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[MRG] MAINT: remove move_to_pos #314

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merged 6 commits into from
May 31, 2021
Merged

[MRG] MAINT: remove move_to_pos #314

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f39fa5d
MAINT: demo what move_to_pos does
jasmainak Apr 8, 2021
5a1a432
DOC: update whats new
jasmainak Apr 8, 2021
5372338
DEMO its numerical precision
jasmainak Apr 23, 2021
76c1ab2
ENH: dummy comment to demo issue with NEURON 8.0
jasmainak May 5, 2021
c418697
set position of sections upon creation
rythorpe May 31, 2021
c4fbd81
update comment and whats_new.rst
rythorpe May 31, 2021
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2 changes: 2 additions & 0 deletions doc/whats_new.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,8 @@ Changelog
Bug
~~~

- Remove rounding error caused by repositioning of NEURON cell sections, by `Mainak Jas`_ and `Ryan Thorpe`_ in `#314 <https://github.com/jonescompneurolab/hnn-core/pull/314>`_

API
~~~
- New API for defining cell-cell connections. Custom connections can be added with :func:`~hnn_core.Network.add_connection`, by `Nick Tolley`_ in `#276 <https://github.com/jonescompneurolab/hnn-core/pull/276>`_
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25 changes: 10 additions & 15 deletions hnn_core/cell.py
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Original file line number Diff line number Diff line change
Expand Up @@ -250,13 +250,22 @@ def _create_sections(self, p_secs, topology):
for height and xz plane for depth. This is opposite for model as a
whole, but convention is followed in this function ease use of gui.
"""
# distance from initial to final root postion
# Resolve: y-coordinate here corresponds to the z-coordinate in
# self.pos[2]
dx = self.pos[0] - self.p_secs['soma']['sec_pts'][0][0]
dy = self.pos[2] - self.p_secs['soma']['sec_pts'][0][1]
dz = self.pos[1] - self.p_secs['soma']['sec_pts'][0][2]

for sec_name in p_secs:
sec = h.Section(name=f'{self.name}_{sec_name}')
self.sections[sec_name] = sec

h.pt3dclear(sec=sec)
for pt in p_secs[sec_name]['sec_pts']:
h.pt3dadd(pt[0], pt[1], pt[2], 1, sec=sec)
h.pt3dadd(pt[0] + dx,
pt[1] + dy,
pt[2] + dz, 1, sec=sec)
Comment on lines +256 to +268
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The consequences of these lines are very confusing to me (still: I realise nothing has changed in that respect in this PR). Are we reorienting the apical sections to align with the Z-axis here?

In any case, we now have a situation where net.pos_dict, Cell.pos and the Section end points are inconsistent, right?

@rythorpe are you planning to address this in the follow-up you mention? I'm working on some qualified opinions about the spacing-issue too, based on "reduced" model literature.

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@jasmainak jasmainak Jun 1, 2021 •
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yes, we should be reorienting the apical sections to align with the Z-axis ... but maybe it's not the case?

The Section end points are specified relative to the Cell.pos or net.pos_dict ...

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now that I think of it, to reorient along the Z-axis, you'd need to do:

dy = self.pos[1] - self.p_secs['soma']['sec_pts'][0][2]

what might be more clear though is to apply a trans matrix first:

trans = [[1, 0, 0], [0, 0, 1], [0, 1, 0]]
self.p_secs['soma']['sec_pts'] = np.dot(trans, self.p_secs['soma']['sec_pts'])

there is a wealth of functions we can copy from MNE :) There is even a function to align along a target axis:

https://github.com/mne-tools/mne-python/blob/b3f4b05b3933a3b73458205c7e786166f90ad1f7/mne/transforms.py#L298

that we can use to our advantage

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I'm not sure I understand your question @cjayb. Are you asking about the implementation in this PR or what we plan to do in later PRs?

If we change the section endpoints in params_default.py, I think we should do that in a separate PR.

sec.L = p_secs[sec_name]['L']
sec.diam = p_secs[sec_name]['diam']
sec.Ra = p_secs[sec_name]['Ra']
Expand Down Expand Up @@ -301,20 +310,6 @@ def build(self, sec_name_apical=None):
f'section of the current cell or None. '
f'Got {sec_name_apical}.')

def move_to_pos(self):
"""Move cell to position."""
x0 = self.sections['soma'].x3d(0)
y0 = self.sections['soma'].y3d(0)
z0 = self.sections['soma'].z3d(0)
dx = self.pos[0] * 100 - x0
dy = self.pos[2] - y0
dz = self.pos[1] * 100 - z0

for s in list(self.sections.values()):
for i in range(s.n3d()):
h.pt3dchange(i, s.x3d(i) + dx, s.y3d(i) + dy,
s.z3d(i) + dz, s.diam3d(i), sec=s)

# two things need to happen here for h:
# 1. dipole needs to be inserted into each section
# 2. a list needs to be created with a Dipole (Point Process) in each
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8 changes: 0 additions & 8 deletions hnn_core/network_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -317,8 +317,6 @@ def _build(self):
self._all_spike_gids = h.Vector()

self._record_spikes()

self.move_cells_to_pos() # position cells in 2D grid
self._connect_celltypes()

if _get_rank() == 0:
Expand Down Expand Up @@ -482,7 +480,6 @@ def _record_spikes(self):
if _PC.gid_exists(gid):
_PC.spike_record(gid, self._spike_times, self._spike_gids)

# aggregate recording all the somatic voltages for pyr
def aggregate_data(self):
"""Aggregate somatic currents, voltages, and dipoles."""
for cell in self._cells:
Expand Down Expand Up @@ -516,11 +513,6 @@ def state_init(self):
elif cell.name == 'L5Basket':
seg.v = -64.9737

def move_cells_to_pos(self):
"""Move cells 3d positions to positions used for wiring."""
for cell in self._cells:
cell.move_to_pos()

def _clear_neuron_objects(self):
"""Clear up NEURON internal gid information.

Expand Down