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,
])
def _widget(self):
""" Create IPython widget for display within a notebook """
try:
return self._cached_widget
except AttributeError:
pass
from ipywidgets import Layout, VBox, HBox, IntText, Button, HTML, Accordion
layout = Layout(width="150px")
if "dashboard" in self.scheduler.services:
link = self.dashboard_link
link = '<p><b>Dashboard: </b><a href="%s" target="_blank">%s</a></p>\n' % (
link,
link,
)
else:
link = ""
title = "<h2>%s</h2>" % type(self).__name__
title = HTML(title)
dashboard = HTML(link)
status = HTML(self._widget_status(), layout=Layout(min_width="150px"))
request = IntText(0, description="Workers", layout=layout)
scale = Button(description="Scale", layout=layout)
minimum = IntText(0, description="Minimum", layout=layout)
maximum = IntText(0, description="Maximum", layout=layout)
adapt = Button(description="Adapt", layout=layout)
accordion = Accordion(
[HBox([request, scale]),
HBox([minimum, maximum, adapt])],
layout=Layout(min_width="500px"),
)
accordion.selected_index = None
accordion.set_title(0, "Manual Scaling")
accordion.set_title(1, "Adaptive Scaling")
box = VBox([title, HBox([status, accordion]), dashboard])
self._cached_widget = box
def adapt_cb(b):
self.adapt(minimum=minimum.value, maximum=maximum.value)
adapt.on_click(adapt_cb)
def scale_cb(b):
with log_errors():
n = request.value
with ignoring(AttributeError):
self._adaptive.stop()
self.scale(n)
scale.on_click(scale_cb)
scheduler_ref = ref(self.scheduler)
def update():
status.value = self._widget_status()
pc = PeriodicCallback(update, 500, io_loop=self.scheduler.loop)
self.scheduler.periodic_callbacks["cluster-repr"] = pc
pc.start()
return box
def multi_label_annotate(examples,
example_labels=None,
options=None,
shuffle=False,
display_fn=display,
include_skip=False,
save_file='annotations'):
"""
Build an interactive widget for annotating a list of input examples.
Parameters
----------
examples: list(any), list of items to annotate
example_labels: list(string), if examples are one large numpy array
options: Dict
dictionary of category names and category classes
ex {'gender':['male', 'female', 'unisex']}
shuffle: bool, shuffle the examples before annotating
display_fn: func, function for displaying an example to the user
Returns
-------
annotations : defaultdict of dicts, dict of annotated examples
(example, {task:[label... label],task2:[label]})
"""
examples = list(examples)
use_example_labels = True
if example_labels is None:
use_example_labels = False
example_labels = examples
if shuffle:
ind_shuff = np.arange(len(examples))
# set seed
random.Random(42).shuffle(ind_shuff)
examples = examples[ind_shuff]
example_labels = example_labels[ind_shuff]
annotation_dict = defaultdict(dict)
all_buttons = []
current_index = -1
def set_label_text():
nonlocal count_label
if current_index < len(examples):
count_label.value = (
'{} examples annotated, {} examples left<br>Asset name: <code>{}</code><hr>'
.format(len(annotation_dict),
len(examples) - current_index,
example_labels[current_index]))
else:
count_label.value = '{} examples annotated, {} examples left<br>Annoation done.<hr>'.format(
len(annotation_dict),
len(examples) - current_index)
def save_current():
nonlocal current_index
np.save(save_file + '{:d}.npy'.format(current_index), annotation_dict)
def show_next():
clear_colors()
nonlocal current_index
current_index += 1
set_label_text()
if current_index >= len(examples):
for btn in buttons:
btn.disabled = True
with out:
clear_output()
return
with out:
clear_output(wait=True)
display_fn(examples[current_index])
def go_back():
clear_colors()
nonlocal current_index
current_index -= 1
if current_index < 0:
print('cannot go back')
return
with out:
clear_output(wait=True)
try:
del annotation_dict[example_labels[current_index]]
set_label_text()
display_fn(examples[current_index])
except KeyError:
print("Key 'testing' not found")
def del_current_annotation():
nonlocal current_index
del annotation_dict[example_labels[current_index]]
current_index -= 1
show_next()
def add_annotation(annotation_dict, annotation, task_name):
if task_name not in annotation_dict[
example_labels[current_index]].keys():
annotation_dict[example_labels[current_index]][task_name] = [
annotation
]
else:
# check if the annotation is already in the `annotation_dict`, if so, that means
# it has been clicked a second time, and we should remove both the color and
# the annotation
if annotation in annotation_dict[
example_labels[current_index]][task_name]:
annotation_dict[example_labels[current_index]][
task_name].remove(annotation)
else:
annotation_dict[example_labels[current_index]][
task_name].append(annotation)
def skip(btn):
show_next()
def done(btn):
show_next()
def save(btn):
save_current()
def back(btn):
go_back()
def clear_annotation(btn):
del_current_annotation()
def clear_colors():
nonlocal all_buttons
for button in all_buttons:
button.style.button_color = None
count_label = HTML()
set_label_text()
display(count_label)
if type(options) == dict:
task_type = 'classification'
else:
raise ValueError('Invalid options. Must be classification dictionary.')
if task_type == 'classification':
for key, value in options.items():
buttons = []
print(key)
for label in value:
btn = MultiLabelButton(description=label, task_name=key)
def on_click(label, task_name, btn):
# if button has a color, clear it! if not, give it a color!
if btn.style.button_color is None:
btn.style.button_color = 'lightgreen'
else:
btn.style.button_color = None
add_annotation(annotation_dict, label, task_name)
btn.button.on_click(
functools.partial(on_click, label, btn.task_name))
buttons.append(btn.button)
all_buttons.append(btn.button)
box = HBox(buttons)
display(box)
print('')
buttons = []
btn = Button(description='done')
btn.on_click(skip)
buttons.append(btn)
btn = Button(description='back')
btn.on_click(back)
buttons.append(btn)
btn = Button(description='clear current')
btn.on_click(clear_annotation)
buttons.append(btn)
btn = Button(description='save')
btn.on_click(save)
buttons.append(btn)
if include_skip:
btn = Button(description='skip')
btn.on_click(skip)
buttons.append(btn)
all_buttons += buttons
box = HBox(buttons)
display(box)
out = Output()
display(out)
show_next()
return annotation_dict
if not o.layout.flex:
o.layout.flex = '0 0 auto'
# export
def carousel(children=(), **layout):
"A horizontally scrolling carousel"
def_layout = dict(overflow='scroll hidden', flex_flow='row', display='flex')
res = Box([], layout=merge(def_layout, layout))
res.observe(_update_children, names='children')
res.children = children
return res
# +
ts = [VBox([widget(im, max_width='192px'), Button(description='click')])
for o in range(3)]
carousel(ts, width='450px')
# -
# export
def _open_thumb(fn, h, w): return Image.open(fn).to_thumb(h, w).convert('RGBA')
# export
class ImagesCleaner:
"A widget that displays all images in `fns` along with a `Dropdown`"
def __init__(self, opts=(), height=128, width=256, max_n=30):
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 __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):
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='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 create_tables():
"""Create essential cbm tables
"""
data_path = config.get_value(['paths', 'temp'])
l_tb = Label("""Add a short name as prefix for the tables,
max 15 characters e.g.:escat2020.""")
try:
with open(normpath(join(data_path, 'tb_prefix')), 'r') as f:
prefix = f.read()
except Exception:
prefix = ''
tb_prefix = Text(value=prefix,
placeholder='xx2010',
description='Table prefix:',
disabled=False)
checkboxes = {}
tbs = db_tables.tables_dict()
for key in tbs:
checkboxes[key] = Checkbox(value=True,
description=tbs[key]['name'],
disabled=False,
indent=False,
layout=Layout(width='150px'))
checkboxes["aois"].value = False
check_box = HBox([checkboxes[t] for t in checkboxes])
bt_create_tb = Button(description='Create tables',
value=False,
disabled=False,
button_style='info',
tooltip='Creat tables',
icon='fa-table')
progress = Output()
def outlog(*text):
with progress:
print(*text)
def on_tb_prefix(change):
with open(normpath(join(data_path, 'tb_prefix')), 'w+') as f:
f.write(tb_prefix.value.replace(' ', '').lower()[:15])
tb_prefix.observe(on_tb_prefix, 'value')
@bt_create_tb.on_click
def bt_create_tb_on_click(b):
progress.clear_output()
tb_prefix_clean = tb_prefix.value.replace(' ', '').lower()[:15]
if tb_prefix.value != '':
for key in tbs:
if checkboxes[key].value is True:
if db.tb_exist(
f"{tb_prefix_clean}_{tbs[key]['table']}") is False:
sql = tbs[key]['sql'].replace('\n',
'').replace(' ', '')
db.execute_sql(sql.format(tb_prefix_clean))
outlog(
f"The table {tb_prefix_clean}_{tbs[key]['table']} is created.."
)
else:
outlog(
f"The table {tb_prefix_clean}_{tbs[key]['table']} already exist."
)
else:
outlog("Please add tables prefix.")
wbox = VBox([l_tb, tb_prefix, check_box, bt_create_tb, progress])
return wbox
def annotate(
examples,
task_type='classification',
options=None,
shuffle=False,
include_next=True,
include_back=True,
stop_at_last_example=True,
use_dropdown=False,
buttons_in_a_row=4,
reset_buttons_after_click=True,
example_process_fn=None,
final_process_fn=None,
display_fn=display,
example_column='example',
value_column='label',
id_column='id',
return_type='dataframe',
):
"""
Build an interactive widget for annotating a list or DataFrame of input examples.
Parameters
----------
examples : list or pandas.DataFrame
This can be a list of any type or a Pandas dataframe.
If using a DataFrame, make sure that at least the example_column
is set to the column holding the examples.
When a DataFrame of a previous annotation is provided, it can
be relabeled and shows previous selected labels.
task_type : str
Possible options are:
- classification
- multilabel-classification
- regression
- captioning
options : list, tuple, or None
Depending on the task this can be:
- list of str for (multilabel) classification.
- tuple with a range for regression tasks
- None (actually ignored) for captioning
shuffle : bool, shuffle the examples before annotating
include_skip : bool, include option to skip example while annotating
include_back : bool, include option to navigate to previous example
use_dropdown : bool, use a dropdown or buttons during classification
buttons_in_a_row : int, number of buttons in a row during classification
reset_buttons_after_click : bool, reset multi-label buttons after each click
example_process_fn : function, hooked function to call after each example fn(ix, labels)
final_process_fn : function, hooked function to call after annotation is done fn(annotations)
display_fn : function, function for displaying an example to the user
Default, it uses the IPython display function
example_column : str, column name which holds all examples. Required when using DataFrame
value_column : str
column to store the result for classification (not for multilabel), regression,
captioning. For multilabel, each option will be a column in the dataframe.
id_column : str, optional
Column name which holds the id of the example. If available, will be shown in
the progress row.
return_type : str, 'dataframe' or 'dict'
By default, annotate will return a DataFrame with the annotations. For compatability,
when return_type is 'dict' it can also return a dictionary with changed annotations.
Returns
-------
annotations : pandas.DataFrame or dict
Depending on return_type it will return a DataFrame (preferred) or a dict with the
annotations.
The dict will have the form: {example: label} and only return the labeled examples that
are changed (using the submit button).
The DataFrame will have a column with the examples and if it is multilabel, a column for
each label. For regular classification, the labeled values are in the value_column. When
a DataFrame is used as input, all other columns such as id, are kept intact.
"""
# Parameter checkes
task_type = task_type.lower()
if task_type not in [
'classification',
'multilabel-classification',
'regression',
'captioning',
]:
raise ValueError(
"task_type should be 'classification', 'multilabel-classification', 'regression', or 'captioning'"
)
if not isinstance(examples, (list, pd.DataFrame)):
raise TypeError('examples should be of type list or pandas.DataFrame')
if task_type == 'regression':
if not isinstance(options, tuple):
raise TypeError(
'options should be of type tuple for regression tasks')
if len(options) != 2 and len(options) != 3:
raise ValueError(
'options should be a tuple (min, max) or (min, max, step)')
if task_type in ['multilabel-classification', 'classification']:
if not isinstance(options, list):
raise TypeError(
'options should be of type list for classification tasks')
return_type = return_type.lower()
if return_type not in ['dataframe', 'dict']:
raise TypeError("return_type should be 'dataframe' or 'dict'")
# create annotations object as DataFrame
if isinstance(examples, pd.DataFrame):
# Examples is a dataframe
annotations = examples.copy()
annotations['changed'] = False
else:
# Examples is a list
annotations = pd.DataFrame({
example_column: examples,
'changed': False,
})
# add options as columns
if isinstance(options, list):
# list of labels
if task_type == 'classification':
annotations[value_column] = ''
else:
for label in options:
if label not in annotations.columns:
annotations[label] = False
elif isinstance(options, tuple):
# regression
if value_column not in annotations.columns:
annotations[value_column] = 0
else:
# captioning
if value_column not in annotations.columns:
annotations[value_column] = ''
# shuffle if needed
if shuffle:
annotations = annotations.sample(frac=1).copy()
current_index = -1
annotations_dict = {}
def set_label_text(index):
"""
Create info string with annotation progress
"""
nonlocal count_label
labeled = len(annotations.loc[annotations['changed']])
str_output = f'{labeled} of {len(annotations)} Examples annotated, Current Position: {index + 1} '
if id_column in annotations.columns and index >= 0 and index < len(
annotations):
ix = annotations.iloc[index].name
str_output += f"(id: {annotations.at[ix, id_column]}) "
count_label.value = str_output
def render(index):
"""
Render current index of the annotation
"""
set_label_text(index)
if index >= len(annotations):
if stop_at_last_example:
print('Annotation done.')
if final_process_fn is not None:
final_process_fn(annotations)
for button in buttons:
button.disabled = True
set_label_text(index - 1)
else:
prev_example()
return
# render buttons
ix = annotations.iloc[index].name
for button in buttons:
if button.description == 'prev':
# disable previous button when at first example
button.disabled = index <= 0
elif button.description == 'next':
# disable skip button when at last example
button.disabled = index >= len(annotations) - 1
elif button.description != 'submit':
if task_type == 'classification':
if annotations.at[ix, value_column] == button.description:
button.icon = 'check'
else:
button.icon = ''
elif task_type == 'multilabel-classification':
button.value = bool(annotations.at[ix, button.description])
# render dropdown
if use_dropdown:
current_value = annotations.at[ix, value_column]
if current_value in dd.options:
dd.value = current_value
# slider while regression
if task_type == 'regression':
slider.value = annotations.at[ix, value_column]
# captioning
if task_type == 'captioning':
ta.value = annotations.at[ix, value_column]
# display new example
with out:
clear_output(wait=True)
display_fn(annotations.at[ix, example_column])
def add_annotation(annotation):
"""
Toggle annotation
"""
if return_type == 'dict':
annotations_dict[annotations.at[current_index,
example_column]] = annotation
ix = annotations.iloc[current_index].name
if task_type == 'multilabel-classification':
for label in options:
annotations.at[ix, label] = label in annotation
else:
# multi-class, regression, captioning
annotations.at[ix, value_column] = annotation
annotations.at[ix, 'changed'] = True
if example_process_fn is not None:
example_process_fn(annotations.at[ix, example_column], annotation)
next_example()
def next_example(button=None):
"""
Increase current index
"""
nonlocal current_index
if current_index < len(annotations):
current_index += 1
render(current_index)
def prev_example(button=None):
"""
Decrease current index
"""
nonlocal current_index
if current_index > 0:
current_index -= 1
render(current_index)
count_label = HTML()
set_label_text(current_index)
display(count_label)
buttons = []
if task_type == 'classification':
if use_dropdown:
dd = Dropdown(options=options)
display(dd)
btn = Button(description='submit')
def on_click(button):
add_annotation(dd.value)
btn.on_click(on_click)
buttons.append(btn)
else:
for label in options:
btn = Button(description=label)
def on_click(lbl, button):
add_annotation(lbl)
btn.on_click(functools.partial(on_click, label))
buttons.append(btn)
elif task_type == 'multilabel-classification':
for label in options:
tgl = ToggleButton(description=label)
buttons.append(tgl)
btn = Button(description='submit', button_style='info')
def on_click(button):
labels_on = []
for tgl_btn in buttons:
if isinstance(tgl_btn, ToggleButton):
if tgl_btn.value:
labels_on.append(tgl_btn.description)
if reset_buttons_after_click:
tgl_btn.value = False
add_annotation(labels_on)
btn.on_click(on_click)
buttons.append(btn)
elif task_type == 'regression':
# check if tuple is int or float
target_type = type(options[0])
if target_type == int:
cls = IntSlider
else:
cls = FloatSlider
# create slider
if len(options) == 2:
min_val, max_val = options
slider = cls(min=min_val, max=max_val)
else:
min_val, max_val, step_val = options
slider = cls(min=min_val, max=max_val, step=step_val)
display(slider)
# submit button
btn = Button(description='submit', value='submit')
def on_click(button):
add_annotation(slider.value)
btn.on_click(on_click)
buttons.append(btn)
elif task_type == 'captioning':
ta = Textarea()
display(ta)
btn = Button(description='submit')
def on_click(button):
add_annotation(ta.value)
btn.on_click(on_click)
buttons.append(btn)
else:
raise ValueError('invalid task type')
if include_back:
btn = Button(description='prev', button_style='info')
btn.on_click(prev_example)
buttons.append(btn)
if include_next:
btn = Button(description='next', button_style='info')
btn.on_click(next_example)
buttons.append(btn)
if len(buttons) > buttons_in_a_row:
box = VBox([
HBox(buttons[x:x + buttons_in_a_row])
for x in range(0, len(buttons), buttons_in_a_row)
])
else:
box = HBox(buttons)
display(box)
out = Output()
display(out)
next_example()
# return object
if return_type == 'dataframe':
return annotations
else:
return annotations_dict
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 _widget(self):
""" Create IPython widget for display within a notebook """
try:
return self._cached_widget
except AttributeError:
pass
from ipywidgets import Layout, VBox, HBox, IntText, Button, HTML, Accordion
layout = Layout(width='150px')
if 'bokeh' in self.scheduler.services:
template = config.get('diagnostics-link',
'http://{host}:{port}/status')
host = self.scheduler.address.split('://')[1].split(':')[0]
port = self.scheduler.services['bokeh'].port
link = template.format(host=host, port=port, **os.environ)
link = '<p><b>Dashboard: </b><a href="%s" target="_blank">%s</a></p>\n' % (
link, link)
else:
link = ''
title = '<h2>%s</h2>' % type(self).__name__
title = HTML(title)
dashboard = HTML(link)
status = HTML(self._widget_status(), layout=Layout(min_width='150px'))
request = IntText(0, description='Workers', layout=layout)
scale = Button(description='Scale', layout=layout)
minimum = IntText(0, description='Minimum', layout=layout)
maximum = IntText(0, description='Maximum', layout=layout)
adapt = Button(description='Adapt', layout=layout)
accordion = Accordion(
[HBox([request, scale]),
HBox([minimum, maximum, adapt])],
layout=Layout(min_width='500px'))
accordion.selected_index = None
accordion.set_title(0, 'Manual Scaling')
accordion.set_title(1, 'Adaptive Scaling')
box = VBox([title, HBox([status, accordion]), dashboard])
self._cached_widget = box
def adapt_cb(b):
self.adapt(minimum=minimum.value, maximum=maximum.value)
adapt.on_click(adapt_cb)
def scale_cb(b):
print('Hello!')
with log_errors():
n = request.value
with ignoring(AttributeError):
self._adaptive.stop()
self.scale(n)
scale.on_click(scale_cb)
scheduler_ref = ref(self.scheduler)
def update():
status.value = self._widget_status()
pc = PeriodicCallback(update, 500, io_loop=self.scheduler.loop)
self.scheduler.periodic_callbacks['cluster-repr'] = pc
pc.start()
return box
def __init__(self, show=True, style=True, Debug=p.DEBUG):
super(MS2Dscene, self).__init__()
# header
# filechooser
self.base = p.BASE
self.filechooser = FI.FileChooser(self.base,
dotd=False,
accept=('2D-MS', ))
self.datap = None
self.MAX_DISP_PEAKS = p.NbMaxDisplayPeaks
self.debug = Debug
# buttons
# load
self.bload = Button(
description='Load', #layout=Layout(width='15%'),
tooltip='load and display experiment')
self.bload.on_click(self.load2D)
# info
self.binfo = Button(
description='Info', #layout=Layout(width='15%'),
tooltip='Info on selected experiment, without loading')
self.binfo.on_click(self.info2D)
# GUI set-up and scene
# tools
self.header = Output()
with self.header:
self.waitarea = Output()
self.buttonbar = HBox([self.bload, self.binfo, self.waitarea])
display(Markdown('---\n# Select an experiment, and load'))
display(self.filechooser)
display(self.buttonbar)
NODATA = HTML("<br><br><h3><i><center>No Data</center></i></h3>")
# 2D spectrum
self.out2D = Output() # the area where 2D is shown
with self.out2D:
display(NODATA)
display(Markdown("use the `Load` button above"))
# 1D spectrum
self.out1D = Output() # the area where 1D is shown
with self.out1D:
display(NODATA)
display(Markdown("After loading, this window will be activated"))
# peaklist
self.peaklist = Output() # the area where peak list is shown
with self.peaklist:
display(
HTML(
"<br><br><h3><i><center>Not implemented yet</center></i></h3>"
))
# # form
# self.outform = Output() # the area where processing parameters are displayed
# with self.outform:
# self.paramform()
# display(self.form)
# Info
self.outinfo = Output() # the area where info is shown
with self.outinfo:
display(NODATA)
self.out2D.clear_output(wait=True)
self.out1D.clear_output(wait=True)
self.outinfo.clear_output(wait=True)
self.peaklist.clear_output(wait=True)
# tabs
self.tabs = widgets.Tab()
self.tabs.children = [
self.out1D, self.out2D, self.peaklist, self.outinfo
]
self.tabs.set_title(0, '1D Extraction')
self.tabs.set_title(1, '2D Display')
self.tabs.set_title(2, 'Peak List')
# self.tabs.set_title(3, 'Processing Parameters')
self.tabs.set_title(3, 'Info')
# self.tabs = VBox([ self.out2D, self.outpp2D, self.out1D, self.outinfo ])
self.box = VBox([self.header, self.tabs])
# self.box = VBox([self.title,
# self.FC,
# HBox([self.bdisp2D, self.bpp2D, self.bdisp1D])
# ])
if style:
FI.injectcss()
if show:
display(self.box)
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 df_input(dfUniprot=DataFrame([])):
num_phylum = len(dfUniprot.PHYLUM.drop_duplicates())
from matplotlib import cm
set3 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Set3(np.arange(12) / 12.)
]
set2 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Set2(np.arange(8) / 8.)
]
set1 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Set1(np.arange(9) / 9.)
]
pastel2 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Pastel2(np.arange(8) / 8.)
]
pastel1 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Pastel1(np.arange(9) / 9.)
]
dark2 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Dark2(np.arange(8) / 8.)
]
paired = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Paired(np.arange(12) / 12.)
]
accent = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Accent(np.arange(8) / 8.)
]
spectral = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.Spectral(np.arange(11) / 11.)
]
tab20 = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.tab20(np.arange(20) / 20.)
]
tab20b = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.tab20b(np.arange(20) / 20.)
]
tab20c = [
matplotlib.colors.rgb2hex(tuple(i))
for i in cm.tab20c(np.arange(20) / 20.)
]
Colors1 = set2 + set1 + dark2 + paired + accent + spectral + tab20 + tab20b + tab20c
Colors2 = accent + spectral + tab20 + tab20b + tab20c + set1 + set2 + dark2 + paired
Colors3 = dark2 + paired + accent + spectral + tab20 + tab20b + tab20c + set1 + set2
Colors4 = tab20b + tab20c + set1 + set2 + dark2 + paired + accent + spectral + tab20
Colors5 = spectral + tab20 + tab20b + tab20c + set1 + set2 + dark2 + paired + accent
pie_colors = {
'Set3': cm.Set3(np.arange(12) / 12.),
'Set2': cm.Set2(np.arange(8) / 8.),
'Set1': cm.Set1(np.arange(9) / 9.),
'Pastel2': cm.Pastel2(np.arange(8) / 8.),
'Pastel1': cm.Pastel1(np.arange(9) / 9.),
'Dark2': cm.Dark2(np.arange(8) / 8.),
'Paired': cm.Paired(np.arange(12) / 12.),
'Accent': cm.Accent(np.arange(8) / 8.),
'Spectral': cm.Spectral(np.arange(11) / 11.),
'tab20': cm.tab20(np.arange(20) / 20.),
'tab20b': cm.tab20b(np.arange(20) / 20.),
'tab20c': cm.tab20c(np.arange(20) / 20.)
}
circle_colors = {
'Colors1': Colors1[0:num_phylum],
'Colors2': Colors2[0:num_phylum],
'Colors3': Colors3[0:num_phylum],
'Colors4': Colors4[0:num_phylum],
'Colors5': Colors5[0:num_phylum]
}
def tax_colors(color_list=circle_colors['Colors1'], taxx=dfUniprot):
tax_cols = [
'Entry', 'Tax_ID', 'KINGDOM', 'PHYLUM', 'CLASS', 'ORDER', 'FAMILY',
'GENUS', 'SPECIES', 'Organism'
]
new2 = taxx[tax_cols].drop_duplicates()
#>>>>>>>>>>>>>>>>>>>>>>>>>>>
phylum0 = new2.groupby(['PHYLUM'
]).Entry.count().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
asign_color = {}
for i, j in zip(phylum0.PHYLUM, color_list):
if i == 'NA':
asign_color[i] = 'black'
else:
asign_color[i] = j
phylum0['phy_col'] = list(asign_color.values())
# distribución de Class
phylum1 = new2.groupby(['PHYLUM', 'CLASS']).Entry.count().reset_index()
class0 = []
class0_colors = []
for i in phylum0.PHYLUM:
for j in phylum1.PHYLUM:
if i == j:
class0_colors.append(asign_color[j])
class0.append(phylum1[phylum1.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
class1 = pd.concat(class0).drop_duplicates()
class1['class_col'] = class0_colors
class0_colors_corregido = []
for index, row in class1.iterrows():
if row.PHYLUM == 'NA':
if row.CLASS == 'NA':
class0_colors_corregido.append(row.class_col)
else:
class0_colors_corregido.append('grey')
else:
if row.CLASS == 'NA':
class0_colors_corregido.append('black')
else:
class0_colors_corregido.append(row.class_col)
class1['class_col'] = class0_colors_corregido
class11 = class1.groupby(['CLASS'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
class11 = class11.merge(class1[['CLASS',
'class_col']].drop_duplicates(),
on='CLASS',
how='left')
# distribución de Order
phylum2 = new2.groupby(['PHYLUM', 'CLASS',
'ORDER']).Entry.count().reset_index()
order0 = []
order0_colors = []
for i in phylum0.PHYLUM:
for j in phylum2.PHYLUM:
if i == j:
order0_colors.append(asign_color[j])
order0.append(phylum2[phylum2.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
order1 = pd.concat(order0).drop_duplicates()
order1['order_col'] = order0_colors
order0_colors_corregido = []
for index, row in order1.iterrows():
if row.PHYLUM == 'NA':
if row.ORDER == 'NA':
order0_colors_corregido.append(row.order_col)
else:
order0_colors_corregido.append('grey')
else:
if row.ORDER == 'NA':
order0_colors_corregido.append('black')
else:
order0_colors_corregido.append(row.order_col)
order1['order_col'] = order0_colors_corregido
order11 = order1.groupby(['ORDER'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
order11 = order11.merge(order1[['ORDER',
'order_col']].drop_duplicates(),
on='ORDER',
how='left')
# distribución de Genus
phylum3 = new2.groupby(['PHYLUM', 'CLASS', 'ORDER',
'GENUS']).Entry.count().reset_index()
genus0 = []
genus0_colors = []
for i in phylum0.PHYLUM:
for j in phylum3.PHYLUM:
if i == j:
genus0_colors.append(asign_color[j])
genus0.append(phylum3[phylum3.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
genus1 = pd.concat(genus0).drop_duplicates()
genus1['genus_col'] = genus0_colors
genus0_colors_corregido = []
for index, row in genus1.iterrows():
if row.PHYLUM == 'NA':
if row.GENUS == 'NA':
genus0_colors_corregido.append(row.genus_col)
else:
genus0_colors_corregido.append('grey')
else:
if row.GENUS == 'NA':
genus0_colors_corregido.append('black')
else:
genus0_colors_corregido.append(row.genus_col)
genus1['genus_col'] = genus0_colors_corregido
genus11 = genus1.groupby(['GENUS'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
genus11 = genus11.merge(genus1[['GENUS',
'genus_col']].drop_duplicates(),
on='GENUS',
how='left')
# distribución de Organism
phylum4 = new2.groupby(
['PHYLUM', 'CLASS', 'ORDER', 'GENUS',
'Organism']).Entry.count().reset_index()
org0 = []
org0_colors = []
for i in phylum0.PHYLUM:
for j in phylum4.PHYLUM:
if i == j:
org0_colors.append(asign_color[j])
org0.append(phylum4[phylum4.PHYLUM == i].sort_values(
by='Entry', ascending=False).reset_index(drop=True))
else:
pass
org1 = pd.concat(org0).drop_duplicates()
org1['org_col'] = org0_colors
org0_colors_corregido = []
for index, row in org1.iterrows():
if row.PHYLUM == 'NA':
if row.Organism == 'NA':
org0_colors_corregido.append(row.org_col)
else:
org0_colors_corregido.append('grey')
else:
if row.Organism == 'NA':
org0_colors_corregido.append('black')
else:
org0_colors_corregido.append(row.org_col)
org1['org_col'] = org0_colors_corregido
org11 = org1.groupby(['Organism'
]).Entry.sum().reset_index().sort_values(
by='Entry',
ascending=False).reset_index(drop=True)
org11 = org11.merge(org1[['Organism', 'org_col']].drop_duplicates(),
on='Organism',
how='left')
os.makedirs('tax', exist_ok=True)
return phylum0.to_csv('tax/phylum0.tsv', sep = '\t', index = None),\
class1.to_csv('tax/class1.tsv', sep = '\t', index = None),\
class11.to_csv('tax/class11.tsv', sep = '\t', index = None),\
order1.to_csv('tax/order1.tsv', sep = '\t', index = None),\
order11.to_csv('tax/order11.tsv', sep = '\t', index = None),\
genus1.to_csv('tax/genus1.tsv', sep = '\t', index = None),\
genus11.to_csv('tax/genus11.tsv', sep = '\t', index = None),\
org1.to_csv('tax/org1.tsv', sep = '\t', index = None),\
org11.to_csv('tax/org11.tsv', sep = '\t', index = None)
alfas = {
'Lineage*': [1, 1, 1, 1, 1],
'Phylum': [1, 0.3, 0.3, 0.3, 0.3],
'Class': [0.3, 1, 0.3, 0.3, 0.3],
'Order': [0.3, 0.3, 1, 0.3, 0.3],
'Genus': [0.3, 0.3, 0.3, 1, 0.3],
'Species': [0.3, 0.3, 0.3, 0.3, 1],
'Gradient1*': [1, 0.85, 0.7, 0.55, 0.4],
'Gradient2*': [0.4, 0.55, 0.7, 0.85, 1],
'Attenuate*': [0.3, 0.3, 0.3, 0.3, 0.3],
'None*': [0, 0, 0, 0, 0]
}
def circle_lineage(alphas=alfas['Phylum']):
#fig, ax = plt.subplots(111, facecolor= 'white')
#fig, ax = plt.subplot(111)
phylum0 = pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA')
class1 = pd.read_csv('tax/class1.tsv', sep='\t').fillna('NA')
order1 = pd.read_csv('tax/order1.tsv', sep='\t').fillna('NA')
genus1 = pd.read_csv('tax/genus1.tsv', sep='\t').fillna('NA')
org1 = pd.read_csv('tax/org1.tsv', sep='\t').fillna('NA')
radio = 0.5
linaje = [phylum0, class1, order1, genus1, org1]
#colores = [list(asign_color.values()), class0_colors, order0_colors, genus0_colors, org0_colors]
colores = ['phy_col', 'class_col', 'order_col', 'genus_col', 'org_col']
pat = []
size = -.205
for i, j, k in zip(linaje, colores, alphas):
size += .205
patches, texts = plt.pie(
i.Entry,
radius=radio + size,
labels=None,
labeldistance=0.8,
rotatelabels=True,
colors=
i[j], # new_colors(valor = len(i.Entry), col = 'nipy_spectral'),
wedgeprops=dict(width=0.2, edgecolor='white', alpha=k),
textprops=dict(size=10))
pat.append(patches)
#plt.legend(pat[0], df_phylum.PHYLUM, loc=2,fontsize=13,labelspacing = 0.4,
# bbox_to_anchor=(1.05, 1),frameon=False)
plt.gca().set(aspect='equal')
plt.title('Root', fontsize=10, x=0.5, y=0.465)
plt.text(-1.8,
1.35,
'Lineage',
fontsize=15,
ha='left',
va='center',
color='black')
#plt.title('Lineage',fontsize=20, fontweight='bold', x = -0.17, y = 1)
#plt.text(1.1, 1.35, linaje_seleccionado, fontsize = 15, ha='left', va='center',
# color='black')
#>>>>>>>>>>>>>>>>>>>>>>>
#### insetplot
#ax2 = plt.axes([0.1, 0.66, 0.13, 0.14])
ax2 = plt.axes([-0.07, 1.71, 0.17, 0.18])
logo = [20, 20, 20, 20, 20, 20, 20, 20]
logo_col = [
'white', 'white', 'black', 'white', 'white', 'white', 'white',
'white'
]
logo_col1 = [
'white', 'white', 'black', 'black', 'black', 'black', 'black',
'black'
]
radio = 0.5
linaje = [logo, logo, logo, logo, logo]
colores = [logo_col1, logo_col, logo_col, logo_col, logo_col]
name_linaje = ['Phylum', 'Class', 'Order', 'Genus', 'Species']
pat = []
size = -.44
pos = -.18
for i, j, k, l in zip(linaje, colores, name_linaje, alphas):
pos += .47
size += .44
ax2.pie(i,
radius=radio + size,
labels=None,
colors=j,
wedgeprops=dict(width=0.35, edgecolor='white', alpha=l),
textprops=dict(size=10))
ax2.text(0.1,
pos,
k,
fontsize=9,
ha='left',
va='center',
fontweight='bold',
alpha=l) #color='black'
def barras_tax(df=DataFrame([]),
column=0,
dim=111,
title='',
row_num=10,
color=['#ff7f0e'],
size_x=8,
size_y=10,
ylabel_text='',
xlabel=10,
ylabel=10,
size_title=15,
size_bartxt=10,
sep=1.2):
if len(df) == 0:
print('Data frame sin datos')
else:
#plt.subplot(dim, facecolor= 'white')
barWidth = 0.9
if row_num == len(df):
ejey = list(df.iloc[0:len(df), 1])
val = max(ejey)
ejex = list(df.iloc[0:len(df), column])
colores = list(df.iloc[0:len(df), 2])
borde = list(
np.repeat('white', len(df.iloc[0:row_num, column])))
linea = list(np.repeat(0, len(df.iloc[0:row_num, column])))
if row_num < len(df):
ejey = list(df.iloc[0:row_num,
1]) + [df.iloc[row_num:len(df), 1].sum()]
val = max(ejey)
ejex = list(df.iloc[0:row_num, column]) + ['Others']
borde = list(
np.repeat('white', len(df.iloc[0:row_num,
column]))) + ['black']
colores = list(df.iloc[0:row_num, 2]) + ['linen']
linea = list(np.repeat(0, len(df.iloc[0:row_num,
column]))) + [1]
if row_num > len(df):
ejey = list(df.iloc[0:len(df), 1])
val = max(ejey)
ejex = list(df.iloc[0:len(df), column])
borde = list(
np.repeat('white', len(df.iloc[0:row_num, column])))
colores = list(df.iloc[0:len(df), 2])
linea = list(np.repeat(0, len(df.iloc[0:row_num, column])))
for i, j, k, l, m in zip(ejex, ejey, borde, colores, linea):
plt.barh(i,
j,
color=l,
align='center',
height=0.7,
linewidth=m,
alpha=1,
edgecolor=k)
plt.gca().spines['right'].set_visible(False)
plt.gca().spines['top'].set_visible(False)
plt.gca().spines['bottom'].set_position(('data', -0.6))
plt.gca().spines['left'].set_visible(False)
plt.title(title, size=size_title, loc='left')
plt.tick_params(axis="y", color="gray")
plt.yticks(size=size_y)
v1 = -50
v2 = 0
v3 = 0
for i in range(10000):
v1 += 50
v2 += 50
v3 += 10
if v1 <= max(list(ejey)) < v2:
#print(v3, v1, val, v2)
escala = v3
plt.xticks(range(0, val, escala), size=size_x) #fontweight='bold'
plt.ylabel(ylabel_text, size=ylabel)
plt.xlabel("Number of Proteins", size=xlabel)
#plt.tick_params(top = 'on', bottom = 'on', right = 'on', left = 'on')
#plt.tick_params(axis='x', which='both', bottom=False, top=False, labelbottom=False)
for j, k in zip(ejey, range(0, len(ejey))):
plt.text(j + sep,
k - 0.2,
j,
size=size_bartxt,
ha='left',
color='black')
import ipywidgets as widgets
from ipywidgets import interact, interactive, fixed, interact_manual, Button, HBox, VBox, IntSlider, Label, IntRangeSlider
from ipywidgets import Checkbox, RadioButtons
from ipywidgets import Button, Layout
alfas = {
'Lineage*': [1, 1, 1, 1, 1],
'Phylum': [1, 0.3, 0.3, 0.3, 0.3],
'Class': [0.3, 1, 0.3, 0.3, 0.3],
'Order': [0.3, 0.3, 1, 0.3, 0.3],
'Genus': [0.3, 0.3, 0.3, 1, 0.3],
'Species': [0.3, 0.3, 0.3, 0.3, 1],
'Gradient1*': [1, 0.85, 0.7, 0.55, 0.4],
'Gradient2*': [0.4, 0.55, 0.7, 0.85, 1],
'Attenuate*': [0.3, 0.3, 0.3, 0.3, 0.3],
'None*': [0, 0, 0, 0, 0]
}
plotss = ['Phylum', 'Class', 'Order', 'Genus', 'Species']
posicion_subplots = []
n = 0.9
while n < 2:
n += 0.1
posicion_subplots.append(np.around(n, 1))
color_a6 = widgets.Dropdown(options=list(circle_colors.keys()),
value='Colors1',
description='Colors:',
disabled=False,
button_style='',
layout=Layout(width='20%', height='25px'))
a6 = widgets.Dropdown(options=list(alfas.keys()),
description='Chart 1:',
value='Phylum',
disabled=False,
button_style='',
layout=Layout(width='20%', height='25px'))
a61 = widgets.Dropdown(options=plotss,
description='Chart 2:',
disabled=False,
button_style='',
layout=Layout(width='20%', height='25px'))
pos_sub1 = widgets.Dropdown(options=posicion_subplots,
value=1.3,
description='xloc1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
pos_sub2 = widgets.Dropdown(options=posicion_subplots,
value=1.3,
description='xloc2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
b6 = widgets.Dropdown(options=list(range(0, 101)),
value=10,
description='rows1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
c6 = widgets.Dropdown(options=list(range(0, 101)),
value=10,
description='rows2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
z6 = widgets.ToggleButton(value=False,
description='Save Chart',
disabled=False,
button_style='',
tooltip='Description')
o6 = widgets.Dropdown(options=[0, 0.25, 0.5, 0.75] + list(range(0, 201)),
value=3,
description='sep1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
o61 = widgets.Dropdown(options=[0, 0.25, 0.5, 0.75] + list(range(0, 201)),
value=3,
description='sep2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
d6 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='size_y1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
d61 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='size_y2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
g6 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='bartxt1:',
disabled=False,
layout=Layout(width='15%', height='25px'))
g61 = widgets.Dropdown(options=list(range(0, 51)),
value=8,
description='bartxt2:',
disabled=False,
layout=Layout(width='15%', height='25px'))
xxx = Button(layout=Layout(width='5%', height='25px'), disabled=True)
xxx.style.button_color = 'white'
yyy = Button(layout=Layout(width='94%', height='5px'), disabled=True)
yyy.style.button_color = 'red'
ww = widgets.HBox([color_a6, xxx, z6])
w6 = widgets.HBox([
a6,
b6,
o6,
d6,
g6,
pos_sub1,
])
w7 = widgets.HBox([
a61,
c6,
o61,
d61,
g61,
pos_sub2,
])
w8 = widgets.VBox([w6, w7, yyy])
######
def col(color_a6):
tax_colors(color_list=circle_colors[color_a6], taxx=dfUniprot)
out7 = widgets.interactive_output(col, {'color_a6': color_a6})
def box1(a6, a61, pos_sub1, pos_sub2, b6, c6, z6, o6, o61, d6, d61, g6,
g61):
yetiquetas_plot1 = {
'Lineage*': 'Phylum',
'Phylum': 'Phylum',
'Class': 'Class',
'Order': 'Order',
'Genus': 'Genus',
'Species': 'Species',
'Gradient1*': 'Phylum',
'Gradient2*': 'Phylum',
'Attenuate*': 'Phylum',
'None*': 'Phylum'
}
plots1 = {
'Lineage*': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA'),
'Phylum': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA'),
'Class': pd.read_csv('tax/class11.tsv', sep='\t').fillna('NA'),
'Order': pd.read_csv('tax/order11.tsv', sep='\t').fillna('NA'),
'Genus': pd.read_csv('tax/genus11.tsv', sep='\t').fillna('NA'),
'Species': pd.read_csv('tax/org11.tsv', sep='\t').fillna('NA'),
'Gradient1*': pd.read_csv('tax/phylum0.tsv',
sep='\t').fillna('NA'),
'Gradient2*': pd.read_csv('tax/phylum0.tsv',
sep='\t').fillna('NA'),
'Attenuate*': pd.read_csv('tax/phylum0.tsv',
sep='\t').fillna('NA'),
'None*': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA')
}
plots2 = {
'Phylum': pd.read_csv('tax/phylum0.tsv', sep='\t').fillna('NA'),
'Class': pd.read_csv('tax/class11.tsv', sep='\t').fillna('NA'),
'Order': pd.read_csv('tax/order11.tsv', sep='\t').fillna('NA'),
'Genus': pd.read_csv('tax/genus11.tsv', sep='\t').fillna('NA'),
'Species': pd.read_csv('tax/org11.tsv', sep='\t').fillna('NA')
}
ax3 = plt.axes([pos_sub2, .97, .3, 0.55])
##>>>>>>>>>>> grafico circular
ax = plt.axes([0, 1, 0.9, 1])
circle_lineage(alphas=alfas[a6])
##>>>>>>>>>>> grafico 1
#ax2 = plt.axes([pos_sub1, 1.51, .3, 0.55])
ax2 = plt.axes([pos_sub1, 1.63, .3, 0.4]) #>>>>>>>>>>
barras_tax(
plots1[a6],
#barras_tax(tax_colors(color_list = circle_colors['Spectral'])[0],
row_num=b6,
color=plots1[a6].iloc[0:b6, 2],
sep=o6,
size_y=d6,
size_bartxt=g6,
ylabel_text=yetiquetas_plot1[a6],
ylabel=10)
##>>>>>>>>>>> grafico 2
ax3 = plt.axes([pos_sub2, .97, .3, 0.55])
barras_tax(
plots2[a61],
#barras_tax(tax_colors(color_list = circle_colors['Spectral'])[0],
row_num=c6,
color=plots2[a61].iloc[0:b6, 2],
sep=o61,
size_y=d61,
size_bartxt=g61,
ylabel_text=yetiquetas_plot1[a61],
ylabel=10)
##>>>>>>>>>>>> save
if z6 == True:
import datetime
plt.savefig('img/Lineage' +
datetime.datetime.now().strftime('%d.%B.%Y_%I-%M%p') +
'.png',
dpi=900,
bbox_inches='tight')
else:
pass
out6 = widgets.interactive_output(
box1, {
'a6': a6,
'a61': a61,
'pos_sub1': pos_sub1,
'pos_sub2': pos_sub2,
'b6': b6,
'c6': c6,
'z6': z6,
'o6': o6,
'o61': o61,
'd6': d6,
'd61': d61,
'g6': g6,
'g61': g61
})
import warnings
warnings.filterwarnings("ignore")
return display(VBox([yyy, ww, w8, out6]))
def upload_shp(path_data, config_path=False):
# Upload
l_up = Label("a. Upload .shp to the server.")
accept_files = ".shp, .cpg, .dbf, .prj, .shx, .sbn, .sbx, .xml"
data_path = config.get_value(['paths', 'temp'])
shp_dist_folder = Text(value=normpath(join(path_data, 'vector')),
placeholder='tmp/',
description='Folder:',
disabled=config_path)
shp_select = FileUpload(
description='Select files:',
icon='plus',
accept=accept_files,
multiple=True # True to accept multiple files upload else False
)
shp_clear = Button(value=False,
disabled=False,
button_style='info',
tooltip='Clear selections.',
icon='broom',
layout=Layout(width='40px'))
shp_upload = Button(value=False,
disabled=False,
button_style='info',
tooltip='Upload foi reference data (.shp).',
icon='fa-upload',
layout=Layout(width='40px'))
progress = Output()
def outlog(*text):
with progress:
print(*text)
@shp_clear.on_click
def shp_clear_on_click(b):
shp_select.value.clear()
shp_select._counter = 0
@shp_upload.on_click
def shp_upload_on_click(b):
progress.clear_output()
os.makedirs(shp_dist_folder.value, exist_ok=True)
for key in shp_select.value:
content = shp_select.value[key]['content']
with open(normpath(join(shp_dist_folder.value, key)), 'wb') as f:
f.write(content)
outlog("All files are uploaded.")
shp_select.value.clear()
shp_select._counter = 0
shp_box = HBox([shp_dist_folder, shp_select, shp_clear, shp_upload])
# Import the .shp to the database
l_imp = Label("""b. Import uploaded .shp to the database. Add a short name,
max 15 characters for the parcels table e.g.:escat2020.""")
imp_select = Dropdown(options=[
s for s in glob.glob(normpath(join(shp_dist_folder.value, '*')))
if '.shp' in s
],
description='Select .shp:',
disabled=False)
imp_refresh = Button(layout=Layout(width='35px'), icon='fa-refresh')
imp_proc = Button(
description='Import .shp file',
value=False,
disabled=False,
button_style='info',
tooltip='Run',
icon='fa-database',
)
imp_truncate = Checkbox(value=False,
description='Remove old entries',
disabled=False)
try:
with open(normpath(join(data_path, 'tb_prefix')), 'r') as f:
name_from_prfix = f.read()
except Exception:
name_from_prfix = None
imp_tb_name = Text(value=name_from_prfix,
placeholder='ms2010',
description='Table name:',
tooltip='A short name max 10 char.',
disabled=False)
def on_imp_tb_name(change):
with open(normpath(join(data_path, 'tb_prefix')), 'w+') as f:
f.write(imp_tb_name.value)
imp_tb_name.observe(on_imp_tb_name, 'value')
@imp_proc.on_click
def imp_proc_on_click(b):
if imp_tb_name is not None:
import subprocess
progress.clear_output()
# tb_name = imp_select.value.split('/')[-1].split('.')[0]
tb_name = imp_tb_name.value.replace(' ', '').lower()[:15]
outlog("Importing .shp to database...")
command = [
'ogr2ogr', '-f', 'PostgreSQL', 'PG:' + db.conn_str(), '-nln',
tb_name, '-nlt', 'PROMOTE_TO_MULTI', '-nlt', 'GEOMETRY',
imp_select.value
]
if imp_truncate.value is True:
command.extend(['--config', 'OGR_TRUNCATE', 'YES'])
if subprocess.call(command) == 0:
progress.clear_output()
outlog(
f"Completed. Total number of rows in table '{tb_name}':",
db.exact_count(tb_name))
else:
outlog("Could not import shp file.")
else:
outlog(
"Please add a name for the parcels table (MAX 15 char e.g.: escat2020)."
)
@imp_refresh.on_click
def imp_refresh_on_click(b):
imp_select.options = [
s for s in glob.glob(f'{shp_dist_folder.value}/*') if '.shp' in s
]
imp_box = HBox(
[imp_tb_name, imp_select, imp_refresh, imp_proc, imp_truncate])
return VBox([l_up, shp_box, l_imp, imp_box, progress])
def button_factory(description, color='lightgray'):
return Button(description=description,
button_style='',
layout=BUTTON_LAYOUT,
style={'button_color': color})
def extraction():
start = DatePicker(description='Start date:', disabled=False)
end = DatePicker(description='End date:', disabled=False)
dates = HBox([start, end])
bt_sig_s2 = Button(description='Sentinel 2',
value=False,
disabled=False,
button_style='info',
tooltip='Run Sentinel 2 extraction',
icon='fa-play')
bt_sig_bs = Button(description='S1 Backscattering',
value=False,
disabled=True,
button_style='info',
tooltip='Run S1 Backscattering extraction',
icon='fa-play')
bt_sig_c6 = Button(description='S1 6-day coherence',
value=False,
disabled=True,
button_style='info',
tooltip='Run S1 6-day coherence extraction',
icon='fa-play')
progress = Output()
def outlog(*text):
with progress:
print(*text)
bt_sg_box = VBox([bt_sig_s2, bt_sig_bs, bt_sig_c6])
tab_box = Tab(children=[bt_sg_box, Text()])
tab_box.set_title(0, 'Procedures')
tab_box.set_title(1, 'VM Workers config')
@bt_sig_s2.on_click
def bt_sig_s2_on_click(b):
progress.clear_output()
with progress:
try:
delta = end.value - start.value
for d in range(delta.days):
pgS2Extract.main(start.value, end.value)
except Exception as err:
outlog(err)
@bt_sig_bs.on_click
def bt_sig_bs_on_click(b):
progress.clear_output()
with progress:
try:
delta = end.value - start.value
for d in range(delta.days):
pgS1bsExtract.extractS1bs(start.value, end.value)
except Exception as err:
outlog(err)
@bt_sig_c6.on_click
def bt_sig_c6_on_click(b):
progress.clear_output()
with progress:
outlog(
"6-day coherence extraction not yet available please check for updates."
)
return VBox([dates, bt_sg_box, progress])
def __init__(self, **kwargs):
super(TaskManager, self).__init__(**kwargs)
# Header
self.checkbox = Checkbox(indent=False,
layout=Layout(flex='1 1 20', width='auto'))
self.cancel_selected = Button(description='Cancel Selected',
tooltip='Cancel all selected tasks')
self.cancel_all = Button(description='Cancell All',
tooltip='Cancel all tasks')
self.refresh = Button(description='Refresh',
tooltip='Refresh Tasks List')
self.autorefresh = ToggleButton(
description='auto-refresh',
tooltip='click to enable/disable autorefresh')
self.slider = IntSlider(min=1, max=10, step=1, value=5)
self.hbox = HBox([
self.checkbox, self.refresh, self.cancel_selected, self.cancel_all,
self.autorefresh, self.slider
])
# Tabs for COMPLETED, FAILED, etc
self.tabs = Tab()
# Tabs index
self.tab_index = {
0: 'RUNNING',
1: 'COMPLETED',
2: 'FAILED',
3: 'CANCELED',
4: 'UNKNOWN'
}
self.taskVBox = VBox()
self.runningVBox = VBox()
self.completedVBox = VBox()
self.failedVBox = VBox()
self.canceledVBox = VBox()
self.unknownVBox = VBox()
self.tab_widgets_rel = {
'RUNNING': self.runningVBox,
'COMPLETED': self.completedVBox,
'FAILED': self.failedVBox,
'CANCELED': self.canceledVBox,
'UNKNOWN': self.unknownVBox
}
# Create Tabs
self.tab_widgets = []
for key, val in self.tab_index.items():
widget = self.tab_widgets_rel[val]
self.tab_widgets.append(widget)
self.tabs.children = self.tab_widgets
self.tabs.set_title(key, val)
''' autorefresh
def update_task_list(widget):
# widget is a VBox
tasklist = ee.data.getTaskList()
widlist = []
for task in tasklist:
accordion = create_accordion(task)
if task.has_key('description'):
name = '{} ({})'.format(task['description'], task['state'])
else:
name = '{} ({})'.format(task['output_url'][0].split('/')[-1], task['state'])
mainacc = Accordion(children=(accordion, ))
mainacc.set_title(0, name)
mainacc.selected_index = None
wid = CheckRow(mainacc)
#wid = CheckRow(accordion)
widlist.append(wid)
widget.children = tuple(widlist)
'''
def loop(widget):
while True:
self.update_task_list()(self.refresh)
time.sleep(self.slider.value)
# First widget
self.update_task_list(vbox=self.runningVBox)(self.refresh)
# self.children = (self.hbox, self.taskVBox)
self.children = (self.hbox, self.tabs)
# Set on_click for refresh button
self.refresh.on_click(self.update_task_list(vbox=self.selected_tab()))
''' autorefresh
thread = threading.Thread(target=loop, args=(self.taskVBox,))
thread.start()
'''
# Set on_clicks
self.cancel_all.on_click(self.cancel_all_click)
self.cancel_selected.on_click(self.cancel_selected_click)
def _dock_add_button(self, name, callback, layout=None):
widget = Button(description=name)
widget.on_click(lambda x: callback())
self._layout_add_widget(layout, widget)
return _IpyWidget(widget)
def create_expanded_button(description, button_style):
return Button(description=description,
button_style=button_style,
layout=Layout(height='auto', width='auto'))
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'
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 = 'lightgreen'
self.random_seed = IntText(value=0,
step=1,
style=style,
layout=widget_layout)
param_name2 = Button(description='scale_factor',
disabled=True,
layout=name_button_layout)
param_name2.style.button_color = 'tan'
self.scale_factor = FloatText(value=300.,
step=10,
style=style,
layout=widget_layout)
param_name3 = Button(description='persistence_time',
disabled=True,
layout=name_button_layout)
param_name3.style.button_color = 'lightgreen'
self.persistence_time = FloatText(value=4.0,
step=0.1,
style=style,
layout=widget_layout)
param_name4 = Button(description='migration_speed',
disabled=True,
layout=name_button_layout)
param_name4.style.button_color = 'tan'
self.migration_speed = FloatText(value=0.25,
step=0.01,
style=style,
layout=widget_layout)
param_name5 = Button(description='adhesion_strength',
disabled=True,
layout=name_button_layout)
param_name5.style.button_color = 'lightgreen'
self.adhesion_strength = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name6 = Button(description='repulsion_strength',
disabled=True,
layout=name_button_layout)
param_name6.style.button_color = 'tan'
self.repulsion_strength = FloatText(value=0.5,
step=0.1,
style=style,
layout=widget_layout)
param_name7 = Button(description='rel_max_adhesion_dist',
disabled=True,
layout=name_button_layout)
param_name7.style.button_color = 'lightgreen'
self.rel_max_adhesion_dist = FloatText(value=1.25,
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='',
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'
units_button7 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button7.style.button_color = 'lightgreen'
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'
row1 = [param_name1, self.random_seed, units_button1, desc_button1]
row2 = [param_name2, self.scale_factor, units_button2, desc_button2]
row3 = [
param_name3, self.persistence_time, units_button3, desc_button3
]
row4 = [param_name4, self.migration_speed, units_button4, desc_button4]
row5 = [
param_name5, self.adhesion_strength, units_button5, desc_button5
]
row6 = [
param_name6, self.repulsion_strength, units_button6, desc_button6
]
row7 = [
param_name7, self.rel_max_adhesion_dist, units_button7,
desc_button7
]
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)
self.tab = VBox([
box1,
box2,
box3,
box4,
box5,
box6,
box7,
])
def annotate(self):
self.count_label = HTML()
self.set_label_text()
display(self.count_label)
self.buttons = []
text_id = self.current_index + 1
if self.task_type == 'classification':
use_dropdown = len(self.options) > self.max_options_dropdown
if use_dropdown:
dd = Dropdown(options=self.options)
display(dd)
else:
for label in self.options:
btn = Button(description=label)
def on_click(label, btn):
self.add_annotation(label)
btn.on_click(functools.partial(on_click, label))
self.buttons.append(btn)
elif self.task_type == 'regression':
target_type = type(options[0])
if target_type == int:
cls = IntSlider
else:
cls = FloatSlider
if len(options) == 2:
min_val, max_val = options
slider = cls(min=min_val, max=max_val)
else:
min_val, max_val, step_val = options
slider = cls(min=min_val, max=max_val, step=step_val)
display(slider)
btn = Button(description='submit')
def on_click(btn):
add_annotation(slider.value)
btn.on_click(on_click)
buttons.append(btn)
ta = Textarea()
display(ta)
btn = Button(description='submit', button_style="success")
def on_click(btn):
self.add_annotation(dd.value, ta.value)
btn.on_click(on_click)
self.buttons.append(btn)
self.box = HBox(self.buttons)
display(self.box)
self.out = Output()
display(self.out)
self.show_next()
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='thanos',
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.thanos_diffusion_coefficient = FloatText(value=100000.0,
step=10000,
style=style,
layout=widget_layout)
param_name2 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.thanos_decay_rate = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name3 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.thanos_initial_condition = FloatText(value=0.0,
style=style,
layout=widget_layout)
param_name4 = Button(description='Dirichlet_boundary_condition',
disabled=True,
layout=name_button_layout)
self.thanos_Dirichlet_boundary_condition = FloatText(
value=1.0, style=style, layout=widget_layout)
self.thanos_Dirichlet_boundary_condition_toggle = Checkbox(
description='on/off',
disabled=False,
style=style,
layout=widget_layout)
menv_var2 = Button(description='avenger',
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.avenger_diffusion_coefficient = FloatText(value=100000.0,
step=10000,
style=style,
layout=widget_layout)
param_name6 = Button(description='decay_rate',
disabled=True,
layout=name_button_layout)
self.avenger_decay_rate = FloatText(value=1,
step=0.1,
style=style,
layout=widget_layout)
param_name7 = Button(description='initial_condition',
disabled=True,
layout=name_button_layout)
self.avenger_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.avenger_Dirichlet_boundary_condition = FloatText(
value=1.0, style=style, layout=widget_layout)
self.avenger_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)
units_button1 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button2 = Button(description='',
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_button3 = Button(description='',
disabled=True,
layout=units_button_layout)
units_button4 = Button(description='',
disabled=True,
layout=units_button_layout)
row_thanos = [
menv_var1,
]
row1 = [
param_name1, self.thanos_diffusion_coefficient, menv_units_button1
]
row2 = [param_name2, self.thanos_decay_rate, menv_units_button2]
row3 = [param_name3, self.thanos_initial_condition, units_button1]
row4 = [
param_name4, self.thanos_Dirichlet_boundary_condition,
units_button2, self.thanos_Dirichlet_boundary_condition_toggle
]
row_avenger = [
menv_var2,
]
row5 = [
param_name5, self.avenger_diffusion_coefficient, menv_units_button5
]
row6 = [param_name6, self.avenger_decay_rate, menv_units_button6]
row7 = [param_name7, self.avenger_initial_condition, units_button3]
row8 = [
param_name8, self.avenger_Dirichlet_boundary_condition,
units_button4, self.avenger_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_thanos = Box(children=row_thanos, 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_avenger = Box(children=row_avenger, 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_thanos,
box1,
box2,
box3,
box4,
box_avenger,
box5,
box6,
box7,
box8,
box9,
box10,
])
def __init__(
self,
path=os.getcwd(),
filename='',
title='',
select_desc='Select',
change_desc='Change',
show_hidden=False,
select_default=False,
use_dir_icons=False,
**kwargs
):
"""Initialize FileChooser object."""
self._default_path = path.rstrip(os.path.sep)
self._default_filename = filename
self._selected_path = None
self._selected_filename = None
self._show_hidden = show_hidden
self._select_desc = select_desc
self._change_desc = change_desc
self._callback = None
self._use_dir_icons = use_dir_icons
# Widgets
self._pathlist = Dropdown(
description="",
layout=Layout(
width='auto',
grid_area='pathlist'
)
)
self._filename = Text(
placeholder='output filename',
layout=Layout(
width='auto',
grid_area='filename'
)
)
self._dircontent = Select(
rows=8,
layout=Layout(
width='auto',
grid_area='dircontent'
)
)
self._cancel = Button(
description='Cancel',
layout=Layout(
width='auto',
display='none'
),
)
self._cancel.button_style='danger'
self._select = Button(
description=self._select_desc,
layout=Layout(width='auto')
)
self._select.button_style='info'
self._title = HTML(
value=title
)
if title == '':
self._title.layout.display = 'none'
# Widget observe handlers
self._pathlist.observe(
self._on_pathlist_select,
names='value'
)
self._dircontent.observe(
self._on_dircontent_select,
names='value'
)
self._filename.observe(
self._on_filename_change,
names='value'
)
self._select.on_click(self._on_select_click)
self._cancel.on_click(self._on_cancel_click)
# Selected file label
self._label = HTML(
value=self._LBL_TEMPLATE.format(
self._LBL_NOFILE,
'black'
),
placeholder='',
description=''
)
# Layout
self._gb = GridBox(
children=[
self._pathlist,
self._filename,
self._dircontent
],
layout=Layout(
display='none',
width='500px',
grid_gap='0px 0px',
grid_template_rows='auto auto',
grid_template_columns='60% 40%',
grid_template_areas='''
'pathlist filename'
'dircontent dircontent'
'''
)
)
buttonbar = HBox(
children=[
self._select,
self._cancel,
self._label
],
layout=Layout(width='auto')
)
# Call setter to set initial form values
self._set_form_values(
self._default_path,
self._default_filename
)
# Use the defaults as the selected values
if select_default:
self._apply_selection()
# Call VBox super class __init__
super().__init__(
children=[
self._title,
self._gb,
buttonbar,
],
layout=Layout(width='auto'),
**kwargs
)
def annotate(examples,
example_labels=None,
options=None,
shuffle=False,
include_skip=True,
display_fn=display):
"""
Build an interactive widget for annotating a list of input examples.
Parameters
----------
examples: list(any), list of items to annotate
example_labels: list(string), if examples are one large numpy array
options: list(any) or tuple(start, end, [step]) or None
if list: list of labels for binary classification task (Dropdown or Buttons)
if tuple: range for regression task (IntSlider or FloatSlider)
if None: arbitrary text input (TextArea)
shuffle: bool, shuffle the examples before annotating
include_skip: bool, include option to skip example while annotating
display_fn: func, function for displaying an example to the user
Returns
-------
annotations : list of tuples, list of annotated examples (example, label)
"""
examples = list(examples)
use_example_labels = True
if example_labels is None:
use_example_labels = False
example_labels = examples
if shuffle:
ind_shuff = np.arange(len(examples))
random.shuffle(ind_shuff)
examples = examples[ind_shuff]
example_labels = example_labels[ind_shuff]
annotations = []
current_index = -1
def set_label_text():
nonlocal count_label
count_label.value = '{} examples annotated, {} examples left'.format(
len(annotations),
len(examples) - current_index)
def show_next():
nonlocal current_index
current_index += 1
set_label_text()
if current_index >= len(examples):
for btn in buttons:
btn.disabled = True
print('Annotation done.')
return
with out:
clear_output(wait=True)
display_fn(examples[current_index])
def add_annotation(annotation):
annotations.append((example_labels[current_index], annotation))
show_next()
def skip(btn):
show_next()
count_label = HTML()
set_label_text()
display(count_label)
if type(options) == list:
task_type = 'classification'
elif type(options) == tuple and len(options) in [2, 3]:
task_type = 'regression'
elif options is None:
task_type = 'captioning'
else:
raise Exception('Invalid options')
buttons = []
if task_type == 'classification':
use_dropdown = len(options) > 5
if use_dropdown:
dd = Dropdown(options=options)
display(dd)
btn = Button(description='submit')
def on_click(btn):
add_annotation(dd.value)
btn.on_click(on_click)
buttons.append(btn)
else:
for label in options:
btn = Button(description=label)
def on_click(label, btn):
add_annotation(label)
btn.on_click(functools.partial(on_click, label))
buttons.append(btn)
elif task_type == 'regression':
target_type = type(options[0])
if target_type == int:
cls = IntSlider
else:
cls = FloatSlider
if len(options) == 2:
min_val, max_val = options
slider = cls(min=min_val, max=max_val)
else:
min_val, max_val, step_val = options
slider = cls(min=min_val, max=max_val, step=step_val)
display(slider)
btn = Button(description='submit')
def on_click(btn):
add_annotation(slider.value)
btn.on_click(on_click)
buttons.append(btn)
else:
ta = Textarea()
display(ta)
btn = Button(description='submit')
def on_click(btn):
add_annotation(ta.value)
btn.on_click(on_click)
buttons.append(btn)
if include_skip:
btn = Button(description='skip')
btn.on_click(skip)
buttons.append(btn)
box = HBox(buttons)
display(box)
out = Output()
display(out)
show_next()
return annotations
'g61': g61
})
import warnings
warnings.filterwarnings("ignore")
return display(VBox([yyy, ww, w8, out6]))
def inputs():
taxonomia_cargada = pd.read_csv('tax_file.tsv', sep='\t').fillna('NA')
return taxonomia_cargada
import tkinter as tk
from tkinter import filedialog
yyy = Button(layout=Layout(width='94%', height='5px'), disabled=True)
yyy.style.button_color = 'red'
xxx = Button(layout=Layout(width='94%', height='5px'), disabled=True)
xxx.style.button_color = 'white'
upload_tax = widgets.Checkbox(description='Upload file',
value=False,
disabled=False)
def file_tax(upload_tax):
if upload_tax == True:
root = tk.Tk()
root.withdraw()
root.attributes("-topmost", True)
file_path = filedialog.askopenfilename()
root.destroy()
def __init__(self, description, task_name):
self.description = description
self.task_name = task_name
self.button = Button(description=description)
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,
])
