Search found 32 matches

by selfdestructo
Fri Apr 29, 2011 7:44 am
Forum: NEURON + Python
Topic: neuron.h.Vector() size argument has no effect
Replies: 4
Views: 2561

neuron.h.Vector() size argument has no effect

Hi, Consider the following Python function, looping over all sections of a morphology, creating membrane current recorders for all segments; def set_imem_recorders(self, tstopms): '''record membrane currents for all compartments''' self.memireclist = neuron.h.List() for sec in neuron.h.allseclist: f...
by selfdestructo
Thu Mar 03, 2011 4:00 am
Forum: NEURON + Python
Topic: Record i_membrane from extracellular in Python
Replies: 2
Views: 2559

Re: Record i_membrane from extracellular in Python

Thanks, that did the trick, so the following works: def set_imem_recorders(self, tstopms): '''record membrane currents for all compartments''' memireclist = self.h.List() for seg in self.h.allseclist: for sec in seg: memirec = self.h.Vector(size=tstopms/self.timeres_python+1) memirec.record(sec._ref...
by selfdestructo
Sun Feb 27, 2011 11:41 am
Forum: NEURON + Python
Topic: Record i_membrane from extracellular in Python
Replies: 2
Views: 2559

Record i_membrane from extracellular in Python

Hi, could use some help with recording float variables. I have some existing .hoc-code I want to transfer to Python; objref memirec,memireclist proc set_imem_recorders() { //Arguments: timeres_python, len(tvec) memireclist = new List() //records passive and capacitive currents forsec allseclist { fo...
by selfdestructo
Wed Dec 15, 2010 9:23 am
Forum: Other questions
Topic: SaveState.save() give segmentation fault
Replies: 4
Views: 1987

Re: SaveState.save() give segmentation fault

Hi again, I did some more testing, and the cause of the issue seem to be due to that I tried to use svstate.save() from the the main script/interpreter. It works for me now if the call to svstate.save() are done within the cell-class itself, not from the interpreter. Now, I only have to see if I can...
by selfdestructo
Wed Dec 15, 2010 5:44 am
Forum: Other questions
Topic: SaveState.save() give segmentation fault
Replies: 4
Views: 1987

Re: SaveState.save() give segmentation fault

A simple test of python + SaveState succeeded on my machine. Can you send me a zip file of all the mod, hoc, py files needed to exhibit the problem. Send to michael dot hines at yale dot edu. Also what version of NEURON are you using on your machine? Hi Michael, I'll see what I can do, as some of t...
by selfdestructo
Fri Dec 10, 2010 7:25 am
Forum: Other questions
Topic: SaveState.save() give segmentation fault
Replies: 4
Views: 1987

SaveState.save() give segmentation fault

Hi, I'm running i NEURON in Python 2.6.6 on OSX 10.6.5, importing neuron.h in a Python class object, 'cell', where cell.h = neuron.h, together with some custom hoc-codes and some mechanisms loaded by the cell-class (A bit too much to show here, unfortunately). I want to run some simulation for some ...
by selfdestructo
Tue Oct 19, 2010 7:33 am
Forum: Other questions
Topic: Reducing morphology (soma) complexity, how?
Replies: 3
Views: 1768

Re: Reducing morphology (soma) complexity, how?

I work with extracellular potential modeling from reconstructed neurons, and the thin cylindrical slabs that we get for multicompartment soma's, do not go well with the line-source approximation of Holt&Koch for the soma compartments. Really? Why? It's just that the line-source method assumes that ...
by selfdestructo
Mon Oct 18, 2010 4:09 am
Forum: Other questions
Topic: Reducing morphology (soma) complexity, how?
Replies: 3
Views: 1768

Reducing morphology (soma) complexity, how?

Hi! I'd just want to know if there exist a simple way of reducing morphology complexity using NEURON, either while converting from .swc- to .hoc-format, or after loading the .hoc-file I just created (redefining things). The reason is that for some morphologies I convert from neuromorpho.org, I end u...
by selfdestructo
Tue Jan 26, 2010 7:43 am
Forum: OS X
Topic: Trying to get python with OS X working
Replies: 2
Views: 4215

Re: Trying to get python with OS X working

I made this sh.-script some time ago to install neuron as python module on 64 bit python on mac os x 10.6. Use at your own risk. #!/bin/sh #Install Neuron with InterViews and nrnpython interphase #create a directory in home directory cd $HOME mkdir nrn64 cd nrn64 #removing old #sudo rm -r /Applicati...
by selfdestructo
Tue Oct 27, 2009 5:54 pm
Forum: OS X
Topic: building py-neuron module on 10.6 problem
Replies: 10
Views: 5111

Re: building py-neuron module on 10.6 problem

I finally had some success. I ended up using the as of today current source tar-balls. For future reference I think I used the following procedure; #building iv; tar xzf iv-17.tar.gz cd iv-17 sh build.sh ./configure --prefix=/Applications/NEURON-7.1/iv --enable-UniversalMacBinary make make install #...
by selfdestructo
Mon Oct 26, 2009 9:41 am
Forum: OS X
Topic: building py-neuron module on 10.6 problem
Replies: 10
Views: 5111

Re: building py-neuron module on 10.6 problem

Well, it turns out that I can compile Neuron with --with-iv by pointing it to the iv-folder included in the precompiled NEURON 7.0 package for OS X 10.4. For it to work, I had to copy the lib folder contained within umac, up in the iv-folder. It was not found otherwise. I tried the same with iv comp...
by selfdestructo
Sun Oct 25, 2009 3:48 pm
Forum: OS X
Topic: building py-neuron module on 10.6 problem
Replies: 10
Views: 5111

Re: building py-neuron module on 10.6 problem

Thanks, removing the lIVhines thing did it, a neuron module is found by Python. It will not load properly though; In [1]: import neuron /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/neuron/__init__.py:92: DeprecationWarning: BaseException.message has been deprecated a...
by selfdestructo
Sat Oct 24, 2009 3:26 pm
Forum: OS X
Topic: building py-neuron module on 10.6 problem
Replies: 10
Views: 5111

building py-neuron module on 10.6 problem

Hi! I'm trying to produce the neuron module for my native Python 2.6.3 installation on a macbook pro 15 with OS X 10.6 (Snow Leopard). I've installed XCode 3.2.1 (full install). I am working with the hg repositories of IV and NEURON. --enable-carbon with configure will not work for neither of these,...
by selfdestructo
Sat Oct 24, 2009 6:30 am
Forum: MSWin
Topic: Neuron as python module in windows 7
Replies: 15
Views: 17655

Re: Neuron as python module in windows 7

Could you share your win 7 experience with us. I want to know is there any performance improvement (running a neuron model) compared to win XP using win 7? win 7 32 bit or 64 bit? Can´t say much about NEURON performance in 7 vs XP in 32b vs 64b mode, as I´ve only used the OS´s on my old Dell Inspir...
by selfdestructo
Mon Oct 19, 2009 4:00 am
Forum: MSWin
Topic: Neuron as python module in windows 7
Replies: 15
Views: 17655

Re: Neuron as python module in windows 7

hines wrote:I installed the windows version of python-2.6.3 and don't see a problem with configure.
You might look at your config.log file to see precisely why it failed.
Yes, I did, didn't get any wiser, and concluded that my Cygwin-installation was to blame :) Thank you for your help!