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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.

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...

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...

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...

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 = ...

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_...

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...

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...

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 ...

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...

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...

As long as Python is installed, you can use Python dictionaries from inside HOC: 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") 1...

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

Looks like something went wrong with the Cython part of the compilation (which provides voxelize2). If you're using Centos 7 and Python 3.4, try recompiling after something like: yum -y install python34-Cython (I understand you may not have sudo rights on this machine, but you ought to be able to in...

NEURON doesn't use cylinders. It uses truncated cones ("frusta of a right circular cone") for the electrophysiology. For 3D reaction-diffusion domains, we use essentially the algorithm of McDougal et al., 2013 to convert Neurolucidia-style point-diameter measurements into watertight surfac...