Merge branch 'tom/max_adu'

5 files changed, 16 insertions, 0 deletions

diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index 3254232b..006af722 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -170,6 +170,10 @@ peak_sep = 6.0
 .br
 ; in which case the value will be used for all *subsequent* panels.
 
+; The maximum value, in ADU, before the pixel will be considered as bad.
+.br
+max_adu = 3500
+
 .PP
 See the "examples" folder for some examples (look at the ones ending in .geom).
 
diff --git a/libcrystfel/src/detector.c b/libcrystfel/src/detector.c
index 94af656f..b7d809df 100644
--- a/libcrystfel/src/detector.c
+++ b/libcrystfel/src/detector.c
@@ -606,6 +606,8 @@ static int parse_field_for_panel(struct panel *panel, const char *key,
 		panel->coffset = atof(val);
 	} else if ( strcmp(key, "res") == 0 ) {
 		panel->res = atof(val);
+	} else if ( strcmp(key, "max_adu") == 0 ) {
+		panel->max_adu = atof(val);
 	} else if ( strcmp(key, "peak_sep") == 0 ) {
 		panel->peak_sep = atof(val);
 	} else if ( strcmp(key, "badrow_direction") == 0 ) {
@@ -743,6 +745,7 @@ struct detector *get_detector_geometry(const char *filename)
 	det->defaults.ssy = 1.0;
 	det->defaults.rigid_group = NULL;
 	det->defaults.adu_per_eV = NAN;
+	det->defaults.max_adu = +INFINITY;
 	strncpy(det->defaults.name, "", 1023);
 
 	do {
@@ -1254,6 +1257,7 @@ int write_detector_geometry(const char *filename, struct detector *det)
 		fprintf(fh, "%s/corner_x = %g\n", p->name, p->cnx);
 		fprintf(fh, "%s/corner_y = %g\n", p->name, p->cny);
 		fprintf(fh, "%s/adu_per_eV = %g\n", p->name, p->adu_per_eV);
+		fprintf(fh, "%s/max_adu = %g\n", p->name, p->max_adu);
 
 		if ( p->no_index ) {
 			fprintf(fh, "%s/no_index = 1\n", p->name);
diff --git a/libcrystfel/src/detector.h b/libcrystfel/src/detector.h
index 02d66cd4..2b4ac5c6 100644
--- a/libcrystfel/src/detector.h
+++ b/libcrystfel/src/detector.h
@@ -65,6 +65,7 @@ struct panel
 	double   peak_sep; /* Characteristic peak separation */
 	char    *rigid_group;  /* Rigid group, or -1 for none */
 	double   adu_per_eV;   /* Number of ADU per eV */
+	double   max_adu;  /* Treat pixel as unreliable if higher than this */
 
 	double fsx;
 	double fsy;
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 78a68185..477d9345 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -211,6 +211,9 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 		val = image->data[idx];
 
+		/* Veto peak if it contains saturation in bg region */
+		if ( val > p->max_adu ) return 1;
+
 		bg_tot += val;
 		bg_tot_sq += pow(val, 2.0);
 		bg_counts++;
@@ -259,6 +262,9 @@ static int integrate_peak(struct image *image, int cfs, int css,
 
 		val = image->data[idx] - bg_mean;
 
+		/* Veto peak if it contains saturation */
+		if ( image->data[idx] > p->max_adu ) return 1;
+
 		pk_counts++;
 		pk_total += val;
 
diff --git a/tests/integration_check.c b/tests/integration_check.c
index 7e812ad5..2d18ac5a 100644
--- a/tests/integration_check.c
+++ b/tests/integration_check.c
@@ -197,6 +197,7 @@ int main(int argc, char *argv[])
 	image.det->panels[0].clen = 1.0;
 	image.det->panels[0].res = 1.0;
 	image.det->panels[0].adu_per_eV = 1.0/1000.0;  /* -> 1 adu per photon */
+	image.det->panels[0].max_adu = +INFINITY;  /* No cutoff */
 
 	image.width = 128;
 	image.height = 128;