Search found 178 matches

by ramcdougal
Tue Jan 03, 2017 10:25 am
Forum: NEURON + Python
Topic: Beginner needs help: Questions arise from tutorials
Replies: 5
Views: 10151

Re: Beginner needs help: Questions arise from tutorials

From the path adjustment: sys.path.append('/Applications/NEURON-7.3/nrn/lib/python') I gather you're running NEURON 7.3 on a Mac. Unless you have a strong reason for using 7.3 try updating to 7.4 (the current release version), and tell us if the problem persists. If so: what version of Python are yo...
by ramcdougal
Thu Sep 29, 2016 12:00 pm
Forum: NEURON + Python
Topic: Python object as argument of hoc function
Replies: 4
Views: 10919

Re: Python object as argument of hoc function

Object arguments (doesn't matter if HOC objects or Python objects) to HOC functions are accessed using positional notation with $o instead of just $. e.g. $o1 instead of $1. A complete example, where for laziness I define the HOC function via h(): from neuron import h # declare a HOC function that j...
by ramcdougal
Fri Jun 10, 2016 9:41 am
Forum: Employment and educational opportunities
Topic: Postdoc Postion: Multiscale Modeling Methods & Simulator Dev
Replies: 0
Views: 15682

Postdoc Postion: Multiscale Modeling Methods & Simulator Dev

Mosaic Multiscale Modeling Postdoctoral Fellowship available for combining cell biology (reaction-diffusion) and electrophysiology in the NEURON simulator (neuron.yale.edu). The position involves an unusual mix of software engineering and science, depending on the candidate’s background and interest...
by ramcdougal
Fri May 20, 2016 2:51 pm
Forum: NEURON + Python
Topic: Guidance on plotting cell's geometry in Python?
Replies: 4
Views: 7541

Re: Guidance on plotting cell's geometry in Python?

where I expect methods to be associated with the section objects and instead they're accessed through the hoc object (my terminology here might be wrong). Is there some guiding rule as to why this is the case? This is a legacy artifact of NEURON's transition from a HOC-based interface which did not...
by ramcdougal
Fri May 20, 2016 9:08 am
Forum: NEURON + Python
Topic: import swc file for network simulation
Replies: 2
Views: 8656

Re: import swc file for network simulation

For an example addressing both (1) and (2), see the load_swc function in https://github.com/ahwillia/PyNeuron-Toolbox/blob/master/PyNeuronToolbox/morphology.py You linked to a prior thread about using SWC morphologies. Remember Ted's cautions : always check the morphology to make sure it is reasonab...
by ramcdougal
Thu May 05, 2016 10:32 am
Forum: NEURON + Python
Topic: AP propagates too slow
Replies: 7
Views: 5860

Re: AP propagates too slow

To set the temperature via Python:

Code: Select all

h.celsius = 20
With important exceptions, the Python interface is essentially the same as the HOC interface, but prefaced with an "h."
by ramcdougal
Mon May 02, 2016 4:38 pm
Forum: UNIX/Linux
Topic: Issue compiling ...geometry3d/surfaces.cpp NEURON v7.4
Replies: 3
Views: 10066

Re: Issue compiling ...geometry3d/surfaces.cpp NEURON v7.4

Here's a patch that fixes the issue present when compiling with newer versions of cython: it changes the tuple position into a list. diff -r b8295be34ae5 share/lib/python/neuron/rxd/geometry3d/surfaces.pyx --- a/share/lib/python/neuron/rxd/geometry3d/surfaces.pyx Mon May 02 14:29:44 2016 +0200 +++ b...
by ramcdougal
Sat Apr 30, 2016 9:27 am
Forum: NEURON + Python
Topic: AP propagates too slow
Replies: 7
Views: 5860

Re: AP propagates too slow

Is the morphology (in particular, the diameter) the same?
by ramcdougal
Tue Apr 26, 2016 3:41 pm
Forum: NEURON + Python
Topic: Export a subset of loaded morphology
Replies: 3
Views: 5632

Re: Export a subset of loaded morphology

Almost. In my example, parent is the index of the parent section; parent_loc is the normalized position within that section. Thus: parent_sec = sec_list[sd['parent']] # not parent_loc, grab from sec_list not sec sec.connect(parent_sec(sd['parent_loc']), sd['section_orientation']) This last line is i...
by ramcdougal
Tue Apr 26, 2016 10:31 am
Forum: NEURON + Python
Topic: Export a subset of loaded morphology
Replies: 3
Views: 5632

Re: Export a subset of loaded morphology

To the best of my knowledge, there is no built-in 1-line solution, but: The key functions and classes are h.parent_connection , h.section_orientation , and h.SectionRef . It's a little tricky to do this right because of the distinction between a "true parent" and a mere "parent". There are two funct...
by ramcdougal
Fri Mar 11, 2016 6:00 pm
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 12080

Re: Neuron as a Python Module Redux

Try permanently setting the PATH environment variable for the system instead of through the command line. (See below.) In addition, make sure you are using the 32 bit NEURON to match your 32 bit Python. For completeness, I just tried the following on a machine starting from no OS, and it worked: Ins...
by ramcdougal
Sat Mar 05, 2016 10:59 am
Forum: MSWin
Topic: Neuron as a Python Module Redux
Replies: 8
Views: 12080

Re: Neuron as a Python Module Redux

Open a DOS prompt (cmd) and try running: set PATH=c:\nrn\bin;%PATH% Then (in the same window), type "python" and "import neuron". Does that work? If so, you can make the change permanent by adding c:\nrn\bin to the PATH environment variable; instructions are available here and elsewhere. A similar p...
by ramcdougal
Wed Dec 30, 2015 10:40 pm
Forum: Reaction-diffusion in NEURON
Topic: calcium diffusion in different shells
Replies: 8
Views: 7339

Re: calcium diffusion in different shells

You are right that cai as defined in those models is not the average calcium concentration. That is by design. cai and cao are the two calcium concentrations made available to ion channel, pump, etc mechanisms defined in NMODL via USEION. As such, they are the concentrations that the mechanism can "...
by ramcdougal
Fri Oct 02, 2015 11:07 am
Forum: NEURON + Python
Topic: Problem with hclass in NEURON 7.4
Replies: 5
Views: 2306

Re: Problem with hclass in NEURON 7.4

One more change should fix that, this time in share/lib/python/neuron/__init__.py : Replace the __new__ method (starts at line 168) with def __new__(cls, *args, **kwds): kwds2 = {'hocbase': cls.htype} if 'sec' in kwds: kwds2['sec'] = kwds['sec'] return hoc.HocObject.__new__(cls, *args, **kwds2) (Dep...
by ramcdougal
Thu Oct 01, 2015 11:40 am
Forum: NEURON + Python
Topic: Problem with hclass in NEURON 7.4
Replies: 5
Views: 2306

Re: Problem with hclass in NEURON 7.4

Sorry about that; ironically, this was caused by an attempt to improve error checking in the hocobj_call function. A fix is to add the line: PyDict_DelItemString(kwds, "hocbase"); at line 182 in src/nrnpython/nrnpy_hoc.cpp (right before the call to hocobj_call). We'll try to update the repository so...