forsec on external object?

[mctavish]

I am trying to write a non-cellular object that operates on other cell objects, gathering information of the sections in the cell. The routines should operate on any generic cell. I simply want to call forall or forsec, but just on whatever cell object I am using. This works fine if the code that gathers the information on the cell is not an object itself (i.e., it is not a template). When the code that gathers the information is also an object, however, I cannot get it to work. Any ideas?

Thanks,
Tom

[ted]

Are you dealing with cell classes that have properly defined "all" subsets? If so, your non-cell class object foo could contain a public proc bar like this
proc bar() {
forsec $o1.all { . . . }
}
and
foo.bar(somecellobjref)
would iterate over just somecellobjref's sections.

[mctavish]

This is a general method, and while I can define "all" in my own cells, I'd like to deal with other cell models that do not have "all" defined. Is there another way?

Thanks,
Tom

[ted]

Beats me. First thing I'd do with any cell class that lacks an all set would be to . . . define an all set. Maybe Michael Hines has a different trick up his sleeve.

[hines]

If you can get any section of an object as the currently accessed section, then you can create a whole cell section list with
http://www.neuron.yale.edu/neuron/stati ... #wholetree
(Of course this won't work in the case an object holds more than one tree , e.g. after multisplit)

WIthout knowing anything about internal section names, sectionlists, or connectivity, the only way I can think of offhand to
create an "all" sectionlist is to use a top level object reference and a top level procedure as in:

Code: Select all

// example cell template
begintemplate Cell
public soma, axon
create soma, axon
endtemplate Cell

// 5 of them for our test
objref cells[5]
for i=0,4 cells[i] = new Cell()

// use the built-in hoc_obj_[0] to create the
// sectionlist. Any global objref would do.
proc cellall() {
        hoc_obj_[0] = new SectionList()
        object_push($o1)
        forall {
                execute("hoc_obj_[0].append()")
        }
        object_pop()
        // for testing
        forsec hoc_obj_[0] { print secname() }
}
 
// test
cellall(cells[1])
cellall(cells[3])

[mctavish]

Thanks! I did not know about wholecell(). I've combined both of these approaches to give me a SectionList in root-to-leaf order without accessing globals:

Code: Select all

objref sl
sl = new SectionList()
object_push(cellObj)
forall {
  execute("sl.wholetree()")
  break  // Stop after the first section
}
object_pop()
// for testing
forsec sl { print secname() }