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-rw-r--r--src/indexamajig.c18
-rw-r--r--src/process_image.c7
-rw-r--r--src/process_image.h1
3 files changed, 17 insertions, 9 deletions
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;