Installing the MATLAB interface to STIR

This page provides instructions on how to install STIR for MATLAB. You will need STIR 3.1 or later for this to work (at present, use the [github version].

Introduction

You will need to use the instructions at Installing STIR with CMake. Here we will give more specific information.

These are instructions on how to install the STIR+MATLAB interface have been tested on a unix system with ubuntu 14.04. It relies on CmakeGui (as usual) and an extension of SWIG that has to be installed first.

Install SWIG

First, prepare your system with some packages

 sudo apt-get install libtool automake autoconf autogen bison 

Get a version of SWIG with preliminary MATLAB support

 mkdir swig
 cd swig
 git clone https://github.com/jaeandersson/swig.git swig_git 

(you could try https://github.com/KrisThielemans/swig.git instead but this is currently out-of-date) and checkout the right branch

 cd swig_git	
 git checkout matlab 

SWIG can now be installed

 ./autogen.sh	
 cd ..
 mkdir build
 cd build	
 ../swig_git/configure	
 make
 sudo make install 

In the case were MATLAB is not installed globally, when use the following flag:

 ../swig_git/configure --with-matlab=[PATH]

Note that the install might fail at the end if it can't find yodl2man, but we don't care. Check with that we now have the right version (should say 3.0.3 or later)

 swig -version 

Install STIR

Follow the instructions on this page up to the point where you started cmake-gui.

• press configure
• press ok
• set CMAKE_BUILD_TYPE to Release
• enable BUILD_SWIG_MATLAB
• If you want want to use openMP for acceleration, enable STIR_OPENMP
• press configure
• check that CMake found the correct SWIG file (not the system one). If it did, replace the SWIG variable and "configure" again
• optionally adjust location of STIR-MATLAB files (MATLAB_DEST variable)
• generate
• close cmake-gui

Then either install STIR as usual

 make    
 sudo make install 

or you could build only the STIR+MATLAB first (just to see if it fails or not)

 make stirMATLAB 

Add path in MATLAB. E.g.

 addpath /usr/local/matlab 

Potential problems

swig complains about mexname

The following error

swig error : Unrecognized option -mexname swig error : Unrecognized option stirMATLAB_wrap 
Use 'swig -help' for available options.

is caused by a slightly out-of-date swig. you can get around it by editing src/swig/CMakeLists.txt and removing -mexname stirMATLAB_wrap from the line (around L107) that sets SWIG_MODULE_stirMATLAB_EXTRA_FLAGS.

run-time errors in MATLAB

On Linux, you might see something like this

Invalid MEX-file '/nobackup/umpw/STIR/STIR-Build/src/swig/stirMATLAB_wrap.mexa64':
/apps1/applications/matlab/R2016a/1/default/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /nobackup/umpw/STIR/STIR-Build/src/swig/stirMATLAB_wrap.mexa64)

you might see something similar on Mac.

This problem is caused by MathWorks making sure that MATLAB works by shipping its own version of system/gcc/dependent libraries, but breaking external code in the mean time. Our recommended solution is to compile EVERYTHING with a MATLAB compatible compiler. Check for instance https://uk.mathworks.com/support/sysreq/previous_releases.html.

On Linux/Mac you can do this as follows

CC=gcc-4.7 CXX=g++4.7 ccmake ...

If you want to use a more recent compiler (or have a corner case where you see the above error anyway), you could try to resolve by pre-loading your shared libraries. In bash, you can do for instance:

LD_PRELOAD=/lib64/libstdc++.so.6:/lib64/libhdf5.so matlab&

In certain systems, you might have to use LD_PRELOAD_64. Also, the exact path of your libraries will change. You can normally find out by locating the stirMATLAB_wrap.mex* file and doing something like

ldd stirMATLAB_wrap.mexa64

Testing

There are a few tests in STIR/src/swig/test/matlab. Just execute these adding the directory where you installed it to your matlab path (e.g. if you choose /usr/local as your CMAKE_INSTALL_PREFIX, in MATLAB do "addpath /usr/local/matlab")

Examples

Get started with the examples in STIR/examples/matlab