Corrspecgui and Release Notes Version 8 5: Difference between pages

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==Correlation Spectroscopy Interface==
Corrspecgui is the interactive version of corrspec. The principles of correlation spectroscopy are shown in the demo of corrspec; in the manual in the chapter 'Tutorial for the correlation spectroscopy function corrspec' and for in depth information: W. Windig, D.E. Margevich, W.P. McKenna, A novel tool for two-dimensional (2D) correlation spectroscopy, Chemometrics and Intelligent Laboratory Systems, 28, 1995, 108-128.


After starting the program the files are read in through the file menu. The cursor is not displayed until pressing the 'Move cursor to max' button, described below. Often the setting 'Z Origin Equal Zero', described below,is turned on in order to simplify the dispersion matrix.  
==Version 8.5==
Version 8.5 of PLS_Toolbox and Solo was released in September, 2017.


Below the buttons the number of pure variables selected is displayed, followed by editable boxes defining the number of contour levels used in the display of the dispersion matrix and to define the offsets. Below the display of the pure variables the cursor position is displayed.
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].


Below, the buttons and menus of corrspecgui will be discussed. The names of the buttons will be displayed by placing the cursor on top of them.
(back to [[Release Notes PLS Toolbox and Solo]])
''Toggle settings display'': turns the settings, displayed on the right, on or off.
''Set pure variable:'' the components defined by the pure variables, indicated by the cross-hair cursor, are eliminated.
''Reset last variable'': undoes the action of the previous 'Set pure variable'.
''Cursor'': enables manual change of cursor position, indicating the pure variables.
''Move cursor to max'': moves the cursor to the maximum in the matrix defined by the setting 'Max Algorithm'.
''Plot At Cursor'': Plots the data at the cursor position in the follow forms:
a) Cursor Variable Plots, a plot of the (pure) variable of the X data set, the (pure) variable of the Y data set, both as a function of axisscale{1} and a plot of both variables, as a visual tool to judge the correlation between these two variables.
b) Cursor Spectrum Plots: a plot of the spectra in the displayed map.
''Inactivate'': Areas that should not be used for pure variables can be inactivated, after which these areas are excluded when the cursor is set to the maximum (by the program of the 'Move cursor to max' button). After clicking one of these buttons the mouse is used to indicate the area to be inactivated. The different inactivate options define whether only the x or y data are inactivated, or both x and y. 
''Reactivate last selection'': Reactivation of the previous inactivated area.
Plot map in 3D: a 3D presentation of the map. Works best with the 'Plot Settings' 'False Color' on. The display can be rotated with the mouse. The button toggles between 3D on and off.
''Resolve spectra'': resolves the data using the pure variables. The resolved results are displayed in the following form:
a)X Spec, X Con, Y spec, Y con, with the resolved spectra and contributions for both X and Y data.
b)X vs Y Con, which shows the resolved X contributions versus the resolved Y contributions, as a tool to judge the correlations between the variables.
c) Maps: the resolved correlation maps.
d) Diagnostics: the original dispersion matrix, the dispersion matrix reconstructed from the resolved components, the sum of the maps shown under the tab 'Maps' and an overlay of these maps, each in a different color.
e) Current plot: clicking on any of the plots mentioned above will display it enlarged under 'Current plot'.


The settings, displayed at the right, have the following functions:
==Overview==
''Load demo data'': loads the data used for the demo in corrspec.
 
''Plot type'': determines plots along the z and y axes of the correlation matrix.
* The primary focus of version 8.5 has been in Calibration Transfer and additional importers.
''Max Algorithm'': defines the matrix of which its maximum determines pure variables.
 
''Dispersion Algorithm'': defines the matrix displayed.
* PLS_Toolbox/Solo 8.5 has been tested extensively with Matlab 2017b prerelease and should be compatible with the coming release.
''Plot Settings'': determines different aspects of the plots.
 
a) Axis type: defines the continuous or discrete character of plots.
* Simplified interface design changes. Various controls have been moved to simplify interfaces. Seldom used settings have been moved to options in several cases (e.g., simplified [[Svm|SVM]] panel).
b) False color: creates false coloring of the dispersion matrix.
 
c) Z Origin Equal Zero: only displays positive values in dispersion matrix.
* The Analysis window's confusion matrix and table toolbar icon now returns classification results for both [http://wiki.eigenvector.com/index.php?title=Sample_Classification_Predictions#Class_Pred_Most_Probable 'most probable'] and [http://wiki.eigenvector.com/index.php?title=Sample_Classification_Predictions#Class_Pred_Strict  'strict'] classifications. In the 'strict' case it also lists the 'strictthreshold' value used.
d) Grid: toggle for grid in dispersion matrix.
 
e) Set X/Y direction: plots the x/y axis regular or in reverse.
==Calibration Transfer==
f) Color bar: inserts color-bar to indicate z values in plot.  
* [[MCCTTool | New Model-centric Calibration Transfer]] - Interface to develop instrument specific models with calibration transfer.
g) Colormap: determines which colormap is used.
 
* [[nlstd| NLSTD]] - Create or apply non-linear instrument transfer models (PLS_Toolbox only).
 
* [[sstcal| SST]] - Spectral Subspace Transformation calibration transfer.
 
* [[Demonstration_Datasets|Corn DSO]] - New calibration transfer demonstration data set added. 80 samples of corn measured on 3 different NIR spectrometers with moisture, oil, protein and starch values for each of the samples is also included.
 
==Importers==
 
* [[shimadzueemreadr]] - Imports Shimadzu EEM formatted text files.
* [[visionairxmlreadr]] - Imports Vision Air formatted XML files (X- & Y-Blocks).
* [[pltreadr]] - Imports Vision Air model files (.plt).
 
* [[aqualogreadr]] - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
 
* [[jascoeemreadr]] - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
 
* [[hitachieemreadr]] - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
 
* [[rawread|RAWREAD]] - Added support for new version format (3 & 4) (See MIA_Toolbox).
 
* [[spgreadr|SPGREADR]] Added new feature, options.spectrumindex now can be an integer, an array of integers (indices, & order doesn't matter), or 'all'. When loading multiple files, options.spectrumindex must be either a single value or 'all'.
 
==Exporters==
 
* [[writeplt]] - Exports EVRI Model structures to Vision Air PLT files.
 
==Other Features and Improvements==
* [[Cooksd| Cook's Distance]] - Calculates Cooks Distance for samples in a regression model.
 
* [[rpls| RPLS]] - A recursive PLS and PCR variable selection algorithm.
 
* [[manhattandist| MANHATTANDIST]] - Calculate Manhattan Distance between rows of a matrix.
 
* [[Confusionmatrix]] and [[Confusiontable]] - Classification results formatting options added. Can now specify use of mostprobable or strict classification rule.  
* [[calcdifference]] - Calculate difference between two datasets.
* Added GLS Weighting to model optimizer.

Revision as of 09:35, 7 February 2019

Version 8.5

Version 8.5 of PLS_Toolbox and Solo was released in September, 2017.

For general product information, see PLS_Toolbox Product Page. For information on Solo, see Solo Product Page.

(back to Release Notes PLS Toolbox and Solo)

Overview

  • The primary focus of version 8.5 has been in Calibration Transfer and additional importers.
  • PLS_Toolbox/Solo 8.5 has been tested extensively with Matlab 2017b prerelease and should be compatible with the coming release.
  • Simplified interface design changes. Various controls have been moved to simplify interfaces. Seldom used settings have been moved to options in several cases (e.g., simplified SVM panel).
  • The Analysis window's confusion matrix and table toolbar icon now returns classification results for both 'most probable' and 'strict' classifications. In the 'strict' case it also lists the 'strictthreshold' value used.

Calibration Transfer

  • NLSTD - Create or apply non-linear instrument transfer models (PLS_Toolbox only).
  • SST - Spectral Subspace Transformation calibration transfer.
  • Corn DSO - New calibration transfer demonstration data set added. 80 samples of corn measured on 3 different NIR spectrometers with moisture, oil, protein and starch values for each of the samples is also included.

Importers

  • aqualogreadr - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
  • jascoeemreadr - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
  • hitachieemreadr - Improved capability of loading multiple files containing samples of varying sizes (PLS_Toolbox only).
  • RAWREAD - Added support for new version format (3 & 4) (See MIA_Toolbox).
  • SPGREADR Added new feature, options.spectrumindex now can be an integer, an array of integers (indices, & order doesn't matter), or 'all'. When loading multiple files, options.spectrumindex must be either a single value or 'all'.

Exporters

  • writeplt - Exports EVRI Model structures to Vision Air PLT files.

Other Features and Improvements

  • RPLS - A recursive PLS and PCR variable selection algorithm.
  • MANHATTANDIST - Calculate Manhattan Distance between rows of a matrix.
  • Confusionmatrix and Confusiontable - Classification results formatting options added. Can now specify use of mostprobable or strict classification rule.
  • calcdifference - Calculate difference between two datasets.
  • Added GLS Weighting to model optimizer.