TIMEleSS Multigrain Wiki

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====== 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
    * ''timelessTiff2edf'' to [[xray_data:convertfileseries|convert series of tiff files into series of EDF files]]
    * ''timelessMccd2edf'' to [[xray_data:convertfileseries|convert series of MarCCD files into series of EDF files]]
    * ''timelessEdf2tiff'' to [[xray_data:convertfileseries|convert a single EDF file into a tiff file]]
    * ''timelessEdf2tiffFileSeries'' to [[xray_data:convertfileseries|convert series of EDF files into series of tiff files]]
    * ''timelessAverageEDF'' to [[xray_data:averageEDF|take the average of two or more EDF images]]
    * ''timelessMeanFileSeries'' to [[xray_data:averageManyEDF|take the mean of two or more EDF images]]
    * ''timelessCreateEmptyImage'' to [[xray_data:empty-image|produce an empty (black) image]]
  * Diffraction pre-processing for diamond anvil cell experiments
    * ''timelessDACShadow'' to [[software:remove-shadow|remove the shadow which is produced during a 3D image acquisition]]
    *  ''timelessDiamondSpotRemoval'' to [[processing:clean-diamond-anvil-cell-data|take out spots from the single-crystal diamond anvils]]
  * Phase identification
    * ''timelessTthHistogram2Maud'', used to [[processing:phase_identification|identify sample phases]], converts a 2theta histogram to an ESG file that you can load in [[software:maud|MAUD]].
  * Grain tools 
    * ''timelessRemoveUsedGVE'', [[processing:remove-used-gve|removes G-vectors which are already indexed byGrainSpotter]]. ''timelessClearGVEGrains'' is more up-to-date with more options to [[processing:remove-used-gve-updated|clear a GVE file from G-vectors which are already assigne to grains]]
    * ''timelessGrainComparison'', which is meant to [[processing:compare-grain-orientations|compare the orientations of grains]] between different sources
    * ''timelessGrainSpotterMerge'', which is meant to [[processing:grainSpotter-merge|merge the output of multiple GrainSpotter runs into one]]
    * ''timelessSaveFLTGrains'' to [[processing:extractGVEGrain|extract the peaks corresponding to a grain]]
    * ''timelessPlotIndexedGrain'' to [[evaluation:evaluategrainindexing|graphically evaluate the indexing quality for a given grain]]
    * ''timelessExtractEulerAngles'' to [[processing:extractEulerAngles|convert a log file (from GrainSpotter) into a list of Euler angles (necessary for MTeX)]]
    * ''timelessFixGSOutput'' to [[processing:fixGSOutput | fix a bogus GrainSpotter output file]]
    * ''timelessExtractGrainSizes'' and ''timelessRelToAbsGrainSize'' to [[evaluation:extractGrainSizes| determine grain sizes]]
  * Peaks management
    * ''timelessClearGVEGrains'' (more up-to-date than ''timelessRemoveUsedGVE'' to [[processing:remove-used-gve|remove G-vectors which are already indexed byGrainSpotter]] )
    * ''timelessSaveFLTGrains''
    * ''timelessClearFLTGrains'' to [[processing:remove-used-flt|remove the already used peaks]]
    * ''timelessPeaksFromCIF'' to [[processing:list-peaks-from-cif|list expected peaks based on a CIF file]]
  * Post-processing
    * ''timelessGrainSpotterMerge'', which is meant to [[processing:grainSpotter-merge|merge the output of multiple GrainSpotter runs into one]]
    * ''timelessTestGSvsGVE'', to be used if you lost track and need to [[evaluation:testGSvsGVE|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 [[evaluation:evaluate indexing statistics]]
    * ''timelessExtractEulerAngles'' to [[processing:extractEulerAngles|convert a log file (from GrainSpotter) into a list of Euler angles (necessary for MTeX)]]