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MAINT: setting up gui cell params default values
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@kmilo9999
kmilo9999 committed Jul 9, 2024
1 parent 9510844 commit 77ef4fc
Showing 1 changed file with 115 additions and 80 deletions.
195 changes: 115 additions & 80 deletions hnn_core/gui/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,84 +26,98 @@
from hnn_core.network import pick_connection
from hnn_core.params import _extract_drive_specs_from_hnn_params
from hnn_core.dipole import _read_dipole_txt
from hnn_core.cells_default import pyramidal
from hnn_core.params_default import (get_L2Pyr_params_default,
get_L5Pyr_params_default)

import base64
import zipfile
import numpy as np
from copy import deepcopy

cell_parameters_dic = {

class CellParamGui():
def __init__(self, cell_type, layer, label, units):
self.layer = layer
self.cell_type = cell_type
self.label = label
self.units = units


cell_parameters_dict = {

"Geometry":
[
('Soma lenght', 'micron'),
('Soma diameter', 'micron'),
('Soma capacitive density', 'F/cm2'),
('Soma resistivity', 'ohm-cm'),
('Dendrite capacitive density', 'F/cm2'),
('Dendrite resistivity', 'ohm-cm'),
('Apical Dendrite Trunk lenght', 'micron'),
('Apical Dendrite 1 lenght', 'micron'),
('Apical Dendrite 1 diameter', 'micron'),
('Apical Dendrite Tuft lenght', 'micron'),
('Apical Dendrite Tuft diameter', 'micron'),
('Oblique Apical Dendrite lenght', 'micron'),
('Oblique Apical Dendrite diameter', 'micron'),
('Basal Dendrite 1 lenght', 'micron'),
('Basal Dendrite 1 diameter', 'micron'),
('Basal Dendrite 2 lenght', 'micron'),
('Basal Dendrite 2 diameter', 'micron'),
('Basal Dendrite 3 lenght', 'micron'),
('Basal Dendrite 3 diameter', 'micron')
('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 1 length', 'micron', 'apicaltrunk_diam'),
('Apical Dendrite 1 diameter', 'micron', 'apical1_L'),
('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')
],
"Synapses":
[
('AMPA reversal', 'mV'),
('AMPA rise time', 'ms'),
('AMPA decay time', 'ms'),
('NMDA reversal', 'mV'),
('NMDA rise time', 'ms'),
('NMDA decay time', 'ms'),
('GABAA reversal', 'mV'),
('GABAA rise time', 'ms'),
('GABAA decay time', 'ms'),
('GABAB reversal', 'mV'),
('GABAB rise time', 'ms'),
('GABAB decay time', 'ms')
('AMPA reversal', 'mV', 'ampa_e'),
('AMPA rise time', 'ms', 'ampa_tau1'),
('AMPA decay time', 'ms', 'ampa_tau2'),
('NMDA reversal', 'mV', 'nmda_e'),
('NMDA rise time', 'ms', 'nmda_tau1'),
('NMDA decay time', 'ms', 'nmda_tau2'),
('GABAA reversal', 'mV', 'gabaa_e'),
('GABAA rise time', 'ms', 'gabaa_tau1'),
('GABAA decay time', 'ms', 'gabaa_tau2'),
('GABAB reversal', 'mV', 'gabab_e'),
('GABAB rise time', 'ms', 'gabab_tau1'),
('GABAB decay time', 'ms', 'gabab_tau2')
],
"Biophysics L2":
[
('Soma Kv channel density', 'S/cm2'),
('Soma Na channel density', 'S/cm2'),
('Soma leak reversal', 'mV'),
('Soma leak channel density', 'S/cm2'),
('Soma Km channel density', 'pS/micron2'),
('Dendrite Kv channel density', 'S/cm2'),
('Dendrite Na channel density', 'S/cm2'),
('Dendrite leak reversal', 'mV'),
('Dendrite leak channel density', 'S/cm2'),
('Dendrite Km channel density', 'pS/micron2')
('Soma Kv channel density', 'S/cm2', 'soma_gkbar_hh2'),
('Soma Na channel density', 'S/cm2', 'soma_gnabar_hh2'),
('Soma leak reversal', 'mV', 'soma_el_hh2'),
('Soma leak channel density', 'S/cm2', 'soma_gl_hh2'),
('Soma Km channel density', 'pS/micron2', 'soma_gbar_km'),
('Dendrite Kv channel density', 'S/cm2', 'dend_gkbar_hh2'),
('Dendrite Na channel density', 'S/cm2', 'dend_gnabar_hh2'),
('Dendrite leak reversal', 'mV', 'dend_el_hh2'),
('Dendrite leak channel density', 'S/cm2', 'dend_gl_hh2'),
('Dendrite Km channel density', 'pS/micron2', 'dend_gbar_km')
],
"Biophysics L5":
[
('Soma Kv channel density', 'S/cm2'),
('Soma Na channel density', 'S/cm2'),
('Soma leak reversal', 'mV'),
('Soma leak channel density', 'S/cm2'),
('Soma Ca channel density', 'pS/micron2'),
('Soma Ca decay time', 'ms'),
('Soma Kca channel density', 'pS/micron2'),
('Soma Km channel density', 'pS/micron2'),
('Soma CaT channel density', 'S/cm2'),
('Soma HCN channel density', 'S/cm2'),
('Dendrite Kv channel density', 'S/cm2'),
('Dendrite Na channel density', 'S/cm2'),
('Dendrite leak reversal', 'mV'),
('Dendrite leak channel density', 'S/cm2'),
('Dendrite KCa channel density', 'pS/micron2'),
('Dendrite Km channel density', 'pS/micron2'),
('Dendrite CaT channel density', 'S/cm2'),
('Dendrite HCN channel density', 'S/cm2')
('Soma Kv channel density', 'S/cm2', 'soma_gkbar_hh2'),
('Soma Na channel density', 'S/cm2', 'soma_gnabar_hh2'),
('Soma leak reversal', 'mV', 'soma_el_hh2'),
('Soma leak channel density', 'S/cm2', 'soma_gl_hh2'),
('Soma Ca channel density', 'pS/micron2', 'soma_gbar_ca'),
('Soma Ca decay time', 'ms', 'soma_taur_cad'),
('Soma Kca channel density', 'pS/micron2', 'soma_gbar_kca'),
('Soma Km channel density', 'pS/micron2', 'soma_gbar_km'),
('Soma CaT channel density', 'S/cm2', 'soma_gbar_cat'),
('Soma HCN channel density', 'S/cm2', 'soma_gbar_ar'),
('Dendrite Kv channel density', 'S/cm2', 'dend_gkbar_hh2'),
('Dendrite Na channel density', 'S/cm2', 'dend_gnabar_hh2'),
('Dendrite leak reversal', 'mV', 'dend_el_hh2'),
('Dendrite leak channel density', 'S/cm2', 'dend_gl_hh2'),
('Dendrite Ca channel density', 'pS/micron2', 'dend_gbar_ca'),
('Dendrite Ca decay time', 'ms', 'dend_taur_cad'),
('Dendrite KCa channel density', 'pS/micron2', 'dend_gbar_kca'),
('Dendrite Km channel density', 'pS/micron2', 'dend_gbar_km'),
('Dendrite CaT channel density', 'S/cm2', 'dend_gbar_cat'),
('Dendrite HCN channel density', 'S/cm2', 'dend_gbar_ar')
]
}

Expand Down Expand Up @@ -1365,30 +1379,36 @@ def add_cell_parameters_tab(network, cell_params_out, cell_pameters_vboxes,
cell_layer_radio_button, cell_type_radio_button,
layout):

cell_types = ["L2", "L5"]
L2_defautl_values = get_L2Pyr_params_default()
L5_default_values = get_L5Pyr_params_default()
cell_types = [("L2", L2_defautl_values), ("L5", L5_default_values)]
style = {'description_width': '235px'}
kwargs = dict(layout=layout, style=style)

# get_cell_params_dic_values(network.cell_types)
for cell_type in cell_types:
layer_parameters = list()
for layer in cell_parameters_dic.keys():
if 'Biophysic' in layer and cell_type not in layer:
for layer in cell_parameters_dict.keys():
if 'Biophysic' in layer and cell_type[0] not in layer:
continue

for parameter in cell_parameters_dic[layer]:
param_name = parameter[0]
param_units = parameter[1]
for parameter in cell_parameters_dict[layer]:
param_name, param_units, params_key = (parameter[0],
parameter[1],
parameter[2])
default_value = get_cell_param_default_value(
f'{cell_type[0]}Pyr_{params_key}', cell_type[1])
description = f"{param_name} ({param_units})"
text_field = BoundedFloatText(value=0.0,
min=0,
max=10.0,
min_value = -1000.0 if param_units not in 'ms' else 0
text_field = BoundedFloatText(value=default_value,
min=min_value,
max=1000.0,
step=0.1,
description=description,
disabled=False,
**kwargs)
layer_parameters.append(text_field)
cell_pameters_key = cell_type + "_" + layer
cell_pameters_key = f'{cell_type[0]}_{layer}'
cell_pameters_vboxes[cell_pameters_key] = VBox(layer_parameters)
layer_parameters.clear()

Expand All @@ -1405,15 +1425,8 @@ def add_cell_parameters_tab(network, cell_params_out, cell_pameters_vboxes,
cell_layer_radio_button.value))


def get_cell_params_dic_values(network_cell_types):
# cell_types = [ct for ct in network_cell_types.keys()
# if "pyramidal" in ct]
...
# for type in cell_types:
# cell_type = network_cell_types[type]
# # get geometry params

# cell_types.sections['soma']
def get_cell_param_default_value(cell_type_key, param_dict):
return param_dict[cell_type_key]


def add_drive_tab(params, log_out, drives_out, drive_widgets, drive_boxes,
Expand Down Expand Up @@ -1549,7 +1562,7 @@ def on_upload_params_change(change, tstop, dt, log_out, drive_boxes,

def _init_network_from_widgets(params, dt, tstop, single_simulation_data,
drive_widgets, connectivity_textfields,
add_drive=True):
cell_pararms_widgets, add_drive=True):
"""Construct network and add drives."""
print("init network")
params['dt'] = dt.value
Expand All @@ -1576,6 +1589,28 @@ def _init_network_from_widgets(params, dt, tstop, single_simulation_data,
single_simulation_data['net'].connectivity[conn_idx][
'probability'] = vbox.children[2].value

# add cell parameters
# Geometry
cell_type_template = dict()
for cell_layer in cell_pararms_widgets.keys():
if 'Geometry' in cell_layer:
float_text_fields = cell_pararms_widgets[cell_layer].children
cell_type = cell_layer.split('_')[0]
# at this point only L2 and L5 should be in the cell_type variable
# althought, it still has the Pyr substring as suffix

Check failure on line 1600 in hnn_core/gui/gui.py

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althought ==> although
geometry_param_list = cell_parameters_dict['Geometry']
for index, geometry_param in enumerate(geometry_param_list):
# proccess a list of tuples (label,units,desc_key)

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proccess ==> process
cell_pameters_key = f'{cell_type}_{geometry_param[2]}'
cell_type_template[cell_pameters_key] = (
float_text_fields[index].value)
l_geometry_template = pyramidal(cell_type,
override_params=cell_type_template)
print(l_geometry_template)
# single_simulation_data['net']._add_cell_type(cell_type,cell_template=l_geometry_template)
# clean dictionary for next cell type geometry
cell_type_template.clear()

if add_drive is False:
return
# add drives to network
Expand Down

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