Export to .hoc with CellBuilder from Python

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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vogdb
Posts: 37
Joined: Sun Aug 13, 2017 9:51 am

Export to .hoc with CellBuilder from Python

Post by vogdb »

Hi! I'm trying now for a week to properly export the currently loaded neuron model. There is only one loaded model in my namespace that I loaded like this.

Code: Select all

h.load_file('Cell_Scnn1a.hoc')
cell_hoc = h.Cell_Scnn1a('/morphologies', 'Scnn1a_473845048_m.swc')
It is absolutely properly exported to nml by

Code: Select all

h.load_file("mview.hoc")
mv = h.ModelView(0)
mv_xml = h.ModelViewXML(mv)
export_filepath = os.path.join('.', 'test.nml')
mv_xml.exportNeuroML(export_filepath, 2)
but when I try

Code: Select all

bld = h.CellBuild(0)
mng = h.CellManage(bld)
f = h.File()
f.wopen('test.hoc')
mng.toplevel = 1 // i tried  toplevel=0 as well
mng.pr(f)
I receive an empty cell in test.hoc. The same output is when I use Cell Builder from GUI. How can I export with CellBuild/CellManage properly from Python?

Code: Select all

proc celldef() {
  topol()
  subsets()
  geom()
  biophys()
  geom_nseg()
}


proc topol() { local i
  basic_shape()
}
proc basic_shape() {
}

objref all
proc subsets() { local i
  objref all
  all = new SectionList()

}
proc geom() {
}
proc geom_nseg() {
}
proc biophys() {
}
celldef()
ted
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Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
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Re: Export to .hoc with CellBuilder from Python

Post by ted »

but when I try
. . .
I receive an empty cell in test.hoc.
You're starting with a model created by executing statements in Cell_Scnn1a.hoc. Where did the CellBuilder referenced by h.CellBuild() come from? If you created it yourself, it's "empty" (except for a soma section). It's not going to know anything about the model that was created by executing statements in Cell_Scnn1a.hoc. And even if you "imported" that model into the CellBuilder, the CellBuilder would only know about the anatomy of that model--its branched architecture, and the geometry of each section.

So even though it is true that the code in

Code: Select all

bld = h.CellBuild(0)
. . .
mng.pr(f)
does not generate a hoc file that, when executed, will recreate the model specified by h.Cellbuild(), fixing it won't be useful to you anyway.
vogdb
Posts: 37
Joined: Sun Aug 13, 2017 9:51 am

Re: Export to .hoc with CellBuilder from Python

Post by vogdb »

Thank you for the response.
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