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software:peaksearch
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software:peaksearch [2018/06/22 15:48] matthias ↷ Page moved from sofware:peaksearch to software:peaksearch |
software:peaksearch [2019/02/20 19:43] (current) smerkel |
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| ====== Peaksearch ====== | ====== Peaksearch ====== | ||
| - | ===== Peaksearch ===== | + | Peaksearch is a peak searching algorithm, part of [[software:imaged11|ImageD11]]. It can be started by typing |
| - | Go to the newly created folder (which is still empty). Then type to the Konsole: | + | peaksearch.py |
| + | in a terminal. | ||
| - | peaksearch.py -n ../XXX/YYY -f 0 -l 111 -d ../XXX/XXgrainm20000.edf -t &&& | + | Peaksearch is used when [[processing:search_for_peaks|searching for peaks]] on the diffraction images. |
| - | + | ||
| - | where //XXX// is a space holder for the directory and //YYY// is a space holder for the stem of the edf image files (everything before the numbers). | + | |
| - | //&&&// 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. | + | More details on peaksearch can be found in the [[https://pythonhosted.org/ImageD11/peaksearching.html|ImageD11 user manual]]. |
| - | From now on, we call the newly created files //processed data//. | + | <code> |
| + | peaksearch.py -h | ||
| + | Usage: peaksearch.py [options] | ||
| - | ===== ImageD11 ===== | + | 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> | ||
| - | Open [[software:imaged11|ImageD11]] by going to the folder where the //processed data// is stored. Now open the program by typing the following to the Konsole: | ||
| - | |||
| - | ImageD11_gui.py | ||
| - | |||
| - | The program should open. In //ImageD11// go to //Transformation//, then //Load filtered peaks// and choose the .flt file you would like to see (You automatically should be in the right folder.). | ||
| - | |||
| - | Then go to //Transformation// and //plot y/z//. You should see a 2D diffraction image of all the spots which passed the threshold. From now on, we call this image //diffraction plot//. You should remember, which file you opened, because ImageD11 doesn't show this anywhere. | ||
| - | |||
| - | //ImageD11// can show only one //diffraction plot// at once. If you want to compare two (or more) //diffraction plots//, you can either save the plots (as .png file) or open a new //ImageD11// in a new tab of the Konsole. | ||
software/peaksearch.1529682490.txt.gz · Last modified: 2019/02/18 10:11 (external edit)
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