Re: Python from Matlab (was: *cochlea*: inner ear models in Python) (Jan Schnupp )

Subject: Re: Python from Matlab (was: *cochlea*: inner ear models in Python)
From:    Jan Schnupp  <jan.schnupp@xxxxxxxx>
Date:    Fri, 22 Aug 2014 12:47:12 +0100

Hi Alain, "calling" python from matlab is easy (as you are probably aware, you can all anything from Matlab using the dos() function, and I often conjure up little python helpers from matlab in this way). The hard part is shifting data between python and matlab in a way that is efficient, elegant and easy to implement, and which works on UNIX based systems as well as on Windows (i.e. no proprietary OLE). You can always hack together a kludge that writes temporary binary files in one environment and reads it in the other (which is what I tend to do), but that is inelegant and has nontrivial overheads. Or you could python and matlab work together on some sort of client/server model. That would be more elegant - the matlab and python parts then wouldn't even have to be on the same machine, but the programming investment is very large. I don't know of any developments to make this sort of stuff easier that are even on the distant horizon. If other list members know of any I would be interested to hear about them. Cheers, J On 22 August 2014 08:44, Alain de Cheveigne <> wrote: > Hi Marek, > > I am looking for the opposite: an easy, efficient and reliable way to call Python from Matlab. My programming environment nowdays is matlab and I can't easily change. The best course that I see is to implement new code in Python and call it from matlab, and make the switch to Python when Python code reaches critical mass. I suspect many people are in a similar position. > > Alain > > > > On 21 Aug 2014, at 11:20, Marek Rudnicki <marek.rudnicki@xxxxxxxx> wrote: > >> Etienne Gaudrain <e.p.c.gaudrain@xxxxxxxx> writes: >> >>> Dear Marek, >>> >>> This looks very promising, I'm glad to finally see the first signs of a >>> shift from Matlab to Python. Thanks a lot for sharing this!! >> >> Dear Etienne >> >> I'm glad you like it. >> >> BTW, if you still have some MATLAB legacy code that you would like to >> use in Python, then matlab_wrapper [1] could be helpful. It allows you >> to call MATLAB functions directly from Python environment (the MATLAB >> process is started in the background), e.g.: >> >> matlab.workspace.sin([0.1, 0.2, 0.3]) >> >> >> Cheers >> Marek >> >> >> [1] >> >> >> >>> On 19/08/2014 14:50, Marek Rudnicki wrote: >>>> Hi all, >>>> >>>> we would like to announce *cochlea* -- a collection of inner ear >>>> models in Python. It was developed in the group of Werner Hemmert [1] >>>> at the Technische Universit√§t M√ľnchen. After a few years of >>>> development, we decided that it is stable and would like to contribute >>>> it to the auditory community. >>>> >>>> >>>> >>>> The main features of the package are: >>>> >>>> - simple to use (each model is implemented as a single Python >>>> function: sound in, spikes out) >>>> - fast (you can generate responses of hundreds or even thousands of >>>> nerve fibers) >>>> - all models have the same interface (easy to make comparisons and >>>> pick the one that best suits your needs) >>>> - up-to-date (recent models included) >>>> >>>> >>>> >>>> Currently implemented models are: >>>> >>>> - Zilany, M. S., Bruce, I. C., & Carney, L. H. (2014). Updated >>>> parameters and expanded simulation options for a model of the >>>> auditory periphery. The Journal of the Acoustical Society of >>>> America, 135(1), 283-286. >>>> - Zilany, M. S., Bruce, I. C., Nelson, P. C., & Carney, >>>> L. H. (2009). A phenomenological model of the synapse between the >>>> inner hair cell and auditory nerve: long-term adaptation with >>>> power-law dynamics. The Journal of the Acoustical Society of >>>> America, 126(5), 2390-2412. >>>> - Holmberg, M. (2007). Speech Encoding in the Human Auditory >>>> Periphery: Modeling and Quantitative Assessment by Means of >>>> Automatic Speech Recognition. PhD thesis, Technical University >>>> Darmstadt. >>>> - MATLAB Auditory Periphery by Meddis et al. (external model, not >>>> implemented in the package, but easily accessible through >>>> matlab_wrapper). >>>> >>>> >>>> >>>> We are really grateful to the authors of those models for allowing us >>>> to use their code it in *cochlea*. We release the package under the >>>> GNU General Public License, so that you are free to copy, use and >>>> modify the code. We also encourage you to contribute back your >>>> changes. >>>> >>>> >>>> The code is distributed on GitHub [2] and the package/documentation >>>> are hosted on the Python Package Index [3]. Check also our demo [4]! >>>> >>>> >>>> If you would like to give a feedback, have questions or found some >>>> problem, do not hesitate to email me or open an issue on GitHub [2]. >>>> >>>> >>>> Thank you and best regards >>>> Marek Rudnicki >>>> >>>> >>>> [1] >>>> [2] >>>> [3] >>>> [4] -- Prof Jan Schnupp University of Oxford Dept. of Physiology, Anatomy and Genetics Sherrington Building - Parks Road Oxford OX1 3PT - UK +44-1865-282012

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Electrical Engineering Dept., Columbia University