Release Notes Version 7 3 1 and Faq import three-way data: Difference between pages

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==Changes and Bug Fixes in Version 7.3.1==
===Issue:===


How do I import three-way data into Solo or PLS_Toolbox?


===Bug Fixes===
===Possible Solutions:===


{| {{table}}
'''Solution 1) Built in EEM importers :'''
| align="center" style="background:#f0f0f0;"|'''File'''
 
| align="center" style="background:#f0f0f0;"|'''Comment'''
If applicable to your file type, use one of the built in EEM importers. There are importers for EEM data from Hitachi, Shimazdu, Horiba and Jasco. Please see this wiki entry for more information on [[Data_Importing_Formats | Data Importing Formats]]
|-
 
| [[modeloptimizergui]]||Add plotting button.
EEM data needs be configured in a specific way such that:
|-
 
| plotloadslimits||Fix for error when plotting of Selectivity Ratio with model cleared.
* '''mode 1''' corresponds to '''samples'''
|-
 
| [[experimentreadr]]||Fix default for cal/val when NO cal/val specified in experiment file.
* <div>'''mode 2''' corresponds to '''emission'''</div>
|-
 
| [[encodexml]]||Remove all control characters other than tab/linefeed/return in strings.
* <div>'''mode 3''' corresponds to '''excitation'''</div>
|-
 
| getcacheindex||Avoid "load xml file" dialog for rare case when cache item is missing information (e.g. when preprocessing description has gotten too long).
The built-in EEM importers will handle this configuration automatically. When importing manually (see below), further manipulation will likely be necessary. Use the Transform &rarr; Permute modes and Transform &rarr; Reshape smenu items to modify your imported data as appropriate.
|-
 
| adjustaxislimitsgui||Add drawnow, user reported error with missing handles.
'''Solution 2) For three-way data with few slabs:'''
|-
 
| [[opusreadr]]||Fix for typo which obscured a real error messages.
<ol style="list-style-type:lower-alpha">
|-
  <li>Import the data slabs into the workspace (browser). The workspace browser is available from the main analysis user interface from the menu item FigBrowser.</li>
| browse_shortcuts||Fix for bug when eigenguide.xml file can't be found.
  <li>Each slab, i.e. each matrix of data is imported individually. Hence, if you have a '''10x8x3''' array, you will import three slabs each of size '''10x8'''.</li>
|-
  <li>Use the mouse to drag slab two onto slab one. In the window that opens choose Augment and then choose augment in the Slabs direction.</li>
| [[plsdaroc]]/[[roccurve]]||Switch orientation of our ROC curves to match general convention of "Specificity"/"Sensitivity" on x and y-axes respt., instead of the reverse.
  <li>A two-slab three-way array has now replaced the first data matrix. More slabs can be added in the same fashion.</li>
|-
</ol>
| [[parsexml]]||Convert from use of "exist()" function to use of java.io.File().isFile (to avoid memory leak).
 
|-
Alternatively, you may also open one slab in the dataset editor and then add additional slabs using File &rarr; Import. After selecting the next slab to import, answer the same questions as in step c above. Repeat for each slab.  
| plotscores_addclassification||Add extra check for non-emptyness to avoid error when using "pred  = plsda(xt,model);"
 
|-
'''Solution 3) For larger three-way data:'''
| trendwaterfall||Use findindx when prepping for waterfall.
 
|}
In the DataSet editor, you can import a full three-way array if you have it organized as a two-way matrix. Upon importing the two-way data, you can reshape to a three-way array using the menu item: Transform &rarr; Fold into 3-way.  
 
For example, you have the above matrices (three slabs) in one table/matrix:
 
  [ Slab1;
  Slab2;
  Slab3 ]
 
hence have the three slabs below each other. Upon importing, use the menu option described above to "Fold into 3-way" and choose three as the number of slabs and the data will be rearranged accordingly. If you are familiar with the MATLAB function <code>reshape</code>, you may also use Transform &rarr; Reshape for other types of rearrangements.  
 
Note: the result of this command will give you slabs in the 3rd mode of the DataSet. If these slabs are separate samples (such as with EEMs), you'll want to use the Transform &rarr; Permute menu to reorder the dimensions. For example, permuting to the order [3 2 1] would swap the order of the 1st and 3rd modes, putting slabs as the first mode.  
 
 
'''Still having problems? Please contact our helpdesk at [mailto:helpdesk@eigenvector.com helpdesk@eigenvector.com]'''
 
[[Category:FAQ]]

Revision as of 10:45, 20 June 2019

Issue:

How do I import three-way data into Solo or PLS_Toolbox?

Possible Solutions:

Solution 1) Built in EEM importers :

If applicable to your file type, use one of the built in EEM importers. There are importers for EEM data from Hitachi, Shimazdu, Horiba and Jasco. Please see this wiki entry for more information on Data Importing Formats

EEM data needs be configured in a specific way such that:

  • mode 1 corresponds to samples
  • mode 2 corresponds to emission
  • mode 3 corresponds to excitation

The built-in EEM importers will handle this configuration automatically. When importing manually (see below), further manipulation will likely be necessary. Use the Transform → Permute modes and Transform → Reshape smenu items to modify your imported data as appropriate.

Solution 2) For three-way data with few slabs:

  1. Import the data slabs into the workspace (browser). The workspace browser is available from the main analysis user interface from the menu item FigBrowser.
  2. Each slab, i.e. each matrix of data is imported individually. Hence, if you have a 10x8x3 array, you will import three slabs each of size 10x8.
  3. Use the mouse to drag slab two onto slab one. In the window that opens choose Augment and then choose augment in the Slabs direction.
  4. A two-slab three-way array has now replaced the first data matrix. More slabs can be added in the same fashion.

Alternatively, you may also open one slab in the dataset editor and then add additional slabs using File → Import. After selecting the next slab to import, answer the same questions as in step c above. Repeat for each slab.

Solution 3) For larger three-way data:

In the DataSet editor, you can import a full three-way array if you have it organized as a two-way matrix. Upon importing the two-way data, you can reshape to a three-way array using the menu item: Transform → Fold into 3-way.

For example, you have the above matrices (three slabs) in one table/matrix:

 [ Slab1;
 Slab2;
 Slab3 ]

hence have the three slabs below each other. Upon importing, use the menu option described above to "Fold into 3-way" and choose three as the number of slabs and the data will be rearranged accordingly. If you are familiar with the MATLAB function reshape, you may also use Transform → Reshape for other types of rearrangements.

Note: the result of this command will give you slabs in the 3rd mode of the DataSet. If these slabs are separate samples (such as with EEMs), you'll want to use the Transform → Permute menu to reorder the dimensions. For example, permuting to the order [3 2 1] would swap the order of the 1st and 3rd modes, putting slabs as the first mode.


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