Subject: Re: *cochlea*: inner ear models in Python From: Nima Maftoon <n_maftoon@xxxxxxxx> Date: Fri, 22 Aug 2014 07:30:25 -0700 List-Archive:<http://lists.mcgill.ca/scripts/wa.exe?LIST=AUDITORY>--1261493821-1065867848-1408717825=:73956 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello Marek,=0A=0ANice to see this. Keep up the great work.=0A=0ANima=0A=0A= =0A=0A________________________________=0A From: Marek Rudnicki <marek.rudni= cki@xxxxxxxx>=0ATo: AUDITORY@xxxxxxxx =0ASent: Thursday, August 21, 20= 14 5:20:58 AM=0ASubject: Re: *cochlea*: inner ear models in Python=0A =0A= =0AEtienne Gaudrain <e.p.c.gaudrain@xxxxxxxx> writes:=0A=0A> Dear Marek,=0A>= =0A> This looks very promising, I'm glad to finally see the first signs of = a=0A> shift from Matlab to Python. Thanks a lot for sharing this!!=0A=0ADea= r Etienne=0A=0AI'm glad you like it.=0A=0ABTW, if you still have some MATLA= B legacy code that you would like to=0Ause in Python, then matlab_wrapper [= 1] could be helpful.=A0 It allows you=0Ato call MATLAB functions directly f= rom Python environment (the MATLAB=0Aprocess is started in the background),= e.g.:=0A=0Amatlab.workspace.sin([0.1, 0.2, 0.3])=0A=0A=0ACheers=0AMarek=0A= =0A=0A[1] https://github.com/mrkrd/matlab_wrapper=0A=0A=0A=0A> On 19/08/201= 4 14:50, Marek Rudnicki wrote:=0A>> Hi all,=0A>>=0A>> we would like to anno= unce *cochlea* -- a collection of inner ear=0A>> models in Python.=A0 It wa= s developed in the group of Werner Hemmert [1]=0A>> at the Technische Unive= rsit=E4t M=FCnchen.=A0 After a few years of=0A>> development, we decided th= at it is stable and would like to contribute=0A>> it to the auditory commun= ity.=0A>>=0A>>=0A>>=0A>> The main features of the package are:=0A>>=0A>>=A0= =A0 - simple to use (each model is implemented as a single Python=0A>>=A0 = =A0 =A0 function: sound in, spikes out)=0A>>=A0 =A0 - fast (you can generat= e responses of hundreds or even thousands of=0A>>=A0 =A0 =A0 nerve fibers)= =0A>>=A0 =A0 - all models have the same interface (easy to make comparisons= and=0A>>=A0 =A0 =A0 pick the one that best suits your needs)=0A>>=A0 =A0 -= up-to-date (recent models included)=0A>>=0A>>=0A>>=0A>> Currently implemen= ted models are:=0A>>=0A>>=A0 =A0 - Zilany, M. S., Bruce, I. C., & Carney, L= . H. (2014). Updated=0A>>=A0 =A0 =A0 parameters and expanded simulation opt= ions for a model of the=0A>>=A0 =A0 =A0 auditory periphery. The Journal of = the Acoustical Society of=0A>>=A0 =A0 =A0 America, 135(1), 283-286.=0A>>=A0= =A0 - Zilany, M. S., Bruce, I. C., Nelson, P. C., & Carney,=0A>>=A0 =A0 = =A0 L. H. (2009). A phenomenological model of the synapse between the=0A>>= =A0 =A0 =A0 inner hair cell and auditory nerve: long-term adaptation with= =0A>>=A0 =A0 =A0 power-law dynamics. The Journal of the Acoustical Society = of=0A>>=A0 =A0 =A0 America, 126(5), 2390-2412.=0A>>=A0 =A0 - Holmberg, M. (= 2007). Speech Encoding in the Human Auditory=0A>>=A0 =A0 =A0 Periphery: Mod= eling and Quantitative Assessment by Means of=0A>>=A0 =A0 =A0 Automatic Spe= ech Recognition. PhD thesis, Technical University=0A>>=A0 =A0 =A0 Darmstadt= .=0A>>=A0 =A0 - MATLAB Auditory Periphery by Meddis et al. (external model,= not=0A>>=A0 =A0 =A0 implemented in the package, but easily accessible thro= ugh=0A>>=A0 =A0 =A0 matlab_wrapper).=0A>>=0A>>=0A>>=0A>> We are really grat= eful to the authors of those models for allowing us=0A>> to use their code = it in *cochlea*.=A0 We release the package under the=0A>> GNU General Publi= c License, so that you are free to copy, use and=0A>> modify the code.=A0 W= e also encourage you to contribute back your=0A>> changes.=0A>>=0A>>=0A>> T= he code is distributed on GitHub [2] and the package/documentation=0A>> are= hosted on the Python Package Index [3].=A0 Check also our demo [4]!=0A>>= =0A>>=0A>> If you would like to give a feedback, have questions or found so= me=0A>> problem, do not hesitate to email me or open an issue on GitHub [2]= .=0A>>=0A>>=0A>> Thank you and best regards=0A>> Marek Rudnicki=0A>>=0A>>= =0A>> [1] http://www.imetum.tum.de/research/bai/home/?L=3D1=0A>> [2] https:= //github.com/mrkrd/cochlea=0A>> [3] https://pythonhosted.org/cochlea/=0A>> = [4] http://nbviewer.ipython.org/github/mrkrd/cochlea/blob/master/examples/c= ochlea_demo.ipynb --1261493821-1065867848-1408717825=:73956 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable <html><body><div style=3D"color:#000; background-color:#fff; font-family:He= lveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;fo= nt-size:10pt"><div><span>Hello Marek,</span></div><div style=3D"color: rgb(= 0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,H= elvetica,Arial,Lucida Grande,sans-serif; background-color: transparent; fon= t-style: normal;"><br><span></span></div><div style=3D"color: rgb(0, 0, 0);= font-size: 13.3333px; font-family: HelveticaNeue,Helvetica Neue,Helvetica,= Arial,Lucida Grande,sans-serif; background-color: transparent; font-style: = normal;"><span>Nice to see this. Keep up the great work.</span></div><div s= tyle=3D"color: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNe= ue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-colo= r: transparent; font-style: normal;"><br><span></span></div><div style=3D"c= olor: rgb(0, 0, 0); font-size: 13.3333px; font-family: HelveticaNeue,Helvet= ica Neue,Helvetica,Arial,Lucida Grande,sans-serif; background-color: transpare= nt; font-style: normal;"><span>Nima</span></div><div><br></div> <div style= =3D"font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Gr= ande, sans-serif; font-size: 10pt;"> <div style=3D"font-family: HelveticaNe= ue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size:= 12pt;"> <div dir=3D"ltr"> <hr size=3D"1"> <font face=3D"Arial" size=3D"2"= > <b><span style=3D"font-weight:bold;">From:</span></b> Marek Rudnicki <= marek.rudnicki@xxxxxxxx><br> <b><span style=3D"font-weight: bold;">To:</sp= an></b> AUDITORY@xxxxxxxx <br> <b><span style=3D"font-weight: bold;"= >Sent:</span></b> Thursday, August 21, 2014 5:20:58 AM<br> <b><span style= =3D"font-weight: bold;">Subject:</span></b> Re: *cochlea*: inner ear models= in Python<br> </font> </div> <div class=3D"y_msg_container"><br>Etienne Ga= udrain <<a ymailto=3D"mailto:e.p.c.gaudrain@xxxxxxxx" href=3D"mailto:e.p.c.gaudrain@xxxxxxxx">e.p.c.gaudrain@xxxxxxxx</a>> writ= es:<br><br>> Dear Marek,<br>><br>> This looks very promising, I'm = glad to finally see the first signs of a<br>> shift from Matlab to Pytho= n. Thanks a lot for sharing this!!<br><br>Dear Etienne<br><br>I'm glad you = like it.<br><br>BTW, if you still have some MATLAB legacy code that you wou= ld like to<br>use in Python, then matlab_wrapper [1] could be helpful. = ; It allows you<br>to call MATLAB functions directly from Python environmen= t (the MATLAB<br>process is started in the background), e.g.:<br><br>matlab= .workspace.sin([0.1, 0.2, 0.3])<br><br><br>Cheers<br>Marek<br><br><br>[1] <= a href=3D"https://github.com/mrkrd/matlab_wrapper" target=3D"_blank">https:= //github.com/mrkrd/matlab_wrapper</a><br><br><br><br>> On 19/08/2014 14:= 50, Marek Rudnicki wrote:<br>>> Hi all,<br>>><br>>> we wo= uld like to announce *cochlea* -- a collection of inner ear<br>>> models in Python. It was developed in the group of Werner Hemmert [1= ]<br>>> at the Technische Universit=E4t M=FCnchen. After a few = years of<br>>> development, we decided that it is stable and would li= ke to contribute<br>>> it to the auditory community.<br>>><br>&= gt;><br>>><br>>> The main features of the package are:<br>&g= t;><br>>> - simple to use (each model is implemented = as a single Python<br>>> function: sound in, spik= es out)<br>>> - fast (you can generate responses of hund= reds or even thousands of<br>>> nerve fibers)<br>= >> - all models have the same interface (easy to make co= mparisons and<br>>> pick the one that best suits = your needs)<br>>> - up-to-date (recent models included)<= br>>><br>>><br>>><br>>> Currently implemented models are:<br>>><br>>> - Zilany, M. S., Bruce, I= . C., & Carney, L. H. (2014). Updated<br>>> p= arameters and expanded simulation options for a model of the<br>>>&nb= sp; auditory periphery. The Journal of the Acoustical Society= of<br>>> America, 135(1), 283-286.<br>>>&n= bsp; - Zilany, M. S., Bruce, I. C., Nelson, P. C., & Carney,<br>= >> L. H. (2009). A phenomenological model of the = synapse between the<br>>> inner hair cell and aud= itory nerve: long-term adaptation with<br>>> powe= r-law dynamics. The Journal of the Acoustical Society of<br>>> = America, 126(5), 2390-2412.<br>>> - Holmbe= rg, M. (2007). Speech Encoding in the Human Auditory<br>>> &nbs= p; Periphery: Modeling and Quantitative Assessment by Means of<br>>> Automatic Speech Recognition. PhD thesi= s, Technical University<br>>> Darmstadt.<br>>&= gt; - MATLAB Auditory Periphery by Meddis et al. (external mod= el, not<br>>> implemented in the package, but eas= ily accessible through<br>>> matlab_wrapper).<br>= >><br>>><br>>><br>>> We are really grateful to the = authors of those models for allowing us<br>>> to use their code it in= *cochlea*. We release the package under the<br>>> GNU General = Public License, so that you are free to copy, use and<br>>> modify th= e code. We also encourage you to contribute back your<br>>> cha= nges.<br>>><br>>><br>>> The code is distributed on GitHub= [2] and the package/documentation<br>>> are hosted on the Python Pac= kage Index [3]. Check also our demo [4]!<br>>><br>>><br>>> If you would like to give a feedb= ack, have questions or found some<br>>> problem, do not hesitate to e= mail me or open an issue on GitHub [2].<br>>><br>>><br>>>= Thank you and best regards<br>>> Marek Rudnicki<br>>><br>>&= gt;<br>>> [1] <a href=3D"http://www.imetum.tum.de/research/bai/home/?= L=3D1" target=3D"_blank">http://www.imetum.tum.de/research/bai/home/?L=3D1<= /a><br>>> [2] <a href=3D"https://github.com/mrkrd/cochlea" target=3D"= _blank">https://github.com/mrkrd/cochlea</a><br>>> [3] <a href=3D"htt= ps://pythonhosted.org/cochlea/" target=3D"_blank">https://pythonhosted.org/= cochlea/</a><br>>> [4] <a href=3D"http://nbviewer.ipython.org/github/= mrkrd/cochlea/blob/master/examples/cochlea_demo.ipynb" target=3D"_blank">ht= tp://nbviewer.ipython.org/github/mrkrd/cochlea/blob/master/examples/cochlea= _demo.ipynb</a><br><br></div> </div> </div> </div></body></html> --1261493821-1065867848-1408717825=:73956--