Search found 179 matches

by ramcdougal
Wed Feb 19, 2020 5:13 pm
Forum: UNIX/Linux
Topic: How do I collect data for plots without IV
Replies: 4
Views: 49

Re: How do I collect data for plots without IV

There's also a HOC version of the programmer's reference at: https://www.neuron.yale.edu/neuron/stat ... index.html
by ramcdougal
Wed Feb 05, 2020 9:32 am
Forum: Reaction-diffusion in NEURON
Topic: length scales and SparseEfficiencyWarning
Replies: 5
Views: 349

Re: length scales and SparseEfficiencyWarning

That's very weird because there's nothing wrong with h('{sw4=new PlotShape(0)}') by itself. There's no way there's a weird character in there, is there? (Non-breaking space, that sort of thing?) Otherwise, my guess is that something badly destabilized NEURON before you got that far. If you're willin...
by ramcdougal
Fri Jan 31, 2020 5:15 pm
Forum: NEURON + Python
Topic: For loop over section's segments in Python and HOC returns different values
Replies: 4
Views: 103

Re: For loop over section's segments in Python and HOC returns different values

Given that you're trying to make a Python version of the HOC... you could change the HOC to do it right using for (x,0), and then validate your Python against that.
by ramcdougal
Fri Jan 31, 2020 5:50 am
Forum: NEURON + Python
Topic: For loop over section's segments in Python and HOC returns different values
Replies: 4
Views: 103

Re: For loop over section's segments in Python and HOC returns different values

The short version, as you've figured out, is that your Python code and your HOC code are not equivalent ; they do different things, but both languages support both types of loops . Density mechanisms (like hh) exist on segments of positive surface area not on the 0 and 1 end points (which by definit...
by ramcdougal
Wed Jan 29, 2020 8:07 pm
Forum: NEURON + Python
Topic: Rset or reboot neuron without exist in python
Replies: 6
Views: 925

Re: Rset or reboot neuron without exist in python

h.finitialize() resets a model (if the mod files, etc were setup right) but it does not reset the simulator . importlib.reload will have no useful effect. It will not cause Sections to disappear, it will not reset the temperature, etc. It's basically only useful for modules that are themselves writ...
by ramcdougal
Wed Jan 29, 2020 12:31 am
Forum: Adding new mechanisms and functions to NEURON
Topic: Interfacing NEURON with other software on runtime
Replies: 4
Views: 147

Re: Interfacing NEURON with other software on runtime

Your specific code doesn't work because you are evaluating the function foo(ns) at the time of your callback (it returns None) and that's what's being set as your callback. (By the order of operations, we evaluate foo(ns) before calling set_callback.) You could fix this by passing in a lambda that e...
by ramcdougal
Fri Jan 17, 2020 9:00 am
Forum: NEURON + Python
Topic: Dynamically accessing vectors in python (_ref_x)
Replies: 5
Views: 155

Re: Dynamically accessing vectors in python (_ref_x)

Think of these things with [] as an array of sections; what that means is that the object you getattr is the array, not any individual section. i.e. do something like this: >>> from neuron import h >>> h('create axon[6]') 1 >>> getattr(h, 'axon')[5] axon[5] >>> sec = getattr(h, 'axon')[5] >>> ptr = ...
by ramcdougal
Tue Jan 14, 2020 4:41 pm
Forum: UNIX/Linux
Topic: Failed to run neuron inside virtual environment in Ubuntu18 with Anaconda (PATH issue?)
Replies: 2
Views: 186

Re: Failed to run neuron inside virtual environment in Ubuntu18 with Anaconda (PATH issue?)

Do you have root access? Assuming so, when you installed with dpkg, I believe you meant for PYTHONPATH to start with /usr/ not with /home/usr/ That worked for me in Ubuntu 19.04: (base) robert@robert-VirtualBox:~/anaconda3/envs/my_env$ cd (base) robert@robert-VirtualBox:~$ conda activate my_env (my_...
by ramcdougal
Mon Jan 13, 2020 2:00 pm
Forum: NEURON + Python
Topic: Dynamically accessing vectors in python (_ref_x)
Replies: 5
Views: 155

Re: Dynamically accessing vectors in python (_ref_x)

I believe you're looking for Python's getattr function: You can get a pointer to the membrane potential at the center of the soma via: ptr = getattr(soma(0.5), '_ref_v') (Here, I'm assuming "soma" is a Python Section object... adjust accordingly for HOC variables, which you can also get by name with...
by ramcdougal
Mon Jan 13, 2020 1:43 pm
Forum: NEURON + Python
Topic: different section names, morphology - h.Section
Replies: 2
Views: 103

Re: different section names, morphology - h.Section

Specify the name attribute when creating a section to give them meaningful names: soma = h.Section(name='soma') Specify both name and cell (and give the cell a reasonable __repr__) for meaningful dot notation: from neuron import h class MyCell: def __repr__(self): return 'MyCell[{}]'.format(self._id...
by ramcdougal
Mon Jan 13, 2020 12:39 pm
Forum: NEURON + Python
Topic: Finding middle of a section
Replies: 4
Views: 89

Re: Finding middle of a section

So it's best to call h.define_shape() preemptively, right after all sections have been created, connected, assigned their geometries via L and diam or pt3dadd statements, and their nseg parameters have been set. And after you do that, every section will have its own pt3d data that will include the ...
by ramcdougal
Mon Jan 13, 2020 11:38 am
Forum: NEURON + Python
Topic: Finding middle of a section
Replies: 4
Views: 89

Re: Finding middle of a section

Neither of those strategies necessarily identifies the coordinates of the center of the section. The second solution doesn't necessarily lead to a point on the section (consider a circular section with evenly spaced 3D points; it would find the center of the circle). The explanation is simple: 3D po...
by ramcdougal
Fri Jan 03, 2020 12:59 pm
Forum: Reaction-diffusion in NEURON
Topic: Cell membrane with PMCA pump
Replies: 2
Views: 163

Re: Cell membrane with PMCA pump

Are you trying to do this with a network model or a single cell? Do you care what happens to the extracellular concentration or do you want to treat that as constant? A way of doing this is to an rxd.Extracellular domain and to use the rxd.membrane() geometry for the plasma membrane. The following e...
by ramcdougal
Wed Jan 01, 2020 2:13 pm
Forum: NEURON + Python
Topic: Associative arrays in HOC
Replies: 5
Views: 236

Re: Associative arrays in HOC

As long as Python is installed, you can use Python dictionaries from inside HOC:

Code: Select all

oc>objref py, d
oc>py = new PythonObject()
oc>d = py.dict()
oc>d.__setitem__("axon", 100)
	NULLobject 
oc>d.__setitem__("soma", 10)
	NULLobject 
oc>d.get("soma")
	10 
oc>d.get("axon")
	100 
by ramcdougal
Wed Jan 01, 2020 2:00 pm
Forum: NEURON + Python
Topic: Converting HOC extracellular to Python
Replies: 3
Views: 150

Re: Converting HOC extracellular to Python

In HOC, if foo is an array, assigning to foo is a syntactic shortcut for assigning to foo[0].