A Pythonic, object-oriented, monkey patch for NEURON
*No ducks were punched during the construction of this monkey patch.
pip install nrn-patch
Be aware that the interface is currently incomplete, this means that most parts
are still "just" NEURON. I've only patched holes I frequently encounter myself
when using the
h.NetCon functions. Feel free to
open an issue or fork this project and open a pull request for missing or broken
parts of the interface.
Python interfaces should be Pythonic, this wrapper offers just that:
- Full Python objects: each wonky C-like NEURON object is wrapped in a full fledged Python object, easily handled and extended through inheritance.
- Duck typed interface: take a look at the magic methods I use and any object you create with those methods present will work just fine with Patch.
- Correct garbage collection, objects connected to eachother don't dissapear: Objects that rely on eachother store a reference to eachother. As is the basis for any sane object oriented interface.
Use it like you would use NEURON. The wrapper doesn't make any changes to the interface, it just patches up some of the more frequent and ridiculous gotchas.
Patch supplies a new HOC interpreter
PythonHocInterpreter which wraps
the standard HOC interpreter
h provided by NEURON. Any objects returned will
PythonHocObjects wrapping their corresponding NEURON object, or
whatever NEURON returns.
When using just Patch the difference between NEURON and Patch objects is handled
transparently, but if you wish to mix interpreters you can transform all Patch
objects back to NEURON objects with
from patch import p import glia as g section = p.Section() point_process = g.insert(section, "AMPA") stim = p.NetStim() stim.start = 10 stim.number = 5 stim.interval = 10 # And here comes the magic! This explicitly defined connection # isn't immediatly garbage collected! What a crazy world we live in. # Has science gone too far? p.NetCon(stim, point_process) # It's fully compatible using __neuron__ from neuron import h nrn_section = h.Section() nrn_section.connect(section.__neuron__())
Known unpatched holes
- When inserting point processes the returned object is unwrapped. This can be resolved using Glia, or by using this syntax:
# In neuron process = h.MyMechanismName(my_section(0.5), *args, **kwargs) # In patch point_process = p.PointProcess(p.MyMechanismName, my_section(0.5), *args, **kwargs)
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