Tools ModelRobustness and Faq obtain or use recompilation license for PLS Toolbox: Difference between pages

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__TOC__
===Issue:===
[[TableOfContents|Table of Contents]] | [[Tools_Cross-Validation|Previous]] | [[Tools_CorrelationMap|Next]]


==Model Robustness Tool==
How do I obtain or use a recompilation license for PLS_Toolbox?


You use the Model Robustness tool to measure the sensitivity of a regression model to artifacts in new spectroscopic measurements. To open the Model Robustness tool, on the Analysis window, click Tools > Model Robustness, and then click Shifts or Interferences.
===Possible Solutions:===


===Shifts===
The standard [http://www.eigenvector.com/software/license_evri.html PLS_Toolbox license] does not permit recompilation of any part of the code without written permission from Eigenvector Research, Inc. This permission is usually in the form of a recompiliation license (for more information on recompilation licenses, see: our [http://www.eigenvector.com/evriblog/?p=27 Blog post on Compiling PLS_Toolbox] ).


The Shifts option measures the sensitivity of a regression model to shifts in x-axis data that are caused by instrument instability-that is, if you have an instrument that is not particularly stable or reproducible over time, what is the impact on predictions using the given model? The Shifts plot is a three-dimensional plot that details the RMSEP (Root Mean Squared Error of Prediction) for the model as a function of shift, where shift is described in terms of the number of variables and the Smoothing window.  
If you have purchased a recompiliation license for PLS_Toolbox and/or other Matlab-based Eigenvector Research products, you can use the following instructions to compile your application including the licensed Eigenvector Research (EVRI) code.


::''Example of a Shifts plot''
# If you were not supplied an ''evrilicense.lic'' file by EVRI, create one by copying the license code supplied for your compilation license (found on the download tab of your EVRI account) into a plain-text file named: ''evrilicense.lic'' The file should consist of the license code on a single line of the file. For example: <pre>12345678-98765432-ab-1234-1234</pre>
# Copy the ''evrilicense.lic'' file into one of the folders on your Matlab path. This could be either one of the PLS_Toolbox folders, or your application's folder.
# Add the ''evrilicense.lic'' file to the "Shared Resources" list in the Matlab project builder. This will assure that the EVRI license gets included in the compiled application.
# Compile your application as usual using Mathworks' standard instructions. The Matlab dependency logic will automatically include the PLS_Toolbox functions in your compiled application. (See note below regarding "blocking" certain functions from being included.)


::[[Image:Tools_ModelRobustness.29.1.1.jpg|417x359px]]
'''Blocking Unnecessary Functions'''
::


::
By default, Matlab's compiler automatically identifies all m-files which are necessary to run your application and includes all of these in the compiler output. Because of the integrated nature of many of the PLS_Toolbox functions, this can lead to "sprawl" - inclusion of many more functions than are actually needed. The follow steps can be taken to reduce the size of a compiled application:
::


Consider the figure above, which shows the model robustness for a regression model with an RMSEC (Root Mean Squared Error of Calibration) of approximately 0.5. As shown in this figure:
* Remove PLS_Toolbox 'dems' folder and 'help' folder from your path prior to compiling. Files in these folders can be large and are unnecessary for compilation.


{|
* Add "dummy" functions to reduce dependencies:
:: One way to help reduce these unnecessary additions is to create empty "shell" functions to overload certain PLS_Toolbox functions. These functions, if placed in a folder above PLS_Toolbox when you are compiling, will shadow (hide) the actual function and help avoid sprawl. In particular the following functions are useful to shadow:


|-
:* analysis.m
:* browse.m
:* plotgui.m
:* browse.m
:* evriinstall.m
:* evrireporterror.m


|
:: These functions will not be called in normal operation and, in most cases, our compilation licenses do not permit their inclusion in your application anyway.
* 1 - Without shift and without smoothing of the variables, the RMSEP indicates that you have test data that is identical to your calibration data and you have performance that is on par for the RMSEC of the model


|}
* Find top level functions and see if you can "manually" determine dependencies. Look at the results of the top level dependency check and see what functions are called from the primary PLS_Toolbox function you're working with. If the dependencies are few, you may be able to iterate over the results (get 'toponly' dependencies from results) and get a smaller subset of dependencies. '''NOTE''': This will require some experimentation and time to work through. The dataset object is extensively used by most function so this folder should almost always be included.


{|
<pre> [fList, pList] = matlab.codetools.requiredFilesAndProducts('peakfind','toponly') </pre>


|-
'''Uninstall the Stats Toolbox '''


|
Although moving the Stats Toolbox below PLS_Toolbox on your MATLAB path (or removing the Stats Toolbox folders altogether) will allow the PLS_Toolbox DataSet Object to function normally, you must uninstall the Stats Toolbox before compiling PLS_Toolbox function that require the DataSet Object.  
* 2 - Shifting a spectrum over by simply one variable increases the RMSEP for the model by almost twelve orders of magnitude, from 0.5 to almost 60.  


|}
The MathWorks states:


{|
"When you compile [a program] into an application and run it, the MATLAB Compiler Run-time references its in-built Dataset function which is higher in its PATH and hence runs the data against this inbuilt Dataset function."


|-
For more information on the DataSet Object history see here:
*[http://www.eigenvector.com/evriblog/?p=10 DataSet Object Conflict]
*[http://www.eigenvector.com/evriblog/?p=11 DataSet Object — Letter to MathWorks March 15, 2007]


|
'''Troubleshooting'''
* 3 - With a combination of shifting and smoothing, the impact on the model is lessened somewhat.


|}
* In some cases PLS_Toolbox may need to be moved out of the default installation folder into a folder with more permissions and/or no spaces in the path. For example, "C:\eigenvector\PLS_Toolbox".
'''Still having problems? Please contact our helpdesk at [mailto:helpdesk@eigenvector.com helpdesk@eigenvector.com]'''


===Interferences===
[[Category:FAQ]]
 
The Interferences option measures the sensitivity of a regression model to the location and width of a new peak in test data-that is, if you have a chemical entity that is present in the test data but that was not reflected in the calibration data, what is the impact on predictions using the given model? The Interferences plot is a three-dimensional plot that details the RMSEP (Root Mean Squared Error of Prediction) for the model as a function of a new peak, where the peak is described in terms of its width and location.
 
::''Example of an Interferences plot''
 
::[[Image:Tools_ModelRobustness.29.1.2.jpg|418x366px]]
::
 
::
::
 
::
::
 
Consider the figure above, which shows the model robustness for a regression model with an RMSEC (Root Mean Squared Error of Calibration) of approximately 0.5. As shown in this figure, the RMSEP for the model can be impacted in one of three ways:
 
{|
 
|-
 
|
* 1 - An interferant area where there is virtually no impact on the RMSEP for the model, no matter how wide the interfering peak is.
 
|}
 
{|
 
|-
 
|
* 2 - An interferant area where there is a slight impact on the RMSEP for the model, but the impact is lessened as the width of the peak increases.
 
|}
 
{|
 
|-
 
|
* 3 - An interference area where there is a significant impact on the RMSEP for the model, but the impact is lessened as the width of the peak increases.
 
|}

Revision as of 11:28, 28 June 2019

Issue:

How do I obtain or use a recompilation license for PLS_Toolbox?

Possible Solutions:

The standard PLS_Toolbox license does not permit recompilation of any part of the code without written permission from Eigenvector Research, Inc. This permission is usually in the form of a recompiliation license (for more information on recompilation licenses, see: our Blog post on Compiling PLS_Toolbox ).

If you have purchased a recompiliation license for PLS_Toolbox and/or other Matlab-based Eigenvector Research products, you can use the following instructions to compile your application including the licensed Eigenvector Research (EVRI) code.

  1. If you were not supplied an evrilicense.lic file by EVRI, create one by copying the license code supplied for your compilation license (found on the download tab of your EVRI account) into a plain-text file named: evrilicense.lic The file should consist of the license code on a single line of the file. For example: 
    12345678-98765432-ab-1234-1234
  2. Copy the evrilicense.lic file into one of the folders on your Matlab path. This could be either one of the PLS_Toolbox folders, or your application's folder.
  3. Add the evrilicense.lic file to the "Shared Resources" list in the Matlab project builder. This will assure that the EVRI license gets included in the compiled application.
  4. Compile your application as usual using Mathworks' standard instructions. The Matlab dependency logic will automatically include the PLS_Toolbox functions in your compiled application. (See note below regarding "blocking" certain functions from being included.)

Blocking Unnecessary Functions

By default, Matlab's compiler automatically identifies all m-files which are necessary to run your application and includes all of these in the compiler output. Because of the integrated nature of many of the PLS_Toolbox functions, this can lead to "sprawl" - inclusion of many more functions than are actually needed. The follow steps can be taken to reduce the size of a compiled application:

  • Remove PLS_Toolbox 'dems' folder and 'help' folder from your path prior to compiling. Files in these folders can be large and are unnecessary for compilation.
  • Add "dummy" functions to reduce dependencies:
One way to help reduce these unnecessary additions is to create empty "shell" functions to overload certain PLS_Toolbox functions. These functions, if placed in a folder above PLS_Toolbox when you are compiling, will shadow (hide) the actual function and help avoid sprawl. In particular the following functions are useful to shadow:
  • analysis.m
  • browse.m
  • plotgui.m
  • browse.m
  • evriinstall.m
  • evrireporterror.m
These functions will not be called in normal operation and, in most cases, our compilation licenses do not permit their inclusion in your application anyway.
  • Find top level functions and see if you can "manually" determine dependencies. Look at the results of the top level dependency check and see what functions are called from the primary PLS_Toolbox function you're working with. If the dependencies are few, you may be able to iterate over the results (get 'toponly' dependencies from results) and get a smaller subset of dependencies. NOTE: This will require some experimentation and time to work through. The dataset object is extensively used by most function so this folder should almost always be included.
 [fList, pList] = matlab.codetools.requiredFilesAndProducts('peakfind','toponly')

Uninstall the Stats Toolbox

Although moving the Stats Toolbox below PLS_Toolbox on your MATLAB path (or removing the Stats Toolbox folders altogether) will allow the PLS_Toolbox DataSet Object to function normally, you must uninstall the Stats Toolbox before compiling PLS_Toolbox function that require the DataSet Object.

The MathWorks states:

"When you compile [a program] into an application and run it, the MATLAB Compiler Run-time references its in-built Dataset function which is higher in its PATH and hence runs the data against this inbuilt Dataset function."

For more information on the DataSet Object history see here:

Troubleshooting

  • In some cases PLS_Toolbox may need to be moved out of the default installation folder into a folder with more permissions and/or no spaces in the path. For example, "C:\eigenvector\PLS_Toolbox".

Still having problems? Please contact our helpdesk at helpdesk@eigenvector.com

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