Rigid group stuff

4 files changed, 88 insertions, 47 deletions

diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index f7ff135e..a30d3ccf 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -480,11 +480,12 @@ static struct panel *new_panel(struct detector *det, const char *name)
 	new = &det->panels[det->n_panels-1];
 	memcpy(new, &det->defaults, sizeof(struct panel));
 
+	strcpy(new->name, name);
+
 	/* Create a new copy of the camera length location if needed */
 	if ( new->clen_from != NULL ) {
 		new->clen_from = strdup(new->clen_from);
 	}
-	strcpy(new->name, name);
 
 	return new;
 }
@@ -537,32 +538,68 @@ static struct badregion *find_bad_region_by_name(struct detector *det,
 }
 
 
-static char *find_or_add_rg(struct detector *det, const char *name)
+static struct rigid_group *find_or_add_rg(struct detector *det,
+                                          const char *name)
 {
 	int i;
-	char **new;
-	char *tmp;
+	struct rigid_group **new;
+	struct rigid_group *rg;
 
-	for ( i=0; i<det->num_rigid_groups; i++ ) {
+	for ( i=0; i<det->n_rigid_groups; i++ ) {
 
-		if ( strcmp(det->rigid_groups[i], name) == 0 ) {
+		if ( strcmp(det->rigid_groups[i]->name, name) == 0 ) {
 			return det->rigid_groups[i];
 		}
 
 	}
 
 	new = realloc(det->rigid_groups,
-	              (1+det->num_rigid_groups)*sizeof(char *));
+	              (1+det->n_rigid_groups)*sizeof(struct rigid_group *));
 	if ( new == NULL ) return NULL;
 
 	det->rigid_groups = new;
 
-	tmp = strdup(name);
-	det->rigid_groups[det->num_rigid_groups] = tmp;
+	rg = malloc(sizeof(struct rigid_group));
+	if ( rg == NULL ) return NULL;
 
-	det->num_rigid_groups++;
+	det->rigid_groups[det->n_rigid_groups++] = rg;
 
-	return tmp;
+	rg->name = strdup(name);
+	rg->panels = NULL;
+	rg->n_panels = 0;
+
+	return rg;
+}
+
+
+static void add_to_rigid_group(struct rigid_group *rg, struct panel *p)
+{
+	struct panel **pn;
+
+	pn = realloc(rg->panels, (1+rg->n_panels)*sizeof(struct panel *));
+	if ( pn == NULL ) {
+		ERROR("Couldn't add panel to rigid group.\n");
+		return;
+	}
+
+	assert(p->rigid_group == rg);
+	rg->panels = pn;
+	rg->panels[rg->n_panels++] = p;
+}
+
+
+static void fix_up_rigid_groups(struct detector *det)
+{
+	int i;
+
+	for ( i=0; i<det->n_panels; i++ ) {
+
+		struct panel *p = &det->panels[i];
+		if ( p->rigid_group != NULL ) {
+			add_to_rigid_group(p->rigid_group, p);
+		}
+
+	}
 }
 
 
@@ -775,7 +812,7 @@ struct detector *get_detector_geometry(const char *filename)
 	det->mask_good = 0;
 	det->mask_bad = 0;
 	det->mask = NULL;
-	det->num_rigid_groups = 0;
+	det->n_rigid_groups = 0;
 	det->rigid_groups = NULL;
 
 	/* The default defaults... */
@@ -1012,6 +1049,10 @@ out:
 
 	}
 
+	/* Fix up rigid group panel pointers now that the panels and RGs have
+	 * stopped being realloc()ed */
+	fix_up_rigid_groups(det);
+
 	find_min_max_d(det);
 
 	if ( reject ) return NULL;
@@ -1026,9 +1067,6 @@ void free_detector_geometry(struct detector *det)
 {
 	int i;
 
-	for ( i=0; i<det->num_rigid_groups; i++ ) {
-		free(det->rigid_groups[i]);
-	}
 	free(det->rigid_groups);
 
 	for ( i=0; i<det->n_panels; i++ ) {
@@ -1062,18 +1100,6 @@ struct detector *copy_geom(const struct detector *in)
 	out->bad = malloc(out->n_bad * sizeof(struct badregion));
 	memcpy(out->bad, in->bad, out->n_bad * sizeof(struct badregion));
 
-	if ( in->rigid_groups != NULL ) {
-
-		out->rigid_groups = malloc(out->num_rigid_groups*sizeof(char *));
-		memcpy(out->rigid_groups, in->rigid_groups,
-		       out->num_rigid_groups*sizeof(char *));
-
-		for ( i=0; i<in->num_rigid_groups; i++ ) {
-			out->rigid_groups[i] = strdup(in->rigid_groups[i]);
-		}
-
-	}
-
 	for ( i=0; i<out->n_panels; i++ ) {
 
 		struct panel *p;
@@ -1088,22 +1114,19 @@ struct detector *copy_geom(const struct detector *in)
 
 	}
 
-	for ( i=0; i<in->num_rigid_groups; i++ ) {
+	for ( i=0; i<in->n_panels; i++ ) {
 
-		int j;
-		char *rg = in->rigid_groups[i];
-		char *rgn = out->rigid_groups[i];
+		struct rigid_group *rg;
 
-		for ( j=0; j<in->n_panels; j++ ) {
+		rg = in->panels[i].rigid_group;
+		if ( rg == NULL ) continue;
 
-			if ( in->panels[j].rigid_group == rg ) {
-				out->panels[j].rigid_group = rgn;
-			}
-
-		}
+		out->panels[i].rigid_group = find_or_add_rg(out, rg->name);
 
 	}
 
+	fix_up_rigid_groups(out);
+
 	return out;
 }
 
@@ -1303,7 +1326,7 @@ int write_detector_geometry(const char *filename, struct detector *det)
 
 		if ( p->rigid_group != NULL ) {
 			fprintf(fh, "%s/rigid_group = %s\n",
-			        p->name, p->rigid_group);
+			        p->name, p->rigid_group->name);
 		}
 
 	}
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 0f9be817..b6a90fbf 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -46,6 +46,15 @@ struct hdfile;
 extern "C" {
 #endif
 
+
+struct rigid_group
+{
+	char *name;
+	struct panel **panels;
+	int n_panels;
+};
+
+
 struct panel
 {
 	char     name[1024];  /* Name for this panel */
@@ -62,7 +71,7 @@ struct panel
 	double   res;      /* Resolution in pixels per metre */
 	char     badrow;   /* 'x' or 'y' */
 	int      no_index; /* Don't index peaks in this panel if non-zero */
-	char    *rigid_group;  /* Rigid group name */
+	struct rigid_group *rigid_group;  /* Rigid group */
 	double   adu_per_eV;   /* Number of ADU per eV */
 	double   max_adu;  /* Treat pixel as unreliable if higher than this */
 
@@ -106,8 +115,8 @@ struct detector
 	unsigned int       mask_bad;
 	unsigned int       mask_good;
 
-	char             **rigid_groups;
-	int                num_rigid_groups;
+	struct rigid_group **rigid_groups;
+	int                n_rigid_groups;
 
 	/* Location of the pixel furthest away from the beam position, which
 	 * will have the largest value of 2theta regardless of camera length
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index 967ffb9c..1a2c0585 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1095,6 +1095,11 @@ static int suitable_reference(struct intcontext *ic, struct peak_box *bx)
 }
 
 
+static void refine_rigid_groups(struct intcontext *ic)
+{
+}
+
+
 static void measure_all_intensities(IntegrationMethod meth, RefList *list,
                                     struct image *image, UnitCell *cell,
                                     double ir_inn, double ir_mid, double ir_out)
@@ -1245,6 +1250,8 @@ static void measure_all_intensities(IntegrationMethod meth, RefList *list,
 		}
 	}
 
+	refine_rigid_groups(&ic);
+
 	free_intcontext(&ic);
 
 	image->num_saturated_peaks = n_saturated;
@@ -1646,6 +1653,8 @@ static void integrate_rings(IntegrationMethod meth, Crystal *cr,
 
 	}
 
+	refine_rigid_groups(&ic);
+
 	free_intcontext(&ic);
 
 	crystal_set_num_saturated_reflections(cr, n_saturated);
diff --git a/libcrystfel/src/reax.c b/libcrystfel/src/reax.c
index 2a599b40..cfc86ba4 100644
--- a/libcrystfel/src/reax.c
+++ b/libcrystfel/src/reax.c
@@ -128,7 +128,7 @@ struct reax_private
 static void fill_and_transform(struct dvec *dir, ImageFeatureList *flist,
                         int nel, double pmax, double *fft_in,
                         fftw_complex *fft_out, fftw_plan plan,
-                        const char *rg, struct detector *det)
+                        const struct rigid_group *rg, struct detector *det)
 {
 	int n, i;
 
@@ -191,7 +191,7 @@ static double check_dir(struct dvec *dir, ImageFeatureList *flist,
                         int nel, double pmax, double *fft_in,
                         fftw_complex *fft_out, fftw_plan plan,
                         struct reax_search *s,
-                        const char *rg, struct detector *det)
+                        const struct rigid_group *rg, struct detector *det)
 {
 	int i;
 	double tot;
@@ -553,7 +553,7 @@ static struct reax_search *search_all_axes(UnitCell *cell, double pmax)
 static double get_model_phase(double x, double y, double z, ImageFeatureList *f,
                               int nel, double pmax, double *fft_in,
                               fftw_complex *fft_out, fftw_plan plan,
-                              int smin, int smax, const char *rg,
+                              int smin, int smax, const struct rigid_group *rg,
                               struct detector *det)
 {
 	struct dvec dir;
@@ -589,7 +589,7 @@ static double get_model_phase(double x, double y, double z, ImageFeatureList *f,
 
 
 static void refine_rigid_group(struct image *image, UnitCell *cell,
-                               const char *rg, double pmax,
+                               const struct rigid_group *rg, double pmax,
                                double *fft_in, fftw_complex *fft_out,
                                fftw_plan plan, int smin, int smax,
                                struct detector *det, struct reax_private *pr)
@@ -716,8 +716,8 @@ static UNUSED void refine_all_rigid_groups(struct image *image, UnitCell *cell,
 {
 	int i;
 
-	for ( i=0; i<image->det->num_rigid_groups; i++ ) {
-		refine_rigid_group(image, cell, image->det->rigid_groups[i],
+	for ( i=0; i<image->det->n_rigid_groups; i++ ) {
+		refine_rigid_group(image, cell, &image->det->rigid_groups[i],
 		                   pmax, fft_in, fft_out, plan, smin, smax,
 		                   det, p);
 	}