I would like to call a matlab function from mathematica. How best to do that?
I have found an ancient post on Wolfram site describing a way to do this, is this still the way to connect the two?
You can try NETLink for this at least under Windows:
In[1]:= Needs["NETLink`"]
matlab = CreateCOMObject["matlab.application"]
Out[2]= «NETObject[COMInterface[MLApp.DIMLApp]]»
And then you can invoke Matlab functions:
In[4]:= matlab#Execute["version"]
Out[4]= "
ans =
7.9.0.529 (R2009b)
"
In[5]:= matlab#Execute["a=2"]
matlab#Execute["a*2"]
Out[5]= "
a =
2
"
Out[6]= "
ans =
4
"
HTH
You can use mEngine. The precompiled Windows MathLink executable works with Mathematica 8. On Windows you may need to add MATLAB to the system path.
The advantage of this compared to the NETLink method is that transferring variables between Mathematica and MATLAB will be as easy as mGet["x"] or mPut["x"]. Although this might be possible with NETLink too, the advantage of mEngine is that you don't need to implement it yourself (which is great if like me you don't know anything about COM or .NET)
I would imagine that this is a difficult problem in general, but can be easily solved with a little programming for a particular case. I'll demonstrate with C#.
I would build a string of calls, like so.
Mathematica calls a C# program, through MathLink. This is near trivial to setup, and Mathematica has a sample project in Mathematica\8.0\SystemFiles\Links\NETLink directory.
C# program calls Matlab. There are several ways to make this call, and this handy link describes how to do it and offers sample code.
C# program returns Matlab results.
All in all I could do this in less than 50 lines of C# code, for a specific problem. Not too much work, in other words. Possible problems are data conversion, but if you want to send back and forth arrays of data, MathLink offers a lot out of the box. Similarly Mathematica can be linked to MATLAB through Java, though I haven't done that myself.
Perhaps the easiest connection could be made through Python. Mathematica offers an installable MathLink python library, located at Mathematica\8.0\SystemFiles\Links\NETLink, and Matlab has an addon library called PyMat, which can be downloaded here, but this package hasn't been maintained for a long time and supports only the most ancient of Matlabs.
Alternatively you can forgo Matlab altogether in favor of SAGE and/or numpy.
There is now a new package for this --- MATLink. It is the most complete such package I am aware of. (Disclaimer: I'm one of the developers of MATLink.)
MATLink lets you ...
seamlessly call MATLAB functions form Mathematica
transfer data between the two systems
Most MATLAB data types are supported, including sparse arrays, structs and cells.
A more complete description is available here. For detailed examples, see the website.
Related
I'm looking for a tool to convert a SBML model into a Matlab function. I've tried SBMLTranslate() function from libSBML but this returns a Matlab struct, not a function. Does anybody know if such tool exists? Thanks
There are at least three efforts in this direction:
Frank Bergmann offers an online service for SBML translation where you can upload an SBML file and it will generate a MATLAB file. The comments at the top of the generated MATLAB file explain how to use the results. The C++ source code is available on SourceForge.
Bergmann's code referenced above was used by Stanley Gu to create sbml2matlab, a Windows standalone program. Off-hand, I don't know whether Gu's version changed or enhanced the algorithm used by the Bergmann version, but it seems likely. (Note: Gu now works at Google and does not maintain this code anymore, as far as I know.)
The Systems Biology Format Converter (SBFC) is a framework written principally by Nicolas Rodriguez; it includes a collection of converters, one of which is an SBML-to-MATLAB converter. This converter is written in Java.
I have not compared the results of the translators myself yet, so cannot speak to the differences or quality of output. If you try them and have any feedback to relate, please let the authors know. Knowing what has or hasn't worked for real users will help improve things in the future.
A final caveat is that all of these have been research projects, so make sure to set your expectations accordingly. (This is not a criticism of the authors; the authors are very good – I know most of them personally – but the reality of academic development work is that we all lack the time and resources to make these systems comprehensive, hardened, polished, and documented to the degree that we wish we could.)
I'm looking for a function in Julia to estimate coefficients for an ARMA process.
For example using the Prediction Error Model as pem and armax in Matlab (part of system identification toolbox) do. pem documentation and armax documentation.
I've looked at the following packages, but can't see that they do what I'm looking for:
TimeSeries.jl
TimeModels.jl
One solution is of course to use Matlab.jl and use the Matlab functions, but I was hoping to do it all in Julia.
If there isn't anything right now, does anyone know of if there are any good Julia functions for multidimensional numerical minimisation (like Newton-Raphson), that can be used for implementing a PEM function?
UPDATE: I've just pushed a module to github called RARIMA.jl. This module can be used to estimate, forecast, and simulate ARIMA models (of which ARMA is a special case). Some of the functions are implemented in Julia, others (particularly estimation) call equivalent R functions using the RCall package which you will need to install and verify it works prior to using RARIMA. The package isn't officially registered (yet), so Pkg.add("RARIMA") won't work for now. If you want to use RARIMA, instead try Pkg.clone("https://github.com/colintbowers/RARIMA.jl"). If this fails, you can file an issue on the repository github page, but be sure to check RCall is installed and working before doing this. Cheers, I'll come back and update here if/when the package is officially registered.
ORIGINAL ANSWER: I just had a glance at the source, and TimeModels does not appear to have any functionality for estimating ARIMA models, although does have one function for simulating them. Given time though, I suspect this will be the package that deals with ARIMA modelling. The TimeSeries package is more about building the object type TimeSeries rather than implementing time series models, so I would be surprised if ARIMA modelling is ever merged into that package.
As near as I can tell, at this point if you want a fully functioning ARIMA package you'll need to use Matlab or R. The R one is very good (see the forecast package written by Rob Hyndman - it is very nice) and is probably easier to interface with from Julia than the Matlab option. Of course, the other option is to start it yourself and merge the code with the TimeModels package :-)
In terms of optimization procedures, Julia has a fair few that are written in Julia, and can be found under the JuliaOpt umbrella. The Optim package in particular is quite popular and well developed. However, most of the people I know who are really into this stuff use NLOpt which is a free open source library callable from many languages (including Julia). I have heard nothing but good things about this library from people who tend to work with this stuff 24/7.
I would like to know which programming languages can be called by matlab.
for example I am quiet sure that matlab can use C function and maybe java.
I need this stuff for an industrial project so I need something that works well.
For example I have found some tutorial to call python function in matlab but they look to me not very good and stable solution.
I am not an expert of the field and my knowledge of matlab is very limited. So please be patience with the answer.
This project is related to machine learning and the software will probably run on a cluster.
EDIT according to this post Embedding Python in MATLAB seems that there are problem when importing numpy using python.
The only reason to use python in this environment is the numpy library.
Without that it is almost useless to me.
Do you think that I will encounter similar problem using java or c calling some mathematics libraries?
Most interfaces are listed here:
http://www.mathworks.de/de/help/matlab/external-interfaces.html
For Python I see different solutions:
COM on Windows platforms. This requires to register an application, check if this is possible and allowed on the cluster.
XMLRPC or SOAP. You may need to use Java-Classes in Matlab, but as you already realised this is very simple. Verify that the cluster has a Java VM available, many run matlab without java.
You can embed python code into c, which allows you to write mex functions which run c code: http://docs.python.org/2/extending/embedding.html
Use the command line interface for python.
Besides the documented limitations, I don't see any problem with these solution. If you are familiar with C or Matlab, I would choose the second or third option. This allows you to write a wrapper to access python with a very fundamental knowledge of matlab.
There are two main methods to achieve this:
Write MEX functions, which is basically C/C++ or Fortran methods, which use Matlab-specific API. You can then call these methods like you would any function written in M-language file. This is described here.
Call external libraries written in Java, .Net, C/C++, and COM servers. This is described here.
Both methods require good understanding of what you are doing, although I would argue that writing MEX function is much harder then referencing an existing library.
I'm not sure about programming language but You can do it by EXE file by running run('C:\someCompiledProgram.exe')
And if you need result you can use:
[status, result] = system('command')
You can read about it here:
http://nf.nci.org.au/facilities/software/Matlab/techdoc/ref/system.html
A friend of mine needs to implement some statistical calculations in hardware.
She wants it to be accomplished using VHDL.
(cross my heart, I haven't written a line of code in VHDL and know nothing about its subtleties)
In particular, she needs a direct analogue of MATLAB's betainc function.
Is there a good package around for doing this?
Any hints on the implementation are also highly appreciated.
If it's not a good idea at all, please tell me about it as well.
Thanks a lot!
There isn't a core available that performs an incomplete beta function in the Xilinx toolset. I can't speak for the other toolsets available, although I would doubt that there is such a thing.
What Xilinx does offer is a set of signal processing blocks, like multipliers, adders and RAM Blocks (amongst other things, filters, FFTs), that can be used together to implement various custom signal transforms.
In order for this to be done, there needs to be a complete understanding of the inner workings of the transform to be applied.
A good first step is to implement the function "manually" in matlab as a proof of concept:
Instead of using the built-in function in matlab, your friend can try to implement the function just using fundamental operators like multipliers and adders.
The results can be compared with those produced by the built-in function for verification.
The concept can then be moved to VHDL using the building blocks that are provided.
Doing this for the incomplete beta function isn't something for the faint-hearted, but it can be done.
As far as I know there is no tool which allow interface of VHDL and matlab.
But interface of VHDL and C is fairly easy, so if you can implement your code(MATLAB's betainc function) in C then it can be done easily with FLI(foreign language interface).
If you are using modelsim below link can be helpful.
link
First of all a word of warning, if you haven't done any VHDL/FPGA work before, this is probably not the best place to start. With VHDL (and other HDL languages) you are basically describing hardware, rather than a sequential line of commands to execute on a processor (as you are with C/C++, etc.). You thus need a completely different skill- and mind-set when doing FPGA-development. Just because something can be written in VHDL, it doesn't mean that it actually can work in an FPGA chip (that it is synthesizable).
With that said, Xilinx (one of the major manufacturers of FPGA chips and development tools) does provide the System Generator package, which interfaces with Matlab and can automatically generate code for FPGA chips from this. I haven't used it myself, so I'm not at all sure if it's usable in your friend's case - but it's probably a good place to start.
The System Generator User guide (link is on the previously linked page) also provides a short introduction to FPGA chips in general, and in the context of using it with Matlab.
You COULD write it yourself. However, the incomplete beta function is an integral. For many values of the parameters (as long as both are greater than 1) it is fairly well behaved. However, when either parameter is less than 1, a singularity arises at an endpoint, making the problem a bit nasty. The point is, don't write it yourself unless you have a solid background in numerical analysis.
Anyway, there are surely many versions in C available. Netlib must have something, or look in Numerical Recipes. Or compile it from MATLAB. Then link it in as nav_jan suggests.
As an alternative to VHDL, you could use MyHDL to write and test your beta function - that can produce synthesisable (ie. can go into an FPGA chip) VHDL (or Verilog as you wish) out of the back end.
MyHDL is an extra set of modules on top of Python which allow hardware to be modelled, verified and generated. Python will be a much more familiar environment to write validation code in than VHDL (which is missing many of the abstract data types you might take for granted in a programming language).
The code under test will still have to be written with a "hardware mindset", but that is usually a smaller piece of code than the test environment, so in some ways less hassle than figuring out how to work around the verification limitations of VHDL.
I have the problem, that I have to access a funktion form a dll in matlab/Simulink in the rtw.
This should work with a s function, but I have the needed parameters in a array of structures organized.
The question is now how I can reach them when I want to call my DLL function?
Or is there a better way (e.g. level 2 Matlab files or something similar)?
The pure simulation (without RTW) worked pretty well with level 2 m files but I am not able to write a tlc file for compiling them. I did not find much on the net and the documentation only about C sources.
Thanks
Christian
For signals in Simulink, what you are asking for is an array of buses. There is similar support for using arrays of structs for parameters. For calling an external function, you might want to look at the legacy code tool. You might also be able to use the MATLAB function block to call your external dll.
In addition to what #MikeT says:
Generating code from Level 2 M-S-Functions is problematic. Read this: http://www.mathworks.co.uk/help/toolbox/simulink/sfg/f7-67622.html#brgscav-1
Also, M-S-functions are generally slow, because they run in the MATLAB interpreter: http://blogs.mathworks.com/seth/2010/10/28/tips-for-simulation-performance/
In the end I coded the problem in C and used an array where I defined to order of the elements. Then I wrote some interface functions to access this "virtual" struct.
This is not very good coding but the easiest way I have found and it is portable.
Thanks