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MAINT: Refactoring ui cell params datastructure #860

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MAINT: Refactoring ui cell params datastructure #860

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066ff87
MAINT: Refactoring ui cell params dictionary. Reimplemented as a nump…
kmilo9999 Aug 13, 2024
4f1da72
MAINT: Removed debuggy import
kmilo9999 Aug 13, 2024
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299 changes: 165 additions & 134 deletions hnn_core/gui/gui.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,108 +41,125 @@
default_network_configuration = (hnn_core_root / 'param' /
'jones2009_base.json')

cell_parameters_dict = {
"Geometry L2":
[
('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 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'),
('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_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_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_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')
]
}
# Define the structured array data type
data_types = np.dtype([
('Label', 'U50'),
('Units', 'U10'),
('Param_Key', 'U20'),
('Layer', 'U15'),
('CELL_TYPE', 'U10')
])

ui_cell_params_data = np.array([
('Soma length', 'micron', 'soma_L',
'Geometry', 'L2 L5'),
('Soma diameter', 'micron', 'soma_diam',
'Geometry', 'L2 L5'),
('Soma capacitive density', 'F/cm2', 'soma_cm',
'Geometry', 'L2 L5'),
('Soma resistivity', 'ohm-cm', 'soma_Ra',
'Geometry', 'L2 L5'),
('Dendrite capacitive density', 'F/cm2', 'dend_cm',
'Geometry', 'L2 L5'),
('Dendrite resistivity', 'ohm-cm', 'dend_Ra',
'Geometry', 'L2 L5'),
('Apical Dendrite Trunk length', 'micron', 'apicaltrunk_L',
'Geometry', 'L2 L5'),
('Apical Dendrite Trunk diameter', 'micron', 'apicaltrunk_diam',
'Geometry', 'L2 L5'),
('Apical Dendrite 1 length', 'micron', 'apical1_L',
'Geometry', 'L2 L5'),
('Apical Dendrite 1 diameter', 'micron', 'apical1_diam',
'Geometry', 'L2 L5'),
('Apical Dendrite 2 length', 'micron', 'apical2_L',
'Geometry', 'L5'),
('Apical Dendrite 2 diameter', 'micron', 'apical2_diam',
'Geometry', 'L5'),
('Apical Dendrite Tuft length', 'micron', 'apicaltuft_L',
'Geometry', 'L2 L5'),
('Apical Dendrite Tuft diameter', 'micron', 'apicaltuft_diam',
'Geometry', 'L2 L5'),
('Oblique Apical Dendrite length', 'micron', 'apicaloblique_L',
'Geometry', 'L2 L5'),
('Oblique Apical Dendrite diameter', 'micron', 'apicaloblique_diam',
'Geometry', 'L2 L5'),
('Basal Dendrite 1 length', 'micron', 'basal1_L',
'Geometry', 'L2 L5'),
('Basal Dendrite 1 diameter', 'micron', 'basal1_diam',
'Geometry', 'L2 L5'),
('Basal Dendrite 2 length', 'micron', 'basal2_L',
'Geometry', 'L2 L5'),
('Basal Dendrite 2 diameter', 'micron', 'basal2_diam',
'Geometry', 'L2 L5'),
('Basal Dendrite 3 length', 'micron', 'basal3_L',
'Geometry', 'L2 L5'),
('Basal Dendrite 3 diameter', 'micron', 'basal3_diam',
'Geometry', 'L2 L5'),
('AMPA reversal', 'mV', 'ampa_e',
'Synapses', 'L2 L5'),
('AMPA rise time', 'ms', 'ampa_tau1',
'Synapses', 'L2 L5'),
('AMPA decay time', 'ms', 'ampa_tau2',
'Synapses', 'L2 L5'),
('NMDA reversal', 'mV', 'nmda_e',
'Synapses', 'L2 L5'),
('NMDA rise time', 'ms', 'nmda_tau1',
'Synapses', 'L2 L5'),
('NMDA decay time', 'ms', 'nmda_tau2',
'Synapses', 'L2 L5'),
('GABAA reversal', 'mV', 'gabaa_e',
'Synapses', 'L2 L5'),
('GABAA rise time', 'ms', 'gabaa_tau1',
'Synapses', 'L2 L5'),
('GABAA decay time', 'ms', 'gabaa_tau2',
'Synapses', 'L2 L5'),
('GABAB reversal', 'mV', 'gabab_e',
'Synapses', 'L2 L5'),
('GABAB rise time', 'ms', 'gabab_tau1',
'Synapses', 'L2 L5'),
('GABAB decay time', 'ms', 'gabab_tau2',
'Synapses', 'L2 L5'),
('Soma Kv channel density', 'S/cm2', 'soma_gkbar_hh2',
'Biophysics', 'L2 L5'),
('Soma Na channel density', 'S/cm2', 'soma_gnabar_hh2',
'Biophysics', 'L2 L5'),
('Soma leak reversal', 'mV', 'soma_el_hh2',
'Biophysics', 'L2 L5'),
('Soma leak channel density', 'S/cm2', 'soma_gl_hh2',
'Biophysics', 'L2 L5'),
('Soma Ca channel density', 'pS/micron2', 'soma_gbar_ca',
'Biophysics', 'L5'),
('Soma Ca decay time', 'ms', 'soma_taur_cad',
'Biophysics', 'L5'),
('Soma Kca channel density', 'pS/micron2', 'soma_gbar_kca',
'Biophysics', 'L5'),
('Soma Km channel density', 'pS/micron2', 'soma_gbar_km',
'Biophysics', 'L2 L5'),
('Soma CaT channel density', 'S/cm2', 'soma_gbar_cat',
'Biophysics', 'L5'),
('Soma HCN channel density', 'S/cm2', 'soma_gbar_ar',
'Biophysics', 'L5'),
('Dendrite Kv channel density', 'S/cm2', 'dend_gkbar_hh2',
'Biophysics', 'L2 L5'),
('Dendrite Na channel density', 'S/cm2', 'dend_gnabar_hh2',
'Biophysics', 'L2 L5'),
('Dendrite leak reversal', 'mV', 'dend_el_hh2',
'Biophysics', 'L2 L5'),
('Dendrite leak channel density', 'S/cm2', 'dend_gl_hh2',
'Biophysics', 'L2 L5'),
('Dendrite Ca channel density', 'pS/micron2', 'dend_gbar_ca',
'Biophysics', 'L5'),
('Dendrite Ca decay time', 'ms', 'dend_taur_cad',
'Biophysics', 'L5'),
('Dendrite KCa channel density', 'pS/micron2', 'dend_gbar_kca',
'Biophysics', 'L5'),
('Dendrite Km channel density', 'pS/micron2', 'dend_gbar_km',
'Biophysics', 'L2 L5'),
('Dendrite CaT channel density', 'S/cm2', 'dend_gbar_cat',
'Biophysics', 'L5'),
('Dendrite HCN channel density', 'S/cm2', 'dend_gbar_ar',
'Biophysics', 'L5')
], dtype=data_types)


class _OutputWidgetHandler(logging.Handler):
Expand Down Expand Up @@ -425,11 +442,13 @@ def __init__(self, theme_color="#802989",
self._init_ui_components()
self.add_logging_window_logger()

def get_cell_parameters_dict(self):
"""Returns the number of elements in the
cell_parameters_dict dictionary.
def count_cell_parametes(self, layer, celltype):
"""Returns cell_parameters dictionary.
This is for testing purposes """
return cell_parameters_dict
selected_elements = ui_cell_params_data[
(ui_cell_params_data['Layer'] == layer) &
(np.char.find(ui_cell_params_data['CELL_TYPE'], celltype) >= 0)]
return len(selected_elements)

def _init_html_download_button(self):
b64 = base64.b64encode("".encode())
Expand Down Expand Up @@ -1479,6 +1498,30 @@ def add_network_connectivity_tab(net, connectivity_out,
return net


def build_cell_params_table(cell_params_data, cell_type,
default_values_function, style):
layer_parameters = []
for row in cell_params_data:
param_name = row['Label']
param_units = row['Units']
param_key = row['Param_Key']
default_value = get_cell_param_default_value(
f'{cell_type}Pyr_{param_key}', default_values_function)
description = f"{param_name} ({param_units})"
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,
**style)
text_field.layout.width = "350px"
layer_parameters.append(text_field)

return layer_parameters


def add_cell_parameters_tab(cell_params_out, cell_pameters_vboxes,
cell_layer_radio_button, cell_type_radio_button,
layout):
Expand All @@ -1488,33 +1531,23 @@ def add_cell_parameters_tab(cell_params_out, cell_pameters_vboxes,
style = {'description_width': '255px'}
kwargs = dict(layout=layout, style=style)

for cell_type in cell_types:
layer_parameters = list()
for layer in cell_parameters_dict.keys():
if ('Biophysic' in layer or 'Geometry' in layer) and \
cell_type[0] not in layer:
continue

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})"
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)
text_field.layout.width = "350px"
layer_parameters.append(text_field)
cell_pameters_key = f'{cell_type[0]} Pyramidal_{layer}'
unique_cell_layers = np.unique(ui_cell_params_data['Layer'])

for layer in unique_cell_layers:
for cell_type, default_values in cell_types:
cell_params_table = (
ui_cell_params_data[
(ui_cell_params_data['Layer'] == layer) &
(np.char.find(ui_cell_params_data['CELL_TYPE'],
cell_type) >= 0)])

layer_parameters = build_cell_params_table(cell_params_table,
cell_type,
default_values,
kwargs)

cell_pameters_key = f'{cell_type} Pyramidal_{layer}'
cell_pameters_vboxes[cell_pameters_key] = VBox(layer_parameters)
layer_parameters.clear()

# clear existing connectivity
cell_params_out.clear_output()
Expand Down Expand Up @@ -1868,8 +1901,6 @@ 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" or 'Geometry' in cell_layer:
cell_parameters_key += f" {cell_type.split(' ')[0]}"

if cell_parameters_key in cell_parameters_list:
cell_type_out.clear_output()
Expand Down
11 changes: 5 additions & 6 deletions hnn_core/tests/test_gui.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -811,12 +811,11 @@ def test_gui_cell_params_widgets(setup_gui):
assert (len(keys) == num_cell_params)

# Check the if the cell params dictionary has been updated
cell_params = gui.get_cell_parameters_dict()
assert (len(cell_params['Geometry L2']) == 20)
assert (len(cell_params['Geometry L5']) == 22)
assert (len(cell_params['Synapses']) == 12)
assert (len(cell_params['Biophysics L2']) == 10)
assert (len(cell_params['Biophysics L5']) == 20)
assert (gui.count_cell_parametes('Geometry', 'L2') == 20)
assert (gui.count_cell_parametes('Geometry', 'L5') == 22)
assert (gui.count_cell_parametes('Synapses', 'L2') == 12)
assert (gui.count_cell_parametes('Biophysics', 'L2') == 10)
assert (gui.count_cell_parametes('Biophysics', 'L5') == 20)


def test_fig_tabs_dropdown_lists(setup_gui):
Expand Down
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