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xray_data:convertfileseries
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xray_data:convertfileseries [2019/01/18 13:31] smerkel |
xray_data:convertfileseries [2019/02/18 10:11] |
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| - | ====== Convert image file series ====== | ||
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| - | ===== Introduction ===== | ||
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| - | Typical diamond anvil cell beamlines generate series of diffraction files in various formats, which are not the EDF format used in further processing. The tools here can be used to convert the files into the proper format. | ||
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| - | 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°. | ||
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| - | 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. | ||
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| - | ===== timelessTiff2edf ===== | ||
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| - | <code> | ||
| - | timelessTiff2edf -h | ||
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| - | usage: timelessTiff2edf -f from -t to -s step -n stem -i first image [OPTIONS] | ||
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| - | 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> | ||
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| - | ===== timelessMccd2edf ===== | ||
| - | |||
| - | <code> | ||
| - | timelessMccd2edf -h | ||
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| - | 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.txt · Last modified: 2019/02/18 10:11 (external edit)
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