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0558c72 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | import ipywidgets
import numpy as np
import pylab as plt
from traitlets import link
#default input parameters
default_capacitance = 1
default_cond_Na = 120
default_cond_K = 36
default_cond_L = 0.3
default_pot_Na = 50
default_pot_K = -77
default_pot_L = -54.387
default_t0 = 0
default_tn = 150
default_deltat = 0.01
#default_amplitude = 10 #Python version
default_amplitude = 0.1 #NeuroML version
default_width = 100
default_translation = 25
#function to reset input values to default on button click
def resetTodefault(_):
slider_capacitance.value = default_capacitance
slider_cond_Na.value = default_cond_Na
slider_cond_K.value = default_cond_K
slider_cond_L.value = default_cond_L
slider_pot_Na.value = default_pot_Na
slider_pot_K.value = default_pot_K
slider_pot_L.value = default_pot_L
time_start.value = default_t0
time_end.value = default_tn
time_step.value = default_deltat
slider_amplitude.value = default_amplitude
slider_width.value = default_width
slider_translation.value = default_translation
def showDefault(response):
if showValue_togglebtn.value:
defalultValues.layout.display = ''
else:
defalultValues.layout.display = 'none'
#function to change slider handle colour when move from default
def highlight_slider():
inputList = [slider_capacitance, slider_cond_Na, slider_cond_K, slider_cond_L, slider_pot_Na, slider_pot_K, slider_pot_L, slider_amplitude, slider_width, slider_translation]
inputDefault = [default_capacitance, default_cond_Na, default_cond_K, default_cond_L, default_pot_Na, default_pot_K, default_pot_L, default_amplitude, default_width, default_translation]
for l, d in zip(inputList,inputDefault):
if l.value == d:
l.style.handle_color = 'white'
else:
l.style.handle_color = 'orange'
#defining the widgets
#Header or texts as HTMLMath to include symbols
header_capacitance = ipywidgets.HTMLMath(value=r"<b> Membrane Capacitance, \(\mu{F}/cm^2\)</b>")
header_conductance = ipywidgets.HTMLMath(value=r"<b> Maximum Conductances, \(mS/cm^2\)</b>")
header_potential = ipywidgets.HTMLMath(value=r"<b> Nernst Reverasal Potentials, \(mV\)</b>")
header_simTime = ipywidgets.HTMLMath(value=r"<b> Simulation Time, \(ms\)</b>")
#header_injCurrent = ipywidgets.HTMLMath(value=r"<b> Injection Current, \(\mu{A}/cm^2\)</b>") #Python version
header_injCurrent = ipywidgets.HTMLMath(value=r"<b> Injection Current, \(nA\)</b>") #NeuroML version
#injCurrent_note = ipywidgets.HTML(value=f"<i>*For injection current duration = 0, the model uses default pulse signal from tutorial</i>")
#slider widgets
slider_capacitance = ipywidgets.FloatSlider(value=default_capacitance,min=0,max=3,step=0.1,description='Capacitance',readout=False,continuous_update=False)
slider_cond_Na = ipywidgets.FloatSlider(value=default_cond_Na,min=0,max=160,step=0.1,description='Sodium',readout=False,continuous_update=False)
slider_cond_K = ipywidgets.FloatSlider(value=default_cond_K,min=0,max=80,step=0.1,description='Potassium',readout=False,continuous_update=False)
slider_cond_L = ipywidgets.FloatSlider(value=default_cond_L,min=0,max=1,step=0.1,description='Leak',readout=False,continuous_update=False)
slider_pot_Na = ipywidgets.FloatSlider(value=default_pot_Na,min=-100,max=100,step=0.1,description='Sodium',readout=False,continuous_update=False)
slider_pot_K = ipywidgets.FloatSlider(value=default_pot_K,min=-100,max=100,step=0.1,description='Potassium',readout=False,continuous_update=False)
slider_pot_L = ipywidgets.FloatSlider(value=default_pot_L,min=-100,max=100,step=0.1,description='Leak',readout=False,continuous_update=False)
slider_amplitude = ipywidgets.FloatSlider(value=default_amplitude,min=-20,max=200,step=0.1,description='Amplitude',readout=False,continuous_update=False)
slider_width = ipywidgets.FloatSlider(value=default_width,min=0,max=500,step=0.1,description='Duration',readout=False,continuous_update=False)
slider_translation = ipywidgets.FloatSlider(value=default_translation,min=0,max=250,step=0.1,description='Time Delay',readout=False,continuous_update=False)
#text box widgets
time_start = ipywidgets.FloatText(value=default_t0,description='Start Time',disabled=True)
time_end = ipywidgets.FloatText(value=default_tn,description='Total Time',disabled=False)
time_step = ipywidgets.FloatText(value=default_deltat,description='Time Step',disabled=False)
#text box widgets to link with sliders (included to type in values for slider inputs also)
textBox_capacitance = ipywidgets.FloatText(value=default_capacitance,step=0.1,layout=ipywidgets.Layout(width='5%'))
textBox_cond_Na = ipywidgets.FloatText(value=default_cond_Na,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_cond_K = ipywidgets.FloatText(value=default_cond_K,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_cond_L = ipywidgets.FloatText(value=default_cond_L,step=0.1,layout=ipywidgets.Layout(width='5%'))
textBox_pot_Na = ipywidgets.FloatText(value=default_pot_Na,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_pot_K = ipywidgets.FloatText(value=default_pot_K,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_pot_L = ipywidgets.FloatText(value=default_pot_L,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_amplitude = ipywidgets.FloatText(value=default_amplitude,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_width = ipywidgets.FloatText(value=default_width,step=1,layout=ipywidgets.Layout(width='5%'))
textBox_translation = ipywidgets.FloatText(value=default_translation,step=1,layout=ipywidgets.Layout(width='5%'))
#linking sliders and textbox for values
link_capacitance = link((slider_capacitance, 'value'), (textBox_capacitance, 'value'))
link_cond_Na = link((slider_cond_Na, 'value'), (textBox_cond_Na, 'value'))
link_cond_K = link((slider_cond_K, 'value'), (textBox_cond_K, 'value'))
link_cond_L = link((slider_cond_L, 'value'), (textBox_cond_L, 'value'))
link_pot_Na = link((slider_pot_Na, 'value'), (textBox_pot_Na, 'value'))
link_pot_K = link((slider_pot_K, 'value'), (textBox_pot_K, 'value'))
link_pot_L = link((slider_pot_L, 'value'), (textBox_pot_L, 'value'))
link_amplitude = link((slider_amplitude, 'value'), (textBox_amplitude, 'value'))
link_width = link((slider_width, 'value'), (textBox_width, 'value'))
link_translation = link((slider_translation, 'value'), (textBox_translation, 'value'))
#define reset button and connect to fucntion call
reset_button = ipywidgets.Button(description="Reset All",button_style='warning',tooltip='Reset to default values for all user inputs')
reset_button.on_click(resetTodefault)
#define toggle button and connect to fucntion call
showValue_togglebtn = ipywidgets.ToggleButton(value=False,description='Default Values',disabled=False,button_style='info',tooltip='Show/Hide default value below') # 'success', 'info', 'warning', 'danger' or ''
showValue_togglebtn.observe(showDefault)
defalultValues = ipywidgets.HTMLMath(value=r"\(C = 1.0\)<br>\(G_{Na} = 120, G_{K} = 36, G_{L} = 0.3\)<br>\(V_{Na} = 50, V_{K} = -77, G_{L} = -54.387\)")
defalultValues.layout.display = 'none'
#define run button and connect to fucntion call
run_button = ipywidgets.Button(description="Run NeuroML",button_style='success',tooltip='Execute NeuroML Model with above inputs and plot results') #NeuroML version
#layout widgets in column using HBox
h1=ipywidgets.HBox([header_capacitance])
h2=ipywidgets.HBox([slider_capacitance, textBox_capacitance])
h3=ipywidgets.HBox([header_conductance])
h4=ipywidgets.HBox([slider_cond_Na,textBox_cond_Na,slider_cond_K,textBox_cond_K,slider_cond_L,textBox_cond_L])
h5=ipywidgets.HBox([header_potential])
h6=ipywidgets.HBox([slider_pot_Na,textBox_pot_Na,slider_pot_K,textBox_pot_K,slider_pot_L,textBox_pot_L])
h7=ipywidgets.HBox([header_simTime])
h8=ipywidgets.HBox([time_start,time_end,time_step])
h9=ipywidgets.HBox([header_injCurrent])
#h10=ipywidgets.HBox([injCurrent_note])
h11=ipywidgets.HBox([slider_amplitude,textBox_amplitude,slider_width,textBox_width,slider_translation,textBox_translation])
h12=ipywidgets.HBox([reset_button,showValue_togglebtn])
h13=ipywidgets.HBox([defalultValues])
#layout vertically all the HBox defined above
modelInputs=ipywidgets.VBox([h1,h2,h3,h4,h5,h6,h7,h8,h9,h11,h12,h13]) |