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software:peaksearch
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software:peaksearch [2019/02/20 19:38] smerkel |
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| ====== Peaksearch ====== | ====== 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 | peaksearch.py -h | ||
| WARNING:xsdimage:lxml library is probably not part of your python installation: disabling xsdimage format | WARNING:xsdimage:lxml library is probably not part of your python installation: disabling xsdimage format | ||
| Line 72: | Line 69: | ||
| Header value to use for rotation width [OmegaStep] | Header value to use for rotation width [OmegaStep] | ||
| --interlaced Interlaced DCT scan | --interlaced Interlaced DCT scan | ||
| - | Usage: peaksearch.py [options] | + | </code> |
| - | + | ||
| - | 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 | + | |
software/peaksearch.txt · Last modified: 2019/02/20 19:43 by smerkel
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