diff options
| author | Thomas White <taw@physics.org> | 2014-03-26 17:48:47 +0100 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2014-03-26 17:48:47 +0100 |
| commit | fddfbb4fd069d914865afc53053574b87ba2d552 (patch) | |
| tree | 6523ca8cd5d9c1c65d4064b433e4197f41aad8ac /src | |
| parent | 372c7db873ffbc538591d66ff1c7a1fc5d390a65 (diff) | |
indexamajig: Don't check SNR with --peaks=hdf5 unless given --check-hdf5-snr
Diffstat (limited to 'src')
| -rw-r--r-- | src/indexamajig.c | 18 | ||||
| -rw-r--r-- | src/process_image.c | 7 | ||||
| -rw-r--r-- | src/process_image.h | 1 |
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; |