secspec.rst

Section and Segment Selection

Since sections share property names eg. a length called :hoc:data:`L` it is always necessary to specify which section is being discussed.

There are three methods of specifying which section a property refers to (with each being compact in some contexts and cumbersome in others). They are given below in order of precedence (highest first).

Dot notation

This takes precedence over the other methods and is described by the syntax :samp:`{sectionname}.varname`. Examples are

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

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

Stack of sections

The syntax is

sectionname {stmt}

and means that the currently selected section during the execution of stmt is sectionname. This method is the most useful for programming since the user has explicit control over the scope of the section and can set several range variables. Notice that after the stmt is executed the currently selected section reverts to the name (if any) it had before sectionname was seen. The programmer is allowed to nest these statements to any level. Avoid the error:

        soma L=10 diam=10

which sets soma.L, then pops the section stack and sets :hoc:data:`diam` for whatever section is then on the stack.

It is important that control flow reach the end of stmt in order to automatically pop the section stack. Therefore, one cannot use the :ref:`continue <hoc_keyword_continue>`, :ref:`break <hoc_keyword_break>`, or :ref:`return <hoc_keyword_return>` statements in stmt.

There is no explicit notion of a section variable in NEURON but the same effect can be obtained with the :hoc:class:`SectionRef` class. The use of :hoc:func:`push_section` for this purpose is not recommended except as a last resort.

Looping over sets of sections is done most often with the :ref:`forall <hoc_keyword_forall>` and :ref:`forsec <hoc_keyword_forsec>` commands.

Default section

The syntax

access sectionname

defines a default section name to be the currently selected section when the first two methods are not in effect. There is often a conceptually privileged section which gets most of the use and it is useful to declare that as the default section. e.g.

access soma

With this, one can, with a minimum of typing, get values of voltage, etc at the command line level.

In general, this statement should only be used once to give default access to a privileged section. It's bad programming practice to change the default access within anything other than an initialization procedure. The "sec { stmt }" form is almost always the right way to use the section stack.

---

.. index::  access (keyword)

access

Syntax:

access section

Description:

Makes section the default currently accessed section. More precisely, it replaces the top of the section stack with the indicated section and so will be the permanent default section only if the section stack is empty or has only one section in it. This is lesser precedence than section stmt which is lesser precedence than section.var

Note:

The access statement should not be used within a procedure or function. In fact the best style is to execute it only once in a program to refer to a priviledged section such as "soma". It can be very confusing when a procedure has the side effect of permanently changing the default section.

Example:

create a, b, c, d
access a
print secname()
b {
        print secname()
        access c        // not recommended. The "go_to" of sections.
        print secname()
        d {print secname()}
        print secname()
} // because the stack has more than one section, c is popped off
print secname()     // and the second "access" was not permanent!

---

.. index::  forall (keyword)

forall

Syntax:

forall stmt

Description:

Loops over all sections, successively making each section the currently accessed section.

Within an object, forall refers to all the sections declared in the object. This is generally the right thing to do when a template creates sections but is inconvenient when a template is constructed which needs to compute using sections external to it. In this case, one can pass a collection of sections into a template function as a :hoc:class:`SectionList` object argument.

The forall is relatively slow, especially when used in conjunction with :hoc:func:`issection` and :hoc:func:`ismembrane` selectors. If you are often iterating over the same sets it is much faster to keep the sets in :hoc:class:`SectionList` objects and use the much faster :ref:`forsec <hoc_keyword_forsec>` command.

The iteration sequence order is undefined but will remain the same for a given sequence of :ref:`create <hoc_keyword_create>` statements.

Example:

create soma, axon, dend[3]
forall {
    print secname()
}

prints the names of all the sections which have been created.

soma
axon
dend[0]
dend[1]
dend[2]

.. seealso::
    :ref:`forsec <hoc_keyword_forsec>`, :ref:`ifsec <hoc_keyword_ifsec>`, :hoc:func:`issection`, :hoc:func:`SectionList`, :hoc:func:`ismembrane`

---

.. index::  ifsec (keyword)

ifsec

Syntax:

ifsec string stmt

ifsec sectionlist stmt

Description:

ifsec string stmt

Executes stmt if string is contained in the name of the currently accessed section. equivalent to :samp:`if(issection({string}))` stmt Note that the regular expression semantics is not the same as that used by issection. To get an exact match use ifsec ^string$

ifsec sectionlist stmt

Executes stmt if the currently accessed section is in the sectionlist.

.. seealso::
    :ref:`forsec <hoc_keyword_forsec>`, :hoc:class:`SectionList`, :hoc:func:`issection`

---

.. index::  forsec (keyword)

forsec

Syntax:

forsec string stmt

forsec sectionlist stmt

Description:

forsec string stmt

equivalent to forall ifsec string stmt but faster. Note that forsec string is equivalent to :samp:`forall if (issection({string})) stmt`

forsec sectionlist

equivalent to forall ifsec sectionlist stmt but very fast.

These provide a very efficient iteration over the list of sections.

Example:

create soma, dend[3], axon
forsec "a" print secname()

create soma, dend[3], axon
objref sl
sl = new SectionList()
for (i = 2; i >= 0; i = i - 1) dend[i] sl.append()
forsec sl print secname()

---

.. hoc:function:: pop_section


    Syntax:
        ``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::
            none

            create soma[5]
            objref stim[5]
            for i=0,4 soma[i] stim[i] = new IClamp(i/4)
            for i=0,4 {
                x = stim[i].get_loc()
                printf("location of %s is %s(%g)\n", stim[i], secname(), x)
                pop_section()
            }

---

.. hoc:function:: push_section


    Syntax:
        ``push_section(number)``

        ``push_section(section_name)``


    Description:
        This function, along with ``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 :hoc:class:`SectionRef`
        or :hoc:class:`SectionList` .


        :samp:`push_section({number})`
            Push the section identified by the number returned by
            this_section, etc. which you desire to be the currently accessed
            section. Any section pushed must have a corresponding 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.


    .. seealso::
        :hoc:class:`SectionRef`