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====== Peaksearch ======

Peaksearch is a peak searching algorithm, part of [[software:imaged11|ImageD11]]. It can be started by typing
    peaksearch.py
in a terminal.

Peaksearch is used when [[processing:search_for_peaks|searching for peaks]] on the diffraction images.

More details on peaksearch can be found in the [[https://pythonhosted.org/ImageD11/peaksearching.html|ImageD11 user manual]].

<code>
peaksearch.py -h
Usage: peaksearch.py [options]

Options:
  -h, --help            show this help message and exit
  -n STEM, --namestem=STEM
                        Name of the files up the digits part  eg mydata in
                        mydata0000.edf
  -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,
                        default=0
  -s SPLINE, --splinefile=SPLINE
                        Spline file for spatial distortion,
                        default=/data/opid11/inhouse/Frelon2K/spatial2k.spline
  -p PERFECT, --perfect_images=PERFECT
                        Ignore spline Y|N, default=N
  -O FLOOD, --flood=FLOOD
                        Flood file, default=None
  -t THRESHOLDS, --threshold=THRESHOLDS
                        Threshold level, you can have several
  --OmegaFromHeader     Read Omega values from headers [default]
  --OmegaOverRide       Override Omega values from headers
  --singleThread        Do single threaded processing
  --profile=PROFILE_FILE
                        Write profiling information (you will want
                        singleThread too)
  -S OMEGASTEP, --step=OMEGASTEP
                        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
  --monitorcol=MONITORCOL
                        Header value for incident beam intensity
  --monitorval=MONITORVAL
                        Incident beam intensity value to normalise to
  --omega_motor=OMEGAMOTOR
                        Header value to use for rotation motor position
                        [Omega]
  --omega_motor_step=OMEGAMOTORSTEP
                        Header value to use for rotation width [OmegaStep]
  --interlaced          Interlaced DCT scan
</code>
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