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-rw-r--r--doc/man/indexamajig.17
-rw-r--r--libcrystfel/src/peaks.c5
-rw-r--r--libcrystfel/src/peaks.h2
-rw-r--r--src/indexamajig.c18
-rw-r--r--src/process_image.c7
-rw-r--r--src/process_image.h1
6 files changed, 27 insertions, 13 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index cb24e916..c0ddd41f 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -315,7 +315,12 @@ Normally, peaks which contain one or more pixels above max_adu (defined in the d
.PD 0
.IP \fB--no-revalidate\fR
.PD
-When using \fB--peaks=hdf5\fR, the peaks will be put through the same checks as if you were using \fB--peaks=zaef\fR. These checks reject peaks which are too close to panel edges, are saturated (unless you use \fB--use-saturated\fR), fall short of the minimum SNR value given by \fB--min-snr\fR, have other nearby peaks (closer than twice the inner integration radius, see \fB--int-radius\fR), or have any part in a bad region. Using this option skips this validation step, and uses the peaks directly.
+When using \fB--peaks=hdf5\fR, the peaks will be put through some of the same checks as if you were using \fB--peaks=zaef\fR. These checks reject peaks which are too close to panel edges, are saturated (unless you use \fB--use-saturated\fR), have other nearby peaks (closer than twice the inner integration radius, see \fB--int-radius\fR), or have any part in a bad region. Using this option skips this validation step, and uses the peaks directly.
+
+.PD 0
+.IP \fB--check-hdf5-snr\fR
+.PD
+With this option with \fB--peaks=hdf5\fR, the peaks will additionally be checked to see that they satisfy the minimum SNR specified with \fB--min-snr\fR.
.PD 0
.IP \fB--no-peaks-in-stream\fR
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 0f5d96a6..6e5d09dd 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -661,7 +661,8 @@ int peak_sanity_check(struct image *image, Crystal **crystals, int n_cryst)
void validate_peaks(struct image *image, double min_snr,
- int ir_inn, int ir_mid, int ir_out, int use_saturated)
+ int ir_inn, int ir_mid, int ir_out, int use_saturated,
+ int check_snr)
{
int i, n;
ImageFeatureList *flist;
@@ -718,7 +719,7 @@ void validate_peaks(struct image *image, double min_snr,
continue;
}
- if ( fabs(intensity)/sigma < min_snr ) {
+ if ( check_snr && (fabs(intensity)/sigma < min_snr) ) {
n_snr++;
continue;
}
diff --git a/libcrystfel/src/peaks.h b/libcrystfel/src/peaks.h
index 09ad5245..433f7d1f 100644
--- a/libcrystfel/src/peaks.h
+++ b/libcrystfel/src/peaks.h
@@ -50,7 +50,7 @@ extern int peak_sanity_check(struct image *image, Crystal **crystals,
extern void validate_peaks(struct image *image, double min_snr,
int ir_inn, int ir_mid, int ir_out,
- int use_saturated);
+ int use_saturated, int check_snr);
extern int integrate_peak(struct image *image, int cfs, int css,
double *pfs, double *pss,
diff --git a/src/indexamajig.c b/src/indexamajig.c
index 3f010b12..019d55a1 100644
--- a/src/indexamajig.c
+++ b/src/indexamajig.c
@@ -3,13 +3,13 @@
*
* Index patterns, output hkl+intensity etc.
*
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
* Copyright © 2012 Richard Kirian
* Copyright © 2012 Lorenzo Galli
*
* Authors:
- * 2010-2013 Thomas White <taw@physics.org>
+ * 2010-2014 Thomas White <taw@physics.org>
* 2011 Richard Kirian
* 2012 Lorenzo Galli
* 2012 Chunhong Yoon
@@ -121,6 +121,7 @@ static void show_help(const char *s)
" Default: 100,000.\n"
" --min-snr=<n> Minimum signal-to-noise ratio for peaks.\n"
" Default: 5.\n"
+" --check-hdf5-snr Check SNR for peaks from --peaks=hdf5.\n"
" --int-radius=<r> Set the integration radii. Default: 4,5,7.\n"
"-e, --image=<element> Use this image from the HDF5 file.\n"
" Example: /data/data0.\n"
@@ -211,6 +212,7 @@ int main(int argc, char *argv[])
iargs.threshold = 800.0;
iargs.min_gradient = 100000.0;
iargs.min_snr = 5.0;
+ iargs.check_hdf5_snr = 0;
iargs.det = NULL;
iargs.peaks = PEAK_ZAEF;
iargs.beam = NULL;
@@ -251,18 +253,22 @@ int main(int argc, char *argv[])
/* Long-only options with no arguments */
{"filter-noise", 0, &iargs.noisefilter, 1},
- {"no-sat-corr", 0, &iargs.satcorr, 0},
- {"sat-corr", 0, &iargs.satcorr, 1},
{"no-check-prefix", 0, &config_checkprefix, 0},
- {"no-closer-peak", 0, &iargs.closer, 0},
{"closer-peak", 0, &iargs.closer, 1},
{"basename", 0, &config_basename, 1},
{"no-peaks-in-stream", 0, &iargs.stream_peaks, 0},
{"no-refls-in-stream", 0, &iargs.stream_refls, 0},
{"integrate-saturated",0, &integrate_saturated, 1},
- {"use-saturated", 0, &iargs.use_saturated, 1},
{"no-use-saturated", 0, &iargs.use_saturated, 0},
{"no-revalidate", 0, &iargs.no_revalidate, 1},
+ {"check-hdf5-snr", 0, &iargs.check_hdf5_snr, 1},
+
+ /* Long-only options which don't actually do anything */
+ {"no-sat-corr", 0, &iargs.satcorr, 0},
+ {"sat-corr", 0, &iargs.satcorr, 1},
+ {"no-closer-peak", 0, &iargs.closer, 0},
+ {"no-check-hdf5-snr", 0, &iargs.check_hdf5_snr, 0},
+ {"use-saturated", 0, &iargs.use_saturated, 1},
/* Long-only options with arguments */
{"peaks", 1, NULL, 2},
diff --git a/src/process_image.c b/src/process_image.c
index d1e3a7de..9c4c740d 100644
--- a/src/process_image.c
+++ b/src/process_image.c
@@ -3,11 +3,11 @@
*
* The processing pipeline for one image
*
- * Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY,
+ * Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY,
* a research centre of the Helmholtz Association.
*
* Authors:
- * 2010-2013 Thomas White <taw@physics.org>
+ * 2010-2014 Thomas White <taw@physics.org>
*
* This file is part of CrystFEL.
*
@@ -128,7 +128,8 @@ void process_image(const struct index_args *iargs, struct pattern_args *pargs,
if ( !iargs->no_revalidate ) {
validate_peaks(&image, iargs->min_snr,
iargs->ir_inn, iargs->ir_mid,
- iargs->ir_out, iargs->use_saturated);
+ iargs->ir_out, iargs->use_saturated,
+ iargs->check_hdf5_snr);
}
break;
diff --git a/src/process_image.h b/src/process_image.h
index 90113ff9..20e6fe2e 100644
--- a/src/process_image.h
+++ b/src/process_image.h
@@ -55,6 +55,7 @@ struct index_args
float threshold;
float min_gradient;
float min_snr;
+ int check_hdf5_snr;
struct detector *det;
IndexingMethod *indm;
IndexingPrivate **ipriv;
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-07 16:13:53 +0000