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.. _secspec:
.. _CurrentlyAccessedSection:
Section and Segment Selection
=============================
Dot notation for properties
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Since sections share property names eg. a length called :data:`L`
it is always necessary to specify *which* section is being discussed;
this is done using dot notation, e.g.
.. code-block::
python
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:
.. code-block::
python
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.*
.. function:: 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:
.. code-block::
python
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()``.)
----
.. function:: 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 :class:`SectionRef`
or :class:`SectionList` .
:samp:`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.
:samp:`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:
.. code-block::
python
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')
.. seealso::
:class:`SectionRef`
|
