Skip to content

Commit

Permalink
WIP make l2/l5 pyr have different geometry
Browse files Browse the repository at this point in the history
  • Loading branch information
@ntolley
ntolley committed Aug 1, 2024
1 parent 773a86d commit a75eb00
Show file tree
Hide file tree
Showing 2 changed files with 81 additions and 7 deletions.
79 changes: 73 additions & 6 deletions hnn_core/gui/gui.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
from collections import defaultdict
from pathlib import Path
from datetime import datetime
from functools import partial
from IPython.display import IFrame, display
from ipywidgets import (HTML, Accordion, AppLayout, BoundedFloatText,
BoundedIntText, Button, Dropdown, FileUpload, VBox,
Expand All @@ -29,6 +30,7 @@
from hnn_core.params_default import (get_L2Pyr_params_default,
get_L5Pyr_params_default)
from hnn_core.hnn_io import dict_to_network
from hnn_core.cells_default import _exp_g_at_dist

import base64
import zipfile
Expand All @@ -41,7 +43,7 @@

cell_parameters_dict = {

"Geometry":
"Geometry L2":
[
('Soma length', 'micron', 'soma_L'),
('Soma diameter', 'micron', 'soma_diam'),
Expand All @@ -53,6 +55,34 @@
('Apical Dendrite Trunk diameter', 'micron', 'apicaltrunk_diam'),
('Apical Dendrite 1 length', 'micron', 'apical1_L'),
('Apical Dendrite 1 diameter', 'micron', 'apical1_diam'),
# ('Apical Dendrite 2 length', 'micron', 'apical2_L'),
# ('Apical Dendrite 2 diameter', 'micron', 'apical2_diam'),
('Apical Dendrite Tuft length', 'micron', 'apicaltuft_L'),
('Apical Dendrite Tuft diameter', 'micron', 'apicaltuft_diam'),
('Oblique Apical Dendrite length', 'micron', 'apicaloblique_L'),
('Oblique Apical Dendrite diameter', 'micron', 'apicaloblique_diam'),
('Basal Dendrite 1 length', 'micron', 'basal1_L'),
('Basal Dendrite 1 diameter', 'micron', 'basal1_diam'),
('Basal Dendrite 2 length', 'micron', 'basal2_L'),
('Basal Dendrite 2 diameter', 'micron', 'basal2_diam'),
('Basal Dendrite 3 length', 'micron', 'basal3_L'),
('Basal Dendrite 3 diameter', 'micron', 'basal3_diam')
],

"Geometry L5":
[
('Soma length', 'micron', 'soma_L'),
('Soma diameter', 'micron', 'soma_diam'),
('Soma capacitive density', 'F/cm2', 'soma_cm'),
('Soma resistivity', 'ohm-cm', 'soma_Ra'),
('Dendrite capacitive density', 'F/cm2', 'dend_cm'),
('Dendrite resistivity', 'ohm-cm', 'dend_Ra'),
('Apical Dendrite Trunk length', 'micron', 'apicaltrunk_L'),
('Apical Dendrite Trunk diameter', 'micron', 'apicaltrunk_diam'),
('Apical Dendrite 1 length', 'micron', 'apical1_L'),
('Apical Dendrite 1 diameter', 'micron', 'apical1_diam'),
('Apical Dendrite 2 length', 'micron', 'apical2_L'),
('Apical Dendrite 2 diameter', 'micron', 'apical2_diam'),
('Apical Dendrite Tuft length', 'micron', 'apicaltuft_L'),
('Apical Dendrite Tuft diameter', 'micron', 'apicaltuft_diam'),
('Oblique Apical Dendrite length', 'micron', 'apicaloblique_L'),
Expand Down Expand Up @@ -1656,7 +1686,8 @@ def _init_network_from_widgets(params, dt, tstop, single_simulation_data,
# Update cell params

update_functions = {
'Geometry': _update_geometry_cell_params,
'L2 Geometry': _update_L2_geometry_cell_params,
'L5 Geometry': _update_L5_geometry_cell_params,
'Synapses': _update_synapse_cell_params,
'L2 Pyramidal_Biophysics': _update_L2_biophysics_cell_params,
'L5 Pyramidal_Biophysics': _update_L5_biophysics_cell_params
Expand All @@ -1669,7 +1700,11 @@ def _init_network_from_widgets(params, dt, tstop, single_simulation_data,
cell_type = vbox_key.split()[0]
update_function(single_simulation_data['net'], cell_type,
cell_param_list.children)
break
break # why is this here?

for cell_type in single_simulation_data['net'].cell_types.keys():
single_simulation_data['net'].cell_types[cell_type]._update_end_pts()
single_simulation_data['net'].cell_types[cell_type]._compute_section_mechs()

if add_drive is False:
return
Expand Down Expand Up @@ -1817,7 +1852,7 @@ def run_button_clicked(widget_simulation_name, log_out, drive_widgets,
def _update_cell_params_vbox(cell_type_out, cell_parameters_list,
cell_type, cell_layer):
cell_parameters_key = f"{cell_type}_{cell_layer}"
if "Biophysics" in cell_layer:
if "Biophysics" or 'Geometry' in cell_layer:
cell_parameters_key += f" {cell_type.split(' ')[0]}"

if cell_parameters_key in cell_parameters_list:
Expand All @@ -1826,7 +1861,7 @@ def _update_cell_params_vbox(cell_type_out, cell_parameters_list,
display(cell_parameters_list[cell_parameters_key])


def _update_geometry_cell_params(net, cell_param_key, param_list):
def _update_L2_geometry_cell_params(net, cell_param_key, param_list):
cell_params = param_list
cell_type = f'{cell_param_key.split("_")[0]}_pyramidal'

Expand All @@ -1848,6 +1883,37 @@ def _update_geometry_cell_params(net, cell_param_key, param_list):
param_indices = [
(6, 7), (8, 9), (10, 11), (12, 13), (14, 15), (16, 17), (18, 19)]

# Dendrite
for section, indices in zip(dendrite_sections, param_indices):
sections[section]._L = cell_params[indices[0]].value
sections[section]._diam = cell_params[indices[1]].value
sections[section]._cm = dendrite_cm
sections[section]._Ra = dendrite_Ra


def _update_L5_geometry_cell_params(net, cell_param_key, param_list):
cell_params = param_list
cell_type = f'{cell_param_key.split("_")[0]}_pyramidal'

sections = net.cell_types[cell_type].sections
# Soma
sections['soma']._L = cell_params[0].value
sections['soma']._diam = cell_params[1].value
sections['soma']._cm = cell_params[2].value
sections['soma']._Ra = cell_params[3].value

# Dendrite common parameters
dendrite_cm = cell_params[4].value
dendrite_Ra = cell_params[5].value

dendrite_sections = [name for name in sections.keys()
if name != 'soma'
]

param_indices = [
(6, 7), (8, 9), (10, 11), (12, 13), (14, 15),
(16, 17), (18, 19), (20, 21)]

# Dentrite
for section, indices in zip(dendrite_sections, param_indices):
sections[section]._L = cell_params[indices[0]].value
Expand Down Expand Up @@ -1953,7 +2019,8 @@ def _update_L5_biophysics_cell_params(net, cell_param_key, param_list):
mechs_params['kca'] = {'gbar_kca': param_list[16].value}
mechs_params['km'] = {'gbar_km': param_list[17].value}
mechs_params['cat'] = {'gbar_cat': param_list[18].value}
mechs_params['ar'] = {'gbar_ar': param_list[19].value}
mechs_params['ar'] = {'gbar_ar': partial(_exp_g_at_dist, zero_val=param_list[19].value,
exp_term=3e-3, offset=0.0)}

update_common_dendrite_sections(sections, mechs_params)

Expand Down
9 changes: 8 additions & 1 deletion hnn_core/tests/test_gui.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
import os

from pathlib import Path
from hnn_core import Dipole, Network
from hnn_core import Dipole, Network, read_params, jones_2009_model
from hnn_core.gui import HNNGUI
from hnn_core.gui._viz_manager import (_idx2figname,
_plot_types,
Expand Down Expand Up @@ -283,6 +283,13 @@ def test_gui_init_network():
assert np.isclose(_single_simulation['net']._inplane_distance, 1.)
assert np.isclose(_single_simulation['net']._layer_separation, 1307.4)

default_network_configuration = read_params(hnn_core_root / 'param' / 'default.json')
net = jones_2009_model(params=default_network_configuration)
for section in _single_simulation['net'].cell_types['L5_pyramidal'].sections:
print(section)
# assert _single_simulation['net'].cell_types['L5_pyramidal'].sections[section].mechs == net.cell_types['L5_pyramidal'].sections[section].mechs
assert _single_simulation['net'].cell_types['L5_pyramidal'].sections[section].L == net.cell_types['L5_pyramidal'].sections[section].L


@requires_mpi4py
@requires_psutil
Expand Down

0 comments on commit a75eb00

Please sign in to comment.