[MRG] check section lengths match L-parameter #373
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cjayb
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Codecov Report
@@ Coverage Diff @@
## master #373 +/- ##
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- Coverage 89.93% 89.81% -0.12%
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Files 16 15 -1
Lines 2930 2897 -33
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- Hits 2635 2602 -33
Misses 295 295
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| for pt in p_secs[sec_name]['sec_pts']: | ||
| h.pt3dadd(pt[0] + dx, | ||
| pt[1] + dy, | ||
| pt[2] + dz, 1, sec=sec) | ||
| # with pt3dconst==0, these will alter the 3d points defined above! |
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So I suppose this essentially functions to define the direction in which the section points?
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That must be it, yes, though the documentation manages to be pretty unclear...
hnn_core/tests/test_cells_default.py
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| @@ -1,6 +1,7 @@ | |||
| import pytest | |||
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| from neuron import h | |||
| from numpy import allclose, abs | |||
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| from numpy import allclose, abs | |
| import numpy as np |
more standard
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the other issue is that you are overriding the abs that comes natively from python that may lead to unexpected issues.
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fix this and I'll merge :)
hnn_core/tests/test_cells_default.py
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| # check that after building, the vertical sections have the length | ||
| # specified in get_L5Pyr_params_default (or overriden in a params file). | ||
| # Note that the lengths implied by _secs_L5Pyr are completely ignored: | ||
| # NEURON extends the sections as needed to match the sec.L 's | ||
| vertical_secs = ['basal_1', 'soma', 'apical_trunk', 'apical_1', 'apical_2', | ||
| 'apical_tuft'] | ||
| for sec_name in vertical_secs: | ||
| sec = l5p.sections[sec_name] | ||
| vert_len = abs(sec.z3d(1) - sec.z3d(0)) | ||
| assert allclose(vert_len, sec.L) |
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this test passes on master ... in other words it's not testing the new functionality
this is why I suggest starting by writing the test first
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or I suppose the point of this PR is only to clarify the code?
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Indeed, this is intended to allow us to close #330 knowing that it won't bite us in the rear end when we start accepting section points other than those hard-coded in the private functions _secs_*{Pyr|Basket}
| @@ -325,10 +325,12 @@ def _create_sections(self, p_secs, topology): | |||
| self.sections[sec_name] = sec | |||
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| h.pt3dclear(sec=sec) | |||
| h.pt3dconst(0, sec=sec) # be explicit, see documentation | |||
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is this needed when there is h.define_shape? I feel one is enough ...
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Neither are really needed (as you pointed out, the code worked before)
pt3dconstis set to '0' by default; I thought I'd make it explicit here to remind ourselves.- from the doc of pt3dadd:
Note: When L is changed, h.define_shape() should be executed to adjust the 3-d info so that branches appear connected.
I think it hasn't been a problem because none of our dendrites branch. Or do the last too basal ones...? I'm uncertain.
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can I just put it on record that I hate strongly dislike Neuron documentation :) Instead of raising sane errors, the onus is on the user to make sure things are executed in certain order with statements like "this may happen if you do this, but it may not be so bad ...".
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I'll counter-sign that one, and you can pick an even stronger word if you'd like ;)
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Thanks @cjayb ! |
Closes #330 by adding a test to check
sec.Lmatches the difference insec.z3d(1) - sec.z3d(0).I added a few lines to
Cellbased on the NEURON docs forpt3dadd: