Search found 81 matches

by patoorio
Wed Sep 04, 2013 8:39 am
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

the export command is a UNIX command not working on WIN Exactly!! As I told you, you have to open a bash command window (A *NIX-like environment that gets installed with neuron, part of MinGW), issue the export commands and run pyhton (or spyder!) from there; then you will be able to import neuron....
by patoorio
Tue Sep 03, 2013 8:22 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

For environment variable in WIN environment variable editor I used NEURONHOME C:\nrn73w64 PYTHONPATH C:\nrn73w64\lib\python You don't have to do it in the Windows environment variables, instead (or in addition to??) you have to do export NEURONHOME /c/nrn73w64 export PYTHONPATH /c/nrn73w64/lib/pyth...
by patoorio
Fri Aug 09, 2013 10:07 am
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

Thanks!
by patoorio
Sat Aug 03, 2013 10:45 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

Hi, The as_numpy() function is giving an error: >>> from neuron import h Unable to load 'mpich2nemesis.dll', error 126 NEURON -- Release 7.3 (901:c736db45853d) 2013-06-29 Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013 See http://www.neuron.yale.edu/neuron/credits >>> vec=h.Vector(10) >...
by patoorio
Wed Jul 31, 2013 9:47 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

It's working!!
The best part is that I can even call spyder from the bash shell and then import neuron. Mods compiled with mknrndll are correctly imported also. I haven't actually run any simulation yet, but be sure that I'll let you know if anything doesnt go as expected.

Thanks a lot.
by patoorio
Thu Jul 18, 2013 4:43 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

Well, I'm still not getting it. With Neuron 7.3 x64, I get the 'no module named hoc' error, unless I add c:\nrn73x64\bin64 to PYTHONPATH as well. It also works to copy hoc.pyd to the c:\nrn73x64\lib\python\neuron folder. In either case, however I get the following error: 'DLL load error: hoc.pyd is ...
by patoorio
Fri Jul 05, 2013 9:18 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

you can extend Python xy with NEURON (but not use any interviews gui) if you install http://www.neuron.yale.edu/ftp/neuron/versions/v7.3/nrn-7.3.x86_64-w64-mingw32-setup.exe and then set the environment variables mentioned in the 16May2012 12:21 post above. Well, I took some time before trying (act...
by patoorio
Sun Jun 30, 2013 3:26 pm
Forum: Other questions
Topic: Cannot use continuous play with Dt?
Replies: 2
Views: 1206

Re: Cannot use continuous play with Dt?

Thanks for the answer!
Yes, it's easy to make a vector; I just wanted to know if the behavior was 'bug or feature'.

Regards
by patoorio
Thu Jun 27, 2013 11:49 am
Forum: Other questions
Topic: Cannot use continuous play with Dt?
Replies: 2
Views: 1206

Cannot use continuous play with Dt?

Hi, The following simple code is giving me a Segmentation fault at init(): load_file("nrngui.hoc") create soma access soma insert hh objref celsiusvec,timevec celsiusvec=new Vector(10) celsiusvec.fill(20) for (i=0;i<=8;i=i+2) {celsiusvec.x[i]=18} tstop = celsiusvec.size()*1000 celsiusvec.play(&celsi...
by patoorio
Mon Jun 03, 2013 12:41 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

Oh, I can see... and I fully understand!
But this is about the GUI, right?
What about version 7.3? Is there anything I can do about it? (compile, etc.?)
by patoorio
Sun Jun 02, 2013 3:14 pm
Forum: MSWin
Topic: Neuron as Python module in Win (again)
Replies: 37
Views: 32350

Re: Neuron as Python module in Win (again)

Hi, I could make it work under Win 8 x64, with the latest Python x,y. However there are two issues: 1) The Neuron version installed by pip is 7.2, not (yet?) 7.3. I really need 7.3 because I'm making use of the as_numpy() function. Will it be updated anytime? Is there anything I can do to help? 2) G...
by patoorio
Fri May 03, 2013 3:30 pm
Forum: NEURON + Python
Topic: array of point processes
Replies: 5
Views: 3799

Re: array of point processes

You are right.
Thanks!

EDIT: And it's waaay much faster!!!
by patoorio
Fri May 03, 2013 10:46 am
Forum: NEURON + Python
Topic: using neuron.h.Graph() through python
Replies: 9
Views: 5617

Re: using neuron.h.Graph() through python

Solved by adding

Code: Select all

h.graphList[0].append(g)
That worked for me.

Also, the behavior of the plot is better if I use

Code: Select all

g.size(0,h.tstop,-80,40)
In this way the time scale will adjust automatically as tstop is changed.

Regards
by patoorio
Fri May 03, 2013 9:13 am
Forum: NEURON + Python
Topic: array of point processes
Replies: 5
Views: 3799

Re: array of point processes

Thank you, Ted! Indeed the lists are very straightforward in pyhton and much similar to the neuron code. I'll also keep lists in mind when doing something similar in hoc again. About your final comment, I thought of that, and my first thought would be that it should be the same. But I had a second t...
by patoorio
Thu May 02, 2013 1:17 pm
Forum: NEURON + Python
Topic: array of point processes
Replies: 5
Views: 3799

array of point processes

Hi, I'm starting to figure out how to do some things in neuron+python. However, I'm kind of new to python yet and I have a (probably) basic question: How do I translate a code like the following into python? objref GABAinp[N_in], GABApre[N_in], GABAconn[N_in] for ii= 0,N_in-1 { GABAinp[ii] = new Exp...