Remove image.num_peaks and num_saturated_peaks

These values were inconsistently set by different parts of the code,
e.g. different peak search methods.  num_saturated_peaks was even set
during final integration.  Now, the peak count is taken from the
ImageFeatureList, so it's authoritative.

7 files changed, 5 insertions, 39 deletions

diff --git a/libcrystfel/src/hdf5-file.c b/libcrystfel/src/hdf5-file.c
index 7aa8165d..ff96adb1 100644
--- a/libcrystfel/src/hdf5-file.c
+++ b/libcrystfel/src/hdf5-file.c
@@ -396,8 +396,6 @@ int get_peaks_cxi_2(struct image *image, struct hdfile *f, const char *p,
 	}
 	image->features = image_feature_list_new();
 
-	image->num_peaks = 0;
-	image->num_saturated_peaks = 0;
 	for ( pk=0; pk<num_peaks; pk++ ) {
 
 		float fs, ss, val;
@@ -416,7 +414,6 @@ int get_peaks_cxi_2(struct image *image, struct hdfile *f, const char *p,
 		ss = ss - p->orig_min_ss;
 
 		image_add_feature(image->features, fs, ss, p, image, val, NULL);
-		image->num_peaks++;
 
 	}
 
@@ -542,8 +539,6 @@ int get_peaks_2(struct image *image, struct hdfile *f, const char *p,
 	}
 	image->features = image_feature_list_new();
 
-	image->num_peaks = 0;
-	image->num_saturated_peaks = 0;
 	for ( i=0; i<size[0]; i++ ) {
 
 		float fs, ss, val;
@@ -563,7 +558,6 @@ int get_peaks_2(struct image *image, struct hdfile *f, const char *p,
 
 		image_add_feature(image->features, fs, ss, p, image, val,
 		                  NULL);
-		image->num_peaks++;
 
 	}
 
diff --git a/libcrystfel/src/image.h b/libcrystfel/src/image.h
index 98cac12c..56f07132 100644
--- a/libcrystfel/src/image.h
+++ b/libcrystfel/src/image.h
@@ -203,12 +203,8 @@ struct image
 	/** Full-width half-maximum bandwidth as a fraction, applied to wavelength */
 	double                  bw;
 
-	/** \name Numbers of peaks.  To be deleted.
-	 * @{ */
-	long long               num_peaks;
-	long long               num_saturated_peaks;
+	/** Resolution estimate based on peaks */
 	double                  peak_resolution;
-	/** @} */
 
 	/** List of peaks found in the image */
 	ImageFeatureList        *features;
diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c
index d9636d9f..5270816b 100644
--- a/libcrystfel/src/integration.c
+++ b/libcrystfel/src/integration.c
@@ -1355,7 +1355,6 @@ static void integrate_prof2d(IntegrationMethod meth,
 	UnitCell *cell;
 	struct intcontext ic;
 	int i;
-	int n_saturated = 0;
 
 	list = crystal_get_reflections(cr);
 	cell = crystal_get_cell(cr);
@@ -1397,8 +1396,6 @@ static void integrate_prof2d(IntegrationMethod meth,
 	}
 
 	free_intcontext(&ic);
-
-	image->num_saturated_peaks = n_saturated;
 }
 
 
diff --git a/libcrystfel/src/peakfinder8.c b/libcrystfel/src/peakfinder8.c
index 2c67a484..30082580 100644
--- a/libcrystfel/src/peakfinder8.c
+++ b/libcrystfel/src/peakfinder8.c
@@ -1196,9 +1196,7 @@ int peakfinder8(struct image *img, int max_n_peaks,
 
 			p = &img->det->panels[pi];
 
-			img->num_peaks += 1;
 			if ( pkdata->max_i[pki] > p->max_adu ) {
-				img->num_saturated_peaks++;
 				if ( !use_saturated ) {
 					continue;
 				}
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index a45a51af..1af901e0 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -485,12 +485,9 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 			continue;
 		}
 
-		if ( saturated ) {
-			image->num_saturated_peaks++;
-			if ( !use_saturated ) {
-				nrej_sat++;
-				continue;
-			}
+		if ( saturated && !use_saturated ) {
+			nrej_sat++;
+			continue;
 		}
 
 		/* Add using "better" coordinates */
@@ -510,8 +507,6 @@ static void search_peaks_in_panel(struct image *image, float threshold,
 		ncull = 0;
 	}
 
-	image->num_peaks += nacc;
-
 	//STATUS("%i accepted, %i box, %i proximity, %i outside panel, "
 	//       "%i failed integration, %i with SNR < %g, %i badrow culled, "
 	//        "%i saturated.\n",
@@ -536,8 +531,6 @@ void search_peaks(struct image *image, float threshold, float min_sq_gradient,
 		image_feature_list_free(image->features);
 	}
 	image->features = image_feature_list_new();
-	image->num_peaks = 0;
-	image->num_saturated_peaks = 0;
 
 	for ( i=0; i<image->det->n_panels; i++ ) {
 
@@ -577,8 +570,6 @@ int search_peaks_peakfinder8(struct image *image, int max_n_peaks,
 		image_feature_list_free(image->features);
 	}
 	image->features = image_feature_list_new();
-	image->num_peaks = 0;
-	image->num_saturated_peaks = 0;
 
 	return peakfinder8(image, max_n_peaks, threshold, min_snr,
 	                   min_pix_count, max_pix_count,
@@ -810,8 +801,6 @@ void validate_peaks(struct image *image, double min_snr,
 	//       n, image_feature_count(flist), n_wtf, n_int, n_snr, n_sat);
 	image_feature_list_free(image->features);
 	image->features = flist;
-	image->num_saturated_peaks = n_sat;
-	image->num_peaks = image_feature_count(flist);
 }
 
 
diff --git a/libcrystfel/src/stream.c b/libcrystfel/src/stream.c
index 5aac2eab..6b8f3565 100644
--- a/libcrystfel/src/stream.c
+++ b/libcrystfel/src/stream.c
@@ -897,8 +897,7 @@ int write_chunk(Stream *st, struct image *i, struct imagefile *imfile,
 
 	}
 
-	fprintf(st->fh, "num_peaks = %lli\n", i->num_peaks);
-	fprintf(st->fh, "num_saturated_peaks = %lli\n", i->num_saturated_peaks);
+	fprintf(st->fh, "num_peaks = %i\n", image_feature_count(i->features));
 	fprintf(st->fh, "peak_resolution = %f nm^-1 or %f A\n",
 	        i->peak_resolution/1e9, 1e10/i->peak_resolution);
 	if ( include_peaks ) {
@@ -1218,7 +1217,6 @@ int read_chunk_2(Stream *st, struct image *image,  StreamReadFlags srf)
 	}
 
 	do {
-		long long num_peaks;
 		int ser;
 		float div, bw;
 
@@ -1263,10 +1261,6 @@ int read_chunk_2(Stream *st, struct image *image,  StreamReadFlags srf)
 			image->bw = bw;
 		}
 
-		if ( sscanf(line, "num_peaks = %lld", &num_peaks) == 1 ) {
-			image->num_peaks = num_peaks;
-		}
-
 		if ( sscanf(line, "Image serial number: %i", &ser) == 1 ) {
 			image->serial = ser;
 		}
diff --git a/src/partial_sim.c b/src/partial_sim.c
index 012b0a59..92f9703c 100644
--- a/src/partial_sim.c
+++ b/src/partial_sim.c
@@ -841,8 +841,6 @@ int main(int argc, char *argv[])
 	image.crystals = NULL;
 	image.n_crystals = 0;
 	image.indexed_by = INDEXING_SIMULATION;
-	image.num_peaks = 0;
-	image.num_saturated_peaks = 0;
 	image.spectrum_size = 0;
 	image.spectrum0 = NULL;
 	image.serial = 0;