Release Notes Version 7 0: Difference between revisions
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* Opens processed data directly in Analysis for immediate model building. | * 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.) | * Steps to process data stored for easy application to new data (in data application mode.) | ||
===[[AnalysisWindow_Layout|Analysis Window]]=== | ===[[AnalysisWindow_Layout|Analysis Window]]=== | ||
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* Cross-validation sub-sets are included as classes to show which samples were in which cross-validation groups. | * Cross-validation sub-sets are included as classes to show which samples were in which cross-validation groups. | ||
* Add support for [[Svmoc|SVM One-Class models]] (command-line only) | * Add support for [[Svmoc|SVM One-Class models]] (command-line only) | ||
===[[Plot_Controls|Plot Controls and Visualization Tools]]=== | ===[[Plot_Controls|Plot Controls and Visualization Tools]]=== | ||
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* Magnify tool now has an easy "resize" corner. | * Magnify tool now has an easy "resize" corner. | ||
* Label points by their axisscale value. | * Label points by their axisscale value. | ||
===[[Trendtool|TrendTool]]=== | ===[[Trendtool|TrendTool]]=== | ||
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* Enable use of imageaxisscale when showing images | * Enable use of imageaxisscale when showing images | ||
* Add new peakfindgui function and tie-ins to PlotGUI and TrendTool to use this automatic peak finding | * Add new peakfindgui function and tie-ins to PlotGUI and TrendTool to use this automatic peak finding | ||
===[[Dataset_editor|DataSet Editor]]=== | ===[[Dataset_editor|DataSet Editor]]=== | ||
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* Add drop support (drop onto tabs imports data) | * Add drop support (drop onto tabs imports data) | ||
* Add classes to identify different data blocks when augmenting new data as columns | * Add classes to identify different data blocks when augmenting new data as columns | ||
===[[Importing_Data|Import / Export]]=== | ===[[Importing_Data|Import / Export]]=== | ||
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*:* improved handling of automatic axis scale names | *:* improved handling of automatic axis scale names | ||
* [[XCLREADR|CSV File Format]] -Allow space, tab, and | as valid automatically-detected delimiters for CSV files (improves drag/drop importing behavior). | * [[XCLREADR|CSV File Format]] -Allow space, tab, and | as valid automatically-detected delimiters for CSV files (improves drag/drop importing behavior). | ||
===Preprocessing and Transformations=== | ===Preprocessing and Transformations=== | ||
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* [[wlsbaseline]] -Add Whittaker filter option to Weighted Least Squares baseline. FAST and better for baselines which don't look like polynomials. | * [[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. | * [[reducennsamples]] -Added access to help within settings dialog. | ||
===New Demo Datasets=== | ===New Demo Datasets=== | ||
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:'''Dupont_BSPC''' -Batch data (10 variables x 36 batches at 100 time intervals) from Nomikos & MacGregor, Technometrics, 37(1), 1995. | :'''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) | :'''OliveOilData''' -Olive Oil FT-IR Classification data from Dahlberg, et. al. Appl. Spectrosc., 51(8), 1118-1124 (1997) | ||
===General Solo Improvements=== | ===General Solo Improvements=== | ||
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* Re-enable docked figures with Solo & Solo+MIA. | * Re-enable docked figures with Solo & Solo+MIA. | ||
* Improved memory performance (java.opts modification). | * Improved memory performance (java.opts modification). | ||
==New Command-line Features and Functions== | ==New Command-line Features and Functions== | ||
*''Full Support for Matlab R2012b'' | *''Full Support for Matlab R2012b'' | ||
===[[EVRIModel Objects]]=== | |||
New [[EVRIModel_Objects|high-level object]] to contain models. Makes working with standard-built models easier and provides an "object-oriented" approach to building new models. | |||
* Build models using simple object-oriented assignments and methods | |||
<pre> | |||
model = evrimodel('pca'); | |||
model.x = data; | |||
model.ncomp = 3; | |||
model.calibrate; | |||
</pre> | |||
* Apply models to new data directly using model methods: | |||
::<tt>prediction = model.apply(newdata);</tt> | |||
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*:* SEARCH -Search for given term in a dso field, mode, and set. | *:* SEARCH -Search for given term in a dso field, mode, and set. | ||
*:* UPDATESET -Add/update a label field (axisscale,label,class) in a DataSet. | *:* UPDATESET -Add/update a label field (axisscale,label,class) in a DataSet. | ||
===Misc New Functions=== | ===Misc New Functions=== |
Revision as of 16:25, 25 September 2012
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
- BatchMaturity analysis type added (PCA model with heterogeneous confidence limits for scores).
- Split data into calibration / validation sets using manual or automatic selection.
- 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).
- Y-block loadings included in bi-plots (PLS).
- Cross-validation results in SSQ table.
- 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.
Scores Plots
(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.
- Add support for SVM One-Class models (command-line only)
Plot Controls and Visualization Tools
- Automatic find and mark peak locations.
- [PlotControlsWindow_Layout_2#Search_Bar|Quick-search bar for selecting]] by labels, axisscales, classes and indexes.
- Plot type button for quick change between various plot types.
- 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).
- 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.
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
- 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
EVRIModel Objects
New high-level object to contain models. Makes working with standard-built models easier and provides an "object-oriented" approach to building new models.
- Build models using simple object-oriented assignments and methods
model = evrimodel('pca'); model.x = data; model.ncomp = 3; model.calibrate;
- Apply models to new data directly using model methods:
- prediction = model.apply(newdata);
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.