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section points and lengths don't match #330
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+1, I can take care of this with a couple of other things I had in mind. @rythorpe did you have a PR upcoming / local changes or can I take a go at the code? |
I can see how this might be a problem if we're using @jasmainak I don't have any local changes yet but was planning on diving into it tonight. If you're cool with waiting, that'd be ideal. |
Okay, go for it! I have other things on my plate for now :) |
Note that Neuron adjusts L and section points so that they match. So, I'm assuming whatever was set later is used for the simulation. Looking at our code, it seems that it is |
Yikes, that's pretty bold behaviour! We should throw mismatch exceptions rather than counting on Neuron. Isn't this related to #314? In the sense that we have to make a choice on what our primary source of geometric information is. In #334 you mentioned that
I really like the idea of storing cell morphology in a file, and infer |
Okay let's think of the right file format then. I'll get the ball rolling here with a table, you guys can edit and make it more detailed:
I think we could delegate the reading to Neuron by the way, same as LFPy folks have done. Then we could get all these different readers for free. Disadvantage might be that some numerical precision might be lost? For the ASC format, I can't figure out if the membrance capacitance and resistivity can be stored. Is that going to be stored in our file as well or do we populate it later? In any case, we need to decide what's the right file format to store the default cells in. I'm leaning towards NeuroML based on the fields I have filled so far ... |
For example (in
params_default.py
):get_L5Pyr_params_default()
:'L5Pyr_apicaltrunk_L': 102.
, but_secs_L5Pyr()
:sec_pts = { ... 'apical_trunk': [[0, 23, 0], [0, 83, 0]], ...
That is, based on the 3D section end points, the apical trunk is 60 microns long, whereas the
L
-parameter is explicitly set to 102. NEURON usesL
in simulations.I propose that this be fixed by adjusting the
sec_pts
to match theL
-values. WDYT? Could be a good First Issue for someone?Related to #165 and #327
Ping @jasmainak @ntolley @rythorpe
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