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| author | Thomas White <taw@physics.org> | 2012-03-13 16:54:01 +0100 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2012-03-13 16:54:01 +0100 |
| commit | 28b098f021b81b5f1fd90361923320540d2d50fa (patch) | |
| tree | f9b5a78190651753298965a75ab7083a2989f87f | |
| parent | 5357af3607a844fe403bc83a87ea8bae74067bbb (diff) | |
| parent | 1c36f47bd3c30b99fcff86e4a1d7dea69f174fbb (diff) | |
Merge branch 'master-new' of ssh://git.bitwiz.org.uk/crystfel into master-new
| -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 5469174a..ac443906 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -75,7 +75,7 @@ which could not be indexed, you might use \fB--record=integrated,peaksifnotindex 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 \fR--min-gradient\fB. 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 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. A minimum peak separation can also be provided in the geometry description file (see \fBman crystfel_geometry\fR for details). This number serves two purposes. Firstly, it is the maximum distance allowed between the peak summit and the foot point (where the gradient exceeds the minimum gradient). Secondly, it is the minimum distance allowed between one peak and another, before the later peak will be rejected. |