SectionRef: child · exists · has_parent · has_trueparent · is_cas · nchild · parent · root · sec · trueparent

SectionRef

Note

Much of this functionality is available in Python through Section methods in recent versions of NEURON. It is, however, sometimes necessary to use this class to interoperate with legacy code.

class SectionRef

Python

Syntax:

sref = n.SectionRef(sec=section)

Description:

SectionRef keeps a pointer/reference to section. If the sec= argument is omitted, the reference is to the currently accessed section.

This class overcomes a HOC limitation where sections were not treated as objects.

HOC

Syntax:

section sref = new SectionRef()

Description:

SectionRef keeps a pointer/reference to a section The reference is to the currently accessed section at the time the object was created.

This class allows sections to be referenced as normal object variables for assignment and passing as arguments.

SectionRef.sec

Python

Syntax:

sref.sec

Description:

Returns the Section the SectionRef references.

from neuron import n

s = n.Section("s")
s2 = n.Section("s2")
sref = n.SectionRef(sec=s2)

print(sref.sec==s)  # False
print(sref.sec==s2) # True

HOC

Syntax:

sref.sec

Description:

special syntax that makes the reference the currently accessed section. This class allows sections to be referenced as normal object variables for assignment and passing as arguments. The usage is

create soma, axon
axon.diam=2
soma.diam=10
access axon
objref s1, s2
soma s1 = new SectionRef()  // s1 holds a reference to the soma
print s1.sec.diam           // print the diameter of the soma
s2 = s1                             // s2 also holds a reference to the soma
s2.sec { psection() }               // print all info about soma
axon s2 = new SectionRef()
proc c() {
    $o1.sec connect $o2.sec(0), 1
}
c(s1, s2)
topology()

This last is a procedure that takes two SectionRef args and connects them end to end.

SectionRef.parent

Python

Syntax:: sref.parent

Description:

Returns the parent of sref.sec.

Warning

If there is a chance that a section does not have a parent then SectionRef.has_parent() should be called first to avoid an execution error. Note that the parent is the current parent of sref.sec, not necessarily the parent when the SectionRef was created.

HOC

Syntax:: sref.parent
Description:: parent of sref.sec becomes the currently accessed section. Generally it is used in a context like sref.parent { statement } just like a normal section name and does NOT need a section_pop If there is a chance that a section does not have a parent then SectionRef.has_parent() should be called first to avoid an execution error. Note that the parent is the current parent of sref.sec, not necessarily the parent when the SectionRef was created.

SectionRef.trueparent

Python

Syntax:

sref.trueparent

Description:

Returns the trueparent of sref.sec.

This is normally identical to SectionRef.parent() except when the parent’s parent_connection() is equal to the parent’s section_orientation().

If there is a chance that a section does not have a trueparent then SectionRef.has_trueparent() should be called first to avoid an execution error.

HOC

Syntax:: sref.trueparent
Description:: trueparent of sref.sec becomes the currently accessed section. This is normally identical to SectionRef.parent() except when the parent’s parent_connection() is equal to the parent’s section_orientation(). If there is a chance that a section does not have a trueparent then SectionRef.has_trueparent() should be called first to avoid an execution error.

SectionRef.child

Python

Syntax:

sref.child[i]

Description:

Returns the ith child of sref.sec. Generally it is used in a context like

for child in sref.child:
    print(child)

Note that the children are the current children of sref.sec, not necessarily the same as when the SectionRef was created since sections may be deleted or re-connected subsequent to the instantiation of the SectionRef.

HOC

Syntax:

sref.child[i]

Description:

the ith child of sref.sec becomes the currently accessed section. Generally it is used in a context like

for i=0, sref.nchild-1 sref.child[i] { statement }

SectionRef.root

Python

Syntax:: sref.root

Description:

Returns the root of sref.sec.

HOC

Syntax:: sref.root
Description:: root of sref.sec becomes the currently accessed section.

SectionRef.has_parent()

Python

Syntax:: boolean = sref.has_parent()
Description:: Returns True if sref.sec has a parent and False if sref.sec is a root section. Invoking sref.parent when sref.sec is a root section will print an error message and halt execution.

Note:

If sec is a Section, then sec.parentseg() is either the segment the section is attached to or None if sec does not have a parent.

HOC

Syntax:: boolean = sref.has_parent
Description:: returns 1 if sref.sec has a parent and 0 if sref.sec is a root section. Invoking sref.parent when sref.sec is a root section will print an error message and halt execution.

SectionRef.has_trueparent()

Python

Syntax:: boolean = sref.has_trueparent()
Description:: returns True if the sref.sec parent node is not the root node and False otherwise. Invoking sref.trueparent when it is the root node will print an error message and halt execution.

HOC

Syntax:: boolean = sref.has_trueparent
Description:: returns 1 if the sref.sec parent node is not the root node and 0 otherwise. Invoking sref.trueparent when it is the root node will print an error message and halt execution.

SectionRef.nchild()

Python

Syntax:: num = sref.nchild()
Description:: Return the number of child sections connected to sref.sec as a float.

Note

To get the number of child sections as an int, use: num = len(sref.child)

HOC

Syntax:: integer = sref.nchild
Description:: Return the number of child sections connected to sref.sec

SectionRef.is_cas()

Python

Syntax:: boolean = sref.is_cas()
Description:: Returns True if this section reference is the currently accessed (default) section, False otherwise.

Note

An equivalent expression is (sref.sec == n.cas()).

HOC

Syntax:: boolean = sref.is_cas()
Description:: Returns 1 if this section reference is the currently accessed section, 0 otherwise.

SectionRef.exists()

Python

Syntax:: boolean = sref.exists()
Description:: Returns True if the referenced section has not been deleted, False otherwise.