Release Notes Version 7 0

Version 7.0 of PLS_Toolbox and Solo was released in October, 2012.

For general product information, see PLS_Toolbox Product Page. For information on Solo, see Solo Product Page. This release was done in conjunction with MIA_Toolbox / Solo+MIA version 2.8

(back to Release Notes PLS Toolbox and Solo)

New Features

Batch Statistical Process Control Tools

• 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.)

Analysis Window

• Add BatchMaturity analysis type (PCA model with heterogeneous confidence limits for scores).
• Add cross-validation (RMSECV and miss-classification information) to SSQ table.
• Allow split of data into calibration / validation samples by automatic or manual selection.
• Add y-block loadings to bi-plot.
• Allow relative (a.k.a. differential) 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).
• Add plotting of 3D surfaces (or other 3D plots) of loadings in multiway analyses.
• Allow changes to included data on preprocessed data plots (conveys changes back to original blocks).
• Enable "Export to Regression Vector" for MLR models.
• Enable cross-validation by default and improve user awareness of options.
• Model Cache "Date" mode now sorts in descending order (for faster access to the most recent models and data)
• Add tucker congruence test and core consistency test for multiway models (warn user if it looks like the "supposed to be one" components in the core are showing signs of degeneracy)
• Add "Resolve" and "Accept" buttons to purity's main figure toolbar (to avoid needing to use menu)

Scores Plots

(see also #Plot Controls and Visualization Tools below)

• Add configurable display options to double-sided scores limits. Display limits as shaded regions, lines, and choose colors.
• View cross-validation subsets as classes to show which samples were in which cross-validation groups.
• Add support for SVMOC (command-line only)

Plot Controls and Visualization Tools

• Add automatic peak location and marking.
• Add quick-search bar for selection by labels, axisscales, and classes.
• Add selector to quickly change between plot types.
• Add "Monotonic" plot type.
• Add 'scatter' and 'line' types to plottype list (so user can FORCE these plot types if auto doesn't do the right thing).
• Add right-click access to quickly adjust axis limits and other plot settings.
• Improve selection appearance.
• Add class statistics information to right-click (shows # and % of samples in each class).
• Add colormap change options to right-click menus (With MIA_Toolbox and Solo+MIA only).
• Add autosize makers option ( automatically adjusts marker sizes to match axes size, if not specified otherwise).
• Improved 3D plot types.
• Improved stacked plots.
• Allow colorby axisscales and index and clarify what will be colored for all types (lines or points).
• Show class notice EACH TIME the plot is updated (allows easier reference for which class we're seeing) and an option to leave the name on at all times.
• Set the "select persistent" feature to default to be OFF.
• Add resize corner to magnify tool.
• Add ability to view an axisscale set as labels on points.

TrendTool

• Allow showing of more than 3 colors in image mode
• Enable use of imageaxisscale when showing images
• Add new peakfindgui function and tie-ins to PlotGUI and TrendTool to use this automatic peak finding

DataSet Editor

• Add support for axistype in labels tabs
• Add bulk selection change to context menus (allows quick selections based on list of all samples)
• Add export to ThermoGalactic SPC file format
• Add drop support (drop onto tabs imports data)
• Add classes to identify different data blocks when augmenting new data as columns

Import / Export

• 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 -Add selection of "tails" mode (improves performance at ends of spectra.)
• classcentroid -Add classcentroid centering preprocessing methods.
• mscorr -Add new 'median' method for robust scaling (and to use with Probabilistic Quotient Normalization - PQN.)
• wlsbaseline -Add Whittaker filter option 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

TODO: Add Descriptions

cancer

Dupont_BSPC

OliveOilData

General Solo and Solo+MIA 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

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.
• spcreadr

  • 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.

classcentriod - Centers data to the centroid of all classes.

evrimodel - EVRI Model Object.

minimizemodel - Shrinks model by removing non-critical information.

plotmontonic - 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.