Search found 97 matches

by eacheon
Fri May 25, 2007 2:14 pm
Forum: NEURON + Python
Topic: Using nrniv with IPython
Replies: 10
Views: 10194

Re: NEURON as a python module

emuller wrote:Are plans to eventually provide neuron as a python module?

i.e:

ipython -pylab

>>> import nrn
>>> ...

What would be the limitations, if any, in taking this route?

cheers,

Eilif
would an nrn.load_dll(path_to_so) be provided so external mechanisms can be loaded?
by eacheon
Sun May 13, 2007 3:02 pm
Forum: NEURON + Python
Topic: Tip of the day
Replies: 11
Views: 11169

eacheon wrote:Nice job, Micheal! You did it so fast!

May I ask why you are reluctant to numpy dependency? My guess is every one is going to use numpy with NEURON so there should not be a dependency issue.
I am sorry, Micheal. I realized you meant the "build dependency"...
by eacheon
Thu May 10, 2007 3:16 am
Forum: NEURON + Python
Topic: Using nrniv with IPython
Replies: 10
Views: 10194

Seems r1729 of NEURON fixed this. I had difficulty building r17: gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21) /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I...
by eacheon
Wed May 09, 2007 11:30 pm
Forum: NEURON + Python
Topic: Using nrniv with IPython
Replies: 10
Views: 10194

I had difficulty building r17: gcc version 4.1.2 20061115 (prerelease) (Debian 4.1.1-21) /bin/bash ../../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/oc -I../../src/parallel -I../../src/nrnjava -I../../src/nrncvode -I../../src/ivos -I../../src/sundials -I. -I../../src...
by eacheon
Wed May 09, 2007 3:41 pm
Forum: NEURON + Python
Topic: Using nrniv with IPython
Replies: 10
Views: 10194

As Micheal pointed out, doNotify() need to be called periodically in a separate thread to make mainmenu reacting to GUI operations. IPython is doing similar things to GTK, Qt GUIs, but it is said to do it via python binding of those toolkits. Does anyone know of existence of an Interview python bind...
by eacheon
Wed May 09, 2007 8:11 am
Forum: NEURON + Python
Topic: Tip of the day
Replies: 11
Views: 11169

Nice job, Micheal! You did it so fast! May I ask why you are reluctant to numpy dependency? My guess is every one is going to use numpy with NEURON so there should not be a dependency issue. At the same time I am not aware python has a way (with standard library) to represent a double vector. Numpy ...
by eacheon
Tue May 08, 2007 6:33 pm
Forum: NEURON + Python
Topic: Tip of the day
Replies: 11
Views: 11169

If I can get the Vectors into python efficiently, I'll switch to python. Do you have a good way to manage to getting hoc's Vectors into python?
by eacheon
Sun May 06, 2007 11:50 pm
Forum: Getting started
Topic: Multiple simulation control
Replies: 4
Views: 4179

An idiom for exploring parameter space is proc explore_params() { local working working = 1 while (working==1) { working = new_params(args2) adjust_params() custom_init() continuerun(tstop) postprocess() savetofiles() } } explore_params(args1) where --new_params() is a function that generates a new...
by eacheon
Sat May 05, 2007 12:40 pm
Forum: Getting started
Topic: NetCon.event not working for me
Replies: 3
Views: 3925

Good question. Your code executes nc.event when the file is first parsed. However, when you initialize, the event is discarded. To quote from 8.2 Basic initialization in NEURON: finitialize() on page 185 of The NEURON Book: Basic initialization in NEURON . . . carries out several actions: 1. t is s...
by eacheon
Sat May 05, 2007 6:18 am
Forum: Getting started
Topic: NetCon.event not working for me
Replies: 3
Views: 3925

NetCon.event not working for me

Hello, NetCon.event doesn't work for me, could you run the following little script and tell me what's wrong with it? When I hit the "init and run" button, there's no synaptic events at 2.5 ms as I expected ... loaderr = load_file("nrngui.hoc") proc morpho_passive_init () { nseg = 1 diam = 20 L = 20 ...
by eacheon
Sun Apr 15, 2007 4:45 pm
Forum: Getting started
Topic: SectionList more methods?
Replies: 1
Views: 2677

SectionList more methods?

Hi, I am wondering are more methods planned to be added into SectionList? Say, supporting intersect operation of 2 sectionLists etc... Right now I find myself always doing something like: objref intersec_seclist intersec_seclist = new SectionList() forsec seclist1 { ifsec seclist2 intersec_seclist.a...
by eacheon
Fri Apr 13, 2007 4:03 pm
Forum: Other questions
Topic: how to read from, and record data into binary files?
Replies: 7
Views: 10318

Re: combining datatypes in binary file

I want to include metadata about the vectors I'm writing to a binary file. Can I include information like descriptions of the experiment, type of data(voltage, conductance, current), location of the recording, etc. for each vector? The corollary of this is would be can I use fread in matlab to read...
by eacheon
Wed Mar 14, 2007 1:13 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Assertion failed: file exp2synT.c, line 249
Replies: 1
Views: 2468

Re: Assertion failed: file exp2synT.c, line 249

Hello, I am getting this error message: Assertion failed: file exp2synT.c, line 249 /home/me/nrn59/nrn/i686/bin/nrniv: _tsav <= t near line 0 during running of my model. The mechanism exp2synT.mod used has the following in its NET_RECEIVE block: NET_RECEIVE(weight (uS)) { VERBATIM fprintf(stderr, "...
by eacheon
Wed Mar 14, 2007 12:49 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Assertion failed: file exp2synT.c, line 249
Replies: 1
Views: 2468

Assertion failed: file exp2synT.c, line 249

Hello, I am getting this error message: Assertion failed: file exp2synT.c, line 249 /home/me/nrn59/nrn/i686/bin/nrniv: _tsav <= t near line 0 during running of my model. The mechanism exp2synT.mod used has the following in its NET_RECEIVE block: NET_RECEIVE(weight (uS)) { VERBATIM fprintf(stderr, "_...
by eacheon
Sun Dec 10, 2006 6:11 pm
Forum: Parallel NEURON
Topic: How to write a parallel FitnessPrimitive
Replies: 5
Views: 12741

I am also interested in parallelized fitting even with only one generator. I have one Multiple Run Fitter as my generator. It tooks minutes to finish one run of the model, I hope this can somehow be improved by rewriting some of my code so when I click on "|| Optimize", NEURON could distribute some ...