def test_zeppelin_with_notebook_handle(self):
load_zeppelin_args = (Resources(), True, True, 1000, 'zeppelin')
io.output_notebook(*load_zeppelin_args)
with pytest.raises(Exception) as ex:
p = Plot()
io.show(p, notebook_handle=True)
assert "Zeppelin doesn't support notebook_handle." == str(ex.value)
def plot_matplobli(self):
from omicexperiment.plotting.plot_bokeh import plot_interactive
fig = plot_interactive(self.data_df)
from bokeh.io import show, output_notebook
output_notebook()
show(fig)
return fig
def render(xmin, xmax, ymin, ymax, numDisplayed):
start_time = time.time()
(xpoints, ypoints) = RDDDB.crossfilter(xmin, xmax, ymin, ymax, numDisplayed)
x = np.random.random(size=numDisplayed) * 100
y = np.random.random(size=numDisplayed) * 100
displayArea = (xmax - xmin) * (ymax - ymin)
radii = math.sqrt(.1 * displayArea/600)
print "Radii size = " + str(radii)
colors = ["#%02x%02x%02x" % (r, g, 100) for r, g in zip(np.floor(50 + 2 * x), np.floor(30 + 2 * y))]
# output to static HTML file (with CDN resources)
# output_file("color_scatter.html", title="color_scatter.py example", mode="cdn")
TOOLS = "resize,crosshair,pan,wheel_zoom,box_zoom,reset,box_select,lasso_select"
# set output to notebook widget environment
output_notebook()
# create a new plot with the tools above, and explicit ranges
p = figure(tools=TOOLS, x_range=(xmin, xmax), y_range=(ymin, ymax))
# add a circle renderer with vecorized colors and sizes
p.circle(xpoints, ypoints, radius=radii, fill_color=colors, fill_alpha=0.6, line_color=None)
end_time = time.time()
print "Time taken to render : " + str(end_time - start_time)
show(p)
def test_args(self, mock_load_notebook):
# call _install_notebook_hook to register the patched `bokeh.io.load_notebook`
from bokeh.io import _install_notebook_hook
_install_notebook_hook()
load_jupyter_args = (Resources(), True, True, 1000)
io.output_notebook(*load_jupyter_args)
self._check_func_called(io._state.output_notebook, ('jupyter',), {})
self._check_func_called(mock_load_notebook, load_jupyter_args, {'notebook_type': 'jupyter'})
def test_noarg(self, mock_load_notebook):
# call _install_notebook_hook to register the patched `bokeh.io.load_notebook`
from bokeh.io import _install_notebook_hook
_install_notebook_hook()
default_load_jupyter_args = (None, False, False, 5000)
io.output_notebook()
self._check_func_called(io._state.output_notebook, ('jupyter',), {})
self._check_func_called(mock_load_notebook, default_load_jupyter_args, {'notebook_type': 'jupyter'})
def cdp_plot(counts_by_ref, seq1, seq2, nt, onscreen, file_fig, file_name, pub,
bok):
"""
Scatter plot of alignments to references
:param counts_by_ref: dict of (x,y) counts for each reference (dict)
:param seq1: x label (str)
:param seq2: y label (str)
:param nt: aligned read length (int)
:param file_fig: output plot to pdf (bool)
:param file_name: output filename (str)
:param onscreen: show plot on screen (bool)
:param pub: publication plot (bool)
"""
results_list = [] # list of results
for counts in counts_by_ref.values():
results_list.append((counts[0] + 0.01, counts[1] + 0.01))
# hack that allows zero values to be plotted on a log scale
results_list = sorted(results_list)
_max = max(results_list[-1][0], results_list[-1][1]) # sets up max x and y scale values
_max += float(_max / 2)
if not bok:
plt.scatter(*list(zip(*results_list)),
s=10,
color=_nt_colour(nt),
marker='o',
label="{0} nt".format(nt))
arrow(0.1, 0.1, _max, _max, color='r')
xscale('log')
yscale('log')
xlim(0.1, _max)
ylim(0.1, _max)
if pub:
_pub_plot()
else:
plt.legend(loc='upper left', fancybox=True, framealpha=0.5)
xlabel(seq1)
ylabel(seq2)
_shared_plot(file_fig, file_name, onscreen)
else:
output_notebook()
x_vals = []
y_vals = []
for point in counts_by_ref.values():
x_vals.append(point[0]+ 0.01)
y_vals.append(point[1]+ 0.01)
p = figure(plot_width=600, plot_height=600,
x_axis_type="log", y_axis_type="log",
x_range=(0.1, _max), y_range=(0.1, _max))
p.circle(x_vals, y_vals, size=5, color=_nt_colour(nt), alpha=0.9)
p.line([0.1,_max],[0.1,_max])
p.xaxis.axis_label = seq1
p.yaxis.axis_label = seq2
show(p)
def den_multi_plot_21_22_24(x_ref, y_fwd_smoothed_21, y_rvs_smoothed_21,
y_fwd_smoothed_22, y_rvs_smoothed_22,
y_fwd_smoothed_24, y_rvs_smoothed_24, file_fig,
file_name, onscreen, x_label, plot_y_lim,
pub=False, bok=False):
"""
21, 22 and 24nt combined alignment profile
:param x_ref: x co-ords (list(int))
:param y_fwd_smoothed_21: 21 nt positive y co-ords (list(float))
:param y_rvs_smoothed_21: 21 nt negative y co-ords (list(float))
:param y_fwd_smoothed_22: 22 nt positive y co-ords (list(float))
:param y_rvs_smoothed_22: 22 nt negative y co-ords (list(float)):
:param y_fwd_smoothed_24: 24 nt positive y co-ords (list(float))
:param y_rvs_smoothed_24: 24 nt negative y co-ords (list(float))
:param nt: aligned read length (int)
:param file_fig: output plot to pdf (bool)
:param file_name: output filename (str)
:param onscreen: show plot on screen (bool)
:param x_label: x label (str)
:param plot_y_lim: + / - y-axis limit (int)
:param pub: publication plot (bool)
"""
if not bok:
plt.plot(x_ref, y_fwd_smoothed_21, color='#00CC00', label='21 nt', lw=2)
plt.plot(x_ref, y_rvs_smoothed_21, color='#00CC00', lw=2)
plt.plot(x_ref, y_fwd_smoothed_22, color='#FF3399', label='22 nt', lw=2)
plt.plot(x_ref, y_rvs_smoothed_22, color='#FF3399', lw=2)
plt.plot(x_ref, y_fwd_smoothed_24, color='#3333FF', label='24 nt', lw=2)
plt.plot(x_ref, y_rvs_smoothed_24, color='#3333FF', lw=2)
axhline(y=0)
if pub:
_pub_plot()
else: # no_publication
xlabel(x_label)
ylabel('Reads per million reads')
plt.rc('font') #remove?
plt.legend(bbox_to_anchor=(0., 1.02, 1., .102), loc=3,
ncol=3, mode="expand", borderaxespad=0., fontsize=12)
_generate_profile(file_fig, file_name, onscreen, plot_y_lim)
else:
##Test bokeh package
output_notebook()
if plot_y_lim!=0:
p = figure(plot_width=700, plot_height=400, y_range=(-plot_y_lim, plot_y_lim))
else:
p = figure(plot_width=700, plot_height=400)
p.line(x_ref, y_fwd_smoothed_21, line_width=2, color="#00CC00", legend= "21 nt", alpha=0.9)
p.line(x_ref, y_rvs_smoothed_21, line_width=2, color="#00CC00", alpha=0.9)
p.line(x_ref, y_fwd_smoothed_22, line_width=2, color="#FF3399", legend= "22 nt", alpha=0.9)
p.line(x_ref, y_rvs_smoothed_22, line_width=2, color="#FF3399", alpha=0.9)
p.line(x_ref, y_fwd_smoothed_24, line_width=2, color="#3333FF", legend= "24 nt", alpha=0.9)
p.line(x_ref, y_rvs_smoothed_24, line_width=2, color="#3333FF", alpha=0.9)
show(p)
def timeplot(data):
#input data is a DataFrame
time = pd.DatetimeIndex(data['ltime'])
#String list to store column names from the third column of the dataframe
columns = []
for x in data.columns[1:]:
columns.append(x)
#change string to float in the data
for x in columns[0:(len(columns)-2)]:
if (type(data[x][0]) is str):
for i in range(len(data[x])):
data[x][i] = float(data[x][i].replace(',',''))
output_notebook()
y = data[columns[1]]
x = time
p = Figure(x_axis_type = 'datetime', title = "TimeSeries Plotting")
source = ColumnDataSource(data=dict(x=x, y=y, d=data))
#create a new columndatasoure to pass column name to CustomJS
source2 = ColumnDataSource(data = dict(columns = columns))
p.line('x', 'y', source = source)
p.xaxis.axis_label = "Time"
p.yaxis.axis_label = "Selected Y"
callback = CustomJS(args = dict(source = source, columns=source2), code="""
var data = source.get('data');
var columns = columns.get('data')['columns'];
var f = cb_obj.get('value');
y = data['y'];
console.log('y');
console.log(y);
var d = data['d'];
//get the index of the chosen column from the widget
for(i = 0; i<columns.length;i++){
if(f[0]==columns[i]){
index = i;
}
}
//make the column transpose since the CustomJS
//takes dataframe as an array of arrays which is
//a row of the DataFrame
for (i = 0; i < d.length; i++) {
y[i] = d[i][index+1];
}
console.log('y');
console.log(y.length);
source.trigger('change');
""")
select = MultiSelect(title="Y_Option:", value=[columns[0]],
options=columns, callback=callback)
layout = vform(select, p)
show(layout)
def visualize_segments(self):
output_notebook()
g = figure(x_axis_type="datetime")
for day in pd.date_range(self.date_start, self.date_end - timedelta(days=1), normalize=True):
mask = (self.newdf.date >= day) & (self.newdf.date < (day + timedelta(days=1)))
g.line(self.times, self.newdf.loc[mask][2])
g.circle([s for s, t in self.segs],
[10 for s, t in self.segs], color="red")
show(g)
def doRender(self, handlerId):
clientHasBokeh = self.options.get("nostore_bokeh", "false") == "true"
if not clientHasBokeh:
output_notebook(hide_banner=True)
data = self.entity.getNextData()
if data is None:
return
x = None
y = None
if isinstance(data, (list,np.ndarray)):
x = list(range(self.windowSize)) if self.glyphRenderer is None else self.glyphRenderer.data_source.data['x']
y = data if self.glyphRenderer is None else self._concatArrays(self.glyphRenderer.data_source.data['y'],data)
if len(y) < self.windowSize:
y = [0]*(self.windowSize-len(y)) + y
elif len(y) > self.windowSize:
y = self._delWindowElements(y)
elif isinstance(data, pandas.core.frame.DataFrame):
pd = pd.drop(pd.index[[0]])
#pd.index = list(range(len(pd.index)))
pd['x'] = list(range(len(pd.index)))
else:
x = data[0]
y = data[1]
if self.glyphRenderer is None:
self.glyphRenderer = self.createGlyphRenderer( self.figure, x, y )
else:
self.updateGlyphRenderer( self.figure, self.glyphRenderer)
if self.glyphRenderer is None:
print("Error: no glyphRenderer found")
return
self.glyphRenderer.data_source.data['x'] = x
self.glyphRenderer.data_source.data['y'] = y
if not self.comms_handle:
state = curstate()
doc = state.document
if self.figure not in doc.roots:
doc.add_root(self.figure)
self.comms_handle = show_doc(self.figure, state, notebook_handle=True)
else:
push_notebook(handle = self.comms_handle)
def __init__(self, data,name='scatter_plot', **kwargs):
output_notebook(hide_banner=True)
self._data = data
mapper = PlotMapper(data, button_type='ddown',button_pos='top', name='mapper', mode='interactive')
if isinstance(data, pd.DataFrame):
tooltip = BokehDataFrameTooltip(data, name='tooltip', mode='interactive')
ToggleMenu.__init__(self, children=[mapper,tooltip], name=name,**kwargs)
else:
ToggleMenu.__init__(self, children=[mapper], name=name,**kwargs)
self.buttons.value = 'mapper'
self.mapper.buttons.value = 'y'
if isinstance(self._data,pd.DataFrame):
self.mapper.y.data_slicer.columns_slicer.dd_selector.value =\
self.mapper.y.data_slicer.columns_slicer.dd_selector.target.options[1]
self.observe(self.update)
self.update_source_df()
self.init_plot()
self.update()
def output_chart(issues_df,output_mode='static'):
import datetime
import bokeh
from bokeh.models import HoverTool
# Add timestamp to title
issues_chart = Bar(issues_df, label='value_delivered',
values='status', agg='count', stack='status',
title=ISSUES_TITLE+" (Updated "+datetime.datetime.now().strftime('%m/%d/%Y')+")",
xlabel="Value Delivered",ylabel="Number of Use Cases",
legend='top_right',
tools='hover',
color=brewer["GnBu"][3]
)
issues_chart.plot_width = DESTINATION_FRAME_WIDTH - (HTML_BODY_MARGIN * 2)
issues_chart.plot_height = DESTINATION_FRAME_HEIGHT - (HTML_BODY_MARGIN * 2)
issues_chart.logo = None
issues_chart.toolbar_location = None
hover = issues_chart.select(dict(type=HoverTool))
hover.tooltips = [ ("Value Delivered", "$x")]
#--- Configure output ---
reset_output()
if output_mode == 'static':
# Static file. CDN is most space efficient
output_file(ISSUES_FILE, title=ISSUES_TITLE,
autosave=False, mode='cdn',
root_dir=None
) # Generate file
save(issues_chart,filename=ISSUES_FILE)
elif output_mode == 'notebook':
output_notebook() # Show inline
show(issues_chart)
else:
# Server (using internal server IP, rather than localhost or external)
session = bokeh.session.Session(root_url = BOKEH_SERVER_IP, load_from_config=False)
output_server("ddod_chart", session=session)
show(issues_chart)
def mc_init_notebook(plot_lib='bokeh', i=1):
lib = plot_lib.lower()
if lib == 'bokeh':
if bp is None:
raise ImportError('bokeh')
if i:
from bokeh.io import output_notebook
output_notebook()
environ.notebook = 2
elif lib == 'matplotlib':
if plt is None:
raise ImportError('matplotlib')
plt.rcParams['figure.figsize'] = (15, 12)
plt.rcParams['font.family'] = 'serif'
plt.rcParams['font.size'] = 20
plt.rcParams['font.serif'] = 'Times New Roman'
plt.rcParams['legend.scatterpoints'] = 1
plt.rcParams['legend.handlelength'] = 0
environ.notebook = 1
else:
raise ValueError('expected bokeh or matplotlib, got {0!r}'.format(plot_lib))
def den_plot(x_ref, y_fwd_smoothed, y_rvs_smoothed, nt, file_fig,
file_name, onscreen, x_label, plot_y_lim, pub=False, bok=False):
"""
Single alignment profile
:param x_ref: x co-ords (list(int))
:param y_fwd_smoothed: positive y co-ords (list(float))
:param y_rvs_smoothed: negative y co-ords (list(float))
:param nt: aligned read length (int)
:param file_fig: output plot to pdf (bool)
:param file_name: output filename (str)
:param onscreen: show plot on screen (bool)
:param x_label: x label (str)
:param plot_y_lim: + / - y-axis limit (int)
:param pub: publication plot (bool)
"""
if not bok:
plt.plot(x_ref, y_fwd_smoothed, color=_nt_colour(nt),
label='{0} nt'.format(nt), lw=2)
plt.plot(x_ref, y_rvs_smoothed, color=_nt_colour(nt), lw=2)
axhline(y=0)
if pub:
_pub_plot()
else:
xlabel(x_label)
ylabel('Reads per million reads')
plt.legend(loc='best', fancybox=True, framealpha=0.5)
_generate_profile(file_fig, file_name, onscreen, plot_y_lim)
else:
output_notebook()
if plot_y_lim!=0:
p = figure(plot_width=700, plot_height=400, y_range=(-plot_y_lim, plot_y_lim))
else:
p = figure(plot_width=700, plot_height=400)
p.line(x_ref, y_fwd_smoothed, line_width=2, color=_nt_colour(nt), legend='{0} nt'.format(nt), alpha=0.9)
p.line(x_ref, y_rvs_smoothed, line_width=2, color=_nt_colour(nt), alpha=0.9)
show(p)
# Standard Library
import re
# Third Party
import numpy as np
from bokeh.io import output_notebook, push_notebook, show
from bokeh.layouts import column, row
from bokeh.models import ColumnDataSource, CustomJS, Div, HoverTool
from bokeh.models.glyphs import Circle, Line, Quad
from bokeh.plotting import figure, show
# First Party
from smdebug.profiler.utils import TimeUnits
output_notebook(hide_banner=True)
class TimelineCharts:
def __init__(
self,
system_metrics_reader,
framework_metrics_reader,
starttime=0,
endtime=None,
select_dimensions=[".*"],
select_events=[".*"],
x=1000,
show_workers=True,
):
self.select_dimensions = select_dimensions
def class_plot(self, change):
global global_handle
nx = len(self.xaxis.value)
ny = len(self.yaxis.value)
selected = self.plot_selection.value
if nx * ny > 0:
reset_output()
output_notebook()
p_all = []
for xxa in self.xaxis.value:
for iax, yya in enumerate(self.yaxis.value):
p = figure(title="Class Output", plot_height=300)
xmax = -1e9
xmin = 1e9
ymax = -1e9
ymin = 1e9
legend_items = []
r = []
for ir, irun in enumerate(self.outp):
name = irun.input.name
if selected.count(name) == 1:
if xxa == 't':
x = irun.out.t
xlab = 'time [h]'
elif xxa == 'h':
x = irun.out.h
xlab = 'h [m]'
elif xxa == 'theta':
x = irun.out.theta
xlab = 'theta [K]'
elif xxa == 'q':
x = irun.out.q * 1000
xlab = 'g [g/kg]'
else:
x = None
xlab = ''
xmax = max(xmax, max(x))
xmin = min(xmin, min(x))
if yya == 't':
y = irun.out.t
ylab = 'time [h]'
elif yya == 'h':
y = irun.out.h
ylab = 'h [m]'
elif yya == 'theta':
y = irun.out.theta
ylab = 'theta [K]'
elif yya == 'q':
y = irun.out.q * 1000
ylab = 'g [g/kg]'
else:
y = None
ylab = ''
ymax = max(ymax, max(y))
ymin = min(ymin, min(y))
#self.r[ir].data_source.data['x'] = x
#self.r[ir].data_source.data['y'] = y
r.append(
p.line(x,
y,
color=self.colors[ir],
legend=name,
line_width=3))
#legend_items.append((name,r[ir]))
p.x_range.start = xmin
p.x_range.end = xmax
p.y_range.start = ymin
p.y_range.end = ymax
p.xaxis.axis_label = xlab
p.yaxis.axis_label = ylab
p.legend.location = "top_left"
p_all.append(p)
# show(column(p_all))
# does not work yet to keep one graph. Idea comes from https://bokeh.pydata.org/en/latest/docs/user_guide/notebook.html
# Or this may work: http://localhost:8889/notebooks/Untitled3.ipynb?kernel_name=python3
if (not global_handle):
global_handle = show(obj=p,
new='tab',
notebook_handle=True)
else:
push_notebook(handle=global_handle)
async def _update(self, device: str, datapoint):
# If a chart has been registered to the device, update it.
if device not in self.data:
self.data[device] = []
self.data[device].append(datapoint)
if self._data_file is not None:
line = json.dumps({
"device": device,
"timestamp": datapoint.timestamp,
"experiment_elapsed_time": datapoint.experiment_elapsed_time,
"data": datapoint.data,
"unit": self.protocol.apparatus[device]._unit,
})
async with aiofiles.open(self._data_file, "a+") as f:
await f.write(line + "\n")
if get_ipython() is None:
return
if not self._graphs_shown:
logger.debug("Graphs not shown. Initializing...")
for sensor, output in self._sensor_outputs.items(): # type: ignore
logger.trace(f"Initializing graph for {sensor}")
# bind the height of the graph to the selected plot height
output.layout.height = f"{self._plot_height}px"
with output:
# create the figure object
p = figure(
title=f"{sensor} data",
plot_height=self._plot_height,
plot_width=600,
)
r = p.line(
source=self._transformed_data[sensor.name],
x="timestamps",
y="datapoints",
color="#2222aa",
line_width=3,
)
p.xaxis.axis_label = "Experiment elapsed time (seconds)"
p.yaxis.axis_label = self._device_name_to_unit[sensor.name]
# since we're in the with-statement, this will show up in the accordion
output_notebook(resources=INLINE, hide_banner=True)
target = show(p, notebook_handle=True)
# save the target and plot for later updating
self._charts[sensor.name] = (target, r)
logger.trace(
f"Sucessfully initialized graph for {sensor.name}")
logger.trace("All graphs successfully initialized")
self._graphs_shown = True
if device in self._transformed_data:
target, r = self._charts[device]
self._transformed_data[device]["datapoints"].append(datapoint.data)
self._transformed_data[device]["timestamps"].append(
datapoint.experiment_elapsed_time)
r.data_source.data["datapoints"] = self._transformed_data[device][
"datapoints"]
r.data_source.data["timestamps"] = self._transformed_data[device][
"timestamps"]
push_notebook(handle=target)
dfs = []
files = file_io.get_matching_files(source)
for f in files:
dfs.append(pd.read_csv(f, names=names))
df = pd.concat(dfs)
if variables.get("target_lambda", False):
df["target"] = df.apply(eval(variables.get("target_lambda", "")),
axis=1)
else:
df["target"] = df["target"].apply(
lambda x: 1 if x == variables.get("trueclass", "true") else 0)
fpr, tpr, thresholds = roc_curve(
df["target"], df[variables.get("true_score_column", "true")])
df = pd.DataFrame({"fpr": fpr, "tpr": tpr, "thresholds": thresholds})
else:
# Load data from generated csv file.
df = pd.read_csv(source, header=None, names=["fpr", "tpr", "thresholds"])
# Create visualization.
output_notebook()
p = figure(tools="pan,wheel_zoom,box_zoom,reset,hover,previewsave")
p.line("fpr", "tpr", line_width=2, source=df)
hover = p.select(dict(type=HoverTool))
hover.tooltips = [("Threshold", "@thresholds")]
show(row(p, sizing_mode="scale_width"))
def interact(self, lc=None):
"""Display an interactive IPython Notebook widget to inspect the data.
The widget will show both the lightcurve and pixel data. By default,
the lightcurve shown is obtained by calling the `to_lightcurve()` method,
unless the user supplies a custom `LightCurve` object.
Note: at this time, this feature only works inside an active Jupyter
Notebook, and tends to be too slow when more than ~30,000 cadences
are contained in the TPF (e.g. short cadence data).
Parameters
----------
lc : LightCurve object
An optional pre-processed lightcurve object to show.
"""
try:
from ipywidgets import interact
import ipywidgets as widgets
from bokeh.io import push_notebook, show, output_notebook
from bokeh.plotting import figure, ColumnDataSource
from bokeh.models import Span, Range1d, LinearAxis, LogColorMapper
from bokeh.layouts import row
from bokeh.models.tools import HoverTool
from IPython.display import display
output_notebook()
except ImportError:
raise ImportError('The quicklook tool requires Bokeh and ipywidgets. '
'See the .interact() tutorial')
ytitle = 'Flux'
if lc is None:
lc = self.to_lightcurve()
ytitle = 'Flux (e/s)'
# Bokeh cannot handle many data points
## https://github.com/bokeh/bokeh/issues/7490
if len(lc.cadenceno) > 30000:
raise RuntimeError('Interact cannot display more than 20000 cadences.')
# Map cadence to index for quick array slicing.
n_lc_cad = len(lc.cadenceno)
n_cad, nx, ny = self.flux.shape
lc_cad_matches = np.in1d(self.cadenceno, lc.cadenceno)
if lc_cad_matches.sum() != n_lc_cad:
raise ValueError("The lightcurve provided has cadences that are not "
"present in the Target Pixel File.")
min_cadence, max_cadence = np.min(self.cadenceno), np.max(self.cadenceno)
cadence_lookup = {cad: j for j, cad in enumerate(self.cadenceno)}
cadence_full_range = np.arange(min_cadence, max_cadence, 1, dtype=np.int)
missing_cadences = list(set(cadence_full_range)-set(self.cadenceno))
# Convert binary quality numbers into human readable strings
qual_strings = []
for bitmask in lc.quality:
flag_str_list = KeplerQualityFlags.decode(bitmask)
if len(flag_str_list) == 0:
qual_strings.append(' ')
if len(flag_str_list) == 1:
qual_strings.append(flag_str_list[0])
if len(flag_str_list) > 1:
qual_strings.append("; ".join(flag_str_list))
# Convert time into human readable strings, breaks with NaN time
# See https://github.com/KeplerGO/lightkurve/issues/116
if (self.time == self.time).all():
human_time = self.timeobj.isot[lc_cad_matches]
else:
human_time = [' '] * n_lc_cad
# Each data source will later become a hover-over tooltip
source = ColumnDataSource(data=dict(
time=lc.time,
time_iso=human_time,
flux=lc.flux,
cadence=lc.cadenceno,
quality_code=lc.quality,
quality=np.array(qual_strings)))
# Provide extra metadata in the title
if self.mission == 'K2':
title = "Quicklook lightcurve for EPIC {} (K2 Campaign {})".format(
self.keplerid, self.campaign)
elif self.mission == 'Kepler':
title = "Quicklook lightcurve for KIC {} (Kepler Quarter {})".format(
self.keplerid, self.quarter)
# Figure 1 shows the lightcurve with steps, tooltips, and vertical line
fig1 = figure(title=title, plot_height=300, plot_width=600,
tools="pan,wheel_zoom,box_zoom,save,reset")
fig1.yaxis.axis_label = ytitle
fig1.xaxis.axis_label = 'Time - 2454833 days [BKJD]'
fig1.step('time', 'flux', line_width=1, color='gray', source=source,
nonselection_line_color='gray', mode="center")
r = fig1.circle('time', 'flux', source=source, fill_alpha=0.3, size=8,
line_color=None, selection_color="firebrick",
nonselection_fill_alpha=0.0, nonselection_line_color=None,
nonselection_line_alpha=0.0, fill_color=None,
hover_fill_color="firebrick", hover_alpha=0.9,
hover_line_color="white")
fig1.add_tools(HoverTool(tooltips=[("Cadence", "@cadence"),
("Time (BKJD)", "@time{0,0.000}"),
("Time (ISO)", "@time_iso"),
("Flux", "@flux"),
("Quality Code", "@quality_code"),
("Quality Flag", "@quality")],
renderers=[r],
mode='mouse',
point_policy="snap_to_data"))
# Vertical line to indicate the cadence shown in Fig 2
vert = Span(location=0, dimension='height', line_color='firebrick',
line_width=4, line_alpha=0.5)
fig1.add_layout(vert)
# Figure 2 shows the Target Pixel File stamp with log screen stretch
fig2 = figure(plot_width=300, plot_height=300,
tools="pan,wheel_zoom,box_zoom,save,reset",
title='Pixel data (CCD {}.{})'.format(
self.module, self.output))
fig2.yaxis.axis_label = 'Pixel Row Number'
fig2.xaxis.axis_label = 'Pixel Column Number'
pedestal = np.nanmin(self.flux[lc_cad_matches, :, :])
stretch_dims = np.prod(self.flux[lc_cad_matches, :, :].shape)
screen_stretch = self.flux[lc_cad_matches, :, :].reshape(stretch_dims) - pedestal
screen_stretch = screen_stretch[np.isfinite(screen_stretch)] # ignore NaNs
screen_stretch = screen_stretch[screen_stretch > 0.0]
vlo = np.min(screen_stretch)
vhi = np.max(screen_stretch)
vstep = (np.log10(vhi) - np.log10(vlo)) / 300.0 # assumes counts >> 1.0!
lo, med, hi = np.nanpercentile(screen_stretch, [1, 50, 95])
color_mapper = LogColorMapper(palette="Viridis256", low=lo, high=hi)
fig2_dat = fig2.image([self.flux[0, :, :] - pedestal], x=self.column,
y=self.row, dw=self.shape[2], dh=self.shape[1],
dilate=False, color_mapper=color_mapper)
# The figures appear before the interactive widget sliders
show(row(fig1, fig2), notebook_handle=True)
# The widget sliders call the update function each time
def update(cadence, log_stretch):
"""Function that connects to the interact widget slider values"""
fig2_dat.glyph.color_mapper.high = 10**log_stretch[1]
fig2_dat.glyph.color_mapper.low = 10**log_stretch[0]
if cadence not in missing_cadences:
index_val = cadence_lookup[cadence]
vert.update(line_alpha=0.5)
if self.time[index_val] == self.time[index_val]:
vert.update(location=self.time[index_val])
else:
vert.update(line_alpha=0.0)
fig2_dat.data_source.data['image'] = [self.flux[index_val, :, :]
- pedestal]
else:
vert.update(line_alpha=0)
fig2_dat.data_source.data['image'] = [self.flux[0, :, :] * np.NaN]
push_notebook()
# Define the widgets that enable the interactivity
play = widgets.Play(interval=10, value=min_cadence, min=min_cadence,
max=max_cadence, step=1, description="Press play",
disabled=False)
play.show_repeat, play._repeat = False, False
cadence_slider = widgets.IntSlider(
min=min_cadence, max=max_cadence,
step=1, value=min_cadence, description='Cadence',
layout=widgets.Layout(width='40%', height='20px'))
screen_slider = widgets.FloatRangeSlider(
value=[np.log10(lo), np.log10(hi)],
min=np.log10(vlo),
max=np.log10(vhi),
step=vstep,
description='Pixel Stretch (log)',
style={'description_width': 'initial'},
continuous_update=False,
layout=widgets.Layout(width='30%', height='20px'))
widgets.jslink((play, 'value'), (cadence_slider, 'value'))
ui = widgets.HBox([play, cadence_slider, screen_slider])
out = widgets.interactive_output(update, {'cadence': cadence_slider,
'log_stretch': screen_slider})
display(ui, out)
def cpu_usage():
from bokeh.layouts import gridplot
from bokeh.plotting import figure, show, helpers
from bokeh.resources import CDN
from bokeh.io import output_notebook, push_notebook
from bokeh.models import ColumnDataSource
output_notebook(resources=CDN)
# Parse the client table to determine how many CPUs are available
num_cpus = 0
client_table = ray.global_state.client_table()
for node_ip, client_list in client_table.items():
for client in client_list:
if "CPU" in client:
num_cpus += client["CPU"]
# Update the plot based on the sliders
def plot_utilization():
# Create the Bokeh plot
time_series_fig = figure(title="CPU Utilization",
tools=["save", "hover", "wheel_zoom",
"box_zoom", "pan"],
background_fill_color="#FFFFFF",
x_range=[0, 1],
y_range=[0, 1])
# Create the data source that the plot will pull from
time_series_source = ColumnDataSource(data=dict(
left=[],
right=[],
top=[]
))
# Plot the rectangles representing the distribution
time_series_fig.quad(left="left",
right="right",
top="top",
bottom=0,
source=time_series_source,
fill_color="#B3B3B3",
line_color="#033649")
# Label the plot axes
time_series_fig.xaxis.axis_label = "Time in seconds"
time_series_fig.yaxis.axis_label = "Number of CPUs used"
handle = show(gridplot(time_series_fig,
ncols=1,
plot_width=500,
plot_height=500,
toolbar_location="below"), notebook_handle=True)
def update_plot(abs_earliest, abs_latest, abs_num_tasks, tasks):
num_buckets = 100
left, right, top = compute_utilizations(abs_earliest,
abs_latest,
abs_num_tasks,
tasks,
num_buckets)
time_series_source.data = {"left": left,
"right": right,
"top": top}
x_range = (max(0, min(left))
if len(left) else 0,
max(right) if len(right) else 1)
y_range = (0, max(top) + 1 if len(top) else 1)
# Define the axis ranges
x_range = helpers._get_range(x_range)
time_series_fig.x_range.start = x_range.start
time_series_fig.x_range.end = x_range.end
y_range = helpers._get_range(y_range)
time_series_fig.y_range.start = y_range.start
time_series_fig.y_range.end = num_cpus
# Push the updated data to the notebook
push_notebook(handle=handle)
get_sliders(update_plot)
plot_utilization()
"""
This module implements the Container class.
"""
import sys
import webbrowser
import random
from tempfile import NamedTemporaryFile
from typing import Any, Dict
from bokeh.io import output_notebook
from bokeh.embed import components
from bokeh.resources import INLINE
from jinja2 import Environment, PackageLoader
from ..utils import is_notebook
output_notebook(INLINE, hide_banner=True) # for offline usage
ENV_LOADER = Environment(loader=PackageLoader("dataprep", "eda/templates"), )
TAB_VISUAL_TYPES = {
"missing_impact_1v1",
"missing_impact",
"categorical_column",
"numerical_column",
"datetime_column",
"cat_and_num_cols",
"two_num_cols",
"two_cat_cols",
"dt_and_num_cols",
"dt_and_cat_cols",
"dt_cat_num_cols",
def show_interact_widget(
tpf,
notebook_url="localhost:8888",
lc=None,
max_cadences=200000,
aperture_mask="default",
exported_filename=None,
transform_func=None,
ylim_func=None,
vmin=None,
vmax=None,
scale="log",
cmap="Viridis256",
):
"""Display an interactive Jupyter Notebook widget to inspect the pixel data.
The widget will show both the lightcurve and pixel data. The pixel data
supports pixel selection via Bokeh tap and box select tools in an
interactive javascript user interface.
Note: at this time, this feature only works inside an active Jupyter
Notebook, and tends to be too slow when more than ~30,000 cadences
are contained in the TPF (e.g. short cadence data).
Parameters
----------
tpf : lightkurve.TargetPixelFile
Target Pixel File to interact with
notebook_url: str
Location of the Jupyter notebook page (default: "localhost:8888")
When showing Bokeh applications, the Bokeh server must be
explicitly configured to allow connections originating from
different URLs. This parameter defaults to the standard notebook
host and port. If you are running on a different location, you
will need to supply this value for the application to display
properly. If no protocol is supplied in the URL, e.g. if it is
of the form "localhost:8888", then "http" will be used.
max_cadences: int
Raise a RuntimeError if the number of cadences shown is larger than
this value. This limit helps keep browsers from becoming unresponsive.
aperture_mask : array-like, 'pipeline', 'threshold', 'default', or 'all'
A boolean array describing the aperture such that `True` means
that the pixel will be used.
If None or 'all' are passed, all pixels will be used.
If 'pipeline' is passed, the mask suggested by the official pipeline
will be returned.
If 'threshold' is passed, all pixels brighter than 3-sigma above
the median flux will be used.
If 'default' is passed, 'pipeline' mask will be used when available,
with 'threshold' as the fallback.
exported_filename: str
An optional filename to assign to exported fits files containing
the custom aperture mask generated by clicking on pixels in interact.
The default adds a suffix '-custom-aperture-mask.fits' to the
TargetPixelFile basename.
transform_func: function
A function that transforms the lightcurve. The function takes in a
LightCurve object as input and returns a LightCurve object as output.
The function can be complex, such as detrending the lightcurve. In this
way, the interactive selection of aperture mask can be evaluated after
inspection of the transformed lightcurve. The transform_func is applied
before saving a fits file. Default: None (no transform is applied).
ylim_func: function
A function that returns ylimits (low, high) given a LightCurve object.
The default is to return an expanded window around the 10-90th
percentile of lightcurve flux values.
scale: str
Color scale for tpf figure. Default is 'log'
vmin: int [optional]
Minimum color scale for tpf figure
vmax: int [optional]
Maximum color scale for tpf figure
cmap: str
Colormap to use for tpf plot. Default is 'Viridis256'
"""
try:
import bokeh
if bokeh.__version__[0] == "0":
warnings.warn("interact() requires Bokeh version 1.0 or later",
LightkurveWarning)
except ImportError:
log.error("The interact() tool requires the `bokeh` Python package; "
"you can install bokeh using e.g. `conda install bokeh`.")
return None
aperture_mask = tpf._parse_aperture_mask(aperture_mask)
if ~aperture_mask.any():
log.error(
"No pixels in `aperture_mask`, finding optimum aperture using `tpf.create_threshold_mask`."
)
aperture_mask = tpf.create_threshold_mask()
if ~aperture_mask.any():
log.error("No pixels in `aperture_mask`, using all pixels.")
aperture_mask = tpf._parse_aperture_mask("all")
if exported_filename is None:
exported_filename = make_default_export_name(tpf)
try:
exported_filename = str(exported_filename)
except:
log.error("Invalid input filename type for interact()")
raise
if ".fits" not in exported_filename.lower():
exported_filename += ".fits"
if lc is None:
lc = tpf.to_lightcurve(aperture_mask=aperture_mask)
tools = "tap,box_select,wheel_zoom,reset"
else:
lc = lc.copy()
tools = "wheel_zoom,reset"
aperture_mask = np.zeros(tpf.flux.shape[1:]).astype(bool)
aperture_mask[0, 0] = True
lc.meta["APERTURE_MASK"] = aperture_mask
if transform_func is not None:
lc = transform_func(lc)
npix = tpf.flux[0, :, :].size
pixel_index_array = np.arange(0, npix, 1).reshape(tpf.flux[0].shape)
# Bokeh cannot handle many data points
# https://github.com/bokeh/bokeh/issues/7490
n_cadences = len(lc.cadenceno)
if n_cadences > max_cadences:
log.error(
f"Error: interact cannot display more than {max_cadences} "
"cadences without suffering significant performance issues. "
"You can limit the number of cadences show using slicing, e.g. "
"`tpf[0:1000].interact()`. Alternatively, you can override "
"this limitation by passing the `max_cadences` argument.")
elif n_cadences > 30000:
log.warning(f"Warning: the pixel file contains {n_cadences} cadences. "
"The performance of interact() is very slow for such a "
"large number of frames. Consider using slicing, e.g. "
"`tpf[0:1000].interact()`, to make interact run faster.")
def create_interact_ui(doc):
# The data source includes metadata for hover-over tooltips
lc_source = prepare_lightcurve_datasource(lc)
tpf_source = prepare_tpf_datasource(tpf, aperture_mask)
# Create the lightcurve figure and its vertical marker
fig_lc, vertical_line = make_lightcurve_figure_elements(
lc, lc_source, ylim_func=ylim_func)
# Create the TPF figure and its stretch slider
pedestal = -np.nanmin(tpf.flux.value) + 1
if scale == "linear":
pedestal = 0
fig_tpf, stretch_slider = make_tpf_figure_elements(
tpf,
tpf_source,
pedestal=pedestal,
fiducial_frame=0,
vmin=vmin,
vmax=vmax,
scale=scale,
cmap=cmap,
tools=tools,
)
# Helper lookup table which maps cadence number onto flux array index.
tpf_index_lookup = {cad: idx for idx, cad in enumerate(tpf.cadenceno)}
# Interactive slider widgets and buttons to select the cadence number
cadence_slider = Slider(
start=np.min(tpf.cadenceno),
end=np.max(tpf.cadenceno),
value=np.min(tpf.cadenceno),
step=1,
title="Cadence Number",
width=490,
)
r_button = Button(label=">", button_type="default", width=30)
l_button = Button(label="<", button_type="default", width=30)
export_button = Button(label="Save Lightcurve",
button_type="success",
width=120)
message_on_save = Div(text=" ", width=600, height=15)
# Callbacks
def _create_lightcurve_from_pixels(tpf,
selected_pixel_indices,
transform_func=transform_func):
"""Create the lightcurve from the selected pixel index list"""
selected_indices = np.array(selected_pixel_indices)
selected_mask = np.isin(pixel_index_array, selected_indices)
lc_new = tpf.to_lightcurve(aperture_mask=selected_mask)
lc_new.meta["APERTURE_MASK"] = selected_mask
if transform_func is not None:
lc_transformed = transform_func(lc_new)
if len(lc_transformed) != len(lc_new):
warnings.warn(
"Dropping cadences in `transform_func` is not "
"yet supported due to fixed time coordinates."
"Skipping the transformation...",
LightkurveWarning,
)
else:
lc_new = lc_transformed
lc_new.meta["APERTURE_MASK"] = selected_mask
return lc_new
def update_upon_pixel_selection(attr, old, new):
"""Callback to take action when pixels are selected."""
# Check if a selection was "re-clicked", then de-select
if (sorted(old) == sorted(new)) & (new != []):
# Trigger recursion
tpf_source.selected.indices = new[1:]
if new != []:
lc_new = _create_lightcurve_from_pixels(
tpf, new, transform_func=transform_func)
lc_source.data["flux"] = lc_new.flux.value
if ylim_func is None:
ylims = get_lightcurve_y_limits(lc_source)
else:
ylims = ylim_func(lc_new)
fig_lc.y_range.start = ylims[0]
fig_lc.y_range.end = ylims[1]
else:
lc_source.data["flux"] = lc.flux.value * 0.0
fig_lc.y_range.start = -1
fig_lc.y_range.end = 1
message_on_save.text = " "
export_button.button_type = "success"
def update_upon_cadence_change(attr, old, new):
"""Callback to take action when cadence slider changes"""
if new in tpf.cadenceno:
frameno = tpf_index_lookup[new]
fig_tpf.select("tpfimg")[0].data_source.data["image"] = [
tpf.flux.value[frameno, :, :] + pedestal
]
vertical_line.update(location=tpf.time.value[frameno])
else:
fig_tpf.select("tpfimg")[0].data_source.data["image"] = [
tpf.flux.value[0, :, :] * np.NaN
]
lc_source.selected.indices = []
def go_right_by_one():
"""Step forward in time by a single cadence"""
existing_value = cadence_slider.value
if existing_value < np.max(tpf.cadenceno):
cadence_slider.value = existing_value + 1
def go_left_by_one():
"""Step back in time by a single cadence"""
existing_value = cadence_slider.value
if existing_value > np.min(tpf.cadenceno):
cadence_slider.value = existing_value - 1
def save_lightcurve():
"""Save the lightcurve as a fits file with mask as HDU extension"""
if tpf_source.selected.indices != []:
lc_new = _create_lightcurve_from_pixels(
tpf,
tpf_source.selected.indices,
transform_func=transform_func)
lc_new.to_fits(
exported_filename,
overwrite=True,
flux_column_name="SAP_FLUX",
aperture_mask=lc_new.meta["APERTURE_MASK"].astype(np.int),
SOURCE="lightkurve interact",
NOTE="custom mask",
MASKNPIX=np.nansum(lc_new.meta["APERTURE_MASK"]),
)
if message_on_save.text == " ":
text = '<font color="black"><i>Saved file {} </i></font>'
message_on_save.text = text.format(exported_filename)
export_button.button_type = "success"
else:
text = '<font color="gray"><i>Saved file {} </i></font>'
message_on_save.text = text.format(exported_filename)
else:
text = (
'<font color="gray"><i>No pixels selected, no mask saved</i></font>'
)
export_button.button_type = "warning"
message_on_save.text = text
def jump_to_lightcurve_position(attr, old, new):
if new != []:
cadence_slider.value = lc.cadenceno[new[0]]
# Map changes to callbacks
r_button.on_click(go_right_by_one)
l_button.on_click(go_left_by_one)
tpf_source.selected.on_change("indices", update_upon_pixel_selection)
lc_source.selected.on_change("indices", jump_to_lightcurve_position)
export_button.on_click(save_lightcurve)
cadence_slider.on_change("value", update_upon_cadence_change)
# Layout all of the plots
sp1, sp2, sp3, sp4 = (
Spacer(width=15),
Spacer(width=30),
Spacer(width=80),
Spacer(width=60),
)
widgets_and_figures = layout(
[fig_lc, fig_tpf],
[
l_button, sp1, r_button, sp2, cadence_slider, sp3,
stretch_slider
],
[export_button, sp4, message_on_save],
)
doc.add_root(widgets_and_figures)
output_notebook(verbose=False, hide_banner=True)
return show(create_interact_ui, notebook_url=notebook_url)
def show_skyview_widget(tpf,
notebook_url="localhost:8888",
magnitude_limit=18):
"""skyview
Parameters
----------
tpf : lightkurve.TargetPixelFile
Target Pixel File to interact with
notebook_url: str
Location of the Jupyter notebook page (default: "localhost:8888")
When showing Bokeh applications, the Bokeh server must be
explicitly configured to allow connections originating from
different URLs. This parameter defaults to the standard notebook
host and port. If you are running on a different location, you
will need to supply this value for the application to display
properly. If no protocol is supplied in the URL, e.g. if it is
of the form "localhost:8888", then "http" will be used.
magnitude_limit : float
A value to limit the results in based on Gaia Gmag. Default, 18.
"""
try:
import bokeh
if bokeh.__version__[0] == "0":
warnings.warn("interact_sky() requires Bokeh version 1.0 or later",
LightkurveWarning)
except ImportError:
log.error(
"The interact_sky() tool requires the `bokeh` Python package; "
"you can install bokeh using e.g. `conda install bokeh`.")
return None
# Try to identify the "fiducial frame", for which the TPF WCS is exact
zp = (tpf.pos_corr1 == 0) & (tpf.pos_corr2 == 0)
(zp_loc, ) = np.where(zp)
if len(zp_loc) == 1:
fiducial_frame = zp_loc[0]
else:
fiducial_frame = 0
def create_interact_ui(doc):
# The data source includes metadata for hover-over tooltips
tpf_source = None
# Create the TPF figure and its stretch slider
fig_tpf, stretch_slider = make_tpf_figure_elements(
tpf,
tpf_source,
fiducial_frame=fiducial_frame,
plot_width=640,
plot_height=600,
)
fig_tpf, r = add_gaia_figure_elements(tpf,
fig_tpf,
magnitude_limit=magnitude_limit)
# Optionally override the default title
if tpf.mission == "K2":
fig_tpf.title.text = (
"Skyview for EPIC {}, K2 Campaign {}, CCD {}.{}".format(
tpf.targetid, tpf.campaign, tpf.module, tpf.output))
elif tpf.mission == "Kepler":
fig_tpf.title.text = (
"Skyview for KIC {}, Kepler Quarter {}, CCD {}.{}".format(
tpf.targetid, tpf.quarter, tpf.module, tpf.output))
elif tpf.mission == "TESS":
fig_tpf.title.text = "Skyview for TESS {} Sector {}, Camera {}.{}".format(
tpf.targetid, tpf.sector, tpf.camera, tpf.ccd)
# Layout all of the plots
widgets_and_figures = layout([fig_tpf, stretch_slider])
doc.add_root(widgets_and_figures)
output_notebook(verbose=False, hide_banner=True)
return show(create_interact_ui, notebook_url=notebook_url)
def notebook(self, flag):
warnings.warn("Chart property 'notebook' was deprecated in 0.11 \
and will be removed in the future.")
from bokeh.io import output_notebook
output_notebook()
sqrt, sin, cos, tan, sec, csc, cot, log, exp, e, asin, acos, atan
#Plotting and fitting
from qexpy.plotting import Plot, MakePlot
from qexpy.fitting import XYDataSet, XYFitter, DataSetFromFile
from qexpy.plot_utils import bk_plot_dataset, bk_add_points_with_error_bars,\
bk_plot_function
__version__ = '1.0.1'
# The following will initialize bokeh if running in a notebook,
# and hacks the _nb_loaded variable which is required for all plots
# to show when Run All is used in a notebook. This bug arrived in
# bokeh 12.1, hopefully they get rid of it...
import qexpy.utils as qu
import bokeh.io as bi
from qexpy.utils import get_data_from_file
if qu.in_notebook():
qu.mpl_output_notebook() # calls matplotlib inline
bi.output_notebook()
qu.bokeh_ouput_notebook_called = True
'''This hack is required as there is a bug in bokeh preventing it
from knowing that it was in fact loaded.
'''
bi._nb_loaded = True
def bokplot(self, title='Placeholder'):
from bokeh.io import output_notebook
from bokeh.plotting import figure, show, output_file
output_notebook()
p1 = figure(title=title,
x_axis_type="datetime",
plot_width=1400,
plot_height=400,
background_fill_color="#EFE8E2")
# check if scaling has been applied
# use the same indices for both cases
if self.scale == True:
# check if ys_train exists, and plot if yes
if self.data['ys_train'] is not None:
if isinstance(self.data['ys_train'], self.pd.DataFrame):
local_y_train = self.data['ys_train'].values.astype(
'float32')
p1.line(self.data['y_train_index'],
local_ys_train.reshape(len(local_ys_train)),
color='#E08E79',
legend='ys_train')
else: # if it's a np array
p1.line(self.data['y_train_index'],
local_y_train.reshape(len(self.data['ys_train'])),
color='#E08E79',
legend='ys_train')
# check if ys_val exists, and plot if yes
if self.data['ys_val'] is not None:
if isinstance(self.data['ys_val'], self.pd.DataFrame):
local_ys_val = self.data['ys_val'].values.astype('float32')
p1.line(self.data['y_val_index'],
local_ys_val.reshape(len(local_ys_val)),
color='#3B8686',
legend='ys_val')
else: # if it's an np.array
p1.line(self.data['y_val_index'],
local_ys_val.reshape(len(self.data['ys_val'])),
color='#3B8686',
legend='ys_val')
if self.scale == False:
if self.data['y_train'] is not None:
if isinstance(self.data['y_train'], self.pd.DataFrame):
local_y_train = self.data['y_train'].values.astype(
'float32')
p1.line(self.data['y_train_index'],
local_y_train.reshape(len(local_y_train)),
color='#E08E79',
legend='y_train')
else: # if it's an np.array
p1.line(self.data['y_train_index'],
local_y_train.reshape(len(local_y_train)),
color='#E08E79',
legend='y_train')
if self.data['y_val'] is not None:
if isinstance(self.data['y_val'], self.pd.DataFrame):
local_y_val = self.data['y_val'].values.astype('float32')
p1.line(self.data['y_val_index'],
local_y_val.reshape(len(local_y_val)),
color='#3B8686',
legend='y_val')
else: # if it's an np.array
p1.line(self.data['y_val_index'],
local_y_val.reshape(len(local_y_val)),
color='#3B8686',
legend='y_val')
# aesthetic mapping
p1.grid.grid_line_alpha = 0.1
p1.xaxis.axis_label = "Date"
p1.yaxis.axis_label = "Price"
p1.legend.location = "top_left"
p1.ygrid.band_fill_alpha = 0.2
show(p1)
def test_noarg(self, mock_load_notebook):
default_load_notebook_args = (None, False, False)
io.output_notebook()
self._check_func_called(io._state.output_notebook, (), {})
self._check_func_called(mock_load_notebook, default_load_notebook_args, {})
import colorsys
import math
import numpy as np
from bokeh.charts import Bar
from bokeh.plotting import figure, ColumnDataSource
import bokeh.io as io
from bokeh.models import HoverTool, OpenURL, TapTool
AVAIL_COLORS = ["#1F77B4", "firebrick", "goldenrod", "aqua", "brown", "chartreuse", "darkmagenta"
"aquamarine", "blue", "red", "blueviolet", "darkorange", "forestgreen", "lime"]
# AVAIL_MARKERS: circle, diamond, triangle, square, inverted_triangle, asterisk,
# circle_cross, circle_x, cross, diamond_cross, square_cross, square_x, asterisk, diamond
io.output_notebook()
class ColorScale():
def __init__(self, num_values, val_min, val_max, middle_color="yellow", reverse=False):
self.num_values = num_values
self.num_val_1 = num_values - 1
self.value_min = val_min
self.value_max = val_max
self.reverse = reverse
self.value_range = self.value_max - self.value_min
self.color_scale = []
if middle_color.startswith("y"): # middle color yellow
hsv_tuples = [(0.0 + ((x * 0.35) / (self.num_val_1)), 0.99, 0.9) for x in range(self.num_values)]
self.reverse = not self.reverse
def __init__(self, gc, name='scatter_plot', **kwargs):
node_mapper_dict = {'size':{'max':100,
'min':5,
'step':0.5,
'high':75,
'low':25,
'default':60,
'map_data':False,
'fixed_active':False,
},
'line_width':{'max':50,
'min':0,
'step':0.5,
'high':5,
'low':1,
'default':2,
'map_data':False,
'fixed_active':False,
},
'fill_alpha':{'max':1.0,
'min':0.,
'step':0.05,
'high':0.95,
'low':0.3,
'default':1.,
'map_data':False,
'fixed_active':False,
},
'line_alpha':{'max':1.0,
'min':0.,
'step':0.05,
'high':0.95,
'low':0.3,
'default':1.,
'map_data':False,
'fixed_active':False,
},
'line_color':{'default_color':'black','map_data':False,'step':0.05,'min':0.0,'low':0.0},
'fill_color':{'default_color':'#11D4CA','map_data':False,'step':0.05,'min':0.0,'low':0.0}
}
edge_mapper_dict = {'size':{'max':100,
'min':5,
'step':0.5,
'high':20,
'low':7,
'default':7,
'map_data':False,
'fixed_active':False,
},
'line_width':{'max':50,
'min':0,
'step':0.5,
'high':5,
'low':1,
'default':2,
'map_data':False,
'fixed_active':False,
},
'fill_alpha':{'max':1.0,
'min':0.,
'step':0.05,
'high':0.95,
'low':0.3,
'default':1.,
'map_data':False,
'fixed_active':False,
},
'line_alpha':{'max':1.0,
'min':0.,
'step':0.05,
'high':0.95,
'low':0.3,
'default':1.,
'map_data':False,
'fixed_active':False,
},
'line_color':{'default_color':'black','map_data':False,'step':0.05,'min':0.0,'low':0.0},
'fill_color':{'default_color':'#EDB021','map_data':False,'step':0.05,'min':0.0,'low':0.0}
}
gc.name = 'gc'
output_notebook(hide_banner=True)
edge_mapper_data = self.prepare_edge_mapper_data(gc)
node_mapper = PlotMapper(gc.node, mapper_dict=node_mapper_dict, button_type='ddown',button_pos='top', name='node_mapper', mode='interactive')
edge_mapper = PlotMapper(edge_mapper_data, mapper_dict=edge_mapper_dict, button_type='ddown',button_pos='top', name='edge_mapper', mode='interactive')
node_tooltip_data = gc.node.combine_first(gc.node_metrics.T)
node_tooltip = BokehDataFrameTooltip(node_tooltip_data, name='node_tooltip')
edge_tooltip = BokehDataFrameTooltip(edge_mapper_data, name='edge_tooltip')
ToggleMenu.__init__(self,
children=[gc,node_mapper,
edge_mapper,
node_tooltip,
edge_tooltip],
name=name,**kwargs)
self.observe(self.update)
self.gc.calculate.observe(self.update)
self.node_mapper.marker.marker_type.observe(self._on_marker_change)
self.edge_mapper.marker.marker_type.observe(self._on_marker_change)
self.update_source_df()
self.init_plot()
self.update()
self._init_layout()
import bisect
from pymongo import MongoClient
import pandas as pd
from bokeh.plotting import show
from bokeh.plotting import figure, show, gridplot, curdoc
from bokeh.io import output_notebook, reset_output
from bokeh.models import Spacer, DatetimeTickFormatter, Legend
from bokeh.resources import INLINE
import numpy as np
import holoviews as hv
from datetime import datetime, timedelta
reset_output()
output_notebook(resources = INLINE, verbose=False, hide_banner=True)
#hv.extension('bokeh')
def print_dict(data):
for key in data:
print(f'{key:<14}: {data[key]:>4}')
def make_histogram_plot(name, hist, edges, x_label=None):
p = figure(title=name + ' distribution', tools='', background_fill_color="#fafafa")
p.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:],
fill_color="navy", line_color="white", alpha=0.5)
p.y_range.start = 0
p.yaxis.formatter.use_scientific = False
if x_label is None:
x_label = name + ' count'
p.xaxis.axis_label = x_label
p.yaxis.axis_label = 'user count'
p.grid.grid_line_color="white"
def test_args(self):
kwargs = dict(url="url", docname="docname", session="session", name="name")
io.output_notebook(**kwargs)
self._check_func_called(io._state.output_notebook, (), kwargs)
wh.groupby(by=['country'])['suicides_no'].sum().reset_index().sort_values(
['suicides_no'], ascending=True).tail(15).country
wh[wh.country.isin(
wh.groupby(by=['country'])['suicides_no'].sum().reset_index().sort_values(
['suicides_no'], ascending=True).tail(5).country)].groupby(
by=['sex', 'country'])['suicides_no'].sum().unstack().plot(
kind='bar', stacked=True)
#wh[wh.country.isin(wh.groupby(by=['country'])['suicides_no'].sum().reset_index().sort_values(['suicides_no'],ascending=True).tail(5).country)].groupby(by=['age','country'])['suicides_no'].sum().unstack().plot(kind='bar',stacked=True)
#https://stackoverflow.com/questions/12096252/use-a-list-of-values-to-select-rows-from-a-pandas-dataframehttps://stackoverflow.com/questions/12096252/use-a-list-of-values-to-select-rows-from-a-pandas-dataframe
#wh[wh.country.isin(wh.groupby(by=['country'])['suicides_no'].sum().reset_index().sort_values(['suicides_no'],ascending=True).tail(5).country)].groupby(by=['year','country'])['suicides_no'].sum().unstack().plot()
#https://gist.github.com/dela3499/e159b388258b5f1a7a3bac42fc0179fd
from bokeh.plotting import figure, output_file, show, ColumnDataSource
from bokeh.models import HoverTool, CategoricalColorMapper
from bokeh.io import output_notebook
output_notebook()
source = ColumnDataSource(data=wh)
hover = HoverTool(
tooltips=[("year",
"@year"), ("sex",
"@sex"), ("country",
"@country"), ("suicides_no",
"@suicides_no")])
p = figure(plot_width=700,
plot_height=700,
tools=[hover],
title="Mouse over the dots")
#https://www.kaggle.com/kanncaa1/visualization-bokeh-tutorial-part-1
def notebook(self, flag):
warnings.warn("Chart property 'notebook' was deprecated in 0.11 \
and will be removed in the future.")
from bokeh.io import output_notebook
output_notebook()
import pandas as pd
import numpy as np
# Bokeh libraries
from bokeh.io import output_file, output_notebook
from bokeh.plotting import figure, show
from bokeh.models import ColumnDataSource
from bokeh.layouts import row, column, gridplot
from bokeh.models.widgets import Tabs, Panel
# Prepare the data
# Determine where the visualization will be rendered
output_file('filename.html') # Render to static HTML, or
output_notebook() # Render inline in a Jupyter Notebook
# Set up the figure(s)
fig = figure() # Instantiate a figure() object
# Connect to and draw the data
# Organize the layout
# Preview and save
show(fig) # See what I made, and save if I like it
def __init__(self, dataf, labels):
output_notebook()
self.dataf = dataf
self.labels = labels
self.charts = []
def load_ipython_extension(shell):
# Initiate bokeh
output_notebook(hide_banner=True)
shell.register_magics(IProfilerMagics)
from bokeh.models import ColumnDataSource, HoverTool, Select, Paragraph, TextInput
from bokeh.layouts import widgetbox, column, row
from ipywidgets import interact
import pandas as pd
df_bokeh = pd.read_csv("Data/cosmetic_TSNE.csv")
"""
This is for Bokeh to create all possible combinations based on the options from category of products and skin type
"""
# cosmetic filtering options
option_1 = ['Moisturizer', 'Cleanser', 'Treatment', 'Face Mask', 'Eye cream', 'Sun protect']
option_2 = ['Combination', 'Dry', 'Normal', 'Oily', 'Sensitive']
output_notebook() # plot will be shown inside the notebook
""" Creating plot, glyphs and adding hover tool"""
# make a source and scatter bokeh plot
source = ColumnDataSource(df_bokeh)
plot = figure(x_axis_label = 'T-SNE 1', y_axis_label = 'T-SNE 2',
width = 500, height = 400)
plot.circle(x = 'X', y = 'Y', source = source,
size = 10, color = '#FF7373', alpha = .8)
plot.background_fill_color = "beige"
plot.background_fill_alpha = 0.2
# add hover tool
hover = HoverTool(tooltips = [
def __init__(self, **options):
if in_ipnb():
from bokeh.io import output_notebook
output_notebook(hide_banner=True)
super(BokehPlotter, self).__init__(**options)
# Import Bokeh modules for interactive plotting
import bokeh.io as bi
import bokeh.plotting as bp
# Set up Bokeh for inline viewing
bi.output_notebook()
# Set up plot
p = bp.figure(width=650, height=400, x_axis_label='x', y_axis_label='dy/dx',
tools='pan,wheel_zoom,box_zoom,resize,reset')
# Populate glyphs
p.circle((x[1:] + x[:-1]) / 2.0, deriv, color='gray', legend='fin. diff.')
p.line(x, deriv_exact, color='black', line_width=2, legend='exact')
# Position legend
p.legend.location = 'top_center'
# Display plot
bp.show(p)
def event_display_interactive(
events,
peaks,
to_pe,
run_id,
context,
bottom_pmt_array=True,
only_main_peaks=False,
only_peak_detail_in_wf=False,
plot_all_pmts=False,
plot_record_matrix=False,
plot_records_threshold=10,
xenon1t=False,
colors=('gray', 'blue', 'green'),
yscale=('linear', 'linear', 'linear'),
log=True,
):
"""
Interactive event display for XENONnT. Plots detailed main/alt
S1/S2, bottom and top PMT hit pattern as well as all other peaks
in a given event.
:param bottom_pmt_array: If true plots bottom PMT array hit-pattern.
:param only_main_peaks: If true plots only main peaks into detail
plots as well as PMT arrays.
:param only_peak_detail_in_wf: Only plots main/alt S1/S2 into
waveform. Only plot main peaks if only_main_peaks is true.
:param plot_all_pmts: Bool if True, colors switched off PMTs instead
of showing them in gray, useful for graphs shown in talks.
:param plot_record_matrix: If true record matrix is plotted below.
waveform.
:param plot_records_threshold: Threshold at which zoom level to display
record matrix as polygons. Larger values may lead to longer
render times since more polygons are shown.
:param xenon1t: Flag to use event display with 1T data.
:param colors: Colors to be used for peaks. Order is as peak types,
0 = Unknown, 1 = S1, 2 = S2. Can be any colors accepted by bokeh.
:param yscale: Defines scale for main/alt S1 == 0, main/alt S2 == 1,
waveform plot == 2. Please note, that the log scale can lead to funny
glyph renders for small values.
:param log: If true color sclae is used for hitpattern plots.
Note:
How to use:
> st.event_display(context,
> run_id,
> time_range=(event['time'],
> event['endtime'])
> )
Warning:
Raises an error if the user queries a time range which contains
more than a single event.
:return: bokeh.plotting.figure instance.
"""
st = context
if len(yscale) != 3:
raise ValueError(
f'"yscale" needs three entries, but you passed {len(yscale)}.')
if not hasattr(st, '_BOKEH_CONFIGURED_NOTEBOOK'):
st._BOKEH_CONFIGURED_NOTEBOOK = True
# Configure show to show notebook:
from bokeh.io import output_notebook
output_notebook()
if len(events) != 1:
raise ValueError('The time range you specified contains more or'
' less than a single event. The event display '
' only works with individual events for now.')
if peaks.shape[0] == 0:
raise ValueError(
'Found an event without peaks this should not had have happened.')
# Select main/alt S1/S2s based on time and endtime in event:
m_other_peaks = np.ones(len(peaks),
dtype=np.bool_) # To select non-event peaks
endtime = strax.endtime(peaks)
signal = {}
if only_main_peaks:
s1_keys = ['s1']
s2_keys = ['s2']
labels = {'s1': 'S1', 's2': 'S2'}
else:
s1_keys = ['s1', 'alt_s1']
s2_keys = ['s2', 'alt_s2']
labels = {'s1': 'MS1', 'alt_s1': 'AS1', 's2': 'MS2', 'alt_s2': 'AS2'}
for s_x in labels.keys():
# Loop over Main/Alt Sx and get store S1/S2 Main/Alt in signals,
# store information about other peaks as "m_other_peaks"
m = (peaks['time']
== events[f'{s_x}_time']) & (endtime == events[f'{s_x}_endtime'])
signal[s_x] = peaks[m]
m_other_peaks &= ~m
# Detail plots for main/alt S1/S2:
fig_s1, fig_s2 = plot_detail_plot_s1_s2(
signal,
s1_keys,
s2_keys,
labels,
colors,
yscale[:2],
)
# PMT arrays:
if not only_main_peaks:
# Plot all keys into both arrays:
top_array_keys = s2_keys + s1_keys
bottom_array_keys = s1_keys + s2_keys
else:
top_array_keys = s2_keys
bottom_array_keys = s1_keys
fig_top, fig_bottom = plot_pmt_arrays_and_positions(top_array_keys,
bottom_array_keys,
signal,
to_pe,
labels,
plot_all_pmts,
xenon1t=xenon1t,
log=log)
m_other_s2 = m_other_peaks & (peaks['type'] == 2)
if np.any(m_other_s2) and not only_main_peaks:
# Now we have to add the positions of all the other S2 to the top pmt array
# if not only main peaks.
fig_top, plot = plot_posS2s(peaks[m_other_s2],
label='OS2s',
fig=fig_top,
s2_type_style_id=2)
plot.visible = False
# Main waveform plot:
if only_peak_detail_in_wf:
# If specified by the user only plot main/alt S1/S2
peaks = peaks[~m_other_peaks]
waveform = plot_event(peaks, signal, labels, events[0], colors, yscale[-1])
# Create tile:
title = _make_event_title(events[0], run_id)
# Put everything together:
if bottom_pmt_array:
upper_row = [fig_s1, fig_s2, fig_top, fig_bottom]
else:
upper_row = [fig_s1, fig_s2, fig_top]
upper_row = bokeh.layouts.Row(children=upper_row)
plots = bokeh.layouts.gridplot(
children=[upper_row, waveform],
sizing_mode='scale_both',
ncols=1,
merge_tools=True,
toolbar_location='above',
)
event_display = bokeh.layouts.Column(
children=[title, plots],
sizing_mode='scale_both',
max_width=1600,
)
# Add record matrix if asked:
if plot_record_matrix:
if st.is_stored(run_id, 'records'):
# Check if records can be found and load:
r = st.get_array(run_id,
'records',
time_range=(events[0]['time'],
events[0]['endtime']))
elif st.is_stored(run_id, 'raw_records'):
warnings.warn(
f'Cannot find records for {run_id}, making them from raw_records instead.'
)
p = st.get_single_plugin(run_id, 'records')
r = st.get_array(run_id,
'raw_records',
time_range=(events[0]['time'],
events[0]['endtime']))
r = p.compute(r, events[0]['time'],
events[0]['endtime'])['records']
else:
warnings.warn(
f'Can neither find records nor raw_records for run {run_id}, proceed without record '
f'matrix.')
plot_record_matrix = False
if plot_record_matrix:
straxen._BOKEH_X_RANGE = None
# First get hook to for x_range:
x_range_hook = lambda plot, element: hook(
plot, x_range=straxen._BOKEH_X_RANGE, debug=False)
# Create datashader plot:
wf, record_points, time_stream = _hvdisp_plot_records_2d(
records=r,
to_pe=to_pe,
t_reference=peaks[0]['time'],
event_range=(waveform.x_range.start, waveform.x_range.end),
config=st.config,
hooks=[x_range_hook],
tools=[],
)
# Create record polygons:
polys = plot_record_polygons(record_points, width=1.1)
records_in_window = polys.apply(get_records_matrix_in_window,
streams=[time_stream],
time_slice=plot_records_threshold)
# Render plot to initialize x_range:
import holoviews as hv
import panel
_ = hv.render(wf)
# Set x-range of event plot:
bokeh_set_x_range(waveform, straxen._BOKEH_X_RANGE, debug=False)
event_display = panel.Column(event_display,
wf * records_in_window,
sizing_mode='scale_width')
return event_display
def get_jupyter(self):
bokeh_plot = self.plot()
output_notebook()
show(bokeh_plot)
import pandas as pd
import numpy as np
import colorsys
import networkx as nx
from bokeh.resources import CDN
from bokeh.io import output_notebook
output_notebook(resources=CDN)
pd.set_option('max_colwidth', 200)
pd.set_option('max_rows', 500)
from bokeh.plotting import figure, output_file, show, ColumnDataSource, save
from bokeh.io import show
from bokeh.models import ColumnDataSource
from bokeh.plotting import figure
def _pseudocolor(val):
"""Convert number to color"""
h = (1.0 - val) * 120 / 360
r, g, b = colorsys.hsv_to_rgb(h, 1., 1.)
return r * 255, g * 255, b * 255
def _rgb2hex(color):
"""Converts a list or tuple of color to an RGB string
Args:
color (list|tuple): the list or tuple of integers (e.g. (127, 127, 127))
def __init__(self, map_size, team_size):
self.draw_init_plot(map_size, team_size)
output_notebook()
self.nb_handle = show(self.plt_combo, notebook_handle=True)
def test_noarg(self, mock_load_notebook):
default_load_notebook_args = (None, False, False)
io.output_notebook()
self._check_func_called(io._state.output_notebook, (), {})
self._check_func_called(mock_load_notebook, default_load_notebook_args,
{})
def __init__(self, **options):
if in_ipnb():
from bokeh.io import output_notebook
output_notebook(hide_banner=True)
super(BokehPlotter, self).__init__(**options)
def test_args(self, mock_load_notebook):
load_notebook_args = (Resources(), True, True)
io.output_notebook(*load_notebook_args)
self._check_func_called(io._state.output_notebook, (), {})
self._check_func_called(mock_load_notebook, load_notebook_args, {})
def test_args(self, mock_load_notebook):
load_notebook_args = (Resources(), True, True)
io.output_notebook(*load_notebook_args)
self._check_func_called(io._state.output_notebook, (), {})
self._check_func_called(mock_load_notebook, load_notebook_args, {})
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Nov 21 16:06:38 2017
@author: jmmauricio
"""
from bokeh.io import output_notebook, show
from bokeh.plotting import figure
from bokeh.models import ColumnDataSource, HoverTool
from bokeh.io import push_notebook
from bokeh.resources import INLINE
output_notebook(INLINE)
def plot_results(grid):
grid.bokeh_tools()
p = figure(width=600, height=400, title='Results')
# trafos:
source = ColumnDataSource(grid.transformer_data)
trafo = p.multi_line(source=source,
xs='x_s',
ys='y_s',
color="green",
alpha=0.5,
line_width=5)
# lines:
def test_args(self, mock_load_notebook):
load_zeppelin_args = (Resources(), True, True, 1000, 'zeppelin')
io.output_notebook(*load_zeppelin_args)
self._check_func_called(io._state.output_notebook, ('zeppelin',), {})
self._check_func_called(mock_load_notebook, load_zeppelin_args, {})
def visualize_portfolio_transform_bokeh(portfolio_state_list,
save_path=None,
is_save=False,
is_show=True,
is_jupyter=True):
"""
["now_price_array", "portfoilo_vector", "mean_cost_price_array", "all_assets", "datetime"]
"""
# テータの取り出し
ticker_names = portfolio_state_list[0].names
colors = d3["Category20"][len(ticker_names)]
all_price_array = np.stack(
[one_state.now_price_array for one_state in portfolio_state_list],
axis=1)
all_portfolio_vector = np.stack(
[one_state.portfolio_vector for one_state in portfolio_state_list],
axis=1)
all_mean_cost_price_array = np.stack([
one_state.mean_cost_price_array for one_state in portfolio_state_list
],
axis=1)
all_assets_array = np.array(
[one_state.all_assets for one_state in portfolio_state_list])
all_datetime_array = np.array([
get_naive_datetime_from_datetime(one_state.datetime)
for one_state in portfolio_state_list
])
x = np.arange(0, len(portfolio_state_list))
# sorceの作成
portfolio_vector_source = {"x": x, "datetime": all_datetime_array}
price_source_x = []
price_source_y = []
mean_cost_price_source_x = []
mean_cost_price_source_y = []
for i, ticker_name in enumerate(ticker_names):
portfolio_vector_source[ticker_name] = all_portfolio_vector[i, :]
price_source_x.append(x)
price_source_y.append(all_price_array[i, :] / all_price_array[i, 0])
mean_cost_price_source_x.append(x)
mean_cost_price_source_y.append(all_mean_cost_price_array[i, :] /
all_mean_cost_price_array[i, 0])
# ホバーツールの設定
#tool_tips = [("x", "@x")]
tool_tips = [("datetime", "@datetime{%F %H:%M:%S}")]
tool_tips.extend([(ticker_name, "@" + ticker_name + "{0.000}")
for ticker_name in ticker_names])
hover_tool = HoverTool(tooltips=tool_tips,
formatters={'@datetime': 'datetime'})
# 描画
p1_text = Div(text=make_ticker_text(all_price_array[:, 0], ticker_names))
p1 = bokeh.plotting.figure(plot_width=1200,
plot_height=500,
title="正規化価格・ポートフォリオ")
p1.add_tools(hover_tool)
p1.extra_y_ranges = {"portfolio_vector": Range1d(start=0, end=3)}
p1.add_layout(LinearAxis(y_range_name="portfolio_vector"), 'right')
p1.vbar_stack(ticker_names,
x='x',
width=1,
color=colors,
y_range_name="portfolio_vector",
source=portfolio_vector_source,
legend_label=ticker_names,
alpha=0.8)
p1.multi_line(xs=price_source_x,
ys=price_source_y,
line_color=colors,
line_width=2)
y_min, y_max = make_y_limit_multi(price_source_y,
lowwer_ratio=0.1,
upper_ratio=0.1)
y_min -= (y_max - y_min) * 0.66 # ポートフォリオ割合のためのオフセット
p1.y_range = Range1d(start=y_min, end=y_max)
p1.yaxis[0].axis_label = "正規化価格"
p1.yaxis[1].axis_label = "保有割合"
p1.xaxis.major_label_overrides = {
str(one_x): str(all_datetime_array[i])
for i, one_x in enumerate(x)
}
p2_text = Div(
text=make_ticker_text(all_mean_cost_price_array[:, 0], ticker_names))
p2 = bokeh.plotting.figure(plot_width=1200,
plot_height=300,
title="正規化平均取得価格・全資産")
p2.multi_line(xs=mean_cost_price_source_x,
ys=mean_cost_price_source_y,
line_color=colors,
line_width=2)
y_min, y_max = make_y_limit_multi(mean_cost_price_source_y,
lowwer_ratio=0.1,
upper_ratio=0.1)
p2.y_range = Range1d(start=y_min, end=y_max)
y_max, y_min = make_y_limit(all_assets_array,
upper_ratio=0.1,
lowwer_ratio=0.1)
p2.extra_y_ranges = {"all_assets": Range1d(start=y_max, end=y_min)}
p2.add_layout(LinearAxis(y_range_name="all_assets"), 'right')
p2.line(x,
all_assets_array,
color="red",
legend_label="all_assets",
line_width=4,
y_range_name="all_assets")
# 疑似的なレジェンドをつける
for ticker_name, color in zip(ticker_names, colors):
p2.line([], [], legend_label=ticker_name, color=color, line_width=2)
p2.yaxis[0].axis_label = "正規化平均取得価格"
p2.yaxis[1].axis_label = "全資産 [円]"
p2.xaxis.major_label_overrides = {
str(one_x): str(all_datetime_array[i])
for i, one_x in enumerate(x)
}
layout_list = [p1_text, p1, p2_text, p2]
created_figure = bokeh.layouts.column(*layout_list)
if is_save:
if save_path.suffix == ".png":
bokeh.io.export_png(created_figure, filename=save_path)
elif save_path.suffix == ".html":
output_file(save_path)
bokeh.io.save(created_figure,
filename=save_path,
title="trading process")
else:
raise Exception(
"The suffix of save_path is must be '.png' or '.html'.")
return None
if is_show:
try:
reset_output()
if is_jupyter:
output_notebook()
show(created_figure)
except:
if is_jupyter:
output_notebook()
show(created_figure)
return None
if not is_save and not is_show:
return layout_list
def test_noarg(self):
default_kwargs = dict(url=None, docname=None, session=None, name=None)
io.output_notebook()
self._check_func_called(io._state.output_notebook, (), default_kwargs)
import numpy as np
from bokeh.plotting import figure, ColumnDataSource
import bokeh.io as io
from bokeh.models import HoverTool
AVAIL_COLORS = [
"#1F77B4", "firebrick", "goldenrod", "aqua", "brown", "chartreuse",
"darkmagenta"
"aquamarine", "blue", "red", "blueviolet", "darkorange", "forestgreen",
"lime"
]
# AVAIL_MARKERS: circle, diamond, triangle, square, inverted_triangle, asterisk,
# circle_cross, circle_x, cross, diamond_cross, square_cross, square_x, asterisk, diamond
io.output_notebook()
class ColorScale():
def __init__(self,
num_values,
val_min,
val_max,
middle_color="yellow",
reverse=False):
self.num_values = num_values
self.num_val_1 = num_values - 1
self.value_min = val_min
self.value_max = val_max
self.reverse = reverse
self.value_range = self.value_max - self.value_min
def task_completion_time_distribution():
from bokeh.models import ColumnDataSource
from bokeh.layouts import gridplot
from bokeh.plotting import figure, show, helpers
from bokeh.io import output_notebook, push_notebook
from bokeh.resources import CDN
output_notebook(resources=CDN)
# Create the Bokeh plot
p = figure(title="Task Completion Time Distribution",
tools=["save", "hover", "wheel_zoom", "box_zoom", "pan"],
background_fill_color="#FFFFFF",
x_range=(0, 1),
y_range=(0, 1))
# Create the data source that the plot pulls from
source = ColumnDataSource(data={
"top": [],
"left": [],
"right": []
})
# Plot the histogram rectangles
p.quad(top="top", bottom=0, left="left", right="right", source=source,
fill_color="#B3B3B3", line_color="#033649")
# Label the plot axes
p.xaxis.axis_label = "Duration in seconds"
p.yaxis.axis_label = "Number of tasks"
handle = show(gridplot(p, ncols=1,
plot_width=500,
plot_height=500,
toolbar_location="below"), notebook_handle=True)
# Function to update the plot
def task_completion_time_update(abs_earliest,
abs_latest,
abs_num_tasks,
tasks):
if len(tasks) == 0:
return
# Create the distribution to plot
distr = []
for task_id, data in tasks.items():
distr.append(data["store_outputs_end"] -
data["get_arguments_start"])
# Create a histogram from the distribution
top, bin_edges = np.histogram(distr, bins="auto")
left = bin_edges[:-1]
right = bin_edges[1:]
source.data = {"top": top, "left": left, "right": right}
# Set the x and y ranges
x_range = (min(left) if len(left) else 0,
max(right) if len(right) else 1)
y_range = (0, max(top) + 1 if len(top) else 1)
x_range = helpers._get_range(x_range)
p.x_range.start = x_range.start
p.x_range.end = x_range.end
y_range = helpers._get_range(y_range)
p.y_range.start = y_range.start
p.y_range.end = y_range.end
# Push updates to the plot
push_notebook(handle=handle)
get_sliders(task_completion_time_update)
def __init__(self, notebook=False):
self.notebook = notebook
if notebook:
output_notebook()
def cluster_usage():
from bokeh.io import show, output_notebook, push_notebook
from bokeh.resources import CDN
from bokeh.plotting import figure
from bokeh.models import (
ColumnDataSource,
HoverTool,
LinearColorMapper,
BasicTicker,
ColorBar,
)
output_notebook(resources=CDN)
# Initial values
source = ColumnDataSource(data={"node_ip_address": ['127.0.0.1'],
"time": ['0.5'],
"num_tasks": ['1'],
"length": [1]})
# Define the color schema
colors = ["#75968f",
"#a5bab7",
"#c9d9d3",
"#e2e2e2",
"#dfccce",
"#ddb7b1",
"#cc7878",
"#933b41",
"#550b1d"]
mapper = LinearColorMapper(palette=colors, low=0, high=2)
TOOLS = "hover, save, xpan, box_zoom, reset, xwheel_zoom"
# Create the plot
p = figure(title="Cluster Usage",
y_range=list(set(source.data['node_ip_address'])),
x_axis_location="above",
plot_width=900,
plot_height=500,
tools=TOOLS,
toolbar_location='below')
# Format the plot axes
p.grid.grid_line_color = None
p.axis.axis_line_color = None
p.axis.major_tick_line_color = None
p.axis.major_label_text_font_size = "10pt"
p.axis.major_label_standoff = 0
p.xaxis.major_label_orientation = np.pi / 3
# Plot rectangles
p.rect(x="time", y="node_ip_address", width="length", height=1,
source=source,
fill_color={"field": "num_tasks", "transform": mapper},
line_color=None)
# Add legend to the side of the plot
color_bar = ColorBar(color_mapper=mapper,
major_label_text_font_size="8pt",
ticker=BasicTicker(desired_num_ticks=len(colors)),
label_standoff=6,
border_line_color=None,
location=(0, 0))
p.add_layout(color_bar, "right")
# Define hover tool
p.select_one(HoverTool).tooltips = [
("Node IP Address", "@node_ip_address"),
("Number of tasks running", "@num_tasks"),
("Time", "@time")
]
# Define the axis labels
p.xaxis.axis_label = "Time in seconds"
p.yaxis.axis_label = "Node IP Address"
handle = show(p, notebook_handle=True)
workers = ray.global_state.workers()
# Function to update the heat map
def heat_map_update(abs_earliest, abs_latest, abs_num_tasks, tasks):
if len(tasks) == 0:
return
earliest = time.time()
latest = 0
node_to_tasks = dict()
# Determine which task has the earlest start time out of the ones
# passed into the update function
for task_id, data in tasks.items():
if data["score"] > latest:
latest = data["score"]
if data["score"] < earliest:
earliest = data["score"]
worker_id = data["worker_id"]
node_ip = workers[worker_id]["node_ip_address"]
if node_ip not in node_to_tasks:
node_to_tasks[node_ip] = {}
node_to_tasks[node_ip][task_id] = data
nodes = []
times = []
lengths = []
num_tasks = []
for node_ip, task_dict in node_to_tasks.items():
left, right, top = compute_utilizations(earliest,
latest,
abs_num_tasks,
task_dict,
100,
True)
for (l, r, t) in zip(left, right, top):
nodes.append(node_ip)
times.append((l + r) / 2)
lengths.append(r - l)
num_tasks.append(t)
# Set the y range of the plot to be the node IP addresses
p.y_range.factors = list(set(nodes))
mapper.low = min(min(num_tasks), 0)
mapper.high = max(max(num_tasks), 1)
# Update plot with new data based on slider and text box values
source.data = {"node_ip_address": nodes,
"time": times,
"num_tasks": num_tasks,
"length": lengths}
push_notebook(handle=handle)
get_sliders(heat_map_update)
def get_jupyter(self):
output_notebook()
show(self.plot())
def plot_process_tree(
data: pd.DataFrame,
schema: ProcSchema = None,
output_var: str = None,
legend_col: str = None,
show_table: bool = False,
**kwargs,
) -> Tuple[figure, LayoutDOM]:
"""
Plot a Process Tree Visualization.
Parameters
----------
data : pd.DataFrame
DataFrame containing one or more Process Trees
schema : ProcSchema, optional
The data schema to use for the data set, by default None
(if None the schema is inferred)
output_var : str, optional
Output variable for selected items in the tree,
by default None
legend_col : str, optional
The column used to color the tree items, by default None
show_table: bool
Set to True to show a data table, by default False.
Other Parameters
----------------
height : int, optional
The height of the plot figure
(the default is 700)
width : int, optional
The width of the plot figure (the default is 900)
title : str, optional
Title to display (the default is None)
Returns
-------
Tuple[figure, LayoutDOM]:
figure - The main bokeh.plotting.figure
Layout - Bokeh layout structure.
Raises
------
ProcessTreeSchemaException
If the data set schema is not valid for the plot.
Notes
-----
The `output_var` variable will be overwritten with any selected
values.
"""
check_kwargs(kwargs, _DEFAULT_KWARGS)
reset_output()
output_notebook()
data, schema, levels, n_rows = _pre_process_tree(data, schema)
if schema is None:
raise ProcessTreeSchemaException(
"Could not infer schema from data set.")
source = ColumnDataSource(data=data)
# Get legend/color bar map
fill_map, color_bar = _create_fill_map(source, legend_col)
max_level = max(levels) + 3
min_level = min(levels)
plot_height: int = kwargs.pop("height", 700)
plot_width: int = kwargs.pop("width", 900)
title: str = kwargs.pop("title", "ProcessTree")
if color_bar:
title += " (color bar = {legend_col})"
visible_range = int(plot_height / 35)
y_start_range = (n_rows - visible_range, n_rows + 1)
b_plot = figure(
title=title,
plot_width=plot_width,
plot_height=plot_height,
x_range=(min_level, max_level),
y_range=y_start_range,
tools=["ypan", "reset", "save", "tap"],
toolbar_location="above",
)
hover = HoverTool(tooltips=_get_tool_tips(schema),
formatters={"TimeGenerated": "datetime"})
b_plot.add_tools(hover)
# dodge to align rectangle with grid
rect_x = dodge("Level", 1.75, range=b_plot.x_range)
rect_plot_params = dict(width=3.5,
height=0.95,
source=source,
fill_alpha=0.4,
fill_color=fill_map)
if color_bar:
b_plot.add_layout(color_bar, "right")
elif legend_col:
rect_plot_params["legend_field"] = legend_col
rect_plot = b_plot.rect(x=rect_x, y="Row", **rect_plot_params)
if legend_col and not color_bar:
b_plot.legend.title = legend_col
text_props = {
"source": source,
"text_align": "left",
"text_baseline": "middle"
}
def x_dodge(x_offset):
return dodge("Level", x_offset, range=b_plot.x_range)
def y_dodge(y_offset):
return dodge("Row", y_offset, range=b_plot.y_range)
b_plot.text(x=x_dodge(0.1),
y=y_dodge(-0.2),
text="cmd",
text_font_size="7pt",
**text_props)
b_plot.text(x=x_dodge(0.1),
y=y_dodge(0.25),
text="Exe",
text_font_size="8pt",
**text_props)
b_plot.text(x=x_dodge(1.8),
y=y_dodge(0.25),
text="PID",
text_font_size="8pt",
**text_props)
# Plot options
_set_plot_option_defaults(b_plot)
b_plot.xaxis.ticker = sorted(levels)
b_plot.xgrid.ticker = sorted(levels)
b_plot.hover.renderers = [rect_plot] # only hover element boxes
# Selection callback
if output_var is not None:
get_selected = _create_js_callback(source, output_var)
b_plot.js_on_event("tap", get_selected)
box_select = BoxSelectTool(callback=get_selected)
b_plot.add_tools(box_select)
range_tool = _create_vert_range_tool(
data=source,
min_y=0,
max_y=n_rows,
plot_range=b_plot.y_range,
width=90,
height=plot_height,
x_col="Level",
y_col="Row",
fill_map=fill_map,
)
plot_elems = row(b_plot, range_tool)
if show_table:
data_table = _create_data_table(source, schema, legend_col)
plot_elems = column(plot_elems, data_table)
show(plot_elems)
return b_plot, plot_elems
def plot_entity_graph(
entity_graph: nx.Graph,
node_size: int = 25,
font_size: Union[int, str] = 10,
height: int = 800,
width: int = 800,
scale: int = 2,
) -> figure:
"""
Plot entity graph with Bokeh.
Parameters
----------
entity_graph : nx.Graph
The entity graph as a networkX graph
node_size : int, optional
Size of the nodes in pixels, by default 25
font_size : int, optional
Font size for node labels, by default 10
Can be an integer (point size) or a string (e.g. "10pt")
width : int, optional
Width in pixels, by default 800
height : int, optional
Image height (the default is 800)
scale : int, optional
Position scale (the default is 2)
Returns
-------
bokeh.plotting.figure
The network plot.
"""
output_notebook()
font_pnt = f"{font_size}pt" if isinstance(font_size, int) else font_size
node_attrs = {
node: attrs["color"]
for node, attrs in entity_graph.nodes(data=True)
}
nx.set_node_attributes(entity_graph, node_attrs, "node_color")
plot = figure(
title="Alert Entity graph",
x_range=(-3, 3),
y_range=(-3, 3),
width=width,
height=height,
)
plot.add_tools(
HoverTool(tooltips=[
("node_type", "@node_type"),
("name", "@name"),
("description", "@description"),
]))
graph_renderer = from_networkx(entity_graph,
nx.spring_layout,
scale=scale,
center=(0, 0))
graph_renderer.node_renderer.glyph = Circle(size=node_size,
fill_color="node_color",
fill_alpha=0.5)
plot.renderers.append(graph_renderer)
# pylint: disable=no-member
# Create labels
for name, pos in graph_renderer.layout_provider.graph_layout.items():
label = Label(
x=pos[0],
y=pos[1],
x_offset=5,
y_offset=5,
text=name,
text_font_size=font_pnt,
)
plot.add_layout(label)
# pylint: enable=no-member
return plot
from bokeh.plotting import figure, output_file, show, ColumnDataSource
from bokeh.models import HoverTool, CustomJS
import pandas as pd
from bokeh.io import output_notebook
import numpy as np
from bokeh.models import (
GMapPlot, GMapOptions, ColumnDataSource, Circle, DataRange1d, PanTool, WheelZoomTool, BoxSelectTool, ResetTool, RedoTool, UndoTool
)
from bokeh.models import GeoJSONDataSource
output_notebook()
#Get Data
df = pd.read_csv("final_no_outlier")
latitude = df['latitude'].tolist()
longitude = df['longitude'].tolist()
price = df['price per room'].tolist()
r = [0.0003] * len(price)
address = df['address'].tolist()
distance = df['edge_distance'].tolist()
sqft = df['sqft per room'].tolist()
food = df['avg_rating'].tolist()
cafes = df['#cafes'].tolist()
pubs = df['#pubs'].tolist()
# Create color span based on price
colors = ["#F1EEF6", "#D4B9DA", "#C994C7", "#DF65B0", "#DD1C77", "#980043"]
def visualize_portfolio_rl_bokeh(portfolio_state_list,
reward_list,
save_path=None,
is_save=False,
is_show=True,
is_jupyter=True):
"""
[datetime]
"""
all_datetime_array = np.array([
get_naive_datetime_from_datetime(one_state.datetime)
for one_state in portfolio_state_list
])
reward_array = np.array(reward_list)
x = np.arange(0, len(portfolio_state_list))
layout_list = visualize_portfolio_transform_bokeh(portfolio_state_list,
is_save=False,
is_show=False)
add_p1 = bokeh.plotting.figure(plot_width=1200,
plot_height=300,
title="報酬")
add_p1.line(x,
reward_array,
legend_label="reward",
line_width=2,
color="green")
add_p1.xaxis.major_label_overrides = {
str(one_x): str(all_datetime_array[i])
for i, one_x in enumerate(x)
}
add_p1.yaxis[0].axis_label = "報酬"
layout_list.extend([add_p1])
created_figure = bokeh.layouts.column(*layout_list)
if is_save:
if save_path.suffix == ".png":
bokeh.io.export_png(created_figure, filename=save_path)
elif save_path.suffix == ".html":
output_file(save_path)
bokeh.io.save(created_figure,
filename=save_path,
title="trading process")
else:
raise Exception(
"The suffix of save_path is must be '.png' or '.html'.")
return None
if is_show:
try:
reset_output()
if is_jupyter:
output_notebook()
show(created_figure)
except:
if is_jupyter:
output_notebook()
show(created_figure)
return None
if not is_save and not is_show:
return layout_list