Search found 74 matches
- Thu Apr 19, 2012 1:49 pm
- Forum: NEURON + Python
- Topic: Section creation
- Replies: 2
- Views: 2799
Re: Section creation
A general idiom for Python cell objects is: from neuron import h class Cell(object): def __init__(self): self.soma = h.Section(name='soma', cell=self) The "cell=self" tells NEURON what Python object this section belongs to. To be honest, I'm not sure if it is really required or poses a pro...
- Thu Apr 05, 2012 12:58 pm
- Forum: Parallel NEURON
- Topic: Splitbit value assignment
- Replies: 2
- Views: 3220
Re: Splitbit value assignment
Thanks for the interest in our model. Basically, our mitral cell is split into three parts: 1) the central Tuft, primary dendrite, soma and axon, 2) left dendrite, 3) right dendrite. Each part must have a unique GID. This is our hashing function to map these sections to GIDs. We could have made a sc...
- Thu May 12, 2011 11:09 am
- Forum: OS X
- Topic: command not found
- Replies: 10
- Views: 12505
Re: command not found
You can download Xcode 3.2.6 for free at http://developer.apple.com/devcenter/mac/index.action. Following the Apple's nickel-and-diming way of getting rich, Xcode 4 requires a free developer registration followed by a $5 download from the App Store.
- Wed Apr 20, 2011 10:33 am
- Forum: OS X
- Topic: installation of NEURON on snow leopard 64 bits
- Replies: 1
- Views: 2848
Re: installation of NEURON on snow leopard 64 bits
You might try this recipe:
viewtopic.php?f=2&t=2191
It uses the Enthought Distribution of Python, which includes scipy....
viewtopic.php?f=2&t=2191
It uses the Enthought Distribution of Python, which includes scipy....
- Fri Mar 25, 2011 4:00 pm
- Forum: NEURON + Python
- Topic: FInitializeHandler example in Python
- Replies: 1
- Views: 2604
FInitializeHandler example in Python
I rewrote the FInitializerHandler example from the hoc reference for python. I had gotten hung up on trying to pass the function as a string to FInitializerHandler(). Turns out you pass the reference.... from neuron import h as nrn nrn.load_file("nrngui.hoc") def fi0(): global a print &quo...
- Tue Mar 08, 2011 9:20 am
- Forum: NEURON + Python
- Topic: Method for moving IClamp
- Replies: 6
- Views: 5354
Re: Method for moving IClamp
Simply using loc() uses the currently accessed section and not the section that the element was placed on. You can do this more explicitly as
Code: Select all
stim.loc(sec(x))
- Tue Feb 01, 2011 11:13 am
- Forum: NEURON + Python
- Topic: Neuron with Enthought Python on Snow Leopard
- Replies: 0
- Views: 4570
Neuron with Enthought Python on Snow Leopard
I have been working with installing NEURON under Enthought Python Distributions. Here is a general recipe for a 32-bit compile: IDIR=${HOME}/neuron IVDIR=iv_epd32 NRNDIR=nrn_epd32 hg clone http://www.neuron.yale.edu/hg/neuron/iv $IVDIR hg clone http://www.neuron.yale.edu/hg/neuron/nrn $NRNDIR cd $IV...
- Fri Jan 07, 2011 3:28 pm
- Forum: NEURON + Python
- Topic: Parallel Neuron: NetCon failed to connect different hosts
- Replies: 4
- Views: 4141
Re: Parallel Neuron: NetCon failed to connect different hosts
Nice use of Sage, Jose! A couple of notes: The Sage worksheet is a bit problematic since the permissions do not allow you to write to the "data" folder from the mpiexec call. Even though the simulation.py file is in the data folder and you can typically write new files there in python with...
- Fri Dec 03, 2010 9:50 am
- Forum: NEURON + Python
- Topic: inserting point process
- Replies: 1
- Views: 2118
Re: inserting point process
Pre is still the currently accessed section.
Try:
Try:
Code: Select all
from neuron import h
ampa=h.gluR(post(0.5))
h.psection(sec=post)
- Thu Dec 02, 2010 4:23 pm
- Forum: NEURON + Python
- Topic: diam(0:1) = A:B in Python
- Replies: 8
- Views: 7376
Re: diam(0:1) = A:B in Python
Good eye, Ted! I was coding what I thought Mike wanted. Here is a hoc equivalent, which is quite comparable to what he wrote before: import numpy from neuron import h as nrn from itertools import izip def taper_diam(sec,zero_bound,one_bound): dx = 1./sec.nseg for (seg, x) in izip(sec, numpy.arange(d...
- Thu Dec 02, 2010 2:19 pm
- Forum: NEURON + Python
- Topic: diam(0:1) = A:B in Python
- Replies: 8
- Views: 7376
Re: diam(0:1) = A:B in Python
This type of linear mapping can be easily handled with numpy's linspace. import numpy from neuron import h as nrn from itertools import izip def taper_diam(sec,zero_bound,one_bound): for (seg, d) in izip(sec, numpy.linspace(zero_bound, one_bound, sec.nseg)): seg.diam=d # Test dend = nrn.Section(name...
- Wed Dec 01, 2010 3:13 pm
- Forum: NEURON + Python
- Topic: More NEURON + Python resources
- Replies: 4
- Views: 31561
More NEURON + Python resources
Here is a list of Python resources with NEURON. Our Sage server equipped with NEURON is a nice resource for example code and recipes. It is a place to try NEURON and Python without installing either on your local machine. To use, visit https://nn.med.yale.edu:8000 and log in with a user id and passw...
- Wed Dec 01, 2010 2:34 pm
- Forum: NEURON + Python
- Topic: NEURON + Python SfN Tutorial Links
- Replies: 0
- Views: 3051
NEURON + Python SfN Tutorial Links
Below is a summary from the NEURON + Python tutorial at SfN. Unfortunately, attachments are not part of the bulletin board, so email me if you are interested in any of the slides. The seminar had two parts: low-level python code delivered by Tom McTavish and higher-level presentations by the other s...
- Tue Nov 09, 2010 3:24 pm
- Forum: NEURON + Python
- Topic: NEURON + Python hands-on tutorial, San Diego 2010
- Replies: 3
- Views: 6882
Re: NEURON + Python hands-on tutorial, San Diego 2010
The response to this seminar has been overwhelming and there are more people on the wait list than there are seats available. We will be placing the seminar materials on the NEURON forum after SfN. Additionally, I have two posters at SfN -- one educational poster Saturday and Sunday (#OOO43), which ...
- Fri Oct 29, 2010 3:18 pm
- Forum: NEURON + Python
- Topic: access the section after loading a morphology file
- Replies: 6
- Views: 5077
Re: access the section after loading a morphology file
the "for sec in h.allsec():" does the trick. Here is a loop that will make a list of tuples containing 3D points, the diameter, and the section name. points3d = [] for sec in h.allsec(): num_points = int(h.n3d()) # Get the number of 3D points in the section for i in range(num_points): x = ...