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Unable to find Import3d_Neurolucida3

Posted: Wed Dec 09, 2020 11:51 am
by NickHananeia

I've been working on an adaptation of a published model, and in attempting to run their code, I get an error in NEURON when their code attempts to load the morphology files, reading

"Import3d_Neurolucida3 is not a template".

I've been running NEURON fine for months on this machine, and I'm unsure why this in particular is causing problems. I've checked the libraries, and the Import3D files are intact and there; it simply seems that this code is unable to invoke it.

Are there any known reasons why this might be happening?

Incidentally I do have the "Python3 permission denied" error every time I run NEURON but since my entire codebase doesn't use Python I've ignored it; I'm wondering if it's related.

Re: Unable to find Import3d_Neurolucida3

Posted: Thu Dec 10, 2020 10:07 am
by ted
It would be helpful to be able to reproduce the problem. Is the code in ModelDB?

Re: Unable to find Import3d_Neurolucida3

Posted: Thu Dec 10, 2020 10:28 am
by NickHananeia
The code is not published in ModelDB; it is posted in the Human Brain Project collaboratory.

If it helps, their invocation of the function looks like this:

Code: Select all

proc load_morphology(/* morphology_dir, morphology_name */) {localobj morph, import, sf, extension
  strdef morph_path
  sprint(morph_path, "%s/%s", "morphology", "2013_03_06_cell03_789_H41_03.ASC")

  sf = new StringFunctions()
  extension = new String()

  morph = new Import3d_Neurolucida3()

  morph.quiet = 1

  import = new Import3d_GUI(morph, 0)

Re: Unable to find Import3d_Neurolucida3

Posted: Thu Dec 10, 2020 4:12 pm
by ted
What would help most would be to see the code in toto. Absent that, the following is only a guess.

At or near the top of your main file--and definitely before there is any statement of the form
foo = new Import3d_Neurolucida()
--insert this statement:


Re: Unable to find Import3d_Neurolucida3

Posted: Fri Dec 11, 2020 2:48 pm
by NickHananeia
Ah, found the problem - their import line was placed in the wrong place relative to the template opening.

Thanks for pointing me in the right direction.