Search found 215 matches
- Wed Dec 30, 2020 5:24 pm
- Forum: NEURON + Python
- Topic: Record and fadvance instead of run
- Replies: 2
- Views: 211
Re: Record and fadvance instead of run
Vectors must be initialized after calling record before advancing . Your other code works with h.run() because a run is basically an h.finitialize(h.v_init) combined with an h.continuerun(h.tstop) . The solution is to declare your timeVector before the h.finitialize call, i.e. something like: timeV...
- Mon Jul 20, 2020 1:34 pm
- Forum: NEURON + Python
- Topic: color or color_list procedures in PlotShape
- Replies: 5
- Views: 715
Re: color or color_list procedures in PlotShape
Hmmm... looks like that example depends on a change introduced about a month ago... so it's available in the "pip install" version for mac/linux or the windows nightly build . (Don't try to pip install on Windows, that will give a VERY old version of NEURON.) Sorry about that. So I guess t...
- Tue Jul 07, 2020 4:48 pm
- Forum: NEURON + Python
- Topic: color or color_list procedures in PlotShape
- Replies: 5
- Views: 715
Re: color or color_list procedures in PlotShape
Unfortunately the .plot for both matplotlib and plotly (available in 8.0 development version) does not currently support the .color or .color_list values and instead always color based on the value of some variable (v, by default). (Note that you can use .mark as in the documentation to highlight sp...
- Mon Jul 06, 2020 9:28 am
- Forum: NEURON Announcements
- Topic: How to cite NEURON
- Replies: 2
- Views: 27068
Re: How to cite NEURON
Thanks for pointing this out.
The old link works now too.
The old link works now too.
- Mon Jun 29, 2020 12:38 pm
- Forum: NEURON + Python
- Topic: Error recording channel current by passing string to Vector.record
- Replies: 3
- Views: 600
Re: Error recording channel current by passing string to Vector.record
Python provides a standard way of using a string to grab a property, namely the getattr function. e.g. if you have a section called soma and you wanted to get a pointer to a specific variable var from the 0.5 location, you could do ptr = getattr(soma(0.5).hh, f'_ref_{var}') Similarly, a second getat...
- Mon Jun 29, 2020 10:32 am
- Forum: Reaction-diffusion in NEURON
- Topic: rxd.plugins interface in Neuron 7.7
- Replies: 2
- Views: 512
Re: rxd.plugins interface in Neuron 7.7
There was a significant revamp of the internals from 7.4 to 7.7 with the intent of speeding up calculations but it likely broke anything that depended on overriding internal functions. What kind of connections do you need? callbacks at each time step? reading and writing concentrations? do you need ...
- Sun Jun 07, 2020 5:46 pm
- Forum: UNIX/Linux
- Topic: .mod files compilation issues
- Replies: 4
- Views: 3467
Re: .mod files compilation issues
Why did you compile NEURON from source?
Do you get this problem if you use the version from
How are you compiling the mod files? The x86_64 should appear in whatever folder you run nrnivmodl from.
Do you get this problem if you use the version from
Code: Select all
pip install neuron
- Sun Jun 07, 2020 5:41 pm
- Forum: MSWin
- Topic: Windows 10, Permission Denied
- Replies: 1
- Views: 2160
Re: Windows 10, Permission Denied
You can't drop onto the main menu window directly, but I believe in Windows you can drop onto the icon . Three other options: (1) Select File - load hoc, change the filter from *.hoc to *.nrm, and then load your model that way. (2) type (using the correct filename): load_file("filename.nrm"...
- Mon Jun 01, 2020 1:44 pm
- Forum: OS X
- Topic: Syntax Warning
- Replies: 1
- Views: 1060
Re: Syntax Warning
This is harmless. You can ignore it. Even though you're not using Python explicitly, NEURON will connect to Python to have it available (and Python is needed to enable certain functions). What happened was there was something in the NEURON internals that did not raise a Python warning until a change...
- Mon Jun 01, 2020 1:35 pm
- Forum: Other questions
- Topic: loop structure
- Replies: 3
- Views: 869
Re: loop structure
You are creating a single file because your file creation is happening once, outside of the for loop. If you look at the Python example, you'll see I'm creating a new file every time with a different filename based on the trial number (trial0.csv, trial1.csv, trial2.csv, ...) You can generate filena...
- Sat May 23, 2020 12:22 pm
- Forum: Other questions
- Topic: loop structure
- Replies: 3
- Views: 869
Re: loop structure
Python, HOC, and most programming languages use a for loop to run the same code a fixed number of times. e.g. in Python, we'd write for trial in range(100): # do stuff here and in HOC, we might write: for (trial = 0; trial < 100; trial += 1) { // do stuff here } NEURON provides the h.Random (or just...
- Fri May 22, 2020 8:32 pm
- Forum: UNIX/Linux
- Topic: help installing on WSL
- Replies: 1
- Views: 597
Re: help installing on WSL
Simple work-around: don't compile NEURON yourself. :) BMTK supports all the way back to NEURON 7.4 which is almost 5 years old, and any guidance you're seeing about issues with NEURON and Anaconda (which we now explicitly suggest using in the NEURON quickstart guide ) pertains to old versions of NEU...
- Tue May 12, 2020 1:06 pm
- Forum: NEURON + Python
- Topic: range morphology and mechanism syntax for sections in python
- Replies: 9
- Views: 2298
Re: range morphology and mechanism syntax for sections in python
Oof. My mistake. Ted is right, of course. The key thing I was missing is that the values should be set based on the position of the center of the segment, which means that they must be strictly inside the interval specified. I was effectively interpolating from the center of the first segment to the...
- Tue May 12, 2020 9:08 am
- Forum: NEURON + Python
- Topic: range morphology and mechanism syntax for sections in python
- Replies: 9
- Views: 2298
Re: range morphology and mechanism syntax for sections in python
You'd have to do it with a for loop. Here's a generic function that does this for you: def range_assignment(sec, var, start, stop): """linearly assign values between start and stop to each segment.var in section""" import numpy as np for seg, val in zip(sec, np.linspace...
- Fri May 08, 2020 5:02 pm
- Forum: Other tools
- Topic: convergence failed repeatedly or with |h|=hmin : err=-7
- Replies: 1
- Views: 944
Re: convergence failed repeatedly or with |h|=hmin : err=-7
The integration advance failed, even when it tried using a really tiny timestep. One possible cause of this is when some of your state variables have found themselves in an invalid place. You could try reducing the atol to see if that helps, because it'll force the system to more carefully track val...