User Tools

Site Tools



Peaksearch is a peak searching algorithm, part of ImageD11. It can be started by typing

in a terminal.

Peaksearch is used when searching for peaks on the diffraction images.

More details on peaksearch can be found in the ImageD11 user manual. -h
Usage: [options]

  -h, --help            show this help message and exit
  -n STEM, --namestem=STEM
                        Name of the files up the digits part  eg mydata in
  -F FORMAT, --format=FORMAT
                        Image File format, eg edf or bruker
  -f FIRST, --first=FIRST
                        Number of first file to process, default=0
  -l LAST, --last=LAST  Number of last file to process
  -o OUTFILE, --outfile=OUTFILE
                        Output filename, default=peaks.spt
  -d DARK, --darkfile=DARK
                        Dark current filename, to be subtracted, default=None
  -D DARKOFFSET, --darkfileoffset=DARKOFFSET
                        Constant to subtract from dark to avoid overflows,
  -s SPLINE, --splinefile=SPLINE
                        Spline file for spatial distortion,
  -p PERFECT, --perfect_images=PERFECT
                        Ignore spline Y|N, default=N
  -O FLOOD, --flood=FLOOD
                        Flood file, default=None
                        Threshold level, you can have several
  --OmegaFromHeader     Read Omega values from headers [default]
  --OmegaOverRide       Override Omega values from headers
  --singleThread        Do single threaded processing
                        Write profiling information (you will want
                        singleThread too)
                        Step size in Omega when you have no header info
  -T OMEGA, --start=OMEGA
                        Start position in Omega when you have no header info
  -k KILLFILE, --killfile=KILLFILE
                        Name of file to create stop the peaksearcher running
  --ndigits=NDIGITS     Number of digits in file numbering [4]
  -P PADDING, --padding=PADDING
                        Is the image number to padded Y|N, e.g. should 1 be
                        0001 or just 1 in image name, default=Y
  -m, --median1D        Computes the 1D median, writes it to file .bkm and
                        subtracts it from image. For liquid background on
                        radially transformed images
                        Header value for incident beam intensity
                        Incident beam intensity value to normalise to
                        Header value to use for rotation motor position
                        Header value to use for rotation width [OmegaStep]
  --interlaced          Interlaced DCT scan
software/peaksearch.txt · Last modified: 2019/02/20 19:43 by smerkel