View source for OpenIGTLink/Matlab

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[[OpenIGTLink | &lt;&lt; OpenIGTLink]]

=About the project=
The objective of this project is to provide OpenIGTLink interface for [http://www.mathworks.com/ Matlab] / [http://www.gnu.org/software/octave/ Octave] to support research and development in image guided therapy (IGT). Matlab and Octave are widely used for prototyping image and signal processing algorithms. They also offer many powerful function sets to handle matrix and coordinate data, which is useful to test and analyze coordinate data exported from tracking and robotic devices.
The OpenIGTLink interface for Matlab / Octave allows importing and exporting several types of data that can be handled in the OpenIGTLink protocol in a Matlab / Octave environment. It provides a rapid prototyping environment, which many researchers and engineers are already familiar with.

This project is a generalization of [[Projects/Slicer3/2007_Project_Week_Slicer_Matlab_Pipeline_for_scalars_and_tensors | Slicer Matlab Pipeline project]] in the 2007 NA-MIC Project Week.

=Demo Videos=
==Scenario 1: Push image data to 3D Slicer from Matlab console (1-way communication) ==
Matlab and 3D Slicer are running on different hosts (the Matlab window is displayed using remote display). A matrix 'I' and 'M' on the Matlab console contain image data and affine transformation respectively. With just a several lines of commands on the Matlab console, the image data is transferred to the 3D Slicer through the network using OpenIGTLink. 

[[Media:OpenIGTLink_Matlab_1way.mov]]


==Scenario 2: Request Matlab to process image data from 3D Slicer (2-way communication)==
Matlab and 3D Slicer are running on different hosts (Matlab window is displayed using remote display). On the Matlab console, an example image processing server ('example_server.m') is running. This example server basically receives an image form external software, apply a filter and return a result. Once the OpenIGTLink connection between the 3D Slicer and the Matlab is established, the example MR image is loaded into the scene on the 3D Slicer, and then pushed to the Matlab through the OpenIGTLink connection. After a few seconds, the Matlab returns the filtered image to the 3D Slicer through the same OpenIGTLink connection. The image is visualized on the 3D Slicer.

[[Media:OpenIGTLink_Matlab_2way.mov]]

==Scenario 3: Send transform (4x4 matrix) from Matlab to 3D Slicer==
Matlab and 3D Slicer are running on different hosts (Matlab window is displayed using remote display). The video demonstrates to manipulate 4x4 matrix on the Matlab console and then transfer to the 3D Slicer through the network using OpenIGTLink.


[[Media:OpenIGTLink_Matlab_tracking.mov]]

=How does it work?=
The OpenIGTLink Matlab interface is implemented as a set of MEX Files, which are C/C++ source codes called from Matlab. Those MEX files simply receive data from Matlab, connect to the OpenIGTLink receiver, serialize the data in an appropriate format using the OpenIGTLink Library, and send it to the receiver.

The usage of the interface is quite simple. The following example Matlab code is sending trancking data to the receiver waiting at port #18944 on the localhost.

 %%% affine transform matrix
 M = [1.0, 0.0, 0.0, 0.0;
      0.0,-1.0, 0.0, 0.0;
      0.0, 0.0, 1.0, 0.0;
      0.0, 0.0, 0.0, 1.0];
 
 IMGDATA.Type = 'TRANSFORM';
 IMGDATA.Name = 'MatlabTrans';
 IMGDATA.Trans = M;
 
 sd = igtlopen('localhost', 18944);
 r = igtlsend(sd, IMGDATA);
 igtlclose(sd);


For tracking data transfer:

 %%% read image data
 fid = fopen('igtlTestImage1.raw', 'r');
 I = fread(fid, [256 256], 'uint8')';
 fclose(fid);
 
 %%% affine transform matrix
 M = [1.0, 0.0, 0.0, 0.0;
      0.0,-1.0, 0.0, 0.0;
      0.0, 0.0, 1.0, 0.0;
      0.0, 0.0, 0.0, 1.0];
 
 IMGDATA.Type = 'IMAGE';
 IMGDATA.Name = 'MatlabImage';
 IMGDATA.Image = I;
 IMGDATA.Trans = M;
 
 %%% send the image data through OpenIGTLink connection
 sd = igtlopen('localhost', 18944);
 r = igtlsend(sd, IMGDATA);
 igtlclose(sd);


=Download & Building OpenIGTLink Mex functions=

==For Windows Users==
*You may download mex binary files for 32-bit and 64-bit Windows built by Dr. Nicolas Herlambang, Ph.D. (Aze Ltd., Japan) from the following link.
**[[File:OpenIGTLinkMex_Win32.zip]] (32 bit).
**[[File:OpenIGTLinkMex_Win64.zip]] (64 bit).

==For Linux Users==
**[[File:OpenIGTLinkMex_Linux64.tar.gz]] (64 bit -- Built on 64-bit FC13 + Matlab 7.10.0 R2010a)

==Install the OpenIGTLink Library==
The instruction can be found in [[OpenIGTLink/Library]]. We recommend to build the library as a static library. (Just to avoid a trouble that Matlab couldn't find shared objects/dynamic link library. In principle, either static or shared library works.)

==Get the Matlab OpenIGTLink interface source code==
The OpenIGTLink/Matlab interface is in the initial stage of development. The source code is available from NA-MIC SandBox repository at

  http://svn.na-mic.org/NAMICSandBox/trunk/MatlabIGTL

==Build MEX files==
CMake configuration (CMakeLists.txt) comes with Matlab OpenIGTLink interface. To build the interface with CMake
in Linux/Mac OS X environment,

 cd <working directory>
 svn co URL: http://svn.na-mic.org/NAMICSandBox/trunk/MatlabIGTL
 mkdir MatlabIGTL-build
 cd MatlabIGTL-build
 ccmake ../MatlabIGTL

This will launch Curses Interface for CMake. Press 'c' to configure and check the following parameters;
 *MEX_COMPILER = (path to Matlab's '''mex''' command or Octave's '''mkoctfile''')
 *OpenIGTLInk_DIR = (path to binary directory of OpenIGTLink)

Then press 'g' to generate a makefile. Press 'q' to quit the CMake interface screen.
Once you find '''Makefile''' in the directory, run make. Several files with extension *.mex (or *.mex<arc-name>) will be generated.

=Contact=
If you have any question, please subscribe to OpenIGTLink ML.
You may also contact to [[User:Tokuda|Junichi Tokuda]] for further information.