Release Notes Version 7 0
Version 7.0 of PLS_Toolbox and Solo was released in October, 2012.
(back to Release Notes PLS Toolbox and Solo)
- 1 New Features in Solo and PLS_Toolbox
- 2 New Command-line Features and Functions
New Features in Solo and PLS_Toolbox
- New top-level data processor to read, align, tag, and arrange batch data into appropriate form for batch analysis.
- Creates data in appropriate format for analysis with these model types:
- Summary PCA (PCA on summary of variables over time)
- Batch Maturity (PCA with heterogeneous confidence limits)
- MPCA (Multiway PCA)
- PARAFAC (Parallel Factor Analysis)
- Summary PARAFAC (PARAFAC on summary of variables over time)
- PARAFAC2 (only available in PLS_Toolbox with MATLAB)
- Graphical and automatic identification of batches and [optional] steps in the imported data.
- Automatic alignment of batches (when necessary) by linear, infilling, or Correlation Optimized Warping.
- Summary methods allow a wide range of statistics to be calculated for each variable.
- Opens processed data directly in Analysis for immediate model building.
- Steps to process data stored for easy application to new data (in data application mode.)
- BatchMaturity analysis type added (PCA model with heterogeneous confidence limits for scores).
- Split data into calibration / validation sets using manual or automatic selection. View Video
- Calculate relative T^2 and Q contributions. New buttons on Plot Controls allow selection of sample(s) as a T or Q reference set. Resulting T or Q contributions are done relative to those selected sample(s). View Video
- Y-block loadings included in bi-plots (PLS).
- Cross-validation results in SSQ table. View Video
- 3D Loadings from multiway methods can be plotted as 3D surfaces (or other 3D plots).
- Change included data directly on preprocessed data plots.
- "Export to Regression Vector" allowed for MLR models.
- Cross-validation default enabled with improved user awareness of options.
- Model Cache "Date" mode now sorts in descending order (for faster access to the most recent models and data)
- Tucker congruence and core consistency test added for multiway models (warn user if it looks like the "supposed to be one" components in the core are showing signs of degeneracy.)
- Purity now has "Resolve" and "Accept" buttons to improve usability.
(see also #Plot Controls and Visualization Tools below)
- Double-sided confidence limits display is more configurable: display as shaded regions, lines, or both and choose color.
- Cross-validation sub-sets are included as classes to show which samples were in which cross-validation groups. View Video
- Add support for SVM One-Class models (command-line only)
- Automatic find and mark peak locations. View Video
- Quick-search bar for selecting by labels, axisscales, classes and indexes. View Video
- Plot type button for quick change between various plot types. View Video
- Plot types "Monotonic", "scatter" and "line" added.
- Right-click access to adjust axis limits and other plot settings.
- Improved appearance of selections, 3D plots, stacked plots, and class set identifiers.
- Class population statistics by right-clicking data (shows # and % of samples in each class). View Video
- Colormap changes by right-clicking image (With MIA_Toolbox and Solo+MIA only).
- Autosize makers option added ( automatically adjusts marker sizes to match axes size, if not specified otherwise).
- Color-by axisscales and index and clarify what will be colored for all types (lines or points).
- Magnify tool now has an easy "resize" corner.
- Label points by their axisscale value.
- Automatically find peaks and place markers at those peaks.
- Images now allow showing of more than 3 markers at a time (MIA_Toolbox and Solo+MIA only).
- Image axisscale is used when displaying images (MIA_Toolbox and Solo+MIA only).
- Axistype (continuous, discrete,...) support in labels tabs.
- Bulk selection changes in label tab context menus (allows quick selections based on list of all samples.)
- Export to ThermoGalactic SPC file format from File menu.
- Data drop support (drop onto tabs imports data.)
- Data augmentation adds classes to identify different data blocks (for column-augment mode.)
- SPC File Format
- Improved multiple file reading (with unequally spaced x-axis)
- improved handling of automatic axis scale names
- CSV File Format -Allow space, tab, and | as valid automatically-detected delimiters for CSV files (improves drag/drop importing behavior).
Preprocessing and Transformations
- savgol -New "tails" mode to improve performance at ends of spectra.
- classcentroid -New class centroid centering preprocessing method.
- mscorr -MSC with new 'median' method for robust scaling (and to use with Probabilistic Quotient Normalization - PQN.)
- wlsbaseline -Whittaker filter option added to Weighted Least Squares baseline. FAST and better for baselines which don't look like polynomials.
- reducennsamples -Added access to help within settings dialog.
New Demo Datasets
- cancer -Fluorescence EEM spectra from images of cervices with various states of cervical cancer.
- Dupont_BSPC -Batch data (10 variables x 36 batches at 100 time intervals) from Nomikos & MacGregor, Technometrics, 37(1), 1995.
- OliveOilData -Olive Oil FT-IR Classification data from Dahlberg, et. al. Appl. Spectrosc., 51(8), 1118-1124 (1997)
General Solo Improvements
- Re-enable docked figures with Solo & Solo+MIA.
- Improved memory performance (java.opts modification).
New Command-line Features and Functions
- Full Support for Matlab R2012b
New high-level object to contain models. Provides an object-oriented approach to building new models and makes working with models and predictions much easier.
- Build models using simple object-oriented assignments and methods
- Apply models to new data directly using model methods: prediction = model.apply(newdata);
- Review results in plots using object methods: model.plotscores, model.plotloads, model.ploteigen
- Access commonly-used results via simple properties: .scores, .predictions, .tcon, .t2 instead of having to remember array indexes and cryptic field names.
- Nearly complete backwards compatibility with existing user code.
Command-line Tool Changes
- Quick Reference Card -New quick reference card ( PLS_Toolbox_Quick_Reference.pdf )
- autoexport -add SPC export functionality.
- chitest -add distribution name and function name to chitest outputs (making it much easier to apply the results).
- coreanal -updated coreanal.m to be able to provide a list of important core values (new optional second output).
- crossval -added output of cvi to help identify which leave-out group each sample was in.
- encode -Increase number of items allowed in each row of "speed" encoded files (makes the encoding MUCH faster)
- ils_esterror -Various improvements to allow different types of error estimates.
- mscorr -Add option.algorithm to include new option 'median', based on Probabilistic Quotient Normalization.
- Improved multiple file reading (with unequally spaced x-axis)
- Improved handling of automatic axis scale names
- svmoc -add support to plot scores from SVM One Class models.
- windowfilter -Added method 'roll' (for processing rows only), slight modification to RH edge indexing during call (is last channel processed?)
- wlsbaseline -Add Whittaker filter option to wlsbaseline and wlsbaselineset (FAST and better for baselines which don't look like polynomials)
- xclreadr -Allow space, tab, and | as valid automatically-detected delimiters for CSV files
- DataSet Object - Changes:
- Decrease dependency on PLS_Toolbox
- Allow assignment directly onto imageaxisscale
- DataSet Object - New Methods:
- FINDSET -Locate a set within a label field (axisscale,label,class) in a DataSet.
- LISTSETS -For a given field and mode list the sets available.
- SEARCH -Search for given term in a dso field, mode, and set.
- UPDATESET -Add/update a label field (axisscale,label,class) in a DataSet.
Misc New Functions
- batchalign - Convert data columns based on matching ref col to target vector.
- batchmaturity - Batch process model and monitoring.
- batchfold - Transform batch data into dataset for analysis.
- classcentroid - Centers data to the centroid of all classes.
- evrimodel - EVRI Model Object.
- minimizemodel - Shrinks model by removing non-critical information.
- plotmonotonic - Plot lines with breaks when the x-value "doubles-back" on itself.
- roccurve - Calculate and display ROC curve(s) for yknown and ypred.
- splitcaltest - Splits randomly ordered data into calibration and test sets.
- unhist -Create a vector whose values follow an empirical distribution.
- writespc - Writes Galactic SPC files.