Compiling and calling other languages

Matlab is an extremely powerful programming environment, but it can still be useful to call other languages for various reasons, such as speed (C) or existence of pre-canned packages (R) or data structures (Java). In this chapter, we show how to do this.

Contents

System Commands

You can execute system commands from Matlab using the system() function or, equivalently, the ! operator.

%system('mspaint');                     % launch mspaint.exe
%!mspaint
system('echo hello world > tmp.txt');  % low level pipe to a file
system('type tmp.txt');                % low level display of a file
system('del tmp.txt');                 % delete the file

hello world  

Eval

Often we do not know precisely which system commands to execute until run time. The eval() function can be very useful in these cases. Eval executes a string specified command as if it were typed at the command prompt or executed in a script or function.

Create 5 files tmp1.txt through tmp5.txt using low level system commands

for i=1:5
   cmd = sprintf('!echo ''%s'' > %s',  sprintf('this is filenum %d', i), sprintf('tmp%d.txt', i))
   eval(cmd)
end
% Now look at the contents of the first file
type tmp1.txt

cmd =

!echo 'this is filenum 1' > tmp1.txt


cmd =

!echo 'this is filenum 2' > tmp2.txt


cmd =

!echo 'this is filenum 3' > tmp3.txt


cmd =

!echo 'this is filenum 4' > tmp4.txt


cmd =

!echo 'this is filenum 5' > tmp5.txt


'this is filenum 1' 

While extremely powerful, eval should only be used when other options have been exhausted as it can result in code that is very difficult to debug. If you want to dynamically determine which function to execute as your program runs, it is much better to pass around function handles.

Calling Java

It is possible to call Java directly from Matlab. To create an object of a java class, you simply need to call the constructor. You must use the fully qualified name, even for classes under java.lang, unless you first import the name space with the import() function, as in this example.

S = java.lang.String('hello')
import java.lang.*;       % import the java.lang namespace
S = String('hello')       % Create a java String object
A = S.substring(0,2)      % Call a method from the java.lang.String class

 
S =
 
hello
 
 
S =
 
hello
 
 
A =
 
he
 

Recall, that java indexes from 0, not 1 as in Matlab

I = Integer(3);            % Create a java.lang.Integer object

When the type returned by a java method is either of type java.lang.Object or a java primitive type, such as int, double, char, boolean, etc, Matlab automatically converts to a Matlab type for you. Similarly, you can pass Matlab data directly to java methods or constructors and Matlab will usually convert the data in a 'reasonable' way as we saw above. If you want to explicitly convert from a java type to a Matlab type, use the char() , double() , cell() , or struct() functions. To use char() , the java class must have an obj.toChar() method and to use double() ,it must have an obj.toDouble() method.

B = char(A)               % convert to a Matlab char array
C = double(I)             % convert to a Matlab double

B =

he


C =

     3

Java objects can be stored in arrays, cell arrays and structs. When you concatenate two java objects, the type of the resulting matrix is the lowest common superclass.

D = [A,I]

 
D =
 
java.lang.Object[]:
    'he'
    [ 3]


 

You can of course, pass java objects to the methods of other java objects.

H = java.util.HashMap();
H.put(S,I);
H.get(S)

ans =

     3

Use the javaArray() function to create a java array. Suppose we wanted a 2D array of Strings as would be created by the java code, String[][] myArray = new String[4][5];

JA = javaArray('java.lang.String',4,5)      % Create a java array of Strings

 
JA =
 
java.lang.String[][]:
 
     []     []     []     []     []
     []     []     []     []     []
     []     []     []     []     []
     []     []     []     []     []


 

You must specify the fully qualified name here, even if you have imported the name space.

While Java indexes from 0, when using Matlab syntax as in the following command, Matlab automatically converts for you and indexing is once again from 1.

JA(3,2) = String('hello')
K = char(JA(3,2))

 
JA =
 
java.lang.String[][]:
 
     []         []     []     []     []
     []         []     []     []     []
     []    'hello'     []     []     []
     []         []     []     []     []


 

K =

hello

The methods() and methodsview() functions can be useful for viewing the public methods of a java object's class.

methods(JA)

Methods for class java.lang.String[][]:

equals     getClass   hashCode   notify     notifyAll  toString   wait       

Static methods can be used as well

Math.random()

ans =

    0.8508

To create objects of java classes, the classes must be on the Matlab java class path. Matlab uses both a static and dynamic path. The static path is loaded when Matlab is started and is defined in the classpath.txt file. To include classes you have written to the static path, edit this file, add the directory name containing your .class files at the bottom, and restart Matlab. They will then be available every time you load Matlab. Classes added to the dynamic path are available right away without having to restart Matlab, but are cleared when Matlab is closed. Also, using classes loaded dynamically is slightly less efficient. To add a directory to the dynamic path use the javaaddpath() function.

javaaddpath(pwd);          % add a directory to the dynamic path
clear java;                                             % clear the dynamic path

Java hash tables

Hash Tables are very useful, and are supported in Java. One can call them easily from Matlab as illustarted in the following example.

hTable = java.util.Hashtable;
hTable.put(0, rand(2,2));
hTable.put(1, 41.287);
hTable.put(2, 'test string');
hTable.put('foo', 'bar');
hTable
hTable.get('foo')
hTable.get(0)

 
hTable =
 
{2.0=test string, foo=bar, 1.0=41.287, 0.0=[[D@12bdbb5}
 

ans =

bar


ans =

    0.0720    0.5681
    0.9673    0.2033

However, Matlab now (as of 2008b) has a containers.map class, which does the same thing, without requiring you to call Java.

Calling R

R is a programming environment and language similar to Matlab but containing somewhat different functionality, and with an emphasis on statistics rather than general numerical computing. Here we describe how to call R functions and obtain the results from within Matlab.

There are three approaches we can take to interface with R.

Calling R using the DCOM interface (Windows only)

This is how you set it up.

You can add the R directory to your windows path for the duration of the Matlab session with the command below: alter the 2.6.2 accordingly. To add it permanently, add the directory to Control Panel -> System -> (Advanced System Settings) -> Environment Variables -> Path, or similar, depending on the version of Windows.

setenv('PATH',[getenv('PATH') ';C:\Program Files\R\R-2.6.2\bin']);

You can then use the COM interface as in this example

Rcon = actxserver('StatConnectorSrv.StatConnector')  % setup connection
Rcon.Init('R');                                      % open R
Rcon.Evaluate('A <- 3');                             % execute an R command, (in R memory space)
A = Rcon.GetSymbol('A')                              % import R data into Matlab
B = [1,2,3];                                         % some Matlab data
Rcon.SetSymbol('B',B);                               % export Matlab data to R
C = Rcon.Evaluate('B <- B +1')                       % execute an R command, get returned data
Rcon.Close;                                          % close connection (remember to do this!)

 
Rcon =
 
	COM.StatConnectorSrv_StatConnector


A =

     3


C =

     2     3     4

Matlab-R link (Windows only)

There is much simpler way to call Matlab. First install this matlab package. This provides the following m-files: openR, closeR, evalR, getRdata, putRdata. We give an example of use below.

The interface can be finicky and will return highly cryptic error messages when anything goes wrong. When exporting Matlab matrices to R for example, it is sometimes necessary to create the variable in R first, assigning it a dummy scalar value.

Here we demonstrate how to use the openR, closeR, evalR, getRdata, and putRdata files. We attempt to classify data using R's randomForest function. The R randomForest package must first be installed in R by going to packages -> install Packages -> (choose a server) -> randomForest

rand('twister',1);                       % seed rand num generator
load fisherIris                          % builtin dataset
[j,j,species] = unique(species);         % convert to numeric class labels instead of strings
ntrain  = 120;                           % number of training cases to use
ntest   = 30;                            % number of test cases to use
perm   = randperm(size(meas,1)        ); % randomly divide data into training and test sets
Xtrain = meas    (perm(1:ntrain    ),:);
Xtest  = meas    (perm(ntrain+1:end),:);
ytrain = species (perm(1:ntrain    ),:);
ytest  = species (perm(ntrain+1:end),:);

openR;                                % open the R connection
evalR('library(randomForest)');       % load the already installed randomForest package
putRdata('Xtrain',Xtrain);            % export the Matlab data to R
evalR('Xtrain <- data.frame(Xtrain)') % randomForest expects an R data frame, create it.
putRdata('ytrain',ytrain);            % export to R
evalR('ytrain <- data.frame(ytrain)');% build frame
putRdata('Xtest',Xtest);              % export to R
evalR('Xtest <- data.frame(Xtest)');  % build frame

Undefined function or variable 'openR'.

Error in ==> external at 200
openR;                                % open the R connection

Here we call the actual randomForest function in R and ask the constructed forest to predict the class labels given the training data.

evalR('rf <- randomForest(Xtrain[1:120,],ytrain[1:120,])');
evalR('yhat <- predict(rf,Xtest[1:30,])');
yhat = getRdata('yhat');                     % import the predictions into Matlab
closeR;                                      % close the R connection
numWrong = sum(round(yhat') ~= ytest)        % How many, out of 30, did it get wrong?

Note, the R random forest function performed regression here not classification so we round the results to approximate the class labels.

Calling Perl

Perl scripts can be run using the perl() function.

fid = fopen('hello.pl','w');
fprintf(fid,'$input = $ARGV[0];\nprint "Hello $input.";');
fclose(fid);
perl('hello.pl','World')

Mex: Calling C, C++, Fortran

Matlab can be extremely fast if you are able to vectorize the code, but when you are faced with loops, executing many many times, Matlab code can be prohibitively slow. It is sometimes necessary, for the sake of speed, to write certain time intensive parts of a Matlab application in a low level language like C. Unfortunately, the process of interfacing with C, C++ and Fortran can be somewhat complicated. We explain here, how to write a simple C function and make it work in Matlab. For more detailed information consult the online documentation at http://www.mathworks.com/access/helpdesk/help/techdoc/matlab.html

We use the mex() function to compile C code for use in Matlab but we must first add the required components to the C source file itself. We import the mex library, which gives us access to various error checking and matrix creation utilities in C.

The gateway function must have the following definition:

void mexFunction(int nlhs, mxArray *plhs[],int nrhs, const mxArray*prhs[])

For an example, see yprime.c. For information on mxCreateDoubleMatrix and other related functions go to help -> contents -> Matlab -> C and Fortran API Reference

Mcc: Exporting Matlab Code to standalone code (requires compiler)

Matlab code can be exported as a stand-alone application or as a shared library for use in Excel, java, C, C++, or .NET applications. The standalone code needs the free Matlab Compile Runtime (MCR) environment. Thus, code that you write in Matlab can be distributed and used by users who do not have Matlab installed, or used inside of larger applications. Furthermore, deployed code is encrypted and thus protected should you not wish to make it open-source.

To create standalone code, you can either type mcc or launch the GUI by typing deploytool. Note that both of these methods require you buy the matlab compiler.

Emlmex: compiling to C for fixed memory functions (requires simulink)

In a certain restricted set of cases, we can compile Matlab m-code to C, for use within Matlab, improving speed. The compiler function is emlmex() and as above, it creates a mexw32 file. As long as this file is on the path, it shadows the original m-code function and is called in its place. The compiler is designed to produce embedded code and compiles functions that do not require any dynamic memory. Such code is extremely fast but requires that the type and size of all of the variables be pre-declared at compile time. This is quite a strong precondition; when it cannot be met, consider the previous approach, or try compiling in 'real time' as described below. The mex compiler must be first setup by following step one of the previous section.

Note that emlmex() is only available if you have either the simulink or fixed-point toolboxes installed.

emlmex() currently does not support: cell arrays, objects, sparse matrices, try/catch blocks, nested functions, matrix element deletion, variables that change size or type, and java.

You must include the following comment as the first line below the function header: %#eml. This affects the warning messages displayed in the editor.

Matlab is usually able to automatically infer the type and size of variables used. Sometimes, however, the assert() function must be used.

m = ones(3,3);                      % suppose this data is passed to the function.
assert(isa(m,'double'));            % declare the type
assert(all (size(m) == [3 3]));     % declare the size

Alternatively, the size and type of the input variables can be specified at compile time using the -eg switch. Below we compile LassoShootingFast, which is a coordinate ascent method for solving L1 regularized least squares, using the following sized of inputs

%emlmex('LassoShootingFast','-eg','{zeros(1000,16),zeros(1000,1),0,zeros(16,1)}');

We could also parameterize the dimensions as follows:

%n = 1000; d = 16;
%emlmex('LassoShootingFast','-eg',[' {zeros(',num2str(n),',',num2str(d),'),zeros(',num2str(n),',1),0,zeros(',num2str(d),',1)}']);

We can call the compiler using the above syntax within another parent function and have it determine the size of the inputs as it runs, before it compiles the subfunction. This gives us the flexibility of determining the input sizes at run time but the speed of a compiled subfunction. Matt Dunham wrote two functions to make this easier: compileAndRun, which compiles the function, calls it, then deletes it; and compileRunAndSave, which compiles the function (for a specific sized input), and saves it.

However, compilation can take a few seconds and so you must be sure that the gain obtained from compilation outweighs the overhead. Use the tic() and toc() functions to time your code both ways and compare. Moreover, compilation is only likely to speed up a function if it contains loops and executes a sufficiently large, (i.e. time consuming) chunk of code. It will not reduce the asymptotic running time of your algorithm and writing emlmex complaint code can be a tedious process; be sure its both possible and worth the effort before you begin. In the case of LassoShootingFast, however, compiling the function did result in code that was about 10 to 100 times faster.

If the m-file to be compiled calls additional functions, emlmex() tries to compile these as well unless they are first declared extrinsic with the command eml.extrinsic('myFunction')

Summary of Useful Functions

Published with MATLAB® 7.8