Add docs/stream-format.txt and clarify count of saturated reflections

2 files changed, 16 insertions, 1 deletions

diff --git a/doc/stream-format.txt b/doc/stream-format.txt
new file mode 100644
index 00000000..b74d50c1
--- /dev/null
+++ b/doc/stream-format.txt
@@ -0,0 +1,15 @@
+CrystFEL stream format
+----------------------
+
+num_peaks: The number of peaks accepted for indexing.  If you used
+  "--use-saturated", this includes the saturated peaks which are also counted by
+  num_saturated_peaks.  If you didn't, then it doesn't.
+
+num_saturated_peaks: The number of saturated peaks, regardless of whether or not
+  they were used for indexing (see --use-saturated).
+
+num_saturated_reflections: The number of saturated reflections, regardless of
+  whether or not they were included in the reflection list
+  (see --integrate-saturated).  Reflections which could not be integrated for
+  some other reason, e.g. because they were close to a panel edge or hit a bad
+  region, are NOT included in this count.
diff --git a/libcrystfel/src/peaks.c b/libcrystfel/src/peaks.c
index 6b2d2b97..4b8a8ee8 100644
--- a/libcrystfel/src/peaks.c
+++ b/libcrystfel/src/peaks.c
@@ -799,7 +799,7 @@ static void integrate_crystal(Crystal *cr, struct image *image, int use_closer,
 		                   &intensity, &sigma, ir_inn, ir_mid, ir_out,
 		                   bgMasks[pnum], &saturated);
 
-		if ( saturated ) {
+		if ( !r && saturated ) {
 			n_saturated++;
 			if ( !integrate_saturated ) r = 1;
 		}