Get rid of "--filter-cm"

This was completely specific to pnCCDs, and not even properly general to the
different configurations there.

1 files changed, 4 insertions, 3 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 8a41e054..2b6bf36d 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -235,14 +235,15 @@ Set the tolerances for unit cell comparison.  \fItol\fR takes the form \fIa\fR,\
 The default is \fB--tolerance=5,5,5,1.5\fR.
 
 .PD 0
-.IP \fB--filter-cm\fR
+.IP \fB--median-filter=\fR\fIn\fR
 .PD
-Attempt to subtract common-mode noise from the image.  The filtered image will be used for the final integration of the peaks (in contrast to \fB--filter-noise\fR.  It is usually better to do a careful job of cleaning the images up before using indexamajig, so this option should not normally be used.
+Apply a median filter with box "radius" \fIn\fR to the image.  Each pixel will be set to the median of the values from a \fI(n+1)\fRx\fI(n+1)\fR square centered on the pixel.  This might help with peak detection if the background is high and/or noisy.  The \fIunfiltered\fR image will be used for the final integration of the peaks.  If you also use \fB--noise-filter\fR, the median filter will be applied first.
+
 
 .PD 0
 .IP \fB--filter-noise\fR
 .PD
-Apply a noise filter to the image with checks 3x3 squares of pixels and sets all of them to zero if any of the nine pixels have a negative value.  This filter may help with peak detection under certain circumstances, and the \fIunfiltered\fR image will be used for the final integration of the peaks.   It is usually better to do a careful job of cleaning the images up before using indexamajig, so this option should not normally be used.
+Apply a noise filter to the image with checks 3x3 squares of pixels and sets all of them to zero if any of the nine pixels have a negative value.  This filter may help with peak detection under certain circumstances.  The \fIunfiltered\fR image will be used for the final integration of the peaks, because the filter is destroys a lot of information from the pattern.  If you also use \fB--median-filter\fR, the median filter will be applied first.
 
 .PD 0
 .IP \fB--no-sat-corr\fR