question about contrib models MorrisLecar

[thierry.r...@gmail.com]

Dear TVB users and developers,

I have installed TVB following along the instructions reported here:

http://docs.thevirtualbrain.org/manuals/ContributorsManual/ContributorsManual.html

and I wanted to use the Morris Lecar model for didactical purposes.

However in my installation I do not have the folder contrib folder, so neither contrib/simulator/models that hosts the morris_lecar.py file.

I have created the folder and placed the morris_lecar file (https://github.com/the-virtual-brain/tvb-root/blob/master/tvb_contrib/tvb/contrib/simulator/models/morris_lecar.py) in that folder. 

Unfortunately even then I am running in the following error:

~/anaconda3/envs/tvb-run/lib/python3.7/site-packages/tvb/contrib/simulator/models/morris_lecar.py in __init__(self, **kwargs) 178 179 """ --> 180 LOG.info('%s: initing...' % str(self)) 181 super(MorrisLecar, self).__init__(**kwargs) 182 ~/anaconda3/envs/tvb-run/lib/python3.7/site-packages/tvb/basic/neotraits/_core.py in __str__(self) 183 184 def __str__(self): --> 185 return trait_object_str(self) 186 187 def _repr_html_(self): ~/anaconda3/envs/tvb-run/lib/python3.7/site-packages/tvb/basic/neotraits/info.py in trait_object_str(self) 133 def trait_object_str(self): 134 cls = type(self) --> 135 summary = self.summary_info() 136 result = ['{} ('.format(cls.__name__)] 137 maxlenk = max(len(k) for k in summary) ~/anaconda3/envs/tvb-run/lib/python3.7/site-packages/tvb/basic/neotraits/_core.py in summary_info(self) 237 cls = type(self) 238 ret = {'Type': cls.__name__} --> 239 if self.title: 240 ret['title'] = str(self.title) 241 AttributeError: 'MorrisLecar' object has no attribute 'title'

The code is:

import tvb.simulator.models as models
from tvb.contrib.simulator.models import morris_lecar
import numpy as np

dt=0.1
integ = integrators.HeunDeterministic(dt=dt)
oscil = morris_lecar.MorrisLecar() #variables_of_interest=['V','N'],gCa=np.array([4.])) - same 

I am wondering if there is maybe a more proper way to install the contrib and how to make it run. 

Thanks in advance.

Thierry

[Lia Domide]

Hi Thierry,

It seems that your environment is not completely set-up. Under `tvb_root` you have folder `tvb_contrib` were python module `tvb.contrib` is hosted.

       cd tvb_contrib

       python setup.py develop --no-deps 

Anyway, after `import tvb.contrib` works, I am able to reproduce your error. 

It seem to be a problem with the way these models (from under tvb_contrib) were translated (apparently incompletely) towards Python 3 and our neo-traits.

To make your example run, you should switch the two lines in morris_lecar.py, constructor MorrisLecar. __init__

       super(MorrisLecar, self).__init__(**kwargs)

       LOG.info('%s: initing...' % str(self))

We will add a task in the following development sprints to have these models fixed.

Let us know how these work for you.

Best,

Lia Domide

TVB technical team