Using cvapp with Neuron_Morpho

NatalieD · Post by **NatalieD** » Fri Sep 14, 2007 4:11 am

Hi.
For some reason I cannot seem to open a file created in Neuron_Morpho with cvapp. My Java knowledge is extremely limited and it took me a while to even run cvapp. I have traced a morphology in Neuron_Morpho, saved it, opened cvapp and tried to "open" the file, but it simply comes up with a box saying "parsing"... and nothing happens. I have no idea where i am going wrong, any help is appreciated!

Post by **ted** » Fri Sep 14, 2007 5:06 pm

If you want to convert morphometric data to a NEURON model, use the Import3D tool--see
the tutorial at http://www.neuron.yale.edu/neuron/docs

livius · Post by **livius** » Thu Nov 08, 2007 7:14 am

NatalieD wrote:Hi.
For some reason I cannot seem to open a file created in Neuron_Morpho with cvapp. My Java knowledge is extremely limited and it took me a while to even run cvapp. I have traced a morphology in Neuron_Morpho, saved it, opened cvapp and tried to "open" the file, but it simply comes up with a box saying "parsing"... and nothing happens. I have no idea where i am going wrong, any help is appreciated!

i have the same problem, now my CVAPP runs but it tells me "parsing" and nothing happens... i have tried to use Neuron-import3d tool but it gives me an error while i'm trying to open .swc files coming from NEUROMANTIC (maybe there are different version of .swc?? i dont think it's a very simple file format)

the error says as follows:
"Can't figure out file format for ./my path/myswcfile.swc"

very strange!!

have you any clue of how to make cvapp work better? or any explanation of the reason of lack of capavility to open .swc by neuron?

thank you very much if you can give me any advice

Livio

Post by **ted** » Thu Nov 08, 2007 9:28 am

If you send me the swc file, I'll try to see what the problem is.
ted dot carnevale at yale dot edu
No rar, doc, or winmail.dat files, please!
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=1048

Can't help you with cvapp; you might try contacting Robert Cannon.

livius · Post by **livius** » Thu Nov 08, 2007 12:32 pm

Thanks Ted, i've sent you an e-mail with my swc
i also tried to contact R.Cannon but haven't managed to efficiently send an email 'caus it turns back to me

do you know an updated address?

thanks if you can help me :)

Post by **ted** » Sat Nov 10, 2007 12:27 pm

The problem was caused by the fact that the user's swc file used the "continental" style of
formatting floating point numbers, i.e. commas as the separator between the whole and
fractional parts. Thus PI would be written as 3,141...

Global search and replace of , with . resolved the issue.

darrenmyatt · Post by **darrenmyatt** » Mon Mar 31, 2008 9:09 am

This particular error has been pointed out to me, and as a consequence later versions of Neuromantic now force the standard decimal point formatting.

Also, you should still be able to load any files created before this fix and then resave them out normally :)

Post by **ted** » Mon Mar 31, 2008 10:28 am

Thanks. I'm sure that international users with detailed morphometric data will welcome this
new feature of Neuromantic.

darrenmyatt · Post by **darrenmyatt** » Mon Mar 31, 2008 10:38 am

ted wrote:Thanks. I'm sure users of NEURON and Neuromantic will welcome this new feature.

It's not so much a new feature as the removal of a horrific bug that I never saw coming ;) I'd never even considered how the behaviour of the program would change under different localisation settings.

Anyway, it was technically fixed in V1.4.5 onwards (which was released in late September 2007), so this hasn't been an issue for a while. I just wanted to confirm this for anyone who comes across this thread.

Using cvapp with Neuron_Morpho

Using cvapp with Neuron_Morpho

[HELP] Using cvapp with Neuron_Morpho