Allow default values in geometry files, and set integration radius seperately

7 files changed, 65 insertions, 30 deletions

diff --git a/doc/examples/cspad-feb2011.geom b/doc/examples/cspad-feb2011.geom
index 3d821517..c51a9746 100644
--- a/doc/examples/cspad-feb2011.geom
+++ b/doc/examples/cspad-feb2011.geom
@@ -1,3 +1,6 @@
+; Parameters common to all panels
+integr_radius = 2.0
+
 ; Quadrant 0, asic 0
 q0a0/min_fs = 0
 q0a0/min_ss = 0
diff --git a/doc/examples/lcls-dec.geom b/doc/examples/lcls-dec.geom
index 349d2b16..f98b42fd 100644
--- a/doc/examples/lcls-dec.geom
+++ b/doc/examples/lcls-dec.geom
@@ -2,6 +2,10 @@ mask = /processing/hitfinder/masks
 mask_good = 0x07
 mask_bad = 0x00
 
+; These default values will be used unless overridden by the per-panel values
+peak_sep = 50.0
+integr_radius = 10.0
+
 upper/min_fs = 0
 upper/max_fs = 1023
 upper/min_ss = 512
@@ -13,7 +17,6 @@ upper/ss = y
 upper/clen = 67.8e-3
 upper/res = 13333.3  ; 75 micron pixel size
 upper/badrow_direction = y
-upper/peak_sep = 50
 
 lower/min_fs = 0
 lower/max_fs = 1023
@@ -26,7 +29,6 @@ lower/ss = y
 lower/clen = 70.8e-3
 lower/res = 13333.3  ; 75 micron pixel size
 lower/badrow_direction = y
-lower/peak_sep = 50
 
 bad_jetneartobeam/min_x = -15.0
 bad_jetneartobeam/max_x = +15.0
diff --git a/doc/examples/lcls-june-r0013-r0128.geom b/doc/examples/lcls-june-r0013-r0128.geom
index 730baf42..943b245f 100644
--- a/doc/examples/lcls-june-r0013-r0128.geom
+++ b/doc/examples/lcls-june-r0013-r0128.geom
@@ -2,6 +2,10 @@ mask = /processing/hitfinder/masks
 mask_good = 0x27
 mask_bad = 0x00
 
+; These default values will be used unless overridden by the per-panel values
+peak_sep = 50.0
+integr_radius = 10.0
+
 ; Upper panel (nearest the beam)
 0/min_fs = 0
 0/max_fs = 1023
@@ -14,7 +18,6 @@ mask_bad = 0x00
 0/clen = 64.78e-3
 0/res = 13333.3  ; 75 micron pixel size
 0/badrow_direction = y
-0/peak_sep = 50
 
 ; Lower panel (furthest from the beam)
 1/min_fs = 0
@@ -28,7 +31,6 @@ mask_bad = 0x00
 1/clen = 67.73e-3
 1/res = 13333.3  ; 75 micron pixel size
 1/badrow_direction = y
-1/peak_sep = 50
 
 bad_jetneartobeam/min_x = -15.0
 bad_jetneartobeam/max_x = +15.0
diff --git a/doc/geometry.txt b/doc/geometry.txt
index bf395e1c..c215d27c 100644
--- a/doc/geometry.txt
+++ b/doc/geometry.txt
@@ -56,10 +56,14 @@ panel0/badrow_direction = -
 ; The resolution (in pixels per metre) for this panel
 panel0/res = 9090.91
 
-; The characteristic peak separation.  The peak detection will assume that
-; genuine peaks are separated by at least this amount.
+; The characteristic peak separation in pixels.  The peak detection will assume
+; that genuine peaks are separated by at least this amount.
 panel0/peak_sep = 6.0
 
+; You need to specify the peak integration radius, which should be a little
+; larger than the actual radii of the peaks in pixels
+panel0/integr_radius = 2.0
+
 ; The camera length (in metres) for this panel
 ; You can also specify the HDF path to a scalar floating point value containing
 ; the camera length in millimetres.
@@ -100,6 +104,9 @@ mask = /processing/hitfinder/masks
 mask_good = 0x27
 mask_bad = 0x00
 
+; Any of the per-panel values can be given without a panel prefix, for example:
+peak_sep = 6.0
+; in which case the value will be used for all *subsequent* panels.
 
 
-See the "examples" folder for some examples.
+See the "examples" folder for some examples (look at the ones ending in .geom).
diff --git a/src/detector.c b/src/detector.c
index b3eb8faa..c542a5a1 100644
--- a/src/detector.c
+++ b/src/detector.c
@@ -306,21 +306,12 @@ static struct panel *new_panel(struct detector *det, const char *name)
 	det->panels = realloc(det->panels, det->n_panels*sizeof(struct panel));
 
 	new = &det->panels[det->n_panels-1];
-	new->min_fs = -1;
-	new->min_ss = -1;
-	new->max_fs = -1;
-	new->max_ss = -1;
-	new->cnx = NAN;
-	new->cny = NAN;
-	new->clen = -1.0;
-	new->res = -1.0;
-	new->badrow = '-';
-	new->no_index = 0;
-	new->peak_sep = 50.0;
-	new->fsx = 1.0;
-	new->fsy = 0.0;
-	new->ssx = 0.0;
-	new->ssy = 1.0;
+	memcpy(new, &det->defaults, sizeof(struct panel));
+
+	/* 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;
@@ -408,6 +399,8 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
 		panel->res = atof(val);
 	} else if ( strcmp(key, "peak_sep") == 0 ) {
 		panel->peak_sep = atof(val);
+	} else if ( strcmp(key, "integr_radius") == 0 ) {
+		panel->integr_radius = atof(val);
 	} else if ( strcmp(key, "badrow_direction") == 0 ) {
 		panel->badrow = val[0]; /* First character only */
 		if ( (panel->badrow != 'x') && (panel->badrow != 'y')
@@ -487,7 +480,11 @@ static void parse_toplevel(struct detector *det, const char *key,
 			det->mask_good = v;
 		}
 
-	} else {
+	}  else if ( strcmp(key, "peak_sep") == 0 ) {
+		det->defaults.peak_sep = atof(val);
+	} else if ( strcmp(key, "integr_radius") == 0 ) {
+		det->defaults.integr_radius = atof(val);
+	} else if ( parse_field_for_panel(&det->defaults, key, val) ) {
 		ERROR("Unrecognised top level field '%s'\n", key);
 	}
 }
@@ -505,11 +502,12 @@ struct detector *get_detector_geometry(const char *filename)
 	fh = fopen(filename, "r");
 	if ( fh == NULL ) return NULL;
 
-	det = malloc(sizeof(struct detector));
+	det = calloc(1, sizeof(struct detector));
 	if ( det == NULL ) {
 		fclose(fh);
 		return NULL;
 	}
+
 	det->n_panels = 0;
 	det->panels = NULL;
 	det->n_bad = 0;
@@ -518,6 +516,25 @@ struct detector *get_detector_geometry(const char *filename)
 	det->mask_bad = 0;
 	det->mask = NULL;
 
+	/* The default defaults... */
+	det->defaults.min_fs = -1;
+	det->defaults.min_ss = -1;
+	det->defaults.max_fs = -1;
+	det->defaults.max_ss = -1;
+	det->defaults.cnx = NAN;
+	det->defaults.cny = NAN;
+	det->defaults.clen = -1.0;
+	det->defaults.res = -1.0;
+	det->defaults.badrow = '-';
+	det->defaults.no_index = 0;
+	det->defaults.peak_sep = 50.0;
+	det->defaults.integr_radius = 10.0;
+	det->defaults.fsx = 1.0;
+	det->defaults.fsy = 0.0;
+	det->defaults.ssx = 0.0;
+	det->defaults.ssy = 1.0;
+	strncpy(det->defaults.name, "", 1023);
+
 	do {
 
 		int n1, n2;
diff --git a/src/detector.h b/src/detector.h
index 42651ebd..0ceff341 100644
--- a/src/detector.h
+++ b/src/detector.h
@@ -39,6 +39,7 @@ struct panel
 	char     badrow;   /* 'x' or 'y' */
 	int      no_index; /* Don't index peaks in this panel if non-zero */
 	double   peak_sep; /* Characteristic peak separation */
+	double   integr_radius;  /* Peak integration radius */
 
 	double fsx;
 	double fsy;
@@ -76,6 +77,8 @@ struct detector
 	char              *mask;
 	unsigned int       mask_bad;
 	unsigned int       mask_good;
+
+	struct panel       defaults;
 };
 
 
diff --git a/src/peaks.c b/src/peaks.c
index 65002538..38825d93 100644
--- a/src/peaks.c
+++ b/src/peaks.c
@@ -160,8 +160,8 @@ int integrate_peak(struct image *image, int cfs, int css,
 	if ( p == NULL ) return 1;
 	if ( p->no_index ) return 1;
 
-	lim = p->peak_sep/4.0;
-	out_lim = 1.0 + lim;
+	lim = p->integr_radius;
+	out_lim = 2.0 + lim;
 	lim_sq = pow(lim, 2.0);
 	out_lim_sq = pow(out_lim, 2.0);
 
@@ -338,15 +338,16 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 			}
 
 			/* Abort if drifted too far from the foot point */
-			if ( distance(mask_fs, mask_ss, fs, ss)
-			   > p->peak_sep ) {
+			if ( distance(mask_fs, mask_ss, fs, ss) >
+			     p->peak_sep/2.0 )
+			{
 				break;
 			}
 
 		} while ( did_something );
 
 		/* Too far from foot point? */
-		if ( distance(mask_fs, mask_ss, fs, ss) > p->peak_sep ) {
+		if ( distance(mask_fs, mask_ss, fs, ss) > p->peak_sep/2.0 ) {
 			nrej_dis++;
 			continue;
 		}
@@ -377,7 +378,7 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 
 		/* Check for a nearby feature */
 		image_feature_closest(image->features, f_fs, f_ss, &d, &idx);
-		if ( d < p->peak_sep ) {
+		if ( d < p->peak_sep/2.0 ) {
 			nrej_pro++;
 			continue;
 		}