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--- software:peaksearch [2019/02/18 11:11] – external edit 127.0.0.1
+++ 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.
+<code>
+peaksearch.py -h
+Usage: peaksearch.py [options]
-From now on, we call the newly created files //processed data//. Proceed with [[software:imaged11|ImageD11]] to look at the //processed data//.
+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
+</code>
-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.