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--- software:peaksearch [2019/02/20 20:38] – smerkel
+++ software:peaksearch [2019/02/20 20:43] (current) – smerkel
@@ Line 1: / Line 1: @@
 ====== Peaksearch ======
-Go to the newly created folder (which is still empty). Then type to the Konsole:
+Peaksearch is a peak searching algorithm, part of [[software:imaged11|ImageD11]]. It can be started by typing
+    peaksearch.py
+in a terminal.
-    peaksearch.py -n ../'directory'/'directory stem' -f 0 -l 111 -d ../'directory'/'median file20000.edf' -t &&&
+Peaksearch is used when [[processing:search_for_peaks|searching for peaks]] on the diffraction images.
-**-f** marks the number of the first image, **-l** the number of the last image.
+More details on peaksearch can be found in the [[https://pythonhosted.org/ImageD11/peaksearching.html|ImageD11 user manual]].
-**&&&** 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 [[software:imaged11|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.
+<code>
 peaksearch.py -h
-WARNING:xsdimage:lxml library is probably not part of your python installation: disabling xsdimage format
-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
-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]
@@ Line 129: / Line 68: @@
                         Header value to use for rotation width [OmegaStep]
   --interlaced          Interlaced DCT scan
+</code>