Merge branch 'master' into taketwo

22 files changed, 345 insertions, 111 deletions

diff --git a/doc/man/render_hkl.1 b/doc/man/render_hkl.1
index d78e3343..eadbba34 100644
--- a/doc/man/render_hkl.1
+++ b/doc/man/render_hkl.1
@@ -93,6 +93,11 @@ The raw numbers of observations of the reflections, without performing the corre
 The default is \fB--weighting=I\fR.
 
 .PD 0
+.IP \fB--scale-top=\fIn\fR
+.PD
+Force the top of the colour scale to correspond to a value of \fIn\fR.  Any value you give for \fB--boost\fR will be ignored.
+
+.PD 0
 .IP \fB--colour-key\fR
 .PD
 Write the selected colour scale out to 'key.pdf' in the current directory.
diff --git a/libcrystfel/src/asdf.c b/libcrystfel/src/asdf.c
index df20f7ef..49917ad9 100644
--- a/libcrystfel/src/asdf.c
+++ b/libcrystfel/src/asdf.c
@@ -322,6 +322,15 @@ static int compare_doubles(const void *a, const void *b)
 }
 
 
+static double max(double a, double b, double c)
+{
+     double m = a;
+     if ( m < b ) m = b;
+     if ( m < c ) m = c;
+     return m;
+}
+
+
 /* Compares tvectors by length */
 static int compare_tvectors(const void *a, const void *b)
 {
@@ -889,12 +898,14 @@ static int find_cell(struct tvector *tvectors, int N_tvectors, double IndexFit,
 	return 0;
 }
 
+
 void swap(int *a, int *b) {
 	int c = *a;
 	*a = *b;
 	*b = c;
 }
 
+
 /* Generate triplets of integers < N_reflections in random sequence */
 static int **generate_triplets(int N_reflections, int N_triplets_max, int *N)
 {
@@ -904,10 +915,13 @@ static int **generate_triplets(int N_reflections, int N_triplets_max, int *N)
 	int N_triplets = N_reflections * (N_reflections - 1) *
 	                                 (N_reflections - 2) / 6;
 
-	if ( N_triplets > N_triplets_max ) N_triplets = N_triplets_max;
+	if ( N_triplets > N_triplets_max || N_reflections > 1000 ) {
+		N_triplets = N_triplets_max;
+	}
 	*N = N_triplets;
 
 	int **triplets = malloc(N_triplets * sizeof(int *));
+
 	if (triplets == NULL) {
 		ERROR("Failed to allocate triplets in generate_triplets!\n");
 		return 0;
@@ -962,6 +976,7 @@ static int **generate_triplets(int N_reflections, int N_triplets_max, int *N)
 	return triplets;
 }
 
+
 static int index_refls(gsl_vector **reflections, int N_reflections,
                        double d_max, double volume_min, double volume_max,
                        double LevelFit, double IndexFit, int N_triplets_max,
@@ -1094,20 +1109,38 @@ int run_asdf(struct image *image, IndexingPrivate *ipriv)
 
 	double LevelFit = 1./1000;
 	double IndexFit = 1./500;
-	double d_max = 220.; // thrice the maximum expected axis length
+	double d_max = 1000.; // thrice the maximum expected axis length
 	double volume_min = 100.;
-	double volume_max = 1000000.;
+	double volume_max = 100000000.;
 
 	int N_triplets_max = 10000; // maximum number of triplets
 
 	struct asdf_private *dp = (struct asdf_private *)ipriv;
 
-	if ( dp->indm & INDEXING_CHECK_CELL_AXES ) {
+	if ( dp->indm & INDEXING_CHECK_CELL_AXES ||
+             dp->indm & INDEXING_CHECK_CELL_COMBINATIONS) {
+		double a, b, c, gamma, beta, alpha;
+		cell_get_parameters(dp->template, &a, &b, &c,
+                                                  &alpha, &beta, &gamma);
+
+		d_max = max(a, b, c) * 3 * 1e10;
+
 		double volume = cell_get_volume(dp->template);
 		double vtol = (dp->ltl[0] + dp->ltl[1] + dp->ltl[2]) / 100 +
 		               dp->ltl[3] / 180 * M_PI;
-		volume_min = volume * (1 - vtol);
-		volume_max = volume * (1 + vtol);
+
+		/* Divide volume constraints by number of lattice points per
+		 * unit cell since asdf always finds primitive cell */
+		int latt_points_per_uc = 1;
+		char centering = cell_get_centering(dp->template);
+		if ( centering == 'A' ||
+		     centering == 'B' ||
+		     centering == 'C' ||
+		     centering == 'I' ) latt_points_per_uc = 2;
+		else if ( centering == 'F' ) latt_points_per_uc = 4;
+
+		volume_min = volume * (1 - vtol)/latt_points_per_uc;
+		volume_max = volume * (1 + vtol)/latt_points_per_uc;
 	}
 
 	int n = image_feature_count(image->features);
diff --git a/libcrystfel/src/geometry.c b/libcrystfel/src/geometry.c
index 266d6267..b968dc06 100644
--- a/libcrystfel/src/geometry.c
+++ b/libcrystfel/src/geometry.c
@@ -52,16 +52,15 @@ static int locate_peak_on_panel(double x, double y, double z, double k,
                                 struct panel *p,
                                 double *pfs, double *pss)
 {
-	double r2, ctt, tta, phi;
+	double ctt, tta, phi;
 	gsl_vector *v;
 	gsl_vector *t;
 	gsl_matrix *M;
 	double fs, ss, one_over_mu;
 
 	/* Calculate 2theta (scattering angle) and azimuth (phi) */
-	r2 = x*x + y*y + z*z;
-	ctt = 1.0 - r2 / (2.0*k*k);  /* cos(2theta) */
-	tta = acos(ctt);
+	tta = atan2(sqrt(x*x+y*y), k+z);
+	ctt = cos(tta);
 	phi = atan2(y, x);
 
 	/* Set up matrix equation */
@@ -637,25 +636,18 @@ void polarisation_correction(RefList *list, UnitCell *cell, struct image *image)
 	      refl != NULL;
 	      refl = next_refl(refl, iter) )
 	{
-		double pol, pa, pb, phi, tt, ool;
+		double pol;
 		double intensity;
-		double xl, yl, zl;
+		double xl, yl;
 		signed int h, k, l;
+		const double P = 1.0;  /* degree of polarisation */
 
 		get_indices(refl, &h, &k, &l);
 
-		/* Polarisation correction assuming 100% polarisation
-		 * along the x direction */
-		xl = h*asx + k*bsx + l*csx;
-		yl = h*asy + k*bsy + l*csy;
-		zl = h*asz + k*bsz + l*csz;
+		xl = (h*asx + k*bsx + l*csx)*image->lambda;
+		yl = (h*asy + k*bsy + l*csy)*image->lambda;
 
-		ool = 1.0 / image->lambda;
-		tt = angle_between(0.0, 0.0, 1.0,  xl, yl, zl+ool);
-		phi = atan2(yl, xl);
-		pa = pow(sin(phi)*sin(tt), 2.0);
-		pb = pow(cos(tt), 2.0);
-		pol = 1.0 - 2.0*(1.0-pa) + (1.0+pb);
+		pol = P*(1.0 - xl*xl) + (1.0-P)*(1.0 - yl*yl);
 
 		intensity = get_intensity(refl);
 		set_intensity(refl, intensity / pol);
diff --git a/libcrystfel/src/index.c b/libcrystfel/src/index.c
index e0bebfa4..e7fd879d 100644
--- a/libcrystfel/src/index.c
+++ b/libcrystfel/src/index.c
@@ -3,12 +3,12 @@
  *
  * Perform indexing (somehow)
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2016 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2010-2011 Richard Kirian <rkirian@asu.edu>
  *   2012      Lorenzo Galli
  *   2013      Cornelius Gati <cornelius.gati@cfel.de>
@@ -434,10 +434,16 @@ static int finished_retry(IndexingMethod indm, int r, struct image *image)
 	}
 }
 
-
 void index_pattern(struct image *image,
                    IndexingMethod *indms, IndexingPrivate **iprivs)
 {
+	index_pattern_2(image, indms, iprivs, NULL);
+}
+
+
+void index_pattern_2(struct image *image, IndexingMethod *indms,
+                     IndexingPrivate **iprivs, int *ping)
+{
 	int n = 0;
 	ImageFeatureList *orig;
 
@@ -465,6 +471,7 @@ void index_pattern(struct image *image,
 			ntry++;
 			done = finished_retry(indms[n], r, image);
 			if ( ntry > 5 ) done = 1;
+			if ( ping != NULL ) (*ping)++;
 
 		} while ( !done );
 
diff --git a/libcrystfel/src/index.h b/libcrystfel/src/index.h
index 23545506..33d568f6 100644
--- a/libcrystfel/src/index.h
+++ b/libcrystfel/src/index.h
@@ -3,13 +3,13 @@
  *
  * Perform indexing (somehow)
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2016 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2010      Richard Kirian
  *   2012      Lorenzo Galli
  *   2015      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
@@ -161,6 +161,9 @@ extern IndexingPrivate **prepare_indexing(IndexingMethod *indm, UnitCell *cell,
 extern void index_pattern(struct image *image,
                           IndexingMethod *indms, IndexingPrivate **iprivs);
 
+extern void index_pattern_2(struct image *image, IndexingMethod *indms,
+                            IndexingPrivate **iprivs, int *ping);
+
 extern void cleanup_indexing(IndexingMethod *indms, IndexingPrivate **privs);
 
 #ifdef __cplusplus
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 789a9d7a..e858172e 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -65,9 +65,11 @@ struct _stream
 
 	int major_version;
 	int minor_version;
+
+	long long int ln;
 };
 
-static int read_peaks(FILE *fh, struct image *image)
+static int read_peaks(Stream *st, struct image *image)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -82,7 +84,8 @@ static int read_peaks(FILE *fh, struct image *image)
 		struct panel *p = NULL;
 		float add_x, add_y;
 
-		rval = fgets(line, 1023, fh);
+		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 		if ( rval == NULL ) continue;
 		chomp(line);
 
@@ -126,7 +129,7 @@ static int read_peaks(FILE *fh, struct image *image)
 }
 
 
-static int read_peaks_2_3(FILE *fh, struct image *image)
+static int read_peaks_2_3(Stream *st, struct image *image)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -142,7 +145,8 @@ static int read_peaks_2_3(FILE *fh, struct image *image)
 		struct panel *p = NULL;
 		float add_x, add_y;
 
-		rval = fgets(line, 1023, fh);
+		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 		if ( rval == NULL ) continue;
 		chomp(line);
 
@@ -269,7 +273,7 @@ static int write_peaks_2_3(struct image *image, FILE *ofh)
 }
 
 
-static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
+static RefList *read_stream_reflections_2_3(Stream *st, struct detector *det)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -290,7 +294,8 @@ static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
 		int r;
 		Reflection *refl;
 
-		rval = fgets(line, 1023, fh);
+		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 		if ( rval == NULL ) continue;
 		chomp(line);
 
@@ -342,7 +347,7 @@ static RefList *read_stream_reflections_2_3(FILE *fh, struct detector *det)
 }
 
 
-static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
+static RefList *read_stream_reflections_2_1(Stream *st, struct detector *det)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -364,7 +369,8 @@ static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
 		int r;
 		Reflection *refl;
 
-		rval = fgets(line, 1023, fh);
+		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 		if ( rval == NULL ) continue;
 		chomp(line);
 
@@ -426,7 +432,7 @@ static RefList *read_stream_reflections_2_1(FILE *fh, struct detector *det)
 }
 
 
-static RefList *read_stream_reflections_2_2(FILE *fh, struct detector *det)
+static RefList *read_stream_reflections_2_2(Stream *st, struct detector *det)
 {
 	char *rval = NULL;
 	int first = 1;
@@ -442,7 +448,8 @@ static RefList *read_stream_reflections_2_2(FILE *fh, struct detector *det)
 		int r;
 		Reflection *refl;
 
-		rval = fgets(line, 1023, fh);
+		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 		if ( rval == NULL ) continue;
 		chomp(line);
 
@@ -887,14 +894,15 @@ int write_chunk(Stream *st, struct image *i, struct hdfile *hdfile,
 }
 
 
-static int find_start_of_chunk(FILE *fh)
+static int find_start_of_chunk(Stream *st)
 {
 	char *rval = NULL;
 	char line[1024];
 
 	do {
 
-		rval = fgets(line, 1023, fh);
+		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 
 		/* Trouble? */
 		if ( rval == NULL ) return 1;
@@ -942,6 +950,7 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 		char c;
 
 		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 
 		/* Trouble? */
 		if ( rval == NULL ) break;
@@ -975,7 +984,8 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 				centering = c;
 				have_cen = 1;
 			} else {
-				ERROR("Duplicate centering ignored.\n");
+				ERROR("Duplicate centering (line %lli) - "
+				      "stream may be corrupted!\n", st->ln);
 			}
 		}
 
@@ -986,7 +996,8 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 				unique_axis = c;
 				have_ua = 1;
 			} else {
-				ERROR("Duplicate unique axis ignored.\n");
+				ERROR("Duplicate unique axis (line %lli) - "
+				      "stream may be corrupted!\n", st->ln);
 			}
 		}
 
@@ -997,7 +1008,8 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 				lattice_type = lattice_from_str(line+15);
 				have_latt = 1;
 			} else {
-				ERROR("Duplicate lattice type ignored.\n");
+				ERROR("Duplicate lattice type (line %lli) - "
+				      "stream may be corrupted!\n", st->ln);
 			}
 		}
 
@@ -1030,13 +1042,13 @@ static void read_crystal(Stream *st, struct image *image, StreamReadFlags srf)
 			/* The reflection list format in the stream diverges
 			 * after 2.2 */
 			if ( AT_LEAST_VERSION(st, 2, 3) ) {
-				reflist = read_stream_reflections_2_3(st->fh,
+				reflist = read_stream_reflections_2_3(st,
                                                       image->det);
 			} else if ( AT_LEAST_VERSION(st, 2, 2) ) {
-				reflist = read_stream_reflections_2_2(st->fh,
+				reflist = read_stream_reflections_2_2(st,
 				          image->det);
 			} else {
-				reflist = read_stream_reflections_2_1(st->fh,
+				reflist = read_stream_reflections_2_1(st,
 				          image->det);
 			}
 			if ( reflist == NULL ) {
@@ -1148,7 +1160,7 @@ int read_chunk_2(Stream *st, struct image *image,  StreamReadFlags srf)
 	int have_filename = 0;
 	int have_ev = 0;
 
-	if ( find_start_of_chunk(st->fh) ) return 1;
+	if ( find_start_of_chunk(st) ) return 1;
 
 	image->lambda = -1.0;
 	image->features = NULL;
@@ -1167,6 +1179,7 @@ int read_chunk_2(Stream *st, struct image *image,  StreamReadFlags srf)
 		float div, bw;
 
 		rval = fgets(line, 1023, st->fh);
+		st->ln++;
 
 		/* Trouble? */
 		if ( rval == NULL ) break;
@@ -1257,9 +1270,9 @@ int read_chunk_2(Stream *st, struct image *image,  StreamReadFlags srf)
 			int fail;
 
 			if ( AT_LEAST_VERSION(st, 2, 3) ) {
-				fail = read_peaks_2_3(st->fh, image);
+				fail = read_peaks_2_3(st, image);
 			} else {
-				fail = read_peaks(st->fh, image);
+				fail = read_peaks(st, image);
 			}
 			if ( fail ) {
 				ERROR("Failed while reading peaks\n");
@@ -1358,6 +1371,8 @@ Stream *open_stream_for_read(const char *filename)
 		return NULL;
 	}
 
+	st->ln = 1;
+
 	return st;
 }
 
@@ -1656,6 +1671,7 @@ void write_geometry_file(Stream *st, const char *geom_filename) {
  */
 int rewind_stream(Stream *st)
 {
+	st->ln = 0;
 	return fseek(st->fh, 0, SEEK_SET);
 }
 
diff --git a/libcrystfel/src/symmetry.c b/libcrystfel/src/symmetry.c
index 503078a7..d675fb30 100644
--- a/libcrystfel/src/symmetry.c
+++ b/libcrystfel/src/symmetry.c
@@ -3,12 +3,12 @@
  *
  * Symmetry
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
- *   2014      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
+ *   2010-2014,2016 Thomas White <taw@physics.org>
+ *   2014           Kenneth Beyerlein <kenneth.beyerlein@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -1088,6 +1088,21 @@ SymOpList *get_pointgroup(const char *sym)
 }
 
 
+void pointgroup_warning(const char *sym)
+{
+	if ( (strcmp(sym, "m") == 0)
+	  || (strcmp(sym, "2/m") == 0)
+	  || (strcmp(sym, "2") == 0) )
+	{
+		ERROR("WARNING: You have specified a monoclinic point group "
+		      "without a unique axis.  The default unique axis is 'c'. "
+		      "If you want unique axis b, append '_uab' to your point "
+		      "group.\n");
+	}
+
+}
+
+
 static void do_op(const IntegerMatrix *op,
                   signed int h, signed int k, signed int l,
                   signed int *he, signed int *ke, signed int *le)
diff --git a/libcrystfel/src/symmetry.h b/libcrystfel/src/symmetry.h
index c29164ef..a61ca96f 100644
--- a/libcrystfel/src/symmetry.h
+++ b/libcrystfel/src/symmetry.h
@@ -3,12 +3,12 @@
  *
  * Symmetry
  *
- * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2014 Thomas White <taw@physics.org>
- *   2014      Kenneth Beyerlein <kenneth.beyerlein@desy.de>
+ *   2010-2014,2016 Thomas White <taw@physics.org>
+ *   2014           Kenneth Beyerlein <kenneth.beyerlein@desy.de>
  *
  * This file is part of CrystFEL.
  *
@@ -90,6 +90,8 @@ extern void describe_symmetry(const SymOpList *s);
 extern int is_centric(signed int h, signed int k, signed int l,
                       const SymOpList *ops);
 
+extern void pointgroup_warning(const char *sym);
+
 extern void add_symop(SymOpList *ops, IntegerMatrix *m);
 extern SymOpList *parse_symmetry_operations(const char *s);
 extern char *get_matrix_name(const IntegerMatrix *m, int row);
diff --git a/src/ambigator.c b/src/ambigator.c
index 659b17dc..f7837721 100644
--- a/src/ambigator.c
+++ b/src/ambigator.c
@@ -1099,6 +1099,7 @@ int main(int argc, char *argv[])
 	if ( s_sym_str == NULL ) {
 		s_sym_str = strdup("1");
 	}
+	pointgroup_warning(s_sym_str);
 	s_sym = get_pointgroup(s_sym_str);
 	if ( s_sym == NULL ) return 1;
 	free(s_sym_str);
@@ -1113,6 +1114,7 @@ int main(int argc, char *argv[])
 		w_sym = NULL;
 		amb = NULL;
 	} else {
+		pointgroup_warning(w_sym_str);
 		w_sym = get_pointgroup(w_sym_str);
 		free(w_sym_str);
 		if ( w_sym == NULL ) return 1;
diff --git a/src/cell_explorer.c b/src/cell_explorer.c
index 914e4740..c8bbb069 100644
--- a/src/cell_explorer.c
+++ b/src/cell_explorer.c
@@ -3,11 +3,11 @@
  *
  * Examine cell parameter histograms
  *
- * Copyright © 2014 Deutsches Elektronen-Synchrotron DESY,
- *                  a research centre of the Helmholtz Association.
+ * Copyright © 2014-2017 Deutsches Elektronen-Synchrotron DESY,
+ *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2014 Thomas White <taw@physics.org>
+ *   2014,2017 Thomas White <taw@physics.org>
  *
  * This file is part of CrystFEL.
  *
@@ -270,6 +270,52 @@ static void draw_axis(cairo_t *cr, HistoBox *b, int width, int height)
 }
 
 
+static void draw_label(cairo_t *cr, HistoBox *b, int width, int height)
+{
+	PangoLayout *layout;
+	PangoFontDescription *fontdesc;
+	PangoRectangle ext;
+	char label[256];
+	double sz;
+
+	layout = pango_cairo_create_layout(cr);
+
+	if ( b->have_fit ) {
+		snprintf(label, 255, "%s = %.2f ± %.2f%s",
+		         b->label, b->fit_b, b->fit_c/sqrt(2), b->units);
+	} else {
+		strncpy(label, b->label, 255);
+	}
+	pango_layout_set_text(layout, label, -1);
+
+	sz = (height*PANGO_SCALE)/10.0;
+
+	fontdesc = pango_font_description_new();
+	pango_font_description_set_family_static(fontdesc, "Serif");
+	pango_font_description_set_style(fontdesc, PANGO_STYLE_ITALIC);
+	pango_font_description_set_absolute_size(fontdesc, sz);
+	pango_layout_set_font_description(layout, fontdesc);
+
+	/* If text is too wide for box, adjust the size so it fits */
+	pango_layout_get_extents(layout, NULL, &ext);
+	if ( ext.width > PANGO_SCALE*(width-20.0) ) {
+		sz = ((double)PANGO_SCALE*(width-20.0) / ext.width)*sz;
+		pango_font_description_set_absolute_size(fontdesc, sz);
+		pango_layout_set_font_description(layout, fontdesc);
+	}
+
+
+	cairo_move_to(cr, 10.0, 10.0);
+	cairo_set_source_rgba(cr, 0.0, 0.0, 0.0, 1.0);
+	pango_cairo_update_layout(cr, layout);
+	pango_cairo_show_layout(cr, layout);
+	cairo_fill(cr);
+
+	g_object_unref(layout);
+	pango_font_description_free(fontdesc);
+}
+
+
 static gboolean draw_sig(GtkWidget *da, GdkEventExpose *event, HistoBox *b)
 {
 	int width, height;
@@ -431,24 +477,7 @@ static gboolean draw_sig(GtkWidget *da, GdkEventExpose *event, HistoBox *b)
 	cairo_restore(cr);
 
 	draw_axis(cr, b, width, height);
-
-	cairo_text_extents_t ext;
-	char label[256];
-
-	cairo_select_font_face(cr, "Serif", CAIRO_FONT_SLANT_ITALIC,
-	                       CAIRO_FONT_WEIGHT_BOLD);
-	cairo_set_font_size(cr, height/10.0);
-
-	if ( b->have_fit ) {
-		snprintf(label, 255, "%s = %.2f ± %.2f%s",
-		         b->label, b->fit_b, b->fit_c/sqrt(2), b->units);
-	} else {
-		strncpy(label, b->label, 255);
-	}
-
-	cairo_text_extents(cr, label, &ext);
-	cairo_move_to(cr, 10.0, 10.0+ext.height);
-	cairo_show_text(cr, label);
+	draw_label(cr, b, width, height);
 
 	cairo_destroy(cr);
 
@@ -1598,9 +1627,9 @@ int main(int argc, char *argv[])
 	w.cols_on[0] = 1;
 	for ( i=1; i<8; i++ ) w.cols_on[i] = 2;
 
-	w.hist_a = histobox_new(&w, " A", "a");
-	w.hist_b = histobox_new(&w, " A", "b");
-	w.hist_c = histobox_new(&w, " A", "c");
+	w.hist_a = histobox_new(&w, " Å", "a");
+	w.hist_b = histobox_new(&w, " Å", "b");
+	w.hist_c = histobox_new(&w, " Å", "c");
 	w.hist_al = histobox_new(&w, "°", "α");
 	w.hist_be = histobox_new(&w, "°", "β");
 	w.hist_ga = histobox_new(&w, "°", "γ");
diff --git a/src/get_hkl.c b/src/get_hkl.c
index 62c9e608..d6efe747 100644
--- a/src/get_hkl.c
+++ b/src/get_hkl.c
@@ -561,18 +561,21 @@ int main(int argc, char *argv[])
 	}
 
 	if ( holo_str != NULL ) {
+		pointgroup_warning(holo_str);
 		holo = get_pointgroup(holo_str);
 		free(holo_str);
 	} else {
 		holo = NULL;
 	}
 	if ( mero_str != NULL ) {
+		pointgroup_warning(mero_str);
 		mero = get_pointgroup(mero_str);
 		free(mero_str);
 	} else {
 		mero = NULL;
 	}
 	if ( expand_str != NULL ) {
+		pointgroup_warning(expand_str);
 		expand = get_pointgroup(expand_str);
 		free(expand_str);
 	} else {
diff --git a/src/im-sandbox.c b/src/im-sandbox.c
index 51cd5903..f5493453 100644
--- a/src/im-sandbox.c
+++ b/src/im-sandbox.c
@@ -3,13 +3,13 @@
  *
  * Sandbox for indexing
  *
- * Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2016 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *   2011      Richard Kirian
  *   2012      Lorenzo Galli
@@ -73,10 +73,18 @@ struct sandbox
 
 	struct index_args *iargs;
 
+	/* Worker processes */
 	int n_proc;
 	pid_t *pids;
-
 	int *running;
+	time_t *last_response;
+	int last_ping[MAX_NUM_WORKERS];
+
+	/* Streams to read from (NB not the same indices as the above) */
+	int n_read;
+	FILE **fhs;
+	int *fds;
+
 	int serial;
 
 	struct sb_shm *shared;
@@ -84,14 +92,6 @@ struct sandbox
 
 	char *tmpdir;
 
-	/* The last time each worker was heard from */
-	time_t *last_response;
-
-	/* Streams to read from */
-	int n_read;
-	FILE **fhs;
-	int *fds;
-
 	/* Final output */
 	Stream *stream;
 };
@@ -124,6 +124,7 @@ static time_t get_monotonic_seconds()
 static void stamp_response(struct sandbox *sb, int n)
 {
 	sb->last_response[n] = get_monotonic_seconds();
+	sb->last_ping[n] = sb->shared->pings[n];
 }
 
 
@@ -131,14 +132,21 @@ static void check_hung_workers(struct sandbox *sb)
 {
 	int i;
 	time_t tnow = get_monotonic_seconds();
-	for ( i=0; i<sb->n_read; i++ ) {
+	for ( i=0; i<sb->n_proc; i++ ) {
+
 		if ( !sb->running[i] ) continue;
+
+		if ( sb->shared->pings[i] != sb->last_ping[i] ) {
+			stamp_response(sb, i);
+		}
+
 		if ( tnow - sb->last_response[i] > 240 ) {
 			STATUS("Worker %i did not respond for 240 seconds - "
 			       "sending it SIGKILL.\n", i);
 			kill(sb->pids[i], SIGKILL);
 			stamp_response(sb, i);
 		}
+
 	}
 }
 
@@ -516,7 +524,6 @@ static void try_read(struct sandbox *sb, TimeAccounts *taccs)
 		/* If the chunk cannot be read, assume the connection
 		 * is broken and that the process will die soon. */
 		time_accounts_set(taccs, TACC_STREAMREAD);
-		stamp_response(sb, i);
 		if ( pump_chunk(sb->fhs[i], ofd) ) {
 			remove_pipe(sb, i);
 		}
@@ -535,6 +542,9 @@ static void start_worker_process(struct sandbox *sb, int slot)
 		return;
 	}
 
+	sb->shared->pings[slot] = 0;
+	sb->last_ping[slot] = 0;
+
 	p = fork();
 	if ( p == -1 ) {
 		ERROR("fork() failed!\n");
diff --git a/src/im-sandbox.h b/src/im-sandbox.h
index b39f9566..b58e4b9e 100644
--- a/src/im-sandbox.h
+++ b/src/im-sandbox.h
@@ -3,13 +3,13 @@
  *
  * Sandbox for indexing
  *
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  * Copyright © 2012 Richard Kirian
  * Copyright © 2012 Lorenzo Galli
  *
  * Authors:
- *   2010-2015 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2011      Richard Kirian
  *   2012      Lorenzo Galli
  *   2012      Chunhong Yoon
@@ -61,6 +61,7 @@ struct sb_shm
 	char queue[QUEUE_SIZE][MAX_EV_LEN];
 	int no_more;
 	char last_ev[MAX_NUM_WORKERS][MAX_EV_LEN];
+	int pings[MAX_NUM_WORKERS];
 
 	pthread_mutex_t totals_lock;
 	int n_processed;
diff --git a/src/partialator.c b/src/partialator.c
index b246571d..09feebb4 100644
--- a/src/partialator.c
+++ b/src/partialator.c
@@ -274,6 +274,12 @@ static void write_custom_split(struct custom_split *csplit, int dsn,
 
 	tmp = insert_into_filename(outfile, csplit->dataset_names[dsn]);
 
+	if ( n_crystalsn == 0 ) {
+		ERROR("Not writing dataset '%s' because it contains no "
+		      "crystals\n", csplit->dataset_names[dsn]);
+		return;
+	}
+
 	STATUS("Writing dataset '%s' to %s (%i crystals)\n",
 	       csplit->dataset_names[dsn], tmp, n_crystalsn);
 	split = merge_intensities(crystalsn, n_crystalsn, nthreads,
@@ -317,6 +323,101 @@ static void show_help(const char *s)
 }
 
 
+static signed int find_first_crystal(Crystal **crystals, int n_crystals,
+                                     struct custom_split *csplit, int dsn)
+{
+	int i;
+
+	for ( i=0; i<n_crystals; i++ ) {
+		const char *fn;
+		struct event *ev;
+		char *evs;
+		char *id;
+		int dsn_crystal;
+
+		fn = crystal_get_image(crystals[i])->filename;
+		ev = crystal_get_image(crystals[i])->event;
+		evs = get_event_string(ev);
+
+		id = malloc(strlen(evs)+strlen(fn)+2);
+		if ( id == NULL ) {
+			ERROR("Failed to allocate ID\n");
+			return -1;
+		}
+		strcpy(id, fn);
+		strcat(id, " ");
+		strcat(id, evs);
+		dsn_crystal = find_dsn_for_id(csplit, id);
+		free(id);
+
+		if ( dsn == dsn_crystal ) return i;
+	}
+	return -1;
+}
+
+
+static void check_csplit(Crystal **crystals, int n_crystals,
+                         struct custom_split *csplit)
+{
+	int i;
+	int n_nosplit = 0;
+	int n_split = 0;
+	int n_cry = 0;
+	int n_nocry = 0;
+
+	STATUS("Checking your custom split datasets...\n");
+
+	for ( i=0; i<n_crystals; i++ ) {
+
+		const char *fn;
+		struct event *ev;
+		char *evs;
+		char *id;
+		int dsn_crystal;
+
+		fn = crystal_get_image(crystals[i])->filename;
+		ev = crystal_get_image(crystals[i])->event;
+		evs = get_event_string(ev);
+
+		id = malloc(strlen(evs)+strlen(fn)+2);
+		if ( id == NULL ) {
+			ERROR("Failed to allocate ID\n");
+			return;
+		}
+		strcpy(id, fn);
+		strcat(id, " ");
+		strcat(id, evs);
+		dsn_crystal = find_dsn_for_id(csplit, id);
+		free(id);
+		if ( dsn_crystal == -1 ) {
+			n_nosplit++;
+		} else {
+			n_split++;
+		}
+
+	}
+
+	for ( i=0; i<csplit->n_datasets; i++ ) {
+
+		/* Try to find a crystal with dsn = i */
+		if ( find_first_crystal(crystals, n_crystals, csplit, i) != -1 )
+		{
+			n_cry++;
+		} else {
+			n_nocry++;
+			STATUS("Dataset %s has no crystals.\n",
+			       csplit->dataset_names[i]);
+		}
+	}
+
+	STATUS("Please check that these numbers match your expectations:\n");
+	STATUS("    Number of crystals assigned to a dataset: %i\n", n_split);
+	STATUS("Number of crystals with no dataset asssigned: %i\n", n_nosplit);
+	STATUS("Number of datasets with at least one crystal: %i\n", n_cry);
+	STATUS("         Number of datasets with no crystals: %i\n", n_nocry);
+}
+
+
 static struct custom_split *load_custom_split(const char *filename)
 {
 	struct custom_split *csplit;
@@ -655,7 +756,6 @@ int main(int argc, char *argv[])
 	int n_iter = 10;
 	RefList *full;
 	int n_images = 0;
-	int n_images_seen = 0;
 	int n_crystals = 0;
 	int n_crystals_seen = 0;
 	char cmdline[1024];
@@ -861,8 +961,10 @@ int main(int argc, char *argv[])
 	}
 
 	if ( sym_str == NULL ) sym_str = strdup("1");
+	pointgroup_warning(sym_str);
 	sym = get_pointgroup(sym_str);
 	free(sym_str);
+	if ( sym == NULL ) return 1;
 
 	if ( pmodel_str != NULL ) {
 		if ( strcmp(pmodel_str, "unity") == 0 ) {
@@ -899,7 +1001,6 @@ int main(int argc, char *argv[])
 
 	/* Fill in what we know about the images so far */
 	n_images = 0;
-	n_images_seen = 0;
 	n_crystals = 0;
 	n_crystals_seen = 0;
 	images = NULL;
@@ -947,8 +1048,6 @@ int main(int argc, char *argv[])
 			return 1;
 		}
 
-		n_images_seen++;
-
 		for ( i=0; i<cur->n_crystals; i++ ) {
 
 			Crystal *cr;
@@ -1001,9 +1100,7 @@ int main(int argc, char *argv[])
 
 		}
 
-		if ( n_crystals > 0 ) {
-			n_images++;
-		}
+		n_images++;
 
 		if ( n_images % 100 == 0 ) {
 			display_progress(n_images, n_crystals);
@@ -1034,6 +1131,8 @@ int main(int argc, char *argv[])
 		}
 	}
 
+	if (csplit != NULL) check_csplit(crystals, n_crystals, csplit);
+
 	/* Make a first pass at cutting out crap */
 	STATUS("Checking patterns.\n");
 	//early_rejection(crystals, n_crystals);
diff --git a/src/pattern_sim.c b/src/pattern_sim.c
index c60b3280..e1e04789 100644
--- a/src/pattern_sim.c
+++ b/src/pattern_sim.c
@@ -533,6 +533,7 @@ int main(int argc, char *argv[])
 	}
 
 	if ( sym_str == NULL ) sym_str = strdup("1");
+	pointgroup_warning(sym_str);
 	sym = get_pointgroup(sym_str);
 	/* sym_str is used below */
 
diff --git a/src/process_hkl.c b/src/process_hkl.c
index 29ef29a1..d2cf640b 100644
--- a/src/process_hkl.c
+++ b/src/process_hkl.c
@@ -692,6 +692,7 @@ int main(int argc, char *argv[])
 	}
 
 	if ( sym_str == NULL ) sym_str = strdup("1");
+	pointgroup_warning(sym_str);
 	sym = get_pointgroup(sym_str);
 	free(sym_str);
 
diff --git a/src/process_image.c b/src/process_image.c
index 62ef732c..bcaee543 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -3,11 +3,11 @@
  *
  * The processing pipeline for one image
  *
- * Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
  *                       a research centre of the Helmholtz Association.
  *
  * Authors:
- *   2010-2015 Thomas White <taw@physics.org>
+ *   2010-2017 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *
  * This file is part of CrystFEL.
@@ -124,6 +124,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	image.indexed_by = INDEXING_NONE;
 
 	time_accounts_set(taccs, TACC_HDF5OPEN);
+	sb_shared->pings[cookie]++;
 	hdfile = hdfile_open(image.filename);
 	if ( hdfile == NULL ) {
 		ERROR("Couldn't open file: %s\n", image.filename);
@@ -131,6 +132,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	}
 
 	time_accounts_set(taccs, TACC_HDF5READ);
+	sb_shared->pings[cookie]++;
 	check = hdf5_read2(hdfile, &image, image.event, 0);
 	if ( check ) {
 		return;
@@ -138,6 +140,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	/* Take snapshot of image before applying horrible noise filters */
 	time_accounts_set(taccs, TACC_FILTER);
+	sb_shared->pings[cookie]++;
 	prefilter = backup_image_data(image.dp, image.det);
 
 	if ( iargs->median_filter > 0 ) {
@@ -149,9 +152,11 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	}
 
 	time_accounts_set(taccs, TACC_RESRANGE);
+	sb_shared->pings[cookie]++;
 	mark_resolution_range_as_bad(&image, iargs->highres, +INFINITY);
 
 	time_accounts_set(taccs, TACC_PEAKSEARCH);
+	sb_shared->pings[cookie]++;
 	switch ( iargs->peaks ) {
 
 		case PEAK_HDF5:
@@ -214,7 +219,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	/* Index the pattern */
 	time_accounts_set(taccs, TACC_INDEXING);
-	index_pattern(&image, iargs->indm, iargs->ipriv);
+	index_pattern_2(&image, iargs->indm, iargs->ipriv,
+	                &sb_shared->pings[cookie]);
 
 	r = chdir(rn);
 	if ( r ) {
@@ -247,6 +253,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	/* Integrate! */
 	time_accounts_set(taccs, TACC_INTEGRATION);
+	sb_shared->pings[cookie]++;
 	integrate_all_4(&image, iargs->int_meth, PMODEL_SCSPHERE,
 	                iargs->push_res,
 	                iargs->ir_inn, iargs->ir_mid, iargs->ir_out,
@@ -255,6 +262,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 	                &sb_shared->term_lock);
 
 	time_accounts_set(taccs, TACC_WRITESTREAM);
+	sb_shared->pings[cookie]++;
 	ret = write_chunk(st, &image, hdfile,
 	                  iargs->stream_peaks, iargs->stream_refls,
 	                  pargs->filename_p_e->ev);
@@ -274,6 +282,7 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 	/* Count crystals which are still good */
 	time_accounts_set(taccs, TACC_TOTALS);
+	sb_shared->pings[cookie]++;
 	pthread_mutex_lock(&sb_shared->totals_lock);
 	any_crystals = 0;
 	for ( i=0; i<image.n_crystals; i++ ) {
diff --git a/src/render_hkl.c b/src/render_hkl.c
index f9398c3d..3996814a 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -90,6 +90,7 @@ static void show_help(const char *s)
 "                            rawcts : the raw number of measurements for the\n"
 "                                     reflection (no 'epsilon' correction).\n"
 "\n"
+"      --scale-top=<n>     Manually set the top of the colour scale\n"
 "      --res-ring=<r>      Draw a resolution ring at <r> Angstroms.\n"
 "      --highres=<r>       Render spots only up to <r> Angstroms.\n"
 "      --no-axes           Do not draw reciprocal space axes.\n"
@@ -477,7 +478,11 @@ static void render_za(UnitCell *cell, RefList *list,
 	/* Use manual scale top if specified */
 	if ( scale_top > 0.0 ) {
 		max_val = scale_top;
+		STATUS("Ignoring boost value (%f) because you used "
+		       "--scale-top\n", boost);
+		boost = 1.0;
 	}
+	STATUS("Top of colour scale = %e\n", max_val/boost);
 
 	scale1 = ((double)wh-border) / (2.0*rmax);
 	scale2 = ((double)ht-border) / (2.0*rmax);
@@ -914,6 +919,7 @@ int main(int argc, char *argv[])
 	if ( sym_str == NULL ) {
 		sym_str = strdup("1");
 	}
+	pointgroup_warning(sym_str);
 	sym = get_pointgroup(sym_str);
 	free(sym_str);
 
diff --git a/tests/first_merge_check b/tests/first_merge_check
index bb1484bd..17b9f87b 100755
--- a/tests/first_merge_check
+++ b/tests/first_merge_check
@@ -38,10 +38,10 @@ cat > first_merge_check_ans.hkl << EOF
 CrystFEL reflection list version 2.0
 Symmetry: 1
    h    k    l          I    phase   sigma(I)   nmeas
-   1    0    0     150.03        -      35.36       2
+   1    0    0     150.00        -      35.36       2
 EOF
 
-src/process_hkl -i first_merge_check.stream -o first_merge_check.hkl
+src/process_hkl -i first_merge_check.stream -o first_merge_check.hkl --no-polarisation
 ex -c '/End of reflections/
 .,$d
 x' first_merge_check.hkl
diff --git a/tests/fourth_merge_check b/tests/fourth_merge_check
index 1c738da7..b0935bc9 100755
--- a/tests/fourth_merge_check
+++ b/tests/fourth_merge_check
@@ -25,7 +25,7 @@ Symmetry: 1
    h    k    l          I    phase   sigma(I)   nmeas
 EOF
 
-src/process_hkl -i fourth_merge_check.stream -o fourth_merge_check.hkl
+src/process_hkl -i fourth_merge_check.stream -o fourth_merge_check.hkl --no-polarisation
 ex -c '/End of reflections/
 .,$d
 x' fourth_merge_check.hkl
diff --git a/tests/second_merge_check b/tests/second_merge_check
index ed2ba9f9..1283cb0a 100755
--- a/tests/second_merge_check
+++ b/tests/second_merge_check
@@ -38,10 +38,10 @@ cat > second_merge_check_ans.hkl << EOF
 CrystFEL reflection list version 2.0
 Symmetry: -1
    h    k    l          I    phase   sigma(I)   nmeas
-   1    0    0     150.03        -      35.36       2
+   1    0    0     150.00        -      35.36       2
 EOF
 
-src/process_hkl -y -1 -i second_merge_check.stream -o second_merge_check.hkl
+src/process_hkl -y -1 -i second_merge_check.stream -o second_merge_check.hkl --no-polarisation
 ex -c '/End of reflections/
 .,$d
 x' second_merge_check.hkl
diff --git a/tests/third_merge_check b/tests/third_merge_check
index 714afb7f..d4f5f9ef 100755
--- a/tests/third_merge_check
+++ b/tests/third_merge_check
@@ -53,10 +53,10 @@ cat > third_merge_check_ans.hkl << EOF
 CrystFEL reflection list version 2.0
 Symmetry: 1
    h    k    l          I    phase   sigma(I)   nmeas
-   1    0    0     133.36        -      27.22       3
+   1    0    0     133.33        -      27.22       3
 EOF
 
-src/process_hkl -i third_merge_check.stream -o third_merge_check.hkl
+src/process_hkl -i third_merge_check.stream -o third_merge_check.hkl --no-polarisation
 ex -c '/End of reflections/
 .,$d
 x' third_merge_check.hkl