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-rw-r--r--libcrystfel/src/peaks.c14
-rw-r--r--libcrystfel/src/peaks.h6
-rw-r--r--src/indexamajig.c20
-rw-r--r--src/process_image.c6
-rw-r--r--src/process_image.h6
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;