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authorValerio Mariani <valerio.mariani@desy.de>2017-03-13 11:26:40 +0100
committerValerio Mariani <valerio.mariani@desy.de>2017-03-13 11:26:40 +0100
commitd757002728ed36686de066aa997ae59817fa322c (patch)
tree1aa5d4eca45b1f7153e9e0d41c4e1ec5bc8efd04
parentb2de09452e8edf050a8679e726f5075abd37e961 (diff)
Added information about max_num_peaks to documentation
-rw-r--r--doc/man/indexamajig.12
1 files changed, 1 insertions, 1 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index b8ed4722..8619fd92 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -47,7 +47,7 @@ You can control the peak detection on the command line. Firstly, you can choose
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.
-If you instead use \fB--peaks=peakfinder8\fR, indexamajig will user the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks. Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion.
+If you instead use \fB--peaks=peakfinder8\fR, indexamajig will user the "peakfinder8" peak finding algorithm describerd in Barty et al. (2014). Pixels above a radius-dependent intensity threshold are considered as candidate peaks (although the user sets an absolute minimum threshold for candidate peaks). Peaks are then only accepted if their signal to noise level over the local background is sufficiently high. Peaks can include multiple pixels and the user can reject a peak if it includes too many or too few. The distance of a peak from the center of the detector can also be used as a filtering criterion. Please notice that the peakfinder8 will not report more than 2048 peaks for each panel: any additional peak is ignored.
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.