# 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].

## Contents

# 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/KrisThielemans/swig.git swig_git

(you could try https://github.com/jaeandersson/swig.git instead which is already a bit more up-to-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is caused by a slightly out-of-date swig.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&

# 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