[MRG] make L5/L2 pyr have different geometry options in GUI (jonescom…

…pneurolab#848)

* WIP make l2/l5 pyr have different geometry

* fix cell params copying and add tests

* fix cell params test

* remove comments

* add back in break

hnn_core/gui/gui.py

@@ -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,
@@ -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
@@ -41,7 +43,7 @@
 
 cell_parameters_dict = {
 
-    "Geometry":
+    "Geometry L2":
     [
         ('Soma length', 'micron', 'soma_L'),
         ('Soma diameter', 'micron', 'soma_diam'),
@@ -64,6 +66,32 @@
         ('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'),
@@ -1459,7 +1487,8 @@ def add_cell_parameters_tab(cell_params_out, cell_pameters_vboxes,
     for cell_type in cell_types:
         layer_parameters = list()
         for layer in cell_parameters_dict.keys():
-            if 'Biophysic' in layer and cell_type[0] not in layer:
+            if ('Biophysic' in layer or 'Geometry' in layer) and \
+                    cell_type[0] not in layer:
                 continue
 
             for parameter in cell_parameters_dict[layer]:
@@ -1658,7 +1687,8 @@ 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
@@ -1671,7 +1701,12 @@ 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  # update needed only once per vbox_key
+
+    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
@@ -1819,7 +1854,7 @@ 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:
@@ -1828,7 +1863,7 @@ 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'
 
@@ -1850,6 +1885,37 @@ 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
@@ -1867,7 +1933,7 @@ def _update_synapse_cell_params(net, cell_param_key, param_list):
     param_indices = [
         (0, 1, 2), (3, 4, 5), (6, 7, 8), (9, 10, 11)]
 
-    # Update Dentrite
+    # Update Dendrite
     for section, indices in zip(synapse_sections, param_indices):
         network_synapses[section]['e'] = cell_params[indices[0]].value
         network_synapses[section]['tau1'] = cell_params[indices[1]].value
@@ -1955,7 +2021,9 @@ 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)
 
@@ -1965,7 +2033,7 @@ def update_common_dendrite_sections(sections, mechs_params):
         name for name in sections.keys() if name != 'soma'
     ]
     for section in dendrite_sections:
-        sections[section].mechs.update(mechs_params)
+        sections[section].mechs.update(deepcopy(mechs_params))
 
 
 def _serialize_simulation(log_out, sim_data, simulation_list_widget):

hnn_core/tests/test_gui.py

@@ -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,
@@ -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, add_drives_from_params=True)
+
+    assert _single_simulation['net'] == net
+
 
 @requires_mpi4py
 @requires_psutil
@@ -774,7 +781,8 @@ def test_gui_cell_params_widgets(setup_gui):
 
     # Check the if the cell params dictionary has been updated
     cell_params = gui.get_cell_parameters_dict()
-    assert (len(cell_params['Geometry']) == 20)
+    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)