Search found 65 matches

by mattions
Sun Jul 15, 2012 2:36 pm
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 10725

Re: Model (hoc file), plotting output in Python

Well there are three more things, which are also written in the paper, which are: 1. the integration with ModelDB, which makes super easy to download, compile and run any model which has been uploaded to ModelDB. If the model provides a mosinit, it just runs out of the box 2. The integration with ma...
by mattions
Wed Jul 11, 2012 12:43 pm
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 10725

Re: Model (hoc file), plotting output in Python

I guess it's mostly correct.

One more diff is that in Neuronvisio the zooming is controlled with the wheel of the mouse, in the shape plot the user needs to select it.
Another one is that Shape Plot is a lot faster than Neuronvisio, however the rendering is not as nice as Neuronvisio.
by mattions
Wed Jul 11, 2012 11:24 am
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 10725

Re: Model (hoc file), plotting output in Python

Hi Ted, as I said I wrote Neuronvisio during my PhD because I had to deal with very tiny spines, and I wanted to see exactly where they were placed. The shape plot from NEURON was able to give a good rough idea, but I need the ability to click on a section to inspect what was the name and the conduc...
by mattions
Wed Jul 11, 2012 6:29 am
Forum: NEURON + Python
Topic: Model (hoc file), plotting output in Python
Replies: 15
Views: 10725

Re: Model (hoc file), plotting output in Python

just want to highlight two points for future reference: - the url for Neuronvisio is http://neuronvisio.org - Neuronvisio does not exclude the ability to NEURON gui at the same time you use Neuronvisio. infact it is possible to load Neuronvisio and Neuron gui at the same time with from neuron import...
by mattions
Tue Apr 24, 2012 3:28 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 10690

Re: Driving synaptic event using vecStim

The problem is tVec does not exist anymore outside the loop, therefore one solution is to create a vector list and add the vectors as you create them. vecStimList = [neuron.h.VecStim() for src in spikeSoures] tVecList = [] # List to hold the Vectors for i, vecStim in enumerate(vecStimList): t = what...
by mattions
Thu Nov 24, 2011 11:05 am
Forum: NEURON + Python
Topic: Saving the integration of Neuron at certain time
Replies: 2
Views: 1487

Re: Saving the integration of Neuron at certain time

Hi Ted,

it does exactly what I need.
Thank you a lot!

Pretty powerful method :)
by mattions
Wed Nov 23, 2011 12:27 pm
Forum: NEURON + Python
Topic: Saving the integration of Neuron at certain time
Replies: 2
Views: 1487

Saving the integration of Neuron at certain time

Hello everyone. Is it possible to save the status of the integration, or to get the integrator to go back in time and restart from a certain time? What I would like to do is to advance neuron till a certain time (let's say t=4) and then have the possibility to go back to t=3 and restart again from t...
by mattions
Tue May 17, 2011 8:42 am
Forum: UNIX/Linux
Topic: Neuron on Ubuntu Natty 11.04
Replies: 2
Views: 2067

Re: Neuron on Ubuntu Natty 11.04

Actually I found out that the problem was a folder with root permission. Deleting the repo and clining again fixed the compilation. Installing the python instead was a bit more tricky. I have no idea why, but using the classic ./configure (no prefix) the python module is installed in two different l...
by mattions
Mon May 16, 2011 12:06 pm
Forum: UNIX/Linux
Topic: Neuron on Ubuntu Natty 11.04
Replies: 2
Views: 2067

Neuron on Ubuntu Natty 11.04

Dear all, I'm trying to install NEURON on the latest ubuntu (11.04) but I run into trouble. This is the error: make[3]: Leaving directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn/src/oc' Making all in nrnoc make[3]: Entering directory `/home/mattions/Work/progs/neuron/neuron-hg/nrn/src/nrnoc'...
by mattions
Fri Jan 14, 2011 10:37 am
Forum: NEURON + Python
Topic: to_python() causes big memory problems
Replies: 8
Views: 5143

Re: to_python() causes big memory problems

hines wrote: ...
The to_python and from_python stil exist but are more or less obsolete since better idioms are now
v = h.Vector(numpy_array)
v = h.Vector(python_list)
python_list = list(v)
numpy_array = numpy.array(v)
...
So it's ok to use it?
by mattions
Fri Jan 14, 2011 6:27 am
Forum: NEURON + Python
Topic: to_python() causes big memory problems
Replies: 8
Views: 5143

Re: to_python() causes big memory problems

If to_python() is deprecated, which inplace operation I can use to move from one HocVector to a numpy array?
by mattions
Fri Dec 10, 2010 12:29 pm
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 10690

Re: Driving synaptic event using vecStim

What is an invalid spike time? There are some times that are not valid? I'm trying those time: 155 160 165 170 175 They are in ms. So the first event should be at 155 ms followed by other 4. I'm switching from NetSource to a VecStim because I need to run event in precomputed time, which are not poss...
by mattions
Fri Dec 10, 2010 6:25 am
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 10690

Re: Driving synaptic event using vecStim

Thanks for the hints Actually I found out that the NetCon weight was zero, the AMPA gbar by default was too small. This works: from neuron import h import neuron.gui soma = h.Section(name='soma') soma.insert('hh') ampa = h.AMPA(0.5, sec=soma) ampa.gbar = 1 # Just increasing, for testing purpose vecS...
by mattions
Thu Dec 09, 2010 5:49 pm
Forum: NEURON + Python
Topic: Driving synaptic event using vecStim
Replies: 21
Views: 10690

Driving synaptic event using vecStim

Dear all, I'm trying to delivery synaptic input at fixed time to a vecevent mod from Neuron example, but with no effect. This is the testcase I'm using to experiment this feature: from neuron import h import neuron.gui soma = h.Section(name='soma') ampa = h.AMPA(0.5, sec=soma) soma.insert('hh') vecS...
by mattions
Thu Jul 15, 2010 4:48 am
Forum: Parallel NEURON
Topic: Activating multithreading from python code
Replies: 1
Views: 1224

Activating multithreading from python code

Dear all, I'm trying to obtain the same effect which I can have using the ParallelComputeTool from NEURON gui through python code: This is what I'm doing: from neuron import h soma = h.Section(name='soma') h.load_file('parcom.hoc') p = h.ParallelComputeTool() p.nthread(4) p.multisplit(True) I think ...