Accessing hoc from Python

Tags: Python, NEURON

22nd January 2009

When running NEURON with Python, the hoc interpreter is still available from within Python, and much of the functionality of NEURON is accessed through the hoc interpreter.

The hoc interpreter is accessible either through the execute() function in the neuron.hoc module, or through the automatically-created h object in the neuron module:

>>> from neuron import h
>>> h
TopLevelHocInterpreter

The h object can be used to access any variable, object reference or function defined in the hoc interpreter, e.g.:

>>> h.dt
0.025000000000000001
>>> h.t
0.0
>>> h.finitialize()
1.0

and is also callable, with any valid hoc command as the argument, e.g.:

>>> h('x = 2')
first instance of x
1
>>> h.x
2.0
>>> h('create soma')
1
>>> h('access soma')
1
>>> h.soma
<nrn.Section object at 0xb7433060>
>>> h.soma(0.5).v
-65.0
>>> h('strdef s')
1
>>> h.s = 'hello'
>>> h.s
'hello'

Note that the return value of the h() call (often 1) is printed to the screen. If you don't like this behaviour, you can always assign the return value to a variable, e.g.:

>>> tmp = h('x=5')
>>>

Note that you cannot assign to a variable that has not already been defined:

>>> h.y = 3
Traceback (most recent call last):
 File "stdin", line 1, in <module>
LookupError: 'y' is not a hoc variable name.

Objects defined in hoc behave in almost all ways like Python objects, e.g.:

>>> h('objref vec')
1
>>> h('vec = new Vector(5)')
1
>>> h('objref list')
1
>>> h('list = new List()')
1
>>> h.list.append(h.vec)
1.0
>>> my_list = h.list
>>> my_list.count()
1.0
>>> my_list.append(h.vec)
2.0
>>> my_vec = h.vec
>>> my_list.append(my_vec)
3.0
>>> my_list.object(2)
Vector[0]

Note that in the example above, there is only a single Vector object - assigning it to a different name or adding it to a list does not copy the Vector:

>>> h.vec.x[0] = 5
>>> my_vec.x[1] = 4
>>> my_list.object(0).x[2] = 3
>>> my_list.object(1).x[3] = 2
>>> h.list.object(2).x[4] = 1
>>> my_vec.printf()
5       4       3       2       1

5.0
>>>

But in some ways, HocObjects do not behave as you might expect. For example, although we showed above that my_vec and h.vec reference the same object:

>>> my_vec == h.vec
False

Also, all HocObjects have the same type, whatever the object type in hoc:

>>> type(my_vec)
<type 'hoc.HocObject'>
>>> type(my_list)
<type 'hoc.HocObject'>

However, listing the object attributes and methods using dir(obj) lists those of the specific hoc object type, and help(obj) gives help about the object's hoc type.