def modify_doc(doc):
plot = Plot(plot_height=400, plot_width=400, x_range=Range1d(0, 1), y_range=Range1d(0, 1), min_border=0)
plot.add_tools(CustomAction(callback=CustomJS(args=dict(s=source), code=RECORD("data", "s.data"))))
button = Button(css_classes=["foo"])
button.js_on_click(CustomJS(args=dict(s=source), code="s.patch({'x': [[1, 100]]})"))
doc.add_root(column(button, plot))
def test_buttonclick_event_callbacks():
button = Button()
test_callback = EventCallback()
button.on_event(events.ButtonClick, test_callback)
assert test_callback.event_name == None
button._trigger_event(events.ButtonClick(button))
assert test_callback.event_name == events.ButtonClick.event_name
def test_displays_button_type(self, typ, bokeh_model_page):
button = Button(button_type=typ, css_classes=["foo"])
page = bokeh_model_page(button)
button = page.driver.find_element_by_css_selector('.foo .bk-btn')
assert typ in button.get_attribute('class')
def root():
scrape_button = Button(label='Scrape Data')
prices = scrape_button.on_click(scrape_prices(url))
#prices = scrape_prices(url)
p = make_hist(prices)
script, div = embed.components(p,scrape_button)
return render_template('histograms.html',script = script,div = div)
class ButtonWrapper(object):
def __init__(self, label, callback):
self.ref = "button-" + make_id()
self.obj = Button(label=label, css_classes=[self.ref])
self.obj.js_on_event('button_click', callback)
def click(self, driver):
button = driver.find_element_by_css_selector(".%s .bk-btn" % self.ref)
button.click()
def modify_doc(doc):
source = ColumnDataSource(dict(x=[1, 2], y=[1, 1]))
plot = Plot(plot_height=400, plot_width=400, x_range=Range1d(0, 1), y_range=Range1d(0, 1), min_border=0)
plot.add_glyph(source, Circle(x='x', y='y', size=20))
plot.add_tools(CustomAction(callback=CustomJS(args=dict(s=source), code=RECORD("data", "s.data"))))
button = Button(css_classes=['foo'])
def cb(event):
source.data=dict(x=[10, 20], y=[10, 10])
button.on_event('button_click', cb)
doc.add_root(column(button, plot))
def test_js_on_click_executes(self, bokeh_model_page):
button = Button(css_classes=['foo'])
button.js_on_click(CustomJS(code=RECORD("clicked", "true")))
page = bokeh_model_page(button)
button = page.driver.find_element_by_css_selector('.foo .bk-btn')
button.click()
results = page.results
assert results == {'clicked': True}
assert page.has_no_console_errors()
def run(doc):
fig = figure(title='random data', width=400, height=200, tools='pan,box_zoom,reset,save')
source = ColumnDataSource(data={'x': [], 'y': []})
fig.line('x', 'y', source=source)
def click(n=100):
source.data = {'x': range(n), 'y': random(n)}
button = Button(label='update', button_type='success')
button.on_click(click)
layout = column(widgetbox(button), fig)
doc.add_root(layout)
click()
def modify_doc(doc):
plot = Plot(plot_height=400, plot_width=400, x_range=Range1d(0, 1), y_range=Range1d(0, 1), min_border=0)
plot.add_tools(CustomAction(callback=CustomJS(args=dict(s=source), code=RECORD("data", "s.data"))))
table = DataTable(columns=[
TableColumn(field="x", title="x", sortable=True),
TableColumn(field="y", title="y", sortable=True)
], source=source, editable=False)
button = Button(css_classes=["foo"])
def cb():
source.stream({'x': [100], 'y': [100]})
button.on_click(cb)
doc.add_root(column(plot, table, button))
def create_previous_event_widget(self):
self.w_previous_event = Button(
label="<",
button_type="default",
width=50
)
self.w_previous_event.on_click(self.on_previous_event_widget_click)
def create_goto_event_index_widget(self):
self.w_goto_event_index = Button(
label="GOTO Index",
button_type="default",
width=100
)
self.w_goto_event_index.on_click(self.on_goto_event_index_widget_click)
def create_goto_event_id_widget(self):
self.w_goto_event_id = Button(
label="GOTO ID",
button_type="default",
width=70
)
self.w_goto_event_id.on_click(self.on_goto_event_id_widget_click)
def test_event_handles_new_callbacks_in_event_callback(self):
from bokeh.models import Button
d = document.Document()
button1 = Button(label="1")
button2 = Button(label="2")
def clicked_1():
button2.on_click(clicked_2)
d.add_root(button2)
def clicked_2():
pass
button1.on_click(clicked_1)
d.add_root(button1)
event_json = json.dumps({"event_name":"button_click","event_values":{"model_id":button1.id}})
try:
d.apply_json_event(event_json)
except RuntimeError:
pytest.fail("apply_json_event probably did not copy models before modifying")
def plot():
import numpy as np
from bokeh.models import Button
from bokeh.palettes import RdYlBu3
from bokeh.plotting import figure, vplot
# create a plots and style its properties
p = figure(x_range=(0, 100), y_range=(0, 100), toolbar_location=None)
p.border_fill_color = 'black'
p.background_fill_color = 'black'
p.outline_line_color = None
p.grid.grid_line_color = None
# add a text renderer to out plots (no data yet)
r = p.text(x=[], y=[], text=[], text_color=[], text_font_size="20pt",
text_baseline="middle", text_align="center")
i = 0
ds = r.data_source
# create a callback that will add a number in a random location
def callback():
nonlocal i
ds.data['x'].append(np.random.random()*70 + 15)
ds.data['y'].append(np.random.random()*70 + 15)
ds.data['text_color'].append(RdYlBu3[i%3])
ds.data['text'].append(str(i))
ds.trigger('data', ds.data, ds.data)
i = i + 1
# add a button widget and configure with the call back
button = Button(label="Press Me")
button.on_click(callback)
plot_this = vplot(button, p)
return plot_this
def test_data_table_selected_highlighting(output_file_url, selenium, screenshot):
# Create a DataTable and Button that sets a selection
data = dict(x = list(range(10)))
source = ColumnDataSource(data=data)
columns = [TableColumn(field="x", title="X")]
data_table = DataTable(source=source, columns=columns)
button = Button(label="Click")
button.callback = CustomJS(args=dict(source=source), code="""
source['selected']['1d'].indices = [1, 2]
source.change.emit();
""")
# Save the table and start the test
save(column(data_table, button))
selenium.get(output_file_url)
assert has_no_console_errors(selenium)
# Click the button to select the rows
button = selenium.find_element_by_class_name('bk-bs-btn')
button.click()
screenshot.assert_is_valid()
def line_scratch():
line_width = 4
line1 = [(0, 1, 2, 3, 4, 5), (0, 1, 2, 3, 4, 5)]
line2 = [(0, 1, 2, 3, 4, 5), (0, 5, 1, 4, 2, 3)]
line3 = [(5, 4, 3, 2, 1), (5, 4, 3, 2, 1)]
plot = figure()
red = plot.line(x=line1[0], y=line1[1], line_width=line_width, color="crimson")
blue = plot.line(x=line2[0], y=line2[1], line_width=line_width)
# purple = plot.line(x=line3[0], y=line3[1], line_width=line_width, color="purple")
button = Button(label="Add Line")
button.on_click(add_line)
curdoc().add_root(vplot(plot, button))
session = push_session(curdoc())
script = autoload_server(model=None, session_id=session.id)
# script, div = components(vplot(plot, button))
return script
def init_controls(self):
btnStop = Button(label="Stop", type="danger")
btnStart = Button(label="Start", type="success")
btnStop.on_click(self.handle_btnStop_press)
btnStart.on_click(self.handle_btnStart_press)
curdoc().add_root(btnStop)
curdoc().add_root(btnStart)
sliderHPThreshold = Slider(start=0, end=500, value=100, step=1, title="High pass threshold")
sliderHPThreshold.on_change('value', self.onChangeHPThreshold)
curdoc().add_root(vplot(sliderHPThreshold))
def do_step(document):
document.clear()
sl, c = next(examples)
p = plot_slice(sl)
b_A = Button(label="Accept")
b_R = Button(label="Reject")
b_A.on_click(functools.partial(callback, sl, c, 'accept'))
b_R.on_click(functools.partial(callback, sl, c, 'reject'))
plot = vplot(p, (hplot(b_A, b_R)))
document.add_root(plot)
ticker1.on_change('value', ticker1_change)
ticker2.on_change('value', ticker2_change)
def selection_change(attrname, old, new):
t1, t2 = ticker1.value, ticker2.value
data = get_data(t1, t2)
selected = source.selected.indices
if selected:
data = data.iloc[selected, :]
update_stats(data, t1, t2)
source.selected.on_change('indices', selection_change)
button = Button(label="Download", button_type="success")
button.js_on_click(
CustomJS(args=dict(source=source),
code=open(join(dirname(__file__), "download.js")).read()))
columns = [
TableColumn(field="t1", title="t1"),
TableColumn(field="t2", title="t2"),
TableColumn(field="t1_returns", title="t1_returns"),
TableColumn(field="t2_returns", title="t2_returns")
]
data_table = DataTable(source=source,
columns=columns,
width=900,
auto_edit=True,
editable=True)
ry_far = x_far[1, :].tolist()
source.data = dict(rx=rx, ry=ry)
source_short.data = dict(rx_short=rx_short, ry_short=ry_short)
source_far.data = dict(rx_far=rx_far, ry_far=ry_far)
# initialize data source
source = ColumnDataSource(data=dict(rx=[], ry=[]))
source_short = ColumnDataSource(data=dict(rx_short=[], ry_short=[]))
source_far = ColumnDataSource(data=dict(rx_far=[], ry_far=[]))
source_datatable = ColumnDataSource(data=dict(shot_alpha=[], shot_error=[]))
app_data = ColumnDataSource(data=dict(alpha=[bv_settings.alpha_init], alpha_left=[bv_settings.alpha_left],
alpha_right=[bv_settings.alpha_right]))
buttonShort = Button(label="shoot shorter")
buttonShort.on_click(shoot_shorter)
buttonFar = Button(label="shoot further")
buttonFar.on_click(shoot_further)
# initialize plot
toolset = "crosshair,pan,reset,resize,wheel_zoom,box_zoom"
# Generate a figure container
plot = Figure(plot_height=bv_settings.fig_height,
plot_width=bv_settings.fig_width,
tools=toolset,
title=bv_settings.title, # obj.text.value,
x_range=[bv_settings.min_x, bv_settings.max_x],
y_range=[bv_settings.min_y, bv_settings.max_y]
)
# Plot the line by the x,y values in the source property
slider = Slider(start=years[0],
end=years[-1],
value=years[0],
step=1,
title="Year")
slider.on_change('value', slider_update)
callback_id = None
def animate():
global callback_id
if button.label == '► Play':
button.label = '❚❚ Pause'
callback_id = curdoc().add_periodic_callback(animate_update, 200)
else:
button.label = '► Play'
curdoc().remove_periodic_callback(callback_id)
button = Button(label='► Play', width=60)
button.on_click(animate)
layout = layout([
[plot],
[slider, button],
], sizing_mode='scale_width')
curdoc().add_root(layout)
curdoc().title = "Gapminder"
def create_next_event_widget(self):
self.w_next_event = Button(label=">", button_type="default", width=50)
self.w_next_event.on_click(self.on_next_event_widget_click)
def KPI_developer_adoption_tab(page_width,DAYS_TO_LOAD=90):
class Thistab(KPI):
def __init__(self, table,cols=[]):
KPI.__init__(self, table,name='developer',cols=cols)
self.table = table
self.df = None
self.checkboxgroup = {}
self.period_to_date_cards = {
'year': self.card('',''),
'quarter': self.card('', ''),
'month': self.card('', ''),
'week': self.card('', '')
}
self.ptd_startdate = datetime(datetime.today().year,1,1,0,0,0)
self.timestamp_col = 'block_timestamp'
self.variable = self.menus['developer_adoption_DVs'][0]
self.datepicker_pop_start = DatePicker(
title="Period start", min_date=self.initial_date,
max_date=dashboard_config['dates']['last_date'], value=dashboard_config['dates']['last_date'])
# ------- DIVS setup begin
self.page_width = page_width
self.KPI_card_div = self.initialize_cards(width=self.page_width,height=1000)
txt = """<hr/><div style="text-align:center;width:{}px;height:{}px;
position:relative;background:black;margin-bottom:200px">
<h1 style="color:#fff;margin-bottom:300px">{}</h1>
</div>""".format(self.page_width, 50, 'Welcome')
self.notification_div = {
'top': Div(text=txt, width=self.page_width, height=20),
'bottom': Div(text=txt, width=self.page_width, height=10),
}
self.section_divider = '-----------------------------------'
self.section_headers = {
'cards': self.section_header_div(
text='Period to date:{}'.format(self.section_divider),
width=int(self.page_width*.5), html_header='h2', margin_top=5,margin_bottom=-155),
'pop': self.section_header_div(
text='Period over period:{}'.format(self.section_divider),
width=int(self.page_width*.5), html_header='h2', margin_top=5, margin_bottom=-155),
'sig_ratio': self.section_header_div(
text='Time series of ratio of DV to significant IVs'.format(self.section_divider),
width=int(self.page_width*.5), html_header='h2', margin_top=5, margin_bottom=-155),
}
# ---------------------- DIVS ----------------------------
def section_header_div(self, text, html_header='h2', width=600, margin_top=150, margin_bottom=-150):
text = """<div style="margin-top:{}px;margin-bottom:-{}px;"><{} style="color:#4221cc;">{}</{}></div>""" \
.format(margin_top, margin_bottom, html_header, text, html_header)
return Div(text=text, width=width, height=15)
def information_div(self, width=400, height=300):
div_style = """
style='width:350px;margin-right:-800px;
border:1px solid #ddd;border-radius:3px;background:#efefef50;'
"""
txt = """
<div {}>
<h4 {}>How to interpret relationships </h4>
<ul style='margin-top:-10px;'>
<li>
</li>
<li>
</li>
<li>
</li>
<li>
</li>
<li>
</li>
<li>
</li>
</ul>
</div>
""".format(div_style, self.header_style)
div = Div(text=txt, width=width, height=height)
return div
# -------------------- CARDS -----------------------------------------
def initialize_cards(self, width, height=250):
try:
txt = ''
for idx,period in enumerate(['year', 'quarter', 'month', 'week']):
design = random.choice(list(KPI_card_css.keys()))
txt += self.card(title='', data='', card_design=design)
text = """<div style="margin-top:100px;display:flex;flex-direction:column;">
{}
</div>""".format(txt)
div = Div(text=text, width=width, height=height)
return div
except Exception:
logger.error('initialize cards', exc_info=True)
# -------------------- GRAPHS -------------------------------------------
def graph_periods_to_date(self,df1,timestamp_filter_col,variable):
try:
dct = {}
for idx,period in enumerate(['week','month','quarter','year']):
all_txt = """<div style="width:{}px;display:flex;flex-direction:row;">"""\
.format(int(self.page_width*.6))
# go to next row
df = self.period_to_date(df1,
timestamp=dashboard_config['dates']['last_date'],
timestamp_filter_col=timestamp_filter_col, period=period)
# get unique instances
df = df.compute()
df = df.drop_duplicates(keep='first')
count = len(df)
gc.collect()
denom = df[variable].sum()
if denom != 0:
payroll_to_date = self.payroll_to_date(period)
cost_per_var = round(payroll_to_date/denom,2)
tmp_var = self.variable.split('_')
title = "{} to date".format(period)
title += "</br>${} per {}".format(cost_per_var,tmp_var[-1])
else:
title = "{} to date".format(period)
design = random.choice(list(KPI_card_css.keys()))
all_txt += self.card(title=title,data=count,card_design=design)
# add the statistically significant point estimates
all_txt += self.calc_sig_effect_card_data(df,interest_var=self.variable, period=period)
all_txt += """</div>"""
print(all_txt)
dct[period] = all_txt
del df
self.update_significant_DV_cards(dct)
except Exception:
logger.error('graph periods to date',exc_info=True)
def graph_period_over_period(self,period):
try:
periods = [period]
start_date = self.pop_start_date
end_date = self.pop_end_date
if isinstance(start_date,date):
start_date = datetime.combine(start_date,datetime.min.time())
if isinstance(end_date,date):
end_date = datetime.combine(end_date,datetime.min.time())
today = datetime.combine(datetime.today().date(),datetime.min.time())
'''
- if the start day is today (there is no data for today),
adjust start date
'''
if start_date == today:
logger.warning('START DATE of WEEK IS TODAY.!NO DATA DATA')
start_date = start_date - timedelta(days=7)
self.datepicker_pop_start.value = start_date
cols = [self.variable,self.timestamp_col, 'day']
df = self.load_df(start_date=start_date,end_date=end_date,cols=cols,timestamp_col='block_timestamp')
if abs(start_date - end_date).days > 7:
if 'week' in periods:
periods.remove('week')
if abs(start_date - end_date).days > 31:
if 'month' in periods:
periods.remove('month')
if abs(start_date - end_date).days > 90:
if 'quarter' in periods:
periods.remove('quarter')
for idx,period in enumerate(periods):
df_period = self.period_over_period(df, start_date = start_date, end_date=end_date,
period=period, history_periods=self.pop_history_periods,
timestamp_col='block_timestamp')
groupby_cols = ['dayset', 'period']
if len(df_period) > 0:
df_period = df_period.groupby(groupby_cols).agg({self.variable: 'sum'})
df_period = df_period.reset_index()
df_period = df_period.compute()
else:
df_period = df_period.compute()
df_period = df_period.rename(index=str, columns={'day': 'dayset'})
prestack_cols = list(df_period.columns)
logger.warning('Line 179:%s', df_period.head(10))
df_period = self.split_period_into_columns(df_period, col_to_split='period',
value_to_copy=self.variable)
# short term fix: filter out the unnecessary first day added by a corrupt quarter functionality
if period == 'quarter':
min_day = df_period['dayset'].min()
logger.warning('LINE 252: MINIUMUM DAY:%s', min_day)
df_period = df_period[df_period['dayset'] > min_day]
logger.warning('line 180 df_period columns:%s', df_period.head(50))
poststack_cols = list(df_period.columns)
title = "{} over {}".format(period, period)
plotcols = list(np.setdiff1d(poststack_cols, prestack_cols))
df_period, plotcols = self.pop_include_zeros(df_period=df_period, plotcols=plotcols, period=period)
if idx == 0:
p = df_period.hvplot.bar('dayset',plotcols,rot=45,title=title,
stacked=False,width=int(self.page_width*.8),height=400,value_label='#')
else:
p += df_period.hvplot.bar('dayset',plotcols,rot=45,title=title,
stacked=False,width=int(self.page_width*.8),height=400,value_label='#')
return p
except Exception:
logger.error('period over period to date', exc_info=True)
# -------------------------------- PLOT TRENDS FOR SIGNIFICANT RATIOS --------------------------
def graph_significant_ratios_ts(self,launch=-1):
try:
df = self.make_significant_ratios_df(self.df,resample_period=self.resample_period,
interest_var=self.variable,
timestamp_col='block_timestamp')
# clean
if self.variable in df.columns:
df = df.drop(self.variable,axis=1)
#df = df.compute()
# plot
return df.hvplot.line(width=int(self.page_width*.8),height=400)
except Exception:
logger.error('graph significant ratios',exc_info=True)
def update_variable(attrname, old, new):
thistab.notification_updater("Calculations underway. Please be patient")
thistab.variable = variable_select.value
thistab.graph_periods_to_date(thistab.df,'block_timestamp',thistab.variable)
thistab.section_header_updater('cards',label='')
thistab.section_header_updater('pop',label='')
thistab.trigger += 1
stream_launch.event(launch=thistab.trigger)
stream_launch_sig_ratio.event(launch=thistab.trigger)
thistab.notification_updater("ready")
def update_period_over_period():
thistab.notification_updater("Calculations underway. Please be patient")
thistab.pop_history_periods = pop_number_select.value
thistab.pop_start_date = thistab.datepicker_pop_start.value # trigger period over period
thistab.pop_end_date = datepicker_pop_end.value
thistab.trigger += 1
stream_launch.event(launch=thistab.trigger)
thistab.notification_updater("ready")
def update_resample(attrname, old, new):
thistab.notification_updater("Calculations underway. Please be patient")
thistab.resample_period = resample_select.value
thistab.trigger += 1
stream_launch_sig_ratio.event(launch=thistab.trigger)
thistab.notification_updater("ready")
def update_history_periods(attrname, old, new):
thistab.notification_updater("Calculations underway. Please be patient")
thistab.pop_history_periods = pop_number_select.value
thistab.trigger += 1
stream_launch.event(launch=thistab.trigger)
thistab.notification_updater("ready")
try:
cols = ['aion_fork','aion_watch','aion_release','aion_issue','aion_push','block_timestamp']
thistab = Thistab(table='account_ext_warehouse', cols=cols)
# ------------------------------------- SETUP ----------------------------
# format dates
first_date_range = thistab.initial_date
last_date_range = datetime.now().date()
last_date = dashboard_config['dates']['last_date']
first_date = datetime(last_date.year,1,1,0,0,0)
thistab.df = thistab.load_df(first_date, last_date,cols,'block_timestamp')
thistab.graph_periods_to_date(thistab.df,timestamp_filter_col='block_timestamp',variable=thistab.variable)
thistab.section_header_updater('cards',label='')
thistab.section_header_updater('pop',label='')
# MANAGE STREAM
# date comes out stream in milliseconds
# --------------------------------CREATE WIDGETS ---------------------------------
thistab.pop_end_date = last_date
thistab.pop_start_date = thistab.first_date_in_period(thistab.pop_end_date, 'week')
stream_launch = streams.Stream.define('Launch',launch=-1)()
stream_launch_sig_ratio = streams.Stream.define('Launch_sigratio',launch=-1)()
datepicker_pop_end = DatePicker(title="Period end", min_date=first_date_range,
max_date=last_date_range, value=thistab.pop_end_date)
pop_number_select = Select(title='Select # of comparative periods',
value=str(thistab.pop_history_periods),
options=thistab.menus['history_periods'])
pop_button = Button(label="Select dates/periods, then click me!",width=15,button_type="success")
variable_select = Select(title='Select variable', value=thistab.variable,
options=thistab.menus['developer_adoption_DVs'])
resample_select = Select(title='Select resample period',
value=thistab.resample_period,
options=thistab.menus['resample_period'])
# --------------------------------- GRAPHS ---------------------------
hv_sig_ratios = hv.DynamicMap(thistab.graph_significant_ratios_ts,
streams=[stream_launch_sig_ratio])
sig_ratios= renderer.get_plot(hv_sig_ratios)
hv_pop_week = hv.DynamicMap(thistab.pop_week,streams=[stream_launch])
pop_week = renderer.get_plot(hv_pop_week)
hv_pop_month = hv.DynamicMap(thistab.pop_month,streams=[stream_launch])
pop_month = renderer.get_plot(hv_pop_month)
hv_pop_quarter = hv.DynamicMap(thistab.pop_quarter, streams=[stream_launch])
pop_quarter = renderer.get_plot(hv_pop_quarter)
# -------------------------------- CALLBACKS ------------------------
variable_select.on_change('value', update_variable)
pop_button.on_click(update_period_over_period) # lags array
resample_select.on_change('value', update_resample)
pop_number_select.on_change('value',update_history_periods)
# -----------------------------------LAYOUT ----------------------------
# put the controls in a single element
controls_ptd = WidgetBox(variable_select, resample_select)
controls_pop = WidgetBox(thistab.datepicker_pop_start,
datepicker_pop_end, pop_number_select,pop_button)
grid_data = [
[thistab.notification_div['top']],
[Spacer(width=20, height=40)],
[thistab.section_headers['sig_ratio']],
[Spacer(width=20, height=25)],
[sig_ratios.state, controls_ptd],
[thistab.section_headers['cards']],
[Spacer(width=20, height=2)],
[thistab.KPI_card_div],
[thistab.section_headers['pop']],
[Spacer(width=20, height=25)],
[pop_week.state,controls_pop],
[pop_month.state],
[pop_quarter.state],
[thistab.notification_div['bottom']]
]
grid = gridplot(grid_data)
# Make a tab with the layout
tab = Panel(child=grid, title='KPI: developer adoption')
return tab
except Exception:
logger.error('rendering err:', exc_info=True)
return tab_error_flag('KPI: developer adoption')
'yellow'
],
factors=syn_factors),
source=depth_sample,
hover_line_color='white')
# Sets up visualization and hover tool.
genome_plot.add_tools(HoverTool(tooltips=TOOLTIPS))
genome_plot.xgrid.grid_line_alpha = 0
configurePlot(genome_plot)
protein_names = protein_annotation(FIRST)
FIRST = False
genome_plot.xaxis.axis_label = "Protein"
# Creates button that allows reset of plot to original state.
reset_button = Button(label="Reset Plot")
reset_button.js_on_click(
CustomJS(args=dict(g=genome_plot),
code="""
g.reset.emit()
"""))
# Creates text input button for user manual input of depth.
ose = TextInput(title='Manually input depth:')
# Creates checkboxes to show different types of mutations.
syngroup = CheckboxGroup(labels=[
"Show synonymous mutations", "Show nonsynonymous mutations",
"Show stopgains and stoplosses", "Show complex mutations",
"Show mutations without longitudinal data"
],
def candlestick_plot():
def obv_indicator(data):
res = talib.OBV(data.close.values, data.volume.values)
return res
def rsi_indicator(data):
res = talib.RSI(data.close.values, timeperiod=14)
return res
def cci_indicator(data):
res = talib.CCI(data.high.values, data.low.values, data.close.values, timeperiod=14)
return res
def technical_indicator(data, indicator):
if indicator == 'CCI':
data['tech'] = cci_indicator(data)
elif indicator == 'RSI':
data['tech'] = rsi_indicator(data)
else:
data['tech'] = obv_indicator(data)
return data
def load_data(obid, start, end, freq='1d'):
print('running....')
data = get_price(obid, start, end, freqency=freq).reset_index()
data['pct_change'] = data['close'].pct_change()
# data.dropna(inplace=True)
data['pct_change'] = data['pct_change'].apply(lambda x: str(round(x * 100, 2)) + '%')
data['index'] = list(np.arange(len(data)))
data['date'] = data['date'].apply(lambda x: x.strftime("%Y%m%d"))
return data
def moving_average(data, selection):
selection_mapping = {k: int(k.split('_')[-1]) for k in selection}
for k, v in selection_mapping.items():
data[k] = data['close'].rolling(window=v).mean()
return data
def update_lines(attr, old, new):
line_0.visible = 0 in average_selection.active
line_1.visible = 1 in average_selection.active
line_2.visible = 2 in average_selection.active
line_3.visible = 3 in average_selection.active
line_4.visible = 4 in average_selection.active
line_5.visible = 5 in average_selection.active
def update_plot(attr, old, new):
indicator = indicator_selection.value
new_data = technical_indicator(data, indicator)
new_source = ColumnDataSource(new_data)
source.data.update(new_source.data)
def update_data():
# global obid, start, end
obid = order_book_id.value
start = start_date.value
end = end_date.value
# 提取数据，均线根据选取与否进行添加
new_data = load_data(obid, start, end)
new_data_1 = moving_average(new_data, average_labels)
new_data_2 = technical_indicator(new_data, indicator_selection.value)
new_source = ColumnDataSource(new_data_2)
new_source_1 = ColumnDataSource(new_data_1)
source.data.update(new_source.data)
source_1.data.update(new_source_1.data)
inc = new_data.close >= new_data.open
dec = new_data.close < new_data.open
inc_source.data = inc_source.from_df(new_data_2.loc[inc])
dec_source.data = dec_source.from_df(new_data_2.loc[dec])
p.title.text = instruments(obid).symbol
p.x_range.end = len(new_data) + 1
p2.xaxis.major_label_overrides = {i: date for i, date in enumerate(new_data['date'])}
today = datetime.now().date()
average_labels = ["MA_5", "MA_10", "MA_20", 'MA_30', 'MA_60', 'MA_120']
average_selection = CheckboxGroup(labels=average_labels, active=[0, 1, 2, 3, 4, 5, 6])
indicator_selection = Select(title='TechnicalIndicator', value='RSI', options=['OBV', 'RSI', 'CCI'])
order_book_id = TextInput(title='StockCode', value='002916.XSHE')
symbol = instruments(order_book_id.value).symbol
start_date = DatePicker(title="StartDate", value='2018-01-01', min_date='2015-01-01', max_date=today)
end_date = DatePicker(title="EndDate", value=today, min_date=start_date.value, max_date=today)
# labels = [average_selection.labels[i] for i in average_selection.active]
data = load_data(order_book_id.value, start_date.value, end_date.value)
# 均线计算
data_1 = moving_average(data, average_labels) # 计算各种长度的均线
# 技术指标计算
data_2 = technical_indicator(data, indicator_selection.value)
source = ColumnDataSource(data_2)
source_1 = ColumnDataSource(data_1)
inc = data.close >= data.open
dec = data.open > data.close
inc_source = ColumnDataSource(data_2.loc[inc])
dec_source = ColumnDataSource(data_2.loc[dec])
TOOLS = 'save, pan, box_zoom, reset, wheel_zoom'
hover = HoverTool(tooltips=[('date', '@date'),
('open', '@open'),
('high', '@high'),
('low', '@low'),
('close', '@close'),
('pct_change', "@pct_change")
]
)
length = len(data)
p = figure(plot_width=1000, plot_height=500, title='{}'.format(symbol), tools=TOOLS, x_range=(0, length + 1))
p.xaxis.visible = False # 隐藏x-axis
p.min_border_bottom = 0
# 均线图
line_0 = p.line(x='index', y='MA_5', source=source_1, color=Spectral6[5])
line_1 = p.line(x='index', y='MA_10', source=source_1, color=Spectral6[4])
line_2 = p.line(x='index', y='MA_20', source=source_1, color=Spectral6[3])
line_3 = p.line(x='index', y='MA_30', source=source_1, color=Spectral6[2])
line_4 = p.line(x='index', y='MA_60', source=source_1, color=Spectral6[1])
line_5 = p.line(x='index', y='MA_120', source=source_1, color=Spectral6[0])
p.segment(x0='index', y0='high', x1='index', y1='low', color='red', source=inc_source)
p.segment(x0='index', y0='high', x1='index', y1='low', color='green', source=dec_source)
p.vbar('index', 0.5, 'open', 'close', fill_color='red', line_color='red', source=inc_source, hover_fill_alpha=0.5)
p.vbar('index', 0.5, 'open', 'close', fill_color='green', line_color='green', source=dec_source,
hover_fill_alpha=0.5)
p.add_tools(hover)
p1 = figure(plot_width=p.plot_width, plot_height=200, x_range=p.x_range, toolbar_location=None)
p1.vbar('index', 0.5, 0, 'volume', color='red', source=inc_source)
p1.vbar('index', 0.5, 0, 'volume', color='green', source=dec_source)
p1.xaxis.visible = False
p2 = figure(plot_width=p.plot_width, plot_height=p1.plot_height, x_range=p.x_range, toolbar_location=None)
p2.line(x='index', y='tech', source=source)
p2.xaxis.major_label_overrides = {i: date for i, date in enumerate(data['date'])}
p2.xaxis.major_label_orientation = pi / 4
p2.min_border_bottom = 0
button = Button(label="ClickToChange", button_type="success")
button.on_click(update_data)
average_selection.inline = True
average_selection.width = 500
average_selection.on_change('active', update_lines)
indicator_selection.on_change('value', update_plot)
widgets = column(row(order_book_id, start_date, end_date, button), row(indicator_selection, average_selection))
layouts = column(widgets, p, p1, p2)
# doc.add_root(pp)
# make a layout
tab = Panel(child=layouts, title='StockPrice')
return tab
class TimeSeries:
def __init__(self, sources, range_categories, custom_title, data_tables):
self.sources = sources
self.range_categories = range_categories
self.current_dvh_group = {n: [] for n in GROUP_LABELS}
# Control Chart layout (Time-Series)
tools = "pan,wheel_zoom,box_zoom,lasso_select,poly_select,reset,crosshair,save"
self.plot = figure(plot_width=1050, plot_height=400, tools=tools, logo=None,
active_drag="box_zoom", x_axis_type='datetime')
self.plot.xaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.plot.yaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.plot.xaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
self.plot.yaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
# plot.min_border_left = min_border
self.plot.min_border_bottom = options.MIN_BORDER
self.plot_data_1 = self.plot.circle('x', 'y', size=options.TIME_SERIES_1_CIRCLE_SIZE,
color=options.GROUP_1_COLOR,
alpha=options.TIME_SERIES_1_CIRCLE_ALPHA,
source=sources.time_1)
self.plot_data_2 = self.plot.circle('x', 'y', size=options.TIME_SERIES_2_CIRCLE_SIZE,
color=options.GROUP_2_COLOR,
alpha=options.TIME_SERIES_2_CIRCLE_ALPHA,
source=sources.time_2)
self.plot_trend_1 = self.plot.line('x', 'y', color=options.GROUP_1_COLOR, source=sources.time_trend_1,
line_width=options.TIME_SERIES_1_TREND_LINE_WIDTH,
line_dash=options.TIME_SERIES_1_TREND_LINE_DASH)
self.plot_trend_2 = self.plot.line('x', 'y', color=options.GROUP_2_COLOR, source=sources.time_trend_2,
line_width=options.TIME_SERIES_2_TREND_LINE_WIDTH,
line_dash=options.TIME_SERIES_2_TREND_LINE_DASH)
self.plot_avg_1 = self.plot.line('x', 'avg', color=options.GROUP_1_COLOR, source=sources.time_bound_1,
line_width=options.TIME_SERIES_1_AVG_LINE_WIDTH,
line_dash=options.TIME_SERIES_1_AVG_LINE_DASH)
self.plot_avg_2 = self.plot.line('x', 'avg', color=options.GROUP_2_COLOR, source=sources.time_bound_2,
line_width=options.TIME_SERIES_2_AVG_LINE_WIDTH,
line_dash=options.TIME_SERIES_2_AVG_LINE_DASH)
self.plot_patch_1 = self.plot.patch('x', 'y', color=options.GROUP_1_COLOR, source=sources.time_patch_1,
alpha=options.TIME_SERIES_1_PATCH_ALPHA)
self.plot_patch_2 = self.plot.patch('x', 'y', color=options.GROUP_2_COLOR, source=sources.time_patch_2,
alpha=options.TIME_SERIES_1_PATCH_ALPHA)
self.plot.add_tools(HoverTool(show_arrow=True,
tooltips=[('ID', '@mrn'),
('Date', '@x{%F}'),
('Value', '@y{0.2f}')],
formatters={'x': 'datetime'}))
self.plot.xaxis.axis_label = "Simulation Date"
self.plot.yaxis.axis_label = ""
# Set the legend
legend_plot = Legend(items=[("Group 1", [self.plot_data_1]),
("Series Average", [self.plot_avg_1]),
("Rolling Average", [self.plot_trend_1]),
("Percentile Region", [self.plot_patch_1]),
("Group 2", [self.plot_data_2]),
("Series Average", [self.plot_avg_2]),
("Rolling Average", [self.plot_trend_2]),
("Percentile Region", [self.plot_patch_2])],
location=(25, 0))
# Add the layout outside the plot, clicking legend item hides the line
self.plot.add_layout(legend_plot, 'right')
self.plot.legend.click_policy = "hide"
plot_options = list(range_categories)
plot_options.sort()
plot_options.insert(0, '')
self.y_axis = Select(value=plot_options[0], options=plot_options, width=300)
self.y_axis.title = "Select a Range Variable"
self.y_axis.on_change('value', self.update_y_axis_ticker)
self.look_back_distance = TextInput(value='1', title="Lookback Distance", width=200)
self.look_back_distance.on_change('value', self.update_plot_trend_ticker)
self.plot_percentile = TextInput(value='90', title="Percentile", width=200)
self.plot_percentile.on_change('value', self.update_plot_trend_ticker)
look_back_units_options = ['Dates with a Sim', 'Days']
self.look_back_units = Select(value=look_back_units_options[0], options=look_back_units_options, width=200)
self.look_back_units.title = 'Lookback Units'
self.look_back_units.on_change('value', self.update_plot_ticker)
# source_time.on_change('selected', plot_update_trend)
self.trend_update_button = Button(label="Update Trend", button_type="primary", width=150)
self.trend_update_button.on_click(self.plot_update_trend)
self.download_time_plot = Button(label="Download Plot Data", button_type="default", width=150)
self.download_time_plot.callback = CustomJS(args=dict(source_1=sources.time_1,
source_2=sources.time_2),
code=open(join(dirname(__file__),
"download_time_plot.js")).read())
# histograms
tools = "pan,wheel_zoom,box_zoom,reset,crosshair,save"
self.histograms = figure(plot_width=1050, plot_height=400, tools=tools, logo=None, active_drag="box_zoom")
self.histograms.xaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.histograms.yaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.histograms.xaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
self.histograms.yaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
self.histograms.min_border_left = options.MIN_BORDER
self.histograms.min_border_bottom = options.MIN_BORDER
self.hist_1 = self.histograms.vbar(x='x', width='width', bottom=0, top='top', source=sources.histogram_1,
color=options.GROUP_1_COLOR, alpha=options.HISTOGRAM_1_ALPHA)
self.hist_2 = self.histograms.vbar(x='x', width='width', bottom=0, top='top', source=sources.histogram_2,
color=options.GROUP_2_COLOR, alpha=options.HISTOGRAM_2_ALPHA)
self.histograms.xaxis.axis_label = ""
self.histograms.yaxis.axis_label = "Frequency"
self.histogram_bin_slider = Slider(start=1, end=100, value=10, step=1, title="Number of Bins")
self.histogram_bin_slider.on_change('value', self.histograms_ticker)
self.histogram_radio_group = RadioGroup(labels=["Absolute Y-Axis", "Relative Y-Axis (to Group Max)"], active=0)
self.histogram_radio_group.on_change('active', self.histograms_ticker)
self.histogram_normaltest_1_text = Div(text="Group 1 Normal Test p-value = ", width=400)
self.histogram_normaltest_2_text = Div(text="Group 2 Normal Test p-value = ", width=400)
self.histogram_ttest_text = Div(text="Two Sample t-Test (Group 1 vs 2) p-value = ", width=400)
self.histogram_ranksums_text = Div(text="Wilcoxon rank-sum (Group 1 vs 2) p-value = ", width=400)
self.histograms.add_tools(HoverTool(show_arrow=True, line_policy='next',
tooltips=[('x', '@x{0.2f}'),
('Counts', '@top')]))
# Set the legend
legend_hist = Legend(items=[("Group 1", [self.hist_1]),
("Group 2", [self.hist_2])],
location=(25, 0))
# Add the layout outside the plot, clicking legend item hides the line
self.histograms.add_layout(legend_hist, 'right')
self.histograms.legend.click_policy = "hide"
self.layout = column(Div(text="<b>DVH Analytics v%s</b>" % options.VERSION),
row(custom_title['1']['time_series'], Spacer(width=50),
custom_title['2']['time_series']),
row(self.y_axis, self.look_back_units, self.look_back_distance,
Spacer(width=10), self.plot_percentile, Spacer(width=10),
self.trend_update_button),
self.plot,
self.download_time_plot,
Div(text="<hr>", width=1050),
row(self.histogram_bin_slider, self.histogram_radio_group),
row(self.histogram_normaltest_1_text, self.histogram_ttest_text),
row(self.histogram_normaltest_2_text, self.histogram_ranksums_text),
self.histograms,
Spacer(width=1000, height=10))
def update_current_dvh_group(self, data):
self.current_dvh_group = data
def update_plot_ticker(self, attr, old, new):
self.update_plot()
def update_y_axis_ticker(self, attr, old, new):
self.update_plot()
def update_plot_trend_ticker(self, attr, old, new):
self.plot_update_trend()
def histograms_ticker(self, attr, old, new):
self.update_histograms()
def update_plot(self):
new = str(self.y_axis.value)
if new:
clear_source_selection(self.sources, 'time_1')
clear_source_selection(self.sources, 'time_2')
if new.startswith('DVH Endpoint: '):
y_var_name = new.split(': ')[1]
y_source_values = self.sources.endpoint_calcs.data[y_var_name]
y_source_uids = self.sources.endpoint_calcs.data['uid']
y_source_mrns = self.sources.endpoint_calcs.data['mrn']
elif new == 'EUD':
y_source_values = self.sources.rad_bio.data['eud']
y_source_uids = self.sources.rad_bio.data['uid']
y_source_mrns = self.sources.rad_bio.data['mrn']
elif new == 'NTCP/TCP':
y_source_values = self.sources.rad_bio.data['ntcp_tcp']
y_source_uids = self.sources.rad_bio.data['uid']
y_source_mrns = self.sources.rad_bio.data['mrn']
else:
y_source = self.range_categories[new]['source']
y_var_name = self.range_categories[new]['var_name']
y_source_values = y_source.data[y_var_name]
y_source_uids = y_source.data['uid']
y_source_mrns = y_source.data['mrn']
self.update_y_axis_label()
sim_study_dates = self.sources.plans.data['sim_study_date']
sim_study_dates_uids = self.sources.plans.data['uid']
x_values = []
skipped = []
colors = []
for v in range(len(y_source_values)):
uid = y_source_uids[v]
try:
sim_study_dates_index = sim_study_dates_uids.index(uid)
current_date_str = sim_study_dates[sim_study_dates_index]
if current_date_str == 'None':
current_date = datetime.now()
else:
current_date = datetime(int(current_date_str[0:4]),
int(current_date_str[5:7]),
int(current_date_str[8:10]))
x_values.append(current_date)
skipped.append(False)
except:
skipped.append(True)
# Get group color
if not skipped[-1]:
if new.startswith('DVH Endpoint') or new in {'EUD', 'NTCP/TCP'} \
or self.range_categories[new]['source'] == self.sources.dvhs:
if new in {'EUD', 'NTCP/TCP'}:
roi = self.sources.rad_bio.data['roi_name'][v]
else:
roi = self.sources.dvhs.data['roi_name'][v]
found = {'Group 1': False, 'Group 2': False}
color = None
if self.current_dvh_group['1']:
r1, r1_max = 0, len(self.current_dvh_group['1'].study_instance_uid)
while r1 < r1_max and not found['Group 1']:
if self.current_dvh_group['1'].study_instance_uid[r1] == uid and \
self.current_dvh_group['1'].roi_name[r1] == roi:
found['Group 1'] = True
color = options.GROUP_1_COLOR
r1 += 1
if self.current_dvh_group['2']:
r2, r2_max = 0, len(self.current_dvh_group['2'].study_instance_uid)
while r2 < r2_max and not found['Group 2']:
if self.current_dvh_group['2'].study_instance_uid[r2] == uid and \
self.current_dvh_group['2'].roi_name[r2] == roi:
found['Group 2'] = True
if found['Group 1']:
color = options.GROUP_1_and_2_COLOR
else:
color = options.GROUP_2_COLOR
r2 += 1
colors.append(color)
else:
if self.current_dvh_group['1'] and self.current_dvh_group['2']:
if uid in self.current_dvh_group['1'].study_instance_uid and \
uid in self.current_dvh_group['2'].study_instance_uid:
colors.append(options.GROUP_1_and_2_COLOR)
elif uid in self.current_dvh_group['1'].study_instance_uid:
colors.append(options.GROUP_1_COLOR)
else:
colors.append(options.GROUP_2_COLOR)
elif self.current_dvh_group['1']:
colors.append(options.GROUP_1_COLOR)
else:
colors.append(options.GROUP_2_COLOR)
y_values = []
y_mrns = []
for v in range(len(y_source_values)):
if not skipped[v]:
y_values.append(y_source_values[v])
y_mrns.append(y_source_mrns[v])
if not isinstance(y_values[-1], (int, long, float)):
y_values[-1] = 0
sort_index = sorted(range(len(x_values)), key=lambda k: x_values[k])
x_values_sorted, y_values_sorted, y_mrns_sorted, colors_sorted = [], [], [], []
for s in range(len(x_values)):
x_values_sorted.append(x_values[sort_index[s]])
y_values_sorted.append(y_values[sort_index[s]])
y_mrns_sorted.append(y_mrns[sort_index[s]])
colors_sorted.append(colors[sort_index[s]])
source_time_1_data = {'x': [], 'y': [], 'mrn': [], 'date_str': []}
source_time_2_data = {'x': [], 'y': [], 'mrn': [], 'date_str': []}
for i in range(len(x_values_sorted)):
if colors_sorted[i] in {options.GROUP_1_COLOR, options.GROUP_1_and_2_COLOR}:
source_time_1_data['x'].append(x_values_sorted[i])
source_time_1_data['y'].append(y_values_sorted[i])
source_time_1_data['mrn'].append(y_mrns_sorted[i])
source_time_1_data['date_str'].append(x_values_sorted[i].strftime("%Y-%m-%d"))
if colors_sorted[i] in {options.GROUP_2_COLOR, options.GROUP_1_and_2_COLOR}:
source_time_2_data['x'].append(x_values_sorted[i])
source_time_2_data['y'].append(y_values_sorted[i])
source_time_2_data['mrn'].append(y_mrns_sorted[i])
source_time_2_data['date_str'].append(x_values_sorted[i].strftime("%Y-%m-%d"))
self.sources.time_1.data = source_time_1_data
self.sources.time_2.data = source_time_2_data
else:
clear_source_data(self.sources, 'time_1')
clear_source_data(self.sources, 'time_2')
self.plot_update_trend()
def plot_update_trend(self):
if self.y_axis.value:
selected_indices = {n: getattr(self.sources, 'time_%s' % n).selected.indices for n in GROUP_LABELS}
for n in GROUP_LABELS:
if not selected_indices[n]:
selected_indices[n] = range(len(getattr(self.sources, 'time_%s' % n).data['x']))
group = {n: {'x': [], 'y': []} for n in GROUP_LABELS}
for n in GROUP_LABELS:
for i in range(len(getattr(self.sources, 'time_%s' % n).data['x'])):
if i in selected_indices[n]:
for v in ['x', 'y']:
group[n][v].append(getattr(self.sources, 'time_%s' % n).data[v][i])
try:
avg_len = int(self.look_back_distance.value)
except:
avg_len = 1
try:
percentile = float(self.plot_percentile.value)
except:
percentile = 90.
# average daily data and keep track of points per day, calculate moving average
group_collapsed = {n: [] for n in GROUP_LABELS}
for n in GROUP_LABELS:
if group[n]['x']:
group_collapsed[n] = collapse_into_single_dates(group[n]['x'], group[n]['y'])
if self.look_back_units.value == "Dates with a Sim":
x_trend, moving_avgs = moving_avg(group_collapsed[n], avg_len)
else:
x_trend, moving_avgs = moving_avg_by_calendar_day(group_collapsed[n], avg_len)
y_np = np.array(group[n]['y'])
upper_bound = float(np.percentile(y_np, 50. + percentile / 2.))
average = float(np.percentile(y_np, 50))
lower_bound = float(np.percentile(y_np, 50. - percentile / 2.))
getattr(self.sources, 'time_trend_%s' % n).data = {'x': x_trend,
'y': moving_avgs,
'mrn': ['Avg'] * len(x_trend)}
getattr(self.sources, 'time_bound_%s' % n).data = {'x': group[n]['x'],
'mrn': ['Bound'] * len(group[n]['x']),
'upper': [upper_bound] * len(group[n]['x']),
'avg': [average] * len(group[n]['x']),
'lower': [lower_bound] * len(group[n]['x'])}
getattr(self.sources, 'time_patch_%s' % n).data = {'x': [group[n]['x'][0], group[n]['x'][-1],
group[n]['x'][-1], group[n]['x'][0]],
'y': [upper_bound, upper_bound, lower_bound, lower_bound]}
else:
for v in ['trend', 'bound', 'patch']:
clear_source_data(self.sources, 'time_%s_%s' % (v, n))
x_var = str(self.y_axis.value)
if x_var.startswith('DVH Endpoint'):
self.histograms.xaxis.axis_label = x_var.split("DVH Endpoint: ")[1]
elif x_var == 'EUD':
self.histograms.xaxis.axis_label = "%s (Gy)" % x_var
elif x_var == 'NTCP/TCP':
self.histograms.xaxis.axis_label = "NTCP or TCP"
else:
if self.range_categories[x_var]['units']:
self.histograms.xaxis.axis_label = "%s (%s)" % (x_var, self.range_categories[x_var]['units'])
else:
self.histograms.xaxis.axis_label = x_var
# Normal Test
s, p = {n: '' for n in GROUP_LABELS}, {n: '' for n in GROUP_LABELS}
for n in GROUP_LABELS:
if group[n]['y']:
s[n], p[n] = normaltest(group[n]['y'])
p[n] = "%0.3f" % p[n]
# t-Test and Rank Sums
pt, pr = '', ''
if group['1']['y'] and group['2']['y']:
st, pt = ttest_ind(group['1']['y'], group['2']['y'])
sr, pr = ranksums(group['1']['y'], group['2']['y'])
pt = "%0.3f" % pt
pr = "%0.3f" % pr
self.histogram_normaltest_1_text.text = "Group 1 Normal Test p-value = %s" % p['1']
self.histogram_normaltest_2_text.text = "Group 2 Normal Test p-value = %s" % p['2']
self.histogram_ttest_text.text = "Two Sample t-Test (Group 1 vs 2) p-value = %s" % pt
self.histogram_ranksums_text.text = "Wilcoxon rank-sum (Group 1 vs 2) p-value = %s" % pr
else:
for n in GROUP_LABELS:
for k in ['trend', 'bound', 'patch']:
clear_source_data(self.sources, "time_%s_%s" % (k, n))
self.histogram_normaltest_1_text.text = "Group 1 Normal Test p-value = "
self.histogram_normaltest_2_text.text = "Group 2 Normal Test p-value = "
self.histogram_ttest_text.text = "Two Sample t-Test (Group 1 vs 2) p-value = "
self.histogram_ranksums_text.text = "Wilcoxon rank-sum (Group 1 vs 2) p-value = "
self.update_histograms()
def update_histograms(self):
if self.y_axis.value != '':
# Update Histograms
bin_size = int(self.histogram_bin_slider.value)
width_fraction = 0.9
for n in GROUP_LABELS:
hist, bins = np.histogram(getattr(self.sources, 'time_%s' % n).data['y'], bins=bin_size)
if self.histogram_radio_group.active == 1:
hist = np.divide(hist, np.float(np.max(hist)))
self.histograms.yaxis.axis_label = "Relative Frequency"
else:
self.histograms.yaxis.axis_label = "Frequency"
width = [width_fraction * (bins[1] - bins[0])] * bin_size
center = (bins[:-1] + bins[1:]) / 2.
getattr(self.sources, 'histogram_%s' % n).data = {'x': center,
'top': hist,
'width': width}
else:
for n in GROUP_LABELS:
clear_source_data(self.sources, 'histogram_%s' % n)
def update_y_axis_label(self):
new = str(self.y_axis.value)
if new:
# If new has something in parenthesis, extract and put in front
new_split = new.split(' (')
if len(new_split) > 1:
new_display = "%s %s" % (new_split[1].split(')')[0], new_split[0])
else:
new_display = new
if new.startswith('DVH Endpoint'):
self.plot.yaxis.axis_label = str(self.y_axis.value).split(': ')[1]
elif new == 'EUD':
self.plot.yaxis.axis_label = 'EUD (Gy)'
elif new == 'NTCP/TCP':
self.plot.yaxis.axis_label = 'NTCP or TCP'
elif self.range_categories[new]['units']:
self.plot.yaxis.axis_label = "%s (%s)" % (new_display, self.range_categories[new]['units'])
else:
self.plot.yaxis.axis_label = new_display
def update_options(self):
new_options = list(self.range_categories)
new_options.extend(['EUD', 'NTCP/TCP'])
for ep in self.sources.endpoint_calcs.data:
if ep.startswith('V_') or ep.startswith('D_'):
new_options.append("DVH Endpoint: %s" % ep)
new_options.sort()
new_options.insert(0, '')
self.y_axis.options = new_options
self.y_axis.value = ''
# hide glyphs by clicking on an entry in a Legend.
p.title.text = 'Click on legend entries to hide the corresponding lines'
p.legend.click_policy = "hide"
# "mute" "hide"
# Vertical line
vline = Span(location=0,
dimension='height',
line_color='black',
line_width=0.5)
# Horizontal line
hline = Span(location=0, dimension='width', line_color='black', line_width=0.5)
p.renderers.extend([vline, hline])
button = Button(label='reset', width=100, align="center")
callback2 = CustomJS(args=dict(p=p, x_slide=x_slider, y_slide=y_slider),
code="""
p.reset.emit();
x_slide.value = [500,1800];
y_slide.value = [-5000,5000];
""")
button.js_on_click(callback2)
# button3 = Button(label='Download 6s',width=100, align="center")
# def export():
# # print('I was clicked')
# df = pandas.read_csv('Cs.csv')
# df = pandas.DataFrame(df, columns= ['wavelength','polarizability'])
# df.to_csv(r'C:\Users\13022\Desktop\website\Bokeh\versionFinal\export_cs.csv', index = False, header=True)
# return send_file('export_cs',
def on_selection_change2(obj, attr, _, inds):
if inds:
[index] = inds
size = [10] * N
size[index] = 40
else:
size = [20] * N
source1.data["size"] = size
session.store_objects(source1)
source2.on_change('selected', on_selection_change2)
reset = Button(label="Reset")
def on_reset_click():
source1.selected = []
source2.selected = []
session.store_objects(source1, source2)
reset.on_click(on_reset_click)
vbox = VBox(children=[reset], width=150)
hbox = HBox(children=[vbox, plot1, plot2])
document.add(hbox)
session.store_document(document)
def create_interact_ui(doc):
fig_tpf, stretch_slider = self._make_echelle_elements(
dnu,
maximum_frequency=maximum_frequency,
minimum_frequency=minimum_frequency,
**kwargs)
maxdnu = self.periodogram.frequency.max().value / 5
# Interactive slider widgets
dnu_slider = Slider(start=0.01,
end=maxdnu,
value=dnu.value,
step=0.01,
title="Delta Nu",
width=290)
r_button = Button(label=">", button_type="default", width=30)
l_button = Button(label="<", button_type="default", width=30)
rr_button = Button(label=">>", button_type="default", width=30)
ll_button = Button(label="<<", button_type="default", width=30)
def update(attr, old, new):
"""Callback to take action when dnu slider changes"""
dnu = SeismologyQuantity(quantity=dnu_slider.value *
u.microhertz,
name='deltanu',
method='echelle')
ep, _, _ = self._clean_echelle(
deltanu=dnu,
minimum_frequency=minimum_frequency,
maximum_frequency=maximum_frequency,
**kwargs)
fig_tpf.select('img')[0].data_source.data['image'] = [ep.value]
fig_tpf.xaxis.axis_label = r'Frequency / {:.3f} Mod. 1'.format(
dnu)
def go_right_by_one_small():
"""Step forward in time by a single cadence"""
existing_value = dnu_slider.value
if existing_value < maxdnu:
dnu_slider.value = existing_value + 0.002
def go_left_by_one_small():
"""Step back in time by a single cadence"""
existing_value = dnu_slider.value
if existing_value > 0:
dnu_slider.value = existing_value - 0.002
def go_right_by_one():
"""Step forward in time by a single cadence"""
existing_value = dnu_slider.value
if existing_value < maxdnu:
dnu_slider.value = existing_value + 0.01
def go_left_by_one():
"""Step back in time by a single cadence"""
existing_value = dnu_slider.value
if existing_value > 0:
dnu_slider.value = existing_value - 0.01
dnu_slider.on_change('value', update)
r_button.on_click(go_right_by_one_small)
l_button.on_click(go_left_by_one_small)
rr_button.on_click(go_right_by_one)
ll_button.on_click(go_left_by_one)
widgets_and_figures = layout(
[fig_tpf, [Spacer(height=20), stretch_slider]], [
ll_button,
Spacer(width=30), l_button,
Spacer(width=25), dnu_slider,
Spacer(width=30), r_button,
Spacer(width=23), rr_button
])
doc.add_root(widgets_and_figures)
def create_goto_event_id_widget(self):
self.w_goto_event_id = Button(label="GOTO ID", button_type="default", width=70)
self.w_goto_event_id.on_click(self.on_goto_event_id_widget_click)
def create_goto_event_index_widget(self):
self.w_goto_event_index = Button(
label="GOTO Index", button_type="default", width=100
)
self.w_goto_event_index.on_click(self.on_goto_event_index_widget_click)
def __init__(self):
self.zoom = 12
self.center = self.start_location
# Set up map
lon_text = TextInput(value='', title='lon:')
lat_text = TextInput(value='', title='lat:')
self.lonlat_text_inputs = [lon_text, lat_text]
self.topo_map = TopoMap(WORKING_POLYGON)
self.folium_fig = self.bokeh_new_class_folium(
lonlat_text_inputs=self.lonlat_text_inputs)
# Set up widgets
self.meters_step = Slider(title="meters_step",
value=400,
start=10,
end=500,
step=10)
self.number_of_points_to_show = Slider(
title="number of points to show", value=2, start=1, end=100)
self.threshold = Slider(title="threshold for class",
value=0,
start=0,
end=1,
step=0.01)
self.test_minimal_resolution = Slider(title="minimal resolution",
value=8,
start=2,
end=50)
get_points_button = Button(label='Get desired points!')
get_points_button.on_click(self.get_points_and_update)
set_working_polygon_button = Button(label='Set working polygon!')
set_working_polygon_button.on_click(self.set_working_polygon)
clean_all_buttun = Button(label='clean all')
clean_all_buttun.on_click(self.clean_all)
clean_text_buttun = Button(label='clean text')
clean_text_buttun.on_click(self.clean_text)
select_class_options = self.topo_map.get_all_available_classes()
self.select_class = Select(title="Option:",
value=select_class_options[0],
options=select_class_options)
get_class_button = Button(label='get_class')
get_class_button.on_click(self.get_points_and_update_for_class)
select_final_model_options = client_lib.get_available_final_model_file_names(
)
self.select_final_model = Select(title="Option:",
value=select_final_model_options[0],
options=select_final_model_options)
final_model_button = Button(label='select final model')
final_model_button.on_click(self.update_final_model)
get_segmentation_map_button = Button(label='get segmentation map')
get_segmentation_map_button.on_click(self.add_segmentation_map)
self.row_mid_column = column(Div(text='get top points of class'),
self.select_class, get_class_button,
get_segmentation_map_button,
self.select_final_model,
final_model_button, Div(text=''))
# Set up layouts and add to document
inputs = row(
column(Div(text='get similar points'), lon_text, lat_text,
get_points_button, set_working_polygon_button,
clean_all_buttun, clean_text_buttun), self.row_mid_column,
column(Div(text='search parameters'), self.meters_step,
self.number_of_points_to_show, self.threshold,
self.test_minimal_resolution))
self.main_panel = row(inputs, self.folium_fig, width=800)
def on_selection_change2(obj, attr, _, inds):
inds = inds["1d"]["indices"]
if inds:
[index] = inds
size = [10] * N
size[index] = 40
else:
size = [20] * N
source1.data["size"] = size
session.store_objects(source1)
source2.on_change("selected", on_selection_change2)
reset = Button(label="Reset")
def on_reset_click():
source1.selected = {"0d": {"flag": False, "indices": []}, "1d": {"indices": []}, "2d": {"indices": []}}
source2.selected = {"0d": {"flag": False, "indices": []}, "1d": {"indices": []}, "2d": {"indices": []}}
session.store_objects(source1, source2)
reset.on_click(on_reset_click)
vbox = VBox(children=[reset], width=150)
hbox = HBox(children=[vbox, plot1, plot2])
document.add(hbox)
session.store_document(document)
]
data_table = DataTable(source=source, columns=columns,
width=300, height=600)
def toggle_callback(attr):
if tide_toggle.active:
# Checked *after* press
tide_toggle.label = "Disable Tides"
else:
tide_toggle.label = "Enable Tides"
tide_toggle = Toggle(label="Enable Tides", callback=toggle_ocean)
tide_toggle.on_click(toggle_callback)
download_button = Button(label="Download data", callback=download_data)
go_button = Button(label="Run model")#, callback=check_fish)
go_button.on_click(update_plots)
# Set up app layout
prods = VBox(gas_exchange_slider, productivity_slider)
river = VBox(river_flow_slider, river_N_slider)
tide_run = HBox(tide_toggle, download_button, go_button)
all_settings = VBox(prods, river, tide_run,
width=400)
# Add to current document
curdoc().add_root(HBox(children=[all_settings, plots]))
def __init__(self, sources, range_categories, custom_title, data_tables):
self.sources = sources
self.range_categories = range_categories
self.current_dvh_group = {n: [] for n in GROUP_LABELS}
# Control Chart layout (Time-Series)
tools = "pan,wheel_zoom,box_zoom,lasso_select,poly_select,reset,crosshair,save"
self.plot = figure(plot_width=1050, plot_height=400, tools=tools, logo=None,
active_drag="box_zoom", x_axis_type='datetime')
self.plot.xaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.plot.yaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.plot.xaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
self.plot.yaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
# plot.min_border_left = min_border
self.plot.min_border_bottom = options.MIN_BORDER
self.plot_data_1 = self.plot.circle('x', 'y', size=options.TIME_SERIES_1_CIRCLE_SIZE,
color=options.GROUP_1_COLOR,
alpha=options.TIME_SERIES_1_CIRCLE_ALPHA,
source=sources.time_1)
self.plot_data_2 = self.plot.circle('x', 'y', size=options.TIME_SERIES_2_CIRCLE_SIZE,
color=options.GROUP_2_COLOR,
alpha=options.TIME_SERIES_2_CIRCLE_ALPHA,
source=sources.time_2)
self.plot_trend_1 = self.plot.line('x', 'y', color=options.GROUP_1_COLOR, source=sources.time_trend_1,
line_width=options.TIME_SERIES_1_TREND_LINE_WIDTH,
line_dash=options.TIME_SERIES_1_TREND_LINE_DASH)
self.plot_trend_2 = self.plot.line('x', 'y', color=options.GROUP_2_COLOR, source=sources.time_trend_2,
line_width=options.TIME_SERIES_2_TREND_LINE_WIDTH,
line_dash=options.TIME_SERIES_2_TREND_LINE_DASH)
self.plot_avg_1 = self.plot.line('x', 'avg', color=options.GROUP_1_COLOR, source=sources.time_bound_1,
line_width=options.TIME_SERIES_1_AVG_LINE_WIDTH,
line_dash=options.TIME_SERIES_1_AVG_LINE_DASH)
self.plot_avg_2 = self.plot.line('x', 'avg', color=options.GROUP_2_COLOR, source=sources.time_bound_2,
line_width=options.TIME_SERIES_2_AVG_LINE_WIDTH,
line_dash=options.TIME_SERIES_2_AVG_LINE_DASH)
self.plot_patch_1 = self.plot.patch('x', 'y', color=options.GROUP_1_COLOR, source=sources.time_patch_1,
alpha=options.TIME_SERIES_1_PATCH_ALPHA)
self.plot_patch_2 = self.plot.patch('x', 'y', color=options.GROUP_2_COLOR, source=sources.time_patch_2,
alpha=options.TIME_SERIES_1_PATCH_ALPHA)
self.plot.add_tools(HoverTool(show_arrow=True,
tooltips=[('ID', '@mrn'),
('Date', '@x{%F}'),
('Value', '@y{0.2f}')],
formatters={'x': 'datetime'}))
self.plot.xaxis.axis_label = "Simulation Date"
self.plot.yaxis.axis_label = ""
# Set the legend
legend_plot = Legend(items=[("Group 1", [self.plot_data_1]),
("Series Average", [self.plot_avg_1]),
("Rolling Average", [self.plot_trend_1]),
("Percentile Region", [self.plot_patch_1]),
("Group 2", [self.plot_data_2]),
("Series Average", [self.plot_avg_2]),
("Rolling Average", [self.plot_trend_2]),
("Percentile Region", [self.plot_patch_2])],
location=(25, 0))
# Add the layout outside the plot, clicking legend item hides the line
self.plot.add_layout(legend_plot, 'right')
self.plot.legend.click_policy = "hide"
plot_options = list(range_categories)
plot_options.sort()
plot_options.insert(0, '')
self.y_axis = Select(value=plot_options[0], options=plot_options, width=300)
self.y_axis.title = "Select a Range Variable"
self.y_axis.on_change('value', self.update_y_axis_ticker)
self.look_back_distance = TextInput(value='1', title="Lookback Distance", width=200)
self.look_back_distance.on_change('value', self.update_plot_trend_ticker)
self.plot_percentile = TextInput(value='90', title="Percentile", width=200)
self.plot_percentile.on_change('value', self.update_plot_trend_ticker)
look_back_units_options = ['Dates with a Sim', 'Days']
self.look_back_units = Select(value=look_back_units_options[0], options=look_back_units_options, width=200)
self.look_back_units.title = 'Lookback Units'
self.look_back_units.on_change('value', self.update_plot_ticker)
# source_time.on_change('selected', plot_update_trend)
self.trend_update_button = Button(label="Update Trend", button_type="primary", width=150)
self.trend_update_button.on_click(self.plot_update_trend)
self.download_time_plot = Button(label="Download Plot Data", button_type="default", width=150)
self.download_time_plot.callback = CustomJS(args=dict(source_1=sources.time_1,
source_2=sources.time_2),
code=open(join(dirname(__file__),
"download_time_plot.js")).read())
# histograms
tools = "pan,wheel_zoom,box_zoom,reset,crosshair,save"
self.histograms = figure(plot_width=1050, plot_height=400, tools=tools, logo=None, active_drag="box_zoom")
self.histograms.xaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.histograms.yaxis.axis_label_text_font_size = options.PLOT_AXIS_LABEL_FONT_SIZE
self.histograms.xaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
self.histograms.yaxis.major_label_text_font_size = options.PLOT_AXIS_MAJOR_LABEL_FONT_SIZE
self.histograms.min_border_left = options.MIN_BORDER
self.histograms.min_border_bottom = options.MIN_BORDER
self.hist_1 = self.histograms.vbar(x='x', width='width', bottom=0, top='top', source=sources.histogram_1,
color=options.GROUP_1_COLOR, alpha=options.HISTOGRAM_1_ALPHA)
self.hist_2 = self.histograms.vbar(x='x', width='width', bottom=0, top='top', source=sources.histogram_2,
color=options.GROUP_2_COLOR, alpha=options.HISTOGRAM_2_ALPHA)
self.histograms.xaxis.axis_label = ""
self.histograms.yaxis.axis_label = "Frequency"
self.histogram_bin_slider = Slider(start=1, end=100, value=10, step=1, title="Number of Bins")
self.histogram_bin_slider.on_change('value', self.histograms_ticker)
self.histogram_radio_group = RadioGroup(labels=["Absolute Y-Axis", "Relative Y-Axis (to Group Max)"], active=0)
self.histogram_radio_group.on_change('active', self.histograms_ticker)
self.histogram_normaltest_1_text = Div(text="Group 1 Normal Test p-value = ", width=400)
self.histogram_normaltest_2_text = Div(text="Group 2 Normal Test p-value = ", width=400)
self.histogram_ttest_text = Div(text="Two Sample t-Test (Group 1 vs 2) p-value = ", width=400)
self.histogram_ranksums_text = Div(text="Wilcoxon rank-sum (Group 1 vs 2) p-value = ", width=400)
self.histograms.add_tools(HoverTool(show_arrow=True, line_policy='next',
tooltips=[('x', '@x{0.2f}'),
('Counts', '@top')]))
# Set the legend
legend_hist = Legend(items=[("Group 1", [self.hist_1]),
("Group 2", [self.hist_2])],
location=(25, 0))
# Add the layout outside the plot, clicking legend item hides the line
self.histograms.add_layout(legend_hist, 'right')
self.histograms.legend.click_policy = "hide"
self.layout = column(Div(text="<b>DVH Analytics v%s</b>" % options.VERSION),
row(custom_title['1']['time_series'], Spacer(width=50),
custom_title['2']['time_series']),
row(self.y_axis, self.look_back_units, self.look_back_distance,
Spacer(width=10), self.plot_percentile, Spacer(width=10),
self.trend_update_button),
self.plot,
self.download_time_plot,
Div(text="<hr>", width=1050),
row(self.histogram_bin_slider, self.histogram_radio_group),
row(self.histogram_normaltest_1_text, self.histogram_ttest_text),
row(self.histogram_normaltest_2_text, self.histogram_ranksums_text),
self.histograms,
Spacer(width=1000, height=10))
def write_segmentation():
save_fiducials(new_pts,'./SEGMENTATIONS_NEW.csv')
def change_range(attr, old, new):
low, high = rangeslider.value
for i in range(12):
leads[i].x_range.start = low
leads[i].x_range.end = high
# Set widgets
rangeslider = RangeSlider(start=0, end=1000, step=1, value=(0,1000), title="X range")
file_selector = Select(value=None, options=nix(None,list_files_bokeh(DATA_DIR)))
textboxold = PreText(text="Original points: \t[]")
textboxnew = PreText(text="New points: \t[]")
retrievebutton = Button(label='Retrieve Segmentation')
storebutton = Button(label='Store Segmentation')
writebutton = Button(label='Write to File')
# Set callbacks
file_selector.on_change('value', file_change)
source.selected.on_change('indices', selection_change)
retrievebutton.on_click(retrieve_segmentation)
storebutton.on_click(save_segmentation)
writebutton.on_click(write_segmentation)
rangeslider.on_change('value',change_range)
# set up layout
textboxes = row(textboxold,textboxnew)
buttons = row(retrievebutton,storebutton,writebutton,rangeslider)
pass
#### WIDGET CREATIONS ####
# OLD VANILLA
# add a button widget and configure with the call back
# button_basic = Button(label="Press Me")
# button_basic.on_click(callback)
#make_bokeh_crossfilter()
# create a button for Select button for input
#menu = [("Bulk Modulus", "B"), ("B'", "dB"), ("Lattice Constant", "a0")]
#select_property = Select(name="Selection", options=menu, value="B")
#select_property.on_click(make_bokeh_crossfilter(axis=value))
# create a button for make crossfilter app
button_crossfilter = Button(label="Make Crossfilter")
button_crossfilter.on_click(make_bokeh_crossfilter)
#create a button for crossfilter_workflwo
button_w_crossfilter = Button(label="Make Crossfilter Workflow")
button_w_crossfilter.on_click(make_wflow_crossfilter)
# put the button and plot in a layout and add to the document
curdoc().add_root(column(button_crossfilter, button_w_crossfilter, p))
doc = curdoc()
'''
Variables
'''
renderer = None
render_callback = None
speed = 0.1
viz_dt = 50 # update every ms
'''
UI
'''
t1 = Div(text='Time:', style={'font-size': '150%'})
t2 = Div(text='N/A', style={'font-size': '150%'})
reset_button = Button(label='⟲ Reset', width=60)
pp_button = Button(label='► Play', width=60, margin=(5, 5, 5, 15))
rec_button = Button(label='⏺️ Record', width=75, margin=(5, 15, 5, 5))
speed_slider = Slider(start=-2.0,
end=1.0,
value=-1.0,
step=0.02,
title='Speed',
width=300)
'''
Callbacks
'''
def update():
global renderer, viz_dt, render_callback
dataSelect = Select(title='Select Data', options=fileNames)
dataSelect.on_change('value', updatePatientCallback)
def increaseCallback():
selects = iP.getSelects(entirePage.children[1].children[0].children)
print(selects)
createInnerPlot.toAddText(selects)
entirePage.children[1] = createInnerPlot(folder, fileName)
return
addButton = Button(label='Add Sentence Outer')
addButton.on_click(increaseCallback)
#-------------------------------------------------------
# Generate information about the first patient
#-------------------------------------------------------
innerPlot = createInnerPlot(folder, fileName)
entirePage = column([dataSelect, innerPlot, addButton])
curdoc().add_root(entirePage)
curdoc().title = "labelData"
class BokehFileViewer(Tool):
name = "BokehFileViewer"
description = ("Interactively explore an event file using the bokeh "
"visualisation package")
port = Int(5006, help="Port to open bokeh server onto").tag(config=True)
disable_server = Bool(False, help="Do not start the bokeh server "
"(useful for testing)").tag(config=True)
aliases = Dict(dict(
port='BokehFileViewer.port',
disable_server='BokehFileViewer.disable_server',
r='EventSourceFactory.product',
f='EventSourceFactory.input_url',
max_events='EventSourceFactory.max_events',
ped='CameraR1CalibratorFactory.pedestal_path',
tf='CameraR1CalibratorFactory.tf_path',
pe='CameraR1CalibratorFactory.pe_path',
ff='CameraR1CalibratorFactory.ff_path',
extractor='ChargeExtractorFactory.product',
extractor_t0='ChargeExtractorFactory.t0',
extractor_window_width='ChargeExtractorFactory.window_width',
extractor_window_shift='ChargeExtractorFactory.window_shift',
extractor_sig_amp_cut_HG='ChargeExtractorFactory.sig_amp_cut_HG',
extractor_sig_amp_cut_LG='ChargeExtractorFactory.sig_amp_cut_LG',
extractor_lwt='ChargeExtractorFactory.lwt',
cleaner='WaveformCleanerFactory.product',
))
classes = List([
EventSourceFactory,
ChargeExtractorFactory,
CameraR1CalibratorFactory,
CameraDL1Calibrator,
WaveformCleanerFactory
])
def __init__(self, **kwargs):
super().__init__(**kwargs)
self._event = None
self._event_index = None
self._event_id = None
self._telid = None
self._channel = None
self.w_next_event = None
self.w_previous_event = None
self.w_event_index = None
self.w_event_id = None
self.w_goto_event_index = None
self.w_goto_event_id = None
self.w_telid = None
self.w_channel = None
self.w_dl1_dict = None
self.wb_extractor = None
self.layout = None
self.reader = None
self.seeker = None
self.extractor = None
self.cleaner = None
self.r1 = None
self.dl0 = None
self.dl1 = None
self.viewer = None
self._updating_dl1 = False
def setup(self):
self.log_format = "%(levelname)s: %(message)s [%(name)s.%(funcName)s]"
kwargs = dict(config=self.config, tool=self)
default_url = get_dataset_path("gamma_test.simtel.gz")
EventSourceFactory.input_url.default_value = default_url
self.reader = EventSourceFactory.produce(**kwargs)
self.seeker = EventSeeker(self.reader, **kwargs)
self.extractor = ChargeExtractorFactory.produce(**kwargs)
self.cleaner = WaveformCleanerFactory.produce(**kwargs)
self.r1 = CameraR1CalibratorFactory.produce(
eventsource=self.reader,
**kwargs
)
self.dl0 = CameraDL0Reducer(**kwargs)
self.dl1 = CameraDL1Calibrator(
extractor=self.extractor,
cleaner=self.cleaner,
**kwargs
)
self.viewer = BokehEventViewer(**kwargs)
# Setup widgets
self.viewer.create()
self.viewer.enable_automatic_index_increment()
self.create_previous_event_widget()
self.create_next_event_widget()
self.create_event_index_widget()
self.create_goto_event_index_widget()
self.create_event_id_widget()
self.create_goto_event_id_widget()
self.create_telid_widget()
self.create_channel_widget()
self.create_dl1_widgets()
self.update_dl1_widget_values()
# Setup layout
self.layout = layout([
[self.viewer.layout],
[
self.w_previous_event,
self.w_next_event,
self.w_goto_event_index,
self.w_goto_event_id
],
[self.w_event_index, self.w_event_id],
[self.w_telid, self.w_channel],
[self.wb_extractor]
])
def start(self):
self.event_index = 0
def finish(self):
if not self.disable_server:
def modify_doc(doc):
doc.add_root(self.layout)
doc.title = self.name
directory = os.path.abspath(os.path.dirname(__file__))
theme_path = os.path.join(directory, "theme.yaml")
template_path = os.path.join(directory, "templates")
doc.theme = Theme(filename=theme_path)
env = jinja2.Environment(
loader=jinja2.FileSystemLoader(template_path)
)
doc.template = env.get_template('index.html')
self.log.info('Opening Bokeh application on '
'http://localhost:{}/'.format(self.port))
server = Server({'/': modify_doc}, num_procs=1, port=self.port)
server.start()
server.io_loop.add_callback(server.show, "/")
server.io_loop.start()
@property
def event_index(self):
return self._event_index
@event_index.setter
def event_index(self, val):
try:
self.event = self.seeker[val]
except IndexError:
self.log.warning("Event Index {} does not exist".format(val))
@property
def event_id(self):
return self._event_id
@event_id.setter
def event_id(self, val):
try:
self.event = self.seeker[str(val)]
except IndexError:
self.log.warning("Event ID {} does not exist".format(val))
@property
def telid(self):
return self._telid
@telid.setter
def telid(self, val):
self.channel = 0
tels = list(self.event.r0.tels_with_data)
if val not in tels:
val = tels[0]
self._telid = val
self.viewer.telid = val
self.update_telid_widget()
@property
def channel(self):
return self._channel
@channel.setter
def channel(self, val):
self._channel = val
self.viewer.channel = val
self.update_channel_widget()
@property
def event(self):
return self._event
@event.setter
def event(self, val):
# Calibrate
self.r1.calibrate(val)
self.dl0.reduce(val)
self.dl1.calibrate(val)
self._event = val
self.viewer.event = val
self._event_index = val.count
self._event_id = val.r0.event_id
self.update_event_index_widget()
self.update_event_id_widget()
self._telid = self.viewer.telid
self.update_telid_widget()
self._channel = self.viewer.channel
self.update_channel_widget()
def update_dl1_calibrator(self, extractor=None, cleaner=None):
"""
Recreate the dl1 calibrator with the specified extractor and cleaner
Parameters
----------
extractor : ctapipe.image.charge_extractors.ChargeExtractor
cleaner : ctapipe.image.waveform_cleaning.WaveformCleaner
"""
if extractor is None:
extractor = self.dl1.extractor
if cleaner is None:
cleaner = self.dl1.cleaner
self.extractor = extractor
self.cleaner = cleaner
kwargs = dict(config=self.config, tool=self)
self.dl1 = CameraDL1Calibrator(
extractor=self.extractor,
cleaner=self.cleaner,
**kwargs
)
self.dl1.calibrate(self.event)
self.viewer.refresh()
def create_next_event_widget(self):
self.w_next_event = Button(label=">", button_type="default", width=50)
self.w_next_event.on_click(self.on_next_event_widget_click)
def on_next_event_widget_click(self):
self.event_index += 1
def create_previous_event_widget(self):
self.w_previous_event = Button(
label="<",
button_type="default",
width=50
)
self.w_previous_event.on_click(self.on_previous_event_widget_click)
def on_previous_event_widget_click(self):
self.event_index -= 1
def create_event_index_widget(self):
self.w_event_index = TextInput(title="Event Index:", value='')
def update_event_index_widget(self):
if self.w_event_index:
self.w_event_index.value = str(self.event_index)
def create_event_id_widget(self):
self.w_event_id = TextInput(title="Event ID:", value='')
def update_event_id_widget(self):
if self.w_event_id:
self.w_event_id.value = str(self.event_id)
def create_goto_event_index_widget(self):
self.w_goto_event_index = Button(
label="GOTO Index",
button_type="default",
width=100
)
self.w_goto_event_index.on_click(self.on_goto_event_index_widget_click)
def on_goto_event_index_widget_click(self):
self.event_index = int(self.w_event_index.value)
def create_goto_event_id_widget(self):
self.w_goto_event_id = Button(
label="GOTO ID",
button_type="default",
width=70
)
self.w_goto_event_id.on_click(self.on_goto_event_id_widget_click)
def on_goto_event_id_widget_click(self):
self.event_id = int(self.w_event_id.value)
def create_telid_widget(self):
self.w_telid = Select(title="Telescope:", value="", options=[])
self.w_telid.on_change('value', self.on_telid_widget_change)
def update_telid_widget(self):
if self.w_telid:
tels = [str(t) for t in self.event.r0.tels_with_data]
self.w_telid.options = tels
self.w_telid.value = str(self.telid)
def on_telid_widget_change(self, _, __, ___):
if self.telid != int(self.w_telid.value):
self.telid = int(self.w_telid.value)
def create_channel_widget(self):
self.w_channel = Select(title="Channel:", value="", options=[])
self.w_channel.on_change('value', self.on_channel_widget_change)
def update_channel_widget(self):
if self.w_channel:
try:
n_chan = self.event.r0.tel[self.telid].waveform.shape[0]
except AttributeError:
n_chan = 1
channels = [str(c) for c in range(n_chan)]
self.w_channel.options = channels
self.w_channel.value = str(self.channel)
def on_channel_widget_change(self, _, __, ___):
if self.channel != int(self.w_channel.value):
self.channel = int(self.w_channel.value)
def create_dl1_widgets(self):
self.w_dl1_dict = dict(
cleaner=Select(title="Cleaner:", value='', width=5,
options=WaveformCleanerFactory.subclass_names),
extractor=Select(title="Extractor:", value='', width=5,
options=ChargeExtractorFactory.subclass_names),
extractor_t0=TextInput(title="T0:", value=''),
extractor_window_width=TextInput(title="Window Width:", value=''),
extractor_window_shift=TextInput(title="Window Shift:", value=''),
extractor_sig_amp_cut_HG=TextInput(title="Significant Amplitude "
"Cut (HG):", value=''),
extractor_sig_amp_cut_LG=TextInput(title="Significant Amplitude "
"Cut (LG):", value=''),
extractor_lwt=TextInput(title="Local Pixel Weight:", value=''))
for val in self.w_dl1_dict.values():
val.on_change('value', self.on_dl1_widget_change)
self.wb_extractor = widgetbox(
PreText(text="Charge Extractor Configuration"),
self.w_dl1_dict['cleaner'],
self.w_dl1_dict['extractor'],
self.w_dl1_dict['extractor_t0'],
self.w_dl1_dict['extractor_window_width'],
self.w_dl1_dict['extractor_window_shift'],
self.w_dl1_dict['extractor_sig_amp_cut_HG'],
self.w_dl1_dict['extractor_sig_amp_cut_LG'],
self.w_dl1_dict['extractor_lwt'])
def update_dl1_widget_values(self):
if self.w_dl1_dict:
for key, val in self.w_dl1_dict.items():
if 'extractor' in key:
if key == 'extractor':
val.value = self.extractor.__class__.__name__
else:
key = key.replace("extractor_", "")
try:
val.value = str(getattr(self.extractor, key))
except AttributeError:
val.value = ''
elif 'cleaner' in key:
if key == 'cleaner':
val.value = self.cleaner.__class__.__name__
else:
key = key.replace("cleaner_", "")
try:
val.value = str(getattr(self.cleaner, key))
except AttributeError:
val.value = ''
def on_dl1_widget_change(self, _, __, ___):
if self.event:
if not self._updating_dl1:
self._updating_dl1 = True
cmdline = []
for key, val in self.w_dl1_dict.items():
if val.value:
cmdline.append('--{}'.format(key))
cmdline.append(val.value)
self.parse_command_line(cmdline)
kwargs = dict(config=self.config, tool=self)
extractor = ChargeExtractorFactory.produce(**kwargs)
cleaner = WaveformCleanerFactory.produce(**kwargs)
self.update_dl1_calibrator(extractor, cleaner)
self.update_dl1_widget_values()
self._updating_dl1 = False
# seasonal attenuation amplitude
saa = Slider(title=SAA_LABEL,
value=SAA_START,
start=SAA_MIN,
end=SAA_MAX,
step=SAA_STEP)
# baseline attenuation
bat = Slider(title=BAT_LABEL,
value=BAT_START,
start=BAT_MIN,
end=BAT_MAX,
step=BAT_STEP)
button = Button(label="Reset", button_type="default")
button2 = Button(label="Vaccinate critical proportion", button_type="default")
button3 = Button(label="Vaccinate 50%", button_type="default")
# text widgets
intro = Div(text='', width=TEXT_WIDTH)
summary = Div(text='', width=TEXT_WIDTH)
stats = Div(text='', width=TEXT_WIDTH)
notes = Div(text='', width=TEXT_WIDTH)
# Assign widgets to the call back function
# updates are on value_throtled because this is too slow for realtime updates
for w in [
population, iinfections, period, period_stdev, latent, h1, p1, drate,
im, ddy, saa, bat
]:
def eda_projects_tab(panel_title):
lags_corr_src = ColumnDataSource(data=dict(variable_1=[],
variable_2=[],
relationship=[],
lag=[],
r=[],
p_value=[]))
class Thistab(Mytab):
def __init__(self, table, cols, dedup_cols=[]):
Mytab.__init__(self, table, cols, dedup_cols)
self.table = table
self.cols = cols
self.DATEFORMAT = "%Y-%m-%d %H:%M:%S"
self.df = None
self.df1 = None
self.df_predict = None
self.day_diff = 1 # for normalizing for classification periods of different lengths
self.df_grouped = ''
self.cl = PythonClickhouse('aion')
self.trigger = 0
self.groupby_dict = {
'project_duration': 'sum',
'project_start_delay': 'mean',
'project_end_delay': 'mean',
'project_owner_age': 'mean',
'project_owner_gender': 'mean',
'milestone_duration': 'sum',
'milestone_start_delay': 'mean',
'milestone_end_delay': 'mean',
'milestone_owner_age': 'mean',
'milestone_owner_gender': 'mean',
'task_duration': 'sum',
'task_start_delay': 'sum',
'task_end_delay': 'mean',
'task_owner_age': 'mean',
'task_owner_gender': 'mean'
}
self.feature_list = list(self.groupby_dict.keys())
self.lag_variable = 'task_duration'
self.lag_days = "1,2,3"
self.lag = 0
self.lag_menu = [str(x) for x in range(0, 100)]
self.strong_thresh = .65
self.mod_thresh = 0.4
self.weak_thresh = 0.25
self.corr_df = None
self.div_style = """
style='width:350px; margin-left:25px;
border:1px solid #ddd;border-radius:3px;background:#efefef50;'
"""
self.header_style = """ style='color:blue;text-align:center;' """
self.variables = sorted(list(self.groupby_dict.keys()))
self.variable = self.variables[0]
self.relationships_to_check = ['weak', 'moderate', 'strong']
self.status = 'all'
self.pm_gender = 'all'
self.m_gender = 'all'
self.t_gender = 'all'
self.type = 'all'
self.pym = PythonMongo('aion')
self.menus = {
'status': ['all', 'open', 'closed'],
'type': [
'all', 'research', 'reconciliation', 'audit', 'innovation',
'construction', 'manufacturing', 'conference'
],
'gender': ['all', 'male', 'female'],
'variables':
list(self.groupby_dict.keys()),
'history_periods':
['1', '2', '3', '4', '5', '6', '7', '8', '9', '10'],
}
self.multiline_vars = {'x': 'manager_gender', 'y': 'remuneration'}
self.timestamp_col = 'project_startdate_actual'
# ------- DIVS setup begin
self.page_width = 1250
txt = """<hr/>
<div style="text-align:center;width:{}px;height:{}px;
position:relative;background:black;margin-bottom:200px">
<h1 style="color:#fff;margin-bottom:300px">{}</h1>
</div>""".format(self.page_width, 50, 'Welcome')
self.notification_div = {
'top': Div(text=txt, width=self.page_width, height=20),
'bottom': Div(text=txt, width=self.page_width, height=10),
}
lag_section_head_txt = 'Lag relationships between {} and...'.format(
self.variable)
self.section_divider = '-----------------------------------'
self.section_headers = {
'lag':
self.section_header_div(text=lag_section_head_txt,
width=600,
html_header='h2',
margin_top=5,
margin_bottom=-155),
'distribution':
self.section_header_div(text='Pre-transform distribution:',
width=600,
html_header='h2',
margin_top=5,
margin_bottom=-155),
'relationships':
self.section_header_div(
text='Relationships between variables:{}'.format(
self.section_divider),
width=600,
html_header='h2',
margin_top=5,
margin_bottom=-155),
'correlations':
self.section_header_div(text='Correlations:',
width=600,
html_header='h3',
margin_top=5,
margin_bottom=-155),
}
# ----- UPDATED DIVS END
# ---------------------- DIVS ----------------------------
def section_header_div(self,
text,
html_header='h2',
width=600,
margin_top=150,
margin_bottom=-150):
text = """<div style="margin-top:{}px;margin-bottom:-{}px;"><{} style="color:#4221cc;">{}</{}></div>""" \
.format(margin_top, margin_bottom, html_header, text, html_header)
return Div(text=text, width=width, height=15)
def notification_updater(self, text):
txt = """<div style="text-align:center;background:black;width:100%;">
<h4 style="color:#fff;">
{}</h4></div>""".format(text)
for key in self.notification_div.keys():
self.notification_div[key].text = txt
def reset_adoption_dict(self, variable):
self.significant_effect_dict[variable] = []
# ////////////// DIVS /////////////////////////////////
def title_div(self, text, width=700):
text = '<h2 style="color:#4221cc;">{}</h2>'.format(text)
return Div(text=text, width=width, height=15)
def corr_information_div(self, width=400, height=300):
div_style = """
style='width:350px; margin-left:-600px;
border:1px solid #ddd;border-radius:3px;background:#efefef50;'
"""
txt = """
<div {}>
<h4 {}>How to interpret relationships </h4>
<ul style='margin-top:-10px;'>
<li>
Positive: as variable 1 increases, so does variable 2.
</li>
<li>
Negative: as variable 1 increases, variable 2 decreases.
</li>
<li>
Strength: decisions can be made on the basis of strong and moderate relationships.
</li>
<li>
No relationship/not significant: no statistical support for decision making.
</li>
<li>
The scatter graphs (below) are useful for visual confirmation.
</li>
<li>
The histogram (right) shows the distribution of the variable.
</li>
</ul>
</div>
""".format(div_style, self.header_style)
div = Div(text=txt, width=width, height=height)
return div
# /////////////////////////////////////////////////////////////
def filter_df(self, df1):
if self.status != 'all':
df1 = df1[df1.status == self.status]
if self.pm_gender != 'all':
df1 = df1[df1.project_owner_gender == self.pm_gender]
if self.m_gender != 'all':
df1 = df1[df1.milestone_owner_gender == self.m_gender]
if self.t_gender != 'all':
df1 = df1[df1.task_owner_gender == self.t_gender]
if self.type != 'all':
df1 = df1[df1.type == self.type]
return df1
def prep_data(self, df1):
try:
'''
df1[self.timestamp_col] = df1[self.timestamp_col].apply(lambda x: datetime(x.year,
x.month,
x.day,
x.hour,0,0))
'''
df1 = df1.set_index(self.timestamp_col)
logger.warning('LINE 195 df:%s', df1.head())
# handle lag for all variables
df = df1.copy()
df = self.filter_df(df)
logger.warning('LINE 199: length before:%s', len(df))
slice = df[['project']]
df = df[list(self.groupby_dict.keys())]
logger.warning('LINE 218: columns:%s', df.head())
df = df.astype(float)
df = pd.concat([df, slice], axis=1)
df = df.groupby('project').resample(self.resample_period).agg(
self.groupby_dict)
logger.warning('LINE 201: length after:%s', len(df))
df = df.reset_index()
vars = self.feature_list.copy()
if int(self.lag) > 0:
for var in vars:
if self.variable != var:
df[var] = df[var].shift(int(self.lag))
df = df.dropna()
self.df1 = df
logger.warning('line 184- prep data: df:%s', self.df.head(10))
except Exception:
logger.error('prep data', exc_info=True)
def lags_plot(self, launch):
try:
df = self.df.copy()
df = df[[self.lag_variable, self.variable]]
cols = [self.lag_variable]
lags = self.lag_days.split(',')
for day in lags:
try:
label = self.lag_variable + '_' + day
df[label] = df[self.lag_variable].shift(int(day))
cols.append(label)
except:
logger.warning('%s is not an integer', day)
df = df.dropna()
self.lags_corr(df)
# plot the comparison
logger.warning('in lags plot: df:%s', df.head(10))
return df.hvplot(x=self.variable,
y=cols,
kind='scatter',
alpha=0.4)
except Exception:
logger.error('lags plot', exc_info=True)
# calculate the correlation produced by the lags vector
def lags_corr(self, df):
try:
corr_dict_data = {
'variable_1': [],
'variable_2': [],
'relationship': [],
'lag': [],
'r': [],
'p_value': []
}
a = df[self.variable].tolist()
for col in df.columns:
if col not in [self.timestamp_col, self.variable]:
# find lag
var = col.split('_')
try:
tmp = int(var[-1])
lag = tmp
except Exception:
lag = 'None'
b = df[col].tolist()
slope, intercept, rvalue, pvalue, txt = self.corr_label(
a, b)
corr_dict_data['variable_1'].append(self.variable)
corr_dict_data['variable_2'].append(col)
corr_dict_data['relationship'].append(txt)
corr_dict_data['lag'].append(lag)
corr_dict_data['r'].append(round(rvalue, 4))
corr_dict_data['p_value'].append(round(pvalue, 4))
lags_corr_src.stream(corr_dict_data,
rollover=(len(corr_dict_data['lag'])))
columns = [
TableColumn(field="variable_1", title="variable 1"),
TableColumn(field="variable_2", title="variable 2"),
TableColumn(field="relationship", title="relationship"),
TableColumn(field="lag", title="lag(days)"),
TableColumn(field="r", title="r"),
TableColumn(field="p_value", title="p_value"),
]
data_table = DataTable(source=lags_corr_src,
columns=columns,
width=500,
height=280)
return data_table
except Exception:
logger.error('lags corr', exc_info=True)
def correlation_table(self, launch):
try:
corr_dict = {
'Variable 1': [],
'Variable 2': [],
'Relationship': [],
'r': [],
'p-value': []
}
# prep df
df = self.df1
# get difference for money columns
df = df.drop(self.timestamp_col, axis=1)
# df = df.compute()
a = df[self.variable].tolist()
for col in self.feature_list:
logger.warning('col :%s', col)
if col != self.variable:
logger.warning('%s:%s', col, self.variable)
b = df[col].tolist()
slope, intercept, rvalue, pvalue, txt = self.corr_label(
a, b)
# add to dict
corr_dict['Variable 1'].append(self.variable)
corr_dict['Variable 2'].append(col)
corr_dict['Relationship'].append(txt)
corr_dict['r'].append(round(rvalue, 4))
corr_dict['p-value'].append(round(pvalue, 4))
df = pd.DataFrame({
'Variable 1': corr_dict['Variable 1'],
'Variable 2': corr_dict['Variable 2'],
'Relationship': corr_dict['Relationship'],
'r': corr_dict['r'],
'p-value': corr_dict['p-value']
})
# logger.warning('df:%s',df.head(23))
return df.hvplot.table(columns=[
'Variable 1', 'Variable 2', 'Relationship', 'r', 'p-value'
],
width=550,
height=200,
title='Correlation between variables')
except Exception:
logger.error('correlation table', exc_info=True)
def non_parametric_relationship_table(self, launch):
try:
corr_dict = {
'Variable 1': [],
'Variable 2': [],
'Relationship': [],
'stat': [],
'p-value': []
}
# prep df
df = self.df1
# get difference for money columns
df = df.drop(self.timestamp_col, axis=1)
# df = df.compute()
# logger.warning('line df:%s',df.head(10))
a = df[self.variable].tolist()
for col in self.feature_list:
logger.warning('col :%s', col)
if col != self.variable:
logger.warning('%s:%s', col, self.variable)
b = df[col].tolist()
stat, pvalue, txt = self.mann_whitneyu_label(a, b)
corr_dict['Variable 1'].append(self.variable)
corr_dict['Variable 2'].append(col)
corr_dict['Relationship'].append(txt)
corr_dict['stat'].append(round(stat, 4))
corr_dict['p-value'].append(round(pvalue, 4))
df = pd.DataFrame({
'Variable 1': corr_dict['Variable 1'],
'Variable 2': corr_dict['Variable 2'],
'Relationship': corr_dict['Relationship'],
'stat': corr_dict['stat'],
'p-value': corr_dict['p-value']
})
# logger.warning('df:%s',df.head(23))
return df.hvplot.table(
columns=[
'Variable 1', 'Variable 2', 'Relationship', 'stat',
'p-value'
],
width=550,
height=200,
title='Non parametric relationship between variables')
except Exception:
logger.error('non parametric table', exc_info=True)
def hist(self, launch):
try:
return self.df.hvplot.hist(y=self.feature_list,
subplots=True,
shared_axes=False,
bins=25,
alpha=0.3,
width=300).cols(4)
except Exception:
logger.warning('histogram', exc_info=True)
def matrix_plot(self, launch=-1):
try:
logger.warning('line 306 self.feature list:%s',
self.feature_list)
df = self.df1
if df is not None:
# thistab.prep_data(thistab.df)
if self.timestamp_col in df.columns:
df = df.drop(self.timestamp_col, axis=1)
df = df.fillna(0)
# logger.warning('line 302. df: %s',df.head(10))
cols_temp = self.feature_list.copy()
if self.variable in cols_temp:
cols_temp.remove(self.variable)
# variable_select.options = cols_lst
p = df.hvplot.scatter(x=self.variable,
y=cols_temp,
width=330,
subplots=True,
shared_axes=False,
xaxis=False).cols(4)
else:
p = df.hvplot.scatter(x=[0, 0, 0], y=[0, 0, 0], width=330)
return p
except Exception:
logger.error('matrix plot', exc_info=True)
def multiline(self, launch=1):
try:
yvar = self.multiline_vars['y']
xvar = self.multiline_vars['x']
df = self.df.copy()
df = df[[xvar, yvar, self.timestamp_col]]
df = df.set_index(self.timestamp_col)
df = df.groupby(xvar).resample(self.resample_period).agg(
{yvar: 'mean'})
df = df.reset_index()
lines = df[xvar].unique()
# split data frames
dfs = {}
for idx, line in enumerate(lines):
dfs[line] = df[df[xvar] == line]
dfs[line] = dfs[line].fillna(0)
logger.warning('LINE 428:%s - %s:', line, dfs[line].head())
if idx == 0:
p = dfs[line].hvplot.line(x=self.timestamp_col,
y=yvar,
width=1200,
height=500).relabel(line)
else:
p *= dfs[line].hvplot.line(x=self.timestamp_col,
y=yvar,
width=2,
height=500).relabel(line)
return p
except Exception:
logger.error('multiline plot', exc_info=True)
def update_variable(attr, old, new):
thistab.notification_updater("Calculations in progress! Please wait.")
thistab.prep_data(thistab.df)
if 'milestone owner gender' == new:
thistab.variable = 'm_gender_code'
if 'project owner gender' == new:
thistab.variable = 'pm_gender_code'
if 'task owner gender' == new:
thistab.variable = 't_gender_code'
if thistab.variable in thistab.adoption_variables['developer']:
thistab.reset_adoption_dict(thistab.variable)
thistab.section_head_updater('lag', thistab.variable)
thistab.trigger += 1
stream_launch_matrix.event(launch=thistab.trigger)
stream_launch_corr.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update_lag_plot_variable(attr, old, new):
thistab.notification_updater("Calculations in progress! Please wait.")
thistab.lag_variable = new
thistab.prep_data(thistab.df)
thistab.trigger += 1
stream_launch_lags_var.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update_IVs(attrname, old, new):
thistab.notification_updater("Calculations in progress! Please wait.")
thistab.pm_gender = pm_gender_select.value
thistab.m_gender = m_gender_select.value
thistab.t_gender = t_gender_select.value
thistab.status = status_select.value
thistab.type = type_select.value
thistab.prep_data(thistab.df)
thistab.trigger += 1
stream_launch_matrix.event(launch=thistab.trigger)
stream_launch_corr.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update_lag(attr, old, new): # update lag & cryptocurrency
thistab.notification_updater("Calculations in progress! Please wait.")
thistab.lag = int(lag_select.value)
thistab.prep_data(thistab.df)
thistab.trigger += 1
stream_launch_matrix.event(launch=thistab.trigger)
stream_launch_corr.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update(attrname, old, new):
thistab.notification_updater(
"Calculations underway. Please be patient")
thistab.df = thistab.pym.load_df(start_date=datepicker_start.value,
end_date=datepicker_end.value,
cols=[],
table=thistab.table,
timestamp_col=thistab.timestamp_col)
thistab.df['project_owner_gender'] = thistab.df[
'project_owner_gender'].apply(lambda x: 1 if x == 'male' else 2)
thistab.df['milestone_owner_gender'] = thistab.df[
'milestone_owner_gender'].apply(lambda x: 1 if x == 'male' else 2)
thistab.df['task_owner_gender'] = thistab.df[
'task_owner_gender'].apply(lambda x: 1 if x == 'male' else 2)
thistab.prep_data(thistab.df)
thistab.trigger += 1
stream_launch_matrix.event(launch=thistab.trigger)
stream_launch_corr.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update_resample(attrname, old, new):
thistab.notification_updater(
"Calculations underway. Please be patient")
thistab.resample_period = new
thistab.prep_data(thistab.df)
thistab.trigger += 1
stream_launch_matrix.event(launch=thistab.trigger)
stream_launch_corr.event(launch=thistab.trigger)
stream_launch.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update_lags_selected():
thistab.notification_updater("Calculations in progress! Please wait.")
thistab.lag_days = lags_input.value
logger.warning('line 381, new checkboxes: %s', thistab.lag_days)
thistab.trigger += 1
stream_launch_lags_var.event(launch=thistab.trigger)
stream_launch.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
def update_multiline(attrname, old, new):
thistab.notification_updater("Calculations in progress! Please wait.")
thistab.multiline_vars['x'] = multiline_x_select.value
thistab.multiline_vars['y'] = multiline_y_select.value
thistab.trigger += 1
stream_launch.event(launch=thistab.trigger)
thistab.notification_updater("Ready!")
try:
# SETUP
table = 'project_composite1'
thistab = Thistab(table, [], [])
# setup dates
first_date_range = datetime.strptime("2013-04-25 00:00:00",
"%Y-%m-%d %H:%M:%S")
last_date_range = datetime.now().date()
last_date = dashboard_config['dates']['last_date'] - timedelta(days=2)
first_date = last_date - timedelta(days=30)
# initial function call
thistab.df = thistab.pym.load_df(start_date=first_date,
end_date=last_date,
cols=[],
table=thistab.table,
timestamp_col=thistab.timestamp_col)
if len(thistab.df) > 0:
thistab.df['manager_gender'] = thistab.df['project_owner_gender']
thistab.df['project_owner_gender'] = thistab.df[
'project_owner_gender'].apply(lambda x: 1
if x == 'male' else 2)
thistab.df['milestone_owner_gender'] = thistab.df[
'milestone_owner_gender'].apply(lambda x: 1
if x == 'male' else 2)
thistab.df['task_owner_gender'] = thistab.df[
'task_owner_gender'].apply(lambda x: 1 if x == 'male' else 2)
logger.warning('LINE 527:columns %s', list(thistab.df.columns))
thistab.prep_data(thistab.df)
# MANAGE STREAM
stream_launch_hist = streams.Stream.define('Launch', launch=-1)()
stream_launch_matrix = streams.Stream.define('Launch_matrix',
launch=-1)()
stream_launch_corr = streams.Stream.define('Launch_corr', launch=-1)()
stream_launch_lags_var = streams.Stream.define('Launch_lag_var',
launch=-1)()
stream_launch = streams.Stream.define('Launch', launch=-1)()
# CREATE WIDGETS
datepicker_start = DatePicker(title="Start",
min_date=first_date_range,
max_date=last_date_range,
value=first_date)
datepicker_end = DatePicker(title="End",
min_date=first_date_range,
max_date=last_date_range,
value=last_date)
variable_select = Select(title='Select variable',
value=thistab.variable,
options=thistab.variables)
lag_variable_select = Select(title='Select lag variable',
value=thistab.lag_variable,
options=thistab.feature_list)
lag_select = Select(title='Select lag',
value=str(thistab.lag),
options=thistab.lag_menu)
type_select = Select(title='Select project type',
value=thistab.type,
options=thistab.menus['type'])
status_select = Select(title='Select project status',
value=thistab.status,
options=thistab.menus['status'])
pm_gender_select = Select(title="Select project owner's gender",
value=thistab.pm_gender,
options=thistab.menus['gender'])
m_gender_select = Select(title="Select milestone owner's gender",
value=thistab.m_gender,
options=thistab.menus['gender'])
t_gender_select = Select(title="Select task owner's gender",
value=thistab.t_gender,
options=thistab.menus['gender'])
resample_select = Select(title='Select resample period',
value='D',
options=['D', 'W', 'M', 'Q'])
multiline_y_select = Select(title='Select comparative DV(y)',
value=thistab.multiline_vars['y'],
options=[
'remuneration', 'delay_start',
'delay_end', 'project_duration'
])
multiline_x_select = Select(
title='Select comparative IV(x)',
value=thistab.multiline_vars['x'],
options=['manager_gender', 'type', 'status'])
lags_input = TextInput(
value=thistab.lag_days,
title="Enter lags (integer(s), separated by comma)",
height=55,
width=300)
lags_input_button = Button(label="Select lags, then click me!",
width=10,
button_type="success")
# --------------------- PLOTS----------------------------------
columns = [
TableColumn(field="variable_1", title="variable 1"),
TableColumn(field="variable_2", title="variable 2"),
TableColumn(field="relationship", title="relationship"),
TableColumn(field="lag", title="lag(days)"),
TableColumn(field="r", title="r"),
TableColumn(field="p_value", title="p_value"),
]
lags_corr_table = DataTable(source=lags_corr_src,
columns=columns,
width=500,
height=200)
hv_matrix_plot = hv.DynamicMap(thistab.matrix_plot,
streams=[stream_launch_matrix])
hv_corr_table = hv.DynamicMap(thistab.correlation_table,
streams=[stream_launch_corr])
hv_nonpara_table = hv.DynamicMap(
thistab.non_parametric_relationship_table,
streams=[stream_launch_corr])
# hv_hist_plot = hv.DynamicMap(thistab.hist, streams=[stream_launch_hist])
hv_lags_plot = hv.DynamicMap(thistab.lags_plot,
streams=[stream_launch_lags_var])
hv_multiline = hv.DynamicMap(thistab.multiline,
streams=[stream_launch])
matrix_plot = renderer.get_plot(hv_matrix_plot)
corr_table = renderer.get_plot(hv_corr_table)
nonpara_table = renderer.get_plot(hv_nonpara_table)
lags_plot = renderer.get_plot(hv_lags_plot)
multiline = renderer.get_plot(hv_multiline)
# setup divs
# handle callbacks
variable_select.on_change('value', update_variable)
lag_variable_select.on_change('value', update_lag_plot_variable)
lag_select.on_change('value', update_lag) # individual lag
resample_select.on_change('value', update_resample)
pm_gender_select.on_change('value', update_IVs)
m_gender_select.on_change('value', update_IVs)
t_gender_select.on_change('value', update_IVs)
datepicker_start.on_change('value', update)
datepicker_end.on_change('value', update)
lags_input_button.on_click(update_lags_selected) # lags array
status_select.on_change('value', update_IVs)
type_select.on_change('value', update_IVs)
multiline_x_select.on_change('value', update_multiline)
multiline_y_select.on_change('value', update_multiline)
# COMPOSE LAYOUT
# put the controls in a single element
controls_lag = WidgetBox(lags_input, lags_input_button,
lag_variable_select)
controls_multiline = WidgetBox(multiline_x_select, multiline_y_select)
controls_page = WidgetBox(datepicker_start, datepicker_end,
variable_select, type_select, status_select,
resample_select, pm_gender_select,
m_gender_select, t_gender_select)
controls_gender = WidgetBox(pm_gender_select, m_gender_select,
t_gender_select)
# create the dashboards
grid = gridplot(
[[thistab.notification_div['top']], [Spacer(width=20, height=70)],
[thistab.section_headers['relationships']],
[Spacer(width=20, height=30)], [matrix_plot.state, controls_page],
[thistab.section_headers['correlations']],
[Spacer(width=20, height=30)],
[corr_table.state,
thistab.corr_information_div()],
[thistab.title_div('Compare levels in a variable', 400)],
[Spacer(width=20, height=30)],
[multiline.state, controls_multiline],
[thistab.section_headers['lag']], [Spacer(width=20, height=30)],
[lags_plot.state, controls_lag], [lags_corr_table],
[thistab.notification_div['bottom']]])
# Make a tab with the layout
tab = Panel(child=grid, title=panel_title)
return tab
except Exception:
logger.error('EDA projects:', exc_info=True)
return tab_error_flag(panel_title)
def __init__(self, server, doc=None, **kwargs):
if doc is not None:
self.doc = weakref.ref(doc)
try:
self.key = doc.session_context.request.arguments.get("key", None)
except AttributeError:
self.key = None
if isinstance(self.key, list):
self.key = self.key[0]
if isinstance(self.key, bytes):
self.key = self.key.decode()
self.task_names = ["All", self.key] if self.key else ["All"]
else:
self.key = None
self.task_names = ["All"]
self.server = server
self.start = None
self.stop = None
self.ts = {"count": [], "time": []}
self.state = profile.create()
data = profile.plot_data(self.state, profile_interval)
self.states = data.pop("states")
self.profile_plot, self.source = profile.plot_figure(data, **kwargs)
changing = [False] # avoid repeated changes from within callback
@without_property_validation
def cb(attr, old, new):
if changing[0] or len(new) == 0:
return
with log_errors():
data = profile.plot_data(self.states[new[0]], profile_interval)
del self.states[:]
self.states.extend(data.pop("states"))
changing[0] = True # don't recursively trigger callback
update(self.source, data)
self.source.selected.indices = old
changing[0] = False
self.source.selected.on_change("indices", cb)
self.ts_source = ColumnDataSource({"time": [], "count": []})
self.ts_plot = figure(
title="Activity over time",
height=150,
x_axis_type="datetime",
active_drag="xbox_select",
tools="xpan,xwheel_zoom,xbox_select,reset",
sizing_mode="stretch_width",
toolbar_location="above",
)
self.ts_plot.line("time", "count", source=self.ts_source)
self.ts_plot.circle(
"time", "count", source=self.ts_source, color=None, selection_color="orange"
)
self.ts_plot.yaxis.visible = False
self.ts_plot.grid.visible = False
def ts_change(attr, old, new):
with log_errors():
selected = self.ts_source.selected.indices
if selected:
start = self.ts_source.data["time"][min(selected)] / 1000
stop = self.ts_source.data["time"][max(selected)] / 1000
self.start, self.stop = min(start, stop), max(start, stop)
else:
self.start = self.stop = None
self.trigger_update(update_metadata=False)
self.ts_source.selected.on_change("indices", ts_change)
self.reset_button = Button(label="Reset", button_type="success")
self.reset_button.on_click(lambda: self.update(self.state))
self.update_button = Button(label="Update", button_type="success")
self.update_button.on_click(self.trigger_update)
self.select = Select(value=self.task_names[-1], options=self.task_names)
def select_cb(attr, old, new):
if new == "All":
new = None
self.key = new
self.trigger_update(update_metadata=False)
self.select.on_change("value", select_cb)
self.root = column(
row(
self.select,
self.reset_button,
self.update_button,
sizing_mode="scale_width",
height=250,
),
self.profile_plot,
self.ts_plot,
**kwargs,
)
text_font_size="20pt",
text_baseline="middle",
text_align="center")
i = 0
ds = r.data_source
# create a callback that will add a number in a random location
def callback():
global i
# BEST PRACTICE --- update .data in one step with a new dict
new_data = dict()
new_data['x'] = ds.data['x'] + [random() * 70 + 15]
new_data['y'] = ds.data['y'] + [random() * 70 + 15]
new_data['text_color'] = ds.data['text_color'] + [RdYlBu3[i % 3]]
new_data['text'] = ds.data['text'] + [str(i)]
ds.data = new_data
i = i + 1
# add a button widget and configure with the call back
button = Button(label="Press Me")
button.on_click(callback)
# put the button and plot in a layout and add to the document
curdoc().add_root(column(button, p))
def __init__(self, server, doc=None, **kwargs):
if doc is not None:
self.doc = weakref.ref(doc)
self.server = server
self.log = self.server.io_loop.profile
self.start = None
self.stop = None
self.ts = {"count": [], "time": []}
self.state = profile.get_profile(self.log)
data = profile.plot_data(self.state, profile_interval)
self.states = data.pop("states")
self.profile_plot, self.source = profile.plot_figure(data, **kwargs)
changing = [False] # avoid repeated changes from within callback
@without_property_validation
def cb(attr, old, new):
if changing[0] or len(new) == 0:
return
with log_errors():
data = profile.plot_data(self.states[new[0]], profile_interval)
del self.states[:]
self.states.extend(data.pop("states"))
changing[0] = True # don't recursively trigger callback
update(self.source, data)
self.source.selected.indices = old
changing[0] = False
self.source.selected.on_change("indices", cb)
self.ts_source = ColumnDataSource({"time": [], "count": []})
self.ts_plot = figure(
title="Activity over time",
height=150,
x_axis_type="datetime",
active_drag="xbox_select",
tools="xpan,xwheel_zoom,xbox_select,reset",
sizing_mode="stretch_width",
toolbar_location="above",
)
self.ts_plot.line("time", "count", source=self.ts_source)
self.ts_plot.circle(
"time", "count", source=self.ts_source, color=None, selection_color="orange"
)
self.ts_plot.yaxis.visible = False
self.ts_plot.grid.visible = False
def ts_change(attr, old, new):
with log_errors():
selected = self.ts_source.selected.indices
if selected:
start = self.ts_source.data["time"][min(selected)] / 1000
stop = self.ts_source.data["time"][max(selected)] / 1000
self.start, self.stop = min(start, stop), max(start, stop)
else:
self.start = self.stop = None
self.trigger_update()
self.ts_source.selected.on_change("indices", ts_change)
self.reset_button = Button(label="Reset", button_type="success")
self.reset_button.on_click(lambda: self.update(self.state))
self.update_button = Button(label="Update", button_type="success")
self.update_button.on_click(self.trigger_update)
self.root = column(
row(self.reset_button, self.update_button, sizing_mode="scale_width"),
self.profile_plot,
self.ts_plot,
**kwargs,
)
x = np.linspace(0, 2, 1000)
y = 1 - (x-1)**2
source = ColumnDataSource(data=dict(x=x, y=y))
p = figure(title="initial title")
p.circle(x=1, y=list(range(0, 11)))
p.line('x', 'y', color="orange", source=source)
slider = Slider(start=0, end=10, step=0.1, value=1)
def scb(attr, old, new):
source.data['y'] = new * y
slider.on_change('value', scb)
combine = Button(label="hold combine")
combine.on_event(ButtonClick, lambda event: doc.hold("combine"))
collect = Button(label="hold collect")
collect.on_event(ButtonClick, lambda event: doc.hold("collect"))
unhold = Button(label="unhold")
unhold.on_event(ButtonClick, lambda event: doc.unhold())
doc.add_root(column(p, slider, combine, collect, unhold))
@repeat(np.linspace(0, 10, 100))
def update(v):
slider.value = v
curdoc().add_periodic_callback(update, 200)
class BokehFileViewer(Tool):
name = "BokehFileViewer"
description = ("Interactively explore an event file using the bokeh "
"visualisation package")
port = Int(5006, help="Port to open bokeh server onto").tag(config=True)
disable_server = Bool(False,
help="Do not start the bokeh server "
"(useful for testing)").tag(config=True)
default_url = get_dataset_path("gamma_test_large.simtel.gz")
EventSource.input_url.default_value = default_url
extractor_product = traits.create_class_enum_trait(
ImageExtractor, default_value="NeighborPeakWindowSum")
aliases = Dict(
dict(
port="BokehFileViewer.port",
disable_server="BokehFileViewer.disable_server",
f="EventSource.input_url",
max_events="EventSource.max_events",
extractor="BokehFileViewer.extractor_product",
))
classes = List([
EventSource,
] + traits.classes_with_traits(ImageExtractor))
def __init__(self, **kwargs):
super().__init__(**kwargs)
self._event = None
self._event_index = None
self._event_id = None
self._telid = None
self._channel = None
self.w_next_event = None
self.w_previous_event = None
self.w_event_index = None
self.w_event_id = None
self.w_goto_event_index = None
self.w_goto_event_id = None
self.w_telid = None
self.w_channel = None
self.w_dl1_dict = None
self.wb_extractor = None
self.layout = None
self.reader = None
self.seeker = None
self.extractor = None
self.calibrator = None
self.viewer = None
self._updating_dl1 = False
# make sure, gzip files are seekable
self.config.SimTelEventSource.back_seekable = True
def setup(self):
self.log_format = "%(levelname)s: %(message)s [%(name)s.%(funcName)s]"
self.reader = EventSource.from_config(parent=self)
self.seeker = EventSeeker(self.reader, parent=self)
self.extractor = ImageExtractor.from_name(
self.extractor_product,
parent=self,
subarray=self.reader.subarray,
)
self.calibrator = CameraCalibrator(
subarray=self.reader.subarray,
parent=self,
image_extractor=self.extractor,
)
self.viewer = BokehEventViewer(parent=self,
subarray=self.reader.subarray)
# Setup widgets
self.viewer.create()
self.viewer.enable_automatic_index_increment()
self.create_previous_event_widget()
self.create_next_event_widget()
self.create_event_index_widget()
self.create_goto_event_index_widget()
self.create_event_id_widget()
self.create_goto_event_id_widget()
self.create_telid_widget()
self.create_channel_widget()
self.create_dl1_widgets()
self.update_dl1_widget_values()
# Setup layout
self.layout = layout([
[self.viewer.layout],
[
self.w_previous_event,
self.w_next_event,
self.w_goto_event_index,
self.w_goto_event_id,
],
[self.w_event_index, self.w_event_id],
[self.w_telid, self.w_channel],
[self.wb_extractor],
])
def start(self):
self.event_index = 0
def finish(self):
if not self.disable_server:
def modify_doc(doc):
doc.add_root(self.layout)
doc.title = self.name
directory = os.path.abspath(os.path.dirname(__file__))
theme_path = os.path.join(directory, "theme.yaml")
template_path = os.path.join(directory, "templates")
doc.theme = Theme(filename=theme_path)
env = jinja2.Environment(
loader=jinja2.FileSystemLoader(template_path))
doc.template = env.get_template("index.html")
self.log.info("Opening Bokeh application on "
"http://localhost:{}/".format(self.port))
server = Server({"/": modify_doc}, num_procs=1, port=self.port)
server.start()
server.io_loop.add_callback(server.show, "/")
server.io_loop.start()
@property
def event_index(self):
return self._event_index
@event_index.setter
def event_index(self, val):
try:
self.event = self.seeker[val]
except IndexError:
self.log.warning(f"Event Index {val} does not exist")
@property
def event_id(self):
return self._event_id
@event_id.setter
def event_id(self, val):
try:
self.event = self.seeker[str(val)]
except IndexError:
self.log.warning(f"Event ID {val} does not exist")
@property
def telid(self):
return self._telid
@telid.setter
def telid(self, val):
self.channel = 0
tels = list(self.event.r0.tels_with_data)
if val not in tels:
val = tels[0]
self._telid = val
self.viewer.telid = val
self.update_telid_widget()
@property
def channel(self):
return self._channel
@channel.setter
def channel(self, val):
self._channel = val
self.viewer.channel = val
self.update_channel_widget()
@property
def event(self):
return self._event
@event.setter
def event(self, val):
self.calibrator(val)
self._event = val
self.viewer.event = val
self._event_index = val.count
self._event_id = val.index.event_id
self.update_event_index_widget()
self.update_event_id_widget()
self._telid = self.viewer.telid
self.update_telid_widget()
self._channel = self.viewer.channel
self.update_channel_widget()
def update_dl1_calibrator(self, extractor=None):
"""
Recreate the dl1 calibrator with the specified extractor and cleaner
Parameters
----------
extractor : ctapipe.image.extractor.ImageExtractor
"""
if extractor is None:
extractor = self.calibrator.image_extractor
self.extractor = extractor
self.calibrator = CameraCalibrator(
subarray=self.reader.subarray,
parent=self,
image_extractor=self.extractor,
)
self.viewer.refresh()
def create_next_event_widget(self):
self.w_next_event = Button(label=">", button_type="default", width=50)
self.w_next_event.on_click(self.on_next_event_widget_click)
def on_next_event_widget_click(self):
self.event_index += 1
def create_previous_event_widget(self):
self.w_previous_event = Button(label="<",
button_type="default",
width=50)
self.w_previous_event.on_click(self.on_previous_event_widget_click)
def on_previous_event_widget_click(self):
self.event_index -= 1
def create_event_index_widget(self):
self.w_event_index = TextInput(title="Event Index:", value="")
def update_event_index_widget(self):
if self.w_event_index:
self.w_event_index.value = str(self.event_index)
def create_event_id_widget(self):
self.w_event_id = TextInput(title="Event ID:", value="")
def update_event_id_widget(self):
if self.w_event_id:
self.w_event_id.value = str(self.event_id)
def create_goto_event_index_widget(self):
self.w_goto_event_index = Button(label="GOTO Index",
button_type="default",
width=100)
self.w_goto_event_index.on_click(self.on_goto_event_index_widget_click)
def on_goto_event_index_widget_click(self):
self.event_index = int(self.w_event_index.value)
def create_goto_event_id_widget(self):
self.w_goto_event_id = Button(label="GOTO ID",
button_type="default",
width=70)
self.w_goto_event_id.on_click(self.on_goto_event_id_widget_click)
def on_goto_event_id_widget_click(self):
self.event_id = int(self.w_event_id.value)
def create_telid_widget(self):
self.w_telid = Select(title="Telescope:", value="", options=[])
self.w_telid.on_change("value", self.on_telid_widget_change)
def update_telid_widget(self):
if self.w_telid:
tels = [str(t) for t in self.event.r0.tels_with_data]
self.w_telid.options = tels
self.w_telid.value = str(self.telid)
def on_telid_widget_change(self, _, __, ___):
if self.telid != int(self.w_telid.value):
self.telid = int(self.w_telid.value)
def create_channel_widget(self):
self.w_channel = Select(title="Channel:", value="", options=[])
self.w_channel.on_change("value", self.on_channel_widget_change)
def update_channel_widget(self):
if self.w_channel:
try:
n_chan = self.event.r0.tel[self.telid].waveform.shape[0]
except AttributeError:
n_chan = 1
channels = [str(c) for c in range(n_chan)]
self.w_channel.options = channels
self.w_channel.value = str(self.channel)
def on_channel_widget_change(self, _, __, ___):
if self.channel != int(self.w_channel.value):
self.channel = int(self.w_channel.value)
def create_dl1_widgets(self):
self.w_dl1_dict = dict(
extractor=Select(
title="Extractor:",
value="",
width=5,
options=BokehFileViewer.extractor_product.values,
),
extractor_window_start=TextInput(title="Window Start:", value=""),
extractor_window_width=TextInput(title="Window Width:", value=""),
extractor_window_shift=TextInput(title="Window Shift:", value=""),
extractor_lwt=TextInput(title="Local Pixel Weight:", value=""),
)
for val in self.w_dl1_dict.values():
val.on_change("value", self.on_dl1_widget_change)
self.wb_extractor = widgetbox(
PreText(text="Charge Extractor Configuration"),
self.w_dl1_dict["extractor"],
self.w_dl1_dict["extractor_window_start"],
self.w_dl1_dict["extractor_window_width"],
self.w_dl1_dict["extractor_window_shift"],
self.w_dl1_dict["extractor_lwt"],
)
def update_dl1_widget_values(self):
if self.w_dl1_dict:
for key, val in self.w_dl1_dict.items():
if "extractor" in key:
if key == "extractor":
val.value = self.extractor.__class__.__name__
else:
key = key.replace("extractor_", "")
try:
val.value = str(getattr(self.extractor, key))
except AttributeError:
val.value = ""
def on_dl1_widget_change(self, _, __, ___):
if self.event:
if not self._updating_dl1:
self._updating_dl1 = True
cmdline = []
for key, val in self.w_dl1_dict.items():
k = key.replace("extractor_", "ImageExtractor.")
if val.value:
cmdline.append(f"--{k}={val.value}")
self.parse_command_line(cmdline)
extractor = ImageExtractor.from_name(self.extractor_product,
parent=self)
self.update_dl1_calibrator(extractor)
self.update_dl1_widget_values()
self._updating_dl1 = False
title='Minimum Age (Inclusive)')
max_age_select = Slider(start=0, end=max(df['age']), value=max(df['age']),
step=1, title='Maximum Age (Inclusive)')
# Create checkboxes for enabling each sex
sex_select = CheckboxGroup(labels=['Male', 'Female'], active=[0, 1])
# Combine all the widgets above into a tabbed pane
selectors = Tabs(tabs=[
Panel(child=HBox(category_select), title='Category'),
Panel(child=HBox(min_size_select, max_size_select), title='Group Size'),
Panel(child=HBox(min_age_select, max_age_select), title='Age'),
Panel(child=HBox(sex_select), title='Sex')
])
generate = Button(label='Generate')
renderer = plot.line([], [], line_width=2, line_alpha=0.75)
def generate_plot(): # Perhaps `regenerate_plot`?
""" Dynamically fit and plot a Kaplan-Meier curve. """
df_ = df.copy()
# Use constraints
for index in range(len(categories)):
if index not in category_select.active:
df_ = df_[df_.category != category_select.labels[index]]
df_ = df_[min_size_select.value <= df_['size']]
df_ = df_[df_['size'] <= max_size_select.value]
def create_next_event_widget(self):
self.w_next_event = Button(label=">", button_type="default", width=50)
self.w_next_event.on_click(self.on_next_event_widget_click)
# drop down hour selector
hour_interval_selector = Select(title='Hour interval',
options=list(time_interval_dict.keys()),
value='00:00')
hour_interval_selector.on_change('value', lambda attr, old, new: update())
# minimum traffic flux slider
flux_slider = Slider(start=0,
end=30,
value=0,
step=1,
width=1,
align='start',
title='Lower limit of total traffic flux')
# allows scaling before update
flux_slider.value = flux_slider.value
flux_slider.on_change('value', lambda attr, old, new: update())
# hourly drop down and minimum flux selector
hour_inputs = widgetbox(hour_interval_selector, sizing_mode='scale_width')
slider_input = widgetbox(flux_slider, sizing_mode='scale_width')
# video time lapse button
button = Button(label='► Play',
width=60,
sizing_mode='scale_width',
name='Traffic time lapse',
align='end')
button.on_click(animate)
def create_previous_event_widget(self):
self.w_previous_event = Button(label="<",
button_type="default",
width=50)
self.w_previous_event.on_click(self.on_previous_event_widget_click)
myStream = tweepy.Stream(auth=api.auth, listener=callback)
myStream.filter(track=topic, async=True)
######## Creating Visualizations ###############
# Heading
heading = PreText(text="""\bANALYZING REAL TIME TWITTER DATA\b""",
height=50,
width=1500)
#------------------------------------------------------------------------------------------------------------------
# Catergory text search
search_1 = TextInput(value="default", title="Search Term 1:")
search_2 = TextInput(value="default", title="Search Term 2:")
button_go = Button(label="Compare", width=100, button_type="success")
#------------------------------------------------------------------------------------------------------------------
# Tweets display
text = "Real Time Tweets-- \n"
current_tweets_plot = PreText(text=text, width=400, height=900)
#------------------------------------------------------------------------------------------------------------------
# Line chart for tweet rate
df_tweet_1 = pd.DataFrame(columns=['Timestamp', 'Tweet', 'rounded_time'])
df_tweet_1 = df_tweet_1.fillna(0)
df_tweet_2 = pd.DataFrame(columns=['Timestamp', 'Tweet', 'rounded_time'])
df_tweet_2 = df_tweet_2.fillna(0)
tweet_rate_plot = figure(title='Tweet Rate(per 5 seconds)',
x_axis_type="datetime",
class BokehFileViewer(Tool):
name = "BokehFileViewer"
description = ("Interactively explore an event file using the bokeh "
"visualisation package")
port = Int(5006, help="Port to open bokeh server onto").tag(config=True)
disable_server = Bool(False,
help="Do not start the bokeh server "
"(useful for testing)").tag(config=True)
aliases = Dict(
dict(
port='BokehFileViewer.port',
disable_server='BokehFileViewer.disable_server',
r='EventSourceFactory.product',
f='EventSourceFactory.input_url',
max_events='EventSourceFactory.max_events',
ped='CameraR1CalibratorFactory.pedestal_path',
tf='CameraR1CalibratorFactory.tf_path',
pe='CameraR1CalibratorFactory.pe_path',
ff='CameraR1CalibratorFactory.ff_path',
extractor='ChargeExtractorFactory.product',
extractor_t0='ChargeExtractorFactory.t0',
extractor_window_width='ChargeExtractorFactory.window_width',
extractor_window_shift='ChargeExtractorFactory.window_shift',
extractor_sig_amp_cut_HG='ChargeExtractorFactory.sig_amp_cut_HG',
extractor_sig_amp_cut_LG='ChargeExtractorFactory.sig_amp_cut_LG',
extractor_lwt='ChargeExtractorFactory.lwt',
cleaner='WaveformCleanerFactory.product',
))
classes = List([
EventSourceFactory, ChargeExtractorFactory, CameraR1CalibratorFactory,
CameraDL1Calibrator, WaveformCleanerFactory
])
def __init__(self, **kwargs):
super().__init__(**kwargs)
self._event = None
self._event_index = None
self._event_id = None
self._telid = None
self._channel = None
self.w_next_event = None
self.w_previous_event = None
self.w_event_index = None
self.w_event_id = None
self.w_goto_event_index = None
self.w_goto_event_id = None
self.w_telid = None
self.w_channel = None
self.w_dl1_dict = None
self.wb_extractor = None
self.layout = None
self.reader = None
self.seeker = None
self.extractor = None
self.cleaner = None
self.r1 = None
self.dl0 = None
self.dl1 = None
self.viewer = None
self._updating_dl1 = False
def setup(self):
self.log_format = "%(levelname)s: %(message)s [%(name)s.%(funcName)s]"
kwargs = dict(config=self.config, tool=self)
default_url = get_dataset_path("gamma_test.simtel.gz")
EventSourceFactory.input_url.default_value = default_url
self.reader = EventSourceFactory.produce(**kwargs)
self.seeker = EventSeeker(self.reader, **kwargs)
self.extractor = ChargeExtractorFactory.produce(**kwargs)
self.cleaner = WaveformCleanerFactory.produce(**kwargs)
self.r1 = CameraR1CalibratorFactory.produce(eventsource=self.reader,
**kwargs)
self.dl0 = CameraDL0Reducer(**kwargs)
self.dl1 = CameraDL1Calibrator(extractor=self.extractor,
cleaner=self.cleaner,
**kwargs)
self.viewer = BokehEventViewer(**kwargs)
# Setup widgets
self.viewer.create()
self.viewer.enable_automatic_index_increment()
self.create_previous_event_widget()
self.create_next_event_widget()
self.create_event_index_widget()
self.create_goto_event_index_widget()
self.create_event_id_widget()
self.create_goto_event_id_widget()
self.create_telid_widget()
self.create_channel_widget()
self.create_dl1_widgets()
self.update_dl1_widget_values()
# Setup layout
self.layout = layout([[self.viewer.layout],
[
self.w_previous_event, self.w_next_event,
self.w_goto_event_index, self.w_goto_event_id
], [self.w_event_index, self.w_event_id],
[self.w_telid, self.w_channel],
[self.wb_extractor]])
def start(self):
self.event_index = 0
def finish(self):
if not self.disable_server:
def modify_doc(doc):
doc.add_root(self.layout)
doc.title = self.name
directory = os.path.abspath(os.path.dirname(__file__))
theme_path = os.path.join(directory, "theme.yaml")
template_path = os.path.join(directory, "templates")
doc.theme = Theme(filename=theme_path)
env = jinja2.Environment(
loader=jinja2.FileSystemLoader(template_path))
doc.template = env.get_template('index.html')
self.log.info('Opening Bokeh application on '
'http://localhost:{}/'.format(self.port))
server = Server({'/': modify_doc}, num_procs=1, port=self.port)
server.start()
server.io_loop.add_callback(server.show, "/")
server.io_loop.start()
@property
def event_index(self):
return self._event_index
@event_index.setter
def event_index(self, val):
try:
self.event = self.seeker[val]
except IndexError:
self.log.warning("Event Index {} does not exist".format(val))
@property
def event_id(self):
return self._event_id
@event_id.setter
def event_id(self, val):
try:
self.event = self.seeker[str(val)]
except IndexError:
self.log.warning("Event ID {} does not exist".format(val))
@property
def telid(self):
return self._telid
@telid.setter
def telid(self, val):
self.channel = 0
tels = list(self.event.r0.tels_with_data)
if val not in tels:
val = tels[0]
self._telid = val
self.viewer.telid = val
self.update_telid_widget()
@property
def channel(self):
return self._channel
@channel.setter
def channel(self, val):
self._channel = val
self.viewer.channel = val
self.update_channel_widget()
@property
def event(self):
return self._event
@event.setter
def event(self, val):
# Calibrate
self.r1.calibrate(val)
self.dl0.reduce(val)
self.dl1.calibrate(val)
self._event = val
self.viewer.event = val
self._event_index = val.count
self._event_id = val.r0.event_id
self.update_event_index_widget()
self.update_event_id_widget()
self._telid = self.viewer.telid
self.update_telid_widget()
self._channel = self.viewer.channel
self.update_channel_widget()
def update_dl1_calibrator(self, extractor=None, cleaner=None):
"""
Recreate the dl1 calibrator with the specified extractor and cleaner
Parameters
----------
extractor : ctapipe.image.charge_extractors.ChargeExtractor
cleaner : ctapipe.image.waveform_cleaning.WaveformCleaner
"""
if extractor is None:
extractor = self.dl1.extractor
if cleaner is None:
cleaner = self.dl1.cleaner
self.extractor = extractor
self.cleaner = cleaner
kwargs = dict(config=self.config, tool=self)
self.dl1 = CameraDL1Calibrator(extractor=self.extractor,
cleaner=self.cleaner,
**kwargs)
self.dl1.calibrate(self.event)
self.viewer.refresh()
def create_next_event_widget(self):
self.w_next_event = Button(label=">", button_type="default", width=50)
self.w_next_event.on_click(self.on_next_event_widget_click)
def on_next_event_widget_click(self):
self.event_index += 1
def create_previous_event_widget(self):
self.w_previous_event = Button(label="<",
button_type="default",
width=50)
self.w_previous_event.on_click(self.on_previous_event_widget_click)
def on_previous_event_widget_click(self):
self.event_index -= 1
def create_event_index_widget(self):
self.w_event_index = TextInput(title="Event Index:", value='')
def update_event_index_widget(self):
if self.w_event_index:
self.w_event_index.value = str(self.event_index)
def create_event_id_widget(self):
self.w_event_id = TextInput(title="Event ID:", value='')
def update_event_id_widget(self):
if self.w_event_id:
self.w_event_id.value = str(self.event_id)
def create_goto_event_index_widget(self):
self.w_goto_event_index = Button(label="GOTO Index",
button_type="default",
width=100)
self.w_goto_event_index.on_click(self.on_goto_event_index_widget_click)
def on_goto_event_index_widget_click(self):
self.event_index = int(self.w_event_index.value)
def create_goto_event_id_widget(self):
self.w_goto_event_id = Button(label="GOTO ID",
button_type="default",
width=70)
self.w_goto_event_id.on_click(self.on_goto_event_id_widget_click)
def on_goto_event_id_widget_click(self):
self.event_id = int(self.w_event_id.value)
def create_telid_widget(self):
self.w_telid = Select(title="Telescope:", value="", options=[])
self.w_telid.on_change('value', self.on_telid_widget_change)
def update_telid_widget(self):
if self.w_telid:
tels = [str(t) for t in self.event.r0.tels_with_data]
self.w_telid.options = tels
self.w_telid.value = str(self.telid)
def on_telid_widget_change(self, _, __, ___):
if self.telid != int(self.w_telid.value):
self.telid = int(self.w_telid.value)
def create_channel_widget(self):
self.w_channel = Select(title="Channel:", value="", options=[])
self.w_channel.on_change('value', self.on_channel_widget_change)
def update_channel_widget(self):
if self.w_channel:
try:
n_chan = self.event.r0.tel[self.telid].waveform.shape[0]
except AttributeError:
n_chan = 1
channels = [str(c) for c in range(n_chan)]
self.w_channel.options = channels
self.w_channel.value = str(self.channel)
def on_channel_widget_change(self, _, __, ___):
if self.channel != int(self.w_channel.value):
self.channel = int(self.w_channel.value)
def create_dl1_widgets(self):
self.w_dl1_dict = dict(
cleaner=Select(title="Cleaner:",
value='',
width=5,
options=WaveformCleanerFactory.subclass_names),
extractor=Select(title="Extractor:",
value='',
width=5,
options=ChargeExtractorFactory.subclass_names),
extractor_t0=TextInput(title="T0:", value=''),
extractor_window_width=TextInput(title="Window Width:", value=''),
extractor_window_shift=TextInput(title="Window Shift:", value=''),
extractor_sig_amp_cut_HG=TextInput(title="Significant Amplitude "
"Cut (HG):",
value=''),
extractor_sig_amp_cut_LG=TextInput(title="Significant Amplitude "
"Cut (LG):",
value=''),
extractor_lwt=TextInput(title="Local Pixel Weight:", value=''))
for val in self.w_dl1_dict.values():
val.on_change('value', self.on_dl1_widget_change)
self.wb_extractor = widgetbox(
PreText(text="Charge Extractor Configuration"),
self.w_dl1_dict['cleaner'], self.w_dl1_dict['extractor'],
self.w_dl1_dict['extractor_t0'],
self.w_dl1_dict['extractor_window_width'],
self.w_dl1_dict['extractor_window_shift'],
self.w_dl1_dict['extractor_sig_amp_cut_HG'],
self.w_dl1_dict['extractor_sig_amp_cut_LG'],
self.w_dl1_dict['extractor_lwt'])
def update_dl1_widget_values(self):
if self.w_dl1_dict:
for key, val in self.w_dl1_dict.items():
if 'extractor' in key:
if key == 'extractor':
val.value = self.extractor.__class__.__name__
else:
key = key.replace("extractor_", "")
try:
val.value = str(getattr(self.extractor, key))
except AttributeError:
val.value = ''
elif 'cleaner' in key:
if key == 'cleaner':
val.value = self.cleaner.__class__.__name__
else:
key = key.replace("cleaner_", "")
try:
val.value = str(getattr(self.cleaner, key))
except AttributeError:
val.value = ''
def on_dl1_widget_change(self, _, __, ___):
if self.event:
if not self._updating_dl1:
self._updating_dl1 = True
cmdline = []
for key, val in self.w_dl1_dict.items():
if val.value:
cmdline.append('--{}'.format(key))
cmdline.append(val.value)
self.parse_command_line(cmdline)
kwargs = dict(config=self.config, tool=self)
extractor = ChargeExtractorFactory.produce(**kwargs)
cleaner = WaveformCleanerFactory.produce(**kwargs)
self.update_dl1_calibrator(extractor, cleaner)
self.update_dl1_widget_values()
self._updating_dl1 = False
def produce_graphs(self, context, doc):
"""
Create timetool data timehistory, timetool vs ipm,
and correlation timehistory graphs.
Parameters
----------
context = zmq.Context()
Creates zmq socket to receive data
doc: bokeh.document (I think)
Bokeh document to be displayed on webpage
"""
port = 5006
socket = context.socket(zmq.SUB)
# MUST BE FROM SAME MACHINE, CHANGE IF NECESSARY!!!
socket.connect("tcp://psanagpu114:%d" % port)
socket.setsockopt(zmq.SUBSCRIBE, b"")
# Note: Cannot name 'timetool' variables in hvTimeTool and hvIpmAmp the same thing
# Otherwise, holoviews will try to sync the axis and throw off the ranges for the plots
# since hvIpmAmp only deals with the last 1000 points whereas hvTimeTool deals with all
# the points
hvTimeTool = hv.DynamicMap(my_partial(hv.Points,
kdims=['timestamp', 'timetool']),
streams=[self.b_timetool]).options(
width=1000,
finalize_hooks=[apply_formatter],
xrotation=45).redim.label(
timestamp='Time in UTC',
timetool='Timetool Data')
hvIpmAmp = hv.DynamicMap(
my_partial(hv.Scatter, kdims=['timetool', 'ipm']),
streams=[self.b_IpmAmp]).options(width=500).redim.label(
timetool='Last 1000 Timetool Data Points',
ipm='Last 1000 Ipm Data Points')
hvCorrTimeHistory = hv.DynamicMap(
my_partial(hv.Scatter, kdims=['timestamp', 'correlation']),
streams=[self.b_corr_timehistory
]).options(width=500,
finalize_hooks=[apply_formatter],
xrotation=45).redim.label(time='Time in UTC')
layout = (hvIpmAmp + hvCorrTimeHistory + hvTimeTool).cols(2)
hvplot = renderer.get_plot(layout)
def push_data_timetool(buffer):
"""
Push data to timetool time history graph
"""
timetool_d = deque(maxlen=self.maxlen)
timetool_t = deque(maxlen=self.maxlen)
if socket.poll(timeout=0):
data_dict = socket.recv_pyobj()
timetool_d = data_dict['tt__FLTPOS_PS']
# Get time from data_dict
timeData = deque(maxlen=self.maxlen)
for time in data_dict['event_time']:
num1 = str(time[0])
num2 = str(time[1])
fullnum = num1 + "." + num2
timeData.append(float(fullnum))
timetool_t = timeData
# Convert time to seconds so bokeh formatter can get correct datetime
times = [1000 * time for time in list(timetool_t)]
data = pd.DataFrame({'timestamp': times, 'timetool': timetool_d})
buffer.send(data)
def push_data_amp_ipm(buffer):
"""
Push data into timetool amp vs ipm graph
"""
timetool_d = deque(maxlen=self.maxlen)
ipm_d = deque(maxlen=self.maxlen)
if socket.poll(timeout=0):
data_dict = socket.recv_pyobj()
timetool_d = data_dict['tt__AMPL']
ipm_d = data_dict[self.switchButton]
data = pd.DataFrame({'timetool': timetool_d, 'ipm': ipm_d})
buffer.send(data)
def push_data_corr_time_history(buffer):
"""
Calculate correlation between timetool amp and ipm and
push to correlation time history graph
"""
timetool_d = deque(maxlen=self.maxlen)
timetool_t = deque(maxlen=self.maxlen)
ipm_d = deque(maxlen=self.maxlen)
if socket.poll(timeout=0):
data_dict = socket.recv_pyobj()
timetool_d = data_dict['tt__FLTPOS_PS']
ipm_d = data_dict[self.switchButton]
# Get time from data_dict
timeData = deque(maxlen=self.maxlen)
for time in data_dict['event_time']:
num1 = str(time[0])
num2 = str(time[1])
fullnum = num1 + "." + num2
timeData.append(float(fullnum))
timetool_t = timeData
# Convert time to seconds so bokeh formatter can get correct datetime
times = [1000 * time for time in list(timetool_t)]
data = pd.DataFrame({'timetool': timetool_d, 'ipm': ipm_d})
data_corr = data['timetool'].rolling(window=120).corr(
other=data['ipm'])
# Start at index 119 so we don't get null data
final_df = pd.DataFrame({
'timestamp': times[119:],
'correlation': data_corr[119:]
})
buffer.send(final_df)
def switch(attr, old, new):
"""
Update drop down menu value
"""
self.switchButton = select.value
self.clear_buffer()
def stop():
"""
Add pause and play functionality to graph
"""
if stopButton.label == 'Play':
stopButton.label = 'Pause'
self.cb_id_timetool = doc.add_periodic_callback(
partial(push_data_timetool, buffer=self.b_timetool), 1000)
self.cb_id_amp_ipm = doc.add_periodic_callback(
partial(push_data_amp_ipm, buffer=self.b_IpmAmp), 1000)
self.cb_id_corr_timehistory = doc.add_periodic_callback(
partial(push_data_corr_time_history,
buffer=self.b_corr_timehistory), 1000)
else:
stopButton.label = 'Play'
doc.remove_periodic_callback(self.cb_id_timetool)
doc.remove_periodic_callback(self.cb_id_amp_ipm)
doc.remove_periodic_callback(self.cb_id_corr_timehistory)
# Start the callback
self.cb_id_timetool = doc.add_periodic_callback(
partial(push_data_timetool, buffer=self.b_timetool), 1000)
self.cb_id_amp_ipm = doc.add_periodic_callback(
partial(push_data_amp_ipm, buffer=self.b_IpmAmp), 1000)
self.cb_id_corr_timehistory = doc.add_periodic_callback(
partial(push_data_corr_time_history,
buffer=self.b_corr_timehistory), 1000)
# Use this to test since ipm2 and ipm3 are too similar to see any differences
# select = Select(title='ipm value:', value='ipm2__sum', options=['ipm2__sum', 'tt__FLTPOS_PS'])
select = Select(title='ipm value:',
value='ipm2__sum',
options=['ipm2__sum', 'ipm3__sum'])
select.on_change('value', switch)
stopButton = Button(label='Pause')
stopButton.on_click(stop)
plot = column(select, stopButton, hvplot.state)
doc.add_root(plot)
def home():
bokeh_width, bokeh_height = 1000, 600
lat, lon = 46.2437, 6.0251
api_key = "AIzaSyB4y5u1q0_-4kVQpSMGkH_dxpnzn8PL-dQ"
print(str(api_key))
def plot(lat, lng, zoom=10, map_type='roadmap'):
from bokeh.io import show
from bokeh.plotting import gmap
from bokeh.models import GMapOptions
gmap_options = GMapOptions(lat=lat,
lng=lng,
map_type=map_type,
zoom=zoom)
p = gmap(api_key,
gmap_options,
title='Pays de Gex',
width=bokeh_width,
height=bokeh_height)
# beware, longitude is on the x axis ;-)
center = p.circle([lng], [lat], size=10, alpha=0.5, color='red')
return p
p = plot(lat, lon, map_type='roadmap')
#---------------------------------------------------
from bokeh.io import curdoc
from bokeh.layouts import column
from bokeh.models import Button, ColumnDataSource
from bokeh.plotting import Figure
from bokeh.embed import components
from bokeh.resources import CDN
from numpy.random import random
xs = []
ys = []
points = ColumnDataSource(data={'x_coord': xs, 'y_coord': ys})
plot = Figure(title="Random Lines", x_range=(0, 1), y_range=(0, 1))
plot.line('x_coord', 'y_coord', source=points)
button = Button(label="Click Me!")
def add_random_line():
"""
Adds a new random point to the line.
"""
x, y = random(2)
newxs = [*points.data['x_coord'], x]
newys = [*points.data['y_coord'], y]
points.data = {'x_coord': newxs, 'y_coord': newys}
button.on_click(add_random_line)
layout = column(button, plot)
curdoc().add_root(layout)
script1, div1, = components(p)
cdn_js = CDN.js_files[0]
cdn_css = CDN.css_files
print(script1)
print('\n============================================')
print(div1)
print('\n============================================')
print(cdn_css)
print('\n============================================')
print(cdn_js)
# return render_template("combine.html",script1=script1,div1=div1, cdn_css=cdn_css,cdn_js=cdn_js)
data_val1 = 'Hard Coded value 1'
data_val2 = 'Hard coded value 2'
templateData = {'data1': data_val1, 'data2': data_val2}
return render_template("combine.html",
**templateData,
script1=script1,
div1=div1,
cdn_css=cdn_css,
cdn_js=cdn_js)
def slider_update(attrname, old, new):
year = slider.value
label.text = str(year)
source.data = data[year]
slider = Slider(start=years[0], end=years[-1], value=years[0], step=1, title="Year")
slider.on_change('value', slider_update)
callback_id = None
def animate():
global callback_id
if button.label == '► Play':
button.label = '❚❚ Pause'
callback_id = curdoc().add_periodic_callback(animate_update, 200)
else:
button.label = '► Play'
curdoc().remove_periodic_callback(callback_id)
button = Button(label='► Play', width=60)
button.on_click(animate)
layout = layout([
[plot],
[slider, button],
], sizing_mode='scale_width')
curdoc().add_root(layout)
curdoc().title = "Gapminder"
class ProfileTimePlot(DashboardComponent):
"""Time plots of the current resource usage on the cluster
This is two plots, one for CPU and Memory and another for Network I/O
"""
def __init__(self, server, doc=None, **kwargs):
if doc is not None:
self.doc = weakref.ref(doc)
try:
self.key = doc.session_context.request.arguments.get("key", None)
except AttributeError:
self.key = None
if isinstance(self.key, list):
self.key = self.key[0]
if isinstance(self.key, bytes):
self.key = self.key.decode()
self.task_names = ["All", self.key] if self.key else ["All"]
else:
self.key = None
self.task_names = ["All"]
self.server = server
self.start = None
self.stop = None
self.ts = {"count": [], "time": []}
self.state = profile.create()
data = profile.plot_data(self.state, profile_interval)
self.states = data.pop("states")
self.profile_plot, self.source = profile.plot_figure(data, **kwargs)
changing = [False] # avoid repeated changes from within callback
@without_property_validation
def cb(attr, old, new):
if changing[0] or len(new) == 0:
return
with log_errors():
data = profile.plot_data(self.states[new[0]], profile_interval)
del self.states[:]
self.states.extend(data.pop("states"))
changing[0] = True # don't recursively trigger callback
update(self.source, data)
self.source.selected.indices = old
changing[0] = False
self.source.selected.on_change("indices", cb)
self.ts_source = ColumnDataSource({"time": [], "count": []})
self.ts_plot = figure(
title="Activity over time",
height=150,
x_axis_type="datetime",
active_drag="xbox_select",
tools="xpan,xwheel_zoom,xbox_select,reset",
sizing_mode="stretch_width",
toolbar_location="above",
)
self.ts_plot.line("time", "count", source=self.ts_source)
self.ts_plot.circle(
"time", "count", source=self.ts_source, color=None, selection_color="orange"
)
self.ts_plot.yaxis.visible = False
self.ts_plot.grid.visible = False
def ts_change(attr, old, new):
with log_errors():
selected = self.ts_source.selected.indices
if selected:
start = self.ts_source.data["time"][min(selected)] / 1000
stop = self.ts_source.data["time"][max(selected)] / 1000
self.start, self.stop = min(start, stop), max(start, stop)
else:
self.start = self.stop = None
self.trigger_update(update_metadata=False)
self.ts_source.selected.on_change("indices", ts_change)
self.reset_button = Button(label="Reset", button_type="success")
self.reset_button.on_click(lambda: self.update(self.state))
self.update_button = Button(label="Update", button_type="success")
self.update_button.on_click(self.trigger_update)
self.select = Select(value=self.task_names[-1], options=self.task_names)
def select_cb(attr, old, new):
if new == "All":
new = None
self.key = new
self.trigger_update(update_metadata=False)
self.select.on_change("value", select_cb)
self.root = column(
row(
self.select,
self.reset_button,
self.update_button,
sizing_mode="scale_width",
height=250,
),
self.profile_plot,
self.ts_plot,
**kwargs,
)
@without_property_validation
def update(self, state, metadata=None):
with log_errors():
self.state = state
data = profile.plot_data(self.state, profile_interval)
self.states = data.pop("states")
update(self.source, data)
if metadata is not None and metadata["counts"]:
self.task_names = ["All"] + sorted(metadata["keys"])
self.select.options = self.task_names
if self.key:
ts = metadata["keys"][self.key]
else:
ts = metadata["counts"]
times, counts = zip(*ts)
self.ts = {"count": counts, "time": [t * 1000 for t in times]}
self.ts_source.data.update(self.ts)
@without_property_validation
def trigger_update(self, update_metadata=True):
async def cb():
with log_errors():
prof = await self.server.get_profile(
key=self.key, start=self.start, stop=self.stop
)
if update_metadata:
metadata = await self.server.get_profile_metadata()
else:
metadata = None
if isinstance(prof, gen.Future):
prof, metadata = await asyncio.gather(prof, metadata)
self.doc().add_next_tick_callback(lambda: self.update(prof, metadata))
self.server.loop.add_callback(cb)
y = np.random.random(size=N) * 100
radii = np.random.random(size=N) * 1.5
colors = [
"#%02x%02x%02x" % (int(r), int(g), 150) for r, g in zip(50+2*x, 30+2*y)
]
p = figure(tools="pan,wheel_zoom,zoom_in,zoom_out,reset")
p.scatter(x, y, radius=radii,
fill_color=colors, fill_alpha=0.6,
line_color=None)
# Add a div to display events and a button to trigger button click events
div = Div(width=1000)
button = Button(label="Button", button_type="success")
layout = column(button, row(p, div))
point_attributes = ['x','y','sx','sy']
pan_attributes = point_attributes + ['delta_x', 'delta_y']
pinch_attributes = point_attributes + ['scale']
wheel_attributes = point_attributes+['delta']
## Register Javascript event callbacks
# Button event
button.js_on_event(events.ButtonClick, display_event(div))
# LOD events
p.js_on_event(events.LODStart, display_event(div))
# remove.py
import numpy as np
from bokeh.io import curdoc
from bokeh.models import Button
from bokeh.plotting import figure, curdoc, vplot
xs = np.random.normal(loc=1.0, size=100)
ys = np.random.normal(loc=1.0, size=100)
TOOLS="pan,wheel_zoom,box_select,lasso_select"
p = figure(tools=TOOLS, plot_width=600, plot_height=600, title=None, min_border=10, min_border_left=50)
r = p.scatter(xs.tolist(), ys.tolist(), size=3, color="#3A5785", alpha=0.6)
source = r.data_source
empty_selection = r.data_source.selected
def callback():
source.selected = empty_selection
button = Button(label="Remove Points", width=20)
button.on_click(callback)
# put the button and plot in a layout and add to the document
curdoc().add_root(vplot(button, p))
def root():
# add a button widget and configure with the call back
button = Button(label="Press Me")
button.on_click(scrape_prices(url))
p = make_hist(prices)
#layout = vform(button, p)
#script, div = embed.components(layout)
script, div = embed.components(p,button)
return render_template('histograms.html',script = script,div = div)
