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author | Thomas White <taw@physics.org> | 2010-11-16 10:05:28 +0100 |
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committer | Thomas White <taw@physics.org> | 2012-02-22 15:27:05 +0100 |
commit | 67bc653a2b13f3cdcd81c7bcd6e7bbc4d60db7f2 (patch) | |
tree | 2e760886add29e57d83ac1909ee826c9268dab1f /doc/indexamajig.txt | |
parent | 0567569d2f97a5c4aae54d6f8b27f0eeb7539b86 (diff) |
Update docs
Diffstat (limited to 'doc/indexamajig.txt')
-rw-r--r-- | doc/indexamajig.txt | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/doc/indexamajig.txt b/doc/indexamajig.txt index a602a87d..f725bee5 100644 --- a/doc/indexamajig.txt +++ b/doc/indexamajig.txt @@ -56,6 +56,36 @@ See doc/geometry for information about how to create a geometry description file. +Peak Detection +-------------- + +You can control the peak detection on the command line. Firstly, you can choose +the peak detection method using "--peaks=<method>". Currently, two possible +values for "method" are available. "hdf5" will take the peak locations from the +HDF5 file. It expects a two dimensional array at /processing/hitfinder/peakinfo +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 x and y +coordinate (see the "Note about data orientation" in geometry.txt for details), +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. + +The "zaef" method uses a simple gradient search after Zaefferer (2000). You can +control the overall threshold and minimum gradient for finding a peak using the +"--threshold" and "--min-gradient" options. Both of these have units of "ADU" +(i.e. units of intensity according to the contents of the HDF5 file). + +A minimum peak separation can also be provided in the geometry description file +(see geometry.txt 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 "by proximity". + +You can suppress peak detection altogether for a panel in the geometry file by +specifying the "no_index" value for the panel as non-zero. + + Cell Reduction -------------- |