Documentation/4.3/Extensions/MatlabBridge - Revision history

Lasso at 15:12, 23 December 2013

2013-12-23T15:12:02Z

Lasso at 17:31, 12 December 2013

2013-12-12T17:31:50Z

Lasso at 16:47, 12 December 2013

2013-12-12T16:47:34Z

Lasso at 16:44, 12 December 2013

2013-12-12T16:44:36Z

Lasso at 05:26, 26 September 2013

2013-09-26T05:26:12Z

Lasso at 04:52, 26 September 2013

2013-09-26T04:52:03Z

UpdateBot: Nightly -> 4.3

2013-09-05T03:35:46Z

Nightly -> 4.3

New page

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'''MatlabBridge is only available for nightly builds, but unfortunately extensions for nightly builds may not be available immediately. If the extension does not appear for your installed Slicer version, then use an earler nightly version of Slicer, such as [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.2.0-2013-07-13-win-amd64.exe&checksum=424bf07b2954fc1956b69a755920b916 this release]'''


{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Andras Lasso (PerkLab, Queen's University), Jean-Christophe Fillion-Robin (Kitware), Kevin Wang (Radiation Medicine Program, Princess Margaret Hospital, University Health Network Toronto), Gabor Fichtinger (PerkLab, Queen's University) 
Contact: Andras Lasso, <email>lasso@cs.queensu.ca</email> 
Project website: http://www.slicerrt.org 
License: [http://www.slicer.org/pages/LicenseText Slicer license]
{{documentation/{{documentation/version}}/module-introduction-logo-gallery
|{{collaborator|logo|sparkit}}|SparKit
|{{collaborator|logo|namic}}|NA-MIC
|{{collaborator|logo|perklab}}|PerkLab
}}


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
{|
[[Image:MatlabBridgeLogo.png|left]]
|
MatlabBridge is an extension of 3D Slicer to allow running Matlab functions directly in 3D Slicer.

Highlights:
* The extension allows running of Matlab functions directly from 3D Slicer: it takes the input from the data loaded into Slicer and visualizes the results in Slicer right after the execution is completed
* If you change any input on the GUI (and the “AutoRun” option is enabled) the bridge automatically re-runs the Matlab script with the updated parameters and shows the new results
* If you change your Matlab function then you can re-run the function and see the updated results with a single click
* The graphical user interface is generated automatically from a standard command-line interface definition XML file (no GUI programming needed)
* You can get started quickly by generating a skeleton Matlab function and interface definition XML file using the Matlab Module Generator module
* No building of 3D Slicer or MEX files, etc. are needed – the only requirements are to download and install 3D Slicer with the MatlabBridge extension and have Matlab on your computer
The Matlab module behaves exactly as any other command-line-interface module, the Matlab engine is started automatically in the background (and it is kept running in the background so that you don’t have to wait for Matlab startup each time you run your function)

Demo videos:
* [http://screencast.com/t/veVw16jB3uk Creating and using a Matlab module]
* [http://screencast.com/t/LcdrCx9l0 Editing and debugging a Matlab module]

Tutorial: [[Media:MatlabBridgeTutorial.pdf|How to create, run, customize Matlab modules]]

|
|}


{{documentation/{{documentation/version}}/extension-section|Modules}}

*[[Documentation/{{documentation/version}}/Modules/MatlabModuleGenerator|Matlab Module Generator]] (in the module list: Developer Tools / Matlab)
*[[Documentation/{{documentation/version}}/Modules/MatlabCommander|Matlab Commander]] (in the module list: Developer Tools / Matlab)


{{documentation/{{documentation/version}}/extension-section|Use Cases}}

<gallery widths="200px" perrow="4">
Image:MatlabBridgeScreenshot1.png|Example Matlab module user interface in Slicer
Image:MatlabBridgeScreenshot2.png|Matlab Bridge modules appear under the Developer Tools / Matlab category
Image:MatlabBridgeScreenshot3.png|A skeleton Matlab script can be created and installed using the Matlab module generator.
Image:MatlabBridgeScreenshot4.png|The Matlab Commander allows running any commands from the user interface or from another Slicer module.
</gallery>


{{documentation/{{documentation/version}}/extension-section|Tutorials}}
*'''[[Media:MatlabBridgeTutorial.pdf|Comprehensive MatlabBridge tutorial: how to create, run, customize Matlab modules]]'''






{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
* Source code: https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/
* Issue tracker: [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u783013 open issues and enhancement requests]
* Design overview: [https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/doc/MatlabBridgeDesign.pptx].

Tested with Matlab R2009b, R2012a, and R2013a on Windows7.


{{documentation/{{documentation/version}}/extension-section|Troubleshooting}}
* Problem: When I try to run my Matlab module, the Matlab process does not start (Matlab window does not appear on the taskbar)
** Solution [on Windows Vista/7/8]: Please go to the Matlab module generator module and in the “Matlab executable” editbox set the path to your “.../bin/matlab.exe” (not to "activate_matlab.exe" or other exe files in the Matlab program directory or any file in the bin/win64 directory).
* Problem: When I try to run my Matlab module, the Matlab process starts (Matlab window appears on the taskbar and it displays the message "Starting OpenIGTLink command server at port 4100 Waiting for client connections..."), but the Matlab module execution fails (in the Slicer error log the "igtl::ClientSocket (...): Failed to connect to server 127.0.0.1:4100" message is displayed)
** Solution [on Windows Vista/7/8]: Firewall settings prevent Matlab-Slicer communication. Please add a firewall exception by the following steps:
**# Start ''cmd.exe'' as administrator (open the Windows Start menu, type "cmd", hit Ctrl + Shift + Enter)
**# Click ''Yes'', if a dialog box appears asking "''Do you want to allow the following program to make changes to this computer?''"
**# Enter the following command: ''netsh firewall add portopening tcp 4100 MatlabBridge''
* Problem: module execution is not completed
** Solution: make sure you've selected .../MATLAB/.../bin/matlab.exe as Matlab executable (and not .../MATLAB/.../bin/win64/MATLAB.exe)



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@@ Line 31: / Line 31: @@
 Demo videos:
-* [http://screencast.com/t/veVw16jB3uk Creating and using a Matlab module]
+* [http://screencast.com/t/TgAVE6Wa8mf Creating and using a Matlab module]
 * [http://screencast.com/t/LcdrCx9l0 Editing and debugging a Matlab module]
@@ Line 59: / Line 59: @@
 *'''[[Media:MatlabBridgeTutorial.pdf|Comprehensive MatlabBridge tutorial: how to create, run, customize Matlab modules]]'''
 *[https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/Examples/ A few example modules]
-* Demo video: [http://screencast.com/t/veVw16jB3uk Creating and using a Matlab module]
+* Demo video: [http://screencast.com/t/TgAVE6Wa8mf Creating and using a Matlab module]
 * Demo video: [http://screencast.com/t/LcdrCx9l0 Editing and debugging a Matlab module]
 <!-- ---------------------------- -->

@@ Line 82: / Line 82: @@
 * Problem: When I try to run my Matlab module, the Matlab process does not start (Matlab window does not appear on the taskbar)
 ** Solution [on Windows Vista/7/8]: Please go to the Matlab module generator module and in the “Matlab executable” editbox set the path to your “.../bin/matlab.exe” (not to "activate_matlab.exe" or other exe files in the Matlab program directory or any file in the bin/win64 directory).
 * Problem: When I try to run my Matlab module, the Matlab process starts (Matlab window appears on the taskbar and it displays the message "Starting OpenIGTLink command server at port 4100 Waiting for client connections..."), but the Matlab module execution fails (in the Slicer error log the "igtl::ClientSocket (...): Failed to connect to server 127.0.0.1:4100" message is displayed)
 ** Solution [on Windows Vista/7/8]: Firewall settings prevent Matlab-Slicer communication. Please add a firewall exception by the following steps:
@@ Line 87: / Line 88: @@
 **# Click ''Yes'', if a dialog box appears asking "''Do you want to allow the following program to make changes to this computer?''"
 **# Enter the following command: ''netsh firewall add portopening tcp 4100 MatlabBridge''
 * Problem: module execution is not completed
 ** Solution: make sure you've selected .../MATLAB/.../bin/matlab.exe as Matlab executable (and not .../MATLAB/.../bin/win64/MATLAB.exe)

@@ Line 57: / Line 57: @@
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 {{documentation/{{documentation/version}}/extension-section|Tutorials}}
-*'''[[Media:MatlabBridgeTutorial.pdf|Comprehensive MatlabBridge tutorial:]] how to create, run, customize Matlab modules - everything that you need to get started'''
+*'''[[Media:MatlabBridgeTutorial.pdf|Comprehensive MatlabBridge tutorial: how to create, run, customize Matlab modules]]'''
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@@ Line 72: / Line 73: @@
 * Issue tracker:  [https://www.assembla.com/spaces/dG15GuCs4r4l4UeJe5cbCb/tickets/report/u783013 open issues and enhancement requests]
 * Design overview: [https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/doc/MatlabBridgeDesign.pptx].
+* Running Matlab modules without accessing a Matlab license: You can run your Matlab modules on a computer that does not have Matlab license. You just have to create an executable with the Matlab compiler: include all the MatlabBridge CommandServer functions (https://subversion.assembla.com/svn/slicerrt/trunk/MatlabBridge/src/MatlabCommander/commandserver/) and your custom .m files as Shared Resources and choose cli_commandserver.m as "Main File". To run the Matlab modules just start the compiled MCR executable before running your module.
-Tested with Matlab R2009b, R2012a, and R2013a on Windows7.
+* Tested with Matlab R2009b, R2012a, and R2013a on Windows7.
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