s/hit/cpeak/

Avoid confusion over the use of the word 'hit'.

11 files changed, 89 insertions, 88 deletions

diff --git a/src/calibrate_detector.c b/src/calibrate_detector.c
index 0d613849..5ca468c6 100644
--- a/src/calibrate_detector.c
+++ b/src/calibrate_detector.c
@@ -168,8 +168,8 @@ static void add_image(void *args, int cookie)
 	image.flags = NULL;
 	image.indexed_cell = NULL;
 	image.filename = pargs->filename;
-	image.hits = NULL;
-	image.n_hits = 0;
+	image.cpeaks = NULL;
+	image.n_cpeaks = 0;
 	image.det = NULL;
 
 	/* View head-on (unit cell is tilted) */
diff --git a/src/cubeit.c b/src/cubeit.c
index ebb21151..ad78704e 100644
--- a/src/cubeit.c
+++ b/src/cubeit.c
@@ -216,8 +216,8 @@ static void sum_image(void *pg, int cookie)
 	image.flags = NULL;
 	image.indexed_cell = NULL;
 	image.filename = apargs->filename;
-	image.hits = NULL;
-	image.n_hits = 0;
+	image.cpeaks = NULL;
+	image.n_cpeaks = 0;
 	image.det = pargs->det;
 
 	/* View head-on (unit cell is tilted) */
diff --git a/src/facetron.c b/src/facetron.c
index fa9754e4..9bef1682 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -87,7 +87,7 @@ static void integrate_image(int mytask, void *tasks)
 {
 	struct integrate_args *all_args = tasks;
 	struct integrate_args *pargs = &all_args[mytask];
-	struct reflhit *spots;
+	struct cpeak *spots;
 	int j, n;
 	struct hdfile *hdfile;
 	struct image *image = pargs->image;
diff --git a/src/geometry.c b/src/geometry.c
index 09865822..cca2d050 100644
--- a/src/geometry.c
+++ b/src/geometry.c
@@ -22,24 +22,24 @@
 #include "peaks.h"
 
 
-#define MAX_HITS (1024)
+#define MAX_CPEAKS (1024)
 
 
-struct reflhit *find_intersections(struct image *image, UnitCell *cell,
-                                   double divergence, double bandwidth,
-                                   int *n, int output)
+struct cpeak *find_intersections(struct image *image, UnitCell *cell,
+                                 double divergence, double bandwidth,
+                                 int *n, int output)
 {
 	double asx, asy, asz;
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
-	struct reflhit *hits;
+	struct cpeak *cpeaks;
 	int np = 0;
 	int hmax, kmax, lmax;
 	double mres;
 	signed int h, k, l;
 
-	hits = malloc(sizeof(struct reflhit)*MAX_HITS);
-	if ( hits == NULL ) {
+	cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
+	if ( cpeaks == NULL ) {
 		*n = 0;
 		return NULL;
 	}
@@ -118,11 +118,11 @@ struct reflhit *find_intersections(struct image *image, UnitCell *cell,
 
 		if ( !found ) continue;
 
-		hits[np].h = h;
-		hits[np].k = k;
-		hits[np].l = l;
-		hits[np].x = xda;
-		hits[np].y = yda;
+		cpeaks[np].h = h;
+		cpeaks[np].k = k;
+		cpeaks[np].l = l;
+		cpeaks[np].x = xda;
+		cpeaks[np].y = yda;
 		np++;
 
 		if ( output ) {
@@ -134,7 +134,7 @@ struct reflhit *find_intersections(struct image *image, UnitCell *cell,
 	}
 
 	*n = np;
-	return hits;
+	return cpeaks;
 }
 
 
@@ -145,7 +145,7 @@ double partiality(struct image *image, signed int h, signed int k, signed int l)
 }
 
 
-double integrate_all(struct image *image, struct reflhit *hits, int n)
+double integrate_all(struct image *image, struct cpeak *cpeaks, int n)
 {
 	double itot = 0.0;
 	int i;
@@ -154,7 +154,7 @@ double integrate_all(struct image *image, struct reflhit *hits, int n)
 
 		float x, y, intensity;
 
-		if ( integrate_peak(image, hits[i].x, hits[i].y, &x, &y,
+		if ( integrate_peak(image, cpeaks[i].x, cpeaks[i].y, &x, &y,
                                     &intensity, NULL, NULL, 0, 0) ) continue;
 
 		itot += intensity;
diff --git a/src/geometry.h b/src/geometry.h
index 3e25a8a3..8ebfc1b2 100644
--- a/src/geometry.h
+++ b/src/geometry.h
@@ -17,13 +17,13 @@
 #include <config.h>
 #endif
 
-extern struct reflhit *find_intersections(struct image *image, UnitCell *cell,
-                                          double divergence, double bandwidth,
-                                          int *n, int output);
+extern struct cpeak *find_intersections(struct image *image, UnitCell *cell,
+                                        double divergence, double bandwidth,
+                                        int *n, int output);
 
 extern double partiality(struct image *image, signed int h,
                          signed int k, signed int l);
-extern double integrate_all(struct image *image, struct reflhit *hits, int n);
+extern double integrate_all(struct image *image, struct cpeak *cpeaks, int n);
 
 
 #endif	/* GEOMETRY_H */
diff --git a/src/image.h b/src/image.h
index 71bf0d3a..4f5052bb 100644
--- a/src/image.h
+++ b/src/image.h
@@ -58,7 +58,8 @@ struct imagefeature {
 typedef struct _imagefeaturelist ImageFeatureList;
 
 
-struct reflhit {
+/* This structure represents a predicted peak in an image */
+struct cpeak {
 	signed int h;
 	signed int k;
 	signed int l;
@@ -79,8 +80,8 @@ struct image {
 	int                     ncells;
 	struct detector         *det;
 	char                    *filename;
-	struct reflhit          *hits;
-	int                     n_hits;
+	struct cpeak            *cpeaks;
+	int                     n_cpeaks;
 
 	int                     id;   /* ID number of the thread
 	                               * handling this image */
diff --git a/src/indexamajig.c b/src/indexamajig.c
index d0260a8e..54d5e630 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -1,7 +1,7 @@
 /*
  * indexamajig.c
  *
- * Find hits, index patterns, output hkl+intensity etc.
+ * Index patterns, output hkl+intensity etc.
  *
  * (c) 2006-2010 Thomas White <taw@physics.org>
  *
@@ -258,8 +258,8 @@ static struct image *get_simage(struct image *template, int alternate)
 	image->f0 = template->f0;
 
 	/* Prevent muppetry */
-	image->hits = NULL;
-	image->n_hits = 0;
+	image->cpeaks = NULL;
+	image->n_cpeaks = 0;
 
 	return image;
 }
@@ -317,8 +317,8 @@ static void process_image(void *pp, int cookie)
 	image.indexed_cell = NULL;
 	image.id = cookie;
 	image.filename = filename;
-	image.hits = NULL;
-	image.n_hits = 0;
+	image.cpeaks = NULL;
+	image.n_cpeaks = 0;
 	image.det = pargs->static_args.det;
 
 	/* View head-on (unit cell is tilted) */
@@ -442,7 +442,7 @@ done:
 	free(image.data);
 	free(image.flags);
 	image_feature_list_free(image.features);
-	free(image.hits);
+	free(image.cpeaks);
 	hdfile_close(hdfile);
 }
 
diff --git a/src/peaks.c b/src/peaks.c
index 0cf7c232..e70ebfe2 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -33,7 +33,7 @@
 
 
 /* Maximum number of peaks which may be predicted by find_projected_peaks() */
-#define MAX_HITS (1024)
+#define MAX_CPEAKS (1024)
 
 /* How close a peak must be to an indexed position to be considered "close"
  * for the purposes of double hit detection and sanity checking. */
@@ -495,12 +495,12 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
 	double ax, ay, az;
 	double bx, by, bz;
 	double cx, cy, cz;
-	struct reflhit *hits;
-	int n_hits = 0;
+	struct cpeak *cpeaks;
+	int n_cpeaks = 0;
 	double alen, blen, clen;
 
-	hits = malloc(sizeof(struct reflhit)*MAX_HITS);
-	if ( hits == NULL ) return 0;
+	cpeaks = malloc(sizeof(struct cpeak)*MAX_CPEAKS);
+	if ( cpeaks == NULL ) return 0;
 
 	/* "Borrow" direction values to get reciprocal lengths */
 	cell_get_reciprocal(cell, &ax, &ay, &az, &bx, &by, &bz, &cx, &cy, &cz);
@@ -547,14 +547,14 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
 			if ( dist > domain_r ) continue;
 		}
 
-		for ( j=0; j<n_hits; j++ ) {
-			if ( (hits[j].h == h) && (hits[j].k == k)
-			                      && (hits[j].l == l) ) {
+		for ( j=0; j<n_cpeaks; j++ ) {
+			if ( (cpeaks[j].h == h) && (cpeaks[j].k == k)
+			                      && (cpeaks[j].l == l) ) {
 
-				if ( dist < hits[j].min_distance ) {
-					hits[j].min_distance = dist;
-					hits[j].x = x;
-					hits[j].y = y;
+				if ( dist < cpeaks[j].min_distance ) {
+					cpeaks[j].min_distance = dist;
+					cpeaks[j].x = x;
+					cpeaks[j].y = y;
 				}
 
 				found = 1;
@@ -563,14 +563,14 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
 		}
 
 		if ( !found ) {
-			hits[n_hits].min_distance = dist;
-			hits[n_hits].x = x;
-			hits[n_hits].y = y;
-			hits[n_hits].h = h;
-			hits[n_hits].k = k;
-			hits[n_hits].l = l;
-			n_hits++;
-			if ( n_hits == MAX_HITS ) {
+			cpeaks[n_cpeaks].min_distance = dist;
+			cpeaks[n_cpeaks].x = x;
+			cpeaks[n_cpeaks].y = y;
+			cpeaks[n_cpeaks].h = h;
+			cpeaks[n_cpeaks].k = k;
+			cpeaks[n_cpeaks].l = l;
+			n_cpeaks++;
+			if ( n_cpeaks == MAX_CPEAKS ) {
 				ERROR("Unit cell is insanely large!\n");
 				goto out;
 			}
@@ -580,11 +580,11 @@ int find_projected_peaks(struct image *image, UnitCell *cell,
 	}
 
 out:
-	STATUS("Found %i reflections\n", n_hits);
-	image->hits = hits;
-	image->n_hits = n_hits;
+	STATUS("Found %i reflections\n", n_cpeaks);
+	image->cpeaks = cpeaks;
+	image->n_cpeaks = n_cpeaks;
 
-	return n_hits;
+	return n_cpeaks;
 }
 
 
@@ -710,10 +710,10 @@ void output_intensities(struct image *image, UnitCell *cell,
 	double bsx, bsy, bsz;
 	double csx, csy, csz;
 
-	if ( image->n_hits == 0 ) {
+	if ( image->n_cpeaks == 0 ) {
 		find_projected_peaks(image, cell, circular_domain, domain_r);
 	}
-	if ( image->n_hits == 0 ) return;
+	if ( image->n_cpeaks == 0 ) return;
 
 	/* Get exclusive access to the output stream if necessary */
 	if ( mutex != NULL ) pthread_mutex_lock(mutex);
@@ -724,7 +724,7 @@ void output_intensities(struct image *image, UnitCell *cell,
 	                          &bsx, &bsy, &bsz,
 	                          &csx, &csy, &csz);
 
-	for ( i=0; i<image->n_hits; i++ ) {
+	for ( i=0; i<image->n_cpeaks; i++ ) {
 
 		float x, y, intensity;
 		double d;
@@ -738,8 +738,8 @@ void output_intensities(struct image *image, UnitCell *cell,
 
 			if ( image->features != NULL ) {
 				f = image_feature_closest(image->features,
-					                  image->hits[i].x,
-					                  image->hits[i].y,
+					                  image->cpeaks[i].x,
+					                  image->cpeaks[i].y,
 					                  &d, &idx);
 			} else {
 				f = NULL;
@@ -773,8 +773,8 @@ void output_intensities(struct image *image, UnitCell *cell,
 				int r;
 
 				r = integrate_peak(image,
-					           image->hits[i].x,
-					           image->hits[i].y,
+					           image->cpeaks[i].x,
+					           image->cpeaks[i].y,
 					           &x, &y, &intensity, &bg, &max,
 					           polar, sa);
 				if ( r ) {
@@ -794,8 +794,8 @@ void output_intensities(struct image *image, UnitCell *cell,
 			int r;
 
 			r = integrate_peak(image,
-				           image->hits[i].x,
-				           image->hits[i].y,
+				           image->cpeaks[i].x,
+				           image->cpeaks[i].y,
 				           &x, &y, &intensity, &bg, &max, polar,
 				           sa);
 			if ( r ) {
@@ -808,11 +808,11 @@ void output_intensities(struct image *image, UnitCell *cell,
 
 		/* Write h,k,l, integrated intensity and centroid coordinates */
 		fprintf(ofh, "%3i %3i %3i %6f (at %5.2f,%5.2f) max=%6f bg=%6f\n",
-		       image->hits[i].h, image->hits[i].k, image->hits[i].l,
+		       image->cpeaks[i].h, image->cpeaks[i].k, image->cpeaks[i].l,
 		       intensity, x, y, max, bg);
 
-		image->hits[i].x = x;
-		image->hits[i].y = y;
+		image->cpeaks[i].x = x;
+		image->cpeaks[i].y = y;
 
 	}
 
@@ -826,12 +826,12 @@ void output_intensities(struct image *image, UnitCell *cell,
 
 		if ( f == NULL ) continue;
 
-		for ( j=0; j<image->n_hits; j++ ) {
+		for ( j=0; j<image->n_cpeaks; j++ ) {
 
 			double d;
 
-			d = pow(image->hits[j].x-f->x, 2.0)
-			  + pow(image->hits[j].y-f->y, 2.0);
+			d = pow(image->cpeaks[j].x-f->x, 2.0)
+			  + pow(image->cpeaks[j].y-f->y, 2.0);
 
 			if ( d < PEAK_CLOSE ) n_foundclose++;
 
@@ -842,7 +842,7 @@ void output_intensities(struct image *image, UnitCell *cell,
 	fprintf(ofh, "Peak statistics: %i peaks found by the peak search out of "
 	       "%i were close to indexed positions. "
 	       "%i indexed positions out of %i were close to detected peaks.\n",
-	       n_foundclose, n_found, n_indclose, image->n_hits);
+	       n_foundclose, n_found, n_indclose, image->n_cpeaks);
 	fprintf(ofh, "%i integrations using indexed locations were aborted because "
 	       "they hit one or more bad pixels.\n", n_veto);
 	fprintf(ofh, "%i integrations using peak search locations were aborted "
diff --git a/src/reintegrate.c b/src/reintegrate.c
index 43db6092..c9de3338 100644
--- a/src/reintegrate.c
+++ b/src/reintegrate.c
@@ -108,8 +108,8 @@ static void process_image(void *pg, int cookie)
 	image.flags = NULL;
 	image.indexed_cell = NULL;
 	image.filename = apargs->filename;
-	image.hits = NULL;
-	image.n_hits = 0;
+	image.cpeaks = NULL;
+	image.n_cpeaks = 0;
 	image.det = pargs->det;
 
 	/* View head-on (unit cell is tilted) */
diff --git a/src/render_hkl.c b/src/render_hkl.c
index e333da7f..4b077ba7 100644
--- a/src/render_hkl.c
+++ b/src/render_hkl.c
@@ -63,9 +63,9 @@ static void show_help(const char *s)
 "                           according to:\n"
 "                            I      : the intensity of the reflection.\n"
 "                            sqrtI  : the square root of the intensity.\n"
-"                            count  : the number of hits for the reflection.\n"
+"                            count  : the number of measurements for the reflection.\n"
 "                                     (after correcting for 'epsilon')\n"
-"                            rawcts : the raw number of hits for the\n"
+"                            rawcts : the raw number of measurements for the\n"
 "                                     reflection (no 'epsilon' correction).\n"
 "\n"
 "      --colour-key        Draw (only) the key for the current colour scale.\n"
diff --git a/src/templates.c b/src/templates.c
index 468612f2..105fa755 100644
--- a/src/templates.c
+++ b/src/templates.c
@@ -43,7 +43,7 @@ struct template {
 	double omega;
 	double phi;
 	int n;
-	struct reflhit *spots;
+	struct cpeak *spots;
 };
 
 
@@ -165,16 +165,16 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
 	for ( phi = 0.0; phi < phi_max-phi_step; phi += phi_step ) {
 
 		int n;
-		struct reflhit *hits;
+		struct cpeak *cpeaks;
 		UnitCell *cell_rot;
 
 		assert(i < n_templates);
 
 		cell_rot = rotate_cell(cell, omega, phi, 0.0);
 
-		hits = find_intersections(&image, cell_rot, 5.0e-3,
+		cpeaks = find_intersections(&image, cell_rot, 5.0e-3,
 		                          3.0/100.0, &n, 0);
-		if ( hits == NULL ) {
+		if ( cpeaks == NULL ) {
 			ERROR("Template calculation failed.\n");
 			return NULL;
 		}
@@ -182,7 +182,7 @@ IndexingPrivate *generate_templates(UnitCell *cell, const char *filename,
 		priv->templates[i].omega = omega;
 		priv->templates[i].phi = phi;
 		priv->templates[i].n = n;
-		priv->templates[i].spots = hits;
+		priv->templates[i].spots = cpeaks;
 		i++;
 
 		free(cell_rot);
@@ -228,7 +228,7 @@ static int fast_integrate_peak(struct image *image, int xp, int yp)
 }
 
 
-static double integrate_all_rot(struct image *image, struct reflhit *hits,
+static double integrate_all_rot(struct image *image, struct cpeak *cpeaks,
                                 int n, double rot)
 {
 	double itot = 0.0;
@@ -243,8 +243,8 @@ static double integrate_all_rot(struct image *image, struct reflhit *hits,
 
 		float xp, yp;
 
-		xp =  cosr*hits[i].x + sinr*hits[i].y;
-		yp = -sinr*hits[i].x + cosr*hits[i].y;
+		xp =  cosr*cpeaks[i].x + sinr*cpeaks[i].y;
+		yp = -sinr*cpeaks[i].x + cosr*cpeaks[i].y;
 
 		itot += fast_integrate_peak(image, rint(xp), rint(yp));
 		num_int++;
@@ -257,7 +257,7 @@ static double integrate_all_rot(struct image *image, struct reflhit *hits,
 
 /* Return the mean of the distances between peaks in the image and peaks from
  * the given template. */
-static double mean_distance(struct image *image, struct reflhit *hits,
+static double mean_distance(struct image *image, struct cpeak *cpeaks,
                             int n, double rot)
 {
 	double dtot = 0.0;
@@ -275,8 +275,8 @@ static double mean_distance(struct image *image, struct reflhit *hits,
 		int j;
 		double min_dsq;
 
-		xp =  cosr*hits[i].x + sinr*hits[i].y;
-		yp = -sinr*hits[i].x + cosr*hits[i].y;
+		xp =  cosr*cpeaks[i].x + sinr*cpeaks[i].y;
+		yp = -sinr*cpeaks[i].x + cosr*cpeaks[i].y;
 
 		/* Compare to every real peak */
 		min_dsq = +INFINITY;