Update docs

1 files changed, 3 insertions, 3 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 1f253aea..b151438c 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -38,7 +38,7 @@ See \fBman crystfel_geometry\fR for information about how to create a geometry d
 
 .SH PEAK DETECTION
 
-You can control the peak detection on the command line.  Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR.  Currently, two values for "method" are available.  \fB--peaks=hdf5\fR will take the peak locations from the HDF5 file.  It expects a two dimensional array at where size in the first dimension is the number of peaks and the size in the second dimension is three.  The first two columns contain the fast scan and slow scan coordinates, the third contains the intensity.  However, the intensity will be ignored since the pattern will always be re-integrated using the unit cell provided by the indexer on the basis of the peaks.  You can tell indexamajig where to find this table inside each HDF5 file using \fB--hdf5-peaks=\fR\fIpath\fR.
+You can control the peak detection on the command line.  Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR.  Currently, two values for "method" are available.  \fB--peaks=hdf5\fR will take the peak locations from the HDF5 file.  It expects a two dimensional array, by default at /processing/hitfinder/peakinfo, whose size in the first dimension equals the number of peaks and whose size in the second dimension is three.  The first two columns contain the fast scan and slow scan coordinates, the third contains the intensity.  However, the intensity will be ignored since the pattern will always be re-integrated using the unit cell provided by the indexer on the basis of the peaks.  You can tell indexamajig where to find this table inside each HDF5 file using \fB--hdf5-peaks=\fR\fIpath\fR.
 
 If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000).  You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-gradient\fR.  The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units.  Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below).  They will also be rejected if the peak is closer than twice the inner integration radius from another peak.
 
@@ -63,7 +63,7 @@ To use this option, 'ipmosflm' must be in your shell's search path.  If you see
 
 .IP \fBreax\fR
 .PD
-Run the DPS algorithm, looking for the axes of your cell.
+Run the DPS algorithm, looking only for lattice repeats which are close to the axes of the unit cell parameters you gave.  In theory, this method is similar to \fBmosflm\fR but should work better because of making better use of the prior cell information you gave.  In practice, it's experimental.
 
 .IP \fBgrainspotter\fR
 .PD
@@ -92,7 +92,7 @@ Check linear combinations of the unit cell basis vectors to see if a cell can be
 
 .IP \fB-bad\fR
 .PD
-Do not check that the cell accounts for any of the peaks as described in \fBdirax\fR above.  Might be useful to debug initial indexing problems, or if there are many multi-crystal patterns and the indexing method has no concept of multiple crystals per pattern (which, at the moment, means all of them).  Can be used with any indexing method, but is generally a bad idea.
+Do not check that the cell accounts for any of the peaks as described in \fBdirax\fR above.  Might be useful to debug initial indexing problems, or if there are many multi-crystal patterns and the indexing method has no concept of multiple crystals per pattern (which, at the moment, means all of them except \fBgrainspotter\fR).  Can be used with any indexing method, but is generally a bad idea.
 
 .IP \fB-nolatt\fR
 .PD