diff options
Diffstat (limited to 'doc/man')
| -rw-r--r-- | doc/man/indexamajig.1 | 2 |
1 files changed, 1 insertions, 1 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 2f06d8d3..11da2445 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -48,7 +48,7 @@ See \fBman crystfel_geometry\fR for information about how to create a geometry d 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. -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 gradient for finding a peak using \fB--threshold\fR and \fB--min-gradient\fR. Both of these have arbitrary units matching the pixel values in the data. +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. |