneg);
-	}
 
-	if ( zero_negs && (nneg > 0) ) {
-		STATUS("For %i reflection pairs, either or both versions had"
-		       " negative intensities which were set to zero.\n", nneg);
-	}
+struct fom_rejections fom_select_reflections(RefList *raw_list,
+                                             RefList **plist_acc,
+                                             UnitCell *cell, SymOpList *sym,
+                                             double rmin_fix, double rmax_fix,
+                                             double sigma_cutoff, int ignore_negs,
+                                             int zero_negs, int mul_cutoff)
+{
+	RefList *list;
+	Reflection *refl;
+	RefListIterator *iter;
+	struct fom_rejections rej;
 
-	if ( nmul > 0 ) {
-		STATUS("%i reflection pairs rejected because either or both"
-		       " versions had too few measurements.\n", nmul);
-	}
+	*plist_acc = NULL;
+
+	rej.common = 0;
+	rej.low_snr = 0;
+	rej.negative_deleted = 0;
+	rej.negative_zeroed = 0;
+	rej.few_measurements = 0;
+	rej.outside_resolution_range = 0;
+	rej.no_bijvoet = 0;
+	rej.centric = 0;
+	rej.nan_inf_value = 0;
+
+	list = reflist_new();
+	if ( list == NULL ) return rej;
+
+	for ( refl = first_refl(raw_list, &iter);
+	      refl != NULL;
+	      refl = next_refl(refl, iter) ) {
+
+		signed int h, k, l;
+		double val, sig;
+		int ig = 0;
+		Reflection *new;
+
+		get_indices(refl, &h, &k, &l);
+
+		val = get_intensity(refl);
+		sig = get_esd_intensity(refl);
+
+		if ( !isfinite(val) || !isfinite(sig) ) {
+			rej.nan_inf_value++;
+			continue;
+		}
+
+		if ( val < sigma_cutoff * sig ) {
+			rej.low_snr++;
+			ig = 1;
+		}
+
+		if ( ignore_negs && (val < 0.0) ) {
+			rej.negative_deleted++;
+			ig = 1;
+		}
+
+		if ( zero_negs && (val < 0.0) ) {
+			set_intensity(refl, 0.0);
+			rej.negative_zeroed++;
+		}
+
+		if ( rmin_fix > 0.0 ) {
+			double res = 2.0*resolution(cell, h, k, l);
+			if ( res < rmin_fix ) {
+				rej.outside_resolution_range++;
+				continue;
+			}
+		}
 
-	if ( nres > 0 ) {
-		STATUS("%i reflection pairs rejected because either or both"
-		       " versions were outside the resolution range.\n", nres);
+		if ( rmax_fix > 0.0 ) {
+			double res = 2.0*resolution(cell, h, k, l);
+			if ( res > rmax_fix ) {
+				rej.outside_resolution_range++;
+				continue;
+			}
+		}
+
+		if ( ig ) continue;
+
+		new = add_refl(list, h, k, l);
+		copy_data(new, refl);
 	}
 
-	if ( nbij > 0 ) {
-		STATUS("%i reflection pairs rejected because either or both"
-		       " versions did not have Bijvoet partners.\n", nres);
+	*plist_acc = list;
+	return rej;
+}
+
+
+int fom_overall_num_reflections(struct fom_context *fctx)
+{
+	int i;
+	long int n = 0;
+
+	for ( i=0; i<fctx->nshells; i++ ) {
+		n += fctx->cts[i];
 	}
+	return n;
+}
+
 
-	if ( ncen > 0 ) {
-		STATUS("%i reflection pairs rejected because they were"
-		       " centric.\n", ncen);
+int fom_shell_num_reflections(struct fom_context *fctx, int i)
+{
+	return fctx->cts[i];
+}
+
+
+int fom_overall_num_possible(struct fom_context *fctx)
+{
+	int i;
+	long int n = 0;
+
+	assert(fctx->fom == FOM_COMPLETENESS);
+
+	for ( i=0; i<fctx->nshells; i++ ) {
+		n += fctx->possible[i];
 	}
+	return n;
+}
+
 
-	return ncom;
+int fom_shell_num_possible(struct fom_context *fctx, int i)
+{
+	assert(fctx->fom == FOM_COMPLETENESS);
+	return fctx->possible[i];
 }