software:timelesstools
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Table of Contents
TIMEleSS tools
Those are a set of tools written for and during the TIMEleSS project.
The source code for the tools is at https://github.com/FABLE-3DXRD/TIMEleSS. The user manuals for each script will be in this wiki.
Installation
Go to https://github.com/FABLE-3DXRD/TIMEleSS and click on the green button “clone or download”. Click on “Download ZIP”. After the download is finished, navigate to the “Downloads” folder and unpack the ZIP folder to a directory of your choice.
Then
- Open the Konsole or any terminal window,
- navigate to the unpacked TIMEleSS directory,
- there should be a file called
setup.py, - Type the following to the Konsole:
python setup.py build, - If you get an error, there might be some of the additional libraries still missing,
- Install the TIMEleSS tools on your system:
python setup.py install.
List of scripts
This list will get longer over time. At present, you will have access to the following commands
- Test
timelessTest, which runs several reading and parsing operations to make sure everything works well,
- Image tools
timelessTiff2edfto convert series of tiff files into series of EDF filestimelessMccd2edfto convert series of MarCCD files into series of EDF filestimelessEdf2tiffto convert a single EDF file into a tiff filetimelessEdf2tiffFileSeriesto convert series of EDF files into series of tiff filestimelessAverageEDFto take the average of two or more EDF imagestimelessMeanFileSeriesto take the mean of two or more EDF imagestimelessCreateEmptyImageto produce an empty (black) image
- Diffraction pre-processing for diamond anvil cell experiments
timelessDACShadowto remove the shadow which is produced during a 3D image acquisitiontimelessDiamondSpotRemovalto take out spots from the single-crystal diamond anvils
- Grain tools
timelessRemoveUsedGVE, removes G-vectors which are already indexed byGrainSpotter. 'timelessClearGVEGrainsis more up-to-date with more options. *timelessGrainComparison, which is meant to compare the orientations of grains between different sources *timelessGrainSpotterMerge, which is meant to merge the output of multiple GrainSpotter runs into one *timelessSaveFLTGrainsto extract the peaks corresponding to a grain *timelessPlotIndexedGrainto graphically evaluate the indexing quality for a given grain *timelessExtractEulerAnglesto convert a log file (from GrainSpotter) into a list of Euler angles (necessary for MTeX) *timelessFixGSOutputto fix a bogus GrainSpotter output file * Peaks management *timelessClearGVEGrains(more up-to-date thantimelessRemoveUsedGVEto remove G-vectors which are already indexed byGrainSpotter ) *timelessSaveFLTGrains*timelessClearFLTGrainsto remove the already used peaks *timelessPeaksFromCIFto list expected peaks based on a CIF file * Post-processing *timelessGrainSpotterMerge, which is meant to merge the output of multiple GrainSpotter runs into one *timelessTestGSvsGVE, to be used if you lost track and need to test which g-vector file was used to perform a GrainSpotter indexing *timelessGSIndexingStatistics, when you run multiple GrainSpotter indexing loop, evaluation of indexing performance can be tricky. Use this script to evaluate indexing statistics *timelessExtractEulerAngles'' to convert a log file (from GrainSpotter) into a list of Euler angles (necessary for MTeX)
software/timelesstools.1604998209.txt.gz · Last modified: by smerkel
