neuron.h: cas

neuron.h.Section

neuron.hoc: execute · hoc_ac

Accessing HOC from Python

This section describes how one can interact with HOC features and the HOC interpreter from Python code.

In many cases, HOC provides features that are natively supported in Python. In these cases, it is usually preferable to use the Python version, which will be familiar to a wider range of people. Nonetheless, in isolated situations the following section may be useful: Python-specific documentation of discouraged HOC features.

Warning

Some of the idioms on this page are out of date, but they still work. See the NEURON Python tutorial for modern idioms.

Note

Most of the following is from the perspective of someone familiar with HOC; for a Python-based introduction to NEURON, see Scripting NEURON Basics

class neuron.hoc.HocObject

Syntax:

from neuron import h

h = neuron.hoc.HocObject()

Description:

Allow access to anything in the Hoc interpreter. h is an instance of a neuron.hoc.HocObject object. Note that there is only one Hoc interpreter, no matter how many interface objects are created, so there is no advantage to creating another.
h("any hoc statement")
Any hoc variable or string in the Hoc world can be accessed in the Python world:
h('strdef s')
h('{x = 3  s = "hello"}')
print(h.x)          # prints 3.0
print(h.s)          # prints hello
And if it is assigned a value in the python world it will be that value in the Hoc world. (Note that any numeric python type becomes a double in Hoc.)
h.x = 25
h.s = 'goodbye'
h('print x, s')    #prints 25 goodbye
Note, however, that new Hoc variables cannot be defined from Python except via, e.g. h('strdef s').

Any hoc object can be handled in Python, and can use Python idioms for that type of object despite being created in hoc. e.g. in hoc, you would have to use vec.size() to get the Vector’s size. This still works in Python, but you can also use the Pythonic len(h.vec):
h('objref vec')
h('vec = new Vector(5)')
print(h.vec)        # prints Vector[0]
print(len(h.vec))   # prints 5.0
There is, however, in pure Python models never a need to create a hoc object; e.g. if no HOC code needed to access the Vector, the above is equivalent to
vec = h.Vector(5)
print(vec)
print(len(vec))
Note that any hoc object method or field may be called, or evaluated/assigned using the normal dot notation which is consistent between hoc and python. However, hoc object methods MUST have the parentheses or else the Python object is not the return value of the method but a method object. ie.
x = h.vec.size     # not 5 but a python callable object
print(x)            # prints: Vector[0].size()
print(x())          # prints 5
This is also true for indices
h.vec.indgen().add(10) # fills elements with 10, 11, ..., 14
print(h.vec[2])    # prints 12.0
x = h.vec.x        # a python indexable object
print(x)           # prints Vector[0].x[?]
print(x[2])        # prints 12.0
Note that the .x notation is not needed in Python for reading or (as of NEURON 7.7) writing to vectors.

The hoc object can be created directly in Python. E.g.
v = h.Vector(range(10, 20))
Iteration over hoc Vector, List, and arrays is supported. e.g.
v = h.Vector(range(10, 14))
for x in v:
  print(x)

l = h.List(); l.append(v); l.append(v); l.append(v)
for x in l:
  print(x)

h('objref o[2][3]')
for x in h.o:
  for y in x:
    print(x, y)
Any hoc Section can be handled in Python. E.g.
h('create soma, axon')
ax = h.axon
makes ax a Python Section which references the hoc axon section. Many hoc functions use the currently accessed section; most of these are now available as section methods, however for user written hoc and in legacy code, a “sec” keyword parameter temporarily makes the Section value the currently accessed section during the scope of the function call. e.g
print(h.secname(sec=ax))
Note

In Python, one can simply:
print(ax)
Or use str(ax) to get the name of the section ax.
Most such functions now have an alternative form that avoids the need for sec=; often they are available as section methods. This is usually listed in the function definition.

Point processes are handled by direct object creation as in
stim = IClamp(ax(1.0))
Many hoc functions use call by reference and return information by changing the value of an argument. These are called from the Python world by passing a HocObject.ref() object. Here is an example that changes a string.
h('proc chgstr() { $s1 = "goodbye" }')
s = h.ref('hello')
print(s[0])          # notice the index to dereference. prints hello
h.chgstr(s)
print(s[0])          # prints goodbye
h.sprint(s, 'value is %d', 2+2)
print(s[0])          # prints value is 4
and here is an example that changes a pointer to a double
h('proc chgval() { $&1 = $2 }')
x = h.ref(5)
print(x[0])          # prints 5.0
h.chgval(x, 1+1)
print(x[0])          # prints 2.0
Finally, here is an example that changes a objref arg.
h('proc chgobj() { $o1 = new List() }')
v = h.ref([1,2,3])  # references a Python object
print(v[0])          # prints [1, 2, 3]
h.chgobj(v)
print(v[0])          # prints List[0]
Unfortunately, the HocObject.ref() is not often useful since it is not really a pointer to a variable. For example consider
h('x = 1')
y = h.ref(h.x)
print(y)                     # prints hoc ref value 1
print(h.x, y[0])             # prints 1.0 1.0
h.x = 2
print(h.x, y[0])             # prints 2.0 1.0
and thus in not what is needed in the most common case of a hoc function holding a pointer to a variable such as Vector.record() or Vector.play(). For this one needs the _ref_varname idiom which works for any hoc variable and acts exactly like a c pointer. eg:
h('x = 1')
y = h._ref_x
print(y)                     # prints pointer to hoc value 1
print(h.x, y[0])             # prints 1.0 1.0
h.x = 2
print(h.x, y[0])             # prints 2.0 2.0
y[0] = 3
print(h.x, y[0])             # prints 3.0 3.0
Of course, this works only for hoc variables, not python variables. For arrays, use all the index arguments and prefix the name with _ref_. The pointer will be to the location indexed and one may access any element beyond the location by giving one more non-negative index. No checking is done with regard to array bounds errors. e.g
v = h.Vector(range(10, 14))
y = v._ref_x[1]    # holds pointer to second element of v
print(v[2], y[1])  # prints 12.0 12.0
y[1] = 50
v.printf()         # prints 10 11 50 13
The idiom is used to record from (or play into) voltage and mechanism variables. eg
from neuron import h
soma = h.Section(name='soma')
soma.insert(h.pas)
v = h.Vector().record(soma(0.5)._ref_v)
pi = h.Vector().record(soma(0.5).pas._ref_i)
ip = h.Vector().record(soma(0.5)._ref_i_pas)
The factory idiom is one way to create Hoc objects and use them in Python.
h('obfunc newvec() { return new Vector($1) }')
v = h.newvec(10).indgen().add(10)
v.printf()          # prints 10 11 ... 19 (not 10.0 ... since printf is a hoc function)
but that idiom is more or less obsolete as the same thing can be accomplished directly as shown a few fragments back. Also consider the minimalist
vt = h.Vector
v = vt(4).indgen().add(10)
or equivalently,
v = h.Vector(range(4)) + 10
Any Python object can be stored in a Hoc List. It is more efficient when navigating the List to use a python callable that avoids repeated lookup of a Hoc method symbol. Note that in the Hoc world a python object is of type PythonObject but python strings and scalars are translated back and forth as strdef and scalar doubles respectively.
h('obfunc newlist() { return new List() }')
my_list = h.newlist()
apnd = my_list.append
apnd([1,2,3])      # Python list in hoc List
apnd(('a', 'b', 'c')) # Python tuple in hoc List
apnd({'a':1, 'b':2, 'c':3}) # Python dictionary in hoc List
for item in my_list:
    print(item)

h('for i=0, List[0].count-1 print List[0].object(i)')
To see all the methods available for a hoc object, use, for example,
dir(h.Vector)
h.anyclass can be subclassed with
class MyVector(neuron.hclass(neuron.h.Vector)) :
  pass

v = MyVector(10)
v.zzz = 'hello' # a new attribute
print(v.size()) # call any base method
If you override a base method such as ‘size’ use
v.baseattr('size')()
to access the base method. Multiple inheritance involving hoc classes probably does not make sense. If you override the __init__ procedure when subclassing a Section, be sure to explicitly initialize the Section part of the instance with
nrn.Section.__init__()
Since nrn.Section is a standard Python class one can subclass it normally with
class MySection(neuron.nrn.Section):
  pass
The hoc setpointer statement is effected in Python as a function call with a syntax for POINT_PROCESS and SUFFIX (density)mechanisms respectively of
h.setpointer(_ref_hocvar, 'POINTER_name', point_proces_object)
h.setpointer(_ref_hocvar, 'POINTER_name', nrn.Mechanism_object)
See nrn/share/examples/nrniv/nmodl/(tstpnt1.py and tstpnt2.py) for examples of usage. For a density mechanism, the ‘POINTER_name’ cannot have the SUFFIX appended. For example if a mechanism with suffix foo has a POINTER bar and you want it to point to t use
h.setpointer(_ref_t, 'bar', sec(x).foo)

neuron.hoc.hoc_ac()

Syntax:

import hoc

double_value = hoc.hoc_ac()

hoc.hoc_ac(double_value)

Description:

Get and set the hoc global scalar, hoc_ac_-variables. This is obsolete since HocObject is far more general.

import hoc
hoc.hoc_ac(25)
hoc.execute('print hoc_ac_') # prints 25
hoc.execute('hoc_ac_ = 17')
print(hoc.hoc_ac())  # prints 17

neuron.h.cas()

Syntax:

sec = h.cas()

Description:

Returns the currently accessed section as a Python Section object.

from neuron import h
h('''
  create soma, dend[3], axon
  access dend[1]
''')

sec = h.cas()
print(sec)

It is generally best to avoid writing code that manipulatesd the section stack. Use Python section objects, sec=, and section methods instead.

class neuron.h.Section

Syntax:

sec = h.Section()

sec = h.Section([name='string', [cell=self])

Description:

The Python Section object allows modification and evaluation of the information associated with a NEURON Conceptual Overview of Sections. The typical way to get a reference to a Section in Python is with neuron.h.cas() or by using the hoc section name as in asec = h.dend[4]. The sec = Section() will create an anonymous Section with a hoc name constructed from “Section” and the Python reference address. Access to Section variables is through standard dot notation. The “anonymous” python section can be given a name with the named parameter and/or associated with a cell object using the named cell parameter. Note that a cell association is required if one anticipates using the gid2cell() method of ParallelContext.

from neuron import h
sec = h.Section()
print(sec)         # prints __nrnsec_0x7fa44eb70000
sec.nseg = 3       # section has 3 segments (compartments)
sec.insert(h.hh)   # all compartments have the hh mechanism
sec.L = 20         # Length of the entire section is 20 um.
for seg in sec:    # iterates over the section compartments
  for mech in seg: # iterates over the segment mechanisms
    print(sec, seg.x, mech.name())

A Python Section can be made the currently accessed section by using its push method. Be sure to use pop_section() when done with it to restore the previous currently accessed section. I.e, given the above fragment,

from neuron import h
h('''
objref p
p = new PythonObject()
{p.sec.push() psection() pop_section()}
''')
#or
print(sec)
h.psection(sec=sec)

When calling a hoc function it is generally preferred to named sec arg style to automatically push and pop the section stack during the scope of the hoc function. ie

h.psection(sec=sec)

The psection section method is different, in that it returns a Python dictionary rather than printing to the screen. It also provides more information, such as reaction-diffusion mechanisms that are present. One could, for example, do

from pprint import pprint
pprint(sec.psection())

The section psection method was added in NEURON 7.6.

With a SectionRef one can, for example,

sr = h.SectionRef(sec=h.dend[2])
sr.root.push(); print(h.secname()); h.pop_section()

or, more compactly and avoiding the modification of the section stack,

sr = h.SectionRef(sec=h.dend[2])
print(sr.root.name(), h.secname(sec=sr.root))

Iteration over sections is accomplished with

for s in h.allsec():
  print(s)

sl = h.SectionList(); sl.wholetree()
for s in sl:
  print(s)

In lieu of using a SectionList, one can get the whole tree containing a given section as a Python list via:

tree_secs = my_sec.wholetree()

(The wholetree section method was added in NEURON 7.7.)

Connecting a child section to a parent section uses the connect method using either

childsec.connect(parentsec, parentx, childx)
childsec.connect(parentsegment, childx)

In the first form parentx and childx are optional with default values of 1 and 0 respectively. childx must be 0 or 1 (orientation of the child). Parentx is in the range [0 - 1] but will actually be connected to the center of the parent segment that contains parentx (or exactly at 0 or 1).

sec.cell() returns the cell object that ‘owns’ the section. The return value is None if no object owns the section (a top level section), the instance of the hoc template that created the section, or the python object specified by the named cell parameter when the python section was created.

Segment

Syntax:
seg = section(x)

Description:
A Segment object is obtained from a Section with the function notation where the argument is 0 <= x <= 1 an the segment is the compartment that contains the location x. The x value of the segment is seg.x and the section is seg.sec . From a Segment one can obtain a Mechanism.

To iterate over segments, use e.g. for seg in sec: print(seg) This does not include 0 area segments at 0 and 1. For those use for seg in sec.allseg():...

Mechanism

Syntax:
mech = segment.mechname

Description:
A Mechanism object is obtained from a Segment. From a Mechanism one can obtain a range variable. The range variable can also be obtained from the segment by using the hoc range variable name that has the mechanism suffix.

To iterate over density mechanisms, use: for mech in seg: print (mech) To get a python list of point processes in a segment: pplist = seg.point_processes()

neuron.hoc.execute()

Syntax:

import neuron

neuron.hoc.execute('any hoc statement')

Description:

Execute any statement or expression using the Hoc interpreter. This is obsolete since the same thing can be accomplished with HocObject with less typing. Note that triple quotes can be used for multiple line statements. A ‘n’ should be escaped as ‘\n’.

hoc.execute('load_file("nrngui.hoc")')

Python-specific documentation of discouraged HOC features

This section contains versions of the HOC documentation for certain features that have been updated to be somewhat Python-specific. You may find them useful, but in general Python-native versions are to be preferred.