Search found 1691 matches

by hines
Wed May 08, 2024 8:43 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 1345

Re: Show Diameter

The above fragments are incomplete and I can't reproduce the figure. Can you send me a zip file with all necessary files and instructions for running?
Please send to Michael.hines@yale.edu
by hines
Thu Apr 25, 2024 6:44 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 1546

Re: Recording variables from ARTIFICIAL_CELL

I'll try to make an example to show the problem.
I'll be interested to see the example.
by hines
Thu Apr 25, 2024 5:09 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 1546

Re: Recording variables from ARTIFICIAL_CELL

I applied the pull request change above to the 8.2 branch (for a future 8.2.5 release) and observe better performance than the master (probably due to ARTIFICIAL_CELLS having better performance when the memory layout is "Array of Structures" rather than the newer "Structure of Array&q...
by hines
Thu Apr 25, 2024 4:04 pm
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 1546

Re: Recording variables from ARTIFICIAL_CELL

I've started a pull request https://github.com/neuronsimulator/nrn/pull/2858 . For now, you can work around the "Optional first arg is not a POINT_PROCESS" error by using hpc.nthread(1) or else creating a section for each thread and putting a POINT_PROCESS in the middle of each Section. On...
by hines
Thu Apr 25, 2024 11:38 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Recording variables from ARTIFICIAL_CELL
Replies: 14
Views: 1546

Re: Recording variables from ARTIFICIAL_CELL

First, it seems to me to be a mistake in the internal NEURON implementation that the following generates an error trec.record(wcs, h._ref_t) erec.record(wcs, wcs._ref_e) That is, I believe the thread that wcs (an ARTIFICIAL CELL) is in is definitely known just as any POINT_PROCESS. An extra section ...
by hines
Tue Apr 09, 2024 6:10 pm
Forum: NEURON + Python
Topic: Python Code Continues Execution Despite HOC Error
Replies: 4
Views: 697

Re: Python Code Continues Execution Despite HOC Error

when an error occurs in the HOC code during a simulation executed from Python, the execution should halt That is what is supposed to happen. Sorry, h('hoc code') does not raise an exception on a hoc error, it returns 0 on failure and 1 on success. It's behavior is similar to https://nrn.readthedocs...
by hines
Wed Apr 03, 2024 10:34 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 1345

Re: Show Diameter

Your example code above worked for me (after prefixing "from neuron import h"). The show diameter feature for pyplot is only available in version 9. For mac, linux you can pip install NEURON-nightly For windows the latest master build is (see the first master label at https://github.com/ne...
by hines
Wed Apr 03, 2024 8:20 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 1345

Re: Show Diameter

After looking around a bit in the github history for nrn, my first impression is that show diameter is supposed to work with plotly. I.e. https://github.com/neuronsimulator/nrn/pull/2404 at the end of June 2023 with the same mode call as works for InterViews GUI PlotShape. After some experimenting, ...
by hines
Tue Apr 02, 2024 11:49 am
Forum: NEURON + Python
Topic: Python Code Continues Execution Despite HOC Error
Replies: 4
Views: 697

Re: Python Code Continues Execution Despite HOC Error

when an error occurs in the HOC code during a simulation executed from Python, the execution should halt That is what is supposed to happen. What kind of computer are you using and what is the NEURON version. A short example would be helpful. E.g. from neuron import h h(''' proc test() { print 1/0 ...
by hines
Tue Apr 02, 2024 11:38 am
Forum: Other questions
Topic: Show Diameter
Replies: 8
Views: 1345

Re: Show Diameter

ps.show(1) At least for the classical InterViews nrn gui, the diameter is shown when the arg to show is 0. (as specified in https://nrn.readthedocs.io/en/8.2.3/python/visualization/shape.html#Shape.show ) Often times, the neurites ar so slender compared to length, it is not easy to see the diameter...
by hines
Thu Feb 22, 2024 9:35 am
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 3485

Re: can't open DISPLAY

A terminal window does open but does not offer a prompt for commands: The launch mechanism dates back to Macos 9. I never learned xcode sufficiently to bring it into the 21st century. Anyway, double clicking on nrngui.app after a few intermediate steps ultimately starts a terminal window that execu...
by hines
Thu Feb 22, 2024 6:44 am
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 3485

Re: can't open DISPLAY

That's great progress. Sadly, I don't know how to diagnose issues at the DISPLAY level of XQuartz so am at a loss as to how to extend the working behavior to launching by double clicking the app icons. When the app icon is launched, does a terminal window pop up? And is the value of DISPLAY in that ...
by hines
Tue Feb 20, 2024 4:54 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 3485

Re: can't open DISPLAY

Yes. The graphics work when nrngui is launched from an xterm. (the xterm was launched from a terminal window)
by hines
Tue Feb 20, 2024 1:42 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 3485

Re: can't open DISPLAY

After installing Sonoma, neurondemo started from a terminal and the graphics works. I do see the <stdin>:149: SyntaxWarning: invalid escape sequence '\.' <stdin>:197: SyntaxWarning: invalid escape sequence '\.' oc> and will try to trace that down. But it does not seem related to the GUI issue. In my...
by hines
Tue Feb 20, 2024 12:46 pm
Forum: OS X
Topic: can't open DISPLAY
Replies: 14
Views: 3485

Re: can't open DISPLAY

I have an Apple M1 Ventura 13.6, xquartz 2.8.5, and a bunch of pythons including python-3.12.2. I'll upgrade to Sonoma 14.3.1 and see what happens.