2020 Vision (Dubious Design Decisions)
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Design decisions relating to ChiToolbox, presented at the Kick-off Meeting for OpenVibSpec, 3 February 2020, in Bochum, Germany. ChiToolbox is an open source MATLAB toolbox for handling data from hyperspectral imaging experiments. https://bitbucket.org/AlexHenderson/ChiToolbox/ https://openvibspec.org/
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2020 Vision (Dubious Design Decisions)
- 1. 2020 VISION ALEX HENDERSON UNIVERSITY OF MANCHESTER THE INTERNATIONAL SOCIETY FOR CLINICAL SPECTROSCOPY SURFACESPECTRA LIMITED alexhenderson.info @AlexHenderson00 @ChiToolbox Kick-off Meeting and Hackathon 3-6 Feb, 2020 Ruhr-University Bochum
- 2. DUBIOUS DESIGN DECISIONS ALEX HENDERSON UNIVERSITY OF MANCHESTER THE INTERNATIONAL SOCIETY FOR CLINICAL SPECTROSCOPY SURFACESPECTRA LIMITED alexhenderson.info @AlexHenderson00 @ChiToolbox Kick-off Meeting and Hackathon 3-6 Feb, 2020 Ruhr-University Bochum
- 4. @clirspec 34 members on steering council
- 5. Travel bursaries available http://spec2020.com 17–22 May, 2020
- 6. Summer School 7–10 July, 2020
- 7. https://springscix.org/ 6–9 April, 2020 Travel bursaries available
- 9. CLIRSPEC DATA Online community for us to share algorithms, code and ideas Hosted on Slack Request an invitation to join Any member can add anyone else http:// tiny.cc / clirspec-data
- 10. CHITOOLBOX •https://bitbucket.org/AlexHenderson/chitoolbox • Open source MATLAB toolbox • Infrared, Raman, secondary ion mass spectrometry (SIMS) • Spectra and hyperspectral images • Library, not a GUI (only 1-2 dialog boxes) • Object oriented design @ChiToolbox
- 11. DESIGN DECISIONS • What worked? • What did not work? • What were the compromises? • What would I do differently?
- 12. OBJECT ORIENTED PROGRAMMING (OOP) • Abstract base classes for spectra, spectral collections and images • Concrete classes for above • ‘Interface’ classes for ‘Raman character’, ‘IR character’ etc. • Multiple inheritance to define technique specific classes • eg. IRSpectrum, RamanImage, (ToF)MSSpectralCollection • Separate classes for pictures, RMieS options, PCA or RF models etc. • Model using classes where possible • Provides type-identification and bespoke functionality
- 13. FILE FORMATS • Agilent (FTIR) • Single FTIR images and mosaicked FTIR images • Biotof (ToFSIMS) • Spectra, hyperspectral image files • Bruker (FTIR) • Opus files and multiple spectra exported as a MAT file • Ionoptika (ToFSIMS) • Hyperspectral image files exported in HDF5 format • Mettler Toledo (FTIR) • Spectra exported in ASCII • Renishaw (Raman) • WiRE Version 4, spectral and hyperspectral images • Thermo Fisher Scientific GRAMS SPC (Generic) • Data stored in spc files Single files can be read using ChiFile. This works out the file format automatically. In addition Readable, but unreleased • Photothermal (FTIR and Raman) • mIRage spectra and hyperspectral images • IONTOF (ToFSIMS) • Hyperspectral images in grd format
- 14. FILE FORMAT ISSUES • Some formats were hacked eg. Agilent • What if example files were specific to certain instrumentation? • Some formats are multi-purpose • Some formats hold only one data type (spectrum, line scan, image etc) • Eg. Agilent single tile format • Some formats can contain any of these data types • Eg. Renishaw • If we read multiple files, what should we do if their contents are of different types?
- 15. REUSE OF EXTERNAL CODE (CREDITED) • Perceptually uniform colormaps • error_ellipse • GSTools • shadedErrorBar • mksqlite • sql_object • cividis • sgolayfilt • RMieS • cluster-toolbox • getSubclasses • GUI Layout Toolbox • DataHash • GetFullPath • m2html • ImportOpus • ME-EMSC • Thresholding Tool • ENVI file reader/writer • read_envihdr
- 16. SOFTWARE LICENCE • ChiToolbox released under GNU General Public License 3.0 (GPL) • External code is GPL, or more liberal (eg. MIT) • GPL ‘infects’ the codebase • User must release any code that intrinsically links to this code • Prefer GNU Lesser General Public License (LGPL) • Your codebase is not affected, but changes must be shared • Unfortunately, LGPL and GPL are not compatible
- 17. MATLAB ISSUES • Tried to make backwardly compatible with R2009a • Too painful • Roughly compatible with R2016a • Trying to reduce toolbox dependencies (eg. Statistics toolbox) • MATLAB OOP not great • Variables pass by value, but handle classes pass by reference. Makes copying difficult • Rolled my own deep copy mechanism (clone)
- 18. DATA TYPES • Single spectrum, spectral collection, hyperspectral image • Continuous data • Did not consider multispectral data (discrete wavenumber) • Discontinuous, cannot take first derivative etc. • Data is a property of the object, not a pointer/function to a data storage type
- 19. METADATA • Separate class from data type • Automatically label plots (eg PCA scores) • Build lists of labels manually labels = ChiClassMembership('mylabels','beta',1, 'gamma',2, 'beta',3, 'alpha',2); • Automatically read from specially designed Excel spreadsheet • Handles logical, category and numeric types • Need to remove label from metadata if removing spectrum from collection
- 20. Users not sure of difference between numeric and category types, when using numbered samples
- 21. DEFAULTS • Try to provide ‘reasonable’ default values • PCA denoising defaults to 30% of PCs retained • Random Forest defaults to 80% training and 20% test sets • Should default to 5-fold cross validation, but takes time • Random Forest defaults to using parallel processing if data set is large • MATLAB is slow to initialise worker pool • All parameters are user-configurable
- 22. VISUALISATION • Graphics use perceptually neutral colormaps • Caters for colour vision deficiency (colour blindness) • Colour-mapped PCA image scores and loadings plots • Dialog box for Raman baseline removal • Asymmetric least squares baseline modelling requires user input • Confidence limits on PCA/CVA* scores plots • Default = 95%, but user variable • RMieS iteration change plot *Canonical variates analysis
- 23. PERCEPTUALLY NEUTRAL COLORMAPS ORIGINAL, FULL COLOUR MATLAB JET COLORMAP
- 24. PERCEPTUALLY NEUTRAL COLORMAPS ORIGINAL, FULL COLOUR MATLAB PARULA COLORMAP
- 25. PERCEPTUALLY NEUTRAL COLORMAPS ORIGINAL, FULL COLOUR PYTHON VIRIDIS COLORMAP Python’s Inferno, Magma, Plasma and Viridis colormaps implemented in MATLAB
- 26. 2020 VISION (IF I HAD A TIME MACHINE) • Developed more tests • Added support for discrete wavenumber data • Separated data storage from data manipulation • Used database (SQLite) to manage metadata • Considered OOP for data storage, but functional programming for operations
- 27. 2020 VISION (IF I HAD A TIME MACHINE) Write it all in Python! …or C++