def __init__(self, net, width="95%", height="550px", play_rate=0.5):
self._ignore_layer_updates = False
self.player = _Player(self, play_rate)
self.player.start()
self.net = net
r = random.randint(1, 1000000)
self.class_id = "picture-dashboard-%s-%s" % (self.net.name, r)
self._width = width
self._height = height
## Global widgets:
style = {"description_width": "initial"}
self.feature_columns = IntText(description="Detail columns:",
value=self.net.config["dashboard.features.columns"],
min=0,
max=1024,
style=style)
self.feature_scale = FloatText(description="Detail scale:",
value=self.net.config["dashboard.features.scale"],
min=0.1,
max=10,
style=style)
self.feature_columns.observe(self.regenerate, names='value')
self.feature_scale.observe(self.regenerate, names='value')
## Hack to center SVG as justify-content is broken:
self.net_svg = HTML(value="""<p style="text-align:center">%s</p>""" % ("",), layout=Layout(
width=self._width, overflow_x='auto', overflow_y="auto",
justify_content="center"))
# Make controls first:
self.output = Output()
controls = self.make_controls()
config = self.make_config()
super().__init__([config, controls, self.net_svg, self.output])
def _create_notebook_widget(self, index=None):
from ipywidgets import (FloatSlider, FloatText, Layout, HBox)
widget_bounds = self._interactive_slider_bounds(index=index)
thismin = FloatText(value=widget_bounds['min'],
description='min',
layout=Layout(flex='0 1 auto',
width='auto'),)
thismax = FloatText(value=widget_bounds['max'],
description='max',
layout=Layout(flex='0 1 auto',
width='auto'),)
current_value = self.value if index is None else self.value[index]
current_name = self.name
if index is not None:
current_name += '_{}'.format(index)
widget = FloatSlider(value=current_value,
min=thismin.value,
max=thismax.value,
step=widget_bounds['step'],
description=current_name,
layout=Layout(flex='1 1 auto', width='auto'))
def on_min_change(change):
if widget.max > change['new']:
widget.min = change['new']
widget.step = np.abs(widget.max - widget.min) * 0.001
def on_max_change(change):
if widget.min < change['new']:
widget.max = change['new']
widget.step = np.abs(widget.max - widget.min) * 0.001
thismin.observe(on_min_change, names='value')
thismax.observe(on_max_change, names='value')
this_observed = functools.partial(self._interactive_update,
index=index)
widget.observe(this_observed, names='value')
container = HBox((thismin, widget, thismax))
return container
def InteractivePlane_Sphere(self, scale="log", fieldvalue="E", compvalue="y"):
def foo(
Update,
Field,
AmpDir,
Component,
Sigma0,
Sigmab,
Sigma1,
Sigma2,
Sus,
d1,
h,
d2,
R,
Scale,
rxOffset,
z,
radius,
itime,
Geometry=True,
Fixed=False,
vmin=None,
vmax=None,
):
if AmpDir == "Direction (B or dBdt)":
Component = "vec"
self.setLayerSphereParam(
d1=d1,
h=h,
d2=d2,
R=R,
sig0=Sigma0,
sigb=Sigmab,
sig1=Sigma1,
sig2=Sigma2,
chi=Sus,
)
self.srcLoc = np.array([0.0, 0.0, z])
self.rxLoc = np.array([[rxOffset, 0.0, z]])
self.radius = radius
if Update:
self.simulate(self.srcLoc, self.rxLoc, self.time, self.radius)
self.getFields(itime)
return self.plotField(
Field=Field,
view=Component,
scale=Scale,
Geometry=Geometry,
itime=itime,
Scenario="Sphere",
Fixed=Fixed,
vmin=vmin,
vmax=vmax,
)
out = widgetify(
foo,
Update=widgets.widget_bool.Checkbox(value=True, description="Update"),
Field=widgets.ToggleButtons(
options=["E", "B", "dBdt", "J", "Model"], value=fieldvalue
),
AmpDir=widgets.ToggleButtons(
options=["None", "Direction (B or dBdt)"], value="None"
),
Component=widgets.ToggleButtons(
options=["x", "y", "z"], value=compvalue, description="Comp."
),
Sigma0=widgets.FloatText(
value=1e-8, continuous_update=False, description="$\sigma_0$ (S/m)"
),
Sigmab=widgets.FloatText(
value=0.01, continuous_update=False, description="$\sigma_b$ (S/m)"
),
Sigma1=widgets.FloatText(
value=0.01, continuous_update=False, description="$\sigma_1$ (S/m)"
),
Sigma2=widgets.FloatText(
value=1.0, continuous_update=False, description="$\sigma_2$ (S/m)"
),
Sus=widgets.FloatText(
value=0.0, continuous_update=False, description="$\chi$"
),
d1=widgets.FloatSlider(
min=0.0,
max=50.0,
step=2.0,
value=0.0,
continuous_update=False,
description="$d_1$ (m)",
),
h=widgets.FloatSlider(
min=2.0,
max=40.0,
step=2.0,
value=20.0,
continuous_update=False,
description="$h$ (m)",
),
d2=widgets.FloatSlider(
min=20.0,
max=80.0,
step=2.0,
value=60.0,
continuous_update=False,
description="$d_2$ (m)",
),
R=widgets.FloatSlider(
min=2.0,
max=40.0,
step=2.0,
value=30.0,
continuous_update=False,
description="$R$ (m)",
),
Scale=widgets.ToggleButtons(options=["log", "linear"], value="linear"),
rxOffset=widgets.FloatSlider(
min=0.0,
max=50.0,
step=2.0,
value=10.0,
continuous_update=False,
description="$\Delta x$(m)",
),
z=widgets.FloatSlider(
min=0.0,
max=50.0,
step=2.0,
value=0.0,
continuous_update=False,
description="$\Delta z$ (m)",
),
radius=widgets.FloatSlider(
min=2.0,
max=50.0,
step=2.0,
value=2.0,
continuous_update=False,
description="Tx radius (m)",
),
itime=widgets.IntSlider(
min=1,
max=70,
step=1,
value=1,
continuous_update=False,
description="Time index",
),
Fixed=widgets.widget_bool.Checkbox(value=False, description="Fixed"),
vmin=FloatText(value=None, description="vmin"),
vmax=FloatText(value=None, description="vmax"),
)
return out
def create_param_widget(self, param, value):
from ipywidgets import Layout, HBox
children = (HBox(), )
if isinstance(value, bool):
from ipywidgets import Label, ToggleButton
p = Label(value=param, layout=Layout(width="10%"))
t = ToggleButton(description=str(value), value=value)
def on_bool_change(change):
t.description = str(change["new"])
self.params[self._method][param] = change["new"]
self.replot_peaks()
t.observe(on_bool_change, names="value")
children = (p, t)
elif isinstance(value, float):
from ipywidgets import FloatSlider, FloatText, BoundedFloatText, Label
from traitlets import link
p = Label(value=param, layout=Layout(flex="0 1 auto", width="10%"))
b = BoundedFloatText(
value=0,
min=1e-10,
layout=Layout(flex="0 1 auto", width="10%"),
font_weight="bold",
)
a = FloatText(value=2 * value,
layout=Layout(flex="0 1 auto", width="10%"))
f = FloatSlider(
value=value,
min=b.value,
max=a.value,
step=np.abs(a.value - b.value) * 0.01,
layout=Layout(flex="1 1 auto", width="60%"),
)
lbl = FloatText(
value=f.value,
layout=Layout(flex="0 1 auto", width="10%"),
disabled=True,
)
link((f, "value"), (lbl, "value"))
def on_min_change(change):
if f.max > change["new"]:
f.min = change["new"]
f.step = np.abs(f.max - f.min) * 0.01
def on_max_change(change):
if f.min < change["new"]:
f.max = change["new"]
f.step = np.abs(f.max - f.min) * 0.01
def on_param_change(change):
self.params[self._method][param] = change["new"]
self.replot_peaks()
b.observe(on_min_change, names="value")
f.observe(on_param_change, names="value")
a.observe(on_max_change, names="value")
children = (p, lbl, b, f, a)
elif isinstance(value, int):
from ipywidgets import IntSlider, IntText, BoundedIntText, Label
from traitlets import link
p = Label(value=param, layout=Layout(flex="0 1 auto", width="10%"))
b = BoundedIntText(
value=0,
min=1e-10,
layout=Layout(flex="0 1 auto", width="10%"),
font_weight="bold",
)
a = IntText(value=2 * value,
layout=Layout(flex="0 1 auto", width="10%"))
f = IntSlider(
value=value,
min=b.value,
max=a.value,
step=1,
layout=Layout(flex="1 1 auto", width="60%"),
)
lbl = IntText(
value=f.value,
layout=Layout(flex="0 1 auto", width="10%"),
disabled=True,
)
link((f, "value"), (lbl, "value"))
def on_min_change(change):
if f.max > change["new"]:
f.min = change["new"]
f.step = 1
def on_max_change(change):
if f.min < change["new"]:
f.max = change["new"]
f.step = 1
def on_param_change(change):
self.params[self._method][param] = change["new"]
self.replot_peaks()
b.observe(on_min_change, names="value")
f.observe(on_param_change, names="value")
a.observe(on_max_change, names="value")
children = (p, lbl, b, f, a)
container = HBox(children)
return container
def __init__(self):
self.output_dir = '.'
# self.output_dir = 'tmpdir'
# self.fig = plt.figure(figsize=(7.2,6)) # this strange figsize results in a ~square contour plot
# initial value
self.field_index = 4
# self.field_index = self.mcds_field.value + 4
tab_height = '500px'
constWidth = '180px'
constWidth2 = '150px'
tab_layout = Layout(
width='900px', # border='2px solid black',
height=tab_height,
) #overflow_y='scroll')
max_frames = 1
self.mcds_plot = interactive(self.plot_substrate,
frame=(0, max_frames),
continuous_update=False)
svg_plot_size = '700px'
self.mcds_plot.layout.width = svg_plot_size
self.mcds_plot.layout.height = svg_plot_size
self.max_frames = BoundedIntText(
min=0,
max=99999,
value=max_frames,
description='Max',
layout=Layout(width='160px'),
)
self.max_frames.observe(self.update_max_frames)
self.field_min_max = {'dummy': [0., 1.]}
# hacky I know, but make a dict that's got (key,value) reversed from the dict in the Dropdown below
self.field_dict = {0: 'dummy'}
self.mcds_field = Dropdown(
options={'dummy': 0},
value=0,
# description='Field',
layout=Layout(width=constWidth))
# print("substrate __init__: self.mcds_field.value=",self.mcds_field.value)
# self.mcds_field.observe(self.mcds_field_cb)
self.mcds_field.observe(self.mcds_field_changed_cb)
# self.field_cmap = Text(
# value='viridis',
# description='Colormap',
# disabled=True,
# layout=Layout(width=constWidth),
# )
self.field_cmap = Dropdown(
options=['viridis', 'jet', 'YlOrRd'],
value='viridis',
# description='Field',
layout=Layout(width=constWidth))
#self.field_cmap.observe(self.plot_substrate)
# self.field_cmap.observe(self.plot_substrate)
self.field_cmap.observe(self.mcds_field_cb)
self.cmap_fixed = Checkbox(
description='Fix',
disabled=False,
# layout=Layout(width=constWidth2),
)
self.save_min_max = Button(
description='Save', #style={'description_width': 'initial'},
button_style=
'success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Save min/max for this substrate',
disabled=True,
layout=Layout(width='90px'))
def save_min_max_cb(b):
# field_name = self.mcds_field.options[]
# field_name = next(key for key, value in self.mcds_field.options.items() if value == self.mcds_field.value)
field_name = self.field_dict[self.mcds_field.value]
# print(field_name)
# self.field_min_max = {'oxygen': [0., 30.], 'glucose': [0., 1.], 'H+ ions': [0., 1.], 'ECM': [0., 1.], 'NP1': [0., 1.], 'NP2': [0., 1.]}
self.field_min_max[field_name][0] = self.cmap_min.value
self.field_min_max[field_name][1] = self.cmap_max.value
# print(self.field_min_max)
self.save_min_max.on_click(save_min_max_cb)
self.cmap_min = FloatText(
description='Min',
value=0,
step=0.1,
disabled=True,
layout=Layout(width=constWidth2),
)
self.cmap_min.observe(self.mcds_field_cb)
self.cmap_max = FloatText(
description='Max',
value=38,
step=0.1,
disabled=True,
layout=Layout(width=constWidth2),
)
self.cmap_max.observe(self.mcds_field_cb)
def cmap_fixed_cb(b):
if (self.cmap_fixed.value):
self.cmap_min.disabled = False
self.cmap_max.disabled = False
self.save_min_max.disabled = False
else:
self.cmap_min.disabled = True
self.cmap_max.disabled = True
self.save_min_max.disabled = True
# self.mcds_field_cb()
self.cmap_fixed.observe(cmap_fixed_cb)
field_cmap_row2 = HBox([self.field_cmap, self.cmap_fixed])
# field_cmap_row3 = HBox([self.save_min_max, self.cmap_min, self.cmap_max])
items_auto = [
self.save_min_max, #layout=Layout(flex='3 1 auto', width='auto'),
self.cmap_min,
self.cmap_max,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='80%')
field_cmap_row3 = Box(children=items_auto, layout=box_layout)
# field_cmap_row3 = Box([self.save_min_max, self.cmap_min, self.cmap_max])
# mcds_tab = widgets.VBox([mcds_dir, mcds_plot, mcds_play], layout=tab_layout)
mcds_params = VBox([
self.mcds_field, field_cmap_row2, field_cmap_row3, self.max_frames
]) # mcds_dir
# mcds_params = VBox([self.mcds_field, field_cmap_row2, field_cmap_row3,]) # mcds_dir
# self.tab = HBox([mcds_params, self.mcds_plot], layout=tab_layout)
# self.tab = HBox([mcds_params, self.mcds_plot])
help_label = Label('select slider: drag or left/right arrows')
row1 = Box([
help_label,
Box([self.max_frames, self.mcds_field, self.field_cmap],
layout=Layout(border='0px solid black',
width='50%',
height='',
align_items='stretch',
flex_direction='row',
display='flex'))
])
row2 = Box([self.cmap_fixed, self.cmap_min, self.cmap_max],
layout=Layout(border='0px solid black',
width='50%',
height='',
align_items='stretch',
flex_direction='row',
display='flex'))
self.tab = VBox([row1, row2, self.mcds_plot])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='tumor_radius',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.tumor_radius = FloatText(value=250.0,
step=10,
style=style,
layout=widget_layout)
param_name2 = Button(description='oncoprotein_mean',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.oncoprotein_mean = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name3 = Button(description='oncoprotein_sd',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.oncoprotein_sd = FloatText(value=0.25,
step=0.01,
style=style,
layout=widget_layout)
param_name4 = Button(description='oncoprotein_min',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.oncoprotein_min = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name5 = Button(description='oncoprotein_max',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.oncoprotein_max = FloatText(value=2,
step=0.1,
style=style,
layout=widget_layout)
param_name6 = Button(description='random_seed',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.random_seed = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
units_button1 = Button(description='micron',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
desc_button1 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
row1 = [param_name1, self.tumor_radius, units_button1, desc_button1]
row2 = [
param_name2, self.oncoprotein_mean, units_button2, desc_button2
]
row3 = [param_name3, self.oncoprotein_sd, units_button3, desc_button3]
row4 = [param_name4, self.oncoprotein_min, units_button4, desc_button4]
row5 = [param_name5, self.oncoprotein_max, units_button5, desc_button5]
row6 = [param_name6, self.random_seed, units_button6, desc_button6]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
label_domain = Label('Domain (micron):')
stepsize = 10
self.xmin = FloatText(
step=stepsize,
# description='$X_{min}$',
description='Xmin',
layout=Layout(width=constWidth),
)
self.ymin = FloatText(
step=stepsize,
description='Ymin',
layout=Layout(width=constWidth),
)
self.zmin = FloatText(
step=stepsize,
description='Zmin',
layout=Layout(width=constWidth),
)
self.xmax = FloatText(
step=stepsize,
description='Xmax',
layout=Layout(width=constWidth),
)
self.ymax = FloatText(
step=stepsize,
description='Ymax',
layout=Layout(width=constWidth),
)
self.zmax = FloatText(
step=stepsize,
description='Zmax',
layout=Layout(width=constWidth),
)
# description='$Time_{max}$',
self.tmax = BoundedFloatText(
min=0.,
max=100000000,
step=stepsize,
description='Max Time',
layout=Layout(width=constWidth),
)
self.xdelta = BoundedFloatText(
min=1.,
description='dx', # '∆x', # Mac: opt-j for delta
layout=Layout(width=constWidth),
)
self.ydelta = BoundedFloatText(
min=1.,
description='dy',
layout=Layout(width=constWidth),
)
self.zdelta = BoundedFloatText(
min=1.,
description='dz',
layout=Layout(width=constWidth),
)
x_row = HBox([self.xmin, self.xmax, self.xdelta])
y_row = HBox([self.ymin, self.ymax, self.ydelta])
z_row = HBox([self.zmin, self.zmax, self.zdelta])
self.omp_threads = BoundedIntText(
min=1,
description='# threads',
layout=Layout(width=constWidth),
)
self.toggle_svg = Checkbox(
description='Cells', # SVG
layout=Layout(width='150px')) # constWidth = '180px'
self.svg_interval = BoundedIntText(
min=1,
max=
99999999, # TODO: set max on all Bounded to avoid unwanted default
description='every',
layout=Layout(width='160px'),
)
def toggle_svg_cb(b):
if (self.toggle_svg.value):
# self.svg_t0.disabled = False
self.svg_interval.disabled = False
else:
# self.svg_t0.disabled = True
self.svg_interval.disabled = True
self.toggle_svg.observe(toggle_svg_cb)
self.toggle_mcds = Checkbox(
description='Subtrates', # Full
layout=Layout(width='180px'),
)
self.mcds_interval = BoundedIntText(
min=0,
max=99999999,
description='every',
layout=Layout(width='160px'),
)
def toggle_mcds_cb(b):
if (self.toggle_mcds.value):
self.mcds_interval.disabled = False
else:
self.mcds_interval.disabled = True
self.toggle_mcds.observe(toggle_mcds_cb)
svg_mat_output_row = HBox([
Label('Plots:'), self.toggle_svg,
HBox([self.svg_interval, Label('min')]), self.toggle_mcds,
HBox([self.mcds_interval, Label('min')])
])
label_blankline = Label('')
label_substrates = Label('Substrates:')
self.substrate = []
self.diffusion_coef = []
self.decay_rate = []
width_cell_params_units = '510px'
width_cell_params_units = '380px'
disable_substrates_flag = False
self.substrate.append(
HBox([
BoundedFloatText(
min=0,
step=0.1,
disabled=True,
value=38,
description='o2: ',
layout=Layout(width=constWidth),
),
Label('mmHg')
],
layout=Layout(width=width_cell_params_units)))
self.substrate.append(
HBox([
BoundedFloatText(
min=0,
step=0.1,
disabled=True,
value=1,
description='Glc: ',
layout=Layout(width=constWidth),
),
],
layout=Layout(width=width_cell_params_units)))
self.substrate.append(
HBox([
BoundedFloatText(
min=0,
step=0.1,
disabled=True,
value=7.25,
description='H+: ',
layout=Layout(width=constWidth),
),
Label('pH')
],
layout=Layout(width=width_cell_params_units)))
self.substrate.append(
HBox([
BoundedFloatText(
min=0,
step=0.1,
disabled=True,
value=1.0,
description='ECM: ',
layout=Layout(width=constWidth),
),
],
layout=Layout(width=width_cell_params_units)))
width_cell_params_units = '450px'
width_cell_params_units = '400px'
self.diffusion_coef.append(
HBox([
BoundedFloatText(
min=0,
max=999999,
step=10.0,
description='diffusion coef',
disabled=disable_substrates_flag,
layout=Layout(width=constWidth),
),
Label('micron^2/min')
],
layout=Layout(width=width_cell_params_units)))
self.diffusion_coef.append(
HBox([
BoundedFloatText(
min=0,
max=999999,
step=10.0,
description='diffusion coef',
disabled=disable_substrates_flag,
layout=Layout(width=constWidth),
),
Label('micron^2/min')
],
layout=Layout(width=width_cell_params_units)))
self.diffusion_coef.append(
HBox([
BoundedFloatText(
min=0,
max=999999,
step=10.0,
description='diffusion coef',
disabled=disable_substrates_flag,
layout=Layout(width=constWidth),
),
Label('micron^2/min')
],
layout=Layout(width=width_cell_params_units)))
width_cell_params_units = '400px'
width_cell_params_units = '380px'
self.decay_rate.append(
HBox([
BoundedFloatText(
min=0,
step=0.01,
description='decay rate',
disabled=disable_substrates_flag,
layout=Layout(width=constWidth),
),
Label('1/min')
],
layout=Layout(width=width_cell_params_units)))
self.decay_rate.append(
HBox([
BoundedFloatText(
min=0,
step=0.00001,
description='decay rate',
disabled=disable_substrates_flag,
layout=Layout(width=constWidth),
),
Label('1/min')
],
layout=Layout(width=width_cell_params_units)))
self.decay_rate.append(
HBox([
BoundedFloatText(
min=0,
step=0.01,
description='decay rate',
disabled=disable_substrates_flag,
layout=Layout(width=constWidth),
),
Label('1/min')
],
layout=Layout(width=width_cell_params_units)))
box_layout = Layout(border='1px solid')
domain_box = VBox([label_domain, x_row, y_row, z_row],
layout=box_layout)
substrates_box = VBox([
label_substrates,
HBox([
self.substrate[0], self.diffusion_coef[0], self.decay_rate[0]
]),
HBox([
self.substrate[1], self.diffusion_coef[1], self.decay_rate[1]
]),
HBox([
self.substrate[2], self.diffusion_coef[2], self.decay_rate[2]
])
],
layout=box_layout)
self.tab = VBox([
domain_box,
HBox([self.tmax, Label('min')]),
self.omp_threads,
svg_mat_output_row,
]) # output_dir, toggle_2D_seed_
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='random_seed',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'tan'
self.random_seed = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
param_name2 = Button(description='motile_cell_persistence_time',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.motile_cell_persistence_time = FloatText(value=15,
step=1,
style=style,
layout=widget_layout)
param_name3 = Button(description='motile_cell_migration_speed',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'tan'
self.motile_cell_migration_speed = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name4 = Button(description='motile_cell_relative_adhesion',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.motile_cell_relative_adhesion = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name5 = Button(description='motile_cell_apoptosis_rate',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'tan'
self.motile_cell_apoptosis_rate = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name6 = Button(
description='motile_cell_relative_cycle_entry_rate',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.motile_cell_relative_cycle_entry_rate = FloatText(
value=0.1, step=0.01, style=style, layout=widget_layout)
param_name7 = Button(description='birth_interval',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'tan'
self.birth_interval = FloatText(value=60,
step=1,
style=style,
layout=widget_layout)
param_name8 = Button(description='volume_total',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.volume_total = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name9 = Button(description='target_fluid_frac',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'tan'
self.target_fluid_frac = FloatText(value=0.75,
step=0.1,
style=style,
layout=widget_layout)
param_name10 = Button(description='fluid_change_rate',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.fluid_change_rate = FloatText(value=0.15,
step=0.01,
style=style,
layout=widget_layout)
param_name11 = Button(description='cytoplasmic_biomass_change_rate',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'tan'
self.cytoplasmic_biomass_change_rate = FloatText(value=0.15,
step=0.01,
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'tan'
units_button2 = Button(description='min',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='micron/min',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'tan'
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'tan'
units_button6 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='min',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'tan'
units_button8 = Button(description='micron^3',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'tan'
units_button10 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'tan'
row0 = [
param_name1,
self.random_seed,
units_button1,
]
row0 = [
param_name2,
self.motile_cell_persistence_time,
units_button2,
]
row0 = [
param_name3,
self.motile_cell_migration_speed,
units_button3,
]
row0 = [
param_name4,
self.motile_cell_relative_adhesion,
units_button4,
]
row0 = [
param_name5,
self.motile_cell_apoptosis_rate,
units_button5,
]
row0 = [
param_name6,
self.motile_cell_relative_cycle_entry_rate,
units_button6,
]
row0 = [
param_name7,
self.birth_interval,
units_button7,
]
row0 = [
param_name8,
self.volume_total,
units_button8,
]
row0 = [
param_name9,
self.target_fluid_frac,
units_button9,
]
row0 = [
param_name10,
self.fluid_change_rate,
units_button10,
]
row0 = [
param_name11,
self.cytoplasmic_biomass_change_rate,
units_button11,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
box0 = Box(children=row0, layout=box_layout)
self.tab = VBox([
box0,
box0,
box0,
box0,
box0,
box0,
box0,
box0,
box0,
box0,
box0,
])
def __init__(self):
micron_units = Label('micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout={'width':'25%'}
widget_layout = {'width': '15%'}
widget2_layout = {'width': '10%'}
units_button_layout ={'width':'15%'}
desc_button_layout={'width':'45%'}
divider_button_layout={'width':'40%'}
div_row1 = Button(description='---Initial Parameters---', disabled=True, layout=divider_button_layout)
param_name1 = Button(description='seeding_method', disabled=True, layout=name_button_layout)
param_name1.style.button_color = 'tan'
self.seeding_method = IntText(
value=1,
step=0.1,
style=style, layout=widget_layout)
div_row2 = Button(description='---Transition Rates---', disabled=True, layout=divider_button_layout)
param_name2 = Button(description='r01', disabled=True, layout=name_button_layout)
param_name2.style.button_color = 'lightgreen'
self.r01 = FloatText(
value=0.01666,
step=0.001,
style=style, layout=widget_layout)
param_name3 = Button(description='r01_fixed_duration', disabled=True, layout=name_button_layout)
param_name3.style.button_color = 'tan'
self.r01_fixed_duration = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name4 = Button(description='r12', disabled=True, layout=name_button_layout)
param_name4.style.button_color = 'lightgreen'
self.r12 = FloatText(
value=0.01666,
step=0.001,
style=style, layout=widget_layout)
param_name5 = Button(description='r12_fixed_duration', disabled=True, layout=name_button_layout)
param_name5.style.button_color = 'tan'
self.r12_fixed_duration = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name6 = Button(description='r23', disabled=True, layout=name_button_layout)
param_name6.style.button_color = 'lightgreen'
self.r23 = FloatText(
value=0.01666,
step=0.001,
style=style, layout=widget_layout)
param_name7 = Button(description='r23_fixed_duration', disabled=True, layout=name_button_layout)
param_name7.style.button_color = 'tan'
self.r23_fixed_duration = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name8 = Button(description='r30', disabled=True, layout=name_button_layout)
param_name8.style.button_color = 'lightgreen'
self.r30 = FloatText(
value=0.01666,
step=0.001,
style=style, layout=widget_layout)
param_name9 = Button(description='r30_fixed_duration', disabled=True, layout=name_button_layout)
param_name9.style.button_color = 'tan'
self.r30_fixed_duration = Checkbox(
value=False,
style=style, layout=widget_layout)
div_row3 = Button(description='---Arresting phase link between G0/G1 and S---', disabled=True, layout=divider_button_layout)
param_name10 = Button(description='r01_arrest', disabled=True, layout=name_button_layout)
param_name10.style.button_color = 'lightgreen'
self.r01_arrest = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name11 = Button(description='oxygen_threshold', disabled=True, layout=name_button_layout)
param_name11.style.button_color = 'tan'
self.oxygen_threshold = FloatText(
value=24,
step=1,
style=style, layout=widget_layout)
param_name12 = Button(description='oxygen_gradient', disabled=True, layout=name_button_layout)
param_name12.style.button_color = 'lightgreen'
self.oxygen_gradient = Checkbox(
value=False,
style=style, layout=widget_layout)
div_row4 = Button(description='---Arresting phase link between S and G2---', disabled=True, layout=divider_button_layout)
param_name13 = Button(description='r12_arrest', disabled=True, layout=name_button_layout)
param_name13.style.button_color = 'tan'
self.r12_arrest = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name14 = Button(description='chemokine_threshold', disabled=True, layout=name_button_layout)
param_name14.style.button_color = 'lightgreen'
self.chemokine_threshold = FloatText(
value=10.0,
step=1,
style=style, layout=widget_layout)
div_row5 = Button(description='---Arresting phase link between G2 an M---', disabled=True, layout=divider_button_layout)
param_name15 = Button(description='r23_arrest', disabled=True, layout=name_button_layout)
param_name15.style.button_color = 'tan'
self.r23_arrest = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name16 = Button(description='pressure_threshold', disabled=True, layout=name_button_layout)
param_name16.style.button_color = 'lightgreen'
self.pressure_threshold = FloatText(
value=1.0,
step=0.1,
style=style, layout=widget_layout)
div_row6 = Button(description='---Arresting phase link between M an G0/G1 (division)---', disabled=True, layout=divider_button_layout)
param_name17 = Button(description='r30_arrest', disabled=True, layout=name_button_layout)
param_name17.style.button_color = 'tan'
self.r30_arrest = Checkbox(
value=False,
style=style, layout=widget_layout)
param_name18 = Button(description='volume_threshold', disabled=True, layout=name_button_layout)
param_name18.style.button_color = 'lightgreen'
self.volume_threshold = FloatText(
value=2490.0,
step=100,
style=style, layout=widget_layout)
units_button1 = Button(description='', disabled=True, layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='', disabled=True, layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='', disabled=True, layout=units_button_layout)
units_button3.style.button_color = 'tan'
units_button4 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button4.style.button_color = 'lightgreen'
units_button5 = Button(description='', disabled=True, layout=units_button_layout)
units_button5.style.button_color = 'tan'
units_button6 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button6.style.button_color = 'lightgreen'
units_button7 = Button(description='', disabled=True, layout=units_button_layout)
units_button7.style.button_color = 'tan'
units_button8 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button8.style.button_color = 'lightgreen'
units_button9 = Button(description='', disabled=True, layout=units_button_layout)
units_button9.style.button_color = 'tan'
units_button10 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button10.style.button_color = 'lightgreen'
units_button11 = Button(description='', disabled=True, layout=units_button_layout)
units_button11.style.button_color = 'tan'
units_button12 = Button(description='', disabled=True, layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='', disabled=True, layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='mmHg', disabled=True, layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='', disabled=True, layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='', disabled=True, layout=units_button_layout)
units_button16.style.button_color = 'lightgreen'
units_button17 = Button(description='', disabled=True, layout=units_button_layout)
units_button17.style.button_color = 'tan'
units_button18 = Button(description='mM', disabled=True, layout=units_button_layout)
units_button18.style.button_color = 'lightgreen'
units_button19 = Button(description='', disabled=True, layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
units_button20 = Button(description='', disabled=True, layout=units_button_layout)
units_button20.style.button_color = 'tan'
units_button21 = Button(description='', disabled=True, layout=units_button_layout)
units_button21.style.button_color = 'lightgreen'
units_button22 = Button(description='', disabled=True, layout=units_button_layout)
units_button22.style.button_color = 'lightgreen'
units_button23 = Button(description='', disabled=True, layout=units_button_layout)
units_button23.style.button_color = 'tan'
units_button24 = Button(description='micron^3', disabled=True, layout=units_button_layout)
units_button24.style.button_color = 'lightgreen'
desc_button2 = Button(description='For seeding one cell => 1, For tissue seeding => 2' , tooltip='For seeding one cell => 1, For tissue seeding => 2', disabled=True, layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='transition rate between G0/G1 and S' , tooltip='transition rate between G0/G1 and S', disabled=True, layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='True if transition rate (r01) are fixed duration.' , tooltip='True if transition rate (r01) are fixed duration.', disabled=True, layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='transition rate between S and G2' , tooltip='transition rate between S and G2', disabled=True, layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='True if transition rate (r12) are fixed duration.' , tooltip='True if transition rate (r12) are fixed duration.', disabled=True, layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='transition rate between G2 and M' , tooltip='transition rate between G2 and M', disabled=True, layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='True if transition rate (r23) are fixed duration.' , tooltip='True if transition rate (r23) are fixed duration.', disabled=True, layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(description='transition rate between M and G0/G1' , tooltip='transition rate between M and G0/G1', disabled=True, layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(description='True if transition rate (r30) are fixed duration.' , tooltip='True if transition rate (r30) are fixed duration.', disabled=True, layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(description='if true and conditions were matched, it arrests phase link.' , tooltip='if true and conditions were matched, it arrests phase link.', disabled=True, layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(description='environmental oxygen threshold for phase transition. If less than threshold, it stops' , tooltip='environmental oxygen threshold for phase transition. If less than threshold, it stops', disabled=True, layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(description='True, if environment has oxygen gradient' , tooltip='True, if environment has oxygen gradient', disabled=True, layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(description='arrest function according to chemokine level' , tooltip='arrest function according to chemokine level', disabled=True, layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(description='environmental chemokine threshold for phase transition. If more, it stops' , tooltip='environmental chemokine threshold for phase transition. If more, it stops', disabled=True, layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(description='arrest function according to pressure level' , tooltip='arrest function according to pressure level', disabled=True, layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(description='cell pressure threshold to stall this phase transition. If more, it stops' , tooltip='cell pressure threshold to stall this phase transition. If more, it stops', disabled=True, layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(description='arrest function according to cell volume' , tooltip='arrest function according to cell volume', disabled=True, layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(description='target cell volume threshold. If less, it does not cycle.' , tooltip='target cell volume threshold. If less, it does not cycle.', disabled=True, layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
row2 = [param_name1, self.seeding_method, units_button2, desc_button2]
row3 = [param_name2, self.r01, units_button4, desc_button3]
row4 = [param_name3, self.r01_fixed_duration, units_button5, desc_button4]
row5 = [param_name4, self.r12, units_button6, desc_button5]
row6 = [param_name5, self.r12_fixed_duration, units_button7, desc_button6]
row7 = [param_name6, self.r23, units_button8, desc_button7]
row8 = [param_name7, self.r23_fixed_duration, units_button9, desc_button8]
row9 = [param_name8, self.r30, units_button10, desc_button9]
row10 = [param_name9, self.r30_fixed_duration, units_button11, desc_button10]
row11 = [param_name10, self.r01_arrest, units_button13, desc_button11]
row12 = [param_name11, self.oxygen_threshold, units_button14, desc_button12]
row13 = [param_name12, self.oxygen_gradient, units_button15, desc_button13]
row14 = [param_name13, self.r12_arrest, units_button17, desc_button14]
row15 = [param_name14, self.chemokine_threshold, units_button18, desc_button15]
row16 = [param_name15, self.r23_arrest, units_button20, desc_button16]
row17 = [param_name16, self.pressure_threshold, units_button21, desc_button17]
row18 = [param_name17, self.r30_arrest, units_button23, desc_button18]
row19 = [param_name18, self.volume_threshold, units_button24, desc_button19]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
self.tab = VBox([
div_row1,
box2,
div_row2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
div_row3,
box11,
box12,
box13,
div_row4,
box14,
box15,
div_row5,
box16,
box17,
div_row6,
box18,
box19,
])
def __init__(self):
# micron_units = HTMLMath(value=r"$\mu M$")
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
# micron_units = Label('microns') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
# tab_height = '400px'
tab_height = '500px'
# tab_layout = Layout(width='900px', # border='2px solid black',
# tab_layout = Layout(width='850px', # border='2px solid black',
# height=tab_height, overflow_y='scroll',)
# np_tab_layout = Layout(width='800px', # border='2px solid black',
# height='350px', overflow_y='scroll',)
# my_domain = [0,0,-10, 2000,2000,10, 20,20,20] # [x,y,zmin, x,y,zmax, x,y,zdelta]
# label_domain = Label('Domain ($\mu M$):')
label_domain = Label('Domain (micron):')
stepsize = 10
disable_domain = False
self.xmin = FloatText(
step=stepsize,
# description='$X_{min}$',
description='Xmin',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.ymin = FloatText(
step=stepsize,
description='Ymin',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.zmin = FloatText(
step=stepsize,
description='Zmin',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.xmax = FloatText(
step=stepsize,
description='Xmax',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.ymax = FloatText(
step=stepsize,
description='Ymax',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.zmax = FloatText(
step=stepsize,
description='Zmax',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
# description='$Time_{max}$',
self.tmax = BoundedFloatText(
min=0.,
max=100000000,
step=stepsize,
description='Max Time',
layout=Layout(width=constWidth),
)
self.xdelta = BoundedFloatText(
min=1.,
description='dx', # '∆x', # Mac: opt-j for delta
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.ydelta = BoundedFloatText(
min=1.,
description='dy',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
self.zdelta = BoundedFloatText(
min=1.,
description='dz',
disabled=disable_domain,
layout=Layout(width=constWidth),
)
"""
self.tdelta = BoundedFloatText(
min=0.01,
description='$Time_{delta}$',
layout=Layout(width=constWidth),
)
"""
"""
self.toggle2D = Checkbox(
description='2-D',
layout=Layout(width=constWidth),
)
def toggle2D_cb(b):
if (self.toggle2D.value):
#zmin.disabled = zmax.disabled = zdelta.disabled = True
zmin.disabled = True
zmax.disabled = True
zdelta.disabled = True
else:
zmin.disabled = False
zmax.disabled = False
zdelta.disabled = False
self.toggle2D.observe(toggle2D_cb)
"""
x_row = HBox([self.xmin, self.xmax, self.xdelta])
y_row = HBox([self.ymin, self.ymax, self.ydelta])
z_row = HBox([self.zmin, self.zmax, self.zdelta])
self.omp_threads = BoundedIntText(
min=1,
max=4,
description='# threads',
layout=Layout(width=constWidth),
)
# self.toggle_prng = Checkbox(
# description='Seed PRNG', style={'description_width': 'initial'}, # e.g. 'initial' '120px'
# layout=Layout(width=constWidth),
# )
# self.prng_seed = BoundedIntText(
# min = 1,
# description='Seed',
# disabled=True,
# layout=Layout(width=constWidth),
# )
# def toggle_prng_cb(b):
# if (toggle_prng.value):
# self.prng_seed.disabled = False
# else:
# self.prng_seed.disabled = True
# self.toggle_prng.observe(toggle_prng_cb)
#prng_row = HBox([toggle_prng, prng_seed])
self.toggle_svg = Checkbox(
description='Cells', # SVG
layout=Layout(width='150px')) # constWidth = '180px'
# self.svg_t0 = BoundedFloatText (
# min=0,
# description='$T_0$',
# layout=Layout(width=constWidth),
# )
# self.svg_interval = BoundedIntText(
self.svg_interval = BoundedFloatText(
min=1,
max=
99999999, # TODO: set max on all Bounded to avoid unwanted default
description='every',
layout=Layout(width='160px'),
)
# self.mcds_interval = BoundedIntText(
self.mcds_interval = BoundedFloatText(
min=1,
max=99999999,
description='every',
# disabled=True,
layout=Layout(width='160px'),
)
# don't let this be > mcds interval
def svg_interval_cb(b):
if (self.svg_interval.value > self.mcds_interval.value):
self.svg_interval.value = self.mcds_interval.value
self.svg_interval.observe(
svg_interval_cb) # BEWARE: when fill_gui, this sets value = 1 !
# don't let this be < svg interval
def mcds_interval_cb(b):
if (self.mcds_interval.value < self.svg_interval.value):
self.mcds_interval.value = self.svg_interval.value
self.mcds_interval.observe(
mcds_interval_cb) # BEWARE: see warning above
def toggle_svg_cb(b):
if (self.toggle_svg.value):
# self.svg_t0.disabled = False
self.svg_interval.disabled = False
else:
# self.svg_t0.disabled = True
self.svg_interval.disabled = True
self.toggle_svg.observe(toggle_svg_cb)
self.toggle_mcds = Checkbox(
# value=False,
description='Subtrates', # Full
layout=Layout(width='180px'),
)
# self.mcds_t0 = FloatText(
# description='$T_0$',
# disabled=True,
# layout=Layout(width=constWidth),
# )
def toggle_mcds_cb(b):
if (self.toggle_mcds.value):
# self.mcds_t0.disabled = False #False
self.mcds_interval.disabled = False
else:
# self.mcds_t0.disabled = True
self.mcds_interval.disabled = True
self.toggle_mcds.observe(toggle_mcds_cb)
svg_mat_output_row = HBox([
Label('Plots:'), self.toggle_svg,
HBox([self.svg_interval, Label('min')]), self.toggle_mcds,
HBox([self.mcds_interval, Label('min')])
])
# to sync, do this
# svg_mat_output_row = HBox( [Label('Plots:'), self.svg_interval, Label('min')])
#write_config_row = HBox([write_config_button, write_config_file])
#run_sim_row = HBox([run_button, run_command_str, kill_button])
# run_sim_row = HBox([run_button, run_command_str])
# run_sim_row = HBox([run_button.w]) # need ".w" for the custom RunCommand widget
label_blankline = Label('')
# toggle_2D_seed_row = HBox([toggle_prng, prng_seed]) # toggle2D
box_layout = Layout(border='1px solid')
# domain_box = VBox([label_domain,x_row,y_row,z_row], layout=box_layout)
domain_box = VBox([label_domain, x_row, y_row], layout=box_layout)
self.tab = VBox([
domain_box,
# label_blankline,
HBox([self.tmax, Label('min')]),
self.omp_threads,
svg_mat_output_row,
# HBox([self.substrate[3], self.diffusion_coef[3], self.decay_rate[3] ]),
]) # output_dir, toggle_2D_seed_
def DataApp():
frequency = FloatText(value=0.5, description="f (Hz)")
zsrc = FloatText(value=-950.0, description="src height (m)")
zrx = FloatText(value=-1000.0, description="rx height (m)")
rho0 = FloatText(value=1e8, description="$\\rho_{0} \ (\Omega m)$")
rho1 = FloatText(value=0.3, description="$\\rho_{1} \ (\Omega m)$")
rho2 = FloatText(value=1.0, description="$\\rho_{2} \ (\Omega m)$")
rho3 = FloatText(value=100.0, description="$\\rho_{3} \ (\Omega m)$")
rho4 = FloatText(value=1.0, description="$\\rho_{4} \ (\Omega m)$")
rv_rh = FloatText(value=1.0, description="$\\rho_{2 \ v} / \\rho_{2 \ h}$")
dz1 = FloatText(value=1000.0, description="dz1 (m)")
dz2 = FloatText(value=1000.0, description="dz2 (m)")
dz3 = FloatText(value=200.0, description="dz3 (m)")
frequency_bg = FloatText(value=0.5, description="f$^{BG}$ (Hz)")
zsrc_bg = FloatText(value=-950.0, description="src height$^{BG}$ (m)")
zrx_bg = FloatText(value=-1000.0, description="rx height$^{BG}$ (m)")
rho0_bg = FloatText(value=1e8, description="$\\rho_{0}^{BG} \ (\Omega m)$")
rho1_bg = FloatText(value=0.3, description="$\\rho_{1}^{BG} \ (\Omega m)$")
rho2_bg = FloatText(value=1.0, description="$\\rho_{2}^{BG} \ (\Omega m)$")
rho3_bg = FloatText(value=1.0, description="$\\rho_{3}^{BG} \ (\Omega m)$")
rho4_bg = FloatText(value=1.0, description="$\\rho_{4}^{BG} \ (\Omega m)$")
rv_rh_bg = FloatText(
value=1.0, description="$\\rho_{2 \ v}^{BG} / \\rho_{2 \ h}^{BG}$")
dz1_bg = FloatText(value=1000.0, description="dz1$^{BG}$ (m)")
dz2_bg = FloatText(value=1000.0, description="dz2$^{BG}$ (m)")
dz3_bg = FloatText(value=200.0, description="dz3$^{BG}$ (m)")
Field = ToggleButtons(options=["E", "H", "Zxy"],
value="E",
description="Field")
Plane = ToggleButtons(options=["XZ", "YZ"],
value="XZ",
description="Plane")
Component = ToggleButtons(options=["x", "y", "z"],
value="x",
description="rx direction")
Complex = ToggleButtons(options=["Real", "Imag", "Amp", "Phase"],
value="Amp",
description="Complex")
scale = ToggleButtons(options=["log", "linear"],
value="log",
description="Scale")
Fixed = widgets.widget_bool.Checkbox(value=False, description="Fixed")
vmin = FloatText(value=None, description="vmin")
vmax = FloatText(value=None, description="vmax")
# __manual = True
out = widgets.interactive_output(
csem_data_app,
{
"frequency": frequency,
"zsrc": zsrc,
"zrx": zrx,
"rho0": rho0,
"rho1": rho1,
"rho2": rho2,
"rho3": rho3,
"rho4": rho4,
"rv_rh": rv_rh,
"dz1": dz1,
"dz2": dz2,
"dz3": dz3,
"frequency_bg": frequency_bg,
"zsrc_bg": zsrc_bg,
"zrx_bg": zrx_bg,
"rho0_bg": rho0_bg,
"rho1_bg": rho1_bg,
"rho2_bg": rho2_bg,
"rho3_bg": rho3_bg,
"rho4_bg": rho4_bg,
"rv_rh_bg": rv_rh_bg,
"dz1_bg": dz1_bg,
"dz2_bg": dz2_bg,
"dz3_bg": dz3_bg,
"Field": Field,
"Plane": Plane,
"Component": Component,
"Complex": Complex,
"scale": scale,
"Fixed": Fixed,
"vmin": vmin,
"vmax": vmax,
},
)
panel = VBox([
frequency, zsrc, zrx, rho0, rho1, rho2, rho3, rho4, rv_rh, dz1, dz2,
dz3
])
panel_bg = VBox([
frequency_bg,
zsrc_bg,
zrx_bg,
rho0_bg,
rho1_bg,
rho2_bg,
rho3_bg,
rho4_bg,
rv_rh_bg,
dz1_bg,
dz2_bg,
dz3_bg,
])
panel_type = VBox(
[Field, Plane, Component, Complex, scale, Fixed, vmin, vmax])
return VBox([HBox([panel, panel_bg]), panel_type, out])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
divider_button_layout = {'width': '40%'}
param_name1 = Button(description='hypoxia_pers_time',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.hypoxia_pers_time = FloatText(value=300,
step=10,
style=style,
layout=widget_layout)
param_name2 = Button(description='fraction_rsp',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.fraction_rsp = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name3 = Button(description='bias_green_rsp',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.bias_green_rsp = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name4 = Button(description='hypoxyprobe',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.hypoxyprobe = Checkbox(value=False,
style=style,
layout=widget_layout)
param_name5 = Button(description='speed_red',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.speed_red = FloatText(value=0.2938,
step=0.01,
style=style,
layout=widget_layout)
param_name6 = Button(description='pers_time_red',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.pers_time_red = FloatText(value=15.0,
step=1,
style=style,
layout=widget_layout)
param_name7 = Button(description='bias_red',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.bias_red = FloatText(value=0.1719,
step=0.01,
style=style,
layout=widget_layout)
param_name8 = Button(description='speed_green',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.speed_green = FloatText(value=0.4755,
step=0.1,
style=style,
layout=widget_layout)
param_name9 = Button(description='pers_time_green',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.pers_time_green = FloatText(value=15.0,
step=1,
style=style,
layout=widget_layout)
param_name10 = Button(description='bias_green',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.bias_green = FloatText(value=0.1791,
step=0.01,
style=style,
layout=widget_layout)
param_name11 = Button(description='initial_tumor_rad',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.initial_tumor_rad = FloatText(value=250.0,
step=10,
style=style,
layout=widget_layout)
param_name12 = Button(description='cell_oxy_cons',
disabled=True,
layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.cell_oxy_cons = FloatText(value=10.0,
step=1,
style=style,
layout=widget_layout)
param_name13 = Button(description='rate_KnToKp',
disabled=True,
layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.rate_KnToKp = FloatText(value=0.00363,
step=0.001,
style=style,
layout=widget_layout)
param_name14 = Button(description='rate_KpToKn',
disabled=True,
layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.rate_KpToKn = FloatText(value=0.00107,
step=0.0001,
style=style,
layout=widget_layout)
param_name15 = Button(description='sigma_S',
disabled=True,
layout=name_button_layout)
param_name15.style.button_color = 'lightgreen'
self.sigma_S = FloatText(value=38.0,
step=1,
style=style,
layout=widget_layout)
param_name16 = Button(description='sigma_T',
disabled=True,
layout=name_button_layout)
param_name16.style.button_color = 'tan'
self.sigma_T = FloatText(value=6.0,
step=0.1,
style=style,
layout=widget_layout)
param_name17 = Button(description='sigma_H',
disabled=True,
layout=name_button_layout)
param_name17.style.button_color = 'lightgreen'
self.sigma_H = FloatText(value=10.0,
step=1,
style=style,
layout=widget_layout)
param_name18 = Button(description='protein_prod_rate',
disabled=True,
layout=name_button_layout)
param_name18.style.button_color = 'tan'
self.protein_prod_rate = FloatText(value=4.8e-4,
step=0.0001,
style=style,
layout=widget_layout)
param_name19 = Button(description='protein_deg_rate',
disabled=True,
layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
self.protein_deg_rate = FloatText(value=6.8e-5,
step=1e-05,
style=style,
layout=widget_layout)
units_button1 = Button(description='min',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='micron/min',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='min',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='micron/min',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='min',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='micron',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
units_button16.style.button_color = 'tan'
units_button17 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
units_button17.style.button_color = 'lightgreen'
units_button18 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button18.style.button_color = 'tan'
units_button19 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
desc_button1 = Button(
description='phenotype persistent time of GFP+ cells',
tooltip='phenotype persistent time of GFP+ cells',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(
description=
'fraction of GFP+ cells with different migration bias (bias_green_rsp)',
tooltip=
'fraction of GFP+ cells with different migration bias (bias_green_rsp)',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(
description='migration bias for GFP + cells (for fraction_rsp)',
tooltip='migration bias for GFP + cells (for fraction_rsp)',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='mark with hypoxyprobe',
tooltip='mark with hypoxyprobe',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='migration speed for DsRed+ cells',
tooltip='migration speed for DsRed+ cells',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(
description='migration persistent time for DsRed+ cells',
tooltip='migration persistent time for DsRed+ cells',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='migration bias for DsRed+ cells',
tooltip='migration bias for DsRed+ cells',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='migration speed for GFP+ cells',
tooltip='migration speed for GFP+ cells',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(
description='migration persistent time for GFP+ cells',
tooltip='migration persistent time for GFP+ cells',
disabled=True,
layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(description='migration bias for GFP+ cells',
tooltip='migration bias for GFP+ cells',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(description='initial tumor radius',
tooltip='initial tumor radius',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(
description='oxygen consumption rate by each cell',
tooltip='oxygen consumption rate by each cell',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(
description=
'transition rate from Ki67- to Ki67+ (for saturated signal)',
tooltip=
'transition rate from Ki67- to Ki67+ (for saturated signal)',
disabled=True,
layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(
description='transition rate from Ki67+ to Ki67-',
tooltip='transition rate from Ki67+ to Ki67-',
disabled=True,
layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(
description=
'oxygen pressure threshold to signal proliferation saturation',
tooltip=
'oxygen pressure threshold to signal proliferation saturation',
disabled=True,
layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(
description='min oxygen pressure to signal proliferation',
tooltip='min oxygen pressure to signal proliferation',
disabled=True,
layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(
description='oxygen pressure threshold to signal hypoxia',
tooltip='oxygen pressure threshold to signal hypoxia',
disabled=True,
layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(description='protein production rate',
tooltip='protein production rate',
disabled=True,
layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(description='protein degradation rate',
tooltip='protein degradation rate',
disabled=True,
layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
row1 = [
param_name1, self.hypoxia_pers_time, units_button1, desc_button1
]
row2 = [param_name2, self.fraction_rsp, units_button2, desc_button2]
row3 = [param_name3, self.bias_green_rsp, units_button3, desc_button3]
row4 = [param_name4, self.hypoxyprobe, units_button4, desc_button4]
row5 = [param_name5, self.speed_red, units_button5, desc_button5]
row6 = [param_name6, self.pers_time_red, units_button6, desc_button6]
row7 = [param_name7, self.bias_red, units_button7, desc_button7]
row8 = [param_name8, self.speed_green, units_button8, desc_button8]
row9 = [param_name9, self.pers_time_green, units_button9, desc_button9]
row10 = [param_name10, self.bias_green, units_button10, desc_button10]
row11 = [
param_name11, self.initial_tumor_rad, units_button11, desc_button11
]
row12 = [
param_name12, self.cell_oxy_cons, units_button12, desc_button12
]
row13 = [param_name13, self.rate_KnToKp, units_button13, desc_button13]
row14 = [param_name14, self.rate_KpToKn, units_button14, desc_button14]
row15 = [param_name15, self.sigma_S, units_button15, desc_button15]
row16 = [param_name16, self.sigma_T, units_button16, desc_button16]
row17 = [param_name17, self.sigma_H, units_button17, desc_button17]
row18 = [
param_name18, self.protein_prod_rate, units_button18, desc_button18
]
row19 = [
param_name19, self.protein_deg_rate, units_button19, desc_button19
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
box15,
box16,
box17,
box18,
box19,
])
def _init_gui(self, **kwargs):
"""Initialize generic GUI controls and observe callbacks."""
mainopts = super(TensorContainer, self)._init_gui(**kwargs)
scn = self.scenes[0]
alo = Layout(width='74px')
rlo = Layout(width='235px')
if self._df is not None:
scn.txx = self._df.loc[0, 'xx']
scn.txy = self._df.loc[0, 'xy']
scn.txz = self._df.loc[0, 'xz']
scn.tyx = self._df.loc[0, 'yx']
scn.tyy = self._df.loc[0, 'yy']
scn.tyz = self._df.loc[0, 'yz']
scn.tzx = self._df.loc[0, 'zx']
scn.tzy = self._df.loc[0, 'zy']
scn.tzz = self._df.loc[0, 'zz']
xs = [
FloatText(value=scn.txx, layout=alo),
FloatText(value=scn.txy, layout=alo),
FloatText(value=scn.txz, layout=alo)
]
ys = [
FloatText(value=scn.tyx, layout=alo),
FloatText(value=scn.tyy, layout=alo),
FloatText(value=scn.tyz, layout=alo)
]
zs = [
FloatText(value=scn.tzx, layout=alo),
FloatText(value=scn.tzy, layout=alo),
FloatText(value=scn.tzz, layout=alo)
]
opt = [0] if self._df is None else [
int(x) for x in self._df.index.values
]
tensorIndex = Dropdown(options=opt, value=opt[0], layout=rlo)
tdxlabel = Label(value='Select the tensor index:')
def _x0(c):
for scn in self.active():
scn.txx = c.new
def _x1(c):
for scn in self.active():
scn.txy = c.new
def _x2(c):
for scn in self.active():
scn.txz = c.new
def _y0(c):
for scn in self.active():
scn.tyx = c.new
def _y1(c):
for scn in self.active():
scn.tyy = c.new
def _y2(c):
for scn in self.active():
scn.tyz = c.new
def _z0(c):
for scn in self.active():
scn.tzx = c.new
def _z1(c):
for scn in self.active():
scn.tzy = c.new
def _z2(c):
for scn in self.active():
scn.tzz = c.new
xs[0].observe(_x0, names='value')
xs[1].observe(_x1, names='value')
xs[2].observe(_x2, names='value')
ys[0].observe(_y0, names='value')
ys[1].observe(_y1, names='value')
ys[2].observe(_y2, names='value')
zs[0].observe(_z0, names='value')
zs[1].observe(_z1, names='value')
zs[2].observe(_z2, names='value')
rlo = Layout(width='234px')
xbox = HBox(xs, layout=rlo)
ybox = HBox(ys, layout=rlo)
zbox = HBox(zs, layout=rlo)
geom = Button(icon='cubes', description=' Geometry', layout=_wlo)
def _change_tensor(tdx=0):
carts = ['x', 'y', 'z']
for i, bra in enumerate(carts):
for j, ket in enumerate(carts):
if i == 0:
xs[j].value = self._df.loc[tdx, bra + ket]
elif i == 1:
ys[j].value = self._df.loc[tdx, bra + ket]
elif i == 2:
zs[j].value = self._df.loc[tdx, bra + ket]
def _geom(b):
for scn in self.active():
scn.geom = not scn.geom
def _tdx(c):
for scn in self.active():
scn.tdx = c.new
_change_tensor(c.new)
geom.on_click(_geom)
tensorIndex.observe(_tdx, names="value")
mainopts.update([('geom', geom), ('tlbl', tdxlabel),
('tidx', tensorIndex), ('xbox', xbox), ('ybox', ybox),
('zbox', zbox)])
return mainopts
def dsc_config(dsc_value):
values = config.read()
ds_db = Dropdown(options=["1"],
value="1",
description='Database:',
disabled=False,
layout=Layout(width='140px'))
try:
with open(f"{config.get_value(['paths','temp'])}tb_prefix",
'r') as f:
code_value = f.read()
except Exception:
code_value = dsc_value
ds_code = Combobox(
value=code_value,
placeholder='abc',
options=[m for m in data_options.eu_ms()] + [''],
description='AOI code:',
ensure_option=False,
disabled=False,
layout=Layout(width='200px'),
tooltip='Lowercase AOI code name for the dataset (5chr max).')
ds_year = BoundedIntText(value=int(dsy.value),
min=1980,
max=2100,
step=1,
description='Dataset year:',
disabled=False,
layout=Layout(width='180px'))
ds_desc = Text(value=values['ds_conf'][dsc_value]['desc'],
description='Description:',
disabled=False)
info_map_text = [
"Set default map view options. ",
"You can get automatically the dataset ", "center coordinates."
]
lat, lon = values['ds_conf'][dsc_value]['center'].split(",")
map_cent_lat = FloatText(value=float(lat),
description='Lat:',
disabled=False,
layout=Layout(width='160px'))
map_cent_lon = FloatText(value=float(lon),
description='Lon:',
disabled=False,
layout=Layout(width='160px'))
map_zoom = BoundedIntText(value=values['ds_conf'][dsc_value]['zoom'],
min=0,
max=20,
step=1,
description='Zoom:',
disabled=False,
layout=Layout(width='140px'))
bt_get_center = Button(layout=Layout(width='40px'),
icon='bullseye',
tooltip='Get center point from database.')
ds_box = HBox([ds_code, ds_year, ds_desc])
map_box = HBox([
Label("Map center: "), map_cent_lat, map_cent_lon, bt_get_center,
map_zoom
])
info_config = Label(
"""Change 'AOI code' value to create a new configuration set or
leave the same 'AOI code' value to configure the selected one.""")
db = int(values['ds_conf'][dsc_value]['db'])
def get_tb_list():
tbls = database.tables(db, None, False)
if tbls is None:
return []
else:
return tbls
tb_dc = Dropdown(options=get_tb_list(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['tables']['dias_catalog'],
get_tb_list(), False),
description='DIAS catalog:',
disabled=False)
tb_pr = Dropdown(options=get_tb_list(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['tables']['parcels'],
get_tb_list(), False),
description='Parcels:',
disabled=False)
def get_pr_columns():
try:
colms = database.table_columns(tb_pr.value, 1, None)
if colms is None:
return []
else:
return colms
except Exception:
return []
tc_id = Dropdown(options=get_pr_columns(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['columns']['parcels_id'],
get_pr_columns(), False),
description='Parcels ID:',
disabled=False,
layout=Layout(width='180px'))
tc_cn = Dropdown(options=get_pr_columns(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['columns']['crop_names'],
get_pr_columns(), False),
description='Crop names:',
disabled=False,
layout=Layout(width='180px'))
tc_cc = Dropdown(options=get_pr_columns(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['columns']['crop_codes'],
get_pr_columns(), False),
description='Crop codes:',
disabled=False,
layout=Layout(width='180px'))
def on_tb_pr_change(change):
tc_id.options = get_pr_columns()
tc_cn.options = get_pr_columns()
tc_cc.options = get_pr_columns()
tb_pr.observe(on_tb_pr_change, 'value')
parcel_box = HBox([tb_pr, tc_id, tc_cn, tc_cc])
tb_s2 = Dropdown(options=get_tb_list(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['tables']['s2'],
get_tb_list(), False),
description='S2 signatures:',
disabled=False)
tb_bs = Dropdown(options=get_tb_list(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['tables']['bs'],
get_tb_list(), False),
description='Backscattering:',
disabled=False)
tb_6c = Dropdown(options=get_tb_list(),
value=config.autoselect(
values['ds_conf'][dsc_value]['years'][str(
ds_year.value)]['tables']['c6'],
get_tb_list(), False),
description='6 day coherence:',
disabled=False)
wb_save = Button(description='Save', disabled=False, icon='save')
@bt_get_center.on_click
def bt_get_center_on_click(b):
import json
center_json = json.loads(
database.getTableCentroid(tb_pr.value)['center'][0])
map_cent_lat.value = round(center_json['coordinates'][1], 2)
map_cent_lon.value = round(center_json['coordinates'][0], 2)
map_zoom.value = 10
@wb_save.on_click
def wb_save_on_click(b):
progress.clear_output()
dscode = ds_code.value
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'tables', 'dias_catalog'
], str(tb_dc.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'tables', 'parcels'
], str(tb_pr.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'columns', 'parcels_id'
], str(tc_id.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'columns', 'crop_names'
], str(tc_cn.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'columns', 'crop_codes'
], str(tc_cc.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'tables', 's2'
], str(tb_s2.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'tables', 'bs'
], str(tb_bs.value))
config.update([
'ds_conf', dscode, 'years',
str(ds_year.value), 'tables', 'c6'
], str(tb_6c.value))
config.update(['ds_conf', dscode, 'db'], str(ds_db.value))
config.update(['ds_conf', dscode, 'desc'], str(ds_desc.value))
config.update(['ds_conf', dscode, 'center'],
f"{map_cent_lat.value},{map_cent_lon.value}")
config.update(['ds_conf', dscode, 'zoom'], str(map_zoom.value))
config.update(['set', 'ds_conf'], str(dscode))
config.update(['set', 'ds_year'], str(ds_year.value))
values = config.read()
ds_c = values['set']['ds_conf']
ds_y = values['set']['ds_year']
dsc.options = [d for d in values['ds_conf']]
dsy.options = [int(y) for y in values['ds_conf'][ds_c]['years']]
dsc.value = ds_c
dsy.value = int(ds_y)
outlog("The configurations are saved.")
return VBox([
info_config, ds_box, parcel_box, tb_dc, tb_s2, tb_bs, tb_6c,
Label(''.join(info_map_text)), map_box, wb_save
])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='Model_Initialization',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.Model_Initialization = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name2 = Button(description='ECM_initialization_parameters',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.ECM_initialization_parameters = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name3 = Button(description='initial_anisotropy',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.initial_anisotropy = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name4 = Button(description='initial_ECM_density',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.initial_ECM_density = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name5 = Button(description='Lesion_intialization',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.Lesion_intialization = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name6 = Button(description='tumor_radius',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.tumor_radius = FloatText(value=175,
step=10,
style=style,
layout=widget_layout)
param_name7 = Button(description='initial_leader_cell_fraction',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.initial_leader_cell_fraction = FloatText(value=0.2,
step=0.01,
style=style,
layout=widget_layout)
param_name8 = Button(description='Cell_properties',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.Cell_properties = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name9 = Button(description='oxygen_uptake',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.oxygen_uptake = FloatText(value=10,
step=1,
style=style,
layout=widget_layout)
param_name10 = Button(description='leader_adhesion',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.leader_adhesion = FloatText(value=5.0,
step=0.1,
style=style,
layout=widget_layout)
param_name11 = Button(description='leader_repulsion',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.leader_repulsion = FloatText(value=25,
step=1,
style=style,
layout=widget_layout)
param_name12 = Button(description='follower_adhesion',
disabled=True,
layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.follower_adhesion = FloatText(value=5.0,
step=0.1,
style=style,
layout=widget_layout)
param_name13 = Button(description='follower_repulsion',
disabled=True,
layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.follower_repulsion = FloatText(value=25,
step=1,
style=style,
layout=widget_layout)
param_name14 = Button(description='default_cell_speed',
disabled=True,
layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.default_cell_speed = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name15 = Button(description='rho_L',
disabled=True,
layout=name_button_layout)
param_name15.style.button_color = 'lightgreen'
self.rho_L = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name16 = Button(description='rho_H',
disabled=True,
layout=name_button_layout)
param_name16.style.button_color = 'tan'
self.rho_H = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name17 = Button(description='rho_I',
disabled=True,
layout=name_button_layout)
param_name17.style.button_color = 'lightgreen'
self.rho_I = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name18 = Button(description='default_persistence_time',
disabled=True,
layout=name_button_layout)
param_name18.style.button_color = 'tan'
self.default_persistence_time = FloatText(value=10.0,
step=1,
style=style,
layout=widget_layout)
param_name19 = Button(description='default_ECM_density_target',
disabled=True,
layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
self.default_ECM_density_target = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name20 = Button(description='default_ECM_sensitivity',
disabled=True,
layout=name_button_layout)
param_name20.style.button_color = 'tan'
self.default_ECM_sensitivity = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name21 = Button(description='default_hysteresis_bias',
disabled=True,
layout=name_button_layout)
param_name21.style.button_color = 'lightgreen'
self.default_hysteresis_bias = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name22 = Button(description='oxygen_migration_bias_for_leaders',
disabled=True,
layout=name_button_layout)
param_name22.style.button_color = 'tan'
self.oxygen_migration_bias_for_leaders = FloatText(
value=0.95, step=0.1, style=style, layout=widget_layout)
param_name23 = Button(description='Microenvironment_parameters',
disabled=True,
layout=name_button_layout)
param_name23.style.button_color = 'lightgreen'
self.Microenvironment_parameters = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name24 = Button(description='chemotactic_substrate_decay_rate',
disabled=True,
layout=name_button_layout)
param_name24.style.button_color = 'tan'
self.chemotactic_substrate_decay_rate = FloatText(value=0.1,
step=0.01,
style=style,
layout=widget_layout)
param_name25 = Button(description='Model_Selection_Parameters',
disabled=True,
layout=name_button_layout)
param_name25.style.button_color = 'lightgreen'
self.Model_Selection_Parameters = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name26 = Button(
description='cell_motility_ECM_interaction_model_selector',
disabled=True,
layout=name_button_layout)
param_name26.style.button_color = 'tan'
self.cell_motility_ECM_interaction_model_selector = Text(
value='previous motility vector based memory',
style=style,
layout=widget_layout)
param_name27 = Button(description='Testing_and_setup_parameters',
disabled=True,
layout=name_button_layout)
param_name27.style.button_color = 'lightgreen'
self.Testing_and_setup_parameters = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name28 = Button(
description='normalize_ECM_influenced_motility_vector',
disabled=True,
layout=name_button_layout)
param_name28.style.button_color = 'tan'
self.normalize_ECM_influenced_motility_vector = Checkbox(
value=False, style=style, layout=widget_layout)
param_name29 = Button(description='duration_of_uE_conditioning',
disabled=True,
layout=name_button_layout)
param_name29.style.button_color = 'lightgreen'
self.duration_of_uE_conditioning = FloatText(value=10,
step=1,
style=style,
layout=widget_layout)
param_name30 = Button(description='freeze_uE_profile',
disabled=True,
layout=name_button_layout)
param_name30.style.button_color = 'tan'
self.freeze_uE_profile = Checkbox(value=False,
style=style,
layout=widget_layout)
param_name31 = Button(description='unit_test_setup',
disabled=True,
layout=name_button_layout)
param_name31.style.button_color = 'lightgreen'
self.unit_test_setup = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
param_name32 = Button(description='march_unit_test_setup',
disabled=True,
layout=name_button_layout)
param_name32.style.button_color = 'tan'
self.march_unit_test_setup = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
param_name33 = Button(description='cell_setup',
disabled=True,
layout=name_button_layout)
param_name33.style.button_color = 'lightgreen'
self.cell_setup = Text(value='lesion',
style=style,
layout=widget_layout)
param_name34 = Button(description='ECM_orientation_setup',
disabled=True,
layout=name_button_layout)
param_name34.style.button_color = 'tan'
self.ECM_orientation_setup = Text(value='random',
style=style,
layout=widget_layout)
param_name35 = Button(description='chemical_field_setup',
disabled=True,
layout=name_button_layout)
param_name35.style.button_color = 'lightgreen'
self.chemical_field_setup = Text(value='none',
style=style,
layout=widget_layout)
param_name36 = Button(description='angle_of_chemical_field_gradient',
disabled=True,
layout=name_button_layout)
param_name36.style.button_color = 'tan'
self.angle_of_chemical_field_gradient = FloatText(value=45.0,
step=1,
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='microns',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='mmHg/min',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='microns/minute',
disabled=True,
layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button16.style.button_color = 'tan'
units_button17 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button17.style.button_color = 'lightgreen'
units_button18 = Button(description='minutes',
disabled=True,
layout=units_button_layout)
units_button18.style.button_color = 'tan'
units_button19 = Button(description='dimenionless',
disabled=True,
layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
units_button20 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button20.style.button_color = 'tan'
units_button21 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button21.style.button_color = 'lightgreen'
units_button22 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button22.style.button_color = 'tan'
units_button23 = Button(description='dimensionlesss',
disabled=True,
layout=units_button_layout)
units_button23.style.button_color = 'lightgreen'
units_button24 = Button(description='1/minutes',
disabled=True,
layout=units_button_layout)
units_button24.style.button_color = 'tan'
units_button25 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button25.style.button_color = 'lightgreen'
units_button26 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button26.style.button_color = 'tan'
units_button27 = Button(description='dimensionlesss',
disabled=True,
layout=units_button_layout)
units_button27.style.button_color = 'lightgreen'
units_button28 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button28.style.button_color = 'tan'
units_button29 = Button(description='minutes',
disabled=True,
layout=units_button_layout)
units_button29.style.button_color = 'lightgreen'
units_button30 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button30.style.button_color = 'tan'
units_button31 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button31.style.button_color = 'lightgreen'
units_button32 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button32.style.button_color = 'tan'
units_button33 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button33.style.button_color = 'lightgreen'
units_button34 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button34.style.button_color = 'tan'
units_button35 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button35.style.button_color = 'lightgreen'
units_button36 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button36.style.button_color = 'tan'
desc_button1 = Button(description='This is a spacer',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='ECM_initialization_parameters',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='Initial ECM anisotropy',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='Initial ECM density',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='Lesion_intialization',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='Initial cell mass radius',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(
description='Average percentage of leaders initialized',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='Cell_properties',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(description='Default cell oxygen uptake rate',
disabled=True,
layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(
description='Strength of leader cells\' cell-cell adhesion',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(
description='Strength of leader cells\' cell-cell repulsion',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(
description='Strength of follower cells\' cell-cell adhesion',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(
description='Strength of follower cells\' cell-cell repulsion',
disabled=True,
layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(description='Base/maximum cell speed',
disabled=True,
layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(
description='Minimum ECM density required for cell motility',
disabled=True,
layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(
description='Maximum ECM density allowing cell motility',
disabled=True,
layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(description='Ideal ECM density cell motility',
disabled=True,
layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(description='Cell directional persistence time',
disabled=True,
layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(description='Cell ECM density target',
disabled=True,
layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
desc_button20 = Button(
description=
'Cell sensitivity to ECM orientation for ECM following type cells',
disabled=True,
layout=desc_button_layout)
desc_button20.style.button_color = 'tan'
desc_button21 = Button(
description=
"Cell's base sensivity to previous cell direction - cell motility history bias",
disabled=True,
layout=desc_button_layout)
desc_button21.style.button_color = 'lightgreen'
desc_button22 = Button(
description='Chemotaxis bias for non-ECM influenced cell types',
disabled=True,
layout=desc_button_layout)
desc_button22.style.button_color = 'tan'
desc_button23 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button23.style.button_color = 'lightgreen'
desc_button24 = Button(description='Chemotactic subsrate decay rate',
disabled=True,
layout=desc_button_layout)
desc_button24.style.button_color = 'tan'
desc_button25 = Button(
description='Allows selection of various cell motility-ECM models',
disabled=True,
layout=desc_button_layout)
desc_button25.style.button_color = 'lightgreen'
desc_button26 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button26.style.button_color = 'tan'
desc_button27 = Button(description='Testing and setup parameters',
disabled=True,
layout=desc_button_layout)
desc_button27.style.button_color = 'lightgreen'
desc_button28 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button28.style.button_color = 'tan'
desc_button29 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button29.style.button_color = 'lightgreen'
desc_button30 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button30.style.button_color = 'tan'
desc_button31 = Button(
description=
'Specifies cell, ECM, and domain parameters for consistent unit tests of ECM influenced mechanics and mechanics influence on ECM: 1 for testing set up, 0 for regular set up',
disabled=True,
layout=desc_button_layout)
desc_button31.style.button_color = 'lightgreen'
desc_button32 = Button(
description=
'Specifies that cells will reset their position to the left boundary and that density is 0.5 for the behavior to ECM march test 1 for march set up, 0 for regular set up',
disabled=True,
layout=desc_button_layout)
desc_button32.style.button_color = 'tan'
desc_button33 = Button(
description=
'Specifies the initial cell setup: single, random, lesion, cells at y = 0, circle of cells, or cells at left boundary/march',
disabled=True,
layout=desc_button_layout)
desc_button33.style.button_color = 'lightgreen'
desc_button34 = Button(
description=
'Specifies the initial ECM orietation: random, horizontal, vertical, circular, or starburst',
disabled=True,
layout=desc_button_layout)
desc_button34.style.button_color = 'tan'
desc_button35 = Button(
description=
'Specifies the chemotatic field gradient orientation: starburst, vertical up, horizontal right, angle, or none',
disabled=True,
layout=desc_button_layout)
desc_button35.style.button_color = 'lightgreen'
desc_button36 = Button(
description=
'Angle of chemical field gradient orientation, specified in degrees',
disabled=True,
layout=desc_button_layout)
desc_button36.style.button_color = 'tan'
row1 = [
param_name1, self.Model_Initialization, units_button1, desc_button1
]
row2 = [
param_name2, self.ECM_initialization_parameters, units_button2,
desc_button2
]
row3 = [
param_name3, self.initial_anisotropy, units_button3, desc_button3
]
row4 = [
param_name4, self.initial_ECM_density, units_button4, desc_button4
]
row5 = [
param_name5, self.Lesion_intialization, units_button5, desc_button5
]
row6 = [param_name6, self.tumor_radius, units_button6, desc_button6]
row7 = [
param_name7, self.initial_leader_cell_fraction, units_button7,
desc_button7
]
row8 = [param_name8, self.Cell_properties, units_button8, desc_button8]
row9 = [param_name9, self.oxygen_uptake, units_button9, desc_button9]
row10 = [
param_name10, self.leader_adhesion, units_button10, desc_button10
]
row11 = [
param_name11, self.leader_repulsion, units_button11, desc_button11
]
row12 = [
param_name12, self.follower_adhesion, units_button12, desc_button12
]
row13 = [
param_name13, self.follower_repulsion, units_button13,
desc_button13
]
row14 = [
param_name14, self.default_cell_speed, units_button14,
desc_button14
]
row15 = [param_name15, self.rho_L, units_button15, desc_button15]
row16 = [param_name16, self.rho_H, units_button16, desc_button16]
row17 = [param_name17, self.rho_I, units_button17, desc_button17]
row18 = [
param_name18, self.default_persistence_time, units_button18,
desc_button18
]
row19 = [
param_name19, self.default_ECM_density_target, units_button19,
desc_button19
]
row20 = [
param_name20, self.default_ECM_sensitivity, units_button20,
desc_button20
]
row21 = [
param_name21, self.default_hysteresis_bias, units_button21,
desc_button21
]
row22 = [
param_name22, self.oxygen_migration_bias_for_leaders,
units_button22, desc_button22
]
row23 = [
param_name23, self.Microenvironment_parameters, units_button23,
desc_button23
]
row24 = [
param_name24, self.chemotactic_substrate_decay_rate,
units_button24, desc_button24
]
row25 = [
param_name25, self.Model_Selection_Parameters, units_button25,
desc_button25
]
row26 = [
param_name26, self.cell_motility_ECM_interaction_model_selector,
units_button26, desc_button26
]
row27 = [
param_name27, self.Testing_and_setup_parameters, units_button27,
desc_button27
]
row28 = [
param_name28, self.normalize_ECM_influenced_motility_vector,
units_button28, desc_button28
]
row29 = [
param_name29, self.duration_of_uE_conditioning, units_button29,
desc_button29
]
row30 = [
param_name30, self.freeze_uE_profile, units_button30, desc_button30
]
row31 = [
param_name31, self.unit_test_setup, units_button31, desc_button31
]
row32 = [
param_name32, self.march_unit_test_setup, units_button32,
desc_button32
]
row33 = [param_name33, self.cell_setup, units_button33, desc_button33]
row34 = [
param_name34, self.ECM_orientation_setup, units_button34,
desc_button34
]
row35 = [
param_name35, self.chemical_field_setup, units_button35,
desc_button35
]
row36 = [
param_name36, self.angle_of_chemical_field_gradient,
units_button36, desc_button36
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
box25 = Box(children=row25, layout=box_layout)
box26 = Box(children=row26, layout=box_layout)
box27 = Box(children=row27, layout=box_layout)
box28 = Box(children=row28, layout=box_layout)
box29 = Box(children=row29, layout=box_layout)
box30 = Box(children=row30, layout=box_layout)
box31 = Box(children=row31, layout=box_layout)
box32 = Box(children=row32, layout=box_layout)
box33 = Box(children=row33, layout=box_layout)
box34 = Box(children=row34, layout=box_layout)
box35 = Box(children=row35, layout=box_layout)
box36 = Box(children=row36, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
box15,
box16,
box17,
box18,
box19,
box20,
box21,
box22,
box23,
box24,
box25,
box26,
box27,
box28,
box29,
box30,
box31,
box32,
box33,
box34,
box35,
box36,
])
def plate_app():
app = widgetify(
plot_Surface_Potentials,
survey=ToggleButtons(
options=[
"Dipole-Dipole", "Dipole-Pole", "Pole-Dipole", "Pole-Pole"
],
value="Dipole-Dipole",
),
dx=FloatSlider(min=1.0,
max=80.0,
step=1.0,
value=10.0,
continuous_update=False),
dz=FloatSlider(min=1.0,
max=40.0,
step=1.0,
value=10.0,
continuous_update=False),
xc=FloatSlider(min=-30.0,
max=30.0,
step=1.0,
value=0.0,
continuous_update=False),
zc=FloatSlider(min=-30.0,
max=0.0,
step=1.0,
value=-10.0,
continuous_update=False),
rotAng=FloatSlider(
min=-90.0,
max=90.0,
step=1.0,
value=0.0,
continuous_update=False,
description="$\\theta$",
),
rhoplate=FloatText(
min=1e-8,
max=1e8,
value=500.0,
continuous_update=False,
description="$\\rho_2$",
),
rhohalf=FloatText(
min=1e-8,
max=1e8,
value=500.0,
continuous_update=False,
description="$\\rho_1$",
),
A=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=-30.25,
continuous_update=False),
B=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=30.25,
continuous_update=False),
M=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=-10.25,
continuous_update=False),
N=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=10.25,
continuous_update=False),
Field=ToggleButtons(
options=["Model", "Potential", "E", "J", "Charge", "Sensitivity"],
value="Model",
),
Type=ToggleButtons(options=["Total", "Primary", "Secondary"],
value="Total"),
Scale=ToggleButtons(options=["Linear", "Log"], value="Linear"),
)
return app
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
widget2_layout = {'width': '10%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
menv_var1 = Button(description='oxygen (mmHg)',
disabled=True,
layout=name_button_layout)
menv_var1.style.button_color = 'tan'
menv_atten = Button(
description=
'Attention! Diffusion is closed in this application to make simulation faster. Initial conditions can be specified still.',
disabled=True,
layout={'width': '75%'})
menv_atten.style.button_color = 'orange'
param_name1 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.oxygen_diffusion_coefficient = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name2 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.oxygen_decay_rate = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name3 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.oxygen_initial_condition = FloatText(value=20.0,
style=style,
layout=widget_layout)
param_name4 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.oxygen_Dirichlet_boundary_condition = FloatText(
value=20.0, style=style, layout=widget_layout)
self.oxygen_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var2 = Button(description='chemokine (mM)',
disabled=True,
layout=name_button_layout)
menv_var2.style.button_color = 'lightgreen'
param_name5 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.chemokine_diffusion_coefficient = FloatText(value=30000.0,
step=1000,
style=style,
layout=widget_layout)
param_name6 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.chemokine_decay_rate = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name7 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.chemokine_initial_condition = FloatText(value=0.0,
style=style,
layout=widget_layout)
param_name8 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.chemokine_Dirichlet_boundary_condition = FloatText(
value=0.0, style=style, layout=widget_layout)
self.chemokine_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
self.calculate_gradient = Checkbox(description='calculate_gradients',
disabled=False,
layout=desc_button_layout)
self.track_internal = Checkbox(description='track_in_agents',
disabled=False,
layout=desc_button_layout)
# ------- micronenv info
menv_units_button1 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button2 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button3 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button4 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button5 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button6 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button7 = Button(description='mM',
disabled=True,
layout=units_button_layout)
menv_units_button8 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
row_atten = [
menv_atten,
]
row_oxygen = [
menv_var1,
]
row1 = [
param_name1, self.oxygen_diffusion_coefficient, menv_units_button1
]
row2 = [param_name2, self.oxygen_decay_rate, menv_units_button2]
row3 = [param_name3, self.oxygen_initial_condition, menv_units_button3]
row4 = [
param_name4, self.oxygen_Dirichlet_boundary_condition,
menv_units_button4, self.oxygen_Dirichlet_boundary_condition_toggle
]
row_chemokine = [
menv_var2,
]
row5 = [
param_name5, self.chemokine_diffusion_coefficient,
menv_units_button5
]
row6 = [param_name6, self.chemokine_decay_rate, menv_units_button6]
row7 = [
param_name7, self.chemokine_initial_condition, menv_units_button7
]
row8 = [
param_name8, self.chemokine_Dirichlet_boundary_condition,
menv_units_button8,
self.chemokine_Dirichlet_boundary_condition_toggle
]
row9 = [
self.calculate_gradient,
]
row10 = [
self.track_internal,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box_atten = Box(children=row_atten)
box_oxygen = Box(children=row_oxygen, layout=box_layout)
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box_chemokine = Box(children=row_chemokine, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
self.tab = VBox([
box_atten,
box_oxygen,
box1,
box2,
box3,
box4,
box_chemokine,
box5,
box6,
box7,
box8,
box9,
box10,
])
def make_config(self):
layout = Layout()
style = {"description_width": "initial"}
checkbox1 = Checkbox(description="Show Targets", value=self.net.config["show_targets"],
layout=layout, style=style)
checkbox1.observe(lambda change: self.set_attr(self.net.config, "show_targets", change["new"]), names='value')
checkbox2 = Checkbox(description="Errors", value=self.net.config["show_errors"],
layout=layout, style=style)
checkbox2.observe(lambda change: self.set_attr(self.net.config, "show_errors", change["new"]), names='value')
hspace = IntText(value=self.net.config["hspace"], description="Horizontal space between banks:",
style=style, layout=layout)
hspace.observe(lambda change: self.set_attr(self.net.config, "hspace", change["new"]), names='value')
vspace = IntText(value=self.net.config["vspace"], description="Vertical space between layers:",
style=style, layout=layout)
vspace.observe(lambda change: self.set_attr(self.net.config, "vspace", change["new"]), names='value')
self.feature_bank = Select(description="Details:", value=self.net.config["dashboard.features.bank"],
options=[""] + [layer.name for layer in self.net.layers],
rows=1)
self.feature_bank.observe(self.regenerate, names='value')
self.control_select = Select(
options=['Test', 'Train'],
value=self.net.config["dashboard.dataset"],
description='Dataset:',
rows=1
)
self.control_select.observe(self.change_select, names='value')
column1 = [self.control_select,
self.zoom_slider,
hspace,
vspace,
HBox([checkbox1, checkbox2]),
self.feature_bank,
self.feature_columns,
self.feature_scale
]
## Make layer selectable, and update-able:
column2 = []
layer = self.net.layers[-1]
self.layer_select = Select(description="Layer:", value=layer.name,
options=[layer.name for layer in
self.net.layers],
rows=1)
self.layer_select.observe(self.update_layer_selection, names='value')
column2.append(self.layer_select)
self.layer_visible_checkbox = Checkbox(description="Visible", value=layer.visible, layout=layout)
self.layer_visible_checkbox.observe(self.update_layer, names='value')
column2.append(self.layer_visible_checkbox)
self.layer_colormap = Select(description="Colormap:",
options=[""] + AVAILABLE_COLORMAPS,
value=layer.colormap if layer.colormap is not None else "", layout=layout, rows=1)
self.layer_colormap_image = HTML(value="""<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap)))
self.layer_colormap.observe(self.update_layer, names='value')
column2.append(self.layer_colormap)
column2.append(self.layer_colormap_image)
## get dynamic minmax; if you change it it will set it in layer as override:
minmax = layer.get_act_minmax()
self.layer_mindim = FloatText(description="Leftmost color maps to:", value=minmax[0], style=style)
self.layer_maxdim = FloatText(description="Rightmost color maps to:", value=minmax[1], style=style)
self.layer_mindim.observe(self.update_layer, names='value')
self.layer_maxdim.observe(self.update_layer, names='value')
column2.append(self.layer_mindim)
column2.append(self.layer_maxdim)
output_shape = layer.get_output_shape()
self.layer_feature = IntText(value=layer.feature, description="Feature to show:", style=style)
self.svg_rotate = Checkbox(description="Rotate", value=layer.visible, layout=layout)
self.layer_feature.observe(self.update_layer, names='value')
column2.append(self.layer_feature)
self.svg_rotate = Checkbox(description="Rotate network",
value=self.net.config["svg_rotate"],
style={"description_width": 'initial'},
layout=Layout(width="52%"))
self.svg_rotate.observe(lambda change: self.set_attr(self.net.config, "svg_rotate", change["new"]), names='value')
self.save_config_button = Button(icon="save", layout=Layout(width="10%"))
self.save_config_button.on_click(self.save_config)
column2.append(HBox([self.svg_rotate, self.save_config_button]))
config_children = HBox([VBox(column1, layout=Layout(width="100%")),
VBox(column2, layout=Layout(width="100%"))])
accordion = Accordion(children=[config_children])
accordion.set_title(0, self.net.name)
accordion.selected_index = None
return accordion
def FieldsApp():
Q1 = interactive(
csem_fields_app,
rho0=FloatText(value=1e8, description="$\\rho_{0} \ (\Omega m)$"),
rho1=FloatText(value=0.3, description="$\\rho_{1} \ (\Omega m)$"),
rho2=FloatText(value=1.0, description="$\\rho_{2} \ (\Omega m)$"),
rho3=FloatText(value=100.0, description="$\\rho_{3} \ (\Omega m)$"),
rho4=FloatText(value=1.0, description="$\\rho_{4} \ (\Omega m)$"),
zsrc=FloatText(value=-950.0, description="src height (m)"),
rv_rh=FloatText(value=1.0,
description="$\\rho_{2 \ v} / \\rho_{2 \ h}$"),
dz1=FloatText(value=1000.0, description="dz1 (m)"),
dz2=FloatText(value=1000.0, description="dz2 (m)"),
dz3=FloatText(value=200.0, description="dz3 (m)"),
frequency=FloatText(value=0.5, description="f (Hz)"),
Field=ToggleButtons(options=["E", "H", "P"], value="E"),
Plane=ToggleButtons(options=["XZ", "YZ"], value="XZ"),
Fixed=widgets.widget_bool.Checkbox(value=False),
vmin=FloatText(value=None),
vmax=FloatText(value=None),
__manual=True,
)
return Q1
def __init__(self):
micron_units = Label('micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout={'width':'25%'}
widget_layout = {'width': '15%'}
units_button_layout ={'width':'15%'}
desc_button_layout={'width':'45%'}
param_name1 = Button(description='immune_activation_time', disabled=True, layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.immune_activation_time = FloatText(
value=20160,
step=1000,
style=style, layout=widget_layout)
param_name2 = Button(description='number_of_immune_cells', disabled=True, layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.number_of_immune_cells = IntText(
value=125,
step=10,
style=style, layout=widget_layout)
param_name3 = Button(description='save_interval_after_therapy_start', disabled=True, layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.save_interval_after_therapy_start = FloatText(
value=60,
step=1,
style=style, layout=widget_layout)
param_name4 = Button(description='immune_apoptosis_rate', disabled=True, layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.immune_apoptosis_rate = FloatText(
value=6.944e-5,
step=1e-05,
style=style, layout=widget_layout)
param_name5 = Button(description='oncoprotein_threshold', disabled=True, layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.oncoprotein_threshold = FloatText(
value=0.1,
step=0.01,
style=style, layout=widget_layout)
param_name6 = Button(description='immune_kill_rate', disabled=True, layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.immune_kill_rate = FloatText(
value=0.8762,
step=0.1,
style=style, layout=widget_layout)
param_name7 = Button(description='immune_attachment_rate', disabled=True, layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.immune_attachment_rate = FloatText(
value=0.72138388,
step=0.1,
style=style, layout=widget_layout)
param_name8 = Button(description='immune_attachment_lifetime', disabled=True, layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.immune_attachment_lifetime = FloatText(
value=90.0,
step=1,
style=style, layout=widget_layout)
param_name9 = Button(description='immune_migration_bias', disabled=True, layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.immune_migration_bias = FloatText(
value=0.679587213,
step=0.1,
style=style, layout=widget_layout)
param_name10 = Button(description='immune_motility_persistence_time', disabled=True, layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.immune_motility_persistence_time = FloatText(
value=10,
step=1,
style=style, layout=widget_layout)
param_name11 = Button(description='immune_migration_speed', disabled=True, layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.immune_migration_speed = FloatText(
value=1.0,
step=0.1,
style=style, layout=widget_layout)
param_name12 = Button(description='tumor_radius', disabled=True, layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.tumor_radius = FloatText(
value=250,
step=10,
style=style, layout=widget_layout)
param_name13 = Button(description='tumor_mean_immunogenicity', disabled=True, layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.tumor_mean_immunogenicity = FloatText(
value=1.0,
step=0.1,
style=style, layout=widget_layout)
param_name14 = Button(description='tumor_immunogenicity_standard_deviation', disabled=True, layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.tumor_immunogenicity_standard_deviation = FloatText(
value=0.25,
step=0.01,
style=style, layout=widget_layout)
units_button1 = Button(description='min', disabled=True, layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='', disabled=True, layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='min', disabled=True, layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='', disabled=True, layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='1/min', disabled=True, layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='min', disabled=True, layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='', disabled=True, layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='min', disabled=True, layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='micron/min', disabled=True, layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='micron', disabled=True, layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='', disabled=True, layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='', disabled=True, layout=units_button_layout)
units_button14.style.button_color = 'tan'
desc_button1 = Button(description='time at which therapy begins', disabled=True, layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='number of immune cells at start of therapy', disabled=True, layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='save (output) interval after therapy begins', disabled=True, layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='immune cell apoptosis rate (d1)', disabled=True, layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='cancer cells are not immunogenic for p below this value (d2)', disabled=True, layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='rate that attached immune cells can apoptose cancer cells (d3)', disabled=True, layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='rate that immune cells can attach to a cell in close contact (d4)', disabled=True, layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='max time immune cells remain attached to a target cell (d5)', disabled=True, layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(description='immune cell migration bias (d6)', disabled=True, layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(description='mean immune cell migration persistence time', disabled=True, layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(description='immune cell migration speed', disabled=True, layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(description='initial tumor radius', disabled=True, layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(description='mean oncoprotein p at start', disabled=True, layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(description='standard deviation of tumor p at start', disabled=True, layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
row1 = [param_name1, self.immune_activation_time, units_button1, desc_button1]
row2 = [param_name2, self.number_of_immune_cells, units_button2, desc_button2]
row3 = [param_name3, self.save_interval_after_therapy_start, units_button3, desc_button3]
row4 = [param_name4, self.immune_apoptosis_rate, units_button4, desc_button4]
row5 = [param_name5, self.oncoprotein_threshold, units_button5, desc_button5]
row6 = [param_name6, self.immune_kill_rate, units_button6, desc_button6]
row7 = [param_name7, self.immune_attachment_rate, units_button7, desc_button7]
row8 = [param_name8, self.immune_attachment_lifetime, units_button8, desc_button8]
row9 = [param_name9, self.immune_migration_bias, units_button9, desc_button9]
row10 = [param_name10, self.immune_motility_persistence_time, units_button10, desc_button10]
row11 = [param_name11, self.immune_migration_speed, units_button11, desc_button11]
row12 = [param_name12, self.tumor_radius, units_button12, desc_button12]
row13 = [param_name13, self.tumor_mean_immunogenicity, units_button13, desc_button13]
row14 = [param_name14, self.tumor_immunogenicity_standard_deviation, units_button14, desc_button14]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
])
def ResLayer_app():
app = widgetify(
plot_Surface_Potentials,
survey=ToggleButtons(options=[
'Dipole-Dipole', 'Dipole-Pole', 'Pole-Dipole', 'Pole-Pole'
],
value='Dipole-Dipole'),
zcLayer=FloatSlider(min=-10.,
max=0.,
step=1.,
value=-10.,
continuous_update=False,
description="$zc_{layer}$"),
dzLayer=FloatSlider(min=0.5,
max=5.,
step=0.5,
value=1.,
continuous_update=False,
description="$dz_{layer}$"),
rhoLayer=FloatText(min=1e-8,
max=1e8,
value=5000.,
continuous_update=False,
description='$\\rho_{2}$'),
xc=FloatSlider(min=-30.,
max=30.,
step=1.,
value=0.,
continuous_update=False),
zc=FloatSlider(min=-30.,
max=-15.,
step=0.5,
value=-25.,
continuous_update=False),
r=FloatSlider(min=1.,
max=10.,
step=0.5,
value=5.,
continuous_update=False),
rhoHalf=FloatText(min=1e-8,
max=1e8,
value=500.,
continuous_update=False,
description='$\\rho_{1}$'),
rhoTarget=FloatText(min=1e-8,
max=1e8,
value=500.,
continuous_update=False,
description='$\\rho_{3}$'),
A=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=-30.25,
continuous_update=False),
B=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=30.25,
continuous_update=False),
M=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=-10.25,
continuous_update=False),
N=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=10.25,
continuous_update=False),
Field=ToggleButtons(
options=['Model', 'Potential', 'E', 'J', 'Charge', 'Sensitivity'],
value='Model'),
Type=ToggleButtons(options=['Total', 'Primary', 'Secondary'],
value='Total'),
Scale=ToggleButtons(options=['Linear', 'Log'], value='Linear'))
return app
def FieldsApp():
Q1 = interactive(csem_fields_app,
rho0=FloatText(value=1e8,
description='$\\rho_{0} \ (\Omega m)$'),
rho1=FloatText(value=0.3,
description='$\\rho_{1} \ (\Omega m)$'),
rho2=FloatText(value=1.,
description='$\\rho_{2} \ (\Omega m)$'),
rho3=FloatText(value=100.,
description='$\\rho_{3} \ (\Omega m)$'),
rho4=FloatText(value=1.,
description='$\\rho_{4} \ (\Omega m)$'),
zsrc=FloatText(value=-950., description='src height (m)'),
rv_rh=FloatText(
value=1.,
description='$\\rho_{2 \ v} / \\rho_{2 \ h}$'),
dz1=FloatText(value=1000., description="dz1 (m)"),
dz2=FloatText(value=1000., description="dz2 (m)"),
dz3=FloatText(value=200., description="dz3 (m)"),
frequency=FloatText(value=0.5, description='f (Hz)'),
Field=ToggleButtons(options=['E', 'H', 'P'], value='E'),
Plane=ToggleButtons(options=['XZ', 'YZ'], value='XZ'),
Fixed=widgets.widget_bool.Checkbox(value=False),
vmin=FloatText(value=None),
vmax=FloatText(value=None),
__manual=True)
return Q1
FROM
dbo.fGetNearbyObjEq({}, {}, {}) AS n
JOIN Star AS s ON n.objID = s.objID
WHERE
g - r BETWEEN -0.5 AND 2.5
AND g BETWEEN 14 and 24
""".format(ra,dec,ang)
return SDSS.query_sql(query, timeout = 600)
#Create widgets
style = {'description_width': 'initial'}
#Boxes and sliders to control the parameters of the query function
RABox = FloatText(value='229.0128', placeholder='', description='Right ascension (degrees)', style=style, disabled=False, grid_area = 'RABox')
RASlider = FloatSlider(value=229.0128, min=0, max=360, continuous_update = False, grid_area = 'RASlider')
DECBox = FloatText(value='-0.1082', placeholder='', description='Declination (degrees)', style=style, disabled=False, grid_area = 'DECBox')
DECSlider = FloatSlider(value=-0.1082, min=-90, max=90, continuous_update = False, grid_area = 'DECSlider')
radBox = FloatText(value='30', placeholder='', description='Radius (arcminutes)', style=style, disabled=False, grid_area = 'radBox')
radSlider = FloatSlider(value=30, min=1, max=120, step=1, continuous_update = False, grid_area = 'radSlider')
#Slider to control the grid size for the Hess diagram
gridSlider = IntSlider(value=100, min=50, max=300, step=1, description='Grid size', style=style, continuous_update = False, grid_area = 'gridSlider')
#Dropdown menu to select the color map for the Hess diagram
hexDrop = Dropdown(options = ['viridis', 'plasma', 'inferno', 'magma', 'hot', 'winter', 'ocean', 'gray', 'binary'],
value = 'viridis',
description = 'Hess diagram colormap',
def DataApp():
frequency = FloatText(value=0.5, description='f (Hz)')
zsrc = FloatText(value=-950., description='src height (m)')
zrx = FloatText(value=-1000., description='rx height (m)')
rho0 = FloatText(value=1e8, description='$\\rho_{0} \ (\Omega m)$')
rho1 = FloatText(value=0.3, description='$\\rho_{1} \ (\Omega m)$')
rho2 = FloatText(value=1., description='$\\rho_{2} \ (\Omega m)$')
rho3 = FloatText(value=100., description='$\\rho_{3} \ (\Omega m)$')
rho4 = FloatText(value=1., description='$\\rho_{4} \ (\Omega m)$')
rv_rh = FloatText(value=1., description='$\\rho_{2 \ v} / \\rho_{2 \ h}$')
dz1 = FloatText(value=1000., description="dz1 (m)")
dz2 = FloatText(value=1000., description="dz2 (m)")
dz3 = FloatText(value=200., description="dz3 (m)")
frequency_bg = FloatText(value=0.5, description='f$^{BG}$ (Hz)')
zsrc_bg = FloatText(value=-950., description='src height$^{BG}$ (m)')
zrx_bg = FloatText(value=-1000., description='rx height$^{BG}$ (m)')
rho0_bg = FloatText(value=1e8, description='$\\rho_{0}^{BG} \ (\Omega m)$')
rho1_bg = FloatText(value=0.3, description='$\\rho_{1}^{BG} \ (\Omega m)$')
rho2_bg = FloatText(value=1., description='$\\rho_{2}^{BG} \ (\Omega m)$')
rho3_bg = FloatText(value=1., description='$\\rho_{3}^{BG} \ (\Omega m)$')
rho4_bg = FloatText(value=1., description='$\\rho_{4}^{BG} \ (\Omega m)$')
rv_rh_bg = FloatText(
value=1., description='$\\rho_{2 \ v}^{BG} / \\rho_{2 \ h}^{BG}$')
dz1_bg = FloatText(value=1000., description="dz1$^{BG}$ (m)")
dz2_bg = FloatText(value=1000., description="dz2$^{BG}$ (m)")
dz3_bg = FloatText(value=200., description="dz3$^{BG}$ (m)")
Field = ToggleButtons(options=['E', 'H', 'Zxy'],
value='E',
description="Field")
Plane = ToggleButtons(options=['XZ', 'YZ'],
value='XZ',
description="Plane")
Component = ToggleButtons(options=['x', 'y', 'z'],
value='x',
description="rx direction")
Complex = ToggleButtons(options=['Real', 'Imag', "Amp", "Phase"],
value='Amp',
description="Complex")
scale = ToggleButtons(options=['log', 'linear'],
value='log',
description="Scale")
Fixed = widgets.widget_bool.Checkbox(value=False, description="Fixed")
vmin = FloatText(value=None, description='vmin')
vmax = FloatText(value=None, description='vmax')
__manual = True
out = widgets.interactive_output(
csem_data_app, {
"frequency": frequency,
"zsrc": zsrc,
"zrx": zrx,
"rho0": rho0,
"rho1": rho1,
"rho2": rho2,
"rho3": rho3,
"rho4": rho4,
"rv_rh": rv_rh,
"dz1": dz1,
"dz2": dz2,
"dz3": dz3,
"frequency_bg": frequency_bg,
"zsrc_bg": zsrc_bg,
"zrx_bg": zrx_bg,
"rho0_bg": rho0_bg,
"rho1_bg": rho1_bg,
"rho2_bg": rho2_bg,
"rho3_bg": rho3_bg,
"rho4_bg": rho4_bg,
"rv_rh_bg": rv_rh_bg,
"dz1_bg": dz1_bg,
"dz2_bg": dz2_bg,
"dz3_bg": dz3_bg,
"Field": Field,
"Plane": Plane,
"Component": Component,
"Complex": Complex,
"scale": scale,
"Fixed": Fixed,
"vmin": vmin,
"vmax": vmax,
})
panel = VBox([
frequency, zsrc, zrx, rho0, rho1, rho2, rho3, rho4, rv_rh, dz1, dz2,
dz3
])
panel_bg = VBox([
frequency_bg, zsrc_bg, zrx_bg, rho0_bg, rho1_bg, rho2_bg, rho3_bg,
rho4_bg, rv_rh_bg, dz1_bg, dz2_bg, dz3_bg
])
panel_type = VBox(
[Field, Plane, Component, Complex, scale, Fixed, vmin, vmax])
return VBox([HBox([panel, panel_bg]), panel_type, out])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
param_name1 = Button(description='Volume',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.Volume = Text(value='"Parameters"',
style=style,
layout=widget_layout)
param_name2 = Button(description='Volume_target_solid_cytoplasmic',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.Volume_target_solid_cytoplasmic = FloatText(value=488.5,
step=10,
style=style,
layout=widget_layout)
param_name3 = Button(description='Volume_target_solid_nuclear',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.Volume_target_solid_nuclear = FloatText(value=135.0,
step=10,
style=style,
layout=widget_layout)
param_name4 = Button(description='Volume_target_fluid_fraction',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.Volume_target_fluid_fraction = FloatText(value=0.75,
step=0.1,
style=style,
layout=widget_layout)
param_name5 = Button(
description='Volume_cytoplasmic_biomass_change_rate',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.Volume_cytoplasmic_biomass_change_rate = FloatText(
value=0.0045, step=0.001, style=style, layout=widget_layout)
param_name6 = Button(description='Volume_nuclear_biomass_change_rate',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.Volume_nuclear_biomass_change_rate = FloatText(
value=0.0055, step=0.001, style=style, layout=widget_layout)
param_name7 = Button(description='Volume_fluid_change_rate',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.Volume_fluid_change_rate = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name8 = Button(description='Volume_calcification_rate',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.Volume_calcification_rate = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name9 = Button(description='Volume_Total',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.Volume_Total = FloatText(value=2494,
step=100,
style=style,
layout=widget_layout)
param_name10 = Button(description='Volume_solid',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.Volume_solid = FloatText(value=623.5,
step=10,
style=style,
layout=widget_layout)
param_name11 = Button(description='Volume_fluid',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.Volume_fluid = FloatText(value=1870.5,
step=100,
style=style,
layout=widget_layout)
param_name12 = Button(description='Volume_fluid_fraction',
disabled=True,
layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.Volume_fluid_fraction = FloatText(value=0.75,
step=0.1,
style=style,
layout=widget_layout)
param_name13 = Button(description='Volume_nuclear',
disabled=True,
layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.Volume_nuclear = FloatText(value=540.0,
step=10,
style=style,
layout=widget_layout)
param_name14 = Button(description='Volume_nuclear_solid',
disabled=True,
layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.Volume_nuclear_solid = FloatText(value=135.0,
step=10,
style=style,
layout=widget_layout)
param_name15 = Button(description='Volume_nuclear_fluid',
disabled=True,
layout=name_button_layout)
param_name15.style.button_color = 'lightgreen'
self.Volume_nuclear_fluid = FloatText(value=405.0,
step=10,
style=style,
layout=widget_layout)
param_name16 = Button(description='Volume_cytoplasmic',
disabled=True,
layout=name_button_layout)
param_name16.style.button_color = 'tan'
self.Volume_cytoplasmic = FloatText(value=1954.0,
step=100,
style=style,
layout=widget_layout)
param_name17 = Button(description='Volume_cytoplasmic_solid',
disabled=True,
layout=name_button_layout)
param_name17.style.button_color = 'lightgreen'
self.Volume_cytoplasmic_solid = FloatText(value=488.5,
step=10,
style=style,
layout=widget_layout)
param_name18 = Button(description='Volume_cytoplasmic_fluid',
disabled=True,
layout=name_button_layout)
param_name18.style.button_color = 'tan'
self.Volume_cytoplasmic_fluid = FloatText(value=1465.5,
step=100,
style=style,
layout=widget_layout)
param_name19 = Button(description='Volume_clacification_fraction',
disabled=True,
layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
self.Volume_clacification_fraction = FloatText(value=0.0,
step=0.01,
style=style,
layout=widget_layout)
param_name20 = Button(
description='Volume_cytoplasmic_to_nuclear_ratio',
disabled=True,
layout=name_button_layout)
param_name20.style.button_color = 'tan'
self.Volume_cytoplasmic_to_nuclear_ratio = FloatText(
value=3.6, step=0.1, style=style, layout=widget_layout)
param_name21 = Button(description='use_function_multiply_by_ratio',
disabled=True,
layout=name_button_layout)
param_name21.style.button_color = 'lightgreen'
self.use_function_multiply_by_ratio = Checkbox(value=False,
style=style,
layout=widget_layout)
param_name22 = Button(description='multiplication_ratio_value',
disabled=True,
layout=name_button_layout)
param_name22.style.button_color = 'tan'
self.multiplication_ratio_value = FloatText(value=2.0,
step=0.1,
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='cubic_micron/min',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='cubic_micron/min',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'tan'
units_button7 = Button(description='cubic_micron/min',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='cubic_micron/min',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'lightgreen'
units_button10 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'tan'
units_button11 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button16.style.button_color = 'tan'
units_button17 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button17.style.button_color = 'lightgreen'
units_button18 = Button(description='cubic_micron',
disabled=True,
layout=units_button_layout)
units_button18.style.button_color = 'tan'
units_button19 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
units_button20 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button20.style.button_color = 'tan'
units_button21 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button21.style.button_color = 'lightgreen'
units_button22 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button22.style.button_color = 'tan'
desc_button1 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
desc_button20 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button20.style.button_color = 'tan'
desc_button21 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button21.style.button_color = 'lightgreen'
desc_button22 = Button(description='',
disabled=True,
layout=desc_button_layout)
desc_button22.style.button_color = 'tan'
row1 = [param_name1, self.Volume, units_button1, desc_button1]
row2 = [
param_name2, self.Volume_target_solid_cytoplasmic, units_button2,
desc_button2
]
row3 = [
param_name3, self.Volume_target_solid_nuclear, units_button3,
desc_button3
]
row4 = [
param_name4, self.Volume_target_fluid_fraction, units_button4,
desc_button4
]
row5 = [
param_name5, self.Volume_cytoplasmic_biomass_change_rate,
units_button5, desc_button5
]
row6 = [
param_name6, self.Volume_nuclear_biomass_change_rate,
units_button6, desc_button6
]
row7 = [
param_name7, self.Volume_fluid_change_rate, units_button7,
desc_button7
]
row8 = [
param_name8, self.Volume_calcification_rate, units_button8,
desc_button8
]
row9 = [param_name9, self.Volume_Total, units_button9, desc_button9]
row10 = [
param_name10, self.Volume_solid, units_button10, desc_button10
]
row11 = [
param_name11, self.Volume_fluid, units_button11, desc_button11
]
row12 = [
param_name12, self.Volume_fluid_fraction, units_button12,
desc_button12
]
row13 = [
param_name13, self.Volume_nuclear, units_button13, desc_button13
]
row14 = [
param_name14, self.Volume_nuclear_solid, units_button14,
desc_button14
]
row15 = [
param_name15, self.Volume_nuclear_fluid, units_button15,
desc_button15
]
row16 = [
param_name16, self.Volume_cytoplasmic, units_button16,
desc_button16
]
row17 = [
param_name17, self.Volume_cytoplasmic_solid, units_button17,
desc_button17
]
row18 = [
param_name18, self.Volume_cytoplasmic_fluid, units_button18,
desc_button18
]
row19 = [
param_name19, self.Volume_clacification_fraction, units_button19,
desc_button19
]
row20 = [
param_name20, self.Volume_cytoplasmic_to_nuclear_ratio,
units_button20, desc_button20
]
row21 = [
param_name21, self.use_function_multiply_by_ratio, units_button21,
desc_button21
]
row22 = [
param_name22, self.multiplication_ratio_value, units_button22,
desc_button22
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
box8,
box9,
box10,
box11,
box12,
box13,
box14,
box15,
box16,
box17,
box18,
box19,
box20,
box21,
box22,
])
def ResLayer_app():
app = widgetify(
PLOT,
manual=True,
survey=ToggleButtons(
options=[
"Dipole-Dipole", "Dipole-Pole", "Pole-Dipole", "Pole-Pole"
],
value="Dipole-Dipole",
),
zcLayer=FloatSlider(
min=-10.0,
max=0.0,
step=1.0,
value=-10.0,
continuous_update=False,
description="$zc_{layer}$",
),
dzLayer=FloatSlider(
min=0.5,
max=5.0,
step=0.5,
value=1.0,
continuous_update=False,
description="$dz_{layer}$",
),
rholayer=FloatText(
min=1e-8,
max=1e8,
value=5000.0,
continuous_update=False,
description="$\\rho_{2}$",
),
xc=FloatSlider(min=-30.0,
max=30.0,
step=1.0,
value=0.0,
continuous_update=False),
zc=FloatSlider(min=-30.0,
max=-15.0,
step=0.5,
value=-25.0,
continuous_update=False),
r=FloatSlider(min=1.0,
max=10.0,
step=0.5,
value=5.0,
continuous_update=False),
rhoTarget=FloatText(
min=1e-8,
max=1e8,
value=500.0,
continuous_update=False,
description="$\\rho_{3}$",
),
rhohalf=FloatText(
min=1e-8,
max=1e8,
value=500.0,
continuous_update=False,
description="$\\rho_{1}$",
),
A=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=-30.25,
continuous_update=False),
B=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=30.25,
continuous_update=False),
M=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=-10.25,
continuous_update=False),
N=FloatSlider(min=-30.25,
max=30.25,
step=0.5,
value=10.25,
continuous_update=False),
Field=ToggleButtons(
options=["Model", "Potential", "E", "J", "Charge", "Sensitivity"],
value="Model",
),
Type=ToggleButtons(options=["Total", "Primary", "Secondary"],
value="Total"),
Scale=ToggleButtons(options=["Linear", "Log"], value="Linear"),
)
return app
def interact_plot_model(self):
Q = interact(
self.plot_model,
m_background=FloatSlider(
min=-2,
max=2,
step=0.05,
value=0.0,
continuous_update=False,
description="m$_{background}$",
),
m1=FloatSlider(
min=-2,
max=2,
step=0.05,
value=1.0,
continuous_update=False,
description="m1",
),
m2=FloatSlider(
min=-2,
max=2,
step=0.05,
value=2.0,
continuous_update=False,
description="m2",
),
m1_center=FloatSlider(
min=-2,
max=2,
step=0.05,
value=0.2,
continuous_update=False,
description="m1$_{center}$",
),
dm1=FloatSlider(
min=0,
max=0.5,
step=0.05,
value=0.2,
continuous_update=False,
description="m1$_{width}$",
),
m2_center=FloatSlider(
min=-2,
max=2,
step=0.05,
value=0.75,
continuous_update=False,
description="m2$_{center}$",
),
sigma_2=FloatSlider(
min=0.01,
max=0.1,
step=0.01,
value=0.07,
continuous_update=False,
description="m2$_{sigma}$",
),
option=SelectMultiple(
options=["kernel", "model", "data"],
value=["model"],
description="option",
),
percentage=FloatText(value=5),
floor=FloatText(value=0.02),
)
return Q
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
menv_var1 = Button(description='resource',
disabled=True,
layout=name_button_layout)
menv_var1.style.button_color = 'tan'
param_name1 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.resource_diffusion_coefficient = FloatText(value=100000,
step=10000,
style=style,
layout=widget_layout)
param_name2 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.resource_decay_rate = FloatText(value=0.1,
step=0.01,
style=style,
layout=widget_layout)
param_name3 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.resource_initial_condition = FloatText(value=0,
style=style,
layout=widget_layout)
param_name4 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.resource_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.resource_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var2 = Button(description='quorum',
disabled=True,
layout=name_button_layout)
menv_var2.style.button_color = 'lightgreen'
param_name5 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.quorum_diffusion_coefficient = FloatText(value=100000,
step=10000,
style=style,
layout=widget_layout)
param_name6 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.quorum_decay_rate = FloatText(value=10,
step=1,
style=style,
layout=widget_layout)
param_name7 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.quorum_initial_condition = FloatText(value=0,
style=style,
layout=widget_layout)
param_name8 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.quorum_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.quorum_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var3 = Button(description='death_signal',
disabled=True,
layout=name_button_layout)
menv_var3.style.button_color = 'tan'
param_name9 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.death_signal_diffusion_coefficient = FloatText(
value=40000, step=1000, style=style, layout=widget_layout)
param_name10 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.death_signal_decay_rate = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name11 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.death_signal_initial_condition = FloatText(value=0,
style=style,
layout=widget_layout)
param_name12 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.death_signal_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.death_signal_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var4 = Button(description='signal',
disabled=True,
layout=name_button_layout)
menv_var4.style.button_color = 'lightgreen'
param_name13 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.signal_diffusion_coefficient = FloatText(value=25000,
step=1000,
style=style,
layout=widget_layout)
param_name14 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.signal_decay_rate = FloatText(value=0.1,
step=0.01,
style=style,
layout=widget_layout)
param_name15 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.signal_initial_condition = FloatText(value=0,
style=style,
layout=widget_layout)
param_name16 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.signal_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.signal_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var5 = Button(description='poison',
disabled=True,
layout=name_button_layout)
menv_var5.style.button_color = 'tan'
param_name17 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.poison_diffusion_coefficient = FloatText(value=50000,
step=1000,
style=style,
layout=widget_layout)
param_name18 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.poison_decay_rate = FloatText(value=20.,
step=1,
style=style,
layout=widget_layout)
param_name19 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.poison_initial_condition = FloatText(value=0,
style=style,
layout=widget_layout)
param_name20 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.poison_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.poison_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
self.calculate_gradient = Checkbox(description='calculate_gradients',
disabled=False,
layout=desc_button_layout)
self.track_internal = Checkbox(description='track_in_agents',
disabled=False,
layout=desc_button_layout)
# ------- micronenv info
menv_units_button1 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button2 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button3 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button4 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button5 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button6 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
menv_units_button9 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button10 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
menv_units_button13 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button14 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button5 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button6 = Button(description='',
disabled=True,
layout=units_button_layout)
menv_units_button17 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button18 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button8 = Button(description='',
disabled=True,
layout=units_button_layout)
row_resource = [
menv_var1,
]
row1 = [
param_name1, self.resource_diffusion_coefficient,
menv_units_button1
]
row2 = [param_name2, self.resource_decay_rate, menv_units_button2]
row3 = [
param_name3, self.resource_initial_condition, menv_units_button3
]
row4 = [
param_name4, self.resource_Dirichlet_boundary_condition,
menv_units_button4,
self.resource_Dirichlet_boundary_condition_toggle
]
row_quorum = [
menv_var2,
]
row5 = [
param_name5, self.quorum_diffusion_coefficient, menv_units_button5
]
row6 = [param_name6, self.quorum_decay_rate, menv_units_button6]
row7 = [param_name7, self.quorum_initial_condition, units_button1]
row8 = [
param_name8, self.quorum_Dirichlet_boundary_condition,
units_button2, self.quorum_Dirichlet_boundary_condition_toggle
]
row_death_signal = [
menv_var3,
]
row9 = [
param_name9, self.death_signal_diffusion_coefficient,
menv_units_button9
]
row10 = [
param_name10, self.death_signal_decay_rate, menv_units_button10
]
row11 = [
param_name11, self.death_signal_initial_condition, units_button3
]
row12 = [
param_name12, self.death_signal_Dirichlet_boundary_condition,
units_button4,
self.death_signal_Dirichlet_boundary_condition_toggle
]
row_signal = [
menv_var4,
]
row13 = [
param_name13, self.signal_diffusion_coefficient,
menv_units_button13
]
row14 = [param_name14, self.signal_decay_rate, menv_units_button14]
row15 = [param_name15, self.signal_initial_condition, units_button5]
row16 = [
param_name16, self.signal_Dirichlet_boundary_condition,
units_button6, self.signal_Dirichlet_boundary_condition_toggle
]
row_poison = [
menv_var5,
]
row17 = [
param_name17, self.poison_diffusion_coefficient,
menv_units_button17
]
row18 = [param_name18, self.poison_decay_rate, menv_units_button18]
row19 = [param_name19, self.poison_initial_condition, units_button7]
row20 = [
param_name20, self.poison_Dirichlet_boundary_condition,
units_button8, self.poison_Dirichlet_boundary_condition_toggle
]
row21 = [
self.calculate_gradient,
]
row22 = [
self.track_internal,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box_resource = Box(children=row_resource, layout=box_layout)
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box_quorum = Box(children=row_quorum, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box_death_signal = Box(children=row_death_signal, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box_signal = Box(children=row_signal, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box_poison = Box(children=row_poison, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
box19 = Box(children=row19, layout=box_layout)
box20 = Box(children=row20, layout=box_layout)
box21 = Box(children=row21, layout=box_layout)
box22 = Box(children=row22, layout=box_layout)
self.tab = VBox([
box_resource,
box1,
box2,
box3,
box4,
box_quorum,
box5,
box6,
box7,
box8,
box_death_signal,
box9,
box10,
box11,
box12,
box_signal,
box13,
box14,
box15,
box16,
box_poison,
box17,
box18,
box19,
box20,
box21,
box22,
])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
widget2_layout = {'width': '10%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
menv_var1 = Button(description='electrical_potential (volt)',
disabled=True,
layout=name_button_layout)
menv_var1.style.button_color = 'tan'
param_name1 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.electrical_potential_diffusion_coefficient = FloatText(
value=0, step=0.01, style=style, layout=widget_layout)
param_name2 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.electrical_potential_decay_rate = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
param_name3 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.electrical_potential_initial_condition = FloatText(
value=0, style=style, layout=widget_layout)
param_name4 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.electrical_potential_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.electrical_potential_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var2 = Button(description='quorum_factor_1',
disabled=True,
layout=name_button_layout)
menv_var2.style.button_color = 'lightgreen'
param_name5 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.quorum_factor_1_diffusion_coefficient = FloatText(
value=50000, step=1000, style=style, layout=widget_layout)
param_name6 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.quorum_factor_1_decay_rate = FloatText(value=0.1,
step=0.01,
style=style,
layout=widget_layout)
param_name7 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.quorum_factor_1_initial_condition = FloatText(
value=0.0, style=style, layout=widget_layout)
param_name8 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.quorum_factor_1_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.quorum_factor_1_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var3 = Button(description='quorum_factor_2',
disabled=True,
layout=name_button_layout)
menv_var3.style.button_color = 'tan'
param_name9 = Button(description='diffusion_coefficient',
disabled=True,
layout=name_button_layout)
self.quorum_factor_2_diffusion_coefficient = FloatText(
value=50000, step=1000, style=style, layout=widget_layout)
param_name10 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.quorum_factor_2_decay_rate = FloatText(value=0.1,
step=0.01,
style=style,
layout=widget_layout)
param_name11 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.quorum_factor_2_initial_condition = FloatText(
value=0.0, style=style, layout=widget_layout)
param_name12 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.quorum_factor_2_Dirichlet_boundary_condition = FloatText(
value=0, style=style, layout=widget_layout)
self.quorum_factor_2_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
self.calculate_gradient = Checkbox(description='calculate_gradients',
disabled=False,
layout=desc_button_layout)
self.track_internal = Checkbox(description='track_in_agents',
disabled=False,
layout=desc_button_layout)
# ------- micronenv info
menv_units_button1 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button2 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button3 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button4 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button5 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button6 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button7 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button8 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button9 = Button(description='micron^2/min',
disabled=True,
layout=units_button_layout)
menv_units_button10 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
menv_units_button11 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
menv_units_button12 = Button(description='mmHg',
disabled=True,
layout=units_button_layout)
row_electrical_potential = [
menv_var1,
]
row1 = [
param_name1, self.electrical_potential_diffusion_coefficient,
menv_units_button1
]
row2 = [
param_name2, self.electrical_potential_decay_rate,
menv_units_button2
]
row3 = [
param_name3, self.electrical_potential_initial_condition,
menv_units_button3
]
row4 = [
param_name4,
self.electrical_potential_Dirichlet_boundary_condition,
menv_units_button4,
self.electrical_potential_Dirichlet_boundary_condition_toggle
]
row_quorum_factor_1 = [
menv_var2,
]
row5 = [
param_name5, self.quorum_factor_1_diffusion_coefficient,
menv_units_button5
]
row6 = [
param_name6, self.quorum_factor_1_decay_rate, menv_units_button6
]
row7 = [
param_name7, self.quorum_factor_1_initial_condition,
menv_units_button7
]
row8 = [
param_name8, self.quorum_factor_1_Dirichlet_boundary_condition,
menv_units_button8,
self.quorum_factor_1_Dirichlet_boundary_condition_toggle
]
row_quorum_factor_2 = [
menv_var3,
]
row9 = [
param_name9, self.quorum_factor_2_diffusion_coefficient,
menv_units_button9
]
row10 = [
param_name10, self.quorum_factor_2_decay_rate, menv_units_button10
]
row11 = [
param_name11, self.quorum_factor_2_initial_condition,
menv_units_button11
]
row12 = [
param_name12, self.quorum_factor_2_Dirichlet_boundary_condition,
menv_units_button12,
self.quorum_factor_2_Dirichlet_boundary_condition_toggle
]
row13 = [
self.calculate_gradient,
]
row14 = [
self.track_internal,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box_electrical_potential = Box(children=row_electrical_potential,
layout=box_layout)
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box_quorum_factor_1 = Box(children=row_quorum_factor_1,
layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box_quorum_factor_2 = Box(children=row_quorum_factor_2,
layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
self.tab = VBox([
box_electrical_potential,
box1,
box2,
box3,
box4,
box_quorum_factor_1,
box5,
box6,
box7,
box8,
box_quorum_factor_2,
box9,
box10,
box11,
box12,
box13,
box14,
])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
divider_button_layout = {'width': '40%'}
param_name1 = Button(description='tumor_transition_rate',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'tan'
self.tumor_transition_rate = FloatText(value=0.0022956841138659324,
step=0.0001,
style=style,
layout=widget_layout)
param_name2 = Button(description='tumor_max_necrosis_rate',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'lightgreen'
self.tumor_max_necrosis_rate = FloatText(value=0.002777777777777778,
step=0.0001,
style=style,
layout=widget_layout)
param_name3 = Button(description='elastic_rate',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'tan'
self.elastic_rate = FloatText(value=0.05,
step=0.01,
style=style,
layout=widget_layout)
param_name4 = Button(description='plastic_rate',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'lightgreen'
self.plastic_rate = FloatText(value=0.0005,
step=0.0001,
style=style,
layout=widget_layout)
param_name5 = Button(description='max_ECM_displacement',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'tan'
self.max_ECM_displacement = FloatText(value=0.75,
step=0.1,
style=style,
layout=widget_layout)
param_name6 = Button(description='tumor_max_pressue',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'lightgreen'
self.tumor_max_pressue = FloatText(value=1.0,
step=0.1,
style=style,
layout=widget_layout)
param_name7 = Button(description='if_random_seed',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'tan'
self.if_random_seed = Checkbox(value=False,
style=style,
layout=widget_layout)
units_button1 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'tan'
units_button2 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'lightgreen'
units_button3 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'tan'
units_button4 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'lightgreen'
units_button5 = Button(description='micron',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'tan'
units_button6 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'lightgreen'
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'tan'
desc_button2 = Button(
description='The proliferation rate of tumor cells',
tooltip='The proliferation rate of tumor cells',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(
description='The maximum necrosis rate of tumor cells',
tooltip='The maximum necrosis rate of tumor cells',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(
description='The elastic force rate for parenchyma',
tooltip='The elastic force rate for parenchyma',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(
description='The plastic reorganization force rate for parenchyma',
tooltip='The plastic reorganization force rate for parenchyma',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(
description='The maximum tolerated displacement for parenchyma',
tooltip='The maximum tolerated displacement for parenchyma',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(
description=
'The maximum pressure threshold for tumor cells proliferation',
tooltip=
'The maximum pressure threshold for tumor cells proliferation',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(
description=
'Boolean variable that used to enable or disable random seeding',
tooltip=
'Boolean variable that used to enable or disable random seeding',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
row2 = [
param_name1, self.tumor_transition_rate, units_button1,
desc_button2
]
row3 = [
param_name2, self.tumor_max_necrosis_rate, units_button2,
desc_button3
]
row4 = [param_name3, self.elastic_rate, units_button3, desc_button4]
row5 = [param_name4, self.plastic_rate, units_button4, desc_button5]
row6 = [
param_name5, self.max_ECM_displacement, units_button5, desc_button6
]
row7 = [
param_name6, self.tumor_max_pressue, units_button6, desc_button7
]
row8 = [param_name7, self.if_random_seed, units_button7, desc_button8]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
self.tab = VBox([
box2,
box3,
box4,
box5,
box6,
box7,
box8,
])
class SubstrateTab(object):
def __init__(self):
self.output_dir = '.'
# self.output_dir = 'tmpdir'
# self.fig = plt.figure(figsize=(7.2,6)) # this strange figsize results in a ~square contour plot
# initial value
self.field_index = 4
# self.field_index = self.mcds_field.value + 4
tab_height = '500px'
constWidth = '180px'
constWidth2 = '150px'
tab_layout = Layout(
width='900px', # border='2px solid black',
height=tab_height,
) #overflow_y='scroll')
max_frames = 1
self.mcds_plot = interactive(self.plot_substrate,
frame=(0, max_frames),
continuous_update=False)
svg_plot_size = '700px'
self.mcds_plot.layout.width = svg_plot_size
self.mcds_plot.layout.height = svg_plot_size
self.max_frames = BoundedIntText(
min=0,
max=99999,
value=max_frames,
description='Max',
layout=Layout(width='160px'),
)
self.max_frames.observe(self.update_max_frames)
self.field_min_max = {'dummy': [0., 1.]}
# hacky I know, but make a dict that's got (key,value) reversed from the dict in the Dropdown below
self.field_dict = {0: 'dummy'}
self.mcds_field = Dropdown(
options={'dummy': 0},
value=0,
# description='Field',
layout=Layout(width=constWidth))
# print("substrate __init__: self.mcds_field.value=",self.mcds_field.value)
# self.mcds_field.observe(self.mcds_field_cb)
self.mcds_field.observe(self.mcds_field_changed_cb)
# self.field_cmap = Text(
# value='viridis',
# description='Colormap',
# disabled=True,
# layout=Layout(width=constWidth),
# )
self.field_cmap = Dropdown(
options=['viridis', 'jet', 'YlOrRd'],
value='viridis',
# description='Field',
layout=Layout(width=constWidth))
#self.field_cmap.observe(self.plot_substrate)
# self.field_cmap.observe(self.plot_substrate)
self.field_cmap.observe(self.mcds_field_cb)
self.cmap_fixed = Checkbox(
description='Fix',
disabled=False,
# layout=Layout(width=constWidth2),
)
self.save_min_max = Button(
description='Save', #style={'description_width': 'initial'},
button_style=
'success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Save min/max for this substrate',
disabled=True,
layout=Layout(width='90px'))
def save_min_max_cb(b):
# field_name = self.mcds_field.options[]
# field_name = next(key for key, value in self.mcds_field.options.items() if value == self.mcds_field.value)
field_name = self.field_dict[self.mcds_field.value]
# print(field_name)
# self.field_min_max = {'oxygen': [0., 30.], 'glucose': [0., 1.], 'H+ ions': [0., 1.], 'ECM': [0., 1.], 'NP1': [0., 1.], 'NP2': [0., 1.]}
self.field_min_max[field_name][0] = self.cmap_min.value
self.field_min_max[field_name][1] = self.cmap_max.value
# print(self.field_min_max)
self.save_min_max.on_click(save_min_max_cb)
self.cmap_min = FloatText(
description='Min',
value=0,
step=0.1,
disabled=True,
layout=Layout(width=constWidth2),
)
self.cmap_min.observe(self.mcds_field_cb)
self.cmap_max = FloatText(
description='Max',
value=38,
step=0.1,
disabled=True,
layout=Layout(width=constWidth2),
)
self.cmap_max.observe(self.mcds_field_cb)
def cmap_fixed_cb(b):
if (self.cmap_fixed.value):
self.cmap_min.disabled = False
self.cmap_max.disabled = False
self.save_min_max.disabled = False
else:
self.cmap_min.disabled = True
self.cmap_max.disabled = True
self.save_min_max.disabled = True
# self.mcds_field_cb()
self.cmap_fixed.observe(cmap_fixed_cb)
field_cmap_row2 = HBox([self.field_cmap, self.cmap_fixed])
# field_cmap_row3 = HBox([self.save_min_max, self.cmap_min, self.cmap_max])
items_auto = [
self.save_min_max, #layout=Layout(flex='3 1 auto', width='auto'),
self.cmap_min,
self.cmap_max,
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='80%')
field_cmap_row3 = Box(children=items_auto, layout=box_layout)
# field_cmap_row3 = Box([self.save_min_max, self.cmap_min, self.cmap_max])
# mcds_tab = widgets.VBox([mcds_dir, mcds_plot, mcds_play], layout=tab_layout)
mcds_params = VBox([
self.mcds_field, field_cmap_row2, field_cmap_row3, self.max_frames
]) # mcds_dir
# mcds_params = VBox([self.mcds_field, field_cmap_row2, field_cmap_row3,]) # mcds_dir
# self.tab = HBox([mcds_params, self.mcds_plot], layout=tab_layout)
# self.tab = HBox([mcds_params, self.mcds_plot])
help_label = Label('select slider: drag or left/right arrows')
row1 = Box([
help_label,
Box([self.max_frames, self.mcds_field, self.field_cmap],
layout=Layout(border='0px solid black',
width='50%',
height='',
align_items='stretch',
flex_direction='row',
display='flex'))
])
row2 = Box([self.cmap_fixed, self.cmap_min, self.cmap_max],
layout=Layout(border='0px solid black',
width='50%',
height='',
align_items='stretch',
flex_direction='row',
display='flex'))
self.tab = VBox([row1, row2, self.mcds_plot])
#---------------------------------------------------
def update_dropdown_fields(self, data_dir):
# print('update_dropdown_fields called --------')
self.output_dir = data_dir
tree = None
try:
fname = os.path.join(self.output_dir, "initial.xml")
tree = ET.parse(fname)
# return
except:
print("Cannot open ", fname, " to get names of substrate fields.")
return
xml_root = tree.getroot()
self.field_min_max = {}
self.field_dict = {}
dropdown_options = {}
uep = xml_root.find('.//variables')
comment_str = ""
field_idx = 0
if (uep):
for elm in uep.findall('variable'):
# print("-----> ",elm.attrib['name'])
self.field_min_max[elm.attrib['name']] = [0., 1.]
self.field_dict[field_idx] = elm.attrib['name']
dropdown_options[elm.attrib['name']] = field_idx
field_idx += 1
# constWidth = '180px'
# print('options=',dropdown_options)
self.mcds_field.value = 0
self.mcds_field.options = dropdown_options
# self.mcds_field = Dropdown(
# # options={'oxygen': 0, 'glucose': 1},
# options=dropdown_options,
# value=0,
# # description='Field',
# layout=Layout(width=constWidth)
# )
def update_max_frames_expected(
self, value): # called when beginning an interactive Run
self.max_frames.value = value # assumes naming scheme: "snapshot%08d.svg"
self.mcds_plot.children[0].max = self.max_frames.value
def update(self, rdir):
self.output_dir = rdir
if rdir == '':
# self.max_frames.value = 0
tmpdir = os.path.abspath('tmpdir')
self.output_dir = tmpdir
all_files = sorted(glob.glob(os.path.join(tmpdir, 'output*.xml')))
if len(all_files) > 0:
last_file = all_files[-1]
self.max_frames.value = int(
last_file[-12:-4]
) # assumes naming scheme: "output%08d.xml"
self.mcds_plot.update()
return
all_files = sorted(glob.glob(os.path.join(rdir, 'output*.xml')))
if len(all_files) > 0:
last_file = all_files[-1]
self.max_frames.value = int(
last_file[-12:-4]) # assumes naming scheme: "output%08d.xml"
self.mcds_plot.update()
def update_max_frames(self, _b):
self.mcds_plot.children[0].max = self.max_frames.value
def mcds_field_changed_cb(self, b):
# print("mcds_field_changed_cb: self.mcds_field.value=",self.mcds_field.value)
if (self.mcds_field.value == None):
return
self.field_index = self.mcds_field.value + 4
field_name = self.field_dict[self.mcds_field.value]
# print('mcds_field_cb: '+field_name)
self.cmap_min.value = self.field_min_max[field_name][0]
self.cmap_max.value = self.field_min_max[field_name][1]
self.mcds_plot.update()
def mcds_field_cb(self, b):
#self.field_index = self.mcds_field.value
# self.field_index = self.mcds_field.options.index(self.mcds_field.value) + 4
# self.field_index = self.mcds_field.options[self.mcds_field.value]
self.field_index = self.mcds_field.value + 4
# field_name = self.mcds_field.options[self.mcds_field.value]
# self.cmap_min.value = self.field_min_max[field_name][0] # oxygen, etc
# self.cmap_max.value = self.field_min_max[field_name][1] # oxygen, etc
# self.field_index = self.mcds_field.value + 4
# print('field_index=',self.field_index)
self.mcds_plot.update()
def plot_substrate(self, frame):
# global current_idx, axes_max, gFileId, field_index
fname = "output%08d_microenvironment0.mat" % frame
xml_fname = "output%08d.xml" % frame
# fullname = output_dir_str + fname
# fullname = fname
full_fname = os.path.join(self.output_dir, fname)
full_xml_fname = os.path.join(self.output_dir, xml_fname)
# self.output_dir = '.'
# if not os.path.isfile(fullname):
if not os.path.isfile(full_fname):
# print("File does not exist: ", full_fname)
# print("No: ", full_fname)
print("Once output files are generated, click the slider."
) # No: output00000000_microenvironment0.mat
return
# tree = ET.parse(xml_fname)
tree = ET.parse(full_xml_fname)
xml_root = tree.getroot()
mins = round(int(float(xml_root.find(
".//current_time").text))) # TODO: check units = mins
hrs = int(mins / 60)
days = int(hrs / 24)
title_str = '%dd, %dh, %dm' % (int(days),
(hrs % 24), mins - (hrs * 60))
info_dict = {}
# scipy.io.loadmat(fullname, info_dict)
scipy.io.loadmat(full_fname, info_dict)
M = info_dict['multiscale_microenvironment']
# global_field_index = int(mcds_field.value)
# print('plot_substrate: field_index =',field_index)
f = M[
self.
field_index, :] # 4=tumor cells field, 5=blood vessel density, 6=growth substrate
# plt.clf()
# my_plot = plt.imshow(f.reshape(400,400), cmap='jet', extent=[0,20, 0,20])
self.fig = plt.figure(figsize=(
7.2, 6)) # this strange figsize results in a ~square contour plot
# fig.set_tight_layout(True)
# ax = plt.axes([0, 0.05, 0.9, 0.9 ]) #left, bottom, width, height
# ax = plt.axes([0, 0.0, 1, 1 ])
# cmap = plt.cm.viridis # Blues, YlOrBr, ...
# im = ax.imshow(f.reshape(100,100), interpolation='nearest', cmap=cmap, extent=[0,20, 0,20])
# ax.grid(False)
N = int(math.sqrt(len(M[0, :])))
grid2D = M[0, :].reshape(N, N)
xvec = grid2D[0, :]
num_contours = 15
# levels = MaxNLocator(nbins=10).tick_values(vmin, vmax)
levels = MaxNLocator(nbins=num_contours).tick_values(
self.cmap_min.value, self.cmap_max.value)
if (self.cmap_fixed.value):
my_plot = plt.contourf(xvec,
xvec,
M[self.field_index, :].reshape(N, N),
levels=levels,
extend='both',
cmap=self.field_cmap.value)
else:
# my_plot = plt.contourf(xvec, xvec, M[self.field_index, :].reshape(N,N), num_contours, cmap=self.field_cmap.value)
my_plot = plt.contourf(xvec,
xvec,
M[self.field_index, :].reshape(N, N),
num_contours,
cmap=self.field_cmap.value)
plt.title(title_str)
plt.colorbar(my_plot)
axes_min = 0
axes_max = 2000
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
divider_button_layout = {'width': '40%'}
param_name1 = Button(description='random_seed',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'lightgreen'
self.random_seed = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
div_row1 = Button(description='---Virus Replication---',
disabled=True,
layout=divider_button_layout)
param_name2 = Button(description='virion_uncoating_rate',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.virion_uncoating_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name3 = Button(description='uncoated_to_RNA_rate',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.uncoated_to_RNA_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name4 = Button(description='protein_synthesis_rate',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.protein_synthesis_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name5 = Button(description='virion_assembly_rate',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.virion_assembly_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
div_row2 = Button(description='---Virus Adsorption and Export---',
disabled=True,
layout=divider_button_layout)
param_name6 = Button(description='virion_export_rate',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.virion_export_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
div_row3 = Button(
description='---ACE2 receptor dynamics with virus binding---',
disabled=True,
layout=divider_button_layout)
param_name7 = Button(description='ACE2_receptors_per_cell',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.ACE2_receptors_per_cell = FloatText(value=1000,
step=100,
style=style,
layout=widget_layout)
param_name8 = Button(description='ACE2_binding_rate',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.ACE2_binding_rate = FloatText(value=0.001,
step=0.0001,
style=style,
layout=widget_layout)
param_name9 = Button(description='ACE2_endocytosis_rate',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.ACE2_endocytosis_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name10 = Button(description='ACE2_cargo_release_rate',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.ACE2_cargo_release_rate = FloatText(value=0.001,
step=0.0001,
style=style,
layout=widget_layout)
param_name11 = Button(description='ACE2_recycling_rate',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.ACE2_recycling_rate = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
div_row4 = Button(description='---Apoptotic Response---',
disabled=True,
layout=divider_button_layout)
param_name12 = Button(description='max_infected_apoptosis_rate',
disabled=True,
layout=name_button_layout)
param_name12.style.button_color = 'tan'
self.max_infected_apoptosis_rate = FloatText(value=0.001,
step=0.0001,
style=style,
layout=widget_layout)
param_name13 = Button(description='max_apoptosis_half_max',
disabled=True,
layout=name_button_layout)
param_name13.style.button_color = 'lightgreen'
self.max_apoptosis_half_max = FloatText(value=500,
step=10,
style=style,
layout=widget_layout)
param_name14 = Button(description='apoptosis_hill_power',
disabled=True,
layout=name_button_layout)
param_name14.style.button_color = 'tan'
self.apoptosis_hill_power = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name15 = Button(description='virus_fraction_released_at_death',
disabled=True,
layout=name_button_layout)
param_name15.style.button_color = 'lightgreen'
self.virus_fraction_released_at_death = FloatText(value=0,
step=0.01,
style=style,
layout=widget_layout)
div_row5 = Button(description='---Initialization Options--',
disabled=True,
layout=divider_button_layout)
param_name16 = Button(description='multiplicity_of_infection',
disabled=True,
layout=name_button_layout)
param_name16.style.button_color = 'tan'
self.multiplicity_of_infection = FloatText(value=0.01,
step=0.001,
style=style,
layout=widget_layout)
param_name17 = Button(description='use_single_infected_cell',
disabled=True,
layout=name_button_layout)
param_name17.style.button_color = 'lightgreen'
self.use_single_infected_cell = Checkbox(value=False,
style=style,
layout=widget_layout)
div_row6 = Button(description='---Visualization Options---',
disabled=True,
layout=divider_button_layout)
param_name18 = Button(description='color_variable',
disabled=True,
layout=name_button_layout)
param_name18.style.button_color = 'tan'
self.color_variable = Text(value='assembled virion',
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'lightgreen'
units_button3 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'tan'
units_button4 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'lightgreen'
units_button5 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'tan'
units_button6 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'lightgreen'
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
units_button8 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'tan'
units_button9 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'tan'
units_button10 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'lightgreen'
units_button11 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'tan'
units_button12 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'lightgreen'
units_button13 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button13.style.button_color = 'tan'
units_button14 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button14.style.button_color = 'lightgreen'
units_button15 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
units_button16 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button16.style.button_color = 'tan'
units_button17 = Button(description='virion',
disabled=True,
layout=units_button_layout)
units_button17.style.button_color = 'lightgreen'
units_button18 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button18.style.button_color = 'tan'
units_button19 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button19.style.button_color = 'lightgreen'
units_button20 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button20.style.button_color = 'lightgreen'
units_button21 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button21.style.button_color = 'tan'
units_button22 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button22.style.button_color = 'lightgreen'
units_button23 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button23.style.button_color = 'lightgreen'
units_button24 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button24.style.button_color = 'tan'
desc_button1 = Button(description='',
tooltip='',
disabled=True,
layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
desc_button2 = Button(
description='rate at which an internalized virion is uncoated',
tooltip='rate at which an internalized virion is uncoated',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(
description=
'rate at which uncoated virion makes its mRNA available',
tooltip='rate at which uncoated virion makes its mRNA available',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button4 = Button(
description='rate at mRNA creates complete set of proteins',
tooltip='rate at mRNA creates complete set of proteins',
disabled=True,
layout=desc_button_layout)
desc_button4.style.button_color = 'tan'
desc_button5 = Button(
description=
'rate at which viral proteins are assembled into complete virion',
tooltip=
'rate at which viral proteins are assembled into complete virion',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(
description='rate at which a virion is exported from a live cell',
tooltip='rate at which a virion is exported from a live cell',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='number of ACE2 receptors per cell',
tooltip='number of ACE2 receptors per cell',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button8 = Button(description='ACE2 receptor-virus binding rate',
tooltip='ACE2 receptor-virus binding rate',
disabled=True,
layout=desc_button_layout)
desc_button8.style.button_color = 'tan'
desc_button9 = Button(
description='ACE2 receptor-virus endocytosis rate',
tooltip='ACE2 receptor-virus endocytosis rate',
disabled=True,
layout=desc_button_layout)
desc_button9.style.button_color = 'lightgreen'
desc_button10 = Button(
description='ACE2 receptor-virus cargo release rate',
tooltip='ACE2 receptor-virus cargo release rate',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(description='ACE2 receptor recycling rate',
tooltip='ACE2 receptor recycling rate',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(
description='maximum rate of cell apoptosis due to viral infection',
tooltip='maximum rate of cell apoptosis due to viral infection',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(
description=
'viral load at which cells reach half max apoptosis rate',
tooltip='viral load at which cells reach half max apoptosis rate',
disabled=True,
layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(
description='Hill power for viral load apoptosis response',
tooltip='Hill power for viral load apoptosis response',
disabled=True,
layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(
description='fraction of internal virus released at cell death',
tooltip='fraction of internal virus released at cell death',
disabled=True,
layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
desc_button16 = Button(
description='multiplicity of infection: virions/cells at t=0',
tooltip='multiplicity of infection: virions/cells at t=0',
disabled=True,
layout=desc_button_layout)
desc_button16.style.button_color = 'tan'
desc_button17 = Button(
description='Infect center cell with one virion (overrides MOI)',
tooltip='Infect center cell with one virion (overrides MOI)',
disabled=True,
layout=desc_button_layout)
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(
description='color cells based on this variable',
tooltip='color cells based on this variable',
disabled=True,
layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
row1 = [param_name1, self.random_seed, units_button1, desc_button1]
row2 = [
param_name2, self.virion_uncoating_rate, units_button3,
desc_button2
]
row3 = [
param_name3, self.uncoated_to_RNA_rate, units_button4, desc_button3
]
row4 = [
param_name4, self.protein_synthesis_rate, units_button5,
desc_button4
]
row5 = [
param_name5, self.virion_assembly_rate, units_button6, desc_button5
]
row6 = [
param_name6, self.virion_export_rate, units_button8, desc_button6
]
row7 = [
param_name7, self.ACE2_receptors_per_cell, units_button10,
desc_button7
]
row8 = [
param_name8, self.ACE2_binding_rate, units_button11, desc_button8
]
row9 = [
param_name9, self.ACE2_endocytosis_rate, units_button12,
desc_button9
]
row10 = [
param_name10, self.ACE2_cargo_release_rate, units_button13,
desc_button10
]
row11 = [
param_name11, self.ACE2_recycling_rate, units_button14,
desc_button11
]
row12 = [
param_name12, self.max_infected_apoptosis_rate, units_button16,
desc_button12
]
row13 = [
param_name13, self.max_apoptosis_half_max, units_button17,
desc_button13
]
row14 = [
param_name14, self.apoptosis_hill_power, units_button18,
desc_button14
]
row15 = [
param_name15, self.virus_fraction_released_at_death,
units_button19, desc_button15
]
row16 = [
param_name16, self.multiplicity_of_infection, units_button21,
desc_button16
]
row17 = [
param_name17, self.use_single_infected_cell, units_button22,
desc_button17
]
row18 = [
param_name18, self.color_variable, units_button24, desc_button18
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box1 = Box(children=row1, layout=box_layout)
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box4 = Box(children=row4, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box8 = Box(children=row8, layout=box_layout)
box9 = Box(children=row9, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
box16 = Box(children=row16, layout=box_layout)
box17 = Box(children=row17, layout=box_layout)
box18 = Box(children=row18, layout=box_layout)
self.tab = VBox([
box1,
div_row1,
box2,
box3,
box4,
box5,
div_row2,
box6,
div_row3,
box7,
box8,
box9,
box10,
box11,
div_row4,
box12,
box13,
box14,
box15,
div_row5,
box16,
box17,
div_row6,
box18,
])
def __init__(self):
micron_units = Label(
'micron') # use "option m" (Mac, for micro symbol)
constWidth = '180px'
tab_height = '500px'
stepsize = 10
#style = {'description_width': '250px'}
style = {'description_width': '25%'}
layout = {'width': '400px'}
name_button_layout = {'width': '25%'}
widget_layout = {'width': '15%'}
widget2_layout = {'width': '10%'}
units_button_layout = {'width': '15%'}
desc_button_layout = {'width': '45%'}
divider_button_layout = {'width': '40%'}
div_row1 = Button(description='---Domain Options---',
disabled=True,
layout=divider_button_layout)
param_name1 = Button(description='type_of_death_model',
disabled=True,
layout=name_button_layout)
param_name1.style.button_color = 'tan'
self.type_of_death_model = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name2 = Button(description='initial_tumor_radius',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'lightgreen'
self.initial_tumor_radius = FloatText(value=150,
step=10,
style=style,
layout=widget_layout)
div_row2 = Button(description='---Apoptosis---',
disabled=True,
layout=divider_button_layout)
param_name3 = Button(description='apoptosis_rate',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.apoptosis_rate = FloatText(value=0.0014,
step=0.0001,
style=style,
layout=widget_layout)
div_row3 = Button(description='---Necrosis---',
disabled=True,
layout=divider_button_layout)
param_name4 = Button(description='necrosis_rate',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.necrosis_rate = FloatText(value=0.00277777777,
step=0.0001,
style=style,
layout=widget_layout)
param_name5 = Button(description='necrosis_type',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.necrosis_type = FloatText(value=2,
step=0.1,
style=style,
layout=widget_layout)
param_name6 = Button(description='o2_necrosis_threshold',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.o2_necrosis_threshold = FloatText(value=5.0,
step=0.1,
style=style,
layout=widget_layout)
param_name7 = Button(description='o2_necrosis_max',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.o2_necrosis_max = FloatText(value=2.5,
step=0.1,
style=style,
layout=widget_layout)
div_row4 = Button(description='---Fluid change rates---',
disabled=True,
layout=divider_button_layout)
param_name8 = Button(description='cytoplasmic_biomass_change_rate',
disabled=True,
layout=name_button_layout)
param_name8.style.button_color = 'tan'
self.cytoplasmic_biomass_change_rate = FloatText(value=0.01666666,
step=0.001,
style=style,
layout=widget_layout)
param_name9 = Button(description='nuclear_biomass_change_rate',
disabled=True,
layout=name_button_layout)
param_name9.style.button_color = 'lightgreen'
self.nuclear_biomass_change_rate = FloatText(value=0.00583333333,
step=0.001,
style=style,
layout=widget_layout)
param_name10 = Button(description='lysed_fluid_change_rate',
disabled=True,
layout=name_button_layout)
param_name10.style.button_color = 'tan'
self.lysed_fluid_change_rate = FloatText(value=0.00083333333,
step=0.0001,
style=style,
layout=widget_layout)
param_name11 = Button(description='unlysed_fluid_change_rate',
disabled=True,
layout=name_button_layout)
param_name11.style.button_color = 'lightgreen'
self.unlysed_fluid_change_rate = FloatText(value=0.01666666,
step=0.001,
style=style,
layout=widget_layout)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button1.style.button_color = 'lightgreen'
units_button2 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2.style.button_color = 'tan'
units_button3 = Button(description='micrometer',
disabled=True,
layout=units_button_layout)
units_button3.style.button_color = 'lightgreen'
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4.style.button_color = 'tan'
units_button5 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button5.style.button_color = 'lightgreen'
units_button6 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button6.style.button_color = 'lightgreen'
units_button7 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'tan'
units_button8 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button8.style.button_color = 'lightgreen'
units_button9 = Button(description='mmHG',
disabled=True,
layout=units_button_layout)
units_button9.style.button_color = 'tan'
units_button10 = Button(description='mmHG',
disabled=True,
layout=units_button_layout)
units_button10.style.button_color = 'lightgreen'
units_button11 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button11.style.button_color = 'lightgreen'
units_button12 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button12.style.button_color = 'tan'
units_button13 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button13.style.button_color = 'lightgreen'
units_button14 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button14.style.button_color = 'tan'
units_button15 = Button(description='1/min',
disabled=True,
layout=units_button_layout)
units_button15.style.button_color = 'lightgreen'
desc_button2 = Button(description='1->apoptosis 2->necrosis',
tooltip='1->apoptosis 2->necrosis',
disabled=True,
layout=desc_button_layout)
desc_button2.style.button_color = 'tan'
desc_button3 = Button(description='initial tumor radius',
tooltip='initial tumor radius',
disabled=True,
layout=desc_button_layout)
desc_button3.style.button_color = 'lightgreen'
desc_button5 = Button(description='mean apoptosis rate',
tooltip='mean apoptosis rate',
disabled=True,
layout=desc_button_layout)
desc_button5.style.button_color = 'lightgreen'
desc_button6 = Button(description='mean necrosis rate',
tooltip='mean necrosis rate',
disabled=True,
layout=desc_button_layout)
desc_button6.style.button_color = 'tan'
desc_button7 = Button(description='1->deterministic 2->stochastic',
tooltip='1->deterministic 2->stochastic',
disabled=True,
layout=desc_button_layout)
desc_button7.style.button_color = 'lightgreen'
desc_button10 = Button(
description='oxygen threshold level for dying with necrotic death',
tooltip='oxygen threshold level for dying with necrotic death',
disabled=True,
layout=desc_button_layout)
desc_button10.style.button_color = 'tan'
desc_button11 = Button(
description=
'oxygen threshold level for maximum rate of necrotic death',
tooltip='oxygen threshold level for maximum rate of necrotic death',
disabled=True,
layout=desc_button_layout)
desc_button11.style.button_color = 'lightgreen'
desc_button12 = Button(
description=
'rate of degradation for solids in the cytoplasm other than the nucleus',
tooltip=
'rate of degradation for solids in the cytoplasm other than the nucleus',
disabled=True,
layout=desc_button_layout)
desc_button12.style.button_color = 'tan'
desc_button13 = Button(
description='rate of degradation for nucleus solids',
tooltip='rate of degradation for nucleus solids',
disabled=True,
layout=desc_button_layout)
desc_button13.style.button_color = 'lightgreen'
desc_button14 = Button(
description=
'rate of fluid change (cytoplasmic fluid) after cell lysis ',
tooltip=
'rate of fluid change (cytoplasmic fluid) after cell lysis ',
disabled=True,
layout=desc_button_layout)
desc_button14.style.button_color = 'tan'
desc_button15 = Button(
description=
'rate of fluid change (cytoplasmic fluid) before cell lysis',
tooltip=
'rate of fluid change (cytoplasmic fluid) before cell lysis',
disabled=True,
layout=desc_button_layout)
desc_button15.style.button_color = 'lightgreen'
row2 = [
param_name1, self.type_of_death_model, units_button2, desc_button2
]
row3 = [
param_name2, self.initial_tumor_radius, units_button3, desc_button3
]
row5 = [param_name3, self.apoptosis_rate, units_button5, desc_button5]
row6 = [param_name4, self.necrosis_rate, units_button7, desc_button6]
row7 = [param_name5, self.necrosis_type, units_button8, desc_button7]
row10 = [
param_name6, self.o2_necrosis_threshold, units_button9,
desc_button10
]
row11 = [
param_name7, self.o2_necrosis_max, units_button10, desc_button11
]
row12 = [
param_name8, self.cytoplasmic_biomass_change_rate, units_button12,
desc_button12
]
row13 = [
param_name9, self.nuclear_biomass_change_rate, units_button13,
desc_button13
]
row14 = [
param_name10, self.lysed_fluid_change_rate, units_button14,
desc_button14
]
row15 = [
param_name11, self.unlysed_fluid_change_rate, units_button15,
desc_button15
]
box_layout = Layout(display='flex',
flex_flow='row',
align_items='stretch',
width='100%')
box2 = Box(children=row2, layout=box_layout)
box3 = Box(children=row3, layout=box_layout)
box5 = Box(children=row5, layout=box_layout)
box6 = Box(children=row6, layout=box_layout)
box7 = Box(children=row7, layout=box_layout)
box10 = Box(children=row10, layout=box_layout)
box11 = Box(children=row11, layout=box_layout)
box12 = Box(children=row12, layout=box_layout)
box13 = Box(children=row13, layout=box_layout)
box14 = Box(children=row14, layout=box_layout)
box15 = Box(children=row15, layout=box_layout)
self.tab = VBox([
div_row1,
box2,
box3,
div_row2,
box5,
div_row3,
box6,
box7,
box10,
box11,
div_row4,
box12,
box13,
box14,
box15,
])
class Dashboard(VBox):
"""
Build the dashboard for Jupyter widgets. Requires running
in a notebook/jupyterlab.
"""
def __init__(self, net, width="95%", height="550px", play_rate=0.5):
self._ignore_layer_updates = False
self.player = _Player(self, play_rate)
self.player.start()
self.net = net
r = random.randint(1, 1000000)
self.class_id = "picture-dashboard-%s-%s" % (self.net.name, r)
self._width = width
self._height = height
## Global widgets:
style = {"description_width": "initial"}
self.feature_columns = IntText(description="Detail columns:",
value=self.net.config["dashboard.features.columns"],
min=0,
max=1024,
style=style)
self.feature_scale = FloatText(description="Detail scale:",
value=self.net.config["dashboard.features.scale"],
min=0.1,
max=10,
style=style)
self.feature_columns.observe(self.regenerate, names='value')
self.feature_scale.observe(self.regenerate, names='value')
## Hack to center SVG as justify-content is broken:
self.net_svg = HTML(value="""<p style="text-align:center">%s</p>""" % ("",), layout=Layout(
width=self._width, overflow_x='auto', overflow_y="auto",
justify_content="center"))
# Make controls first:
self.output = Output()
controls = self.make_controls()
config = self.make_config()
super().__init__([config, controls, self.net_svg, self.output])
def propagate(self, inputs):
"""
Propagate inputs through the dashboard view of the network.
"""
if dynamic_pictures_check():
return self.net.propagate(inputs, class_id=self.class_id, update_pictures=True)
else:
self.regenerate(inputs=input)
def goto(self, position):
if len(self.net.dataset.inputs) == 0 or len(self.net.dataset.targets) == 0:
return
if self.control_select.value == "Train":
length = len(self.net.dataset.train_inputs)
elif self.control_select.value == "Test":
length = len(self.net.dataset.test_inputs)
#### Position it:
if position == "begin":
self.control_slider.value = 0
elif position == "end":
self.control_slider.value = length - 1
elif position == "prev":
if self.control_slider.value - 1 < 0:
self.control_slider.value = length - 1 # wrap around
else:
self.control_slider.value = max(self.control_slider.value - 1, 0)
elif position == "next":
if self.control_slider.value + 1 > length - 1:
self.control_slider.value = 0 # wrap around
else:
self.control_slider.value = min(self.control_slider.value + 1, length - 1)
self.position_text.value = self.control_slider.value
def change_select(self, change=None):
"""
"""
self.update_control_slider(change)
self.regenerate()
def update_control_slider(self, change=None):
self.net.config["dashboard.dataset"] = self.control_select.value
if len(self.net.dataset.inputs) == 0 or len(self.net.dataset.targets) == 0:
self.total_text.value = "of 0"
self.control_slider.value = 0
self.position_text.value = 0
self.control_slider.disabled = True
self.position_text.disabled = True
for child in self.control_buttons.children:
if not hasattr(child, "icon") or child.icon != "refresh":
child.disabled = True
return
if self.control_select.value == "Test":
self.total_text.value = "of %s" % len(self.net.dataset.test_inputs)
minmax = (0, max(len(self.net.dataset.test_inputs) - 1, 0))
if minmax[0] <= self.control_slider.value <= minmax[1]:
pass # ok
else:
self.control_slider.value = 0
self.control_slider.min = minmax[0]
self.control_slider.max = minmax[1]
if len(self.net.dataset.test_inputs) == 0:
disabled = True
else:
disabled = False
elif self.control_select.value == "Train":
self.total_text.value = "of %s" % len(self.net.dataset.train_inputs)
minmax = (0, max(len(self.net.dataset.train_inputs) - 1, 0))
if minmax[0] <= self.control_slider.value <= minmax[1]:
pass # ok
else:
self.control_slider.value = 0
self.control_slider.min = minmax[0]
self.control_slider.max = minmax[1]
if len(self.net.dataset.train_inputs) == 0:
disabled = True
else:
disabled = False
self.control_slider.disabled = disabled
self.position_text.disbaled = disabled
self.position_text.value = self.control_slider.value
for child in self.control_buttons.children:
if not hasattr(child, "icon") or child.icon != "refresh":
child.disabled = disabled
def update_zoom_slider(self, change):
if change["name"] == "value":
self.net.config["svg_scale"] = self.zoom_slider.value
self.regenerate()
def update_position_text(self, change):
# {'name': 'value', 'old': 2, 'new': 3, 'owner': IntText(value=3, layout=Layout(width='100%')), 'type': 'change'}
self.control_slider.value = change["new"]
def get_current_input(self):
if self.control_select.value == "Train" and len(self.net.dataset.train_targets) > 0:
return self.net.dataset.train_inputs[self.control_slider.value]
elif self.control_select.value == "Test" and len(self.net.dataset.test_targets) > 0:
return self.net.dataset.test_inputs[self.control_slider.value]
def get_current_targets(self):
if self.control_select.value == "Train" and len(self.net.dataset.train_targets) > 0:
return self.net.dataset.train_targets[self.control_slider.value]
elif self.control_select.value == "Test" and len(self.net.dataset.test_targets) > 0:
return self.net.dataset.test_targets[self.control_slider.value]
def update_slider_control(self, change):
if len(self.net.dataset.inputs) == 0 or len(self.net.dataset.targets) == 0:
self.total_text.value = "of 0"
return
if change["name"] == "value":
self.position_text.value = self.control_slider.value
if self.control_select.value == "Train" and len(self.net.dataset.train_targets) > 0:
self.total_text.value = "of %s" % len(self.net.dataset.train_inputs)
if self.net.model is None:
return
if not dynamic_pictures_check():
self.regenerate(inputs=self.net.dataset.train_inputs[self.control_slider.value],
targets=self.net.dataset.train_targets[self.control_slider.value])
return
output = self.net.propagate(self.net.dataset.train_inputs[self.control_slider.value],
class_id=self.class_id, update_pictures=True)
if self.feature_bank.value in self.net.layer_dict.keys():
self.net.propagate_to_features(self.feature_bank.value, self.net.dataset.train_inputs[self.control_slider.value],
cols=self.feature_columns.value, scale=self.feature_scale.value, html=False)
if self.net.config["show_targets"]:
if len(self.net.output_bank_order) == 1: ## FIXME: use minmax of output bank
self.net.display_component([self.net.dataset.train_targets[self.control_slider.value]],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
else:
self.net.display_component(self.net.dataset.train_targets[self.control_slider.value],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
if self.net.config["show_errors"]: ## minmax is error
if len(self.net.output_bank_order) == 1:
errors = np.array(output) - np.array(self.net.dataset.train_targets[self.control_slider.value])
self.net.display_component([errors.tolist()],
"errors",
class_id=self.class_id,
minmax=(-1, 1))
else:
errors = []
for bank in range(len(self.net.output_bank_order)):
errors.append( np.array(output[bank]) - np.array(self.net.dataset.train_targets[self.control_slider.value][bank]))
self.net.display_component(errors, "errors", class_id=self.class_id, minmax=(-1, 1))
elif self.control_select.value == "Test" and len(self.net.dataset.test_targets) > 0:
self.total_text.value = "of %s" % len(self.net.dataset.test_inputs)
if self.net.model is None:
return
if not dynamic_pictures_check():
self.regenerate(inputs=self.net.dataset.test_inputs[self.control_slider.value],
targets=self.net.dataset.test_targets[self.control_slider.value])
return
output = self.net.propagate(self.net.dataset.test_inputs[self.control_slider.value],
class_id=self.class_id, update_pictures=True)
if self.feature_bank.value in self.net.layer_dict.keys():
self.net.propagate_to_features(self.feature_bank.value, self.net.dataset.test_inputs[self.control_slider.value],
cols=self.feature_columns.value, scale=self.feature_scale.value, html=False)
if self.net.config["show_targets"]: ## FIXME: use minmax of output bank
self.net.display_component([self.net.dataset.test_targets[self.control_slider.value]],
"targets",
class_id=self.class_id,
minmax=(-1, 1))
if self.net.config["show_errors"]: ## minmax is error
if len(self.net.output_bank_order) == 1:
errors = np.array(output) - np.array(self.net.dataset.test_targets[self.control_slider.value])
self.net.display_component([errors.tolist()],
"errors",
class_id=self.class_id,
minmax=(-1, 1))
else:
errors = []
for bank in range(len(self.net.output_bank_order)):
errors.append( np.array(output[bank]) - np.array(self.net.dataset.test_targets[self.control_slider.value][bank]))
self.net.display_component(errors, "errors", class_id=self.class_id, minmax=(-1, 1))
def toggle_play(self, button):
## toggle
if self.button_play.description == "Play":
self.button_play.description = "Stop"
self.button_play.icon = "pause"
self.player.resume()
else:
self.button_play.description = "Play"
self.button_play.icon = "play"
self.player.pause()
def prop_one(self, button=None):
self.update_slider_control({"name": "value"})
def regenerate(self, button=None, inputs=None, targets=None):
## Protection when deleting object on shutdown:
if isinstance(button, dict) and 'new' in button and button['new'] is None:
return
## Update the config:
self.net.config["dashboard.features.bank"] = self.feature_bank.value
self.net.config["dashboard.features.columns"] = self.feature_columns.value
self.net.config["dashboard.features.scale"] = self.feature_scale.value
inputs = inputs if inputs is not None else self.get_current_input()
targets = targets if targets is not None else self.get_current_targets()
features = None
if self.feature_bank.value in self.net.layer_dict.keys() and inputs is not None:
if self.net.model is not None:
features = self.net.propagate_to_features(self.feature_bank.value, inputs,
cols=self.feature_columns.value,
scale=self.feature_scale.value, display=False)
svg = """<p style="text-align:center">%s</p>""" % (self.net.to_svg(
inputs=inputs,
targets=targets,
class_id=self.class_id,
highlights={self.feature_bank.value: {
"border_color": "orange",
"border_width": 30,
}}))
if inputs is not None and features is not None:
html_horizontal = """
<table align="center" style="width: 100%%;">
<tr>
<td valign="top" style="width: 50%%;">%s</td>
<td valign="top" align="center" style="width: 50%%;"><p style="text-align:center"><b>%s</b></p>%s</td>
</tr>
</table>"""
html_vertical = """
<table align="center" style="width: 100%%;">
<tr>
<td valign="top">%s</td>
</tr>
<tr>
<td valign="top" align="center"><p style="text-align:center"><b>%s</b></p>%s</td>
</tr>
</table>"""
self.net_svg.value = (html_vertical if self.net.config["svg_rotate"] else html_horizontal) % (
svg, "%s details" % self.feature_bank.value, features)
else:
self.net_svg.value = svg
def make_colormap_image(self, colormap_name):
from .layers import Layer
if not colormap_name:
colormap_name = get_colormap()
layer = Layer("Colormap", 100)
minmax = layer.get_act_minmax()
image = layer.make_image(np.arange(minmax[0], minmax[1], .01),
colormap_name,
{"pixels_per_unit": 1,
"svg_rotate": self.net.config["svg_rotate"]}).resize((300, 25))
return image
def set_attr(self, obj, attr, value):
if value not in [{}, None]: ## value is None when shutting down
if isinstance(value, dict):
value = value["value"]
if isinstance(obj, dict):
obj[attr] = value
else:
setattr(obj, attr, value)
## was crashing on Widgets.__del__, if get_ipython() no longer existed
self.regenerate()
def make_controls(self):
layout = Layout(width='100%', height="100%")
button_begin = Button(icon="fast-backward", layout=layout)
button_prev = Button(icon="backward", layout=layout)
button_next = Button(icon="forward", layout=layout)
button_end = Button(icon="fast-forward", layout=layout)
#button_prop = Button(description="Propagate", layout=Layout(width='100%'))
#button_train = Button(description="Train", layout=Layout(width='100%'))
self.button_play = Button(icon="play", description="Play", layout=layout)
step_down = Button(icon="sort-down", layout=Layout(width="95%", height="100%"))
step_up = Button(icon="sort-up", layout=Layout(width="95%", height="100%"))
up_down = HBox([step_down, step_up], layout=Layout(width="100%", height="100%"))
refresh_button = Button(icon="refresh", layout=Layout(width="25%", height="100%"))
self.position_text = IntText(value=0, layout=layout)
self.control_buttons = HBox([
button_begin,
button_prev,
#button_train,
self.position_text,
button_next,
button_end,
self.button_play,
up_down,
refresh_button
], layout=Layout(width='100%', height="100%"))
length = (len(self.net.dataset.train_inputs) - 1) if len(self.net.dataset.train_inputs) > 0 else 0
self.control_slider = IntSlider(description="Dataset index",
continuous_update=False,
min=0,
max=max(length, 0),
value=0,
layout=Layout(width='100%'))
if self.net.config["dashboard.dataset"] == "Train":
length = len(self.net.dataset.train_inputs)
else:
length = len(self.net.dataset.test_inputs)
self.total_text = Label(value="of %s" % length, layout=Layout(width="100px"))
self.zoom_slider = FloatSlider(description="Zoom",
continuous_update=False,
min=0, max=1.0,
style={"description_width": 'initial'},
layout=Layout(width="65%"),
value=self.net.config["svg_scale"] if self.net.config["svg_scale"] is not None else 0.5)
## Hook them up:
button_begin.on_click(lambda button: self.goto("begin"))
button_end.on_click(lambda button: self.goto("end"))
button_next.on_click(lambda button: self.goto("next"))
button_prev.on_click(lambda button: self.goto("prev"))
self.button_play.on_click(self.toggle_play)
self.control_slider.observe(self.update_slider_control, names='value')
refresh_button.on_click(lambda widget: (self.update_control_slider(),
self.output.clear_output(),
self.regenerate()))
step_down.on_click(lambda widget: self.move_step("down"))
step_up.on_click(lambda widget: self.move_step("up"))
self.zoom_slider.observe(self.update_zoom_slider, names='value')
self.position_text.observe(self.update_position_text, names='value')
# Put them together:
controls = VBox([HBox([self.control_slider, self.total_text], layout=Layout(height="40px")),
self.control_buttons], layout=Layout(width='100%'))
#net_page = VBox([control, self.net_svg], layout=Layout(width='95%'))
controls.on_displayed(lambda widget: self.regenerate())
return controls
def move_step(self, direction):
"""
Move the layer stepper up/down through network
"""
options = [""] + [layer.name for layer in self.net.layers]
index = options.index(self.feature_bank.value)
if direction == "up":
new_index = (index + 1) % len(options)
else: ## down
new_index = (index - 1) % len(options)
self.feature_bank.value = options[new_index]
self.regenerate()
def make_config(self):
layout = Layout()
style = {"description_width": "initial"}
checkbox1 = Checkbox(description="Show Targets", value=self.net.config["show_targets"],
layout=layout, style=style)
checkbox1.observe(lambda change: self.set_attr(self.net.config, "show_targets", change["new"]), names='value')
checkbox2 = Checkbox(description="Errors", value=self.net.config["show_errors"],
layout=layout, style=style)
checkbox2.observe(lambda change: self.set_attr(self.net.config, "show_errors", change["new"]), names='value')
hspace = IntText(value=self.net.config["hspace"], description="Horizontal space between banks:",
style=style, layout=layout)
hspace.observe(lambda change: self.set_attr(self.net.config, "hspace", change["new"]), names='value')
vspace = IntText(value=self.net.config["vspace"], description="Vertical space between layers:",
style=style, layout=layout)
vspace.observe(lambda change: self.set_attr(self.net.config, "vspace", change["new"]), names='value')
self.feature_bank = Select(description="Details:", value=self.net.config["dashboard.features.bank"],
options=[""] + [layer.name for layer in self.net.layers],
rows=1)
self.feature_bank.observe(self.regenerate, names='value')
self.control_select = Select(
options=['Test', 'Train'],
value=self.net.config["dashboard.dataset"],
description='Dataset:',
rows=1
)
self.control_select.observe(self.change_select, names='value')
column1 = [self.control_select,
self.zoom_slider,
hspace,
vspace,
HBox([checkbox1, checkbox2]),
self.feature_bank,
self.feature_columns,
self.feature_scale
]
## Make layer selectable, and update-able:
column2 = []
layer = self.net.layers[-1]
self.layer_select = Select(description="Layer:", value=layer.name,
options=[layer.name for layer in
self.net.layers],
rows=1)
self.layer_select.observe(self.update_layer_selection, names='value')
column2.append(self.layer_select)
self.layer_visible_checkbox = Checkbox(description="Visible", value=layer.visible, layout=layout)
self.layer_visible_checkbox.observe(self.update_layer, names='value')
column2.append(self.layer_visible_checkbox)
self.layer_colormap = Select(description="Colormap:",
options=[""] + AVAILABLE_COLORMAPS,
value=layer.colormap if layer.colormap is not None else "", layout=layout, rows=1)
self.layer_colormap_image = HTML(value="""<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap)))
self.layer_colormap.observe(self.update_layer, names='value')
column2.append(self.layer_colormap)
column2.append(self.layer_colormap_image)
## get dynamic minmax; if you change it it will set it in layer as override:
minmax = layer.get_act_minmax()
self.layer_mindim = FloatText(description="Leftmost color maps to:", value=minmax[0], style=style)
self.layer_maxdim = FloatText(description="Rightmost color maps to:", value=minmax[1], style=style)
self.layer_mindim.observe(self.update_layer, names='value')
self.layer_maxdim.observe(self.update_layer, names='value')
column2.append(self.layer_mindim)
column2.append(self.layer_maxdim)
output_shape = layer.get_output_shape()
self.layer_feature = IntText(value=layer.feature, description="Feature to show:", style=style)
self.svg_rotate = Checkbox(description="Rotate", value=layer.visible, layout=layout)
self.layer_feature.observe(self.update_layer, names='value')
column2.append(self.layer_feature)
self.svg_rotate = Checkbox(description="Rotate network",
value=self.net.config["svg_rotate"],
style={"description_width": 'initial'},
layout=Layout(width="52%"))
self.svg_rotate.observe(lambda change: self.set_attr(self.net.config, "svg_rotate", change["new"]), names='value')
self.save_config_button = Button(icon="save", layout=Layout(width="10%"))
self.save_config_button.on_click(self.save_config)
column2.append(HBox([self.svg_rotate, self.save_config_button]))
config_children = HBox([VBox(column1, layout=Layout(width="100%")),
VBox(column2, layout=Layout(width="100%"))])
accordion = Accordion(children=[config_children])
accordion.set_title(0, self.net.name)
accordion.selected_index = None
return accordion
def save_config(self, widget=None):
self.net.save_config()
def update_layer(self, change):
"""
Update the layer object, and redisplay.
"""
if self._ignore_layer_updates:
return
## The rest indicates a change to a display variable.
## We need to save the value in the layer, and regenerate
## the display.
# Get the layer:
layer = self.net[self.layer_select.value]
# Save the changed value in the layer:
layer.feature = self.layer_feature.value
layer.visible = self.layer_visible_checkbox.value
## These three, dealing with colors of activations,
## can be done with a prop_one():
if "color" in change["owner"].description.lower():
## Matches: Colormap, lefmost color, rightmost color
## overriding dynamic minmax!
layer.minmax = (self.layer_mindim.value, self.layer_maxdim.value)
layer.minmax = (self.layer_mindim.value, self.layer_maxdim.value)
layer.colormap = self.layer_colormap.value if self.layer_colormap.value else None
self.layer_colormap_image.value = """<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap))
self.prop_one()
else:
self.regenerate()
def update_layer_selection(self, change):
"""
Just update the widgets; don't redraw anything.
"""
## No need to redisplay anything
self._ignore_layer_updates = True
## First, get the new layer selected:
layer = self.net[self.layer_select.value]
## Now, let's update all of the values without updating:
self.layer_visible_checkbox.value = layer.visible
self.layer_colormap.value = layer.colormap if layer.colormap != "" else ""
self.layer_colormap_image.value = """<img src="%s"/>""" % self.net._image_to_uri(self.make_colormap_image(layer.colormap))
minmax = layer.get_act_minmax()
self.layer_mindim.value = minmax[0]
self.layer_maxdim.value = minmax[1]
self.layer_feature.value = layer.feature
self._ignore_layer_updates = False