Go to the newly created folder (which is still empty). Then type to the Konsole:

  peaksearch.py -n ../'directory'/'directory stem' -f 0 -l 111 -d ../'directory'/'median file20000.edf' -t &&&

-f marks the number of the first image, -l the number of the last image.

&&& is a space holder for the intensity threshold. You can also add more than one threshold by exceeding the code by another -t &&& -t &&& -t &&& …, depending on how many thresholds you want to test.

From now on, we call the newly created files processed data. Proceed with ImageD11 to look at the processed data.

Sometimes the algorithm does not work because it cannot read the median file. You can try to run PeakSearch without typing -d median_file.edf. Sometimes this works.

peaksearch.py -h WARNING:xsdimage:lxml library is probably not part of your python installation: disabling xsdimage format Usage: peaksearch.py [options]

Options:

1. h, –help show this help message and exit
2. 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

Usage: peaksearch.py [options]

Options:

1. h, –help show this help message and exit
2. 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