indexamajig: Don't check SNR with --peaks=hdf5 unless given --check-hdf5-snr

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;