Lauetools. A software package for Laue microdiffraction data analysis. /
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1 Lauetools A software package for Laue microdiffraction data analysis /
2 Motivations
3 Motivations ImageJ LAUE raw data XMAS fit2d Some codes
4 Motivations LAUE raw data LaueTools makes data flow easier
5 Motivations Fast data acquisition rate But slow analysis rate X-ray Microdiffraction Analysis Software (XMAS) by N. Tamura GREAT but: -Black box -Poorly documented -Low intermediate user input -No new functionalities -No bashable Lauetools is for increasing scientific throughput of µlaue - online/offline analysis - help on data acquisition strategy - GUI, command line, bashable - open-source: - stimulate development and maintenance - user control of codes and models - interactions between mechanics, physics, Xtallographers, programmer
6 Motivations Codes in python OO, script, easy prototyping open-source multi-platform matlab-like libraries: matplotlib numpy stats, optimisation graph, bayes wxpython Modularity,Separated routines, classes Interactive python interface with C, JAVA, Fortran
7 LAUETOOLS flow chart Raw Images Set Images Labelling Image 0 Image 1... Image n Image(s) processing Reference structure data (Ang.distances Peaks list Previous analysed data ) Peak & Blobs Search Data & Tools selection Automatic Analysis settings USER Modelling Indexing Fitting Calibration Strain & orientation Solving Orientation Solving Blobs analysis Calibration parameter Crystal Structure Orientation & strain Distribution Results presentation
8 LAUETOOLS implementation GUI in wxpython LaueTool.py Visualisation Indexing Structure refinement Results visualisation 3D visualisation in PyOpenGL laue3d.py Data representation Quick U estimation Strain & Energy effect readmccd.py fit2dintensity.py gnomon.py laue.py findorient.py calibrate.py geometry calibration calcdef.py graingraph.py find2thetachi.py recognition.py image data reading digital processing, numerical operations 2D intensity profile fitting projection on to gnomonic plane Hough transform data and reference matching Laue pattern simulation orientation matrix U determination detector and experiment camera vision + minimisation process Strain determination (B matrix) cliques finding coordinates transforms spot and zone recognition
9 LAUETOOLS world Image Binary data ~ TIFF+header prefix_####.ext prefix_.#### ####: 4 digits integer number Ext: mccd, tiff, spe IMAGE PROCESSING LAUETOOL PIL ImageJ plugins PEAK SEARCH FIT2D Batch, Python subprocess LAUETOOL XMAS (indexation dependent) ImageJ plugin Peaks list Ascii multicolumns data file prefix_####.ext Ext: peaks,pic, CALIBRATION LAUETOOL XMAS Peaks list Ascii multiicolumns data file prefix_####.cor INDEXATION LAUETOOL automatic manual computer-aided Indexed Peaks list Ascii multiicolumns data file prefix_####.ind STRUCTURE REFINEMENT LAUETOOL
10 Simulation LAUETOOLS current status General and pedagogical tool (laue3d) Input: Detector geometry: transmission, backreflection, side, top Spectral Range Materials parameters multigrains orientation matrix (U) lattice matrix (B) some transforms on U,B: twins, mosaicity, strain gradient Output: Ascii file Spot objects list Plot
11 LAUETOOLS current status Simulation Data pre-processing Basic Grain mapping (most intense peak) Peak search (basic, digital processing) Indexing manual -> automatic brute force (trials and errors) image comparing (in Hough space) (~ no peak search) information selection (Human-computer collaboration) gnomonic projection hough space cliques spot & zone axis recognition
12 LAUETOOLS current status Simulation Data pre-processing Indexing Structure solving Detector calibration: refinement, camera & perspective vision Strain Refinement Visualisation Data representation & manual indexing Graphical User Interface: data visualisation & indexing Only ideas and trials for results visualisation
13 LAUETOOLS perspectives - Automatic indexing & structure refinement of file series - Documentation - Autonomy in pre-processing - Open-source dev, cvs, executables distribution - Workshop on «microlaue Diffraction and analysis» - More physics & Xtallography & metallurgy models input - Quantifying experts performance and scopes - More experts for indexing - Parallel computing - Upcoming techniques - 3D microlaue Diffraction - Laue spot tomography - intensity harvesting Interactions with TotalCryst & Fable (algorithms & Laue plugins) Extension of image viewer and other tools: Images slicing, plot vs exp. Conditions statistics and geometrical maths
14 Data analysis and visualisation tools mosaic Images set navigator & processing plotmesh
15 Fast human found orientation matrix Strain simulation
16 Transmission Back-reflection
17
18 Slip system activated! 3% tetragonal strain along a*,b*,c*
19
20
21 Human-aided indexing Automatic indexing
22
23 Fingerprint of one crystal orientation: φ1, φ2, φ3 Only few non zeros pixels Data most intense pixel
24 mosaic 2D microlaue pattern ROI Grain mapping
25 Images set navigator & processing ROI Laue Pattern 2D intensity fitting Navigation on images dataset : Full Pattern results, batchable Mapcanvas.py fit2dintensity.py
26 Plotmesh 2D fluorescence mapping visualisation (sub)micropostioning Sample alignement Chemical element localisation Data from J. Keckes on BM32 Tomography s sinogram Data from P. Bleuet on BM32
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