Using Import3D on Mac

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.

Using Import3D on Mac

Postby neuromau » Thu Jul 27, 2017 9:46 am

I am having an issue using Import3D on Mac OS. I just uninstalled and reinstalled NEURON to be sure, and it is still happening. It claims a syntax error (but I didn't see what was erroneous-looking in the read_nlcda3.hoc file near line 1018).

Code: Select all
$ nrngui
NEURON -- VERSION 7.4 (1380:90539e842093) 90539e842093
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits

loading membrane mechanisms from /model/dir/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
BGate.mod BTGate.mod ExpGABAab.mod ...
oc>/Applications/NEURON-7.4/nrn/x86_64/bin/nrniv: syntax error
in import3d/read_nlcda3.hoc near line 1018
      spines()
        ^
        xopen("import3d/r...")
      xopen("import3d.hoc")
    execute1("{xopen("im...")
  load_file("import3d.hoc")
/Applications/NEURON-7.4/nrn/x86_64/bin/nrniv: makeimport3dtool undefined function
in import3d/read_nlcda3.hoc near line 1
^
        makeimport3dtool()
       
oc>print neuronhome()
/Applications/NEURON-7.4/nrn/share/nrn
oc>for r=0,9 {print nrnversion(r)}
first instance of r
7.4
NEURON -- VERSION 7.4 (1380:90539e842093) 90539e842093
VERSION 7.4 (1380:90539e842093)
90539e842093
90539e842093
1380
'--prefix=/Applications/NEURON-7.4/nrn' '--with-paranrn=dynamic' '--with-nrnpython=dynamic' '--disable-rx3d'
/Applications/NEURON-7.4/nrn/x86_64/bin/nrniv -dll /model/dir/x86_64/.libs/libnrnmech.so /Applications/NEURON-7.4/nrn/share/nrn/lib/hoc/nrngui.hoc -
x86_64-apple-darwin15.0.0
1


Is it likely that I have a setting wrong somewhere? Also, I am still on Yosemite, not sure if that makes a difference.
neuromau
 
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Re: Using Import3D on Mac

Postby ted » Thu Jul 27, 2017 11:48 am

That's a pretty old version of NEURON. There have been many bug fixes since, including some to Import3d (although I don't recall seeing the particular bug you ran into). Are you unable to use a more recent version?
ted
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Re: Using Import3D on Mac

Postby neuromau » Thu Jul 27, 2017 12:20 pm

I checked the alpha folder and found an installer from July 4, so installed that instead (other version I installed was listed as the most recent general release for Mac on the downloads page).

I still get the same error although on a different line number now:

Code: Select all
oc>/Applications/NEURON-7.5/nrn/x86_64/bin/nrniv: syntax error
in import3d/read_nlcda3.hoc near line 1028
             spines()
                  ^
        xopen("import3d/r...")
      xopen("import3d.hoc")
    execute1("{xopen("im...")
  load_file("import3d.hoc")
/Applications/NEURON-7.5/nrn/x86_64/bin/nrniv: makeimport3dtool undefined function
in import3d/read_nlcda3.hoc near line 1
^
        makeimport3dtool()

oc>
oc>print neuronhome()
/Applications/NEURON-7.5/nrn/share/nrn
oc>for r=0,9 {print nrnversion(r)}
first instance of r
7.5
NEURON -- VERSION 7.5 master (2f94790) 2017-07-04
VERSION 7.5 master (2f94790)
2f94790
2017-07-04
1620
'--prefix=/Applications/NEURON-7.5/nrn' '--with-paranrn=dynamic' '--with-nrnpython=dynamic' '--with-pyexe=python3' 'CYTHON=/Users/hines/anaconda2/bin/cython'
/Applications/NEURON-7.5/nrn/x86_64/bin/nrniv -dll /model/dir/x86_64/.libs/libnrnmech.so /Applications/NEURON-7.5/nrn/share/nrn/lib/hoc/nrngui.hoc -
x86_64-apple-darwin16.6.0
1


I've found that if I open read_nlcda3.hoc and comment out the definitions for proc treepoints() through proc branchend(), I can get the tool to load and seemingly work ok ( import morphology files and export hoc files that look reasonable). If I haven't done something likely to cause major errors by commenting out those lines, then I think I have a workaround for now.
neuromau
 
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Re: Using Import3D on Mac

Postby hines » Fri Jul 28, 2017 7:28 am

I wonder if "spines" has become a reserved word due to using it as the name of a mod file SUFFIX or POINT_PROCESS. I get the same error if I replace spines() with hh().

If this is the case, it is a flaw in hoc name space handling that I will look into fixing. But for now the fix would be to change the name of the SUFFIX in the mod file along with any thing that uses insert spines
or xxx_spines. If this is the case, it has nothing to do with the mac version as opposed to mswin or linux.
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Re: Using Import3D on Mac

Postby neuromau » Fri Jul 28, 2017 8:22 am

Ah, of course! I am working with a different model in my Mac, one that does have a "spines" mod file. I should have realized that right away! Thank you, I'll rename that suffix in the file.
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Joined: Mon Apr 20, 2009 7:02 pm


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