value=0.0,
description=r'$k_z$',
continuous_update=False)
Nk_path_slider = widgets.IntSlider(min=5,
max=50,
step=5,
value=10,
description=r'$N_k$',
continuous_update=False)
Nk_FS_slider = widgets.IntSlider(min=5,
max=50,
step=5,
value=10,
description=r'$N_{FS}$',
continuous_update=False)
reset_button = widgets.Button(description="Reset")
def reset_values(b):
ui.children[1].children[2].value = 10
ui.children[1].children[1].value = 10
ui.children[0].children[0].value = 0.0
ui.children[0].children[1].value = 0.0
ui.children[0].children[2].value = 1.0
ui.children[0].children[3].value = 1.0
ui.children[1].children[0].value = 0.0
reset_button.on_click(reset_values)
out = widgets.interactive_output(
def true_false(option_1, bool_1, option_2, bool_2, option_3, bool_3, option_4,
bool_4, button_text_1, button_text_2):
#Convert string to HTMLMath so equations can be displayed
TF_question_1 = widgets.HTMLMath(value=option_1)
TF_question_2 = widgets.HTMLMath(value=option_2)
TF_question_3 = widgets.HTMLMath(value=option_3)
TF_question_4 = widgets.HTMLMath(value=option_4)
#Create true and false bottons
button1_1 = widgets.Button(description=button_text_1)
button1_2 = widgets.Button(description=button_text_2)
button2_1 = widgets.Button(description=button_text_1)
button2_2 = widgets.Button(description=button_text_2)
button3_1 = widgets.Button(description=button_text_1)
button3_2 = widgets.Button(description=button_text_2)
button4_1 = widgets.Button(description=button_text_1)
button4_2 = widgets.Button(description=button_text_2)
button1_1.style.button_color = 'Whitesmoke'
button1_2.style.button_color = 'Whitesmoke'
button2_1.style.button_color = 'Whitesmoke'
button2_2.style.button_color = 'Whitesmoke'
button3_1.style.button_color = 'Whitesmoke'
button3_2.style.button_color = 'Whitesmoke'
button4_1.style.button_color = 'Whitesmoke'
button4_2.style.button_color = 'Whitesmoke'
#Display buttons in front of each question
container1 = widgets.HBox(children=[button1_1, button1_2, TF_question_1])
container2 = widgets.HBox(children=[button2_1, button2_2, TF_question_2])
container3 = widgets.HBox(children=[button3_1, button3_2, TF_question_3])
container4 = widgets.HBox(children=[button4_1, button4_2, TF_question_4])
#Place true or false questions in an array so they can be shuffled
containers = [container1, container2, container3, container4]
random.shuffle(containers)
#Reassign containers and display
container1 = containers[0]
container2 = containers[1]
container3 = containers[2]
container4 = containers[3]
display(container1, container2, container3, container4)
print(" ", end='\r')
def on_button1_1_clicked(b):
if bool_1 == True:
print("Correct! ", end='\r')
button1_1.style.button_color = 'Moccasin'
button1_2.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button1_1.style.button_color = 'Lightgray'
button1_2.style.button_color = 'Whitesmoke'
def on_button1_2_clicked(b):
if bool_1 == False:
print("Correct! ", end='\r')
button1_1.style.button_color = 'Whitesmoke'
button1_2.style.button_color = 'Moccasin'
else:
print("Try again.", end='\r')
button1_1.style.button_color = 'Whitesmoke'
button1_2.style.button_color = 'Lightgray'
def on_button2_1_clicked(b):
if bool_2 == True:
print("Correct! ", end='\r')
button2_1.style.button_color = 'Moccasin'
button2_2.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button2_1.style.button_color = 'Lightgray'
button2_2.style.button_color = 'Whitesmoke'
def on_button2_2_clicked(b):
if bool_2 == False:
print("Correct! ", end='\r')
button2_1.style.button_color = 'Whitesmoke'
button2_2.style.button_color = 'Moccasin'
else:
print("Try again.", end='\r')
button2_1.style.button_color = 'Whitesmoke'
button2_2.style.button_color = 'Lightgray'
def on_button3_1_clicked(b):
if bool_3 == True:
print("Correct! ", end='\r')
button3_1.style.button_color = 'Moccasin'
button3_2.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button3_1.style.button_color = 'Lightgray'
button3_2.style.button_color = 'Whitesmoke'
def on_button3_2_clicked(b):
if bool_3 == False:
print("Correct! ", end='\r')
button3_1.style.button_color = 'Whitesmoke'
button3_2.style.button_color = 'Moccasin'
else:
print("Try again.", end='\r')
button3_1.style.button_color = 'Whitesmoke'
button3_2.style.button_color = 'Lightgray'
def on_button4_1_clicked(b):
if bool_4 == True:
print("Correct! ", end='\r')
button4_1.style.button_color = 'Moccasin'
button4_2.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button4_1.style.button_color = 'Lightgray'
button4_2.style.button_color = 'Whitesmoke'
def on_button4_2_clicked(b):
if bool_4 == False:
print("Correct! ", end='\r')
button4_1.style.button_color = 'Whitesmoke'
button4_2.style.button_color = 'Moccasin'
else:
print("Try again.", end='\r')
button4_1.style.button_color = 'Whitesmoke'
button4_2.style.button_color = 'Lightgray'
button1_1.on_click(on_button1_1_clicked)
button1_2.on_click(on_button1_2_clicked)
button2_1.on_click(on_button2_1_clicked)
button2_2.on_click(on_button2_2_clicked)
button3_1.on_click(on_button3_1_clicked)
button3_2.on_click(on_button3_2_clicked)
button4_1.on_click(on_button4_1_clicked)
button4_2.on_click(on_button4_2_clicked)
if choice == 0:
edge_list = self.tests.free_edges
elif choice == 1:
edge_list = self._class_positive_set(
random.choice(list(self.extractor.classes)))
edge = random.choice(edge_list)
self.current_case = edge
classes = self.extractor.extract(edge)
for cla in self.extractor.classes:
self.class_to_check[cla].value = cla in classes
with self.output:
self.output.clear_output()
print(self.tests.edge_to_text[edge])
print()
print(str(edge))
def run(self, case=None, keywords=None):
self.propose_case(case=case, keywords=keywords)
checks_box = widgets.HBox(self.checkboxes)
button = widgets.Button(description='Add Case')
buttons_box = widgets.HBox([button])
def button_callback(b):
classes = set(cla for cla in self.extractor.classes
if self.class_to_check[cla].value)
self.tests.add_case(self.current_case, classes)
self.propose_case(keywords=keywords)
button.on_click(button_callback)
return widgets.VBox([self.output, checks_box, buttons_box])
def status(self, ohlcvs):
"""Strategy list widgets.
Choose which strategy to implement on widgets GUI.
Args:
ohlcvs: A dataframe of symbol.
Returns:
widget GUI
"""
import ipywidgets as widgets
ret = pd.DataFrame()
full_results = []
for method in self._trading_methods:
for symbol in method.symbols:
ohlcv = ohlcvs[(symbol, method.freq)]
result = method.strategy.backtest(ohlcv,
method.variables, filters=method.filters, freq=method.freq)
ret[method.name + '-' + symbol + '-' + method.freq] = result.cumulative_returns
weight_btc = method.weight_btc
if isinstance(weight_btc, dict):
weight_btc = (weight_btc[symbol]
if symbol in weight_btc else weight_btc['default'])
full_results.append({
'name': method.name,
'symbol': symbol,
'freq': method.freq,
'weight': weight_btc,
'portfolio': result,
'trading_method': method,
'signal': result.cash().iloc[-1] == 0,
})
method_dropdown = widgets.Dropdown(options=[m.name + '-' + str(i) for i, m in enumerate(self._trading_methods)])
symbol_dropdown = widgets.Dropdown(options=[symbol + '-' + freq for symbol, freq in ohlcvs.keys()])
backtest_btn = widgets.Button(description='status')
backtest_panel = widgets.Output()
option_panel = widgets.Output()
def plotly_df(df):
"""Display plot.
"""
# Plot
fig = px.line()
for sname, s in df.items():
fig.add_scatter(x=s.index, y=s.values, name=sname) # Not what is desired - need a line
# fig.show()
@backtest_panel.capture(clear_output=True)
def backtest(_):
"""Display single strategy backtest result.
"""
method_id = int(method_dropdown.value.split('-')[-1])
history_id = tuple(symbol_dropdown.value.split('-'))
ohlcv = ohlcvs[history_id]
strategy = self._trading_methods[method_id].strategy
svars = self._trading_methods[method_id].variables
filters = self._trading_methods[method_id].filters
strategy.backtest(ohlcv, variables=svars, filters=filters, freq=history_id[-1], plot=True)
backtest_btn.on_click(backtest)
dropdowns = widgets.HBox([method_dropdown, symbol_dropdown, backtest_btn])
with option_panel:
plotly_df(ret)
display(pd.DataFrame(full_results))
return widgets.VBox([option_panel, dropdowns, backtest_panel])
global nonosol, n, nonostate, sol_n
nonostate = get_nono(change["new"])
n = Nonogram(nonostate)
nonosol = a_star_search(n)
#print(nonosol)
def rhchange(change):
global rhsol, b, rhstate, sol_b
rhstate = get_rh(change["new"])
b = RushHour(rhstate)
rhsol = a_star_search(b, gac=False)
#print(rhsol)
dropnono.observe(nonochange, names="value")
droprh.observe(rhchange, names="value")
button = widgets.Button(description="Replay Rush Hour-solution")
nonobutton = widgets.Button(description="Replay Nonogram-solution")
def on_button_clicked(button):
sol_b = RushHour(rhstate)
for s in rhsol:
sol_b.set_state(s)
time.sleep(0.1)
#print(rhsol)
def on_nonobutton_clicked(button):
sol_n = Nonogram(nonostate)
for s in nonosol:
sol_n.set_state(s)
sol_n.display_state()
time.sleep(0.1)
def rotation_example():
#from plotly.offline import init_notebook_mode, iplot, plot
#from ipywidgets import HBox
import plotly.graph_objs as go
#import numpy as np
#import random
from math import radians, cos, sin, sqrt, tan, atan
import ipywidgets as widgets
from IPython.display import Markdown, display, clear_output, HTML
#init_notebook_mode(connected=True)
square_clicked4 = True
triangle_clicked4 = False
clockwise_rotation = True
counterclockwise_rotation = False
current_point = 0
square_button4 = widgets.Button(
description='Square',
disabled=False,
button_style='success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Click me',
)
triangle_button4 = widgets.Button(
description='Triangle',
disabled=False,
button_style='', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Click me',
)
rotation_choice = widgets.Dropdown(
options=[('', 0), ('Point A', 1), ('Point B', 2), ('Point C', 3),
('Point D', 4), ('Point E', 5), ('Origin', 6)],
value=0,
description='',
)
clockwise_button = widgets.Button(
description='Clockwise',
disabled=False,
button_style='success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Click me',
)
counterclockwise_button = widgets.Button(
description='Counter-Clockwise',
disabled=False,
button_style='', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Click me',
)
text_widget4 = widgets.HTML("<strong>Object: </strong>")
text2_widget4 = widgets.HTML("<strong>Rotation Direction: </strong>")
text3_widget4 = widgets.HTML("<strong>Rotation Point: </strong>")
choice_widget4 = widgets.HBox(
children=[text_widget4, square_button4, triangle_button4])
rotation_widget4 = widgets.HBox(
children=[text2_widget4, clockwise_button, counterclockwise_button])
point_widget4 = widgets.HBox(children=[text3_widget4, rotation_choice])
input_widget4 = widgets.VBox(
children=[choice_widget4, rotation_widget4, point_widget4])
rotation_choice.layout.width = '150px'
def rotation(p):
point = p
data4 = []
data4.append(
dict(visible=True,
line=dict(color='#00FF00', width=3),
mode='lines+markers+text',
name='Original',
hoverinfo='x+y',
text=['A', 'B', 'C', 'D', ''],
textposition='top left',
textfont=dict(color='#ff0000'),
x=[1, 1, 4, 4, 1],
y=[1, 4, 4, 1, 1]))
data4.append(
dict(visible=True,
line=dict(color='#00CED1', width=3),
mode='lines+markers+text',
name='Translation',
hoverinfo='x+y',
text=['A', 'B', 'C', 'D', ''],
textposition='top left',
textfont=dict(color='#ff0000'),
x=[1, 1, 4, 4, 1],
y=[1, 4, 4, 1, 1]))
temp_degrees = 0
rotationX = 0
rotationY = 0
x0 = 0
x1 = 0
x2 = 0
x3 = 0
y0 = 0
y1 = 0
y2 = 0
y3 = 0
steps4 = []
steps5 = []
for i in range(37):
temp_degrees = radians((36 - i) * 10)
if (point == 1):
rotationX = 1
rotationY = 1
x0 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (1 - rotationY)**2))
y0 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (1 - rotationY)**2))
x1 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (4 - rotationY)**2))
y1 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (4 - rotationY)**2))
x2 = rotationX + cos(temp_degrees + atan(
(4 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(4 - rotationY)**2))
y2 = rotationY + sin(temp_degrees + atan(
(4 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(4 - rotationY)**2))
x3 = rotationX + cos(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
y3 = rotationY + sin(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
elif (point == 2):
rotationX = 1
rotationY = 4
x0 = rotationX + cos(temp_degrees - 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (1 - rotationY)**2))
y0 = rotationY + sin(temp_degrees - 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (1 - rotationY)**2))
x1 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (4 - rotationY)**2))
y1 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (4 - rotationY)**2))
x2 = rotationX + cos(temp_degrees + atan(
(4 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(4 - rotationY)**2))
y2 = rotationY + sin(temp_degrees + atan(
(4 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(4 - rotationY)**2))
x3 = rotationX + cos(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
y3 = rotationY + sin(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
elif (point == 3):
rotationX = 4
rotationY = 4
x0 = rotationX - cos(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
y0 = rotationY - sin(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
x1 = rotationX - cos(temp_degrees + atan(
(4 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(4 - rotationY)**2))
y1 = rotationY - sin(temp_degrees + atan(
(4 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(4 - rotationY)**2))
x2 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (4 - rotationY)**2))
y2 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (4 - rotationY)**2))
x3 = rotationX + cos(temp_degrees - 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (1 - rotationY)**2))
y3 = rotationY + sin(temp_degrees - 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (1 - rotationY)**2))
elif (point == 4):
rotationX = 4
rotationY = 1
x0 = rotationX - cos(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
y0 = rotationY - sin(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
x1 = rotationX - cos(temp_degrees + atan(
(4 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(4 - rotationY)**2))
y1 = rotationY - sin(temp_degrees + atan(
(4 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(4 - rotationY)**2))
x2 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (4 - rotationY)**2))
y2 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (4 - rotationY)**2))
x3 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (1 - rotationY)**2))
y3 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (1 - rotationY)**2))
elif (point == 5):
rotationX = (4 - 1) / 2 + 1
rotationY = (4 - 1) / 2 + 1
x0 = rotationX - cos(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
y0 = rotationY - sin(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
x1 = rotationX - cos(temp_degrees + atan(
(4 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(4 - rotationY)**2))
y1 = rotationY - sin(temp_degrees + atan(
(4 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(4 - rotationY)**2))
x2 = rotationX + cos(temp_degrees + atan(
(4 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(4 - rotationY)**2))
y2 = rotationY + sin(temp_degrees + atan(
(4 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(4 - rotationY)**2))
x3 = rotationX + cos(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
y3 = rotationY + sin(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
elif (point == 6):
rotationX = 0
rotationY = 0
tempX = rotationX + cos(temp_degrees + atan(
(2.5 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(2.5 - rotationY)**2))
tempY = rotationY + sin(temp_degrees + atan(
(2.5 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(2.5 - rotationY)**2))
x0T = tempX - 1.5
y0T = tempY - 1.5
x1T = tempX - 1.5
y1T = tempY + 1.5
x2T = tempX + 1.5
y2T = tempY + 1.5
x3T = tempX + 1.5
y3T = tempY - 1.5
rotationX = tempX
rotationY = tempY
x0 = rotationX - cos(temp_degrees + atan(
(y0T - rotationY) /
(x0T - rotationX))) * (sqrt((x0T - rotationX)**2 +
(y0T - rotationY)**2))
y0 = rotationY - sin(temp_degrees + atan(
(y0T - rotationY) /
(x0T - rotationX))) * (sqrt((x0T - rotationX)**2 +
(y0T - rotationY)**2))
x1 = rotationX - cos(temp_degrees + atan(
(y1T - rotationY) /
(x1T - rotationX))) * (sqrt((x1T - rotationX)**2 +
(y1T - rotationY)**2))
y1 = rotationY - sin(temp_degrees + atan(
(y1T - rotationY) /
(x1T - rotationX))) * (sqrt((x1T - rotationX)**2 +
(y1T - rotationY)**2))
x2 = rotationX + cos(temp_degrees + atan(
(y2T - rotationY) /
(x2T - rotationX))) * (sqrt((x2T - rotationX)**2 +
(y2T - rotationY)**2))
y2 = rotationY + sin(temp_degrees + atan(
(y2T - rotationY) /
(x2T - rotationX))) * (sqrt((x2T - rotationX)**2 +
(y2T - rotationY)**2))
x3 = rotationX + cos(temp_degrees + atan(
(y3T - rotationY) /
(x3T - rotationX))) * (sqrt((x3T - rotationX)**2 +
(y3T - rotationY)**2))
y3 = rotationY + sin(temp_degrees + atan(
(y3T - rotationY) /
(x3T - rotationX))) * (sqrt((x3T - rotationX)**2 +
(y3T - rotationY)**2))
step = dict(method='update',
args=[{
'x[0]': [1, x0],
'x[1]': [1, x1],
'x[2]': [4, x2],
'x[3]': [4, x3],
'x[4]': [1, x0],
'y[0]': [1, y0],
'y[1]': [4, y1],
'y[2]': [4, y2],
'y[3]': [1, y3],
'y[4]': [1, y0]
}],
label=str(i * 10) + "°")
steps4.append(step)
step2 = dict(method='update',
args=[{
'x[0]': [1, x0],
'x[1]': [1, x1],
'x[2]': [4, x2],
'x[3]': [4, x3],
'x[4]': [1, x0],
'y[0]': [1, y0],
'y[1]': [4, y1],
'y[2]': [4, y2],
'y[3]': [1, y3],
'y[4]': [1, y0]
}],
label=str((36 - i) * 10) + "°")
steps5.insert(0, step2)
if (clockwise_rotation):
sliders4 = [
dict(active=0,
currentvalue={
"prefix": "Clockwise Rotation: ",
},
pad={"t": 35},
steps=steps4)
]
else:
sliders4 = [
dict(active=0,
currentvalue={
"prefix": "Counter-Clockwise Rotation: ",
},
pad={"t": 35},
steps=steps5)
]
title = ''
if (point == 1):
title = 'Rotation about Point A'
elif (point == 2):
title = 'Rotation about Point B'
elif (point == 3):
title = 'Rotation about Point C'
elif (point == 4):
title = 'Rotation about Point D'
elif (point == 5):
title = 'Rotation about Point E'
elif (point == 6):
title = 'Rotation about the Origin'
layout4 = go.Layout(
title=title,
sliders=sliders4,
showlegend=False,
hovermode='closest',
yaxis=dict(
title='',
ticklen=5,
dtick=1,
gridwidth=2,
range=[-10, 10],
showgrid=True,
),
xaxis=dict(
title='',
ticklen=5,
dtick=1,
gridwidth=2,
range=[-10, 10],
showgrid=True,
),
autosize=True,
#width=750,
height=725,
annotations=[
dict(
x=1.0,
y=-0.10,
showarrow=False,
text='X Axis',
xref='paper',
yref='paper',
font=dict(size=14, ),
),
dict(
x=-0.06,
y=1.0,
showarrow=False,
text='Y Axis',
textangle=-90,
xref='paper',
yref='paper',
font=dict(size=14, ),
),
],
)
fig4 = dict(data=data4, layout=layout4)
if (not (point == 0)):
clear_output()
display(Markdown("<img src='images/pointplot2.png' align='left'>"))
display(input_widget4)
iplot(fig4, filename='filename')
def rotationT(p):
pointT = p
dataT4 = []
dataT4.append(
dict(visible=True,
line=dict(color='#00FF00', width=3),
mode='lines+markers+text',
name='Original',
hoverinfo='x+y',
text=['A', 'B', 'C', ''],
textposition='top left',
textfont=dict(color='#ff0000'),
x=[1, 2.5, 4, 1],
y=[1, 4, 1, 1]))
dataT4.append(
dict(visible=True,
line=dict(color='#00CED1', width=3),
mode='lines+markers+text',
name='Rotation',
hoverinfo='x+y',
text=['A', 'B', 'C', ''],
textposition='top left',
textfont=dict(color='#ff0000'),
x=[1, 2.5, 4, 1],
y=[1, 4, 1, 1]))
temp_degrees = 0
rotationX = 0
rotationY = 0
xT0 = 0
xT1 = 0
xT2 = 0
yT0 = 0
yT1 = 0
yT2 = 0
stepsT4 = []
stepsT5 = []
for i in range(37):
temp_degrees = radians((36 - i) * 10)
if (pointT == 1):
rotationX = 1
rotationY = 1
xT0 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (1 - rotationY)**2))
yT0 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(1 - rotationX)**2 + (1 - rotationY)**2))
xT1 = rotationX + cos(temp_degrees + atan(
(4 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(4 - rotationY)**2))
yT1 = rotationY + sin(temp_degrees + atan(
(4 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(4 - rotationY)**2))
xT2 = rotationX + cos(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
yT2 = rotationY + sin(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
elif (pointT == 2):
rotationX = 2.5
rotationY = 4
xT0 = rotationX - cos(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
yT0 = rotationY - sin(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
xT1 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(2.5 - rotationX)**2 + (4 - rotationY)**2))
yT1 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(2.5 - rotationX)**2 + (4 - rotationY)**2))
xT2 = rotationX + cos(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
yT2 = rotationY + sin(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
elif (pointT == 3):
rotationX = 4
rotationY = 1
xT0 = rotationX - cos(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
yT0 = rotationY - sin(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
xT1 = rotationX - cos(temp_degrees + atan(
(4 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(4 - rotationY)**2))
yT1 = rotationY - sin(temp_degrees + atan(
(4 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(4 - rotationY)**2))
xT2 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (1 - rotationY)**2))
yT2 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(4 - rotationX)**2 + (1 - rotationY)**2))
elif (pointT == 4):
rotationX = (4 - 1) / 2 + 1
rotationY = (4 - 1) / 2 + 1
xT0 = rotationX - cos(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
yT0 = rotationY - sin(temp_degrees + atan(
(1 - rotationY) /
(1 - rotationX))) * (sqrt((1 - rotationX)**2 +
(1 - rotationY)**2))
xT1 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(2.5 - rotationX)**2 + (4 - rotationY)**2))
yT1 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(2.5 - rotationX)**2 + (4 - rotationY)**2))
xT2 = rotationX + cos(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
yT2 = rotationY + sin(temp_degrees + atan(
(1 - rotationY) /
(4 - rotationX))) * (sqrt((4 - rotationX)**2 +
(1 - rotationY)**2))
elif (pointT == 5):
rotationX = 0
rotationY = 0
tempTX = rotationX + cos(temp_degrees + atan(
(2.5 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(2.5 - rotationY)**2))
tempTY = rotationY + sin(temp_degrees + atan(
(2.5 - rotationY) /
(2.5 - rotationX))) * (sqrt((2.5 - rotationX)**2 +
(2.5 - rotationY)**2))
xT0T = tempTX - 1.5
yT0T = tempTY - 1.5
xT1T = tempTX
yT1T = tempTY + 1.5
xT2T = tempTX + 1.5
yT2T = tempTY - 1.5
rotationX = tempTX
rotationY = tempTY
xT0 = rotationX - cos(temp_degrees + atan(
(yT0T - rotationY) /
(xT0T - rotationX))) * (sqrt((xT0T - rotationX)**2 +
(yT0T - rotationY)**2))
yT0 = rotationY - sin(temp_degrees + atan(
(yT0T - rotationY) /
(xT0T - rotationX))) * (sqrt((xT0T - rotationX)**2 +
(yT0T - rotationY)**2))
xT1 = rotationX + cos(temp_degrees + 1.5707963268) * (sqrt(
(xT1T - rotationX)**2 + (yT1T - rotationY)**2))
yT1 = rotationY + sin(temp_degrees + 1.5707963268) * (sqrt(
(xT1T - rotationX)**2 + (yT1T - rotationY)**2))
xT2 = rotationX + cos(temp_degrees + atan(
(yT2T - rotationY) /
(xT2T - rotationX))) * (sqrt((xT2T - rotationX)**2 +
(yT2T - rotationY)**2))
yT2 = rotationY + sin(temp_degrees + atan(
(yT2T - rotationY) /
(xT2T - rotationX))) * (sqrt((xT2T - rotationX)**2 +
(yT2T - rotationY)**2))
step = dict(method='update',
args=[{
'x[0]': [1, xT0],
'x[1]': [2.5, xT1],
'x[2]': [4, xT2],
'x[3]': [1, xT0],
'y[0]': [1, yT0],
'y[1]': [4, yT1],
'y[2]': [1, yT2],
'y[3]': [1, yT0]
}],
label=str(i * 10) + "°")
stepsT4.append(step)
step2 = dict(method='update',
args=[{
'x[0]': [1, xT0],
'x[1]': [2.5, xT1],
'x[2]': [4, xT2],
'x[3]': [1, xT0],
'y[0]': [1, yT0],
'y[1]': [4, yT1],
'y[2]': [1, yT2],
'y[3]': [1, yT0]
}],
label=str((36 - i) * 10) + "°")
stepsT5.insert(0, step2)
if (clockwise_rotation):
slidersT4 = [
dict(active=0,
currentvalue={
"prefix": "Clockwise Rotation: ",
},
pad={"t": 35},
steps=stepsT4)
]
else:
slidersT4 = [
dict(active=0,
currentvalue={
"prefix": "Counter-Clockwise Rotation: ",
},
pad={"t": 35},
steps=stepsT5)
]
title = ''
if (pointT == 1):
title = 'Rotation about Point A'
elif (pointT == 2):
title = 'Rotation about Point B'
elif (pointT == 3):
title = 'Rotation about Point C'
elif (pointT == 4):
title = 'Rotation about Point D'
elif (pointT == 5):
title = 'Rotation about the Origin'
layoutT4 = go.Layout(
title=title,
sliders=slidersT4,
showlegend=False,
hovermode='closest',
yaxis=dict(
title='',
ticklen=5,
dtick=1,
gridwidth=2,
range=[-10, 10],
showgrid=True,
),
xaxis=dict(
title='',
ticklen=5,
dtick=1,
gridwidth=2,
range=[-10, 10],
showgrid=True,
),
autosize=True,
#width=750,
height=725,
annotations=[
dict(
x=1.0,
y=-0.10,
showarrow=False,
text='X Axis',
xref='paper',
yref='paper',
font=dict(size=14, ),
),
dict(
x=-0.06,
y=1.0,
showarrow=False,
text='Y Axis',
textangle=-90,
xref='paper',
yref='paper',
font=dict(size=14, ),
),
],
)
figT4 = dict(data=dataT4, layout=layoutT4)
if (not (pointT == 0)):
clear_output()
display(Markdown("<img src='images/pointplot4.png' align='left'>"))
display(input_widget4)
iplot(figT4, filename='filename')
def graph_rotation(change):
global current_point
current_point = change.new
if (square_clicked4):
rotation(change.new)
elif (triangle_clicked4):
rotationT(change.new)
def square_update4(change):
global square_clicked4
global triangle_clicked4
if (not (square_clicked4)):
square_clicked4 = True
triangle_clicked4 = False
square_button4.button_style = 'success'
triangle_button4.button_style = ''
rotation_choice.options = [('', 0), ('Point A', 1), ('Point B', 2),
('Point C', 3), ('Point D', 4),
('Point E', 5), ('Origin', 6)]
rotation_choice.value = 0
clear_output()
display(Markdown("<img src='images/pointplot2.png' align='left'>"))
display(input_widget4)
def triangle_update4(change):
global square_clicked4
global triangle_clicked4
if (not (triangle_clicked4)):
triangle_clicked4 = True
square_clicked4 = False
square_button4.button_style = ''
triangle_button4.button_style = 'success'
rotation_choice.options = options = [('', 0), ('Point A', 1),
('Point B', 2),
('Point C', 3),
('Point D', 4), ('Origin', 5)]
rotation_choice.value = 0
clear_output()
display(Markdown("<img src='images/pointplot4.png' align='left'>"))
display(input_widget4)
def clockwise_update(change):
global clockwise_rotation
global counterclockwise_rotation
global current_point
if (not (clockwise_rotation)):
clockwise_rotation = True
counterclockwise_rotation = False
clockwise_button.button_style = "success"
counterclockwise_button.button_style = ""
clear_output()
if (square_clicked4):
display(
Markdown("<img src='images/pointplot2.png' align='left'>"))
if (current_point == 0):
display(input_widget4)
rotation(current_point)
else:
display(
Markdown("<img src='images/pointplot4.png' align='left'>"))
if (current_point == 0):
display(input_widget4)
rotationT(current_point)
def counterclockwise_update(change):
global clockwise_rotation
global counterclockwise_rotation
global current_point
if (not (counterclockwise_rotation)):
clockwise_rotation = False
counterclockwise_rotation = True
clockwise_button.button_style = ""
counterclockwise_button.button_style = "success"
clear_output()
if (square_clicked4):
display(
Markdown("<img src='images/pointplot2.png' align='left'>"))
if (current_point == 0):
display(input_widget4)
rotation(current_point)
else:
display(
Markdown("<img src='images/pointplot4.png' align='left'>"))
if (current_point == 0):
display(input_widget4)
rotationT(current_point)
square_button4.on_click(square_update4)
triangle_button4.on_click(triangle_update4)
clockwise_button.on_click(clockwise_update)
counterclockwise_button.on_click(counterclockwise_update)
rotation_choice.observe(graph_rotation, names='value')
display(Markdown("<img src='images/pointplot2.png' align='left'>"))
display(input_widget4)
rotation(0)
def __init__(self, file):
self.filename = file
self.noMaterials = 0
self.noObjects = 0
self.matAll = []
self.objAll = []
self.widgetList = []
self.objectList = []
self.wfList = []
self.wfAll = []
self.srcAll = []
self.rcAll = []
self.goList = []
self.goAll = []
self.rem = []
self.accNames = [
'Space', 'Materials', 'Objects', 'Source/Receiver',
'Geometry Output'
]
self.add_mat = wd.Button(value=False,
description='Add material',
disabled=False)
self.widgetList = [
self.add_mat,
wd.Label('free_space : Built-in identifier for air',
layout=wd.Layout(width='30%',
margin='-35px 0px 0px 200px')),
wd.Label(
'pec : Built-in identifier for a perfect electric conductor',
layout=wd.Layout(width='50%', margin='-10px 0px 10px 200px'))
]
self.add_obj = wd.Button(value=False,
description='Add object',
disabled=False)
self.rem_obj = wd.Button(value=False,
description='Remove last object',
disabled=False)
self.objectList = [
wd.HBox([self.add_obj, self.rem_obj],
layout=wd.Layout(margin='10px 0px 20px 0px'))
]
self.wrFile = wd.Button(value=False,
description='Write input file',
disabled=False,
layout=wd.Layout(height='30px',
width='40%',
margin='10px 0px 20px 20px'))
self.dd = [
wd.Dropdown(options=[
' ', 'Edge', 'Plate', 'Triangle', 'Box', 'Sphere', 'Cylinder'
],
description='Object {}:'.format(i + 1),
disabled=False,
layout=wd.Layout(margin='20px 0px 10px -20px'))
for i in range(20)
]
self.ddwf = wd.Dropdown(options=[
' ', 'gaussian', 'gaussiandot', 'gaussiandotnorm',
'gaussiandotdot', 'gaussiandotdotnorm', 'ricker', 'gaussianprime',
'gaussiandoubleprime', 'sine', 'contsine'
],
description='Waveform: ',
disabled=False,
layout=wd.Layout(width='23%',
margin='2px 5px 10px 0px'))
self.ddsrc = wd.Dropdown(options=[
' ', 'hertzian_dipole', 'voltage_source', 'magnetic_dipole'
],
description='Source: ',
disabled=False,
layout=wd.Layout(width='23%',
margin='2px 5px 10px 0px'))
self.dom = [wd.Text(layout=wd.Layout(width='15%')) for i in range(3)]
self.sp = [wd.Text(layout=wd.Layout(width='15%')) for i in range(3)]
self.time_window = wd.Text(layout=wd.Layout(width='15%'))
self.title = wd.Text(layout=wd.Layout(width='50%'))
self.msg = wd.Text(layout=wd.Layout(width='15%'))
self.intRes = wd.Text(
layout=wd.Layout(width='11%', margin='10px 0px 0px 0px'))
self.wfAll.append(
[wd.Text(layout=wd.Layout(width='15%')) for i in range(3)])
self.srcAll.append(
[wd.Text(layout=wd.Layout(width='13%')) for i in range(4)])
self.rcAll.append(
[wd.Text(layout=wd.Layout(width='13%')) for i in range(3)])
self.steps = [wd.Text(layout=wd.Layout(width='15%')) for i in range(6)]
self.goAll.append(
[wd.Text(layout=wd.Layout(width='13%')) for i in range(9)])
self.goAll[0].append(wd.Text(layout=wd.Layout(width='25%')))
self.spaceList = [
wd.HBox([
wd.Label('Title: ', layout=wd.Layout(width='20%')), self.title
]),
wd.HBox([
wd.Label('', layout=wd.Layout(width='25%')),
wd.Label('X', layout=wd.Layout(width='15%')),
wd.Label('Y', layout=wd.Layout(width='15%')),
wd.Label('Z', layout=wd.Layout(width='15%'))
]),
wd.HBox([
wd.Label('Domain: ', layout=wd.Layout(width='20%')),
self.dom[0], self.dom[1], self.dom[2]
]),
wd.HBox([
wd.Label('', layout=wd.Layout(width='25%')),
wd.Label('dx', layout=wd.Layout(width='15%')),
wd.Label('dy', layout=wd.Layout(width='15%')),
wd.Label('dz', layout=wd.Layout(width='15%'))
]),
wd.HBox([
wd.Label('Spacing: ', layout=wd.Layout(width='20%')),
self.sp[0], self.sp[1], self.sp[2]
]),
wd.HBox([
wd.Label('Time Window: ', layout=wd.Layout(width='20%')),
self.time_window
]),
wd.HBox([
wd.Label('Messages(y/n): ', layout=wd.Layout(width='20%')),
self.msg
])
]
self.propLabels = wd.HBox([
wd.Label('', layout=wd.Layout(width='10%')),
wd.Label('Relative Permittivity', layout=wd.Layout(width='15%')),
wd.Label('\t\t\tConductivity', layout=wd.Layout(width='15%')),
wd.Label('Relative Permeability', layout=wd.Layout(width='15%')),
wd.Label('Magnetic Loss', layout=wd.Layout(width='15%')),
wd.Label('Name', layout=wd.Layout(width='25%'))
])
self.srList = [
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='12%')),
wd.Label('Type', layout=wd.Layout(width='11.5%')),
wd.Label('Scaling of max amplitude',
layout=wd.Layout(width='17%')),
wd.Label('Center frequency', layout=wd.Layout(width='17%')),
wd.Label('Name', layout=wd.Layout(width='5%'))
],
layout=wd.Layout(margin='10px 0px 10px 0px')),
wd.HBox([
self.ddwf, self.wfAll[0][0], self.wfAll[0][1], self.wfAll[0][2]
]),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='12%')),
wd.Label('Type', layout=wd.Layout(width='11%')),
wd.Label('Polarization (x,y or z)',
layout=wd.Layout(width='19%')),
wd.Label('X', layout=wd.Layout(width='12%')),
wd.Label('Y', layout=wd.Layout(width='13%')),
wd.Label('Z', layout=wd.Layout(width='15%')),
],
layout=wd.Layout(margin='10px 0px 10px 0px')),
wd.HBox([
self.ddsrc, self.srcAll[0][0], self.srcAll[0][1],
self.srcAll[0][2], self.srcAll[0][3]
]),
wd.HBox([
wd.Label(
'If voltage source specify internal resistance (Ohm):',
layout=wd.Layout(width='30%', margin='10px 0px 0px 87px')),
self.intRes
]),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='14%')),
wd.Label('X', layout=wd.Layout(width='13%')),
wd.Label('Y', layout=wd.Layout(width='12%')),
wd.Label('Z', layout=wd.Layout(width='9%'))
],
layout=wd.Layout(margin='10px 0px 0px 0px')),
wd.HBox([
wd.Label('Receiver: ',
layout=wd.Layout(width='6.2%',
margin='0px 0px 20px 25px')),
self.rcAll[0][0], self.rcAll[0][1], self.rcAll[0][2]
]),
wd.HBox([
wd.Label(
'For B-scan specify increments to move sources and receivers:',
layout=wd.Layout(width='40%', margin='10px 0px 0px 5px'))
]),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='17%')),
wd.Label('x', layout=wd.Layout(width='15%')),
wd.Label('y', layout=wd.Layout(width='15%')),
wd.Label('z', layout=wd.Layout(width='15%'))
]),
wd.HBox([
wd.Label('Source steps: ', layout=wd.Layout(width='10%')),
self.steps[0], self.steps[1], self.steps[2]
]),
wd.HBox([
wd.Label('Receiver steps: ', layout=wd.Layout(width='10%')),
self.steps[3], self.steps[4], self.steps[5]
],
layout=wd.Layout(margin='0px 0px 20px 0px'))
]
self.goList = [
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='5%')),
wd.Label('X start', layout=wd.Layout(width='13%')),
wd.Label('Y start', layout=wd.Layout(width='13%')),
wd.Label('Z start', layout=wd.Layout(width='13%')),
wd.Label('X end', layout=wd.Layout(width='13%')),
wd.Label('Y end', layout=wd.Layout(width='13%')),
wd.Label('Z end', layout=wd.Layout(width='9%'))
],
layout=wd.Layout(margin='10px 0px 0px 0px')),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='1%')), self.goAll[0][0],
self.goAll[0][1], self.goAll[0][2], self.goAll[0][3],
self.goAll[0][4], self.goAll[0][5]
]),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='6%')),
wd.Label('dx', layout=wd.Layout(width='13%')),
wd.Label('dy', layout=wd.Layout(width='13%')),
wd.Label('dz', layout=wd.Layout(width='9%'))
],
layout=wd.Layout(margin='10px 0px 0px 0px')),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='1%')), self.goAll[0][6],
self.goAll[0][7], self.goAll[0][8]
]),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='3%')),
wd.Label('Geometry filename (no extension)',
layout=wd.Layout(width='22%'))
],
layout=wd.Layout(margin='10px 0px 0px 0px')),
wd.HBox([
wd.Label(' ', layout=wd.Layout(width='1%')), self.goAll[0][9]
],
layout=wd.Layout(margin='0px 0px 20px 0px')), self.wrFile
]
self.add_mat.on_click(self.on_button_clicked)
self.add_obj.on_click(self.on_button_clicked2)
self.rem_obj.on_click(self.on_button_clicked3)
self.wrFile.on_click(self.write_file)
[self.dd[i].observe(self.on_change, 'value') for i in range(20)]
self.gb = wd.GridBox(
children=self.spaceList,
layout=wd.Layout(grid_template_columns="repeat(1, 500px)"))
self.gb2 = wd.GridBox(
children=self.widgetList,
layout=wd.Layout(grid_template_columns="repeat(1, 900px)"))
self.gb3 = wd.GridBox(
children=self.objectList,
layout=wd.Layout(grid_template_columns="repeat(1, 1100px)"))
self.gb4 = wd.GridBox(
children=self.srList,
layout=wd.Layout(grid_template_columns="repeat(1, 1000px)"))
self.gb5 = wd.GridBox(
children=self.goList,
layout=wd.Layout(grid_template_columns="repeat(1, 900px)"))
self.acc = wd.Accordion(
children=[self.gb, self.gb2, self.gb3, self.gb4, self.gb5])
for i in range(5):
self.acc.set_title(i, self.accNames[i])
display(self.acc)
def base_path(file_path, param, base_number):
"""!@brief Display base to Jupyter notebook given a file path
This function displays the options for the base. If the @a file_path does
not exist, this function displays nothing.
@param file_path (str) Path to a file containing the 3D structure of the base molecule
@param param (dict) @a options._options_dict['Base']
@param base_number The number of the new base
@returns None; @a jupyter_widgets.input_options is modified in place
@sa upload_base
@sa input_options
@sa options._options_dict
@sa view_nglview
"""
if not os.path.isfile(file_path):
# Check if the requested file is in the "pnab/data" directory
file_path = os.path.join(__path__[0], 'data', file_path)
if not os.path.isfile(file_path):
# Unset the values for backbone parameters and return
param['linker']['default'][0] = param['linker']['default'][1] = 1
return
# Show molecule using NGLView with atom numbers
num_atoms = view_nglview(file_path, label=True)
# Display widgets for base-to-backbone connection
linker1 = widgets.Dropdown(value=param['linker']['default'][0], options=range(1, num_atoms + 1), layout=widgets.Layout(width='100px'))
linker2 = widgets.Dropdown(value=param['linker']['default'][1], options=range(1, num_atoms + 1), layout=widgets.Layout(width='100px'))
# Add help box
help_box = widgets.Button(description='?', tooltip=param['linker']['long_glossory'], layout=widgets.Layout(width='4%'))
box = widgets.HBox([help_box, widgets.Label(param['linker']['glossory'], layout={'width': '400px'}), linker1, linker2])
# Display
display(box)
# Code
code = widgets.Text(value=param['code']['default'], description=param['code']['glossory'], style={'description_width': 'initial'}, layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['code']['long_glossory'], layout=widgets.Layout(width='4%'))
box = widgets.HBox([help_box, code])
display(box)
# Name
name = widgets.Text(value=param['name']['default'], description=param['name']['glossory'], style={'description_width': 'initial'}, layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['name']['long_glossory'], layout=widgets.Layout(width='4%'))
box = widgets.HBox([help_box, name])
display(box)
# Pair name
pair_name = widgets.Text(value=param['pair_name']['default'], description=param['pair_name']['glossory'], style={'description_width': 'initial'}, layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['pair_name']['long_glossory'], layout=widgets.Layout(width='4%'))
box = widgets.HBox([help_box, pair_name])
display(box)
# Align
align = widgets.Checkbox(value=param['align']['default'], indent=False, description=param['align']['glossory'], style={'description_width': 'initial'}, layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['align']['long_glossory'], layout=widgets.Layout(width='4%'))
box = widgets.HBox([help_box, align])
display(box)
# Add widgets to the widgets dictionary
input_options['Base %i' %base_number] = {'file_path': file_path, 'linker': [linker1, linker2], 'code': code, 'name': name, 'pair_name': pair_name, 'align': align}
def helical_parameters(param):
"""
Display widgets for specifying helical parameters. It also displays an image illustrating
the used helical parameters.
@param param (dict) @a options._options_dict['HelicalParameters']
@returns None; @a jupyter_widgets.input_options is modified in place
@sa input_options
@sa display_options_widgets
@sa options._options_dict
"""
display(widgets.HTML(value='<H3>Helical Parameters</H3>'))
# Display an image showing the helical parameters for DNA and RNA
display(Image(os.path.join(__path__[0], 'images', 'helical_parameters.jpg'), width=800))
param_dict = {}
# Add widget to the widgets dictionary
input_options['HelicalParameters'] = {}
def helical_or_step(mode, param):
if mode == 'Helical':
excluded_parameters = ['shift', 'slide', 'rise', 'tilt', 'roll', 'twist']
input_options['HelicalParameters']['is_helical'] = True
else:
excluded_parameters = ['x_displacement', 'y_displacement', 'h_rise', 'inclination', 'tip', 'h_twist']
input_options['HelicalParameters']['is_helical'] = False
for k in param:
if k == 'is_helical' or k in excluded_parameters:
continue
param_dict[k] = []
default = [param[k]['default'][0], param[k]['default'][1], param[k]['default'][2]] # [beginning point, end point, number of steps]
# Set angles
if k in ['inclination', 'tip', 'h_twist', 'roll', 'tilt', 'twist', 'buckle', 'propeller', 'opening']:
param_dict[k].append(widgets.FloatRangeSlider(value=[default[0], default[1]], min=-180, max=180, step=0.01, readout_format='.2f'))
# Set distances
else: # h_rise, x-displacement, y-displacement, rise, slide, shift, stretch, shear, stagger
# limit maxium and minimum distance values to be between -20 and 20 and 0.01 Angstrom step size
param_dict[k].append(widgets.FloatRangeSlider(value=[default[0], default[1]], min=-20, max=20, step=0.01, readout_format='.3f'))
# Add the number of steps widgets
param_dict[k].append(widgets.BoundedIntText(value=default[2], min=1, max=1000, step=1, description='Steps'))
help_box = widgets.Button(description='?', tooltip=param[k]['long_glossory'], layout=widgets.Layout(width='3%'))
box = widgets.HBox([help_box, widgets.Label(param[k]['glossory'], layout={'width': '200px'}), param_dict[k][0], param_dict[k][1]])
display(box)
# Add widgets for helical parameter k to the widgets dictionary
input_options['HelicalParameters'][k] = [param_dict[k][0], param_dict[k][1]]
default = 'Helical' if param['is_helical']['default'] else 'Step'
help_box = widgets.Button(description='?', tooltip=param['is_helical']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, widgets.interactive(helical_or_step, mode=widgets.Dropdown(value=default,
options=['Helical', 'Step'],
description="Base step scheme",
style={'description_width': 'initial'},
#layout={'width': '75%'}
),
param=widgets.fixed(param))]))
def state_problem(self):
# show title and statement
super().state_problem()
# show expressions used in problem
if len(self.expression) == 1:
if type(self.expression[0] == str):
display(Markdown(self.expression[0]))
else:
display(Math(latex(self.expression[0])))
if len(self.expression) > 1:
for i in range(len(self.expression)):
if type(self.expression[i] == str):
display(
Markdown("**(" + str(i + 1) + ")** " +
self.expression[i]))
else:
display(
Math("**(" + str(i + 1) + ")** \quad" +
latex(self.expression[i])))
if self.input_widget:
# if input_widget flag is set and multiple inputs required,
# display instructions
if self.num_inputs > 1:
display(Markdown("*Separate multiple answers by comma(s).*"))
# next create text widget and button
# Setup text input field
self.input_field = widgets.Text(value='',
placeholder='Type here',
description='Answer: ',
continuous_update=False,
disabled=False)
self.input_field.observe(self.on_enter, names='value')
# Submit button
self.submit_button = widgets.Button(
description='Submit',
disabled=False,
button_style=
'success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Check answer',
)
self.submit_button.on_click(self.on_submit)
# Put widgets in box
display(widgets.Box([self.input_field, self.submit_button]))
else:
#if not, display cell instructions
display(Markdown("*Enter the answer(s) in the cell below.*"))
if self.output_widget:
# Add dedicated output area
self.out = widgets.Output()
display(self.out)
def display_gui(wti_index, corpus):
compute_callback = compute_most_discriminating_terms
display_callback = display_most_discriminating_terms
lw = lambda w: widgets.Layout(width=w)
include_pos_tags = [ 'ADJ', 'VERB', 'NUM', 'ADV', 'NOUN', 'PROPN' ]
normalize_options = {
'Lemma': spacy.attrs.LEMMA,
'Lower': spacy.attrs.LOWER,
'Orth': spacy.attrs.ORTH
}
party_preset_options = wti_index.get_party_preset_options()
parties_options = [ x for x in wti_index.get_countries_list() if x not in ['ALL', 'ALL OTHER'] ]
signed_years = { d._.meta['signed_year'] for d in corpus }
period_default = (min(signed_years), max(signed_years))
gui = types.SimpleNamespace(
progress=widgets.IntProgress(value=0, min=0, max=5, step=1, description='', layout=lw('90%')),
group1=widgets.SelectMultiple(description='Group 1', options=parties_options, value=[], rows=7, layout=lw('250px')),
group2=widgets.SelectMultiple(description='Group 2', options=parties_options, value=[], rows=7, layout=lw('250px')),
group1_preset=widgets_config.dropdown('Presets', party_preset_options, None, layout=lw('250px')),
group2_preset=widgets_config.dropdown('Presets', party_preset_options, None, layout=lw('250px')),
top_n_terms=widgets.IntSlider(description='#terms', min=10, max=1000, value=100, tooltip='The total number of most discriminating terms to return for each group'),
max_n_terms=widgets.IntSlider(description='#top', min=1, max=2000, value=2000, tooltip='Only consider terms whose document frequency is within the top # terms out of all terms'),
include_pos=widgets.SelectMultiple(description='POS', options=include_pos_tags, value=include_pos_tags, rows=7, layout=lw('150px')),
period1=widgets.IntRangeSlider(description='Period', min=period_default[0], max=period_default[1], value=period_default, layout=lw('250px')),
period2=widgets.IntRangeSlider(description='Period', min=period_default[0], max=period_default[1], value=period_default, layout=lw('250px')),
closed_region=widgets.ToggleButton(description='Closed regions', icon='check', value=True, disabled=False, layout=lw('140px')),
sync_period=widgets.ToggleButton(description='Sync period', icon='check', value=False, disabled=False, layout=lw('140px'), tooltop='HEJ'),
normalize=widgets.Dropdown(description='Normalize', options=normalize_options, value=spacy.attrs.LEMMA, layout=lw('200px')),
compute=widgets.Button(description='Compute', icon='', button_style='Success', layout=lw('120px')),
output=widgets.Output(layout={'border': '1px solid black'})
)
boxes = widgets.VBox([
widgets.HBox([
widgets.VBox([
gui.group1,
gui.group1_preset,
gui.period1
]),
widgets.VBox([
gui.group2,
gui.group2_preset,
gui.period2
]),
widgets.VBox([
gui.include_pos,
gui.closed_region,
gui.sync_period,
], layout=widgets.Layout(align_items='flex-end')),
widgets.VBox([
gui.top_n_terms,
gui.max_n_terms,
gui.normalize,
gui.compute
],layout=widgets.Layout(align_items='flex-end')), # layout=widgets.Layout(align_items='flex-end')),
# widgets.VBox([
# gui.compute,
# widgets.HTML(
# '<b>#terms</b> is the number of most discriminating<br>terms to return for each group.<br>' +
# '<b>#top</b> Consider only terms with a frequency<br>within the top #top terms out of all terms<br>'
# '<b>Closed region</b> If checked, then <u>both</u> treaty parties<br>must be within selected region'
# )
# ])
]),
gui.output
])
display(boxes)
def on_group1_preset_change(change):
if gui.group1_preset.value is None:
return
gui.group1.value = gui.group1.options if 'ALL' in gui.group1_preset.value else gui.group1_preset.value
def on_group2_preset_change(change):
if gui.group2_preset.value is None:
return
gui.group2.value = gui.group2.options if 'ALL' in gui.group2_preset.value else gui.group2_preset.value
def on_period1_change(change):
if gui.sync_period.value:
gui.period2.value = gui.period1.value
def on_period2_change(change):
if gui.sync_period.value:
gui.period1.value = gui.period2.value
gui.group1_preset.observe(on_group1_preset_change, names='value')
gui.group2_preset.observe(on_group2_preset_change, names='value')
gui.period1.observe(on_period1_change, names='value')
gui.period2.observe(on_period2_change, names='value')
def compute_callback_handler(*_args):
gui.output.clear_output()
with gui.output:
try:
gui.compute.disabled = True
df = compute_callback(
wti_index=wti_index,
corpus=corpus,
group1=gui.group1.value,
group2=gui.group2.value,
top_n_terms=gui.top_n_terms.value,
max_n_terms=gui.max_n_terms.value,
include_pos=gui.include_pos.value,
period1=gui.period1.value,
period2=gui.period2.value,
closed_region=gui.closed_region.value,
normalize=gui.normalize.value
)
if df is not None:
display_callback(df)
else:
logger.info('No data for selected groups or periods.')
except Exception as ex:
logger.error(ex)
finally:
gui.compute.disabled = False
gui.compute.on_click(compute_callback_handler)
return gui
def set_button_launcher(desc):
button = widgets.Button(
description=desc,
layout={"width": "max-content"},
)
return button
def plot(dset, **kwargs):
defaults = {'name': '', 'show_comment': False, 'show_title': True, 'auto_copy': True,
'cmap': 'plasma', 'reverse': False, 'auto_scale': True,
'offset': 0., 'xlog': False, 'ylog': False}
defaults.update(kwargs)
if isinstance(dset, xr.DataArray):
dset = xr.Dataset({dset.name:dset})
# We must use a weak reference to hdf so that it can be released properly
# when not used, since otherwise ipywidgets.interact captures all the arguments.
dset_ref = weakref.ref(dset)
data_keys = dset.data_vars.keys()
name = defaults['name']
if name not in data_keys:
name = data_keys[-1]
name_widget = ip.Dropdown(options=data_keys, description='name', value=name)
show_comment = ip.ToggleButton(description='show note', value=defaults['show_comment'])
show_title = ip.Checkbox(description='show title', value=defaults['show_title'])
auto_copy = ip.Checkbox(description='auto copy', value=defaults['auto_copy'])
comment_widget = ip.HTML(value='<pre><code>{0}</code></pre>'.format(dset.attrs.get("comment", '')))
comment_widget.layout.display = 'none'
def __show_comment_changed(change):
comment_widget.layout.display = '' if show_comment.value else 'none'
__show_comment_changed(None)
show_comment.observe(__show_comment_changed, 'value')
copy_position_button = ip.Button(description='Copy (x, y)')
copy_distance_button = ip.Button(description='Copy (dx, dy)')
copy_position_button.layout.width = copy_distance_button.layout.width = '300px'
def __copy_val(btn):
try:
text = str(btn.value).decode('utf8')
win32clipboard.OpenClipboard()
win32clipboard.EmptyClipboard()
win32clipboard.SetClipboardText(text, win32clipboard.CF_UNICODETEXT)
win32clipboard.CloseClipboard()
except: # Ignore errors
pass
copy_distance_button.on_click(__copy_val)
copy_position_button.on_click(__copy_val)
sub_widgets = []
plot_widgets = []
plot_fig = []
def _plot_2D(data, facet_dict, fname, data_label):
maps = [cm for cm in plt.colormaps() if not cm.endswith("_r")]
for k in ('magma', 'inferno', 'plasma', 'viridis'):
maps.remove(k)
maps.insert(0, k)
#maps.sort()
cmap_widget = ip.Dropdown(description='cmap', options=maps, value=defaults['cmap'])
reverse_widget = ip.Checkbox(description='reverse', value=defaults['reverse'])
robust_widget = ip.Checkbox(description='auto scale', value=defaults['auto_scale'])
min_v, max_v = np.min(data), np.max(data)
scale_widget = ip.FloatRangeSlider(min=min_v, max=max_v, step=(max_v-min_v)/100., value=(min_v, max_v), continuous_update=False)
scale_widget.layout.visibility = 'hidden'
def __robust_changed(change):
scale_widget.layout.visibility = 'hidden' if robust_widget.value else ''
robust_widget.observe(__robust_changed, 'value')
def __replot(change):
cmap = cmap_widget.value
if reverse_widget.value:
cmap += '_r'
if not facet_dict:
plt.figure(figsize=(6,4.5))
if robust_widget.value:
data.plot(cmap=cmap, robust=True, **facet_dict)
else:
min_v, max_v = scale_widget.value
data.plot(cmap=cmap, vmin=min_v, vmax=max_v, **facet_dict)
plt.gca().collections[-1].colorbar.set_label(data_label)
ws = [cmap_widget, reverse_widget, robust_widget, scale_widget]
return ws, __replot
def _plot_1D(data_list, fname, data_label):
offset_widget = ip.FloatText(description='offset', value=defaults['offset'])
def __replot(change):
offset = offset_widget.value
for i in range(len(data_list)):
(data_list[i] + offset * i).plot()
plt.ylabel(data_label)
ws = [offset_widget]
return ws, __replot
def _update_plot(change):
if plot_widgets:
plot_widgets.pop().close()
dset = dset_ref()
facets = []
idx = []
for c in sub_widgets[0].children:
if c.value == 'facet':
facets.append(len(idx))
idx.append(slice(None))
else:
idx.append(c.value)
data = dset[name_widget.value][tuple(idx)]
faceted_dims = len(data.shape) - len(facets)
if faceted_dims > 2 and len(facets) < 2:
for i in range(len(data.shape)):
if i not in facets:
facets.append(i)
faceted_dims -= 1
if faceted_dims == 2 or len(facets) == 2:
break
try:
units = dset[name_widget.value].units
data_label = '{0} ({1})'.format(name_widget.value, units)
except:
data_label = name_widget.value
fname = dset.attrs.get('filename', '')
if faceted_dims == 2: # 2D plot
facet_dict = {}
if facets:
facet_dict['col'] = data.dims[facets[-1]]
if len(facets) == 2:
facet_dict['row'] = data.dims[facets[0]]
widgets, plot_func = _plot_2D(data, facet_dict, fname, data_label)
else: # Make stacked line plots
s = list(data.shape)
i = len(s) - 1
while i > 0:
if i not in facets:
break
i -= 1
s[i] = 1
dl = []
for idx in np.ndindex(tuple(s)):
j = list(idx)
j[i] = slice(None)
dl.append(data[tuple(j)])
widgets, plot_func = _plot_1D(dl, fname, data_label)
xscale_widget = ip.Checkbox(description='xlog', value=defaults['xlog'])
yscale_widget = ip.Checkbox(description='ylog', value=defaults['ylog'])
padding_widget = ip.FloatSlider(description='pad', min=0., max=1.0, step=0.1, value=0.2, continuous_update=False)
widgets.extend([xscale_widget, yscale_widget, padding_widget])
def __plot_wrapper(change):
if plot_fig:
plt.close(plot_fig.pop())
clear_output(wait=True)
plot_func(change)
fig = plt.gcf()
plot_fig.append(fig)
if show_title.value:
fig.suptitle(fname, fontsize=16, y=1.02)
# Workaround for tha lack of png transparency support in Windows
fig.patch.set_facecolor('white')
fig.patch.set_alpha(1.0)
if xscale_widget.value:
plt.gca().set_xscale('log')
if yscale_widget.value:
plt.gca().set_yscale('log')
# Adjust axis formatters
for ax in fig.axes:
for xyax in [ax.xaxis, ax.yaxis]:
if type(xyax.get_major_formatter()) == ScalarFormatter:
fmt = ScalarFormatter(useMathText=True, useOffset=False)
fmt.set_powerlimits((-3, 3))
xyax.set_major_formatter(fmt)
cid = []
prev_clicked = [0, 0]
def __adjust(event):
# Adjust figure padding to accomodate the suptitle and axis labels
# Call this only once after the figure is displayed
fig.canvas.mpl_disconnect(cid[0])
bb = fig.bbox_inches.padded(padding_widget.value)
adjust_bbox(fig, bb)
fig.set_size_inches(bb.bounds[2], bb.bounds[3], forward=True)
if auto_copy.value:
copy2clipboard(fig, pad_inches=padding_widget.value)
def __clicked(event):
copy_position_button.value = (event.xdata, event.ydata)
copy_position_button.description = 'Copy (x,y)=(%f,%f)' % copy_position_button.value
copy_distance_button.value = (event.xdata - prev_clicked[0], event.ydata - prev_clicked[1])
copy_distance_button.description = 'Copy (dx,dy)=(%f,%f)' % copy_distance_button.value
prev_clicked[0] = event.xdata
prev_clicked[1] = event.ydata
cid.append(fig.canvas.mpl_connect('draw_event', __adjust))
fig.canvas.mpl_connect('button_press_event', __clicked)
for w in widgets:
w.observe(__plot_wrapper, 'value')
plot_widgets.append(ip.HBox(widgets))
display(plot_widgets[0])
__plot_wrapper(None)
def _update(change):
if sub_widgets:
sub_widgets.pop().close()
dset = dset_ref()
index_widgets = []
for dim in dset[name_widget.value].dims:
coord = dset[name_widget.value].coords[dim]
indexes = OrderedDict({':': slice(None)})
indexes['facet'] = 'facet'
for i in range(len(coord)):
indexes[float(coord[i])] = i
drop = ip.Dropdown(description=dim, options=indexes)
drop.observe(_update_plot, 'value')
index_widgets.append(drop)
sub_widgets.append(ip.HBox(index_widgets))
display(sub_widgets[0])
_update_plot(None)
for w in [name_widget, show_title]:
w.observe(_update, 'value')
display(comment_widget)
display(ip.HBox([name_widget, show_comment, show_title, auto_copy]))
_update(None)
display(ip.HBox([copy_position_button, copy_distance_button]))
for key, column_names in columns.items():
visible = key in selections
for c in column_names:
try:
glyphs[c].visible = visible
except AttributeError:
for glyph in glyphs[c]:
glyph.visible = visible
push_notebook(handle=pn)
##
next_store = widgets.Button(
description='Next store',
disabled=False,
button_style='info', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Click me',
icon='check')
store_text = widgets.Text(value=str(stores.min() - 1),
placeholder='Type something',
description='Store:',
disabled=False)
def update_store_text(*args):
s = int(store_text.value)
if s < stores.max():
store_text.value = str(s + 1)
def polynomial_regression():
"""Polynomial regression example"""
regression_config = {"degree": 1}
sc_x = LinearScale(min=-100, max=100)
sc_y = LinearScale(min=-100, max=100)
scat = Scatter(
x=[], y=[], scales={"x": sc_x, "y": sc_y}, colors=["orange"], enable_move=True
)
lin = Lines(
x=[], y=[], scales={"x": sc_x, "y": sc_y}, line_style="dotted", colors=["blue"]
)
def update_line(change=None):
if len(scat.x) == 0 or len(scat.y) == 0 or scat.x.shape != scat.y.shape:
lin.x = []
lin.y = []
return
pipe = make_pipeline(
PolynomialFeatures(degree=regression_config["degree"]), LinearRegression()
)
pipe.fit(scat.x.reshape(-1, 1), scat.y)
with lin.hold_sync():
if len(lin.x) == 0:
lin.x = np.linspace(sc_x.min, sc_x.max)
lin.y = pipe.predict(np.linspace(sc_x.min, sc_x.max).reshape(-1, 1))
update_line()
# update line on change of x or y of scatter
scat.observe(update_line, names=["x", "y"])
with scat.hold_sync():
scat.enable_move = False
scat.interactions = {"click": "add"}
ax_x = Axis(scale=sc_x, tick_format="0.0f", label="x")
ax_y = Axis(scale=sc_y, tick_format="0.0f", orientation="vertical", label="y")
fig = Figure(marks=[scat, lin], axes=[ax_x, ax_y])
# reset reset_button
reset_button = widgets.Button(description="Reset")
def on_button_clicked(change=None):
with scat.hold_sync():
scat.x = []
scat.y = []
dropdown_w.value = None
reset_button.on_click(on_button_clicked)
# polynomial degree slider
degree = widgets.IntSlider(
value=regression_config["degree"], min=1, max=5, step=1, description="Degree"
)
def degree_change(change):
regression_config["degree"] = change["new"]
update_line()
degree.observe(degree_change, names="value")
# dropdown for dataset selection
dropdown_w = widgets.Dropdown(
options=fake_datasets(ndim=2), value=None, description="Dataset:"
)
def dropdown_on_change(change):
if change["type"] == "change" and change["name"] == "value":
if change["new"] is not None:
x, y = fake_datasets(name=change["new"])
with scat.hold_sync():
scat.x = x.flatten()
scat.y = y.flatten()
dropdown_w.observe(dropdown_on_change)
return VBox(
(
widgets.HTML("<h1>Polynomial regression</h1>"),
reset_button,
dropdown_w,
degree,
fig,
)
)
def algorithm(chosen_algorithm, param):
"""!@brief Display search parameters based on the chosen algorithm
There are six search algorithms and each one has a set of input parameters.
The search algorithms are:
- Systematic Search: Requires specifying the dihedral angle step size, @a dihedral_step.
- Monte Carlo Search: Requires specifying the number of steps, @a num_steps,
and the Monte Carlo temperature, @a monte_carlo_temperature.
- Weighted Monte Carlo Search: Also requires specifying the weighting temperature, @a weighting_temperature.
- Random Search: Requires specifying the number of steps, @a num_steps.
- Weighted Random Search: Also requires specifying the weighting temperature, @a weighting_temperature.
- Genetic Algorithm Search: Requires specifying the number of generations, @a num_steps,
the population size, @a population_size, the mutation_rate, @a mutation_rate,
and the crossover rate, @a crossover_rate.
@param chosen_algorithm (str) The chosen algorithm
@param param (dict) @a options._options_dict['RuntimeParameters']
@returns None; @a jupyter_widgets.input_options is modified in place
@sa runtime_parameters
@sa input_options
@sa options._options_dict
"""
chosen_algorithm = chosen_algorithm.lower()
# Add widget to the widgets dictionary
input_options['RuntimeParameters']['search_algorithm'] = chosen_algorithm
# Systematic search algorithm needs a dihedral step size
if chosen_algorithm == 'systematic search':
dihedral_step = widgets.BoundedFloatText(value=param['dihedral_step']['default'],
min=0.0,
max=360.0,
description=param['dihedral_step']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['dihedral_step']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, dihedral_step]))
input_options['RuntimeParameters']['dihedral_step'] = dihedral_step
# The other five algorithms require specifying the random number seed and the number of steps or generation
else:
# Random number generator seed
seed = widgets.BoundedIntText(value=param['seed']['default'], min=0, max=2**32-1,
description=param['seed']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['seed']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, seed]))
input_options['RuntimeParameters']['seed'] = seed
# Number of steps or generations
num_steps = widgets.BoundedIntText(value=param['num_steps']['default'], min=1, max=1e100,
description=param['num_steps']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['num_steps']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, num_steps]))
input_options['RuntimeParameters']['num_steps'] = num_steps
# If the algorithm weights the dihedral angle probability profile, we need to specify the temperature
# used in the weighting
if "weighted" in chosen_algorithm:
weighting_temperature = widgets.BoundedFloatText(value=param['weighting_temperature']['default'], min=1, max=1e100,
description=param['weighting_temperature']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['weighting_temperature']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, weighting_temperature]))
input_options['RuntimeParameters']['weighting_temperature'] = weighting_temperature
# Specify the temperature for the Monte Carlo procedure
if "monte carlo search" in chosen_algorithm:
monte_carlo_temperature = widgets.BoundedFloatText(value=param['monte_carlo_temperature']['default'], min=1, max=1e100,
description=param['monte_carlo_temperature']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['monte_carlo_temperature']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, monte_carlo_temperature]))
input_options['RuntimeParameters']['monte_carlo_temperature'] = monte_carlo_temperature
# Specify population size, mutation rate, and crossover rate for genetic algorithm
if 'genetic algorithm search' in chosen_algorithm:
population_size = widgets.BoundedIntText(value=param['population_size']['default'], min=1, max=1e100,
description=param['population_size']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['population_size']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, population_size]))
input_options['RuntimeParameters']['population_size'] = population_size
mutation_rate = widgets.BoundedFloatText(value=param['mutation_rate']['default'], min=0, max=1,
description=param['mutation_rate']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['mutation_rate']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, mutation_rate]))
input_options['RuntimeParameters']['mutation_rate'] = mutation_rate
crossover_rate = widgets.BoundedFloatText(value=param['crossover_rate']['default'], min=0, max=1,
description=param['crossover_rate']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['crossover_rate']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, crossover_rate]))
input_options['RuntimeParameters']['crossover_rate'] = crossover_rate
import ipywidgets as widgets
from IPython.display import display, HTML
button = widgets.Button(description="Submit Solution")
name_box = widgets.Text(value='', description='Name:')
email_box = widgets.Text(value='', description='Email:')
js = """
<script>
alert('asdf');
function findCellsByTag(tagName) {
return Jupyter.notebook.get_cells().filter(
({metadata: {tags}}) => tags && tags.includes(tagName));
}
</script>
"""
display(HTML(js))
def on_clicked(b):
name = name_box.value
email = email_box.value
print(name, email)
js = """
<script>
console.log('here');
var submit_cell = findCellsByTag('code')[0];
var text = submit_cell.get_text();
alert(text);
</script>
"""
display(HTML(js))
def runtime_parameters(param):
"""!@brief Runtime parameter widget for use in Jupyter notebook
Displays widgets for specifying runtime parameters.
@param param (dict) @a options._options_dict['RuntimeParameters']
@returns None; @a jupyter_widgets.input_options is modified in place
@sa algorithm
@sa input_options
@sa display_options_widgets
@sa options._options_dict
"""
display(widgets.HTML(value='<H3>Runtime Parameters</H3>'))
input_options['RuntimeParameters'] = {}
# Search algorithm
display(widgets.HTML(value='<H4>Search Algorithm</H4>'))
dropdown = widgets.Dropdown(value=param['search_algorithm']['default'].title(),
options=['Weighted Monte Carlo Search', 'Monte Carlo Search', 'Weighted Random Search', 'Random Search', 'Genetic Algorithm Search', 'Systematic Search'],
description=param['search_algorithm']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
search_algorithm = widgets.interactive_output(algorithm, {'chosen_algorithm':dropdown, 'param':widgets.fixed(param)})
help_box = widgets.Button(description='?', tooltip=param['search_algorithm']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, dropdown]))
display(search_algorithm)
# Maximum number of accepted candidates
num_candidates = widgets.BoundedIntText(value=param['num_candidates']['default'], min=1, max=2**32-1,
description=param['num_candidates']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['num_candidates']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, num_candidates]))
input_options['RuntimeParameters']['num_candidates'] = num_candidates
display(widgets.HTML(value='<H4>Distance and Energy Thresholds</H4>'))
# Distance and energy thresholds
# Threshold for the distance
max_distance = widgets.BoundedFloatText(value=param['max_distance']['default'], min=0.0,
description=param['max_distance']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['max_distance']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, max_distance]))
input_options['RuntimeParameters']['max_distance'] = max_distance
# Force field
ff_type = widgets.Dropdown(value=param['ff_type']['default'], options=['GAFF', 'MMFF94', 'MMFF94s', 'UFF', 'GHEMICAL'],
description=param['ff_type']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['ff_type']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, ff_type]))
input_options['RuntimeParameters']['ff_type'] = ff_type
# Energy filters
input_options['RuntimeParameters']['energy_filter'] = []
for i in range(5):
minimum = 0 if i < 3 else -1e10 # Put the minimum value to zero for bonded terms
label = param['energy_filter']['glossory'].split('\n')[i]
energy_filter = widgets.BoundedFloatText(value=param['energy_filter']['default'][i], min=minimum, max=1e10,
description=label,
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['energy_filter']['long_glossory'].split('\n')[i], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, energy_filter]))
input_options['RuntimeParameters']['energy_filter'].append(energy_filter)
display(widgets.HTML(value='<H4>Structural Parameters</H4>'))
# Base sequence
strand = widgets.Text(value=''.join(param['strand']['default']),
description=param['strand']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['strand']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, strand]))
input_options['RuntimeParameters']['strand'] = strand
# Pair adenine with uracil? Default is A-T base pair
pair_A_U = widgets.Checkbox(value=param['pair_A_U']['default'], indent=False,
description=param['pair_A_U']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['pair_A_U']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, pair_A_U]))
input_options['RuntimeParameters']['pair_A_U'] = pair_A_U
# Is hexad
is_hexad = widgets.Checkbox(value=param['is_hexad']['default'], indent=False,
description=param['is_hexad']['glossory'],
style={'description_width': 'initial'},
layout={'width': '75%'})
help_box = widgets.Button(description='?', tooltip=param['is_hexad']['long_glossory'], layout=widgets.Layout(width='3%'))
display(widgets.HBox([help_box, is_hexad]))
input_options['RuntimeParameters']['is_hexad'] = is_hexad
# Build strand
input_options['RuntimeParameters']['build_strand'] = []
help_box = widgets.Button(description='?', tooltip=param['build_strand']['long_glossory'], layout=widgets.Layout(width='3%'))
box = [help_box, widgets.Label(param['build_strand']['glossory'])]
for i in range(6):
build_strand = widgets.Checkbox(value=param['build_strand']['default'][i], indent=False, layout={'width': '50px'})
input_options['RuntimeParameters']['build_strand'].append(build_strand)
box.append(build_strand)
box = widgets.HBox(box, layout={'width':'100%'})
display(box)
# Orientation of each strand in the hexad
input_options['RuntimeParameters']['strand_orientation'] = []
help_box = widgets.Button(description='?', tooltip=param['strand_orientation']['long_glossory'], layout=widgets.Layout(width='3%'))
box = [help_box, widgets.Label(param['strand_orientation']['glossory'])]
for i in range(6):
strand_orientation = widgets.Checkbox(value=param['strand_orientation']['default'][i], indent=False, layout={'width': '50px'})
input_options['RuntimeParameters']['strand_orientation'].append(strand_orientation)
box.append(strand_orientation)
box = widgets.HBox(box, layout={'width':'100%'})
display(box)
def render_create_interface(cloud_list, cloud_index):
service = cloud_list[cloud_index]
if not service.check_setup():
instances = []
else:
instances = service.get_instances_info()
group_list = ["Create Group"]
for instance in instances:
group_name = instance['Group Name']
if group_name not in group_list and group_name != '':
group_list.append(group_name)
group_list.sort(key=str.lower)
group_dropdown = widgets.Dropdown(
options=group_list,
description="Group: ",
)
new_group_text = widgets.Text(value='',
placeholder='New Group Name',
disabled=False)
def on_change(change):
if (group_dropdown.value == "Create Group"):
new_group_text.disabled = False
else:
new_group_text.disabled = True
group_dropdown.observe(on_change)
name_row_arr = [group_dropdown, new_group_text]
name_row = widgets.HBox(name_row_arr)
size_list = service.get_size_list()
value = service.get_default_size()
size_dropdown = widgets.Dropdown(
options=size_list,
description="Size: ",
value=value,
)
num_instances = widgets.BoundedIntText(value=1,
min=1,
max=20,
step=1,
description='How Many?',
disabled=False)
create_button = widgets.Button(description='Create Instance')
def create_button_clicked(b):
if (new_group_text.value == ''
and group_dropdown.value == 'Create Group'):
print("Please enter a group name")
else:
# def create_instance(self,group,size,region):
group = group_dropdown.value
if (group == "Create Group"):
group = new_group_text.value
service.create_instance(group, size_dropdown.value,
num_instances.value)
create_button.on_click(create_button_clicked)
size_region_row = [size_dropdown, num_instances]
sr_row = widgets.HBox(size_region_row)
if service.check_setup():
display(name_row)
display(sr_row)
display(create_button)
else:
fn = "./src/plugins/" + service.name + "Service/" + service.name + "Setup.txt"
html_as_str = open(fn, 'r').read()
setup = widgets.HTML(value=html_as_str)
display(setup)
def display_options_widgets(param, input_file, uploaded=False):
"""!@brief Display all widgets in Jupyter notebook given an input file
If @a input_file is provided, then it updates the default options in
@a options._options_dict to display the user-defined options. If @a
input_file is "Upload file", then an ipywidgets.FileUpload widget is displayed.
This function also displays a widget for running the program after the
user defines all the options.
@param param (dict) @a options._options_dict
@param input_file (str) Input file
@param uploaded (bool) Whether a file is uploaded by the user or not
@returns None
@sa backbone
@sa bases
@sa helical_parameters
@sa runtime_parameters
@sa upload_input
@sa run
@sa user_input_file
@sa options._options_dict
"""
if input_file == "Upload file":
# Display a widget for uploading input file
w = widgets.interactive(upload_input, param=widgets.fixed(param), f=widgets.FileUpload(accept='', multiple=False, description="Input File"))
help_box = widgets.Button(description='?', tooltip='Upload your input file here. The file will be copied to the current folder.', layout=widgets.Layout(width='4%'))
display(widgets.HBox([help_box, w]))
return
# If the file is not uploaded, then we are using one of the example files
# in the pnab/data directory
if not uploaded:
input_file = os.path.join(__path__[0], 'data', input_file)
options = yaml.load(open(input_file, 'r'), yaml.FullLoader)
# Clean dictionary from additional bases if they are not defined in the options
# This is necessary when the user switches from an input file that has additional bases to one that does not
num_defined_bases = len([k for k in param if 'Base' in k]) - 1 # Subtract the item from the main options
for i in range(1, num_defined_bases + 1):
param.pop('Base %i' %i)
input_options.pop('Base %i' %i)
# Update the default options to display those provided by the user
for k1, v1 in options.items():
if 'Base' in k1:
param[k1] = copy.deepcopy(param['Base'])
for k2, v2 in options[k1].items():
param[k1][k2]['default'] = options[k1][k2]
# Display all options widgets
backbone(param['Backbone'])
bases_param = {k:val for k, val in param.items() if 'Base' in k}
bases(bases_param)
helical_parameters(param['HelicalParameters'])
runtime_parameters(param['RuntimeParameters'])
# Display run widget
button = widgets.Button(description='Run', tooltip='Click here to run the program with the provided options. Once the program finishes, the results will be displayed below.')
button.on_click(run)
display(button)
start_func=run_sim_func,
done_func=run_done_func,
cachename='pc4cancerimmune',
showcache=False,
outcb=outcb)
else:
if (hublib_flag):
run_button = RunCommand(start_func=run_sim_func,
done_func=run_done_func,
cachename='pc4cancerimmune',
showcache=False,
outcb=outcb)
else:
run_button = widgets.Button(
description='Run',
button_style=
'success', # 'success', 'info', 'warning', 'danger' or ''
tooltip='Run a simulation',
)
run_button.on_click(run_button_cb)
if nanoHUB_flag or hublib_flag:
read_config = widgets.Dropdown(
description='Load Config',
options=get_config_files(),
tooltip='Config File or Previous Run',
)
read_config.style = {
'description_width': '%sch' % str(len(read_config.description) + 1)
}
read_config.observe(read_config_cb, names='value')
from __future__ import print_function
import ipywidgets as widgets
from IPython.display import display
button = widgets.Button(description="Tip resonance shape")
display(button)
def on_button_clicked(b):
print(
"[SWE] Titta på https://en.wikipedia.org/wiki/Resonance_(particle_physics)"
)
print(
"[ENG] Check out https://en.wikipedia.org/wiki/Resonance_(particle_physics)"
)
button.on_click(on_button_clicked)
# In[2]:
import ipywidgets as widgets
from IPython.display import display
# In[3]:
#Basic styling
# In[4]:
button = widgets.Button(
description='Hello World!',
width=100, # Integers are interpreted as pixel measurements.
height='2em', # em is valid HTML unit of measurement.
color='lime', # Colors can be set by name,
background_color='#0022FF', # and also by color code.
border_color='cyan')
display(button)
# In[5]:
#Parent/child relationships
# In[6]:
from IPython.display import display
float_range = widgets.FloatSlider()
string = widgets.Text(value='hi')
def create_ui(self):
# Create the active UI components. Height and width are specified in 'em' units. This is
# a html size specification, size relative to current font size.
self.viewing_checkbox = widgets.RadioButtons(
description='Mode:',
options=['edit', 'drag', 'rotate'],
value='edit')
self.viewing_checkbox.observe(self.draw_centroid)
self.noise_button = widgets.Button(description='Add Noise',
width='7em',
height='3em')
self.noise_button.on_click(self.noise)
self.outlier_button = widgets.Button(description='Add Outlier',
width='7em',
height='3em')
self.outlier_button.on_click(self.outlier)
self.bias1_button = widgets.Button(description='Bias (FRE<TRE)',
width='7em',
height='3em')
self.bias1_button.on_click(self.bias_1)
self.bias2_button = widgets.Button(description='Bias (FRE>TRE)',
width='7em',
height='3em')
self.bias2_button.on_click(self.bias_2)
self.clear_fiducial_button = widgets.Button(
description='Clear Fiducials', width='7em', height='3em')
self.clear_fiducial_button.on_click(self.clear_fiducials)
self.clear_target_button = widgets.Button(description='Clear Targets',
width='7em',
height='3em')
self.clear_target_button.on_click(self.clear_targets)
self.reset_button = widgets.Button(description='Reset',
width='7em',
height='3em')
self.reset_button.on_click(self.reset_indexes)
self.register_button = widgets.Button(description='Register',
width='7em',
height='3em')
self.register_button.on_click(self.register)
# Layout of UI components. This is pure ugliness because we are not using a UI toolkit. Layout is done
# using the box widget and padding so that the visible UI components are spaced nicely.
bx0 = widgets.Box(padding=2, children=[self.viewing_checkbox])
bx1 = widgets.Box(padding=15, children=[self.noise_button])
bx2 = widgets.Box(padding=15, children=[self.outlier_button])
bx3 = widgets.Box(padding=15, children=[self.bias1_button])
bx4 = widgets.Box(padding=15, children=[self.bias2_button])
bx5 = widgets.Box(padding=15, children=[self.clear_fiducial_button])
bx6 = widgets.Box(padding=15, children=[self.clear_target_button])
bx7 = widgets.Box(padding=15, children=[self.reset_button])
bx8 = widgets.Box(padding=15, children=[self.register_button])
return widgets.HBox(children=[
bx0,
widgets.VBox(children=[
widgets.HBox([bx1, bx2, bx3, bx4]),
widgets.HBox(children=[bx5, bx6, bx7, bx8])
])
])
import ipywidgets as widgets
from pytube import YouTube
from IPython.display import display
text=widgets.Label("Youtube Downloader")
Link=widgets.Text(placeholder="Enter the Link here",description='Link')
Button=widgets.Button(description='HQ VIDEO',icon='fa-youtube-square') #font_awesome is used for the icon
Button1=widgets.Button(description='AUDIO',icon='fa-music')
display(text,Link,Button,Button1)
def Download_Video(a):
link=str(Link.value)
obj=YouTube(link)
video=obj.streams.filter(progressive=True,file_extension='mp4')
for mp4 in video:
video.get_highest_resolution().download(output_path="#path need to be saved") #getting highest resolution
print("Downloaded Succesfully in path")
def Download_Audio(a):
link=str(Link.value)
obj=YouTube(link)
obj.streams.get_audio_only().download(output_path="#path need to be saved") #getting only auido
print("Downloaded Succesfully in path")
Button.on_click(Download_Video)
Button1.on_click(Download_Audio)
def _make_widgets(self):
self._main_label = widgets.HTML("<b>PyDSS Data Viewer</b>")
text_layout_long = widgets.Layout(width="400px")
text_layout_med = widgets.Layout(width="200px")
text_layout_short = widgets.Layout(width="100px")
button_layout = widgets.Layout(width="200px")
path = "" if self._defaults[
"project_path"] is None else self._defaults["project_path"]
self._project_path_text = widgets.Text(
path,
description="Project Path",
layout=text_layout_long,
placeholder="pydss_projects/project1/",
)
self._load_project_btn = widgets.Button(description="Load project",
layout=button_layout)
self._load_project_btn.on_click(self._on_load_project_click)
self._scenario_label = widgets.HTML("Scenario", layout=text_layout_med)
self._elem_class_label = widgets.HTML("Element Class",
layout=text_layout_med)
self._elem_prop_label = widgets.HTML("Element Property",
layout=text_layout_med)
self._prop_available_options_label = widgets.HTML("Options")
self._prop_options_label = widgets.HTML("Element Property Options",
layout=text_layout_med)
self._num_elems_label = widgets.HTML("Number of Elements",
layout=text_layout_med)
self._elem_regex_label = widgets.HTML("Element Name Regex",
layout=text_layout_med)
self._start_time_label = widgets.HTML("Start Time",
layout=text_layout_med)
self._end_time_label = widgets.HTML("End Time", layout=text_layout_med)
self._resolution_label = widgets.HTML("Resolution",
layout=text_layout_med)
self._moving_avg_cb = widgets.Checkbox(value=False,
description="Moving Average",
disabled=True)
self._window_label = widgets.HTML("Moving Average Window",
layout=text_layout_med)
self._window_text = widgets.Text(value="4")
self._scenario_dd = widgets.Dropdown(
options=self._scenario_names,
value=self._scenario_names[0],
disabled=True,
)
self._scenario_dd.observe(self._on_scenario_change, names="value")
self._elem_class_dd = widgets.Dropdown(
options=self._element_classes,
value=self._element_classes[0],
disabled=True,
)
self._elem_class_dd.observe(self._on_elem_class_change, names="value")
self._elem_prop_dd = widgets.Dropdown(
options=self._element_props,
value=self._element_props[0],
disabled=True,
)
self._elem_prop_dd.observe(self._on_elem_prop_change, names="value")
self._prop_available_options_text = widgets.Text(disabled=True)
self._prop_options_text = widgets.Text(disabled=True)
self._num_elems_text = widgets.Text(disabled=True)
self._elem_regex_text = widgets.Text(disabled=True,
placeholder="p1udt.*")
self._elem_names_select = widgets.SelectMultiple(
options=[""],
value=[""],
rows=5,
description="Elements",
disabled=True,
)
self._start_time_text = widgets.Text(disabled=True)
self._end_time_text = widgets.Text(disabled=True)
self._resolution_text = widgets.Text(disabled=True)
self._load_dataframe_btn = widgets.Button(
description="Load DataFrame",
layout=button_layout,
disabled=True,
tooltip="Load DataFrame into `app.df`",
)
self._load_dataframe_btn.on_click(self._on_load_dataframe_click)
self._plot_btn = widgets.Button(description="Plot",
layout=button_layout)
self._plot_btn.on_click(self._on_plot_click)
self._aggregation_label = widgets.HTML("Aggregation",
layout=text_layout_short)
self._aggregation_dd = widgets.Dropdown(
options=["None", "Min/Mean/Max", "Sum"],
value="None",
disabled=True,
)
self._real_only_cb = widgets.Checkbox(
value=True, description="Exclude imaginary parts", disabled=True)
self._reset_btn = widgets.Button(description="Reset",
layout=button_layout)
self._reset_btn.on_click(self._on_reset_click)
self._plot_output = widgets.Output()
def multiple_choice(option_1, option_2, option_3, option_4):
option_list = [option_1, option_2, option_3, option_4]
answer = option_list[0]
letters = ["<b>(A)</b> ", "<b>(B)</b> ", "<b>(C)</b> ", "<b>(D)</b> "]
#Randomly shuffle the options
random.shuffle(option_list)
#Print the letters (A) to (D) in sequence with randomly chosen options
for i in range(4):
option_text = option_list.pop()
option_text_2 = letters[i] + option_text
option_output = widgets.HTMLMath(value=option_text_2)
display(option_output)
#Stores the correct answer
if option_text == answer:
letter_answer = letters[i]
button1 = widgets.Button(description="(A)")
button2 = widgets.Button(description="(B)")
button3 = widgets.Button(description="(C)")
button4 = widgets.Button(description="(D)")
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Whitesmoke'
container = widgets.HBox(children=[button1, button2, button3, button4])
display(container)
print(" ", end='\r')
def on_button1_clicked(b):
if "<b>(A)</b> " == letter_answer:
print("Correct! ", end='\r')
button1.style.button_color = 'Moccasin'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button1.style.button_color = 'Lightgray'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Whitesmoke'
def on_button2_clicked(b):
if "<b>(B)</b> " == letter_answer:
print("Correct! ", end='\r')
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Moccasin'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Lightgray'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Whitesmoke'
def on_button3_clicked(b):
if "<b>(C)</b> " == letter_answer:
print("Correct! ", end='\r')
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Moccasin'
button4.style.button_color = 'Whitesmoke'
else:
print("Try again.", end='\r')
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Lightgray'
button4.style.button_color = 'Whitesmoke'
def on_button4_clicked(b):
if "<b>(D)</b> " == letter_answer:
print("Correct! ", end='\r')
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Moccasin'
else:
print("Try again.", end='\r')
button1.style.button_color = 'Whitesmoke'
button2.style.button_color = 'Whitesmoke'
button3.style.button_color = 'Whitesmoke'
button4.style.button_color = 'Lightgray'
button1.on_click(on_button1_clicked)
button2.on_click(on_button2_clicked)
button3.on_click(on_button3_clicked)
button4.on_click(on_button4_clicked)
def build(self):
'''Create user interface widgets'''
tabs = [];
# Tab 1: Welcome ======================================================
content = []
content.append(self.section(self.WELCOME1_TITLE,self.WELCOME1_TEXT))
content.append(self.section(self.WELCOME2_TITLE,self.WELCOME2_TEXT))
tabs.append(ui.VBox(content))
# Tab 2: Samples ======================================================
content = []
# CSS (stle) and start the table
table = '''<style>
.sample_cell {padding-right: 32px }
.sample_even {background : White }
.sample_odd {background : Gainsboro}
</style><table>'''
samp_hdrs,samp_data = self.model.get_samples()
for item in samp_hdrs:
table += '<th class="sample_cell">' + item + '</th>'
for i,line in enumerate(samp_data):
if i % 2 == 0:
table += '<tr class="sample_even">'
else:
table += '<tr class="sample_odd">'
for item in line:
table += '<td class="sample_cell">' + item + '</td>'
table += '</tr>'
table += '</table>'
widgets = []
widgets.append(ui.HTML(value=table))
content.append(self.section(self.SAMPLES1_TITLE,widgets))
tabs.append(ui.VBox(content))
# Tab 3: Filter ======================================================
self.filter_txt_gene = ui.Text(description='',value='',placeholder=self.FILTER1_HINT ) # Test: Sevir.9G584100/5G108900
self.filter_txt_func = ui.Text(description='',value='',placeholder=self.FILTER2_HINT )
self.filter_txt_tpm = ui.Text(description=self.FILTER6_TEXT,value=self.DEFAULT_TPM ,placeholder='NA')
self.filter_txt_pval = ui.Text(description=self.FILTER8_TEXT,value=self.DEFAULT_PVAL,placeholder='NA')
self.filter_txt_fdr = ui.Text(description=self.FILTER9_TEXT,value=self.DEFAULT_FDR ,placeholder='NA')
self.filter_conditons = [] # Created in loop below
self.filter_btn_apply = ui.Button(description=self.FILTER_APPLY,icon='filter',layout=self.LO20)
self.filter_ddn_ndisp = ui.Dropdown(options=['25','50','100',self.ALL],layout=self.LO10)
self.filter_html_output = ui.HTML(self.EMPTY_LIST_MSG)
self.filter_btn_refexp = ui.Button(description=self.FILTER_REFEXP,icon='download',layout=self.LO20)
content = []
widgets = []
widgets.append(ui.HTML(value=self.FILTER1_TEXT))
widgets.append(ui.HTML(value=self.FILTER1_TEXT_2))
widgets.append(self.filter_txt_gene)
content.append(self.section(self.FILTER1_TITLE,widgets))
widgets = []
widgets.append(ui.HTML(value=self.FILTER2_TEXT))
widgets.append(self.filter_txt_func)
content.append(self.section(self.FILTER2_TITLE,widgets))
widgets = []
widgets.append(ui.HTML(value=self.FILTER5_TEXT))
widgets.append(self.filter_txt_tpm)
widgets.append(ui.HTML(value=self.FILTER7_TEXT))
widgets.append(self.filter_txt_pval)
widgets.append(self.filter_txt_fdr )
# Conditions ("Set expressions tests..."): matrix of 3-state buttons
# Title
widgets.append(ui.HTML(value=self.FILTER_CONDS_TITLE))
# Column headers (2 rows of headers)
widgets.append(ui.HTML('<style> .ctrhdr {text-align: center; font-weight: bold;} </style>'))
div = '<div class="ctrhdr">'
vid = '</div>'
row = []
row.append(ui.Label(value='' ,layout=self.LO15 ))
row.append(ui.HTML(div+self.FILTER_CONDS_MIN_HDR1+vid,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
row.append(ui.HTML(div+self.FILTER_CONDS_DIF_HDR1+vid,layout=ui.Layout(width=self.FILTER_CONDS_COL_DBLWI)))
widgets.append(ui.HBox(row))
row = []
row.append(ui.HTML( self.FILTER_CONDS_CON_HDR ,layout=self.LO15 ))
row.append(ui.HTML(div+self.FILTER_CONDS_MIN_HDR2 +vid,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
row.append(ui.HTML(div+self.FILTER_CONDS_DIF_HDR2O+vid,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
row.append(ui.HTML(div+self.FILTER_CONDS_DIF_HDR2U+vid,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
widgets.append(ui.HBox(row))
# Buttons
for item in self.model.cond:
row = []
row.append(ui.Label(value=item ,layout=self.LO15 ))
row.append(ui.Button(icon=self.FILT_CLR,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
row.append(ui.Button(icon=self.FILT_CLR,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
row.append(ui.Button(icon=self.FILT_CLR,layout=ui.Layout(width=self.FILTER_CONDS_COL_WIDTH)))
self.filter_conditons.append((row[1],row[2],row[3]))
widgets.append(ui.HBox(row))
content.append(self.section(self.FILTER3_TITLE,widgets))
# "Filtered gene list"
widgets = []
row = []
row.append(self.filter_btn_apply)
row.append(ui.HTML('<div style="text-align: right;">'+self.FILTER15_TEXT+'</div>',layout=self.LO15))
row.append(self.filter_ddn_ndisp)
row.append(ui.HTML('<div style="text-align: left;">' +self.FILTER16_TEXT+'</div>',layout=self.LO10))
widgets.append(ui.HBox(row))
widgets.append(ui.HBox([self.filter_html_output],layout={'width':'90vw'})) # Cause horiz. scrollbar (was: 1200)
content.append(self.section(self.FILTER4_TITLE,widgets))
# "Export"
self.filter_out_export = ui.Output(layout={'border': '1px solid black'})
row = self.section(self.FILTER24_TITLE,[ui.VBox([self.filter_btn_refexp,self.filter_out_export])])
#row.selected_index = None
content.append(row)
tabs.append(ui.VBox(content))
# Tab 4: Plot-experiment ======================================================
content = []
content.append(self.section(self.PLOTEX1_TITLE,self.PLOTEX1_TEXT))
# Plot line graphs ---
self.plotex_ddn_selex_lg = ui.Dropdown(options=[self.EMPTY]+self.model.exps,value=None,disabled=True)
widgets = []
row = []
row.append(ui.HTML(value=self.PLOTEX2_TEXT))
row.append(ui.Label(value='',layout=ui.Layout(width='60%'))) # Cheat: spacer
widgets.append(ui.HBox(row))
widgets.append(self.plotex_ddn_selex_lg)
widgets.append(self.ctrl.plotter.line_plot) # Use widget from plotter
content.append(self.section(self.PLOTEX2_TITLE,widgets))
# Plot heatmaps ---
self.plotex_ddn_selex_hm = ui.Dropdown(options=[self.EMPTY,self.ALL]+self.model.exps,value=None,disabled=True)
self.plotex_img_dispp_hm = ui.Output()
self.ctrl.plotter.out_plot_msg(self.plotex_img_dispp_hm,self.ctrl.plotter.HEAT_INIT_TITLE)
widgets = []
row = []
row.append(ui.HTML(value=self.PLOTEX3_TEXT))
row.append(ui.Label(value='',layout=ui.Layout(width='60%'))) # Cheat: spacer
widgets.append(ui.HBox(row))
widgets.append(self.plotex_ddn_selex_hm)
widgets.append(self.plotex_img_dispp_hm)
content.append(self.section(self.PLOTEX3_TITLE,widgets))
tabs.append(ui.VBox(content))
# Tab 5: Plot-coexpression ======================================================
# Get list of networks and sort them using inline function that parses out numeric portion of network name
networks = sorted(self.model.get_networks(),key=lambda x: int(x.split('_')[1]))
# Build display/value pairs as list of tuples for use in dropdown menu
disp_vals = []
for i,net in enumerate(networks):
#disp_vals.append((net.replace('_',' '),net) )
disp_vals.append((net.split('_')[1],net) )
self.plotco_ddn_netw = ui.Dropdown(options=[(self.EMPTY,self.EMPTY)]+disp_vals,value=None,disabled=True)
# Download button
self.plotco_btn_modu = ui.Button(description=self.FILTER_REFEXP,icon='download',layout=self.LO20)
# Create a fixed width data selection widet
self.plotco_sel_modu = ui.Select(rows=10,options=[],value=None,layout={'width':'99%'})
self.plotco_sel_modu.add_class('selmono') # Use JavaScript to spec fixed-width font (see custom CSS)
# Module selection # NOTE If using latest ver of Jupyter, consider using grid widet instead of fixed font select widget
# Create a fixed width header widget that will match data widget
header = [self.MODULE_HEADER[0][:-2],self.MODULE_HEADER[1][:-2]] # Hide last 2 cols, tho they're used in export/download
header = self.columnize(self.MODULE_HEADER[0][:-2],header)
header = ui.Select(options=header,disabled=True,value=None,layout=ui.Layout(height='3em',width='99%'))
header.add_class('selmono') # Use JavaScript to spec fixed-width font (see custom CSS)
content = []
# Image
with open('images/DecayRates.png','rb') as handle:
image = handle.read()
widgets = []
widgets.append(ui.HTML(self.PLOTCO1_TEXT_A))
widgets.append(ui.Image(value=image,format='png',width=500,height=259))
widgets.append(ui.HTML(self.PLOTCO1_TEXT_B))
content.append(self.section(self.PLOTEX1_TITLE,widgets))
# Select Network Graph
widgets = []
widgets.append(ui.HTML(value=self.PLOTCO1_LABEL))
widgets.append(self.plotco_ddn_netw)
row = []
row.append(ui.HTML(value=self.PLOTCO3_TEXT))
row.append(ui.Label(value='',layout=ui.Layout(width='60%'))) # Cheat: spacer
widgets.append(ui.HBox(row))
widgets.append(ui.HBox([ui.VBox([header,self.plotco_sel_modu],layout={'width':'100%'})])) # was: ,layout={'width':'90vw'}
content.append(self.section(self.PLOTCO1_TITLE,widgets))
# "Export"
self.plotco_out_export = ui.Output(layout={'border': '1px solid black'})
row = self.section(self.FILTER24_TITLE,[ui.VBox([self.plotco_btn_modu,self.plotco_out_export])])
row.selected_index = None
content.append(row)
# Network Graph of Selected Module NOTE Uses widget created by plotter
content.append(self.section(self.PLOTCO2_TITLE,[self.ctrl.plotter.net_plot]))
tabs.append(ui.VBox(content))
# Tab 6: Plot-differentialy ======================================================
content = []
content.append(self.section(self.PLOTEX1_TITLE,self.PLOTDE1_TEXT))
self.plotdif_sel_title = ui.HTML(value=self.PLOTDE4_TEXT,layout={'width':'99%'})
self.plotdif_sel_genes = ui.SelectMultiple(rows=10,options=[],value=[],layout={'width':'99%'})
self.plotdif_img_disp = ui.Output()
self.plotdif_btn_plot = ui.Button(description=self.PLOTDE2_TEXT,icon='bar-chart',layout=self.LO20)
self.ctrl.plotter.out_plot_msg(self.plotdif_img_disp,self.ctrl.plotter.DIF_INIT_TITLE)
widgets = []
widgets.append(self.plotdif_sel_title)
widgets.append(self.plotdif_sel_genes)
widgets.append(self.plotdif_btn_plot)
widgets.append(ui.Label(value='',layout=ui.Layout(width='60%'))) # Cheat: spacer
widgets.append(self.plotdif_img_disp)
widgets.append(ui.Label(value='',layout=ui.Layout(width='60%'))) # Cheat: spacer
content.append(self.section(self.PLOTDE3_TEXT,widgets))
tabs.append(ui.VBox(content))
# Tab bar ======================================================
self.tabs = ui.Tab()
for i in range(len(self.TABS)):
self.tabs.set_title(i,self.TABS[i])
self.tabs.children = tuple(tabs)
def __init__(self, **kwargs):
computer_image = ipw.HTML(
'<img width="200px" src="./miscellaneous/images/computer.png">')
# Computer ssh settings
self._inp_username = ipw.Text(description="SSH username:"******"350px"),
style=STYLE)
self._inp_password = ipw.Password(description="SSH password:"******"130px"),
style=STYLE)
self._inp_computer_hostname = ipw.Text(
description="Computer name:",
layout=ipw.Layout(width="350px"),
style=STYLE)
# Proxy ssh settings
self._use_proxy = ipw.Checkbox(value=False, description='Use proxy')
self._use_proxy.observe(self.on_use_proxy_change, names='value')
self._inp_proxy_address = ipw.Text(description="Proxy server address:",
layout=ipw.Layout(width="350px"),
style=STYLE)
self._use_diff_proxy_username = ipw.Checkbox(
value=False,
description='Use different username and password',
layout={'width': 'initial'})
self._use_diff_proxy_username.observe(
self.on_use_diff_proxy_username_change, names='value')
self._inp_proxy_username = ipw.Text(
value='',
description="Proxy server username:"******"350px"),
style=STYLE)
self._inp_proxy_password = ipw.Password(
value='',
description="Proxy server password:"******"138px"),
style=STYLE)
# Setup ssh button and output
self._btn_setup_ssh = ipw.Button(description="Setup ssh")
self._btn_setup_ssh.on_click(self.on_setup_ssh)
self._setup_ssh_out = ipw.Output()
# Check whether some settings were already provided
predefine_settings(self, **kwargs)
# Defining widgets positions
computer_ssh_box = ipw.VBox([
self._inp_computer_hostname, self._inp_username,
self._inp_password, self._use_proxy
],
layout=ipw.Layout(width="400px"))
self._proxy_user_password_box = ipw.VBox(
[self._inp_proxy_username, self._inp_proxy_password],
layout={'visibility': 'hidden'})
self._proxy_ssh_box = ipw.VBox([
self._inp_proxy_address, self._use_diff_proxy_username,
self._proxy_user_password_box
],
layout={
'visibility': 'hidden',
'width': '400px'
})
children = [
ipw.HBox([computer_image, computer_ssh_box, self._proxy_ssh_box]),
self._btn_setup_ssh, self._setup_ssh_out
]
super(SshComputerSetup, self).__init__(children, **kwargs)
def single_run(data_dir="", id=""):
if not os.path.exists(data_dir):
raise FileNotFoundError("No directory found named: " + data_dir)
run_summary = RunSummary(data_dir=data_dir, id=id)
sedov_solution = SedovSolution(E_0,
run_summary.overview.background_density,
run_summary.overview.metallicity)
#### PASS TO PLOTTER ####
num_checkpoints = len(run_summary.filenames)
# log_R_max = round(np.log10(run_summary.df["Radius"].max()), 2)
# log_R_min = max(log_R_max-4,
# round(np.log10(run_summary.df["Radius"].min()), 2)+1)
R_min = run_summary.df["Radius"].min()
R_min = 0
R_max = run_summary.df["Radius"].max()
if type(single_run.previous_widget) is widgets.Box:
single_run.previous_widget.close()
w = interactive(
plotter,
run_summary=fixed(run_summary),
sedov_solution=fixed(sedov_solution),
xlim=FloatRangeSlider(
min=R_min,
max=R_max,
step=0.01 * (R_max - R_min),
value=(R_min, R_max),
),
checkpoint_index=IntSlider(min=0,
max=num_checkpoints - 1,
step=0,
value=num_checkpoints - 1),
y_axis_variable=Dropdown(options=cols_plot, value="Density"),
x_axis_variable=RadioButtons(options=["Radius", "M_int", "zones"]),
label=fixed("numeric"),
density_in_mH_cm3=fixed(False),
verbose=fixed(True),
)
w1 = widgets.Button(description=u"\u23EA")
def show_first(b):
checkpoint_slider = w.children[5]
checkpoint_slider.value = checkpoint_slider.min
w1.on_click(show_first)
wl = widgets.Button(description=u"\u276E")
def show_prev(b):
checkpoint_slider = w.children[5]
if checkpoint_slider.value > checkpoint_slider.min:
checkpoint_slider.value -= 1
wl.on_click(show_prev)
w2 = widgets.Button(description=u"\u25BA")
# w2.stop = False
def play(b):
checkpoint_slider = w.children[5]
for i in range(checkpoint_slider.value + 1, checkpoint_slider.max + 1):
plt.gcf()
checkpoint_slider.value = i
# plt.show()
# time.sleep(.1)
# if b.stop:
# break
w2.on_click(play)
# wp = widgets.Button(description=u"p")
# def pause(b):
# w2.stop=True
# wp.on_click(pause)
wr = widgets.Button(description=u"\u276F")
def show_next(b):
checkpoint_slider = w.children[5]
if checkpoint_slider.value < checkpoint_slider.max:
checkpoint_slider.value += 1
wr.on_click(show_next)
w3 = widgets.Button(description=u"\u23E9")
def show_last(b):
checkpoint_slider = w.children[5]
checkpoint_slider.value = checkpoint_slider.max
w3.on_click(show_last)
w_buttons = widgets.HBox(children=[w1, wl, w2, wr, w3])
w.children = tuple([_w for _w in w.children] + [w_buttons])
single_run.previous_widget = w
display(w)
# display(w_buttons)
return run_summary