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authorThomas White <taw@physics.org>2021-01-08 11:45:35 +0100
committerThomas White <taw@physics.org>2021-01-08 13:16:38 +0100
commit3410f0a68f889bc6d94f52904abe5a68ba2fe19a (patch)
tree809da5df1c5c21d85989aeb8907d72c80b6a848b /doc
parentd6bfd45c3cd48023532fcc40021a8c98d18e05bf (diff)
Update documentation about max_adu, and add a warning
Diffstat (limited to 'doc')
-rw-r--r--doc/man/crystfel_geometry.52
-rw-r--r--doc/man/indexamajig.12
2 files changed, 2 insertions, 2 deletions
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index dad5d3d0..8797ef3d 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -221,7 +221,7 @@ The corner of this panel, defined as the first point in the panel to appear in t
.PD 0
.IP \fBmax_adu\fR
-The maximum value, in ADU, before the pixel will be considered as bad. That is, the saturation value for the panel.
+The saturation value for the panel. You can use this to exclude saturated peaks from the peak search or to avoid integrating saturated reflections. However, usually it's best to include saturated peaks, and exclude saturated reflections with the --max-adu option of process_hkl and partialator. Therefore you should avoid setting this parameter - a warning will be displayed if you do.
.PD 0
.IP \fBflag_lessthan
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 98c15237..1cca53ba 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -143,7 +143,7 @@ Center the peak boxes iteratively on the actual peak locations. The opposite is
.IP \fB-sat\fR
.PD
-Normally, reflections which contain one or more pixels above max_adu (defined in the detector geometry file) will not be integrated and written to the stream. Using this option skips this check, and allows saturated reflections to be passed to the later merging stages. This is not usually a good idea, but might be your only choice if there are many saturated reflections. The opposite is \fB-nosat\fR, which is the default for all integration methods.
+Normally, reflections which contain one or more pixels above max_adu (defined in the detector geometry file) will not be integrated and written to the stream. Using this option skips this check, and allows saturated reflections to be passed to the later merging stages. The opposite is \fB-nosat\fR, which is the default for all integration methods. However, note that the saturation check will only be done if max_adu is set in the geometry file. Usually, it's better to exclude saturated reflections at the merging stage. The the documentation for max_adu in crystfel_geometry(5).
.IP \fB-grad\fR
.PD