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xray_data:convertfileseries
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xray_data:convertfileseries [2019/01/18 13:19] smerkel created |
xray_data:convertfileseries [2019/02/18 10:11] (current) |
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| - | Convert! | + | ====== Convert image file series ====== |
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| + | ===== Introduction ===== | ||
| + | |||
| + | Typical diamond anvil cell beamlines generate series of diffraction files in various formats, which are not the [[fileformat:edf|EDF]] format used in further processing. The tools here can be used to convert the files into the proper format. | ||
| + | |||
| + | Data collected at step scans have a starting ω position, an end ω position, and a step size δω. Diffraction are collected at each ω and save in files such as ''name-0000.tif'', ''name-0001.tif'', etc. For instance, if you collect data from -2° to +2° with a step size of 1.0°, starting from image 5, with a stem ''mydata'', you will save the following data files | ||
| + | * ''mydata-0005.tif'' for a scan between ω = -2.0° to -1.0° with an average ω of -1.5°, | ||
| + | * ''mydata-0006.tif'' for a scan between ω = -1.0° to -0.0° with an average ω of -0.5°, | ||
| + | * ''mydata-0007.tif'' for a scan between ω = +0.0° to +1.0° with an average ω of -0.5°, | ||
| + | * ''mydata-0008.tif'' for a scan between ω = +1.0° to +2.0° with an average ω of -1.5°. | ||
| + | |||
| + | The scripts ''timelessTiff2edf'' and ''timelessMccd2edf'', which are both part of the [[software:timelesstools|TIMEleSS tools]], are meant to convert such file series into series of EDF files. | ||
| + | |||
| + | Watch out! You can generate vast amount of data! You may want to include such scripts into larger scripts as you develop your data processing strategy. | ||
| + | |||
| + | ===== timelessTiff2edf ===== | ||
| + | |||
| + | <code> | ||
| + | timelessTiff2edf -h | ||
| + | |||
| + | usage: timelessTiff2edf -f from -t to -s step -n stem -i first image [OPTIONS] | ||
| + | |||
| + | Creates a list of EDF files based on a collection of TIFF files This is part | ||
| + | of the TIMEleSS project http://timeless.texture.rocks | ||
| + | |||
| + | optional arguments: | ||
| + | -h, --help show this help message and exit | ||
| + | -f FROM, --from FROM Start for omega scan (in degrees, required) | ||
| + | -t TO, --to TO End for omega scan (in degrees, required) | ||
| + | -s STEP, --step STEP Omega step (in degrees, required) | ||
| + | -n STEM, --stem STEM Stem for images files (required) | ||
| + | -i IMAGEFIRST, --imagefirst IMAGEFIRST | ||
| + | Number of first image file in series (required) | ||
| + | -p TIFFIMAGEPATH, --tiffimagepath TIFFIMAGEPATH | ||
| + | Path to tiff images. Default is ./ | ||
| + | -e EDFIMAGEPATH, --edfimagepath EDFIMAGEPATH | ||
| + | Path in which to save edf images. Default is ./ | ||
| + | -x EXTENSION, --extension EXTENSION | ||
| + | Extension for tiff files. Default is tif | ||
| + | -d NDIGITS, --ndigits NDIGITS | ||
| + | Number of digits for file number. Default is 4 | ||
| + | </code> | ||
| + | |||
| + | |||
| + | ===== timelessMccd2edf ===== | ||
| + | |||
| + | <code> | ||
| + | timelessMccd2edf -h | ||
| + | |||
| + | usage: timelessMccd2edf -f from -t to -s step -n stem -i first image [OPTIONS] | ||
| + | |||
| + | Creates a list of EDF files based on a collection of MarCCD files This is part | ||
| + | of the TIMEleSS project http://timeless.texture.rocks | ||
| + | |||
| + | optional arguments: | ||
| + | -h, --help show this help message and exit | ||
| + | -f FROM, --from FROM Start for omega scan (in degrees, required) | ||
| + | -t TO, --to TO End for omega scan (in degrees, required) | ||
| + | -s STEP, --step STEP Omega step (in degrees, required) | ||
| + | -n STEM, --stem STEM Stem for images file (required) | ||
| + | -i IMAGEFIRST, --imagefirst IMAGEFIRST | ||
| + | Number of first image file in series (required) | ||
| + | -p MCCDIMAGEPATH, --mccdimagepath MCCDIMAGEPATH | ||
| + | Path to MarCCD images. Default is ./ | ||
| + | -e EDFIMAGEPATH, --edfimagepath EDFIMAGEPATH | ||
| + | Path in which to save edf images. Default is ./ | ||
| + | -x EXTENSION, --extension EXTENSION | ||
| + | Extension for MarCCD files. Default is mccd | ||
| + | -d NDIGITS, --ndigits NDIGITS | ||
| + | Number of digits for file number. Default is 4 | ||
| + | </code> | ||
xray_data/convertfileseries.1547817589.txt.gz · Last modified: 2019/02/18 10:11 (external edit)
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