Search found 41 matches

by sgratiy
Fri May 16, 2014 8:32 pm
Forum: Parallel NEURON
Topic: Saving vector at each time step - not associated with cell
Replies: 16
Views: 16681

Re: Saving vector at each time step - not associated with ce

Ted, your understanding is precisely correct about my plan for calculating the CSD. Althought I assume some symmetry about the cell distribution, so my CSD will vary along the depth of the cortex only. I am glad to know that the proc advanace() does exist and can be used. Looking forward to learning...
by sgratiy
Thu May 15, 2014 8:20 pm
Forum: Parallel NEURON
Topic: Saving vector at each time step - not associated with cell
Replies: 16
Views: 16681

Saving vector at each time step - not associated with cell

My model is run in parallel using python as interpreter. I need to save a vector of CSDs at every time step which results from summign currents for entire population of cells. So this vector is not a range variable and it is not associated with any particular cell. For serial implentation I used to ...
by sgratiy
Thu May 15, 2014 1:02 pm
Forum: NEURON + Python
Topic: Accessing segment area
Replies: 2
Views: 2088

Re: Accessing segment area

it works, thanks.
by sgratiy
Tue May 13, 2014 6:53 pm
Forum: NEURON + Python
Topic: Accessing segment area
Replies: 2
Views: 2088

Accessing segment area

How can I access the segment area form Python? For example, I have a hoc objet L2_PC[0] and the the following does not work >>> h.L2_PC[0].dend[14](0.1).area Traceback (most recent call last): File "stdin", line 1, in <module> AttributeError: 'nrn.Segment' object has no attribute 'area' I thought th...
by sgratiy
Tue May 13, 2014 3:41 pm
Forum: NEURON + Python
Topic: Accessing all sections of a particular cell from a list
Replies: 1
Views: 2357

Accessing all sections of a particular cell from a list

I have a python class which defines the population via a list class PL2PC: def __init__(self, morph_fname, n_cells): self.cell = [] for ic in range(0,n_cells): self.cell.append(h.L2_PC(morph_fname)) First question: Is this the proper way of defining a list of cells? Now the main question: I want to ...
by sgratiy
Thu May 08, 2014 7:02 pm
Forum: NEURON + Python
Topic: Cannot access range variable from external mechanism
Replies: 2
Views: 1956

Cannot access range variable from external mechanism

I have problems with accessing a range variable defined in the custom mechanism when using python as a interpreter. However, when working directly in neuron I have no problem: I create a cell object L2_BC[0] from class where I insert a custom mechanism xtra.mod (see at the end of file for the code) ...
by sgratiy
Fri Apr 13, 2012 3:28 pm
Forum: Getting started
Topic: Exporting vectors to .dat file afte each time step
Replies: 5
Views: 3545

Re: Exporting vectors to .dat file afte each time step

It looks like I was too quick to declare a victory. I am having issues with specifying the proper output format such that it would not stick adjacent elements in the vector together in the ASCII file. I have written the following 'save_results' procedure which prints each raw vector from the list at...
by sgratiy
Wed Apr 11, 2012 2:05 pm
Forum: Other questions
Topic: future development of the NEURON
Replies: 1
Views: 1292

future development of the NEURON

I am curious, what is the planned future for the NEURON? Are there new versions to be expected? Perhaps, new GUI?

Thanks
by sgratiy
Tue Apr 10, 2012 7:55 pm
Forum: The GUI
Topic: Shape plot does not reload properly
Replies: 4
Views: 7506

Re: Shape plot does not reload properly

Since I did not get the reply to the last question, I figured that I must have asked for something too obvious. So I did figure out the colormap thing on my own. In case someone else needs to specify a custom colormap, you can use similar definition immediately after psh_v = new PlotShape(0) psh_v.c...
by sgratiy
Mon Apr 09, 2012 5:03 pm
Forum: The GUI
Topic: Shape plot does not reload properly
Replies: 4
Views: 7506

Re: Shape plot does not reload properly

Ted, thanks for such a detailed response. I have looked at your code and used the .exec_menu("Show Diam") and .exec_menu("Shape Plot") commands to "activate" the desired Shape Plot features. It works! Perhaps, the next version of NEURON should include .exec_menu statements when saving Shape Plots in...
by sgratiy
Thu Apr 05, 2012 6:38 pm
Forum: The GUI
Topic: Shape plot does not reload properly
Replies: 4
Views: 7506

Shape plot does not reload properly

I created the Shape plot of transmembrane voltage with specified custom variable scale and the specified "shape style". Then, I saved the session into the .ses file. However, upon reloading this .ses file the specified custom variable scale and the shape style are lost. The scale reverts back to [-8...
by sgratiy
Wed Apr 04, 2012 8:26 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Changing NEURON's default units
Replies: 2
Views: 1850

Re: Changing NEURON's default units

Ted, thanks for a quick response. This is a very nice and cleaver solution to my problem. However, I decided that since the units of distributed current and conductance cannot be easily changed throughout the NEURON, it would be best to avoid introducing custom units for some currents. Future user o...
by sgratiy
Wed Apr 04, 2012 8:00 pm
Forum: Getting started
Topic: Exporting vectors to .dat file afte each time step
Replies: 5
Views: 3545

Re: Exporting vectors to .dat file afte each time step

Thanks Ted, I followed your suggestions to use List and the custom myrun() procedure. Very elegant indeed.
by sgratiy
Tue Apr 03, 2012 5:41 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Changing NEURON's default units
Replies: 2
Views: 1850

Changing NEURON's default units

It seems that the NMODL allows to change some units but not the other. I have read the units tutorial http://www.neuron.yale.edu/neuron/static/docs/units/units.html but I am still confused. For instance, I was able to changed the units of conductance g to (mS/cm2), however, I cannot change the units...