Other Deployment Resources and Release Notes Version 7 0: Difference between pages
(Difference between pages)
Jump to navigation
Jump to search
imported>Jeremy No edit summary |
imported>Jeremy |
||
Line 1: | Line 1: | ||
Version 7.0 of PLS_Toolbox and Solo was released in October, 2012. | |||
For general product information, see [http://www.eigenvector.com/software/pls_toolbox.htm PLS_Toolbox Product Page]. For information on Solo, see [http://www.eigenvector.com/software/solo.htm Solo Product Page]. This release was done in conjunction with [[Release_Notes_MIA_Toolbox_Version_2_8|MIA_Toolbox / Solo+MIA version 2.8]] | |||
(back to [[Release Notes PLS Toolbox and Solo]]) | |||
==New Features== | |||
===[[Bspcgui|Batch Statistical Process Control Tools]]=== | |||
* New [[Bspcgui|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.) | |||
===[[AnalysisWindow_Layout|Analysis Window]]=== | |||
* [[Batchmaturity|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. | |||
===[[Model_Building:_Plotting_Scores|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|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|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|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 | |||
''' | ===[[Importing_Data|Import / Export]]=== | ||
* | |||
* [[SPCREADR|SPC File Format]] | |||
*:* Improved multiple file reading (with unequally spaced x-axis) | |||
*:* 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). | |||
===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'' | |||
===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_Objects|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. |
Revision as of 15:57, 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)
- 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
- 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
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.