From cc55abcff6e91d57e8226fa8a4265b667c20ceb0 Mon Sep 17 00:00:00 2001
From: Thomas White <taw@physics.org>
Date: Thu, 13 Oct 2016 17:03:05 +0200
Subject: validate_peaks(): Remove drifting and proximity checks, and use
 original coordinates

We trust the HDF5 peaks, even if we can't see a peak there.  That means
we can't reliably take a centroid and "improve" the coordinates.  In
some cases, the centroiding procedure seems to be making the peak
coordinates worse than they were originally.

Now, the only remaining checks are:
1. Is the peak in a bad region of the detector?
2. Is it saturated? (but --use-saturated is the default)
3. If --check-hdf5-snr, is it above the minimum SNR?
---
 libcrystfel/src/peaks.c | 30 ++++++------------------------
 1 file changed, 6 insertions(+), 24 deletions(-)

(limited to 'libcrystfel/src/peaks.c')

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 7fc30ef7..cb2a9f5a 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -609,7 +609,7 @@ void validate_peaks(struct image *image, double min_snr,
 {
 	int i, n;
 	ImageFeatureList *flist;
-	int n_wtf, n_int, n_dft, n_snr, n_prx, n_sat;
+	int n_wtf, n_int, n_snr, n_sat;
 
 	flist = image_feature_list_new();
 	if ( flist == NULL ) return;
@@ -617,13 +617,11 @@ void validate_peaks(struct image *image, double min_snr,
 	n = image_feature_count(image->features);
 
 	/* Loop over peaks, putting each one through the integrator */
-	n_wtf = 0;  n_int = 0;  n_dft = 0;  n_snr = 0;  n_prx = 0;  n_sat = 0;
+	n_wtf = 0;  n_int = 0;  n_snr = 0;  n_sat = 0;
 	for ( i=0; i<n; i++ ) {
 
 		struct imagefeature *f;
 		int r;
-		double d;
-		int idx;
 		double f_fs, f_ss;
 		double intensity, sigma;
 		int saturated;
@@ -649,36 +647,20 @@ void validate_peaks(struct image *image, double min_snr,
 			}
 		}
 
-		/* It is possible for the centroid to fall outside the image */
-		if ( (f_fs < 0) || (f_fs > f->p->w)
-		  || (f_ss < 0) || (f_ss > f->p->h) )
-		{
-			n_dft++;
-			continue;
-		}
-
 		if ( check_snr && (fabs(intensity)/sigma < min_snr) ) {
 			n_snr++;
 			continue;
 		}
 
-		/* Check for a nearby feature */
-		image_feature_closest(flist, f_fs, f_ss, f->p, &d, &idx);
-		if ( d < 2.0*ir_inn ) {
-			n_prx++;
-			continue;
-		}
-
 		/* Add using "better" coordinates */
-		image_add_feature(flist, f_fs, f_ss, f->p, image, intensity,
+		image_add_feature(flist, f->fs, f->ss, f->p, image, intensity,
 		                  NULL);
 
 	}
 
-	//STATUS("HDF5: %i peaks, validated: %i.  WTF: %i, integration: %i,"
-	//       " drifted: %i, SNR: %i, proximity: %i, saturated: %i\n",
-	//       n, image_feature_count(flist),
-	//       n_wtf, n_int, n_dft, n_snr, n_prx, n_sat);
+	//STATUS("HDF5: %i peaks, validated: %i.  WTF: %i, integration: %i, "
+	//       "SNR: %i, saturated: %i\n",
+	//       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;
-- 
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