Merge branch 'valerio/peakfinder8'

1 files changed, 30 insertions, 3 deletions

diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index d7f59f9d..8619fd92 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -47,6 +47,8 @@ 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 (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.
 
 
@@ -270,7 +272,7 @@ This option is here for historical purposes only, to disable a correction which
 .PD 0
 .IP \fB--threshold=\fR\fIthres\fR
 .PD
-Set the overall threshold for peak detection using \fB--peaks=zaef\fR to \fIthres\fR, which has the same units as the detector data.  The default is \fB--threshold=800\fR.
+Set the overall threshold for peak detection using \fB--peaks=zaef\fR or \fB--peaks=peakfinder8\fR to \fIthres\fR, which has the same units as the detector data.  The default is \fB--threshold=800\fR.
 
 .PD 0
 .IP \fB--min-gradient=\fR\fIgrad\fR
@@ -280,12 +282,37 @@ Set the square of the gradient threshold for peak detection using \fB--peaks=zae
 .PD 0
 .IP \fB--min-snr=\fR\fIsnr\fR
 .PD
-Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR.  The default is \fB--min-snr=5\fR.
+Set the minimum I/sigma(I) for peak detection when using \fB--peaks=zaef\fR or \fB--peaks=peakfinder8\fR.  The default is \fB--min-snr=5\fR.
+
+.PD 0
+.IP \fB--min-pix-count=\fR\fIcnt\fR
+.PD
+Accepts peaks only if they include more than \fR\fIcnt\fR pixels, when using \fB--peaks=peakfinder8\fR.  The default is \fB--min-pix-count=2\fR.
+
+.PD 0
+.IP \fB--max-pix-count=\fR\fIcnt\fR
+.PD
+Accepts peaks only if they include less than \fR\fIcnt\fR pixels, when using \fB--peaks=peakfinder8\fR.  The default is \fB--max-pix-count=200\fR.
+
+.PD 0
+.IP \fB--local-bg-radius=\fR\fIr\fR
+.PD
+Radius (in pixels) used for the estimation of the local background when using \fB--peaks=peakfinder8\fR.  The default is \fB--local-bg-radius=3\fR.
+
+.PD 0
+.IP \fB--min-res=\fR\fIpx\fR
+.PD
+Only accept peaks if they lay at more than \fR\fIpx\fR pixels from the center of the detector when using \fB--peaks=peakfinder8\fR.  The default is \fB--min-res=0\fR.
+
+.PD 0
+.IP \fB--max-res=\fR\fIpx\fR
+.PD
+Only accept peaks if they lay at less than \fR\fIpx\fR pixels from the center of the detector when using \fB--peaks=peakfinder8\fR.  The default is \fB--max-res=1200\fR.
 
 .PD 0
 .IP \fB--copy-hdf5-field=\fR\fIpath\fR
 .PD
-Copy the information from \fIpath\fR in the HDF5 file into the output stream.  The information must be a single scalar value.  This option is sometimes useful to allow data to be separated after indexing according to some condition such the presence of an optical pump pulse.  You can give this option as many times as you need to copy multiple bits of information.
+Copy the information from \fR\fIpath\fR in the HDF5 file into the output stream.  The information must be a single scalar value.  This option is sometimes useful to allow data to be separated after indexing according to some condition such the presence of an optical pump pulse.  You can give this option as many times as you need to copy multiple bits of information.
 
 .PD 0
 .IP "\fB-j\fR \fIn\fR"