Getting Ready for the new Release

[Michele Mattioni]

Hello people,

I'm thinking to release a new version of Neuronvisio, with the new Mac Instruction from Tom (uhuh!)

I've update the number of models available on ModelDb, shipped with Neuronvisio.

There are some issues standing there for now (https://github.com/mattions/neuronvisio/issues), but most of them are either on NEURON side, so we can't do too much about it, unless we know it has been solved.

If everybody is happy, I'm planning to just have a small release and go to 0.8.6.

What do you think? Any stopholder?

Cheers,

Michele

--
Michele Mattioni, PhD
http://michelemattioni.me

[Mike Vella]

Good idea!

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[Michele Mattioni]

Hello guys,

thanks to the reporting from Tom and the nice work on the docs, we have improved the support on MacOS and closed several issues. 

It was written in the doc, but it was not super clear before, so I rephrase it now:

"if the model does not have a mosinit.hoc, Neuronvisio cannot load it, because does not know what to load as master file. You can always load the relevant file following the section Hoc Intergration or Python integration."

You can find more info here http://neuronvisio.org/gettingstarted.html#loading-a-neuron-model-from-modeldb

If somebody with the Mac can try the development version and let me know if the open command works as expected, I'm planning to release the new version today or tomorrow.

you can install the development version with

   pip install --upgrade git+https://github.com/mattions/neuronvisio.git#egg=Neuronvisio

or if you are running it from your fork, just pull from upstream the latest commit.

Cheers,

Michele

[Mike Vella]

Michele, is neuronvisio neuroML-compatible? you may be interested to know that I have just released a stable libNeuroML: https://github.com/NeuralEnsemble/libNeuroML

[Michele Mattioni]

Neuronvisio is NeuroML compatible from day 1 using the NeuroML parser from NEURON:

http://neuronvisio.org/gettingstarted.html#loading-a-file

Cheers,

Michele.

[Tom Close]

Hi Michele, 

I can confirm that your fixes work, and everything else appears to be working as it should.

The only other issue that I ran into was updating the scaled text property in the visio when sliding the time. However, this turns out to be caused by a small bug in Mayavi when using it with VTK version 5.10 (which is the what is currently installed by the procedure I posted).

It is (a little ironically) caused by them incorrectly checking the VTK version. The required patch can be found here

https://github.com/mluessi/mayavi/commit/15b0774659932596dab27363fa8eefdb855fda8f#mayavi/modules/text.py

which is very easy to apply manually if you know what you are doing. However, I don't know the best way to incorporate this with the neuronvisio package you created which installs mayavi. The fix should now be in the mayavi trunk so you could probably point to that if you like, but that may cause other problems I suppose. The other alternative would be just to disable the text in visio when the vtk version is 5.10 (5.11 should work) until the next release of Mayavi since the time is already displayed in the main controls.

Great work again Michele. It is nice to be able to quickly browse the models on ModelDB, plot their morphologies and test them out. I have to say after my quick little dabble that a tool like this is pretty important because he morphologies in some of them look quite weird and for some of them the hoc code doesn't run. Maybe you need to incorporate a little ratings button on the side!

Cheers,

Tom 

[Michele Mattioni]

Hi Tom,

On Fri, Mar 8, 2013 at 3:35 AM, Tom Close <tclos...@gmail.com> wrote:

Hi Michele, 

I can confirm that your fixes work, and everything else appears to be working as it should.

that's cool :)

 

The only other issue that I ran into was updating the scaled text property in the visio when sliding the time. However, this turns out to be caused by a small bug in Mayavi when using it with VTK version 5.10 (which is the what is currently installed by the procedure I posted).

It is (a little ironically) caused by them incorrectly checking the VTK version. The required patch can be found here

https://github.com/mluessi/mayavi/commit/15b0774659932596dab27363fa8eefdb855fda8f#mayavi/modules/text.py

which is very easy to apply manually if you know what you are doing. However, I don't know the best way to incorporate this with the neuronvisio package you created which installs mayavi. The fix should now be in the mayavi trunk so you could probably point to that if you like, but that may cause other problems I suppose. The other alternative would be just to disable the text in visio when the vtk version is 5.10 (5.11 should work) until the next release of Mayavi since the time is already displayed in the main controls.

Ok. I've changed the install_requires to use pip with paver, so now we are pointing to the latest master of Mayavi. When they will release will pick a proper release.

 

Great work again Michele. It is nice to be able to quickly browse the models on ModelDB, plot their morphologies and test them out. I have to say after my quick little dabble that a tool like this is pretty important because he morphologies in some of them look quite weird and for some of them the hoc code doesn't run. Maybe you need to incorporate a little ratings button on the side!

Thank you very much!

For the rating, I think it's more fair to have what runs automatically, and what needs the user intervation. I think a rating system will be a minefield, but hey, I guess we can think about it.

This issue is the one which we could discuss and decide what to do: https://github.com/mattions/neuronvisio/issues/52

Or we can carry on with the ML.

Anyway, is somebody wants to take a stab, just let me know.

Cheers,

Michele