def show(sample_size):
global session
global scatter_plot
global source
global pie_chart_source
global line_chart_source
global slider
DB.__init__(sample_size)
min_time = DB.min_time()
max_time = DB.max_time()
print min_time
print min_time
xs, ys, color, time = DB.get_current()
xs = [xs[i] for i,v in enumerate(time) if time[i] == min_time]
ys = [ys[i] for i,v in enumerate(time) if time[i] == min_time]
color = [color[i] for i,v in enumerate(time) if time[i] == min_time]
time_dict = Counter(time)
pie_chart_source = ColumnDataSource(data=ChartMath.compute_color_distribution('x', 'y', 'color', color))
line_chart_source = ColumnDataSource(data=dict(x=[key for key in time_dict], y=[time_dict[key] for key in time_dict]))
source = ColumnDataSource(data=dict(x=xs, y=ys, color=color))
scatter_plot = Figure(plot_height=800,
plot_width=1200,
title="Plot of Voters",
tools="pan, reset, resize, save, wheel_zoom",
)
scatter_plot.circle('x', 'y', color='color', source=source, line_width=0, line_alpha=0.001, fill_alpha=0.5, size=15)
scatter_plot.patches('x', 'y', source=state_source, fill_alpha=0.1, line_width=3, line_alpha=1)
scatter_plot.x_range.on_change('end', update_coordinates)
line_chart = Figure(title="Distribution over Time", plot_width=350, plot_height=350)
line_chart.line(x='x', y='y', source=line_chart_source)
pie_chart_plot = Figure(plot_height=350,
plot_width=350,
title="Voter Distribution",
x_range=(-1, 1),
y_range=(-1, 1))
pie_chart_plot.wedge(x=0, y=0, source=pie_chart_source, radius=1, start_angle="x", end_angle="y", color="color")
slider = Slider(start=min_time, end=max_time, value=min_time, step=1, title="Time")
slider.on_change('value', update_coordinates)
h = hplot(scatter_plot, vplot(pie_chart_plot, line_chart))
vplot(slider, h, width=1600, height=1800)
session = push_session(curdoc())
session.show()
#script = autoload_server(scatter_plot, session_id=session.id)
session.loop_until_closed()
def run(input_files, output_files):
# Read reaction sequences
sequs = gazelib.io.load_json(input_files[0])
# Collect figures here.
figs = []
for sequence in sequs:
srts = []
# Trials
for trial in sequence:
if trial['heuristic_saccade_validity']:
srts.append(trial['srt'])
else:
srts.append(0)
# To milliseconds
srts = list(map(to_milliseconds, srts))
d = {
'SRT': srts,
'Trial': list(range(1,13))
}
p = Bar(d, label='Trial', values='SRT', color='black')
figs.append(p)
# Visualization with bokeh. Combine figures in vertical layout.
p = plotting.vplot(*figs)
plotting.output_file(output_files[0],
'Saccadic reaction time variability')
plotting.save(p)
def make_washmap_map_tools_linked():
data = get_data_with_countries(wat_stats, san_stats)
source = ColumnDataSource(data)
wat_map = construct_water_map_tools(source)
wat_text = construct_water_text(source)
wat_key = construct_key(WATER_COLOR_RANGE)
return hplot(vplot(wat_map), vplot(wat_text, wat_key))
def make_washmap_map_tools_linked():
data = get_data_with_countries(wat_stats, san_stats)
source = ColumnDataSource(data)
wat_map = construct_water_map_tools(source)
wat_text = construct_water_text(source)
wat_key = construct_key(WATER_COLOR_RANGE)
return hplot(vplot(wat_map), vplot(wat_text, wat_key))
def __init__(self, title, legends, n_images_train=0, n_images_test=0, n_cols_images=3, axisx="Epochs",
axisy="Values", line_width=4, alpha=0.8, line_dash=[4, 4], plot_width=800, plot_height=400):
# Save some parameters
self.n_lines_plot = len(legends)
self.n_images_train = n_images_train
self.n_images_test = n_images_test
# prepare output to server
output_server(title)
cursession().publish()
# Create the figure plot
if self.n_lines_plot > 0:
p_plot, self.data_plot = self.create_figure_plot(title, legends, axisx=axisx, axisy=axisy,
line_width=line_width, alpha=alpha, line_dash=line_dash,
plot_width=plot_width, plot_height=plot_height)
if n_images_train > 0:
# Create black images as initialization
img = np.zeros((64, 256, 3))
img_batch = []
for i in xrange(n_images_train):
img_batch.append(img)
# Create the training image grid
p_images_train, self.data_img_train = self.create_grid_images(img_batch, name='img_train', n_cols=n_cols_images)
if n_images_test > 0:
# Create black images as initialization
img = np.zeros((64, 256, 3))
img_batch = []
for i in xrange(n_images_test):
img_batch.append(img)
# Create the testing image grid
p_images_test, self.data_img_test = self.create_grid_images(img_batch, name='img_test', n_cols=n_cols_images)
# Create a vertical grid with the plot and the train and test images
if self.n_lines_plot > 0 and n_images_train > 0 and n_images_test > 0:
p = vplot(p_plot, p_images_train, p_images_test)
elif self.n_lines_plot > 0 and n_images_train > 0 and n_images_test <= 0:
p = vplot(p_plot, p_images_train)
else:
print 'ERROR: Not implemented combination. Please, do it!'
# Show the plot
show(p)
def generate_plots(execs,
plot_list=('cpu_bars', 'gpu_bars', 'user_total_memusage')):
monitor_methods = list()
if any('gpu' in pltname for pltname in plot_list):
monitor_methods.append('gpus_mon')
if any('cpu' in pltname for pltname in plot_list):
monitor_methods.append('cpus_mon')
_hplots = list()
panels = list()
monitors = list()
change_streams = list()
for name, ex in execs.items():
changes = ChangeStream(source_fun=update_notebook_source)
mon = RessourceMonitor(changes, async_exec=ex[0], normal_exec=ex[1])
plot_gen = BokehPlots(changes, async_exec=ex[0], normal_exec=ex[1])
plt = vplot(*[getattr(plot_gen, plt).__call__()
for plt in plot_list])
hostname = ex[1](['hostname'], stdout=PIPE).communicate()[0].decode().strip('\r\n ')
panels.append(Panel(title=hostname, child=plt))
_hplots.append(plt)
for mon_method in monitor_methods:
monitors.append(getattr(mon, mon_method))
change_streams.append(changes)
tabs = Tabs(tabs=panels)
return hplot(tabs), monitors, change_streams
def make_washmap_all():
data = get_data_with_countries(wat_stats, san_stats)
source = ColumnDataSource(data)
source.selected = [30]
line_data = get_line_data('Morocco')
line_source = ColumnDataSource(line_data)
wat_map = construct_water_map_tools(source)
wat_line = construct_water_line(line_source)
wat_text = construct_water_text(source)
wat_key = construct_key(WATER_COLOR_RANGE)
san_map = construct_san_map_tools(source)
san_line = construct_san_line(line_source)
san_text = construct_san_text(source)
san_key = construct_key(SANITATION_COLOR_RANGE)
tabs = Tabs(tabs=[
Panel(title="Water",
child=layout_components(wat_map, wat_line, wat_text, wat_key)),
Panel(title="Sanitation",
child=layout_components(san_map, san_line, san_text, san_key))
])
year = Slider(title="Year",
name='year',
value=1990,
start=1990,
end=2012,
step=1)
return vplot(tabs, year)
def plot(output_directory, normalized_counts, chromosome, cell_types):
bp.output_file(output_directory + "/" + chromosome + ".html", mode="cdn")
plots = []
summary = plot_summary(normalized_counts, chromosome)
if summary:
plots.append(summary)
else:
# if summary can't be plotted, then rest probably can't be plotted either,
# so return without even saving the file (the file is never created on disk if not saved)
return
for cell_type in cell_types:
logging.debug(" - plotting %s", cell_type)
bin_number = []
count = []
condition = "(file_key == 0) & (chromosome == '%s') & (cell_type == '%s')" % (chromosome, cell_type)
for row in normalized_counts.where(condition):
bin_number.append(row["bin_number"])
count.append(row["count"])
plot = bp.figure()
plot.title = "%s counts per bin" % cell_type
plot.scatter(bin_number, count)
plots.append(plot)
bp.save(bp.vplot(*plots))
def main(options, args):
logger = log.get_logger("ginga", options=options)
# create a new plot with default tools, using figure
fig = figure(x_range=[0, 600],
y_range=[0, 600],
plot_width=600,
plot_height=600,
toolbar_location=None)
viewer = ib.CanvasView(logger)
viewer.set_figure(fig)
def load_file(path):
image = AstroImage(logger)
image.load_file(path)
viewer.set_image(image)
def load_file_cb(attr_name, old_val, new_val):
#print(attr_name, old_val, new_val)
load_file(new_val)
# add a entry widget and configure with the call back
dstdir = options.indir
path_w = TextInput(value=dstdir, title="File:")
path_w.on_change('value', load_file_cb)
if len(args) > 0:
load_file(args[0])
# put the path widget and viewer in a layout and add to the document
curdoc().add_root(vplot(fig, path_w))
def _make_figures(self,ep,trainerr,metvals):
self._datasources = []
figures = []
fig = figure(title='Total Training Cost',x_axis_label='Epoch',y_axis_label='Cost')
fig.line([ep],[trainerr],name='plot')
ds = fig.select(dict(name='plot'))[0].data_source
self._datasources.append(ds)
if self._plotmetricmean:
figures.append(fig)
fig = figure(title='Metric Mean',x_axis_label='Epoch',y_axis_label='Mean')
fig.line([ep],[np.nanmean(metvals)],name='plot')
ds = fig.select(dict(name='plot'))[0].data_source
self._datasources.append(ds)
figures.append(fig)
for mv,(mk,m) in zip(metvals,self.metrics):
if m.metric in xnn.metrics.metric_names:
name = xnn.metrics.metric_names[m.metric]
else:
name = m.metric.__name__
fig = figure(title=mk,x_axis_label='Epoch',y_axis_label=name)
fig.line([ep],[mv],name='plot')
ds = fig.select(dict(name='plot'))[0].data_source
self._datasources.append(ds)
figures.append(fig)
allfigs = vplot(*figures)
push()
def plot(output_directory, normalized_counts, chromosome, cell_types):
bp.output_file(output_directory + "/" + chromosome + ".html", mode="cdn")
plots = []
summary = plot_summary(normalized_counts, chromosome)
if summary:
plots.append(summary)
else:
# if summary can't be plotted, then rest probably can't be plotted either,
# so return without even saving the file (the file is never created on disk if not saved)
return
for cell_type in cell_types:
logging.debug(" - plotting %s", cell_type)
bin_number = []
count = []
condition = "(file_key == 0) & (chromosome == '%s') & (cell_type == '%s')" % (chromosome, cell_type)
for row in normalized_counts.where(condition):
bin_number.append(row["bin_number"])
count.append(row["count"])
plot = bp.figure()
plot.title = "%s counts per bin" % cell_type
plot.scatter(bin_number, count)
plots.append(plot)
bp.save(bp.vplot(*plots))
def _draw_multiple_line_plot(filename, title, X, y, colors, legend, line_dash, line_width, x_axis_type, x_axis_label, y_axis_label, y_start=0, y_end=10, width=800, height=400):
#output_file(filename, title=title)
p1 = figure(x_axis_type = x_axis_type, plot_width=width, plot_height=height, y_range=(y_start, y_end))
for i in range(len(y)):
p1.line(X[i], y[i], color=colors[i], legend=legend[i], line_dash=line_dash[i], line_width=line_width[i])
#p1.multi_line(X, y, color=colors, legend=legend, line_dash=line_dash, line_width=line_width)
# p1.multi_line(xs=X,
# ys=y,
# line_color=colors,
# line_width=5)
p1.title = title
#p1.grid.grid_line_color='Black'
#p.ygrid[0].grid_line_alpha=0.5
p1.legend.orientation = "bottom_left"
p1.grid.grid_line_alpha=0.75
p1.xaxis.axis_label = x_axis_label
p1.yaxis.axis_label = y_axis_label
p1.ygrid.band_fill_color="olive"
p1.ygrid.band_fill_alpha = 0.25
p1.ygrid.minor_grid_line_color = 'navy'
p1.ygrid.minor_grid_line_alpha = 0.1
save(vplot(p1), filename=filename, title=title)
def notebook(*tunnels):
from bokeh.io import show
execs = dict()
if tunnels:
for tunnel in tunnels:
t_args = re.findall('([\'"]([^"\']+)["\'])|([^ ]+)', tunnel)
t_args = [a[-1] if a[-1] else a[-1] for a in t_args]
t_args = [a.strip(' ') for a in t_args]
execs['_'.join(t_args)] = make_ssh_subprocess(*t_args)
else:
execs['localhost'] = async_subprocess, Popen
_hplots = list()
monitors = list()
change_streams = list()
for ex in execs.values():
changes = ChangeStream(source_fun=update_notebook_source)
mon = RessourceMonitor(changes, async_exec=ex[0], normal_exec=ex[1])
plot_gen = BokehPlots(changes, async_exec=ex[0], normal_exec=ex[1])
_hplots.append(
vplot(plot_gen.cpu_bars(False), plot_gen.gpu_bars(),
plot_gen.user_total_memusage()))
monitors.append(mon)
change_streams.append(changes)
plots = hplot(*_hplots)
show(plots)
loop = asyncio.get_event_loop()
loop.run_until_complete(
asyncio.gather(*(mon.gpus_mon(loop=loop) for mon in monitors),
*(mon.cpus_mon() for mon in monitors),
*(changes.start() for changes in change_streams)))
def make_washmap_all():
data = get_data_with_countries(wat_stats, san_stats)
source = ColumnDataSource(data)
source.selected = [30]
line_data = get_line_data("Morocco")
line_source = ColumnDataSource(line_data)
wat_map = construct_water_map_tools(source)
wat_line = construct_water_line(line_source)
wat_text = construct_water_text(source)
wat_key = construct_key(WATER_COLOR_RANGE)
san_map = construct_san_map_tools(source)
san_line = construct_san_line(line_source)
san_text = construct_san_text(source)
san_key = construct_key(SANITATION_COLOR_RANGE)
tabs = Tabs(
tabs=[
Panel(title="Water", child=layout_components(wat_map, wat_line, wat_text, wat_key)),
Panel(title="Sanitation", child=layout_components(san_map, san_line, san_text, san_key)),
]
)
year = Slider(title="Year", name="year", value=1990, start=1990, end=2012, step=1)
return vplot(tabs, year)
def __init__(self, addr=None, interval=1000.00, loop=None):
if addr is None:
scheduler = default_executor().scheduler
if isinstance(scheduler, rpc):
addr = (scheduler.ip, 9786)
elif isinstance(scheduler, Scheduler):
addr = ('127.0.0.1', scheduler.services['http'].port)
self.addr = addr
self.interval = interval
self.display_notebook = False
if is_kernel() and not curstate().notebook:
output_notebook()
assert curstate().notebook
self.task_source, self.task_table = task_table_plot()
self.worker_source, self.worker_table = worker_table_plot()
self.output = vplot(self.worker_table, self.task_table)
self.client = AsyncHTTPClient()
self.loop = loop or IOLoop.current()
self.loop.add_callback(self.update)
self._pc = PeriodicCallback(self.update, self.interval, io_loop=self.loop)
self._pc.start()
def worker_table_plot(width=600, height="auto", **kwargs):
""" Column data source and plot for host table """
names = ['workers', 'cpu', 'memory-percent', 'memory', 'cores', 'processes',
'processing', 'latency', 'last-seen', 'disk-read', 'disk-write',
'network-send', 'network-recv']
source = ColumnDataSource({k: [] for k in names})
columns = {name: TableColumn(field=name, title=name) for name in names}
slow_names = ['workers', 'cores', 'processes', 'memory',
'latency', 'last-seen']
slow = DataTable(source=source, columns=[columns[n] for n in slow_names],
width=width, height=height, **kwargs)
slow.columns[3].formatter = NumberFormatter(format='0.0 b')
slow.columns[4].formatter = NumberFormatter(format='0.00000')
slow.columns[5].formatter = NumberFormatter(format='0.000')
fast_names = ['workers', 'cpu', 'memory-percent', 'processing',
'disk-read', 'disk-write', 'network-send', 'network-recv']
fast = DataTable(source=source, columns=[columns[n] for n in fast_names],
width=width, height=height, **kwargs)
fast.columns[1].formatter = NumberFormatter(format='0.0 %')
fast.columns[2].formatter = NumberFormatter(format='0.0 %')
fast.columns[4].formatter = NumberFormatter(format='0 b')
fast.columns[5].formatter = NumberFormatter(format='0 b')
fast.columns[6].formatter = NumberFormatter(format='0 b')
fast.columns[7].formatter = NumberFormatter(format='0 b')
table = vplot(slow, fast)
return source, table
def run(input_files, output_files):
# Read reaction sequences
stats = gazelib.io.load_json(input_files[0])
# Collect figures here.
figs = []
# Sequence completeness distribution
d = {
'num saccades captured': stats['total']['completeness'],
'sequences': [1] * len(stats['total']['completeness'])
}
p = Bar(d, agg='count', label='num saccades captured', values='sequences', color='black')
figs.append(p)
# Saccademodel MSE distribution
mses = stats['total']['all_mses']
d = { 'MSE': list(filter(lambda x: x < 0.1, mses)) }
p = Histogram(d, bins=40, values='MSE', color='black')
figs.append(p)
# Visualization with bokeh. Combine figures in vertical layout.
p = plotting.vplot(*figs)
plotting.output_file(output_files[0],
'Saccadic reaction time variability')
plotting.save(p)
def _create_grid_plot_of_trends(df, X, col_list, filename):
width = 600
height = 400
color_palette = [ 'Black', 'Red', 'Purple', 'Green', 'Brown', 'Yellow', 'Cyan', 'Blue', 'Orange', 'Pink']
i = 0
#2 columns, so number of rows is total /2
row_index = 0
row_list = []
row = []
for col in col_list[1:]: #skip the date column
# create a new plot
s1 = figure(x_axis_type = 'datetime', width=width, plot_height=height, title=col + ' trend')
#seasonal decompae to extract seasonal trends
decomposition = seasonal_decompose(np.array(df[col]), model='additive', freq=15)
s1.line(X, decomposition.trend, color=color_palette[i % len(color_palette)], alpha=0.5, line_width=2)
row.append(s1)
if len(row) == 2:
row_copy = copy.deepcopy(row)
row_list.append(row_copy)
row = []
i = 0
i += 1
# put all the plots in a grid layout
p = gridplot(row_list)
save(vplot(p), filename=filename, title='trends')
def get_plot(self, mode="v"):
if not (mode is 'v' or mode is 'h'):
raise MeteoStation.InvalidPlotArgument()
if mode is 'v':
return vplot(*self.figs)
else:
return hplot(*self.figs)
def bokeh2(X):
Y = de_mean_matrix(X)
TOOLS="resize,crosshair,pan,wheel_zoom,box_zoom,reset,previewsave,box_select"
hover = HoverTool(
tooltips=[
("index", "$index"),
("(x,y)", "($x, $y)"),
("desc", "@desc"),
]
)
bplt.output_file("data.html", title="Rescaling")
s1 = bplt.figure(width=500, plot_height=250, title="Data", tools=[hover, TOOLS])
s1.scatter(X[:,0].A1, X[:,1].A1, marker="circle",
line_color="#6666ee", fill_color="#ee6666",
fill_alpha=0.5, size=12)
s2 = bplt.figure(width=500, plot_height=250, title="De-meaned", tools=TOOLS)
s2.scatter(Y[:,0].A1, Y[:,1].A1, marker="circle",
line_color="#6666ee", fill_color="#ee6666",
fill_alpha=0.5, size=12)
# put all the plots in a VBox
p = bplt.vplot(s1, s2)
# show the results
bplt.show(p)
def notebook(*tunnels):
from bokeh.io import show
execs = dict()
if tunnels:
for tunnel in tunnels:
t_args = re.findall('([\'"]([^"\']+)["\'])|([^ ]+)', tunnel)
t_args = [a[-1] if a[-1] else a[-1] for a in t_args]
t_args = [a.strip(' ') for a in t_args]
execs['_'.join(t_args)] = make_ssh_subprocess(*t_args)
else:
execs['localhost'] = async_subprocess, Popen
_hplots = list()
monitors = list()
change_streams = list()
for ex in execs.values():
changes = ChangeStream(source_fun=update_notebook_source)
mon = RessourceMonitor(changes, async_exec=ex[0], normal_exec=ex[1])
plot_gen = BokehPlots(changes, async_exec=ex[0], normal_exec=ex[1])
_hplots.append(vplot(plot_gen.cpu_bars(False), plot_gen.gpu_bars(),
plot_gen.user_total_memusage()))
monitors.append(mon)
change_streams.append(changes)
plots = hplot(*_hplots)
show(plots)
loop = asyncio.get_event_loop()
loop.run_until_complete(asyncio.gather(
*(mon.gpus_mon(loop=loop) for mon in monitors),
*(mon.cpus_mon() for mon in monitors),
*(changes.start() for changes in change_streams)
))
def chart_results(self):
portfolios = self.db.get_all_portfolios()
portfolio_results = {
'portfolios': portfolios,
'overview' : {
'ytd' : self.average_performance('difference_ytd', portfolios),
'1year' : self.average_performance('difference_1year', portfolios)
}
}
portfolio_results['overview']['results_ytd'] = self.outperform(portfolio_results['overview']['ytd'])
portfolio_results['overview']['results_1year'] = self.outperform(portfolio_results['overview']['1year'])
num_points = len(portfolios)
pprint(num_points)
now = time.time()
dates =[]
moneyky_perf=[]
portfolio_perf=[]
#Form the lists
for each in portfolios:
dates.append(each['date'])
moneyky_perf.append(float(each['difference_ytd']))
portfolio_perf.append(float(each['difference_1year']))
TOOLS = "reset,save"
r = figure(x_axis_type = "datetime", tools=TOOLS, plot_width=800, plot_height=400)
r.line(dates, portfolio_perf, legend='Monkey ytd', color="firebrick", alpha=0.8, line_width=4)
r.line(dates, moneyky_perf, legend='Monkey 1 Year', color="navy", alpha=0.8, line_width=4)
r.title = "Moneyky vs Benchmark Performance"
r.grid.grid_line_alpha=100
return (vplot(r)), portfolio_results # return the plot
def get_plot(self, mode="v"): if not(mode is 'v' or mode is 'h'): raise MeteoStation.InvalidPlotArgument() if mode is 'v': return vplot(*self.figs) else: return hplot(*self.figs)
def __init__(self, addr=None, interval=1000.00, loop=None):
if addr is None:
scheduler = default_executor().scheduler
if isinstance(scheduler, rpc):
addr = (scheduler.ip, 9786)
elif isinstance(scheduler, Scheduler):
addr = ('127.0.0.1', scheduler.services['http'].port)
self.addr = addr
self.interval = interval
self.display_notebook = False
if is_kernel() and not curstate().notebook:
output_notebook()
assert curstate().notebook
self.task_source, self.task_table = task_table_plot()
self.worker_source, self.worker_table = worker_table_plot()
self.output = vplot(self.worker_table, self.task_table)
self.client = AsyncHTTPClient()
self.loop = loop or IOLoop.current()
self.loop.add_callback(self.update)
self._pc = PeriodicCallback(self.update, self.interval, io_loop=self.loop)
self._pc.start()
def main(options, args):
logger = log.get_logger("ginga", options=options)
# create a new plot with default tools, using figure
fig = figure(x_range=[0,600], y_range=[0,600], plot_width=600, plot_height=600,
toolbar_location=None)
viewer = ib.CanvasView(logger)
viewer.set_figure(fig)
def load_file(path):
image = AstroImage(logger)
image.load_file(path)
viewer.set_image(image)
def load_file_cb(attr_name, old_val, new_val):
#print(attr_name, old_val, new_val)
load_file(new_val)
# add a entry widget and configure with the call back
dstdir = options.indir
path_w = TextInput(value=dstdir, title="File:")
path_w.on_change('value', load_file_cb)
if len(args) > 0:
load_file(args[0])
# put the path widget and viewer in a layout and add to the document
curdoc().add_root(vplot(fig, path_w))
def visualize_data(data_output_file):
from bokeh.plotting import figure, output_file, save, vplot
from bokeh.models import ColumnDataSource, FactorRange
plots = []
# output to static HTML file
output_file(data_output_file, title='Eye Tracking Data', mode='cdn')
for file_name, file_data in data.iteritems():
# prepare the data
line_types = [line_data[0] for line_data in file_data]
#line_types_top = [line_data[0] + '2.0' for line_data in file_data]
#line_types_bot = [line_data[0] + '1.0' for line_data in file_data]
times = [line_data[1] for line_data in file_data]
start_times = [line_data[2] for line_data in file_data]
end_times = [line_data[3] for line_data in file_data]
descs = [line_data[4] for line_data in file_data]
#x0 = [0 for type_ in line_types]
'''source = ColumnDataSource({
'time': times,
'start': start_times,
'end': end_times,
'line_types_top': line_types_top,
'line_types_bot': line_types_bot,
})'''
source = ColumnDataSource({
'x': [(t1 + t2)/2 for t1, t2 in zip(start_times, end_times)],
'y': line_types,
'width': times,
'height': [0.7 for _ in line_types],
'fill_color': ['red' if 'Incorrect' in desc \
else 'green' for desc in descs]
})
# create a new plot
plot = figure(
tools='pan,reset,save',
title=file_name, y_range=FactorRange(factors=line_types[::-1]),
x_range=[0, sum(times)],
x_axis_label='Time (ms)', y_axis_label='Line Type'
)
plot.rect(x='x', y='y', width='width', height='height', \
fill_color='fill_color', source=source)
#plot.quad(left='start', right='end', \
# top='line_types_top', bottom='line_types_bot', source=source)
# add some renderers
#plot.segment(x0, line_types, times, line_types, \
# line_width=2, line_color="green")
plots.append(plot)
# show the results
save(vplot(*plots))
def make_interactive(plot):
plot = add_legend(plot)
for year in years:
fertility = fertility_df[year]
fertility.name = 'fertility'
life = life_expectancy_df[year]
life.name = 'life'
population = population_df_size[year]
population.name = 'population'
new_df = pd.concat([fertility, life, population, region_color], axis=1)
sources['_' + str(year)] = ColumnDataSource(new_df)
dictionary_of_sources = dict(zip([x for x in years], ['_%s' % x for x in years]))
js_source_array = str(dictionary_of_sources).replace("'", "")
# Add the slider
code = """
var year = slider.get('value'),
sources = %s,
new_source_data = sources[year].get('data');
renderer_source.set('data', new_source_data);
renderer_source.trigger('change');
text_source.set('data', {'year': [String(year)]});
text_source.trigger('change');
""" % js_source_array
callback = CustomJS(args=sources, code=code)
slider = Slider(start=years[0], end=years[-1], value=1, step=1, title="Year", callback=callback)
callback.args["slider"] = slider
callback.args["renderer_source"] = renderer_source
callback.args["text_source"] = text_source
return vplot(plot, slider)
def insertPlot(self, plotSets):
plotSets = [wrapper.plot for wrapper in plotSets]
layout = vplot( *plotSets )
# output_file("les_mis.html") ?????????????????
# show(layout)
for plot in plotSets:
plot.toolbar_location = None
return layout
def plot_summaries(output_directory, normalized_counts, chromosomes):
bp.output_file(output_directory + "/summary.html", mode="cdn")
plots = []
for chromosome in chromosomes:
plot = plot_summary(normalized_counts, chromosome)
if plot:
plots.append(plot)
bp.save(bp.vplot(*plots))
def plot_summaries(output_directory, normalized_counts, chromosomes):
bp.output_file(output_directory + "/summary.html", mode="cdn")
plots = []
for chromosome in chromosomes:
plot = plot_summary(normalized_counts, chromosome)
if plot:
plots.append(plot)
bp.save(bp.vplot(*plots))
def insertPlot(self, plotSets):
plotSets = [wrapper.plot for wrapper in plotSets]
layout = vplot(*plotSets)
# output_file("les_mis.html") ?????????????????
# show(layout)
for plot in plotSets:
plot.toolbar_location = None
return layout
def make_washmap_map_tools_linked_tabbed():
data = get_data_with_countries(wat_stats, san_stats)
source = ColumnDataSource(data)
source.selected = [30]
wat_map = construct_water_map_tools(source)
wat_text = construct_water_text(source)
wat_key = construct_key(WATER_COLOR_RANGE)
san_map = construct_san_map_tools(source)
san_text = construct_san_text(source)
san_key = construct_key(SANITATION_COLOR_RANGE)
tabs = Tabs(
tabs=[
Panel(title="Water", child=hplot(vplot(wat_map), vplot(wat_text, wat_key))),
Panel(title="Sanitation", child=hplot(vplot(san_map), vplot(san_text, san_key))),
]
)
return vplot(tabs)
def make_washmap_map_tools_linked_tabbed():
data = get_data_with_countries(wat_stats, san_stats)
source = ColumnDataSource(data)
source.selected = [30]
wat_map = construct_water_map_tools(source)
wat_text = construct_water_text(source)
wat_key = construct_key(WATER_COLOR_RANGE)
san_map = construct_san_map_tools(source)
san_text = construct_san_text(source)
san_key = construct_key(SANITATION_COLOR_RANGE)
tabs = Tabs(tabs=[
Panel(title="Water",
child=hplot(vplot(wat_map), vplot(wat_text, wat_key))),
Panel(title="Sanitation",
child=hplot(vplot(san_map), vplot(san_text, san_key)))
])
return vplot(tabs)
def create_simple_layout(obj):
# TODO: Seems that DateRangeSlider is broken on latest release. It'd be
# nice to add it when issue is fixed
# start = datetime.date(2010, 1, 1)#'2010-01-01'
# end = datetime.date(2015, 1, 1)#'2015-01-01'
# obj.dr = DateRangeSlider(
# title="Period:", name="period", value=(start, end),
# bounds=(start, end), range=(dict(days=1), None)
# )
# Get the widget for all available plugins and add them
interval_plugins = {pl.name: getattr(obj, pl.name)
for pl in obj._interval_plugins}
names = dict(
js_list_of_sources=str({k: k for k in interval_plugins.keys()}).replace("'", "")
)
code = callbacks.window_selector % names
objs = dict(interval_plugins)
callback = Callback(args=objs, code=code)
obj.window_selector.callback = callback
callback.args['interval_selector'] = obj.window_selector
# configure button to open pump and dump detection (Poulson Algorithm)
code = callbacks.btn_detect_pumps % names
callback = Callback(args=objs, code=code)
obj.btn_detect_pumps.callback = callback
main_view = plotting.hplot(
plotting.vplot(
obj.ts_filters_plot,
obj.main_plot,
# obj.cp_plot,
# obj.trends_plot
),
)
# add spams table to spams tab
obj.spam_tab.child = plotting.hplot(obj.spam_table)
# create
obj.vpeaks = plotting.vplot(obj.PEAKS)
obj.children = [plotting.vplot(
main_view,
)]
def acc_loss_visual(history, result_path, script_name, file_time_global):
"""
Plot accuracy and loss
"""
acc_arr = np.array(history['acc'], dtype=float)
loss_arr = np.array(history['loss'], dtype=float)
val_acc_arr = np.array(history['val_acc'], dtype=float)
val_loss_arr = np.array(history['val_loss'], dtype=float)
output_file(
os.path.join(
result_path,
"legends_" + script_name + "_" + file_time_global + ".html"))
p1 = figure()
p1.title = "Training and Cross validation accuracy"
p1.xaxis.axis_label = 'Iterations'
p1.yaxis.axis_label = 'Accuracy'
p1.circle(range(0, len(acc_arr)),
acc_arr,
color="green",
legend="Train_Acc")
p1.line(range(0, len(acc_arr)),
acc_arr,
line_color="green",
legend="Train_Acc")
p1.circle(range(0, len(val_acc_arr)),
val_acc_arr,
color="orange",
legend="Val_Acc")
p1.line(range(0, len(val_acc_arr)),
val_acc_arr,
line_color="orange",
legend="Val_Acc")
p2 = figure()
p2.title = "Training and Cross validation loss_error"
p2.xaxis.axis_label = 'Iterations'
p2.yaxis.axis_label = 'Loss_error'
p2.circle(range(0, len(loss_arr)),
loss_arr,
color="green",
legend="Train_loss")
p2.line(range(0, len(loss_arr)),
loss_arr,
line_color="green",
legend="Train_loss")
p2.circle(range(0, len(val_loss_arr)),
val_loss_arr,
color="orange",
legend="Val_loss")
p2.line(range(0, len(val_loss_arr)),
val_loss_arr,
line_color="orange",
legend="Val_loss")
p = vplot(p1, p2)
show(p)
def create_layout(obj):
# Get the widget for all available plugins and add them
interval_plugins = {pl.name: getattr(obj, pl.name)
for pl in obj._interval_plugins}
names = dict(
js_list_of_sources=str({k: k for k in interval_plugins.keys()}).replace("'", "")
)
code = callbacks.window_selector % names
objs = dict(interval_plugins)
callback = Callback(args=objs, code=code)
obj.window_selector.callback = callback
callback.args['interval_selector'] = obj.window_selector
# configure button to open pump and dump detection (Poulson Algorithm)
code = callbacks.btn_detect_pumps % names
callback = Callback(args=objs, code=code)
obj.btn_detect_pumps.callback = callback
# add all elements of the main dashboard
main_view = plotting.hplot(
plotting.vplot(
obj.ts_filters_plot, obj.main_plot,
),
)
# add spams table to spams tab
obj.spam_tab.child = plotting.hplot(obj.spam_table)
# create
obj.vpeaks = plotting.vplot(obj.PEAKS)
# vsteinberg = plotting.vplot(obj.TICKS_IN_ROW)
obj.children = [plotting.vplot(
# obj.symbol,
# obj.tabs,
main_view,
# vpeaks, # add peaks plugin dialog view
# vsteinberg,
# obj.dialog_loading,
)]
def pages_timeseries(response):
parse_datetime = lambda x: datetime.datetime.strptime(x, "%Y-%m-%dT%H:%M:%S.%f")
parsed_dates = [parse_datetime(x[1]) for x in response]
dates = sorted(parsed_dates)
plot = figure(plot_width=584, x_axis_type="datetime", x_axis_label="Dates",
y_axis_label="Number Fetched")
plot.line(x=dates, y=range(len(dates)))
button = Button(label="Press Me")
session = push_session(curdoc())
script = autoload_server(vplot(plot, button), session_id=session.id)
return script
def create_grph(lst, df, stock):
TOOLS = "pan,wheel_zoom,box_zoom,reset,save"
#Just figure out how to divide the graph to make it nicer
fig_list = []
if u'Closing' in lst:
output_file("./templates/stock.html", title=stock)
a = figure(x_axis_type="datetime", tools=TOOLS)
a.line(df['Date'],
df['Closing'],
color='#1F78B4',
legend='Closing Prices')
a.title = "%s Closing Prices" % (stock)
a.grid.grid_line_alpha = 0.3
fig_list.append('a')
if u'Adjusted' in lst:
output_file("./templates/stock.html", title=stock)
b = figure(x_axis_type="datetime", tools=TOOLS)
b.line(df['Date'],
df['Adj Closing'],
color='#FF0000',
legend='Adjusted Closing Prices')
b.title = "%s Adjusted Closing Prices" % (stock)
b.grid.grid_line_alpha = 0.3
fig_list.append('b')
if u'Volume' in lst:
output_file("./templates/stock.html", title=stock)
c = figure(x_axis_type="datetime", tools=TOOLS)
c.line(df['Date'], df['Volume'], color='#228B22', legend='Volumes')
c.title = "%s Volumes" % (stock)
c.grid.grid_line_alpha = 0.3
fig_list.append('c')
if 'a' in fig_list and 'b' in fig_list and 'c' in fig_list:
p = vplot(hplot(a, b), c)
elif 'a' in fig_list and 'b' in fig_list:
p = hplot(a, b)
elif 'a' in fig_list and 'c' in fig_list:
p = hplot(a, c)
elif 'b' in fig_list and 'c' in fig_list:
p = hplot(b, c)
elif 'a' in fig_list:
p = a
elif 'b' in fig_list:
p = b
elif 'c' in fig_list:
p = c
save(p)
return None
def gpu_bars(self, vertical=True, **kwargs):
gpus = sorted(RessourceMonitor.gpus_comb(subproc_exec=self.normal_exec),
key=itemgetter(0))
devices, free_mems, loads = tuple(zip(*gpus))
max_free = max(free_mems) * 1.5
source = ColumnDataSource(self._bar_source(devices,
('free', list(free_mems)),
('load', list(loads))))
def waiter():
change = yield GPUComb
while not self.terminated:
self._drop_in(source.data, 'load', change.dev, change.load)
self._drop_in(source.data, 'free', change.dev, change.free)
change = yield source
self.change_consumer.register_waiter(waiter())
name_range = FactorRange(factors=source.data['name'])
def makefig(name_range, val_range, val_name, title, ylabel):
kwargs['x_range'] = name_range
kwargs['y_range'] = val_range
kwargs['x_axis_label'] = 'device'
kwargs['y_axis_label'] = ylabel
if not vertical:
self._swapaxes(kwargs)
return figure(**kwargs, tools=[], title=title)
p1, p2 = (makefig(name_range, Range1d(0, 100), 'load', 'GPU load', '%'),
makefig(name_range, Range1d(0, max_free), 'free',
'GPU free memory', 'MiB'))
if vertical:
p = vplot(p1, p2)
p1.quad(left='name_low', right='name_high', top='load',
bottom='zeros', source=source)
p2.quad(left='name_low', right='name_high', top='free',
bottom='zeros', source=source)
else:
p = hplot(p1, p2)
p1.quad(left='zeros', right='load', top='name_high',
bottom='name_low', source=source)
p2.quad(left='zeros', right='free', top='name_high',
bottom='name_low', source=source)
p1.add_tools(HoverTool(tooltips=[('load', "@load")]))
p2.add_tools(HoverTool(tooltips=[('free', "@free")]))
return p
def main():
# Parse command line arguments
parser = argparse.ArgumentParser()
parser.add_argument('--counts', '-c', required=True)
parser.add_argument('--prefix', '-p')
parser.add_argument('--title', '-t')
parser.add_argument('--bins', '-b', type=int)
parser.add_argument('--y-label', '-y')
parser.add_argument('--x-label', '-x')
args = parser.parse_args()
if args.title:
title = args.title
else:
title = 'Generic Histogram'
if args.prefix:
output_filename = args.prefix + '.html'
else:
output_filename = 'histogram.html'
if args.bins:
bins = args.bins
else:
bins = 10 # Bokeh default
y_label = ""
if args.y_label:
y_label = args.y_label
x_label = ""
if args.x_label:
x_label = args.x_label
# Bokeh magic setup
output_file(output_filename)
fig = figure(title=title, tools="pan,wheel_zoom,save",
background_fill="#E8DDCB")
fig.left[0].formatter.use_scientific = False
fig.xaxis.axis_label = x_label
fig.yaxis.axis_label = y_label
# Read input file and save counts
counts = []
with open(args.counts, 'r') as countfile:
for line in countfile:
counts.append(int(line.strip()))
# Convert to numpy array, then to histogram, then show
np_counts = np.array(counts)
hist, edges = np.histogram(counts, bins=bins, density=False)
fig.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:],
fill_color="#036564", line_color="#033649",\
)
show(vplot(fig))
def make_plots():
data = pd.read_csv("static/running_data.csv", index_col=False)
time = [to_dt(x) for x in data.Time]
dt = max(time)
last_time = datetime.datetime(dt.year, dt.month, dt.day, dt.hour, dt.minute)
x_name = "date (last updated: " + str(last_time) +")"
acc = data.Accuracy
auc = data["ROC-AUC"]
tp = data["True pos."]
tn = data["True neg."]
fp = data["False pos."]
fn = data["False neg."]
# Accuracy and AUC
plot1 = figure(title='Model performance metrics',
x_axis_label=x_name,
x_axis_type='datetime',
y_axis_label='Score')
plot1.line(time, acc, color = 'black', legend='accuracy', line_width=3)
plot1.line(time, auc, color='blue', legend='ROC AUC', line_width=3)
plot1.line(time, tp, color='green', legend='True positive')
plot1.line(time, tn, color='green', legend='True negative',line_dash=[4, 4])
plot1.line(time, fp, color='red', legend='False positive')
plot1.line(time, fn, color='red', legend='False negative',line_dash=[4, 4])
plot1.legend.location = "bottom_left"
plot1.y_range = Range1d(0,1)
plot2 = figure(title='Model performance metrics',
x_axis_label=x_name,
x_axis_type='datetime',
y_axis_label='Score')
plot2.line(time, tp/(tp + fn), color='black',
legend='Sensitivity = true positive / actual positive',
line_width = 3)
plot2.line(time, tn/(fp + tn), color='blue',
legend='Specificity = true negative / actual negative',
line_width = 3)
plot2.legend.location = "bottom_left"
plot2.y_range = Range1d(0, 1)
# Combine the plots
p = vplot(plot1, plot2)
output_file("templates/runningscore.html")
save(p)
def main(options, args):
logger = log.get_logger("ginga", options=options)
TOOLS = "pan,wheel_zoom,box_select,tap"
# create a new plot with default tools, using figure
fig = figure(x_range=[0, 600],
y_range=[0, 600],
plot_width=600,
plot_height=600,
tools=TOOLS)
viewer = ib.CanvasView(logger)
viewer.set_figure(fig)
## box_select_tool = fig.select(dict(type=BoxSelectTool))
## box_select_tool.select_every_mousemove = True
#tap_tool = fig.select_one(TapTool).renderers = [cr]
# open a session to keep our local document in sync with server
session = push_session(curdoc())
#curdoc().add_periodic_callback(update, 50)
def load_file(path):
image = AstroImage(logger)
image.load_file(path)
viewer.set_image(image)
def load_file_cb(attr_name, old_val, new_val):
#print(attr_name, old_val, new_val)
load_file(new_val)
# add a entry widget and configure with the call back
dstdir = options.indir
path_w = TextInput(value=dstdir, title="File:")
path_w.on_change('value', load_file_cb)
curdoc().add_root(vplot(fig, path_w))
if len(args) > 0:
load_file(args[0])
# open the document in a browser
session.show()
# run forever
session.loop_until_closed()
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)
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)
def initPlotArea(self, style=None):
self.plotArea = figure(plot_width=100,
plot_height=100,
background_fill="#c1c1c1",
border_fill="#c1c1c1",
min_border=0)
self.plotArea.xaxis.visible = False
self.plotArea.yaxis.visible = False
self.plotArea.toolbar_location = None
self.scatter = self.plotArea.scatter([0], [0],
marker=style.lower(),
size=88)
self.html = vplot(self.plotArea)
self.drawSymbol(self.html)
return self.html
def build_plot():
global PLOTS
global NEW_PTS
args = request.args
color = colors[getitem(args, 'color', 'Black')]
_from = int(getitem(args, '_from', 0))
to = int(getitem(args, 'to', 10))
x = list(range(_from, to + 1))
model1 = get_forecast_data(model1_file)
model2 = get_forecast_data(model2_file)
for city in ['denver', 'ny', 'chicago', 'seattle', 'sf']:
for cartype in ['uberX', 'uberXL', 'uberBLACK', 'uberSUV']:
p, ds = create_plots(model1, model2, city, cartype)
PLOTS.append(p)
NEW_PTS.append((city, cartype, ds))
ps = vplot(PLOTS[0])
def symbol_val(self, color=None, size=None, outLine=None, visible=None):
symbol = self.scatter.glyph
if color:
symbol.fill_color = color
if size is not None:
symbol.size = size
# if outLine:
# self.symbol_outLine(**outLine)
if visible is not None:
symbol.visible = visible
# self.val.update({'color' : symbol.fill_color})
# self.val.update({'size' : symbol.size})
# # self.val.update({'outLine' : self.outLine})
# self.val.update({'visible' : symbol.visible})
# return self.val
self.html = vplot(self.plotArea)
self.drawSymbol(self.html)
return self.html
def bokeh2(X):
Y = de_mean_matrix(X)
TOOLS = "resize,crosshair,pan,wheel_zoom,box_zoom,reset,previewsave,box_select"
hover = HoverTool(tooltips=[
("index", "$index"),
("(x,y)", "($x, $y)"),
("desc", "@desc"),
])
bplt.output_file("data.html", title="Rescaling")
s1 = bplt.figure(width=500,
plot_height=250,
title="Data",
tools=[hover, TOOLS])
s1.scatter(X[:, 0].A1,
X[:, 1].A1,
marker="circle",
line_color="#6666ee",
fill_color="#ee6666",
fill_alpha=0.5,
size=12)
s2 = bplt.figure(width=500,
plot_height=250,
title="De-meaned",
tools=TOOLS)
s2.scatter(Y[:, 0].A1,
Y[:, 1].A1,
marker="circle",
line_color="#6666ee",
fill_color="#ee6666",
fill_alpha=0.5,
size=12)
# put all the plots in a VBox
p = bplt.vplot(s1, s2)
# show the results
bplt.show(p)
def plot_multi_test():
nelem = 100
samples = np.squeeze(
np.dstack([np.random.normal(size=nelem),
np.random.normal(size=nelem)]))
bwlist = [approx_bandwidth(samples[:, k]) for k in range(samples.shape[1])]
bandwidths = np.array(bwlist)
support = build_support_nd(samples, bandwidths)
pdf = np.zeros(support.shape[0], dtype=np.float64)
print('bandwidths', bandwidths)
print('support', support.shape)
print('samples', samples.shape)
multi_kde_seq(support, samples, bandwidths, pdf)
kde = sm.nonparametric.KDEMultivariate(samples, var_type='cc', bw=bwlist)
expect_pdf = kde.pdf(support)
# Plotting
output_file("kde_multi.html")
cm = RGBColorMapper(0, 1, palettes.Spectral11)
p1 = figure(title="KDE")
p1.square(support[:, 0],
support[:, 1],
size=5,
color=cm.color(pdf / np.ptp(pdf)))
p2 = figure(title="KDE-SM")
p2.square(support[:, 0],
support[:, 1],
size=5,
color=cm.color(expect_pdf / np.ptp(expect_pdf)))
show(vplot(p1, p2))
def worker_table_plot(width=600, height="auto", **kwargs):
""" Column data source and plot for host table """
names = [
'workers', 'cpu', 'memory-percent', 'memory', 'cores', 'processes',
'processing', 'latency', 'last-seen', 'disk-read', 'disk-write',
'network-send', 'network-recv'
]
source = ColumnDataSource({k: [] for k in names})
columns = {name: TableColumn(field=name, title=name) for name in names}
slow_names = [
'workers', 'cores', 'processes', 'memory', 'latency', 'last-seen'
]
slow = DataTable(source=source,
columns=[columns[n] for n in slow_names],
width=width,
height=height,
**kwargs)
slow.columns[3].formatter = NumberFormatter(format='0.0 b')
slow.columns[4].formatter = NumberFormatter(format='0.00000')
slow.columns[5].formatter = NumberFormatter(format='0.000')
fast_names = [
'workers', 'cpu', 'memory-percent', 'processing', 'disk-read',
'disk-write', 'network-send', 'network-recv'
]
fast = DataTable(source=source,
columns=[columns[n] for n in fast_names],
width=width,
height=height,
**kwargs)
fast.columns[1].formatter = NumberFormatter(format='0.0 %')
fast.columns[2].formatter = NumberFormatter(format='0.0 %')
fast.columns[4].formatter = NumberFormatter(format='0 b')
fast.columns[5].formatter = NumberFormatter(format='0 b')
fast.columns[6].formatter = NumberFormatter(format='0 b')
fast.columns[7].formatter = NumberFormatter(format='0 b')
table = vplot(slow, fast)
return source, table
def worker_table_plot(width=600, height=100, **kwargs):
""" Column data source and plot for host table """
names = ['workers', 'cpu', 'memory-percent', 'memory', 'cores', 'processes',
'processing', 'latency', 'last-seen', 'disk-read', 'disk-write',
'network-send', 'network-recv']
source = ColumnDataSource({k: [] for k in names})
columns = {name: TableColumn(field=name, title=name) for name in names}
slow_names = ['workers', 'cores', 'processes', 'memory',
'latency', 'last-seen']
slow = DataTable(source=source, columns=[columns[n] for n in slow_names],
width=width, height=height, **kwargs)
fast_names = ['workers', 'cpu', 'memory-percent', 'processing',
'disk-read', 'disk-write', 'network-send', 'network-recv']
fast = DataTable(source=source, columns=[columns[n] for n in fast_names],
width=width, height=height, **kwargs)
table = vplot(slow, fast)
return source, table
def make_interactive(plot):
plot = add_legend(plot)
for year in years:
fertility = fertility_df[year]
fertility.name = 'fertility'
life = life_expectancy_df[year]
life.name = 'life'
population = population_df_size[year]
population.name = 'population'
new_df = pd.concat([fertility, life, population, region_color], axis=1)
sources['_' + str(year)] = ColumnDataSource(new_df)
dictionary_of_sources = dict(
zip([x for x in years], ['_%s' % x for x in years]))
js_source_array = str(dictionary_of_sources).replace("'", "")
# Add the slider
code = """
var year = slider.get('value'),
sources = %s,
new_source_data = sources[year].get('data');
renderer_source.set('data', new_source_data);
renderer_source.trigger('change');
text_source.set('data', {'year': [String(year)]});
text_source.trigger('change');
""" % js_source_array
callback = CustomJS(args=sources, code=code)
slider = Slider(start=years[0],
end=years[-1],
value=1,
step=1,
title="Year",
callback=callback)
callback.args["slider"] = slider
callback.args["renderer_source"] = renderer_source
callback.args["text_source"] = text_source
return vplot(plot, slider)
def setScatterSymbol(self, val="Circle"):
models = bokeh.models.glyphs
changeVal = self.scatter.glyph.changed_properties_with_values()
glyph = {
"Circle": models.Circle(**changeVal),
"CircleX": models.CircleX(**changeVal),
"Cross": models.Cross(**changeVal),
"Diamond": models.Diamond(**changeVal),
"DiamondCross": models.DiamondCross(**changeVal),
"Square": models.Square(**changeVal),
"SquareX": models.SquareX(**changeVal),
"InvertedTriangle": models.InvertedTriangle(**changeVal),
"Triangle": models.Triangle(**changeVal),
"X": models.X(**changeVal),
"Asterisk": models.Asterisk(**changeVal)
}
self.scatter.set(glyph=glyph[val])
self.html = vplot(self.plotArea)
self.drawSymbol(self.html)
return self.html
def plot_uni_test():
samples = mixture_rvs([.25, .75],
size=10000,
dist=[stats.norm, stats.norm],
kwargs=(dict(loc=-1, scale=.5), dict(loc=1,
scale=.5)))
bandwidth = approx_bandwidth(samples)
print('bandwidth', bandwidth)
print('size', samples.size)
support = build_support(samples, bandwidth)
pdf = np.zeros_like(support)
uni_kde_seq(support, samples, bandwidth, pdf)
# Plotting
output_file("kde.html")
p1 = figure(title="Hist")
hist, edges = np.histogram(samples, bins=50, density=True)
p1.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:])
p2 = figure(title="KDE")
p2.line(support, pdf)
p2.circle(x=support, y=pdf, size=5)
p3 = figure(title="KDE-SM")
kde = sm.nonparametric.KDEUnivariate(samples)
kde.fit(kernel="gau")
p3.line(kde.support, kde.density)
print(samples.size)
print(len(kde.support), len(kde.density))
print(kde.density.sum())
show(vplot(p1, p2, p3))
def index():
# Create layout
c_map = climate_map()
ts = timeseries()
l = legend()
t = title()
map_legend = hplot(c_map, l)
layout = vplot(t, map_legend, ts)
plot_resources = RESOURCES.render(
js_raw=INLINE.js_raw,
css_raw=INLINE.css_raw,
js_files=INLINE.js_files,
css_files=INLINE.css_files,
)
script, div = components(layout, INLINE)
html = flask.render_template(
'embed.html',
plot_script=script,
plot_div=div,
plot_resources=plot_resources,
)
return encode_utf8(html)
# Read counts into a list
barcode_counts = []
with open(sys.argv[1], 'r') as counts:
for line in counts:
barcode_counts.append(int(line.strip()))
output_file('histogram.html')
p1 = figure(title="Barcode Read Counts",
tools="save,box_zoom,pan,ywheel_zoom",
background_fill="#E8DDCB")
barcode_counts = np.array(barcode_counts)
# TODO manually set bins
hist, edges = np.histogram(barcode_counts,
density=False,
bins=[
0, 100, 200, 300, 400, 500, 600, 700, 800, 900,
1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500,
5000, 7500, 10000
])
p1.quad(top=hist, bottom=0, left=edges[:-1], right=edges[1:],
fill_color="#036564", line_color="#033649",\
)
p1.xaxis.axis_label = 'Number of Reads'
p1.yaxis.axis_label = 'Barcode Count'
show(vplot(p1))
def gpu_bars(self, vertical=True, **kwargs):
gpus = sorted(
RessourceMonitor.gpus_comb(subproc_exec=self.normal_exec),
key=itemgetter(0))
devices, free_mems, loads = tuple(zip(*gpus))
max_free = max(free_mems) * 1.5
source = ColumnDataSource(
self._bar_source(devices, ('free', list(free_mems)),
('load', list(loads))))
def waiter():
change = yield GPUComb
while not self.terminated:
self._drop_in(source.data, 'load', change.dev, change.load)
self._drop_in(source.data, 'free', change.dev, change.free)
change = yield source
self.change_consumer.register_waiter(waiter())
name_range = FactorRange(factors=source.data['name'])
def makefig(name_range, val_range, val_name, title, ylabel):
kwargs['x_range'] = name_range
kwargs['y_range'] = val_range
kwargs['x_axis_label'] = 'device'
kwargs['y_axis_label'] = ylabel
if not vertical:
self._swapaxes(kwargs)
return figure(**kwargs, tools=[], title=title)
p1, p2 = (makefig(name_range, Range1d(0, 100), 'load', 'GPU load',
'%'),
makefig(name_range, Range1d(0, max_free), 'free',
'GPU free memory', 'MiB'))
if vertical:
p = vplot(p1, p2)
p1.quad(left='name_low',
right='name_high',
top='load',
bottom='zeros',
source=source)
p2.quad(left='name_low',
right='name_high',
top='free',
bottom='zeros',
source=source)
else:
p = hplot(p1, p2)
p1.quad(left='zeros',
right='load',
top='name_high',
bottom='name_low',
source=source)
p2.quad(left='zeros',
right='free',
top='name_high',
bottom='name_low',
source=source)
p1.add_tools(HoverTool(tooltips=[('load', "@load")]))
p2.add_tools(HoverTool(tooltips=[('free', "@free")]))
return p