Changed sig_fac to min_snr

5 files changed, 26 insertions, 26 deletions

diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 1ec4ae59..6c48bd3a 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -572,8 +572,8 @@ int search_peaks_peakfinder8(struct image *image, int max_n_peaks,
 
 #ifdef HAVE_FDIP
 
-int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix,
-                             float sig_fac_peak_pix, float sig_fac_whole_peak,
+int search_peaks_peakfinder9(struct image *image, float min_snr_biggest_pix,
+                             float min_snr_peak_pix, float min_snr_whole_peak,
                              float min_sig, float min_peak_over_neighbour,
                              int window_radius)
 {
@@ -591,9 +591,9 @@ int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix,
 	image->num_peaks = 0;
 	image->num_saturated_peaks = 0;
 
-	accuracy_consts.sigmaFactorBiggestPixel = sig_fac_biggest_pix;
-	accuracy_consts.sigmaFactorPeakPixel = sig_fac_peak_pix;
-	accuracy_consts.sigmaFactorWholePeak = sig_fac_whole_peak;
+	accuracy_consts.minSNR_biggestPixel = min_snr_biggest_pix;
+	accuracy_consts.minSNR_peakPixel = min_snr_peak_pix;
+	accuracy_consts.minSNR_wholePeak = min_snr_whole_peak;
 	accuracy_consts.minimumSigma = min_sig;
 	accuracy_consts.minimumPeakOversizeOverNeighbours = min_peak_over_neighbour;
 	accuracy_consts.windowRadius = window_radius;
@@ -659,8 +659,8 @@ int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix,
 
 #else
 
-int search_peaks_peakfinder9(struct image *image, float sig_fac_biggest_pix,
-                             float sig_fac_peak_pix, float sig_fac_whole_peak,
+int search_peaks_peakfinder9(struct image *image, float min_snr_biggest_pix,
+                             float min_snr_peak_pix, float min_snr_whole_peak,
                              float min_sig, float min_peak_over_neighbour,
                              int window_radius)
 {
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 06ca8e6c..3abef729 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -57,9 +57,9 @@ extern int search_peaks_peakfinder8(struct image *image, int max_n_peaks,
                                     int max_res, int use_saturated);
 
 extern int search_peaks_peakfinder9(struct image *image,
-                                    float sig_fac_biggest_pix,
-                                    float sig_fac_peak_pix,
-                                    float sig_fac_whole_peak, float min_sig,
+                                    float min_snr_biggest_pix,
+                                    float min_snr_peak_pix,
+                                    float min_snr_whole_peak, float min_sig,
                                     float min_peak_over_neighbour,
                                     int window_radius);
 
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 9e265191..97024b54 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -112,9 +112,9 @@ static void show_help(const char *s)
 "                            (peakfinder8 only) Default: 1200\n"
 "     --window-radius=<n>          (peakFinder9 only) defines the radius in which the "
 "                                  local background is estimated\n"
-"     --sig-fac-biggest-pix=<n>    (peakFinder9 only) min snr of the biggest pixel in "
+"     --min-snr-biggest-pix=<n>    (peakFinder9 only) min snr of the biggest pixel in "
 "                                  the peak\n"
-"     --sig-fac-peak-pix=<n>       (peakFinder9 only) min snr of a peak pixel\n"
+"     --min-snr-peak-pix=<n>       (peakFinder9 only) min snr of a peak pixel\n"
 "     --min-sig=<n>                (peakFinder9 only) minimum standard deviation of "
 "                                 the background\n"
 "     --min-peak-over-neighbour=<n>    (peakFinder9 only) just for speed. Biggest pixel"
@@ -270,9 +270,9 @@ int main(int argc, char *argv[])
 	iargs.min_res = 0;
 	iargs.max_res = 1200;
 	iargs.local_bg_radius = 3;
-	iargs.sig_fac_biggest_pix = 7.0;    /* peak finder 9  */
-	iargs.sig_fac_peak_pix = 6.0;
-	iargs.sig_fac_whole_peak = 9.0;
+	iargs.min_snr_biggest_pix = 7.0;    /* peak finder 9  */
+	iargs.min_snr_peak_pix = 6.0;
+	iargs.min_snr_whole_peak = 9.0;
 	iargs.min_sig = 11.0;
 	iargs.min_peak_over_neighbour = -INFINITY;
 	iargs.window_radius = 3;
@@ -421,8 +421,8 @@ int main(int argc, char *argv[])
 		{"serial-start",             1, NULL,        344},
 		{"felix-domega",             1, NULL,        345},
 		{"felix-max-internal-angle", 1, NULL,        346},
-		{"sig-fac-biggest-pix"              ,1, NULL,347},
-		{"sig-fac-peak-pix"                 ,1, NULL,348},
+		{"min-snr-biggest-pix"              ,1, NULL,347},
+		{"min-snr-peak-pix"                 ,1, NULL,348},
 		{"min-sig"                          ,1, NULL,349},
 		{"min-peak-over-neighbour"          ,1, NULL,350},
 		{"window-radius"                    ,1, NULL,351},
@@ -525,7 +525,7 @@ int main(int argc, char *argv[])
 
 			case 311 :
 			iargs.min_snr = strtof(optarg, NULL);
-			iargs.sig_fac_whole_peak = iargs.min_snr;
+			iargs.min_snr_whole_peak = iargs.min_snr;
 			break;
 
 			case 313 :
@@ -754,11 +754,11 @@ int main(int argc, char *argv[])
 			break;
 
 			case 347:
-			iargs.sig_fac_biggest_pix = strtof(optarg, NULL);
+			iargs.min_snr_biggest_pix = strtof(optarg, NULL);
 			break;
 
 			case 348:
-			iargs.sig_fac_peak_pix = strtof(optarg, NULL);
+			iargs.min_snr_peak_pix = strtof(optarg, NULL);
 			break;
 
 			case 349:
diff --git a/src/process_image.c b/src/process_image.c
index 57f40142..e8bcd911 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -225,9 +225,9 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
 
 		case PEAK_PEAKFINDER9:
 		if ( search_peaks_peakfinder9(&image,
-		                              iargs->sig_fac_biggest_pix,
-		                              iargs->sig_fac_peak_pix,
-		                              iargs->sig_fac_whole_peak,
+		                              iargs->min_snr_biggest_pix,
+		                              iargs->min_snr_peak_pix,
+		                              iargs->min_snr_whole_peak,
 		                              iargs->min_sig,
 		                              iargs->min_peak_over_neighbour,
 		                              iargs->window_radius) )
diff --git a/src/process_image.h b/src/process_image.h
index e44de48f..924b8ac4 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -85,9 +85,9 @@ struct index_args
 	int max_pix_count;
 	int local_bg_radius;
 	int min_peaks;
-	float sig_fac_biggest_pix;
-	float sig_fac_peak_pix;
-	float sig_fac_whole_peak;
+	float min_snr_biggest_pix;
+	float min_snr_peak_pix;
+	float min_snr_whole_peak;
 	float min_sig;
 	float min_peak_over_neighbour;
 	int window_radius;