Topology

Section
   connect        delete_section  nseg          section_owner  
   create         disconnect     section_exists  topology

create

Topology

SYNTAX

create

DESCRIPTION

This is an nrniv command which creates a list of section names. Existing sections with the same names are destroyed and recreated. The create statement may occur within procedures, but the names must have been previously declared with a create statement at the command level.

EXAMPLES

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]

SEE ALSO

connect , insert , forall

connect

Topology

SYNTAX

connect section(0or1), x
connect section(0or1), parent(x)

DESCRIPTION

The first form connects the section at end 0 or 1 to the currently accessed section at position x. An alternative syntax is the second form in which the parent section is explicitly indicated. If a section is connected twice a Notice is printed on the standard error device saying that the section has been reconnected (the last connection takes precedence). To avoid the notice, disconnect the section first with the function "disconnect()". If sections are inadvertently connected in a loop, an error will be generated when the internal data structures are created and the user will be required to disconnect one of the sections forming the loop.

EXAMPLES

execute following example 
 create soma, axon, dendrite[3]
 connect axon(0), soma(0)
 soma for i=0,2 {
   connect dendrite[i](0), 1
 }
 topology()
 objref s
 s = new Shape()

topology

Topology

SYNTAX

topology()

DESCRIPTION

Print the topology of how the sections are connected together.

delete_section

Topology

SYNTAX

delete_section()

DESCRIPTION

Delete the currently accessed section from the main section list which is used in computation. forall delete_section will remove all sections.

Note: deleted sections still exist (even though SectionRef . exists returns 0 and an error will result if one attempts to access the section) so that other objects (such as section lists and Shapes) which hold pointers to these sections will still work. When the last pointer to a section is destroyed, the section memory will be freed.

section_exists

Topology

SYNTAX

boolean = section_exists("name", [index], [object])

DESCRIPTION

Returns 1 if the section defined by the args exists and can be used as a currently accessed section. Otherwise, returns 0. The index is optional and if nonzero, can be incorporated into the name as a literal value such as dend[25]. If the optional object arg is present, that is the context, otherwise the context is the top level. "name" should not contain the object prefix. Even if a section is multiply dimensioned, use a single index value.

section_owner

Topology

SYNTAX

section_owner()

DESCRIPTION

Return the object that created the currently accessed section. If the section was created from the top level, The NULLobject is returned. If the section was created as a Python section and the first constructor arg is a Python object or the keyword argument, cell = ..., is used, a PythonObject wrapper is returned. I.e. in the Python world, it is the Python cell object.

disconnect

Topology

SYNTAX

disconnect()

DESCRIPTION

Disconnect the currently accessed section from its parent. Such a parent can be reconnected with the connect statement.

nseg

Topology

DESCRIPTION

Number of segments (compartments) in the currently accessed section. When a section is created, nseg is 1. In versions prior to 3.2, changing nseg throws away all "inserted" mechanisms including diam (if 3-d points do not exist). PointProcesss, connectivity, L, and 3-d point information remain unchanged.

Starting in version 3.2, a change to nseg re-uses information contained in the old segments.

If nseg is increased, all old segments are relocated to their nearest new locations (no instance variables are modified and no pointers to data in those segments become invalid). and new segments are allocated and given mechanisms and values that are identical to the old segment in which the center of the new segment is located. This means that increasing nseg by an odd factor preserves the locations of all previous data (including all Point Processes) and, if PARAMETER range variables are constant, that all the new segments have the proper PARAMETER values. (It generally doesn't matter that ASSIGNED and STATE values do not get interpolated since those values are computed with fadvance()). If range variables are not constant then the hoc expressions used to set them should be re-executed.

If nseg is decreased then all the new segments are in fact those old segments that were nearest the centers of the new segments. Unused old segments are freed (and thus any existing pointers to variables in those freed segments are invalid). This means that decreasing nseg by an odd factor preserves the locations of all previous data. However POINT PROCESSES not located at the centers of the new segments will be discarded.

The intention is to guarantee that the following sequence 

        run() //sim1
        forall nseg *= oddfactor
        run() //sim2
        forall nseg /= oddfactor
        run() //sim3
will produce identical simulations for sim1 and sim3. And sim2 will be oddfactor^2 more accurate with regard to spatial discretization error.

neuron/neuron/topology.hel : May 13 2012