Fix/clarify peak coordinates for rearranged panels

4 files changed, 53 insertions, 15 deletions

diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 519de050..276dd268 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -75,10 +75,12 @@ struct panel
 {
 	char     name[1024];  /* Name for this panel */
 
+	/* Position of panel in the data block in memory (see below) */
 	int      min_fs;  /* Smallest FS value considered to be in the panel */
 	int      max_fs;  /* Largest FS value considered to be in this panel */
 	int      min_ss;  /* ... and so on */
 	int      max_ss;
+
 	double   cnx;       /* Location of corner (min_fs,min_ss) in pixels */
 	double   cny;
 	double   coffset;
@@ -105,6 +107,9 @@ struct panel
 	double xss;
 	double yss;
 
+	/* Position of the panel in the data block in the file.  The panels may
+	 * get moved around when the file is loaded (see hdf5_read2()),
+	 * especially if the panels come from different HDF5 elements. */
 	int orig_min_fs;
 	int orig_max_fs;
 	int orig_min_ss;
diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index fac07c43..42408fa1 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -191,6 +191,26 @@ int hdfile_set_image(struct hdfile *f, const char *path,
 }
 
 
+/* Like find_panel(), but uses the original panel bounds, i.e. referring to
+ * what's in the HDF5 file */
+struct panel *find_orig_panel(struct detector *det, double fs, double ss)
+{
+	int p;
+
+	for ( p=0; p<det->n_panels; p++ ) {
+		if ( (fs >= det->panels[p].orig_min_fs)
+		  && (fs < det->panels[p].orig_max_fs+1)
+		  && (ss >= det->panels[p].orig_min_ss)
+		  && (ss < det->panels[p].orig_max_ss+1) )
+		{
+			return &det->panels[p];
+		}
+	}
+
+	return NULL;
+}
+
+
 int get_peaks(struct image *image, struct hdfile *f, const char *p)
 {
 	hid_t dh, sh;
@@ -260,10 +280,14 @@ int get_peaks(struct image *image, struct hdfile *f, const char *p)
 		ss = buf[tw*i+1];
 		val = buf[tw*i+2];
 
-		p = find_panel(image->det, fs, ss);
+		p = find_orig_panel(image->det, fs, ss);
 		if ( p == NULL ) continue;
 		if ( p->no_index ) continue;
 
+		/* Convert coordinates to match rearranged panels in memory */
+		fs = fs - p->orig_min_fs + p->min_fs;
+		ss = ss - p->orig_min_ss + p->min_ss;
+
 		image_add_feature(image->features, fs, ss, image, val, NULL);
 
 	}
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index cb152088..cf891f96 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -210,12 +210,15 @@ static void write_peaks_2_3(struct image *image, FILE *ofh)
 		r = get_q(image, f->fs, f->ss, NULL, 1.0/image->lambda);
 		q = modulus(r.u, r.v, r.w);
 
-		p = find_panel(image->det,f->fs,f->ss);
-		write_fs = f->fs-p->min_fs+p->orig_min_fs;
-		write_ss = f->ss-p->min_ss+p->orig_min_ss;
+		p = find_panel(image->det, f->fs, f->ss);
+
+		/* Convert coordinates to match arrangement of panels in HDF5
+		 * file */
+		write_fs = f->fs - p->min_fs + p->orig_min_fs;
+		write_ss = f->ss - p->min_ss + p->orig_min_ss;
 
 		fprintf(ofh, "%7.2f %7.2f %10.2f  %10.2f   %s\n",
-			   write_fs, write_ss, q/1.0e9, f->intensity, p->name);
+		        write_fs, write_ss, q/1.0e9, f->intensity, p->name);
 
 	}
 
diff --git a/src/dw-hdfsee.c b/src/dw-hdfsee.c
index a73b4abf..4dd04940 100644
--- a/src/dw-hdfsee.c
+++ b/src/dw-hdfsee.c
@@ -8,7 +8,7 @@
  * Copyright © 2012 Richard Kirian
  *
  * Authors:
- *   2009-2013 Thomas White <taw@physics.org>
+ *   2009-2014 Thomas White <taw@physics.org>
  *   2014      Valerio Mariani
  *   2014      Takanori Nakane
  *   2012      Richard Kirian
@@ -1017,7 +1017,6 @@ static void load_features_from_file(struct image *image, const char *filename)
 	do {
 		char line[1024];
 		float intensity, sigma, fs, ss;
-		float add_fs, add_ss;
 		char phs[1024];
 		char pn[32];
 		int r;
@@ -1029,24 +1028,28 @@ static void load_features_from_file(struct image *image, const char *filename)
 		if ( rval == NULL ) continue;
 		chomp(line);
 
-		/* Try long format (from stream) */
+		/* Try long reflection format (from stream) */
 		r = sscanf(line, "%i %i %i %f %s %f %f %f %f %s",
 		                   &h, &k, &l, &intensity, phs, &sigma, &cts,
 		                   &fs, &ss, pn);
 
 		if ( r == 10 ) {
+
 			char name[32];
 			snprintf(name, 31, "%i %i %i", h, k, l);
-
 			p = find_panel_by_name(image->det, pn);
 
-			add_fs = fs-p->orig_min_fs+p->min_fs;
-			add_ss = ss-p->orig_min_ss+p->min_ss;
-			image_add_feature(image->features, add_fs, add_ss,
+			/* Convert coordinates to match rearranged panels in
+			 * memory */
+			fs = fs-p->orig_min_fs+p->min_fs;
+			ss = ss-p->orig_min_ss+p->min_ss;
+
+			image_add_feature(image->features, fs, ss,
 			                  image, 1.0, strdup(name));
 			continue;
 		}
 
+		/* Try long peak format from stream */
 		r = sscanf(line, "%f %f %f %f %s", &fs, &ss, &d,
 		           &intensity, pn);
 		if ( r != 5 ) continue;
@@ -1056,9 +1059,12 @@ static void load_features_from_file(struct image *image, const char *filename)
 			ERROR("Unable to find panel %s\n", pn);
 		} else {
 
-			add_fs = fs - p->orig_min_fs + p->min_fs;
-			add_ss = ss - p->orig_min_ss + p->min_ss;
-			image_add_feature(image->features, add_fs, add_ss,
+			/* Convert coordinates to match rearranged panels in
+			 * memory */
+			fs = fs - p->orig_min_fs + p->min_fs;
+			ss = ss - p->orig_min_ss + p->min_ss;
+
+			image_add_feature(image->features, fs, ss,
 			                  image, 1.0, "peak");
 		}