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gui.py
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"""IPywidgets GUI."""
# Authors: Mainak Jas <[email protected]>
# Huzi Cheng <[email protected]>
import codecs
import io
import logging
import mimetypes
import multiprocessing
import sys
import urllib.parse
import urllib.request
from collections import defaultdict
from pathlib import Path
from datetime import datetime
from IPython.display import IFrame, display
from ipywidgets import (HTML, Accordion, AppLayout, BoundedFloatText,
BoundedIntText, Button, Dropdown, FileUpload, VBox,
HBox, IntText, Layout, Output, RadioButtons, Tab, Text,
Checkbox)
from ipywidgets.embed import embed_minimal_html
import hnn_core
from hnn_core import (JoblibBackend, MPIBackend, jones_2009_model, read_params,
simulate_dipole)
from hnn_core.gui._logging import logger
from hnn_core.gui._viz_manager import _VizManager, _idx2figname
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.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_dict = {
"Geometry":
[
('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')
],
"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')
]
}
class _OutputWidgetHandler(logging.Handler):
def __init__(self, output_widget, *args, **kwargs):
super(_OutputWidgetHandler, self).__init__(*args, **kwargs)
self.out = output_widget
def emit(self, record):
formatted_record = self.format(record)
new_output = {
'name': 'stdout',
'output_type': 'stream',
'text': formatted_record + '\n'
}
self.out.outputs = (new_output, ) + self.out.outputs
class HNNGUI:
"""HNN GUI class
Parameters
----------
theme_color : str
The theme color of the whole dashboard.
total_height : int
The height of the GUI (in pixel, same for all following parameters).
total_width : int
The width of the GUI.
header_height : int
The height of the header.
button_height : int
The height of buttons.
operation_box_height : int
The operation_box_height of operations box.
drive_widget_width : int
The width of GUI drive box.
left_sidebar_width : int
The width of left sidebad.
log_window_height : int
The height of logging window.
status_height : int
The height of status bar.
dpi : int
The screen dpi.
Attributes
----------
layout : dict
The styling configuration of GUI.
params : dict
The parameters to use for constructing the network.
simulation_data : dict
Simulation related objects, such as net and dpls.
widget_tstop : Widget
Simulation stop time widget.
widget_dt : Widget
Simulation step size widget.
widget_ntrials : Widget
Widget that controls the number of trials in a single simulation.
widget_backend_selection : Widget
Widget that selects the backend used in simulations.
widget_viz_layout_selection : Widget
Widget that selects the layout of visualization window.
widget_mpi_cmd : Widget
Widget that specify the mpi command to use when the backend is
MPIBackend.
widget_n_jobs : Widget
Widget that specify the cores in multi-trial simulations.
widget_drive_type_selection : Widget
Widget that is used to select the drive to be added to the network.
widget_location_selection : Widget.
Widget that specifies the location of network drives. Could be proximal
or distal.
add_drive_button : Widget
Clickable widget that is used to add a drive to the network.
run_button : Widget
Clickable widget that triggers simulation.
load_button : Widget
Clickable widget that receives uploaded parameter files.
delete_drive_button : Widget
Clickable widget that clear all existing network drives.
plot_outputs_dict : list
A list of visualization panel outputs.
plot_dropdown_types_dict : list
A list of dropdown menus that control the plot types in
plot_outputs_dict.
drive_widgets : list
A list of network drive widgets added by add_drive_button.
drive_boxes : list
A list of network drive layouts.
connectivity_textfields : list
A list of boxes that control the weight and probability of connections
in the network.
"""
def __init__(self, theme_color="#8A2BE2",
total_height=800,
total_width=1300,
header_height=50,
button_height=30,
operation_box_height=60,
drive_widget_width=200,
left_sidebar_width=576,
log_window_height=150,
status_height=30,
dpi=96,
):
# set up styling.
self.total_height = total_height
self.total_width = total_width
viz_win_width = self.total_width - left_sidebar_width
main_content_height = self.total_height - status_height
config_box_height = main_content_height - (log_window_height +
operation_box_height)
self.layout = {
"dpi": dpi,
"header_height": f"{header_height}px",
"theme_color": theme_color,
"btn": Layout(height=f"{button_height}px", width='auto'),
"run_btn": Layout(height=f"{button_height}px", width='10%'),
"btn_full_w": Layout(height=f"{button_height}px", width='100%'),
"del_fig_btn": Layout(height=f"{button_height}px", width='auto'),
"log_out": Layout(border='1px solid gray',
height=f"{log_window_height - 10}px",
overflow='auto'),
"viz_config": Layout(width='99%'),
"simulations_list": Layout(width=f'{left_sidebar_width - 50}px'),
"visualization_window": Layout(
width=f"{viz_win_width - 10}px",
height=f"{main_content_height - 10}px",
border='1px solid gray',
overflow='scroll'),
"visualization_output": Layout(
width=f"{viz_win_width - 50}px",
height=f"{main_content_height - 100}px",
border='1px solid gray',
overflow='scroll'),
"left_sidebar": Layout(width=f"{left_sidebar_width}px",
height=f"{main_content_height}px"),
"left_tab": Layout(width=f"{left_sidebar_width}px",
height=f"{config_box_height}px"),
"operation_box": Layout(width=f"{left_sidebar_width}px",
height=f"{operation_box_height}px",
flex_wrap="wrap",
),
"config_box": Layout(width=f"{left_sidebar_width}px",
height=f"{config_box_height - 100}px"),
"drive_widget": Layout(width="auto"),
"drive_textbox": Layout(width='270px', height='auto'),
# simulation status related
"simulation_status_height": f"{status_height}px",
"simulation_status_common": "background:gray;padding-left:10px",
"simulation_status_running": "background:orange;padding-left:10px",
"simulation_status_failed": "background:red;padding-left:10px",
"simulation_status_finished": "background:green;padding-left:10px",
}
self._simulation_status_contents = {
"not_running":
f"""<div style='{self.layout['simulation_status_common']};
color:white;'>Not running</div>""",
"running":
f"""<div style='{self.layout['simulation_status_running']};
color:white;'>Running...</div>""",
"finished":
f"""<div style='{self.layout['simulation_status_finished']};
color:white;'>Simulation finished</div>""",
"failed":
f"""<div style='{self.layout['simulation_status_failed']};
color:white;'>Simulation failed</div>""",
}
# load default parameters
self.params = self.load_parameters()
# In-memory storage of all simulation and visualization related data
self.simulation_data = defaultdict(lambda: dict(net=None, dpls=list()))
# Simulation parameters
self.widget_tstop = BoundedFloatText(
value=170, description='tstop (ms):', min=0, max=1e6, step=1,
disabled=False)
self.widget_dt = BoundedFloatText(
value=0.025, description='dt (ms):', min=0, max=10, step=0.01,
disabled=False)
self.widget_ntrials = IntText(value=1, description='Trials:',
disabled=False)
self.widget_simulation_name = Text(value='default',
placeholder='ID of your simulation',
description='Name:',
disabled=False)
self.widget_backend_selection = Dropdown(options=[('Joblib', 'Joblib'),
('MPI', 'MPI')],
value='Joblib',
description='Backend:')
self.widget_mpi_cmd = Text(value='mpiexec',
placeholder='Fill if applies',
description='MPI cmd:', disabled=False)
self.widget_n_jobs = BoundedIntText(value=1, min=1,
max=multiprocessing.cpu_count(),
description='Cores:',
disabled=False)
self.load_data_button = FileUpload(
accept='.txt,.csv', multiple=False,
style={'button_color': self.layout['theme_color']},
layout=self.layout['btn'],
description='Load data',
button_style='success')
# Create save simulation widget wrapper
self.save_simuation_button = self._init_html_download_button()
self.simulation_list_widget = Dropdown(options=[],
value=None,
description='',
layout={'width': '15%'})
# Drive selection
self.widget_drive_type_selection = RadioButtons(
options=['Evoked', 'Poisson', 'Rhythmic', 'Tonic'],
value='Evoked',
description='Drive:',
disabled=False,
layout=self.layout['drive_widget'])
self.widget_location_selection = RadioButtons(
options=['proximal', 'distal'], value='proximal',
description='Location', disabled=False,
layout=self.layout['drive_widget'])
self.add_drive_button = create_expanded_button(
'Add drive', 'primary', layout=self.layout['btn'],
button_color=self.layout['theme_color'])
# Dashboard level buttons
self.run_button = create_expanded_button(
'Run', 'success', layout=self.layout['run_btn'],
button_color=self.layout['theme_color'])
self.load_connectivity_button = FileUpload(
accept='.json,.param', multiple=False,
style={'button_color': self.layout['theme_color']},
description='Load local network connectivity',
layout=self.layout['btn_full_w'], button_style='success')
self.load_drives_button = FileUpload(
accept='.json,.param', multiple=False,
style={'button_color': self.layout['theme_color']},
description='Load external drives', layout=self.layout['btn'],
button_style='success')
self.delete_drive_button = create_expanded_button(
'Delete drives', 'success', layout=self.layout['btn'],
button_color=self.layout['theme_color'])
self.cell_type_radio_buttons = RadioButtons(
options=['L2 Pyramidal', 'L5 Pyramidal'],
description='Cell type:')
self.cell_layer_radio_buttons = RadioButtons(
options=['Geometry', 'Synapses', 'Biophysics'],
description='Cell Properties:')
# Plotting window
# Visualization figure related dicts
self.plot_outputs_dict = dict()
self.plot_dropdown_types_dict = dict()
self.plot_sim_selections_dict = dict()
# Add drive section
self.drive_widgets = list()
self.drive_boxes = list()
# Connectivity list
self.connectivity_widgets = list()
# Cell parameter list
self.cell_pameters_widgets = dict()
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.
This is for testing purposes """
return cell_parameters_dict
def _init_html_download_button(self):
b64 = base64.b64encode("".encode())
payload = b64.decode()
# Initialliting HTML code for download button
self.html_download_button = '''
<a download="{filename}" href="data:text/csv;base64,{payload}"
download>
<button style="background:{color_theme}; height:{btn_height}"
class=" jupyter-button
mod-warning" {is_disabled} >Save Simulation</button>
</a>
'''
# Create widget wrapper
return (
HTML(self.html_download_button.
format(payload=payload,
filename={""},
is_disabled="disabled",
btn_height=self.layout['run_btn'].height,
color_theme=self.layout['theme_color'])))
def add_logging_window_logger(self):
handler = _OutputWidgetHandler(self._log_out)
handler.setFormatter(
logging.Formatter('%(asctime)s - [%(levelname)s] %(message)s'))
logger.addHandler(handler)
def _init_ui_components(self):
"""Initialize larger UI components and dynamical output windows.
It's not encouraged for users to modify or access attributes in this
part.
"""
# dynamic larger components
self._drives_out = Output() # tab to add new drives
self._connectivity_out = Output() # tab to tune connectivity.
self._cell_params_out = Output()
self._log_out = Output()
self.viz_manager = _VizManager(self.data, self.layout)
# detailed configuration of backends
self._backend_config_out = Output()
# static parts
# Running status
self._simulation_status_bar = HTML(
value=self._simulation_status_contents['not_running'])
self._log_window = HBox([self._log_out], layout=self.layout['log_out'])
self._operation_buttons = HBox(
[self.run_button, self.load_data_button,
self.save_simuation_button,
self.simulation_list_widget],
layout=self.layout['operation_box'])
# title
self._header = HTML(value=f"""<div
style='background:{self.layout['theme_color']};
text-align:center;color:white;'>
HUMAN NEOCORTICAL NEUROSOLVER</div>""")
@property
def analysis_config(self):
"""Provides everything viz window needs except for the data."""
return {
"viz_style": self.layout['visualization_output'],
# widgets
"plot_outputs": self.plot_outputs_dict,
"plot_dropdowns": self.plot_dropdown_types_dict,
"plot_sim_selections": self.plot_sim_selections_dict,
"current_sim_name": self.widget_simulation_name.value,
}
@property
def data(self):
"""Provides easy access to simulation-related data."""
return {"simulation_data": self.simulation_data}
@staticmethod
def load_parameters(params_fname=None):
"""Read parameters from file."""
if not params_fname:
# by default load default.json
hnn_core_root = Path(hnn_core.__file__).parent
params_fname = hnn_core_root / 'param/default.json'
return read_params(params_fname)
def _link_callbacks(self):
"""Link callbacks to UI components."""
def _handle_backend_change(backend_type):
return handle_backend_change(backend_type.new,
self._backend_config_out,
self.widget_mpi_cmd,
self.widget_n_jobs)
def _add_drive_button_clicked(b):
return add_drive_widget(self.widget_drive_type_selection.value,
self.drive_boxes, self.drive_widgets,
self._drives_out, self.widget_tstop,
self.widget_location_selection.value,
layout=self.layout['drive_textbox'])
def _delete_drives_clicked(b):
self._drives_out.clear_output()
# black magic: the following does not work
# global drive_widgets; drive_widgets = list()
while len(self.drive_widgets) > 0:
self.drive_widgets.pop()
self.drive_boxes.pop()
def _on_upload_connectivity(change):
return on_upload_params_change(
change, self.widget_tstop, self.widget_dt,
self._log_out, self.drive_boxes, self.drive_widgets,
self._drives_out, self._connectivity_out,
self.connectivity_widgets, self._cell_params_out,
self.cell_pameters_widgets, self.cell_layer_radio_buttons,
self.cell_type_radio_buttons, self.layout['drive_textbox'],
"connectivity")
def _on_upload_drives(change):
return on_upload_params_change(
change, self.widget_tstop, self.widget_dt,
self._log_out, self.drive_boxes, self.drive_widgets,
self._drives_out, self._connectivity_out,
self.connectivity_widgets, self._cell_params_out,
self.cell_pameters_widgets, self.cell_layer_radio_buttons,
self.cell_type_radio_buttons, self.layout['drive_textbox'],
"drives")
def _on_upload_data(change):
return on_upload_data_change(change, self.data, self.viz_manager,
self._log_out)
def _run_button_clicked(b):
return run_button_clicked(
self.widget_simulation_name, self._log_out, self.drive_widgets,
self.data, self.widget_dt, self.widget_tstop,
self.widget_ntrials, self.widget_backend_selection,
self.widget_mpi_cmd, self.widget_n_jobs, self.params,
self._simulation_status_bar, self._simulation_status_contents,
self.connectivity_widgets, self.viz_manager,
self.simulation_list_widget, self.cell_pameters_widgets)
def _simulation_list_change(value):
_simulation_data, file_extension = (
_serialize_simulation(self._log_out,
self.data,
self.simulation_list_widget))
result_file = f"{value.new}{file_extension}"
if file_extension == ".csv":
b64 = base64.b64encode(_simulation_data.encode())
else:
b64 = base64.b64encode(_simulation_data)
payload = b64.decode()
self.save_simuation_button.value = (
self.html_download_button.format(
payload=payload, filename=result_file,
is_disabled="", btn_height=self.layout['run_btn'].height,
color_theme=self.layout['theme_color']))
def _driver_type_change(value):
self.widget_location_selection.disabled = (
True if value.new == "Tonic" else False)
def _cell_type_radio_change(value):
_update_cell_params_vbox(self._cell_params_out,
self.cell_pameters_widgets,
value.new,
self.cell_layer_radio_buttons.value)
def _cell_layer_radio_change(value):
_update_cell_params_vbox(self._cell_params_out,
self.cell_pameters_widgets,
self.cell_type_radio_buttons.value,
value.new)
self.widget_backend_selection.observe(_handle_backend_change, 'value')
self.add_drive_button.on_click(_add_drive_button_clicked)
self.delete_drive_button.on_click(_delete_drives_clicked)
self.load_connectivity_button.observe(_on_upload_connectivity,
names='value')
self.load_drives_button.observe(_on_upload_drives, names='value')
self.run_button.on_click(_run_button_clicked)
self.load_data_button.observe(_on_upload_data, names='value')
self.simulation_list_widget.observe(_simulation_list_change, 'value')
self.widget_drive_type_selection.observe(_driver_type_change, 'value')
self.cell_type_radio_buttons.observe(_cell_type_radio_change,
'value')
self.cell_layer_radio_buttons.observe(_cell_layer_radio_change,
'value')
def compose(self, return_layout=True):
"""Compose widgets.
Parameters
----------
return_layout : bool
If the method returns the layout object which can be rendered by
IPython.display.display() method.
"""
simulation_box = VBox([
VBox([
self.widget_simulation_name, self.widget_tstop, self.widget_dt,
self.widget_ntrials, self.widget_backend_selection,
self._backend_config_out]),
], layout=self.layout['config_box'])
connectivity_configuration = Tab()
connectivity_box = VBox([
HBox([self.load_connectivity_button, ]),
self._connectivity_out,
])
cell_parameters = VBox([
HBox([self.cell_type_radio_buttons,
self.cell_layer_radio_buttons]),
self._cell_params_out
])
connectivity_configuration.children = [connectivity_box,
cell_parameters]
connectivity_configuration.titles = ['Connectivity',
'Cell parameters']
drive_selections = VBox([
self.add_drive_button, self.widget_drive_type_selection,
self.widget_location_selection],
layout=Layout(flex="1"))
drives_options = VBox([
HBox([
VBox([self.load_drives_button, self.delete_drive_button],
layout=Layout(flex="1")),
drive_selections,
]), self._drives_out
])
config_panel, figs_output = self.viz_manager.compose()
# Tabs for left pane
left_tab = Tab()
left_tab.children = [
simulation_box, connectivity_configuration, drives_options,
config_panel,
]
titles = ('Simulation', 'Network', 'External drives',
'Visualization')
for idx, title in enumerate(titles):
left_tab.set_title(idx, title)
self.app_layout = AppLayout(
header=self._header,
left_sidebar=VBox([
VBox([left_tab], layout=self.layout['left_tab']),
self._operation_buttons,
self._log_window,
], layout=self.layout['left_sidebar']),
right_sidebar=figs_output,
footer=self._simulation_status_bar,
pane_widths=[
self.layout['left_sidebar'].width, '0px',
self.layout['visualization_window'].width
],
pane_heights=[
self.layout['header_height'],
self.layout['visualization_window'].height,
self.layout['simulation_status_height']
],
)
self._link_callbacks()
# initialize drive and connectivity ipywidgets
load_drive_and_connectivity(self.params, self._log_out,
self._drives_out, self.drive_widgets,
self.drive_boxes, self._connectivity_out,
self.connectivity_widgets,
self._cell_params_out,
self.cell_pameters_widgets,
self.cell_layer_radio_buttons,
self.cell_type_radio_buttons,
self.widget_tstop, self.layout)
if not return_layout:
return
else:
return self.app_layout
def show(self):
display(self.app_layout)
def capture(self, width=None, height=None, extra_margin=100, render=True):
"""Take a screenshot of the current GUI.
Parameters
----------
width : int | None
The width of iframe window use to show the snapshot.
height : int | None
The height of iframe window use to show the snapshot.
extra_margin: int
Extra margin in pixel for the GUI.
render : bool
Will return an IFrame object if False
Returns
-------
snapshot : An iframe snapshot object that can be rendered in notebooks.
"""
file = io.StringIO()
embed_minimal_html(file, views=[self.app_layout], title='')
if not width:
width = self.total_width + extra_margin
if not height:
height = self.total_height + extra_margin
content = urllib.parse.quote(file.getvalue().encode('utf8'))
data_url = f"data:text/html,{content}"
screenshot = IFrame(data_url, width=width, height=height)
if render:
display(screenshot)
else:
return screenshot
def run_notebook_cells(self):
"""Run all but the last cells sequentially in a Jupyter notebook.
To properly use this function:
1. Put this into the penultimate cell.
2. init the HNNGUI in a single cell.
3. Hit 'run all' button to run the whole notebook and it will
selectively run twice.
"""
js_string = """
function sleep(ms) {
return new Promise(resolve => setTimeout(resolve, ms));
}
function getRunningStatus(idx){
const htmlContent = Jupyter.notebook.get_cell(idx).element[0];
return htmlContent.childNodes[0].childNodes[0].textContent;
}
function cellContainsInitOrMarkdown(idx){
const cell = Jupyter.notebook.get_cell(idx);
if(cell.cell_type!=='code'){
return true;
}
else{
const textVal = cell.element[0].childNodes[0].textContent;
return textVal.includes('HNNGUI()') || textVal.includes(
'HNNGUI');
}
}
function cellContainsRunCells(idx){
const textVal = Jupyter.notebook.get_cell(
idx).element[0].childNodes[0].textContent;
return textVal.includes('run_notebook_cells()');
}
async function runNotebook() {
console.log("run notebook cell by cell");
const cellHtmlContents = Jupyter.notebook.element[0].children[0];
const nCells = cellHtmlContents.childElementCount;
console.log(`In total we have ${nCells} cells`);
for(let i=1; i<nCells-1; i++){
if(cellContainsRunCells(i)){
break
}
else if(cellContainsInitOrMarkdown(i)){
console.log(`Skip init or markdown cell ${i}...`);
continue
}
else{
console.log(`About to execute cell ${i}..`);
Jupyter.notebook.execute_cells([i]);
while (getRunningStatus(i).includes("*")){
console.log("Still running, wait for another 2 secs");
await sleep(2000);
}
await sleep(1000);
}
}
console.log('Done');
}
runNotebook();
"""
return js_string
# below are a series of methods that are used to manipulate the GUI
def _simulate_upload_data(self, file_url):
uploaded_value = _prepare_upload_file(file_url)
self.load_data_button.set_trait('value', uploaded_value)
def _simulate_upload_connectivity(self, file_url):
uploaded_value = _prepare_upload_file(file_url)
self.load_connectivity_button.set_trait('value', uploaded_value)
def _simulate_upload_drives(self, file_url):
uploaded_value = _prepare_upload_file(file_url)
self.load_drives_button.set_trait('value', uploaded_value)
def _simulate_left_tab_click(self, tab_title):
# Get left tab group object
left_tab = self.app_layout.left_sidebar.children[0].children[0]
# Check that the title is in the tab group
if tab_title in left_tab.titles:
# Simulate the user clicking on the tab
left_tab.selected_index = left_tab.titles.index(tab_title)
else:
raise ValueError("Tab title does not exist.")
def _simulate_make_figure(self,):
self._simulate_left_tab_click("Visualization")
self.viz_manager.make_fig_button.click()
def _simulate_viz_action(self, action_name, *args, **kwargs):
"""A shortcut to call simulated actions in _VizManager.
Parameters
----------
action_name : str
The action to take. For example, to call `_simulate_add_fig` in
_VizManager, you can run `_simulate_viz_action("add_fig")`
args : list
Optional positional parameters passed to the called method.
kwargs: dict
Optional keyword parameters passed to the called method.
"""
self._simulate_left_tab_click("Visualization")
action = getattr(self.viz_manager, f"_simulate_{action_name}")
action(*args, **kwargs)
def _prepare_upload_file_from_local(path):
path = Path(path)
with open(path, 'rb') as file:
content = memoryview(file.read())
last_modified = datetime.fromtimestamp(path.stat().st_mtime)
upload_structure = [{
'name': path.name,
'type': mimetypes.guess_type(path)[0],
'size': path.stat().st_size,
'content': content,
'last_modified': last_modified
}]
return upload_structure
def _prepare_upload_file_from_url(file_url):
file_name = file_url.split("/")[-1]
data = urllib.request.urlopen(file_url)
content = bytearray()
for line in data:
content.extend(line)
upload_structure = [{
'name': file_name,
'type': mimetypes.guess_type(file_url)[0],
'size': len(content),
'content': memoryview(content),
'last_modified': datetime.now()
}]
return upload_structure
def _prepare_upload_file(path):
""" Simulates output of the FileUpload widget for testing.
Unit tests for the GUI simulate user upload of files. File source can
either be local or from a URL. This function returns the data structure
of the ipywidget FileUpload widget, a list of dictionaries with file
attributes.
"""
try:
uploaded_value = _prepare_upload_file_from_local(path)
except (FileNotFoundError, OSError):
uploaded_value = _prepare_upload_file_from_url(path)
return uploaded_value
def _update_nested_dict(original, new, skip_none=True):
""" Updates dictionary values from another dictionary
Will update nested dictionaries in the structure. New items from the
update dictionary are added and omitted items are retained from the
original dictionary. By default, will not pass None values from the update
dictionary.
Parameters
----------
original : dict
Dictionary to update
new : dict
Dictionary with new values for updating
skip_none : bool, default True
None values in the new dictionary are not passed to the updated
dictionary by when True. If False None values will be passed to the
updated dictionary.
Returns dict
-------
"""
updated = original.copy()
for key, value in new.items():
if (isinstance(value, dict) and
key in updated and
isinstance(updated[key], dict)):
updated[key] = _update_nested_dict(updated[key], value, skip_none)
elif (value is not None) or (not skip_none):
updated[key] = value
else:
pass
return updated
def create_expanded_button(description, button_style, layout, disabled=False,
button_color="#8A2BE2"):
return Button(description=description, button_style=button_style,
layout=layout, style={'button_color': button_color},
disabled=disabled)
def _get_connectivity_widgets(conn_data):
"""Create connectivity box widgets from specified weight and probability"""
style = {'description_width': '150px'}
style = {}
sliders = list()
for receptor_name in conn_data.keys():
w_text_input = BoundedFloatText(
value=conn_data[receptor_name]['weight'], disabled=False,
continuous_update=False, min=0, max=1e6, step=0.01,
description="weight", style=style)
conn_widget = VBox([
HTML(value=f"""<p>
Receptor: {conn_data[receptor_name]['receptor']}</p>"""),
w_text_input, HTML(value="<hr style='margin-bottom:5px'/>")
])
conn_widget._belongsto = {
"receptor": conn_data[receptor_name]['receptor'],
"location": conn_data[receptor_name]['location'],
"src_gids": conn_data[receptor_name]['src_gids'],
"target_gids": conn_data[receptor_name]['target_gids'],
}
sliders.append(conn_widget)
return sliders
def _get_cell_specific_widgets(layout, style, location, data=None):
default_data = {
'weights_ampa': {
'L5_pyramidal': 0.,
'L2_pyramidal': 0.,
'L5_basket': 0.,
'L2_basket': 0.
},
'weights_nmda': {
'L5_pyramidal': 0.,
'L2_pyramidal': 0.,
'L5_basket': 0.,
'L2_basket': 0.
},
'delays': {
'L5_pyramidal': 0.1,
'L2_pyramidal': 0.1,
'L5_basket': 0.1,
'L2_basket': 0.1
},
}
if isinstance(data, dict):
default_data = _update_nested_dict(default_data, data)
kwargs = dict(layout=layout, style=style)
cell_types = ['L5_pyramidal', 'L2_pyramidal', 'L5_basket', 'L2_basket']
if location == "distal":
cell_types.remove('L5_basket')
weights_ampa, weights_nmda, delays = dict(), dict(), dict()
for cell_type in cell_types:
weights_ampa[f'{cell_type}'] = BoundedFloatText(
value=default_data['weights_ampa'][cell_type],
description=f'{cell_type}:', min=0, max=1e6, step=0.01, **kwargs)
weights_nmda[f'{cell_type}'] = BoundedFloatText(
value=default_data['weights_nmda'][cell_type],
description=f'{cell_type}:', min=0, max=1e6, step=0.01, **kwargs)