pop_section · push_section

Section and Segment Selection

Dot notation for properties

Since sections share property names eg. a length called L it is always necessary to specify which section is being discussed; this is done using dot notation, e.g.

dendrite[2].L = dendrite[1].L + dendrite[0].L
axon.v = soma.v
print(soma.gnabar)
axon.nseg *= 3

This notation is necessary when one needs to refer to more than one section within a single statement.

sec= for functions

Many NEURON functions refer to a specific Section. In recent versions of NEURON, most of these either are available as section methods or take a section or segment directly. For older code or for the remaining exceptions, the active section may be specified using a sec= keyword argument.

For example:

my_iclamp = h.IClamp(0.25, sec=soma)   # better to use h.IClamp(soma(0.25)) though
num_pts_3d = h.n3d(sec=apical)         # could get the same value as an int via apical.n3d()

Default section

If no sec= keyword argument is specified, the functions will use NEURON’s default Section (sometimes called the currently accessed section), which can be identified via h.cas(). The default Section is controlled by a stack; it is initially the first Section created but entries may be pushed onto or popped off of the stack by the following commands. Use this only as a last resort.

pop_section()

Syntax:

h.pop_section()

Description:

Take the currently accessed section off the section stack. This can only be used after a function which pushes a section on the section stack such as point_process.getloc().

Example:

from neuron import h

soma = h.Section(name='soma')
apical = h.Section(name='apical')
stims = [h.IClamp(soma(i / 4.)) for i in range(5)] + [h.IClamp(apical(0.5))]
for stim in stims:
    x = stim.get_loc()
    print("location of %s is %s(%g)" % (stim, h.secname(), x))
    h.pop_section()

(Note: in this example as nseg=1, the current clamps will either be at position 0, 0.5, or 1.)

(Note: a more Pythonic way to get the location of the point-process stim is to use seg = stim.get_segment(), but this is shown as an example of using h.pop_section().)

---

push_section()

Syntax:

h.push_section(number)

h.push_section(section_name)

Description:

This function, along with h.pop_section() should only be used as a last resort. It will place a specified section on the top of the section stack, becoming the current section to which all operations apply. It is probably always better to use SectionRef or SectionList .

push_section(number)

Push the section identified by the number returned by h.this_section(), etc. which you desire to be the currently accessed section. Any section pushed must have a corresponding h.pop_section() later or else the section stack will be corrupted. The number is not guaranteed to be the same across separate invocations of NEURON.

push_section(section_name)

Push the section identified by the name obtained from sectionname(strdef). Note: at this time the implementation iterates over all sections to find the proper one; so do not use in loops.

Example:

from neuron import h

soma = h.Section(name='soma')
apical = h.Section(name='apical')

# get a number to allow pushing by number
soma_id = h.this_section(sec=soma)

# push by name
h.push_section('apical')

# push by number
h.push_section(soma_id)

# RuntimeError -- no such section
h.push_section('basal')

See also

SectionRef