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

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===Purpose===
===Issue:===


Reads one or more ASCII XY or XY... files into a DataSet object.
How do I obtain or use a recompilation license for PLS_Toolbox?


===Synopsis===
===Possible Solutions:===


:out = xyreadr(file,delim,options)
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] ).


===Description===
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.


Reads standard XY ASCII files in which the first column is a column of axisscale values (wavelengths, retention times, etc) and the second and possibly subsequent column(s) are values measured at the corresponding axisscale values. Returns a DataSet object with the first column of the file as the axisscale and all subsequent columns (both in the same file and in multiple files) concatenated and transposed as rows.  
# 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.)


It is '''REQUIRED''' that, if multiple files are being read, they must all have the same X range. If this is not true, the import may fail.
'''Blocking Unnecessary Functions'''


====Inputs====
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:


* '''file''' = One of the following identifications of files to read:
* 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.
: '''a)'''  a single string identifying the file to read
::  ('example.txt')
: '''b)'''  a cell array of strings giving multiple files to read
::  ({'example_a' 'example_b' 'example_c'})
: '''c)'''  an empty array indicating that the user should be prompted to locate the file(s) to read
::  ([])
* '''delim''' = An optional string used to specify the delimiter character.
::Supported delimiters include:
:* ''''tab''''  or  '\t' or sprintf('\t')
:* ''''space''''  or  ' '
:* ''''comma''''  or  ','
:* ''''semi''''  or  ';'
:* ''''bar''''    or  '|'
::If (delim) is omitted, the file will be searched for a delimiter common to all rows of the file and producing an equal number of columns in the result.


====Outputs====
* 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:


* '''out''' = a DataSet object with the first column of the file(s) stored as the axisscale{2} values and all subsequent column(s) stored as rows of data.
:* analysis.m
:* browse.m
:* plotgui.m
:* browse.m
:* evriinstall.m
:* evrireporterror.m


===Options:===
:: 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.


*'''commentcharacter''': [<nowiki>''</nowiki>] any line that starts with the given character will be considered a comment and parsed into the"comment" field of the DataSet object. Deafult is no comment character. Example: '%' uses % as a commentcharacter.
* 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.


* '''headerrows''': [{0}] number of header rows to expect in the file.
<pre> [fList, pList] = matlab.codetools.requiredFilesAndProducts('peakfind','toponly') </pre>


* '''waitbar''': [ 'off' |{'on'} ] governs use of waitbars to show progress.
'''Uninstall the Stats Toolbox '''


===See Also===
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.


[[autoimport]], [[areadr]], [[dataset]], [[xclgetdata]], [[xclreadr]]
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'''
 
* 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]'''
 
[[Category:FAQ]]

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