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 __plot_control_chart(self, index):
plot_args = self.__conf.plot_args[index]
annotations = self.__conf.annotations[index]
if not annotations:
annotations = PlotAnnotationContainer()
plot = Figure(plot_height=500, plot_width=600,
x_range=FactorRange(factors=self.__factors,
name='x_factors'))
plot.toolbar.logo = None
plot.title.text = 'Control chart'
hover_tool = self.__create_tooltips()
plot.add_tools(hover_tool)
plot.xaxis.major_label_orientation = pi / 4
plot.xaxis.major_label_standoff = 10
if not self.__values['_calc_value'].empty:
if 'color' not in plot_args:
plot_args['color'] = 'navy'
if 'alpha' not in plot_args:
plot_args['alpha'] = 0.5
self.__values['s_fac'] = self.__factors
col_ds = ColumnDataSource(self.__values, name='control_data')
col_ds.js_on_change('data', CustomJS(code="refresh_maps();"))
plot.circle('s_fac', '_calc_value', source=col_ds, name='circle',
**plot_args)
plot.line('s_fac', '_calc_value', source=col_ds, name='line',
**plot_args)
min_anno, max_anno = annotations.calc_min_max_annotation(
self.__values['_calc_value'])
annotations.plot(plot, self.__values['_calc_value'])
anno_range = max_anno - min_anno
if anno_range and not isnan(anno_range):
plot.y_range.start = min_anno - anno_range
plot.y_range.end = max_anno + anno_range
return plot
def plot_light_curve_source(figure: Figure,
data_source: ColumnDataSource,
time_column_name: str = 'Time (BTJD)',
flux_column_name: str = 'Relative flux',
color_value_column_name: str = 'Time (BTJD)'):
"""
Plots the light curve data source on the passed figure.
:param figure: The figure to plot to.
:param data_source: The data source containing the light curve data.
:param time_column_name: The name of the time column whose values will be used on the x axis.
:param flux_column_name: The name of the flux column whose values will be used on the y axis.
:param color_value_column_name: The name of the column whose values will be used to determine data point color.
"""
mapper = LinearColorMapper(
palette='Plasma256',
low=np.min(data_source.data[color_value_column_name]),
high=np.max(data_source.data[color_value_column_name]))
colors = {'field': color_value_column_name, 'transform': mapper}
figure.circle(time_column_name,
flux_column_name,
source=data_source,
fill_color=colors,
fill_alpha=0.1,
line_color=colors,
line_alpha=0.4)
def qqnorm_viz(
actual_qs: np.ndarray,
theory_qs: np.ndarray,
col: str,
plot_width: int,
plot_height: int,
) -> Panel:
"""
Render a qq plot
"""
tooltips = [("x", "@x"), ("y", "@y")]
fig = Figure(
plot_width=plot_width,
plot_height=plot_height,
title=f"{col}",
tools="hover",
toolbar_location=None,
tooltips=tooltips,
)
fig.circle(
x=theory_qs,
y=actual_qs,
size=3,
color=PALETTE[0],
)
all_values = np.concatenate((theory_qs, actual_qs))
fig.line(
x=[np.min(all_values), np.max(all_values)],
y=[np.min(all_values), np.max(all_values)],
color="red",
)
tweak_figure(fig, "qq")
fig.xaxis.axis_label = "Normal Quantiles"
fig.yaxis.axis_label = f"Quantiles of {col}"
return Panel(child=fig, title="QQ normal plot")
def construct_figure(self, x, y, metric):
# workaround to format date in the hover tool at the moment bokeh
source = ColumnDataSource(data=dict(x=x, y=y, time=[e.strftime('%d %b %Y') for e in x]))
hover = HoverTool(
tooltips=[
("Date", "@time"),
("Return", "@y{0.0%}"),
]
)
# create a new plot with a a datetime axis type
p2 = Figure(x_axis_type="datetime", title=metric,toolbar_location="above",
tools=[hover, 'box_zoom, box_select, crosshair,resize, reset, save, wheel_zoom'])
# add renderers
p2.circle(x, y, size=8, color='black', alpha=0.2, legend=metric, source=source)
p2.line(x, y, color='navy', legend=metric, source=source)
# NEW: customize by setting attributes
# p2.title = metric
p2.legend.location = "top_left"
p2.grid.grid_line_alpha = 0
p2.xaxis.axis_label = 'Date'
p2.yaxis.axis_label = metric
p2.ygrid.band_fill_color = "olive"
p2.ygrid.band_fill_alpha = 0.1
p2.xaxis.formatter = DatetimeTickFormatter(formats={'days': ['%d %b'], 'months': ['%b %Y']})
p2.yaxis.formatter = NumeralTickFormatter(format="0.0%")
# format="0.0%"
return p2
def plot1():
# copy/pasted from Bokeh Getting Started Guide - used as an example
grouped = autompg.groupby("yr")
mpg = grouped.mpg
avg, std = mpg.mean(), mpg.std()
years = list(grouped.groups)
american = autompg[autompg["origin"] == 1]
japanese = autompg[autompg["origin"] == 3]
p = Figure(title="MPG by Year (Japan and US)")
p.vbar(x=years,
bottom=avg - std,
top=avg + std,
width=0.8,
fill_alpha=0.2,
line_color=None,
legend="MPG 1 stddev")
p.circle(x=japanese["yr"],
y=japanese["mpg"],
size=10,
alpha=0.5,
color="red",
legend="Japanese")
p.triangle(x=american["yr"],
y=american["mpg"],
size=10,
alpha=0.3,
color="blue",
legend="American")
p.legend.location = "top_left"
return json.dumps(json_item(p, "myplot"))
def create_figure():
xs, ys, colors, sizes = model.get_axes_values()
fig_args = dict(tools='pan', plot_height=600, plot_width=800)
if model.x_field in model.discrete_column_names and model.y_field in model.discrete_column_names:
figure = Figure(x_range=xs, y_range=ys, **fig_args)
figure.axis.major_label_orientation = math.pi / 4
elif model.x_field in model.discrete_column_names:
figure = Figure(x_range=xs, **fig_args)
figure.xaxis.major_label_orientation = math.pi / 4
elif model.y_field in model.discrete_column_names:
figure = Figure(y_range=ys, **fig_args)
figure.yaxis.major_label_orientation = math.pi / 4
else:
figure = Figure(**fig_args)
figure.circle(x=xs, y=ys, color=colors, size=sizes, line_color="white", alpha=0.8)
figure.toolbar_location = None
figure.xaxis.axis_label = model.x_field
figure.yaxis.axis_label = model.y_field
figure.background_fill_color = model.background_fill
figure.border_fill_color = model.background_fill
figure.axis.axis_line_color = "white"
figure.axis.axis_label_text_color = "white"
figure.axis.major_label_text_color = "white"
figure.axis.major_tick_line_color = "white"
figure.axis.minor_tick_line_color = "white"
figure.axis.minor_tick_line_color = "white"
figure.grid.grid_line_dash = [6, 4]
figure.grid.grid_line_alpha = .3
return figure
def plotnorm(data, circleinds=[], crossinds=[], edgeinds=[], url_path=None, fileroot=None,
tools="hover,tap,pan,box_select,wheel_zoom,reset", plot_width=450, plot_height=400):
""" Make a light-weight norm figure """
fields = ['zs', 'sizes', 'colors', 'abssnr', 'key', 'snrs']
if not circleinds: circleinds = range(len(data['snrs']))
source = ColumnDataSource(data = dict({(key, tuple([value[i] for i in circleinds if i not in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
norm = Figure(plot_width=plot_width, plot_height=plot_height, toolbar_location="left", x_axis_label='SNR observed',
y_axis_label='SNR expected', tools=tools, webgl=True)
norm.circle('abssnr', 'zs', size='sizes', line_color=None, fill_color='colors', fill_alpha=0.2, source=source)
if crossinds:
sourceneg = ColumnDataSource(data = dict({(key, tuple([value[i] for i in crossinds]))
for (key, value) in data.iteritems() if key in fields}))
norm.cross('abssnr', 'zs', size='sizes', line_color='colors', line_alpha=0.3, source=sourceneg)
if edgeinds:
sourceedge = ColumnDataSource(data = dict({(key, tuple([value[i] for i in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
norm.circle('abssnr', 'zs', size='sizes', line_color='colors', fill_color='colors', source=sourceedge, line_alpha=0.5, fill_alpha=0.2)
hover = norm.select(dict(type=HoverTool))
hover.tooltips = OrderedDict([('SNR', '@snrs'), ('key', '@key')])
if url_path and fileroot:
url = '{}/cands_{}[email protected]'.format(url_path, fileroot)
taptool = norm.select(type=TapTool)
taptool.callback = OpenURL(url=url)
return norm
def line_plot(ticker, alias, x_range=None):
p = Figure(
title=alias, x_range=x_range, x_axis_type='datetime',
plot_width=1000, plot_height=200, title_text_font_size="10pt",
tools="pan,wheel_zoom,box_select,reset"
)
p.circle('date', ticker, size=2, source=source, nonselection_alpha=0.02)
return p
def plot_lang(self, fig: Figure, lang: str, source: ColumnDataSource):
col = next(COLORS)
common_kw = {
"line_color": col,
"source": source,
"legend_label": f"{lang} Code Count",
}
fig.circle("x", "y", fill_color="white", size=8, **common_kw)
fig.line("x", "y", line_width=2, **common_kw)
def create_2d_plot(self) -> Figure:
fig = Figure(width=300, height=300, x_range=(-2, 2), y_range=(-2, 2))
fig.circle(x='x', y='y', color='color', source=self.data_source)
fig.segment(x0='x',
y0='y',
x1='xn',
y1='yn',
color='color',
line_dash='dotted',
source=self.data_source)
return fig
def Main():
parser = argparse.ArgumentParser()
parser.add_argument("-st", dest="stationId", nargs='*')
parser.add_argument("-ct", dest="cityName", nargs='*')
parser.add_argument("-pr", dest="percentage", nargs='*')
parser.add_argument("-tc1", dest="taskColor1", nargs='*')
args = parser.parse_args()
for i in range(len(args.stationId)):
Data, Date, Max, Min = prepareCSVData(args.cityName[i])
plotDate = Data['right']
source = ColumnDataSource(data=Data)
AverageTemp = []
for index in range(len(Min)):
Average = (Min[index] + Max[index]) / 2
AverageTemp.append(Average)
plot_graph = Figure(x_axis_type="datetime",
plot_width=1000,
title="2016 Daily Growing Degree Days- " +
args.cityName[i],
toolbar_location=None)
color = "#ADD8E6"
for j in range(len(args.percentage)):
minPer, MaxPer = getComputePercentage(Min, Max, args.percentage[j])
plot_graph.quad(top=MaxPer,
bottom=minPer,
left='left',
right='right',
source=source,
color=color,
legend="percentile " + str(args.percentage[j]) +
"-" + str(100 - int(args.percentage[j])))
color = "#D2B48C"
plot_graph.circle(Max,
Min,
alpha=0.9,
color="#0000FF",
fill_alpha=0.2,
size=10,
source=source,
legend='2016')
plot_graph.line(plotDate,
AverageTemp,
source=source,
line_color='Red',
line_width=0.5,
legend='Average')
plot_graph.xaxis.axis_label = "MONTHS"
plot_graph.yaxis.axis_label = "Daily Accumulation Celcius"
plot_graph.grid[0].ticker.desired_num_ticks = 12
output_file("./plots/secTask-1" + args.cityName[i] + ".html",
title="2016 Daily Growing Degree Days-(" +
args.cityName[i] + ")")
save(plot_graph)
def plot1():
# copy/pasted from Bokeh Getting Started Guide
x = linspace(-6, 6, 100)
y = cos(x)
p = Figure(width=500, height=500, toolbar_location="below",
title="Plot 1")
p.circle(x, y, size=7, color="firebrick", alpha=0.5)
# following above points:
# + pass plot object 'p' into json_item
# + wrap the result in json.dumps and return to frontend
return bokeh.embed.json_item(p, "myplot")
def create_fig(self, sources):
"""
Implementation of :meth:`LivePlot.create_fig` to set up the bokeh figure
"""
fig = Figure(background_fill_color= None,
toolbar_location = None,
x_range=[-100, 100], y_range=[-100, 100], tools="", **self._fig_args)
# Remove existing axes and grid
fig.xgrid.grid_line_color = None
fig.ygrid.grid_line_color = None
fig.axis.visible = False
# Draw circular grid
th = np.linspace(0, 360, 100)
# Draw visibility field
self.vis_horizon = 10
#fig.patch(*pol2rect([90 - self.vis_horizon]*len(th), th), color='lightgray')
fig.patch(*azel2rect(th, [self.vis_horizon]*len(th)), color='lightgray')
for r in [0, 20, 40, 60, 80]:
fig.line(*azel2rect(th, [r]*len(th)), line_dash='dashed')
for th in np.arange(0,360,45):
fig.line(*azel2rect([th,th], [0,90]), line_dash='dashed')
# Add grid labels
lx,ly = azel2rect([0, 90, 180, 270], [0]*4)
lx[1] -= 30
lx[2] -= 20
ly[0] -= 10
lx[0] -= 10
src_labels = ColumnDataSource(dict(
labels= ['N (0)', 'E (90)', 'S (180)', 'W (270)'],
label_x= lx,
label_y =ly))
fig.add_layout(LabelSet(x='label_x', y='label_y', text='labels', source=src_labels))
fig.line(source=sources['dpass'], x='x', y = 'y', line_width=2)
fig.circle(source=sources['ant_cmd'], x='x', y='y', size=20, fill_color=None)
fig.circle(source=sources['ant_cur'], x='x', y='y', size=10, color='green')
fig.circle(source=sources['sat'], x= 'x', y ='y', size=10, color= 'yellow')
return fig
class ScatterDiagram(Component):
def __init__(self, environment: Environment):
super().__init__()
self.environment = environment
self.data_source = ColumnDataSource(
data=dict(x_axis=[], y_axis=[], color=[]))
self.diagram = Figure(plot_width=400, plot_height=400)
self.x_axis_menu = Select(title="x axis",
value="radius",
options=list(BlobStatistics))
self.y_axis_menu = Select(title="y axis",
value="speed",
options=list(BlobStatistics))
self.color_menu = Select(title="colours",
value="time of birth",
options=list(BlobStatistics))
self.color_mapper = LinearColorMapper(palette='Cividis11')
self.color_bar = ColorBar(color_mapper=self.color_mapper,
location=(0, 0))
self.diagram.circle('x_axis',
'y_axis',
color={
'field': 'color',
'transform': self.color_mapper
},
source=self.data_source)
self.diagram.add_layout(self.color_bar, 'right')
self.component = column(
self.diagram,
row(self.x_axis_menu, self.y_axis_menu, self.color_menu))
def refresh(self):
self.data_source.data = {
'x_axis': [
BlobStatistics[self.x_axis_menu.value](organism,
self.environment)
for organism in self.environment.organisms.organism_list
],
'y_axis': [
BlobStatistics[self.y_axis_menu.value](organism,
self.environment)
for organism in self.environment.organisms.organism_list
],
'color': [
BlobStatistics[self.color_menu.value](organism,
self.environment)
for organism in self.environment.organisms.organism_list
]
}
def make_plot(source, AverageTemp, Parcentile_5_Min, Parcentile_5_Max,
Parcentile_25_Min, Parcentile_25_Max, MinTemp, MaxTemp, plotDate,
cityName):
plot = Figure(title='Optional Task # 1 : Growing Degree-day for ' +
cityName,
x_axis_type="datetime",
plot_width=1000,
title_text_font_size='12pt',
tools="",
toolbar_location=None)
colors = Blues4[0:3]
plot.circle(MaxTemp,
MinTemp,
alpha=0.9,
color="#66ff33",
fill_alpha=0.2,
size=10,
source=source,
legend='2015')
plot.quad(top=Parcentile_5_Max,
bottom=Parcentile_5_Min,
left='left',
right='right',
source=source,
color="#e67300",
legend="Percentile 5-95")
plot.quad(top=Parcentile_25_Max,
bottom=Parcentile_25_Min,
left='left',
right='right',
source=source,
color="#66ccff",
legend="percentile 25-75")
plot.line(plotDate,
AverageTemp,
source=source,
line_color='Red',
line_width=0.75,
legend='AverageTemp')
plot.border_fill_color = "whitesmoke"
plot.xaxis.axis_label = "Months"
plot.yaxis.axis_label = "Temperature (C)"
plot.axis.major_label_text_font_size = "10pt"
plot.axis.axis_label_text_font_size = "12pt"
plot.axis.axis_label_text_font_style = "bold"
plot.x_range = DataRange1d(range_padding=0.0, bounds=None)
plot.grid.grid_line_alpha = 0.3
plot.grid[0].ticker.desired_num_ticks = 12
return plot
def make_line(self):
'''
makes a bokeh line chart with markers
'''
p = Figure(x_axis_label=self.xlabel,
y_axis_label=self.ylabel,
title=self.title)
p.line(y='y', x='x', source=self.source_visible)
p.circle(y='y',
x='x',
source=self.source_visible,
size=4,
hover_fill_color='firebrick',
hover_line_color='white')
return p
def _add_nodes(G: nx.Graph,
plot: Figure) -> Union[ColumnDataSource, GlyphRenderer]:
"""Add nodes from G to the plot.
Args:
G (nx.Graph): Networkx graph.
plot (figure): Plot to add the nodes to.
Returns:
Union[ColumnDataSource, GlyphRenderer]: node source and glyphs.
"""
nodes_df = pd.DataFrame([G.nodes[u] for u in sorted(G.nodes())])
nodes_src = ColumnDataSource(data=nodes_df.to_dict(orient='list'))
nodes_glyph = plot.circle(x='x',
y='y',
size=NODE_SIZE,
level=NODE_LEVEL,
line_color='line_color',
fill_color='fill_color',
line_width='line_width',
nonselection_fill_alpha=1,
nonselection_line_alpha=1,
source=nodes_src)
return nodes_src, nodes_glyph
def init_plot(self):
x = fft.rfftfreq(self.CHUNK_SIZE) * self.SAMPLE_RATE
x_max = x[-1]
self.init_y = linspace(0, x_max, len(x))
y = self.init_y
source = ColumnDataSource(data=dict(x=x, y=y))
# TODO: range and size (toolbar), maybe could be user settings
plot = Figure(plot_height=400,
plot_width=800,
title="freq anal",
tools="crosshair,pan,reset,resize,save,wheel_zoom",
x_range=[0, x_max],
y_range=[0, 15])
rad = x_max / float(len(x))
data = plot.circle('x',
'y',
source=source,
line_color=None,
radius=rad)
self.data_source = data.data_source
# TODO: maybe not the best place
curdoc().add_root(plot)
def jwst_noise(result_dict, plot=True, output_file='noise.html'):
"""Plot background
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'noise.html'
Return
------
x : numpy array
micron
y : numpy array
1D noise (ppm)
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,reset,save" #saturation
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['error_w_floor'] * 1e6
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
ymed = np.median(y)
plot_noise_1d1 = Figure(
tools=TOOLS, #responsive=True,
x_axis_label='Wavelength (micron)',
y_axis_label='Error on Spectrum (PPM)',
title="Error Curve",
plot_width=800,
plot_height=300,
y_range=[0, 2.0 * ymed])
ymed = np.median(y)
plot_noise_1d1.circle(x, y, line_width=4, alpha=.7)
if plot:
outputfile(output_file)
show(plot_noise_1d1)
return x, y
def gen_fig(shape, source, tool=''):
'''function to generate either a circle or line graph'''
p = Figure(plot_width=500, plot_height=500,\
title='Selected - Sample by Wave', tools = [tool])
p.title_text_color = "CadetBlue"
p.title_text_font = "helvetica"
p.xaxis.axis_label = "Wave"
p.xaxis.axis_label_text_font_size = '9pt'
p.yaxis.axis_label = "Sample Size"
p.yaxis.axis_label_text_font_size = '9pt'
if shape == 'circle':
p.circle('Years', 'SampleSize', source=source,\
size=10, color="CadetBlue", alpha=0.5)
elif shape == 'line':
p.line('Years', 'SampleSize', source=source,\
line_width=3, color='CadetBlue',line_alpha=0.7)
return p
def plotstat(data, circleinds=None, crossinds=None, edgeinds=None, url_path=None, fileroot=None,
tools="hover,tap,pan,box_select,wheel_zoom,reset", plot_width=450, plot_height=400):
""" Make a light-weight stat figure """
fields = ['imkur', 'specstd', 'sizes', 'colors', 'snrs', 'key']
if not circleinds: circleinds = range(len(data['snrs']))
# set ranges
datalen = len(data['dm'])
inds = circleinds + crossinds + edgeinds
specstd = [data['specstd'][i] for i in inds]
specstd_min = min(specstd)
specstd_max = max(specstd)
imkur = [data['imkur'][i] for i in inds]
imkur_min = min(imkur)
imkur_max = max(imkur)
source = ColumnDataSource(data = dict({(key, tuple([value[i] for i in circleinds if i not in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
stat = Figure(plot_width=plot_width, plot_height=plot_height, toolbar_location="left", x_axis_label='Spectral std',
y_axis_label='Image kurtosis', x_range=(specstd_min, specstd_max),
y_range=(imkur_min, imkur_max), tools=tools, webgl=True)
stat.circle('specstd', 'imkur', size='sizes', line_color=None, fill_color='colors', fill_alpha=0.2, source=source)
if crossinds:
sourceneg = ColumnDataSource(data = dict({(key, tuple([value[i] for i in crossinds]))
for (key, value) in data.iteritems() if key in fields}))
stat.cross('specstd', 'imkur', size='sizes', line_color='colors', line_alpha=0.3, source=sourceneg)
if edgeinds:
sourceedge = ColumnDataSource(data = dict({(key, tuple([value[i] for i in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
stat.circle('specstd', 'imkur', size='sizes', line_color='colors', fill_color='colors', source=sourceedge, line_alpha=0.5, fill_alpha=0.2)
hover = stat.select(dict(type=HoverTool))
hover.tooltips = OrderedDict([('SNR', '@snrs'), ('key', '@key')])
if url_path and fileroot:
url = '{}/cands_{}[email protected]'.format(url_path, fileroot)
taptool = stat.select(type=TapTool)
taptool.callback = OpenURL(url=url)
return stat
def plotdmt(data, circleinds=[], crossinds=[], edgeinds=[], url_path=None, fileroot=None,
tools="hover,tap,pan,box_select,wheel_zoom,reset", plot_width=950, plot_height=500):
""" Make a light-weight dm-time figure """
fields = ['dm', 'time', 'sizes', 'colors', 'snrs', 'key']
if not circleinds: circleinds = range(len(data['snrs']))
# set ranges
datalen = len(data['dm'])
inds = circleinds + crossinds + edgeinds
dm = [data['dm'][i] for i in inds]
dm_min = min(min(dm), max(dm)/1.2)
dm_max = max(max(dm), min(dm)*1.2)
time = [data['time'][i] for i in inds]
time_min = min(time)
time_max = max(time)
source = ColumnDataSource(data = dict({(key, tuple([value[i] for i in circleinds if i not in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
dmt = Figure(plot_width=plot_width, plot_height=plot_height, toolbar_location="left", x_axis_label='Time (s; relative)',
y_axis_label='DM (pc/cm3)', x_range=(time_min, time_max), y_range=(dm_min, dm_max),
webgl=True, tools=tools)
dmt.circle('time', 'dm', size='sizes', fill_color='colors', line_color=None, fill_alpha=0.2, source=source)
if crossinds:
sourceneg = ColumnDataSource(data = dict({(key, tuple([value[i] for i in crossinds]))
for (key, value) in data.iteritems() if key in fields}))
dmt.cross('time', 'dm', size='sizes', fill_color='colors', line_alpha=0.3, source=sourceneg)
if edgeinds:
sourceedge = ColumnDataSource(data = dict({(key, tuple([value[i] for i in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
dmt.circle('time', 'dm', size='sizes', line_color='colors', fill_color='colors', line_alpha=0.5, fill_alpha=0.2, source=sourceedge)
hover = dmt.select(dict(type=HoverTool))
hover.tooltips = OrderedDict([('SNR', '@snrs'), ('key', '@key')])
if url_path and fileroot:
# url = '{}/cands_{}_sc@scan-seg@seg-i@candint-dm@[email protected]'.format(url_path, fileroot)
url = '{}/cands_{}[email protected]'.format(url_path, fileroot)
taptool = dmt.select(type=TapTool)
taptool.callback = OpenURL(url=url)
return dmt
def plotloc(data, circleinds=[], crossinds=[], edgeinds=[], url_path=None, fileroot=None,
tools="hover,tap,pan,box_select,wheel_zoom,reset", plot_width=450, plot_height=400):
""" Make a light-weight loc figure """
fields = ['l1', 'm1', 'sizes', 'colors', 'snrs', 'key']
if not circleinds: circleinds = range(len(data['snrs']))
# set ranges
datalen = len(data['dm'])
inds = circleinds + crossinds + edgeinds
l1 = [data['l1'][i] for i in inds]
l1_min = min(l1)
l1_max = max(l1)
m1 = [data['m1'][i] for i in inds]
m1_min = min(m1)
m1_max = max(m1)
source = ColumnDataSource(data = dict({(key, tuple([value[i] for i in circleinds if i not in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
loc = Figure(plot_width=plot_width, plot_height=plot_height, toolbar_location="left", x_axis_label='l1 (rad)', y_axis_label='m1 (rad)',
x_range=(l1_min, l1_max), y_range=(m1_min,m1_max), tools=tools, webgl=True)
loc.circle('l1', 'm1', size='sizes', line_color=None, fill_color='colors', fill_alpha=0.2, source=source)
if crossinds:
sourceneg = ColumnDataSource(data = dict({(key, tuple([value[i] for i in crossinds]))
for (key, value) in data.iteritems() if key in fields}))
loc.cross('l1', 'm1', size='sizes', line_color='colors', line_alpha=0.3, source=sourceneg)
if edgeinds:
sourceedge = ColumnDataSource(data = dict({(key, tuple([value[i] for i in edgeinds]))
for (key, value) in data.iteritems() if key in fields}))
loc.circle('l1', 'm1', size='sizes', line_color='colors', fill_color='colors', source=sourceedge, line_alpha=0.5, fill_alpha=0.2)
hover = loc.select(dict(type=HoverTool))
hover.tooltips = OrderedDict([('SNR', '@snrs'), ('key', '@key')])
if url_path and fileroot:
url = '{}/cands_{}[email protected]'.format(url_path, fileroot)
taptool = loc.select(type=TapTool)
taptool.callback = OpenURL(url=url)
return loc
def jwst_noise(result_dict, plot=True, output_file= 'noise.html'):
"""Plot background
Parameters
----------
result_dict : dict
Dictionary from pandexo output. If parameter space was run in run_pandexo
make sure to restructure the input as a list of dictionaries without they key words
that run_pandexo assigns.
plot : bool
(Optional) True renders plot, Flase does not. Default=True
output_file : str
(Optional) Default = 'noise.html'
Return
------
x : numpy array
micron
y : numpy array
1D noise (ppm)
See Also
--------
jwst_1d_spec, jwst_1d_bkg, jwst_1d_flux, jwst_1d_snr, jwst_2d_det, jwst_2d_sat
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save" #saturation
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['error_w_floor']*1e6
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
ymed = np.median(y)
plot_noise_1d1 = Figure(tools=TOOLS,#responsive=True,
x_axis_label='Wavelength (micron)',
y_axis_label='Error on Spectrum (PPM)', title="Error Curve",
plot_width=800, plot_height=300, y_range = [0,2.0*ymed])
ymed = np.median(y)
plot_noise_1d1.circle(x, y, line_width = 4, alpha = .7)
if plot:
outputfile(output_file)
show(plot_noise_1d1)
return x,y
def _replacement_plot(self, source):
start = self.now - datetime.timedelta(days=self.RECOATING_PERIOD)
start_timestamp = datetime.datetime(start.year, start.month, start.day, 0, 0, 0, 0).timestamp()
end_timestamp = datetime.datetime(self.now.year, self.now.month, self.now.day, 0, 0, 0, 0).timestamp()
x_range = DataRange1d(start=1000 * start_timestamp, end=1000 * end_timestamp)
y_range = DataRange1d(start=0, end=120)
plot = Figure(x_axis_type='datetime',
x_range=x_range,
y_range=y_range,
tools=['tap'],
toolbar_location=None)
# required recoated segments
plot.line(x=[start, self.now],
y=[0, 91],
legend='required recoated segments',
line_width=2,
line_color='blue')
# recoated segments
plot.line(x='ReplacementDate',
y='RecoatingsSinceYearStart',
source=source,
legend='recoated segments',
line_width=2,
color='orange')
plot.circle(x='ReplacementDate',
y='RecoatingsSinceYearStart',
source=source,
legend='recoated segments',
size=6,
color='orange')
date_format = '%d %b %Y'
formats = dict(hours=[date_format], days=[date_format], months=[date_format], years=[date_format])
plot.xaxis[0].formatter = DatetimeTickFormatter(formats=formats)
plot.legend.location = 'top_left'
plot.min_border_top = 20
plot.min_border_bottom = 30
return plot
def add_geom(fig: Figure, geom: BaseGeometry, **kwargs):
"""Add Shapely geom into Bokeh plot.
Args:
fig (Figure):
geom (BaseGeometry):
"""
if isinstance(geom, Point):
fig.circle(*geom.xy, **kwargs)
elif isinstance(geom, LineString):
fig.line(*geom.xy, **kwargs)
elif isinstance(geom, Polygon):
fig.patch(*geom.exterior.xy, **kwargs)
elif isinstance(geom, BaseMultipartGeometry):
for item in geom:
add_geom(fig, item, **kwargs)
else:
raise TypeError('Object geom {geom} no instance of {types}.'.format(
geom=geom, types=BaseGeometry))
def construct_best_odds_figure(self, x, y, z, t, trade_id, sticker):
# workaround to format date in the hover tool at the moment bokeh does not supported in the tool tips
source_back_odds = ColumnDataSource(data=dict(x=x, y=y, time=[e.strftime('%d-%m-%Y %H:%M:%S') for e in x]))
hover = HoverTool(
tooltips=[
("index", "$index"),
("x", "@time"),
("y", "@y"),
],
active=False
)
# create a new plot with a a datetime axis type
p2 = Figure(plot_width=1000, plot_height=600, title=sticker, toolbar_location="above", x_axis_type="datetime",
tools=[hover, 'box_zoom, box_select, crosshair, resize, reset, save, wheel_zoom'])
orders = self.map_trade_id_to_orders[trade_id, sticker]
for order in orders:
a = [order.placed_dt]
b = [order.price]
source_placed = ColumnDataSource(data=dict(a=a, b=b, time=[a[0].strftime('%d-%m-%Y %H:%M:%S')]))
p2.square(a, b, legend="placed", fill_color="red", line_color="red", size=8, source=source_placed)
p2.circle(x, y, size=8, color='navy', alpha=0.2, legend="best back odds", source=source_back_odds)
p2.line(x, y, color='navy', legend="best back odds", source=source_back_odds)
# lay odds
source_lay_odds = ColumnDataSource(data=dict(z=z, t=t, time=[e.strftime('%d-%m-%Y %H:%M:%S') for e in z]))
p2.triangle(z, t, size=8, color='green', alpha=0.2, legend="best lay odds", source=source_lay_odds)
p2.line(z, t, color='green', legend="best lay odds", source=source_lay_odds)
# NEW: customize by setting attributes
# p2.title = sticker
p2.legend.location = "top_left"
p2.grid.grid_line_alpha = 0
p2.xaxis.axis_label = 'Date'
p2.yaxis.axis_label = "Best odds"
p2.ygrid.band_fill_color = "olive"
p2.ygrid.band_fill_alpha = 0.1
return p2
def make_plot(source,AverageTemp,Parcentile_5_Min,Parcentile_5_Max,Parcentile_25_Min,Parcentile_25_Max,MinTemp,MaxTemp,plotDate,cityName):
plot = Figure(title='Optional Task # 1 : Growing Degree-day for '+cityName, x_axis_type="datetime", plot_width=1000, title_text_font_size='12pt', tools="", toolbar_location=None)
colors = Blues4[0:3]
plot.circle(MaxTemp,MinTemp, alpha=0.9, color="#66ff33", fill_alpha=0.2, size=10,source=source,legend ='2015')
plot.quad(top=Parcentile_5_Max, bottom=Parcentile_5_Min, left='left',right='right',
source=source,color="#e67300", legend="Percentile 5-95")
plot.quad(top=Parcentile_25_Max, bottom=Parcentile_25_Min,left='left',right='right',
source=source,color="#66ccff",legend="percentile 25-75")
plot.line(plotDate,AverageTemp,source=source,line_color='Red', line_width=0.75, legend='AverageTemp')
plot.border_fill_color = "whitesmoke"
plot.xaxis.axis_label = "Months"
plot.yaxis.axis_label = "Temperature (C)"
plot.axis.major_label_text_font_size = "10pt"
plot.axis.axis_label_text_font_size = "12pt"
plot.axis.axis_label_text_font_style = "bold"
plot.x_range = DataRange1d(range_padding=0.0, bounds=None)
plot.grid.grid_line_alpha = 0.3
plot.grid[0].ticker.desired_num_ticks = 12
return plot
def show_light_curve(self, light_curve_path: Path):
"""
Shows a figure of the light curve at the passed path.
:param light_curve_path: The path of the light curve.
"""
fluxes, times = self.load_fluxes_and_times_from_fits_file(
light_curve_path)
figure = Figure(title=str(light_curve_path),
x_axis_label='Flux',
y_axis_label='Time',
active_drag='box_zoom')
color = 'mediumblue'
figure.line(times, fluxes, line_color=color, line_alpha=0.1)
figure.circle(times,
fluxes,
line_color=color,
line_alpha=0.4,
fill_color=color,
fill_alpha=0.1)
figure.sizing_mode = 'stretch_width'
show(figure)
def make_plots(linesources, pointsources):
plots = []
i=0
for linesource, pointsource in zip(linesources, pointsources):
fig = Figure(title=None, toolbar_location=None, tools=[],
x_axis_type="datetime",
width=300, height=70)
fig.xaxis.visible = False
if i in [0, 9] :
fig.xaxis.visible = True
fig.height = 90
fig.yaxis.visible = False
fig.xgrid.visible = True
fig.ygrid.visible = False
fig.min_border_left = 10
fig.min_border_right = 10
fig.min_border_top = 5
fig.min_border_bottom = 5
if not i in [0, 9]:
fig.xaxis.major_label_text_font_size = "0pt"
#fig.yaxis.major_label_text_font_size = "0pt"
fig.xaxis.major_tick_line_color = None
fig.yaxis.major_tick_line_color = None
fig.xaxis.minor_tick_line_color = None
fig.yaxis.minor_tick_line_color = None
fig.background_fill_color = "whitesmoke"
fig.line(x='date', y="y", source=linesource)
fig.circle(x='date', y='y', size=5, source=pointsource)
fig.text(x='date', y='y', text='text', x_offset=5, y_offset=10, text_font_size='7pt', source=pointsource)
fig.title.align = 'left'
fig.title.text_font_style = 'normal'
plots.append(fig)
i+=1
return plots
def handle_submit(self):
filename_sentence_pairs = utils.get_sentences(self.text_input.value)
sentences = [pair[1] for pair in filename_sentence_pairs]
encodings = utils.get_encodings(sentences)
embedding = self.projector.fit_transform(encodings)
tooltip_sentences = []
for sentence in sentences:
index = sentence.lower().index(self.text_input.value)
subsentence = sentence[max(index-settings.TEXT_TOOLTIP_WINDOW_SIZE, 0):\
min(settings.TEXT_TOOLTIP_WINDOW_SIZE+index, len(sentence))]
if len(subsentence) < len(sentence):
subsentence = '...' + subsentence + '...'
tooltip_sentences.append(subsentence)
filename_to_color = dict()
for filename, _ in filename_sentence_pairs:
if filename not in filename_to_color:
filename_to_color[filename] = self.COLORS[len(
filename_to_color)]
color = [
filename_to_color[filename]
for filename, _ in filename_sentence_pairs
]
source = ColumnDataSource(data=dict(x=embedding[:, 0],
y=embedding[:, 1],
text=tooltip_sentences,
fill_color=color))
figure = Figure(tooltips=[('text', '@text')])
figure.circle('x',
'y',
fill_color='fill_color',
radius=0.05,
line_color=None,
source=source)
self.layout.children[-1] = column(figure, sizing_mode='stretch_both')
def plotCorrelation(res):
from bokeh.models import HoverTool,ColumnDataSource
from bokeh.plotting import Figure
width=600
height=600
plot = Figure(title='',title_text_font_size="11pt",
plot_width=width, plot_height=height,
x_axis_label='method1',y_axis_label='method2',
tools="pan, wheel_zoom, resize, hover, reset, save",
background_fill="#FAFAFA")
x=res['perc_x']
y=res['perc_y']
source = ColumnDataSource(data=dict(x=x,y=y, protein=res.locus_tag))
plot.circle(x,y, color='blue', line_color='gray',fill_alpha=0.5, size=10, source=source)
hover = plot.select(dict(type=HoverTool))
hover.tooltips = OrderedDict([
("binders1", "@x"),
("binders2", "@y"),
("protein", "@protein"),
])
js,html = embedPlot(plot)
return html
def create_figure():
xs, ys, colors, sizes = model.get_axes_values()
fig_args = dict(tools='pan', plot_height=600, plot_width=800)
if model.x_field in model.discrete_column_names and model.y_field in model.discrete_column_names:
figure = Figure(x_range=xs, y_range=ys, **fig_args)
figure.axis.major_label_orientation = math.pi / 4
elif model.x_field in model.discrete_column_names:
figure = Figure(x_range=xs, **fig_args)
figure.xaxis.major_label_orientation = math.pi / 4
elif model.y_field in model.discrete_column_names:
figure = Figure(y_range=ys, **fig_args)
figure.yaxis.major_label_orientation = math.pi / 4
else:
figure = Figure(**fig_args)
figure.circle(x=xs,
y=ys,
color=colors,
size=sizes,
line_color="white",
alpha=0.8)
figure.toolbar_location = None
figure.xaxis.axis_label = model.x_field
figure.yaxis.axis_label = model.y_field
figure.background_fill_color = model.background_fill
figure.border_fill_color = model.background_fill
figure.axis.axis_line_color = "white"
figure.axis.axis_label_text_color = "white"
figure.axis.major_label_text_color = "white"
figure.axis.major_tick_line_color = "white"
figure.axis.minor_tick_line_color = "white"
figure.axis.minor_tick_line_color = "white"
figure.grid.grid_line_dash = [6, 4]
figure.grid.grid_line_alpha = .3
return figure
def map():
x_range = (-10000000, -11000000)
y_range = (3500000, 5200000)
plot = Figure(
tools=TOOLS, title="Power Plant Locations", plot_width=1000, plot_height=500, x_range=x_range, y_range=y_range
)
plot.add_tile(STAMEN_TONER)
plot.axis.visible = False
plot.xgrid.grid_line_color = None
plot.ygrid.grid_line_color = None
m1 = plot.circle(x="lat", y="lon", source=source_map_bwr, size="size", fill_alpha=0, line_width=2, color="red")
m2 = plot.square(x="lat", y="lon", source=source_map_pwr, size="size", fill_alpha=0, line_width=2, color="red")
plot.select(dict(type=HoverTool)).tooltips = [("Plant Name", "@name"), ("Reactor and Containment", "@type")]
return plot
def init_plot(self):
x = fft.rfftfreq(self.CHUNK_SIZE)*self.SAMPLE_RATE
x_max = x[-1]
self.init_y = linspace(0, x_max, len(x))
y = self.init_y
source = ColumnDataSource(data=dict(x=x, y=y))
# TODO: range and size (toolbar), maybe could be user settings
plot = Figure(plot_height=400, plot_width=800, title="freq anal",
tools="crosshair,pan,reset,resize,save,wheel_zoom",
x_range=[0, x_max], y_range=[0, 15])
rad = x_max/float(len(x))
data = plot.circle('x', 'y', source=source, line_color=None, radius=rad)
self.data_source = data.data_source
# TODO: maybe not the best place
curdoc().add_root(plot)
# Create Column Data Source that will be used by the plot
source = ColumnDataSource(
data=dict(x=[], y=[], color=[], title=[], year=[], revenue=[]))
hover = HoverTool(tooltips=[("Title", "@title"), ("Year",
"@year"), ("$", "@revenue")])
p = Figure(plot_height=600,
plot_width=800,
title="",
toolbar_location=None,
tools=[hover])
p.circle(x="x",
y="y",
source=source,
size=7,
color="color",
line_color=None,
fill_alpha="alpha")
def select_movies():
genre_val = genre.value
director_val = director.value.strip()
cast_val = cast.value.strip()
selected = movies[(movies.Reviews >= reviews.value)
& (movies.BoxOffice >= (boxoffice.value * 1e6)) &
(movies.Year >= min_year.value) &
(movies.Year <= max_year.value) &
(movies.Oscars >= oscars.value)]
if (genre_val != "All"):
import pandas as pd
from bokeh.plotting import Figure, show, output_file, ColumnDataSource
from bokeh.models import HoverTool
df = pd.read_csv('mean_success_housing.csv')
df['success_metric'] = df['_c0']
print df.head()
source1 = ColumnDataSource(data=df)
hover1 = HoverTool(tooltips=[("zipcode","@zipcode"),
("success_metric","@success_metric")])
p = Figure(title='Mean Success by zip vs Housing Costs',
x_axis_label='$/sq. ft.',
y_axis_label='success_metric',
tools=['crosshair,resize,reset,save', hover1])
p.circle('2016_02', 'success_metric', color='red',alpha=0.4, source=source1)
output_file("mean_success_housing.html", title="Success vs Housing cost")
show(p)
def plot():
# FIGURES AND X-AXIS
fig1 = Figure(title = 'Dive Profile', plot_width = WIDTH, plot_height = HEIGHT, tools = TOOLS)
fig2 = Figure(title = 'Dive Controls', plot_width = WIDTH, plot_height = HEIGHT, tools = TOOLS, x_range=fig1.x_range)
fig3 = Figure(title = 'Attitude', plot_width = WIDTH, plot_height = HEIGHT, tools = TOOLS, x_range=fig1.x_range)
figs = gridplot([[fig1],[fig2],[fig3]])
# Formatting x-axis
timeticks = DatetimeTickFormatter(formats=dict(seconds =["%b%d %H:%M:%S"],
minutes =["%b%d %H:%M"],
hourmin =["%b%d %H:%M"],
hours =["%b%d %H:%M"],
days =["%b%d %H:%M"],
months=["%b%d %H:%M"],
years =["%b%d %H:%M %Y"]))
fig1.xaxis.formatter = timeticks
fig2.xaxis.formatter = timeticks
fig3.xaxis.formatter = timeticks
# removing gridlines
fig1.xgrid.grid_line_color = None
fig1.ygrid.grid_line_color = None
fig2.xgrid.grid_line_color = None
fig2.ygrid.grid_line_color = None
fig3.xgrid.grid_line_color = None
fig3.ygrid.grid_line_color = None
# INPUT WIDGETS
collection_list = CONN[DB].collection_names(include_system_collections=False)
gliders = sorted([platformID for platformID in collection_list if len(platformID)>2])
gliders = Select(title = 'PlatformID', value = gliders[0], options = gliders)
prev_glider = Button(label = '<')
next_glider = Button(label = '>')
glider_controlbox = HBox(children = [gliders, prev_glider, next_glider], height=80)
chunkations = Select(title = 'Chunkation', value = 'segment', options = ['segment', '24hr', '30days', '-ALL-'])
chunk_indicator = TextInput(title = 'index', value = '0')
prev_chunk = Button(label = '<')
next_chunk = Button(label = '>')
chunk_ID = PreText(height=80)
chunk_controlbox = HBox(chunkations,
HBox(chunk_indicator, width=25),
prev_chunk, next_chunk,
chunk_ID,
height = 80)
control_box = HBox(glider_controlbox,
chunk_controlbox)
# DATA VARS
deadby_date = ''
depth = ColumnDataSource(dict(x=[],y=[]))
vert_vel = ColumnDataSource(dict(x=[],y=[]))
mbpump = ColumnDataSource(dict(x=[],y=[]))
battpos = ColumnDataSource(dict(x=[],y=[]))
pitch = ColumnDataSource(dict(x=[],y=[]))
mfin = ColumnDataSource(dict(x=[],y=[]))
cfin = ColumnDataSource(dict(x=[],y=[]))
mroll = ColumnDataSource(dict(x=[],y=[]))
mheading = ColumnDataSource(dict(x=[],y=[]))
cheading = ColumnDataSource(dict(x=[],y=[]))
# AXIS setup
colors = COLORS[:]
fig1.y_range.flipped = True
fig1.yaxis.axis_label = 'm_depth (m)'
fig1.extra_y_ranges = {'vert_vel': Range1d(start=-50, end=50),
'dummy': Range1d(start=0, end=100)}
fig1.add_layout(place = 'right',
obj = LinearAxis(y_range_name = 'vert_vel',
axis_label = 'vertical velocity (cm/s)'))
fig1.add_layout(place = 'left',
obj = LinearAxis(y_range_name = 'dummy',
axis_label = ' '))
fig1.yaxis[1].visible = False
fig1.yaxis[1].axis_line_alpha = 0
fig1.yaxis[1].major_label_text_alpha = 0
fig1.yaxis[1].major_tick_line_alpha = 0
fig1.yaxis[1].minor_tick_line_alpha = 0
fig2.yaxis.axis_label = 'pitch (deg)'
fig2.y_range.start, fig2.y_range.end = -40,40
fig2.extra_y_ranges = {'battpos': Range1d(start=-1, end = 1),
'bpump': Range1d(start=-275, end=275)}
fig2.add_layout(place = 'right',
obj = LinearAxis(y_range_name = 'battpos',
axis_label = 'battpos (in)'))
fig2.add_layout(place = 'left',
obj = LinearAxis(y_range_name = 'bpump',
axis_label = 'bpump (cc)'))
fig2.yaxis[1].visible = False # necessary for spacing. later gets set to true
fig3.yaxis.axis_label = 'fin/roll (deg)'
fig3.y_range.start, fig3.y_range.end = -30, 30
fig3.extra_y_ranges = {'heading': Range1d(start=0, end=360), #TODO dynamic avg centering
'dummy': Range1d(start=0, end=100)}
fig3.add_layout(place = 'right',
obj = LinearAxis(y_range_name = 'heading',
axis_label = 'headings (deg)'))
fig3.add_layout(place = 'left',
obj = LinearAxis(y_range_name = 'dummy',
axis_label = ' '))
fig3.yaxis[1].visible = False
fig3.yaxis[1].axis_line_alpha = 0
fig3.yaxis[1].major_label_text_alpha = 0
fig3.yaxis[1].major_tick_line_alpha = 0
fig3.yaxis[1].minor_tick_line_alpha = 0
# PLOT OBJECTS
fig1.line( 'x', 'y', source = depth, legend = 'm_depth', color = 'red')
fig1.circle('x', 'y', source = depth, legend = 'm_depth', color = 'red')
fig1.line( 'x', 'y', source = vert_vel, legend = 'vert_vel', color = 'green', y_range_name = 'vert_vel')
fig1.circle('x', 'y', source = vert_vel, legend = 'vert_vel', color = 'green', y_range_name = 'vert_vel')
fig1.renderers.append(Span(location = 0, dimension = 'width', y_range_name = 'vert_vel',
line_color= 'green', line_dash='dashed', line_width=1))
fig2.line( 'x', 'y', source = pitch, legend = "m_pitch", color = 'indigo')
fig2.circle('x', 'y', source = pitch, legend = "m_pitch", color = 'indigo')
fig2.line( 'x', 'y', source = battpos, legend = 'm_battpos', color = 'magenta', y_range_name = 'battpos')
fig2.circle('x', 'y', source = battpos, legend = 'm_battpos', color = 'magenta', y_range_name = 'battpos')
fig2.line( 'x', 'y', source = mbpump, legend = "m_'bpump'", color = 'blue', y_range_name = 'bpump')
fig2.circle('x', 'y', source = mbpump, legend = "m_'bpump'", color = 'blue', y_range_name = 'bpump')
fig2.renderers.append(Span(location = 0, dimension = 'width',
line_color= 'black', line_dash='dashed', line_width=1))
fig3.line( 'x', 'y', source = mfin, legend = 'm_fin', color = 'cyan')
fig3.circle('x', 'y', source = mfin, legend = 'm_fin', color = 'cyan')
fig3.line( 'x', 'y', source = cfin, legend = 'c_fin', color = 'orange')
fig3.circle('x', 'y', source = cfin, legend = 'c_fin', color = 'orange')
fig3.line( 'x', 'y', source = mroll, legend = 'm_roll', color = 'magenta')
fig3.circle('x', 'y', source = mroll, legend = 'm_roll', color = 'magenta')
fig3.line( 'x', 'y', source = mheading, legend = 'm_heading', color = 'blue', y_range_name = 'heading')
fig3.circle('x', 'y', source = mheading, legend = 'm_heading', color = 'blue', y_range_name = 'heading')
fig3.line( 'x', 'y', source = cheading, legend = 'c_heading', color = 'indigo', y_range_name = 'heading')
fig3.circle('x', 'y', source = cheading, legend = 'c_heading', color = 'indigo', y_range_name = 'heading')
fig3.renderers.append(Span(location = 0, dimension = 'width', y_range_name = 'default',
line_color= 'black', line_dash='dashed', line_width=1))
# CALLBACK FUNCS
def update_data(attrib,old,new):
g = gliders.value
chnk = chunkations.value
chindex = abs(int(chunk_indicator.value))
depth.data = dict(x=[],y=[])
vert_vel.data = dict(x=[],y=[])
mbpump.data = dict(x=[],y=[])
battpos.data = dict(x=[],y=[])
pitch.data = dict(x=[],y=[])
mfin.data = dict(x=[],y=[])
cfin.data = dict(x=[],y=[])
mroll.data = dict(x=[],y=[])
mheading.data = dict(x=[],y=[])
cheading.data = dict(x=[],y=[])
depth.data,startend = load_sensor(g, 'm_depth', chnk, chindex)
if chnk == 'segment':
xbd = startend[2]
chunk_ID.text = '{} {} \n{} ({}) \nSTART: {} \nEND: {}'.format(g, xbd['mission'],
xbd['onboard_filename'], xbd['the8x3_filename'],
e2ts(xbd['start']), e2ts(xbd['end']))
if len(set(depth.data['x']))<=1 and attrib == 'chunk':
if old > new:
next_chunk.clicks += 1
else:
prev_chunk.clicks += 1
return
elif len(set(depth.data['x']))<=1 and chunk_indicator.value == 0:
chunk_indicator.value = 1
elif chnk in ['24hr', '30days']:
chunk_ID.text = '{} \nSTART: {} \nEND: {}'.format(g, e2ts(startend[0]), e2ts(startend[1]))
elif chnk == '-ALL-':
chunk_ID.text = '{} \nSTART: {} \nEND: {}'.format(g,e2ts(depth.data['x'][0] /1000),
e2ts(depth.data['x'][-1]/1000))
vert_vel.data = calc_vert_vel(depth.data)
mbpump.data,_ = load_sensor(g, 'm_de_oil_vol', chnk, chindex)
if len(mbpump.data['x']) > 1:
#for yax in fig2.select('mbpump'):
# yax.legend = 'm_de_oil_vol'
pass
else:
mbpump.data,_ = load_sensor(g, 'm_ballast_pumped', chnk, chindex)
#for yax in fig2.select('mbpump'):
# yax.legend = 'm_ballast_pumped'
battpos.data,_ = load_sensor(g, 'm_battpos', chnk, chindex)
pitch.data,_ = load_sensor(g, 'm_pitch', chnk, chindex)
pitch.data['y'] = [math.degrees(y) for y in pitch.data['y']]
mfin.data,_ = load_sensor(g, 'm_fin', chnk, chindex)
cfin.data,_ = load_sensor(g, 'c_fin', chnk, chindex)
mroll.data,_ = load_sensor(g, 'm_roll', chnk, chindex)
mheading.data,_ = load_sensor(g, 'm_heading', chnk, chindex)
cheading.data,_ = load_sensor(g, 'c_heading', chnk, chindex)
mfin.data['y'] = [math.degrees(y) for y in mfin.data['y']]
cfin.data['y'] = [math.degrees(y) for y in cfin.data['y']]
mheading.data['y'] = [math.degrees(y) for y in mheading.data['y']]
cheading.data['y'] = [math.degrees(y) for y in cheading.data['y']]
mroll.data['y'] = [math.degrees(y) for y in mroll.data['y']]
fig1.yaxis[1].visible = True
fig2.yaxis[1].visible = True
fig3.yaxis[1].visible = True
#GLIDER SELECTS
def glider_buttons(increment):
ops = gliders.options
new_index = ops.index(gliders.value) + increment
if new_index >= len(ops):
new_index = 0
elif new_index < 0:
new_index = len(ops)-1
gliders.value = ops[new_index]
chunkation_update(None, None, None) #reset chunk indicator and clicks
def next_glider_func():
glider_buttons(1)
def prev_glider_func():
glider_buttons(-1)
def update_glider(attrib,old,new):
chunk_indicator.value = '0'
#update_data(None,None,None)
gliders.on_change('value', update_glider)
next_glider.on_click(next_glider_func)
prev_glider.on_click(prev_glider_func)
#CHUNK SELECTS
def chunkation_update(attrib,old,new):
chunk_indicator.value = '0'
prev_chunk.clicks = 0
next_chunk.clicks = 0
update_data(None,None,None)
if new == '-ALL-':
chunk_indicator.value = '-'
def chunk_func():
chunkdiff = prev_chunk.clicks - next_chunk.clicks
if chunkdiff < 0:
prev_chunk.clicks = 0
next_chunk.clicks = 0
chunkdiff = 0
print (chunkdiff)
chunk_indicator.value = str(chunkdiff)
def chunk_indicator_update(attrib,old,new):
try:
if abs(int(old)-int(new))>1: #manual update, triggers new non-manual indicator update, ie else clause below
prev_chunk.clicks = int(new)
next_chunk.clicks = 0
else:
update_data('chunk',int(old),int(new))
print("UPDATE", old, new)
except Exception as e:
print(type(e),e, old, new)
chunkations.on_change('value', chunkation_update)
chunk_indicator.on_change('value', chunk_indicator_update)
next_chunk.on_click(chunk_func)
prev_chunk.on_click(chunk_func)
update_data(None,None,None)
return vplot(control_box, figs)
start=0.00, end=0.40, step=0.01)
x_axis = Select(title="X Axis", options=sorted(axis_map.keys()), value='Annual Income')
y_axis = Select(title='Y Axis', options=sorted(axis_map.keys()), value='Expected ROI')
# Create Column Data Source that will be used by the plot
source = ColumnDataSource(data=dict(x=[], y=[], color=[], title=[], year=[], revenue=[]))
hover = HoverTool(tooltips=[('Interest Rate', '@interest_rate%'),
('Payments / Income', '@payments_to_income%'),
('FICO', '@fico')
])
p = Figure(plot_height=600, plot_width=800, title='', toolbar_location=None, tools=[hover])
p.circle(x='x', y='y', source=source, size=7, color='blue', line_color=None, alpha=0.8)
# Remove scientific notation
yaxis = p.select(dict(type=Axis, layout='left'))[0]
yaxis.formatter.use_scientific = False
p.xaxis[0].formatter = yaxis.formatter
def select_notes():
"""
Filters the dataframe into notes that satisfy all constraints in web app
"""
selected = df[
(df.annual_inc >= min_income.value * 1000) &
(df.default_prob <= max_default.value) &
def correlation():
"the scatter plot"
args = flask.request.args
xattr = args.get("x", "atomic_number")
yattr = args.get("y", "covalent_radius_pyykko")
categ = args.get("categ", "name_series")
data = get_data()
properties = get_property_names(data)
categories = get_category_names()
fig = Figure(title="{} vs {}".format(properties[xattr], properties[yattr]),
plot_width=PLOT_WIDTH,
plot_height=PLOT_HEIGHT,
tools="box_zoom,pan,resize,save,reset",
toolbar_location="above",
toolbar_sticky=False,
)
fig.xaxis.axis_label = properties[xattr]
fig.yaxis.axis_label = properties[yattr]
ccm = get_color_mapper(categ, data)
if categ == "None":
legend = None
color_dict = "#1F77B4"
else:
legend = categ
color_dict = {"field": categ, "transform": ccm}
fig.circle(x=xattr, y=yattr, fill_alpha=0.7, size=10,
source=ColumnDataSource(data=data),
fill_color=color_dict,
line_color=color_dict,
legend=legend)
if categ != "None":
fig.legend.location = (0, 0)
fig.legend.plot = None
fig.add_layout(fig.legend[0], "right")
hover = HoverTool(tooltips=HOVER_TOOLTIPS)
fig.add_tools(hover)
script, div = components(fig)
js_resources = INLINE.render_js()
css_resources = INLINE.render_css()
html = render_template(
"correlations.html",
plot_script=script,
plot_div=div,
properties=properties,
categories=categories,
xselected=xattr,
yselected=yattr,
catselected=categ,
js_resources=js_resources,
css_resources=css_resources,
)
return encode_utf8(html)
from bokeh.io import curdoc
from bokeh.layouts import column, row
from bokeh.plotting import ColumnDataSource, Figure
from bokeh.models.widgets import Select, TextInput
def get_data(N):
return dict(x=random(size=N), y=random(size=N), r=random(size=N) * 0.03)
source = ColumnDataSource(data=get_data(200))
p = Figure(tools="", toolbar_location=None)
r = p.circle(x='x', y='y', radius='r', source=source,
color="navy", alpha=0.6, line_color="white")
COLORS = ["black", "firebrick", "navy", "olive", "goldenrod"]
select = Select(title="Color", value="navy", options=COLORS)
input = TextInput(title="Number of points", value="200")
def update_color(attrname, old, new):
r.glyph.fill_color = select.value
select.on_change('value', update_color)
def update_points(attrname, old, new):
N = int(input.value)
source.data = get_data(N)
input.on_change('value', update_points)
dataset_type = Select(title = "Dataset", value='movielens_1m', options = ['All', 'All MovieLens', 'movielens_1m', 'Last_FM', 'git'])
checkbox_button_group = CheckboxGroup(labels=labels, active = [0,1,2])
checkbox_button_group_content = CheckboxGroup(labels=c_labels, active = [0])
hover = HoverTool(tooltips=[
("Dataset","@dataset"),
("User Vector","@user_vector"),
("Content Vector", "@content_vector"),
("Algorithm", "@alg_type"),
("Num_preds", "@num_run")
])
p = Figure(plot_height=600, plot_width=800, title="", toolbar_location=None, tools=[hover])
p.circle(x="x", y="y", source=source, size=7, color="color", line_color=None)
def select_run():
num_preds_val = num_preds.value
alg_type_val = alg_type.value
dataset_val = dataset_type.value
selected = hermes_data
# selected = movies[
# (movies.Reviews >= reviews.value) &
# (movies.BoxOffice >= (boxoffice.value * 1e6)) &
# (movies.Year >= min_year.value) &
# (movies.Year <= max_year.value) &
# (movies.Oscars >= oscars.value)
# ]
if num_preds_val != 'All':
def create_component_jwst(result_dict):
"""Generate front end plots JWST
Function that is responsible for generating the front-end interactive plots for JWST.
Parameters
----------
result_dict : dict
the dictionary returned from a PandExo run
Returns
-------
tuple
A tuple containing `(script, div)`, where the `script` is the
front-end javascript required, and `div` is a dictionary of plot
objects.
"""
noccultations = result_dict['timing']['Number of Transits']
# select the tools we want
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
#Define units for x and y axis
punit = result_dict['input']['Primary/Secondary']
p=1.0
if punit == 'fp/f*': p = -1.0
else: punit = '('+punit+')^2'
if result_dict['input']['Calculation Type'] =='phase_spec':
x_axis_label='Time (secs)'
frac = 1.0
else:
x_axis_label='Wavelength [microns]'
frac = result_dict['timing']['Num Integrations Out of Transit']/result_dict['timing']['Num Integrations In Transit']
electrons_out = result_dict['RawData']['electrons_out']
electrons_in = result_dict['RawData']['electrons_in']
var_in = result_dict['RawData']['var_in']
var_out = result_dict['RawData']['var_out']
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['spectrum_w_rand']
err = result_dict['FinalSpectrum']['error_w_floor']
y_err = []
x_err = []
for px, py, yerr in zip(x, y, err):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
source = ColumnDataSource(data=dict(x=x, y=y, y_err=y_err, x_err=x_err, err=err,
electrons_out=electrons_out, electrons_in=electrons_in, var_in=var_in, var_out=var_out,
p=var_in*0+p,nocc=var_in*0+noccultations, frac = var_in*0+frac))
original = ColumnDataSource(data=dict(x=x, y=y, y_err=y_err, x_err=x_err, err=err, electrons_out=electrons_out, electrons_in=electrons_in, var_in=var_in, var_out=var_out))
ylims = [min(result_dict['OriginalInput']['model_spec'])- 0.1*min(result_dict['OriginalInput']['model_spec']),
0.1*max(result_dict['OriginalInput']['model_spec'])+max(result_dict['OriginalInput']['model_spec'])]
xlims = [min(result_dict['FinalSpectrum']['wave']), max(result_dict['FinalSpectrum']['wave'])]
plot_spectrum = Figure(plot_width=800, plot_height=300, x_range=xlims,
y_range=ylims, tools=TOOLS,#responsive=True,
x_axis_label=x_axis_label,
y_axis_label=punit,
title="Original Model with Observation")
plot_spectrum.line(result_dict['OriginalInput']['model_wave'],result_dict['OriginalInput']['model_spec'], color= "black", alpha = 0.5, line_width = 4)
plot_spectrum.circle('x', 'y', source=source, line_width=3, line_alpha=0.6)
plot_spectrum.multi_line('x_err', 'y_err', source=source)
callback = CustomJS(args=dict(source=source, original=original), code="""
// Grab some references to the data
var sdata = source.get('data');
var odata = original.get('data');
// Create copies of the original data, store them as the source data
sdata['x'] = odata['x'].slice(0);
sdata['y'] = odata['y'].slice(0);
sdata['y_err'] = odata['y_err'].slice(0);
sdata['x_err'] = odata['x_err'].slice(0);
sdata['err'] = odata['err'].slice(0);
sdata['electrons_out'] = odata['electrons_out'].slice(0);
sdata['electrons_in'] = odata['electrons_in'].slice(0);
sdata['var_in'] = odata['var_in'].slice(0);
sdata['var_out'] = odata['var_out'].slice(0);
// Create some variables referencing the source data
var x = sdata['x'];
var y = sdata['y'];
var y_err = sdata['y_err'];
var x_err = sdata['x_err'];
var err = sdata['err'];
var p = sdata['p'];
var frac = sdata['frac'];
var og_ntran = sdata['nocc'];
var electrons_out = sdata['electrons_out'];
var electrons_in = sdata['electrons_in'];
var var_in = sdata['var_in'];
var var_out = sdata['var_out'];
var f = wbin.get('value');
var ntran = ntran.get('value');
var wlength = Math.pow(10.0,f);
var ind = [];
ind.push(0);
var start = 0;
for (i = 0; i < x.length-1; i++) {
if (x[i+1] - x[start] >= wlength) {
ind.push(i+1);
start = i;
}
}
if (ind[ind.length-1] != x.length) {
ind.push(x.length);
}
var xout = [];
var foutout = [];
var finout = [];
var varinout = [];
var varoutout = [];
var xslice = [];
var foutslice = [];
var finslice = [];
var varoutslice = [];
var varinslice = [];
function add(a, b) {
return a+b;
}
for (i = 0; i < ind.length-1; i++) {
xslice = x.slice(ind[i],ind[i+1]);
foutslice = electrons_out.slice(ind[i],ind[i+1]);
finslice = electrons_in.slice(ind[i],ind[i+1]);
varinslice = var_in.slice(ind[i],ind[i+1]);
varoutslice = var_out.slice(ind[i],ind[i+1]);
xout.push(xslice.reduce(add, 0)/xslice.length);
foutout.push(foutslice.reduce(add, 0));
finout.push(finslice.reduce(add, 0));
varinout.push(varinslice.reduce(add, 0));
varoutout.push(varoutslice.reduce(add, 0));
xslice = [];
foutslice = [];
finslice = [];
varinslice = [];
varoutslice = [];
}
var new_err = 1.0;
var rand = 1.0;
for (i = 0; i < x.length; i++) {
new_err = Math.pow((frac[i]/foutout[i]),2)*varinout[i] + Math.pow((finout[i]*frac[i]/Math.pow(foutout[i],2)),2)*varoutout[i];
new_err = Math.sqrt(new_err)*Math.sqrt(og_ntran[i]/ntran);
rand = new_err*(Math.random()-Math.random());
y[i] = p[i]*((1.0 - frac[i]*finout[i]/foutout[i]) + rand);
x[i] = xout[i];
x_err[i][0] = xout[i];
x_err[i][1] = xout[i];
y_err[i][0] = y[i] + new_err;
y_err[i][1] = y[i] - new_err;
}
source.trigger('change');
""")
#var_tot = (frac/electrons_out)**2.0 * var_in + (electrons_in*frac/electrons_out**2.0)**2.0 * var_out
sliderWbin = Slider(title="binning", value=np.log10(x[1]-x[0]), start=np.log10(x[1]-x[0]), end=np.log10(max(x)/2.0), step= .05, callback=callback)
callback.args["wbin"] = sliderWbin
sliderTrans = Slider(title="Num Trans", value=noccultations, start=1, end=50, step= 1, callback=callback)
callback.args["ntran"] = sliderTrans
layout = column(row(sliderWbin,sliderTrans), plot_spectrum)
#out of transit 2d output
out = result_dict['PandeiaOutTrans']
# Flux 1d
x, y = out['1d']['extracted_flux']
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
plot_flux_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength [microns]',
y_axis_label='Flux (e/s)', title="Out of Transit Flux Rate",
plot_width=800, plot_height=300)
plot_flux_1d1.line(x, y, line_width = 4, alpha = .7)
tab1 = Panel(child=plot_flux_1d1, title="Total Flux")
# BG 1d
x, y = out['1d']['extracted_bg_only']
y = y[~np.isnan(y)]
x = x[~np.isnan(y)]
plot_bg_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength [microns]',
y_axis_label='Flux (e/s)', title="Background",
plot_width=800, plot_height=300)
plot_bg_1d1.line(x, y, line_width = 4, alpha = .7)
tab2 = Panel(child=plot_bg_1d1, title="Background Flux")
# SNR 1d accounting for number of occultations
x= out['1d']['sn'][0]
y = out['1d']['sn'][1]
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
y = y*np.sqrt(noccultations)
plot_snr_1d1 = Figure(tools=TOOLS,
x_axis_label=x_axis_label,
y_axis_label='SNR', title="Pandeia SNR",
plot_width=800, plot_height=300)
plot_snr_1d1.line(x, y, line_width = 4, alpha = .7)
tab3 = Panel(child=plot_snr_1d1, title="SNR")
# Error bars (ppm)
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['error_w_floor']*1e6
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
ymed = np.median(y)
plot_noise_1d1 = Figure(tools=TOOLS,#responsive=True,
x_axis_label=x_axis_label,
y_axis_label='Error on Spectrum (PPM)', title="Error Curve",
plot_width=800, plot_height=300, y_range = [0,2.0*ymed])
ymed = np.median(y)
plot_noise_1d1.circle(x, y, line_width = 4, alpha = .7)
tab4 = Panel(child=plot_noise_1d1, title="Error")
#Not happy? Need help picking a different mode?
plot_spectrum2 = Figure(plot_width=800, plot_height=300, x_range=xlims,y_range=ylims, tools=TOOLS,
x_axis_label=x_axis_label,
y_axis_label=punit, title="Original Model",y_axis_type="log")
plot_spectrum2.line(result_dict['OriginalInput']['model_wave'],result_dict['OriginalInput']['model_spec'],
line_width = 4,alpha = .7)
tab5 = Panel(child=plot_spectrum2, title="Original Model")
#create set of five tabs
tabs1d = Tabs(tabs=[ tab1, tab2,tab3, tab4, tab5])
# Detector 2d
data = out['2d']['detector']
xr, yr = data.shape
plot_detector_2d = Figure(tools="pan,wheel_zoom,box_zoom,resize,reset,hover,save",
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="2D Detector Image",
plot_width=800, plot_height=300)
plot_detector_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
#2d tabs
#2d snr
data = out['2d']['snr']
data[np.isinf(data)] = 0.0
xr, yr = data.shape
plot_snr_2d = Figure(tools=TOOLS,
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="Signal-to-Noise Ratio",
plot_width=800, plot_height=300)
plot_snr_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
tab1b = Panel(child=plot_snr_2d, title="SNR")
#saturation
data = out['2d']['saturation']
xr, yr = data.shape
plot_sat_2d = Figure(tools=TOOLS,
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="Saturation",
plot_width=800, plot_height=300)
plot_sat_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
tab2b = Panel(child=plot_sat_2d, title="Saturation")
tabs2d = Tabs(tabs=[ tab1b, tab2b])
result_comp = components({'plot_spectrum':layout,
'tabs1d': tabs1d, 'det_2d': plot_detector_2d,
'tabs2d': tabs2d})
return result_comp
indye = set(indb).intersection(
indt).intersection(set(indyey).union(indyex))
noerrorlegend = bandname if len(indne) == 0 else ''
source = ColumnDataSource(
data=dict(
x=[phototime[i] for i in indne],
y=[photoAB[i] for i in indne],
err=[photoABerrs[i] for i in indne],
desc=[photoband[i] for i in indne],
instr=[photoinstru[i] for i in indne],
src=[photoevent[i] for i in indne]
)
)
p1.circle('x', 'y', source=source, color=bandcolorf(band),
legend='', size=2, line_alpha=0.75, fill_alpha=0.75)
source = ColumnDataSource(
data=dict(
x=[phototime[i] for i in indye],
y=[photoAB[i] for i in indye],
err=[photoABerrs[i] for i in indye],
desc=[photoband[i] for i in indye],
instr=[photoinstru[i] for i in indye],
src=[photoevent[i] for i in indye]
)
)
p1.circle('x', 'y', source=source, color=bandcolorf(band),
legend=bandname, size=2, line_alpha=0.75, fill_alpha=0.75)
p1.legend.label_text_font_size = '8pt'
### Step 3: Build the charts
# Build state bar chart
state_bar_chart = Bar(build_state_data(), label="state",
values='complaint_count', toolbar_location=None,
title="Complaints by State", width=1300, height=200,
ylabel="", xlabel="", color="#2cb34a")
# Build zip code scatter plot
zip_data = build_zip_data()
zip_source.data = dict(x = zip_data["median_income"],
y = zip_data["complaint_count"])
zip_scatter_plot = Figure(plot_height=500, plot_width=1000,
title="Complaints by Median Income",
title_text_font_size='14pt', x_range=Range1d(0,100000))
zip_scatter_plot.circle(x="x", y="y", source=zip_source, size=4,
color="#addc91", line_color=None, fill_alpha="0.95")
zip_xaxis = zip_scatter_plot.select(dict(type=Axis, layout="below"))[0]
zip_xaxis.formatter.use_scientific = False
# Build the data table
columns = [
TableColumn(field="labels", title="Label"),
TableColumn(field="data", title="Data")
]
data_table = DataTable(source=table_source, columns=columns,
height=150, width=250)
table_source.data = build_data_table()
### Step 4: Construct the document
from bokeh.plotting import Figure, output_file, show, ColumnDataSource
from bokeh.models import HBox
from bokeh.models.widgets import Slider, Select
# from bokeh.sampledata.autompg import autompg as am
cir_x=[10]
cir_y=[10]
cir_size=[10]
cir_source = ColumnDataSource(data=dict(
x1=cir_x,
y1=cir_y,
sz=cir_size))
p1 = Figure(plot_width=300, plot_height=300)
p1.circle('x1', 'y1', size='sz', color='red', source=cir_source)
my_slider = Slider(start=0, end=100, step=1, value=50, title="Circle Radius")
def update_size(attrname, old, new):
new_sz = [my_slider.value]
cir_source.data = dict(x1=cir_x, y1=cir_y, sz=new_sz)
for w in [my_slider]:
w.on_change('value', update_size)
hlayout = HBox(my_slider, p1)
output_file('circle1.html')
curdoc().add_root(hlayout)
#show(hlayout)
y=[evhys[i] for i in ind],
ra=[evras[i] for i in ind],
dec=[evdecs[i] for i in ind],
event=[evnames[i] for i in ind],
claimedtype=[evtypes[i] for i in ind]))
if ct == 'Unknown':
tcolor = 'black'
falpha = 0.0
else:
tcolor = colors[ci]
falpha = 1.0
glyphs.append(
p1.circle('x',
'y',
source=source,
color=tcolor,
fill_alpha=falpha,
legend=ct,
size=glsize))
hover = HoverTool(tooltips=tt, renderers=glyphs)
p1.add_tools(hover)
p1.legend.location = "bottom_center"
p1.legend.orientation = "horizontal"
p1.legend.label_text_font_size = '7pt'
p1.legend.label_width = 20
p1.legend.label_height = 8
p1.legend.glyph_height = 8
p1.legend.spacing = 0
# set up initial data
n_samples = 1500
n_clusters = 2
algorithm = 'MiniBatchKMeans'
dataset = 'Noisy Circles'
X, y = get_dataset(dataset, n_samples)
X, y_pred = clustering(X, algorithm, n_clusters)
spectral = np.hstack([Spectral6] * 20)
colors = [spectral[i] for i in y]
# set up plot (styling in theme.yaml)
plot = Figure(toolbar_location=None, title=algorithm)
source = ColumnDataSource(data=dict(x=X[:, 0], y=X[:, 1], colors=colors))
plot.circle('x', 'y', fill_color='colors', line_color=None, source=source)
# set up widgets
clustering_algorithms= [
'MiniBatchKMeans',
'AffinityPropagation',
'MeanShift',
'SpectralClustering',
'Ward',
'AgglomerativeClustering',
'DBSCAN',
'Birch'
]
datasets_names = [
'Noisy Circles',
def update_explorer():
games = pd.read_csv('static/games_full.csv')
games["color"] = "blue"
games.fillna(0, inplace=True)
axis_map = {
"Year Published": "yearpublished",
"Average Rating": "bayes_avg_rating",
"Boardgamegeek Rank": "rank",
"Min Players": "minplayers",
"Max Players": "maxplayers",
"Min Playtime": "minplaytime",
"Max Playtime": "maxplaytime",
"Min Age": "minage"
}
ordered_keys = [
"Year Published",
"Average boardgamegeek Rating",
"Rank",
"Min Players",
"Max Players",
"Min Playtime",
"Max Playtime",
"Min Age"
]
# Create Column Data Source that will be used by the plot
source = ColumnDataSource(data=dict(x=[], y=[], color=[], name=[], year=[], thumbnail=[]))
hover = HoverTool(
tooltips="""
<section style="width:350px; float:left; padding:10px;">
<img src="@img" height="42" alt="@name" width="42" style="float: left; margin: 0px 15px 15px 0px;" border="2"></img>
<span style="font-size: 17px; font-weight: bold;">@name (@year)</span>
</section>
""")
x_axis = Select(title="X Axis", options=ordered_keys, value="Year Published")
y_axis = Select(title="Y Axis", options=ordered_keys, value="Average boardgamegeek Rating")
filter = {}
filter['minplayers'] = request.args.get('minplayers', type=int)
filter['maxplayers'] = request.args.get('maxplayers', type=int)
filter['minplaytime'] = request.args.get('minplaytime', type=int)
filter['maxplaytime'] = request.args.get('maxplaytime', type=int)
filter['minyear'] = request.args.get("minyear", type=int)
filter['maxyear'] = request.args.get("maxyear", type=int)
filter['minage'] = request.args.get("minage", type=int)
filter['rank'] = request.args.get("rank", type=int)
x_axis = request.args.get("xaxis")
y_axis = request.args.get("yaxis")
p = Figure(plot_height=600, plot_width=750, title="", toolbar_location=None, tools=[hover])
p.circle(x="x", y="y", source=source, size=7, color="color", line_color=None, fill_alpha=0.25)
def select_games():
selected = games[
(games["maxplayers"] <= filter['maxplayers']) &
(games["minplayers"] >= filter['minplayers']) &
(games["maxplaytime"] <= filter['maxplaytime']) &
(games["minplaytime"] >= filter['minplaytime']) &
(games["yearpublished"] >= filter['minyear']) &
(games["yearpublished"] <= filter['maxyear']) &
(games["minage"] >= filter['minage']) &
(games["rank"] <= filter['rank'])
]
return selected
def update(attrname, old, new):
df = select_games()
x_name = axis_map[x_axis]
y_name = axis_map[y_axis]
p.xaxis.axis_label = x_axis
p.yaxis.axis_label = y_axis
p.title = "%d games selected" % len(df)
source.data = dict(
x=df[x_name],
y=df[y_name],
color=df["color"],
name=df["name"],
year=df["yearpublished"],
img=df['thumbnail'].apply(lambda s: 'http:'+str(s))
)
update(None, None, None) # initial view
script, div = components(p)
return jsonify(plot=render_template('explore_plot.html',script=script, div=div), flag = 0)
plot_field = Figure(plot_height=400,
plot_width=400,
tools=toolset,
title="Vector valued function",
x_range=[curveintegral_settings.x_min, curveintegral_settings.x_max],
y_range=[curveintegral_settings.y_min, curveintegral_settings.y_max]
)
# remove grid from plot
plot_field.grid[0].grid_line_alpha = 0.0
plot_field.grid[1].grid_line_alpha = 0.0
# Plot the direction field
plot_field.segment('x0', 'y0', 'x1', 'y1', source=source_segments)
plot_field.patches('xs', 'ys', source=source_patches)
plot_field.circle('x', 'y', source=source_basept, color='blue', size=1.5)
# Plot curve
plot_field.line('x', 'y', source=source_curve, color='black', legend='curve')
# Plot parameter point
plot_field.scatter('x', 'y', source=source_param, color='black', legend='c(t)')
# Plot corresponding tangent vector
plot_field.segment('x0', 'y0', 'x1', 'y1', source=source_param, color='black')
plot_field.patches('xs', 'ys', source=source_param, color='black')
# Generate a figure container for the integral value
plot_integral = Figure(title_text_font_size="12pt",
plot_height=200,
plot_width=400,
title="Integral along curve",
x_range=[curveintegral_settings.parameter_min, curveintegral_settings.parameter_max],
y_range=[-10,10]
director = TextInput(title="Director name contains")
cast = TextInput(title="Cast names contains")
x_axis = Select(title="X Axis", options=sorted(axis_map.keys()), value="Tomato Meter")
y_axis = Select(title="Y Axis", options=sorted(axis_map.keys()), value="Number of Reviews")
# Create Column Data Source that will be used by the plot
source = ColumnDataSource(data=dict(x=[], y=[], color=[], title=[], year=[], revenue=[]))
hover = HoverTool(tooltips=[
("Title","@title"),
("Year", "@year"),
("$", "@revenue")
])
p = Figure(plot_height=600, plot_width=800, title="", toolbar_location=None, tools=[hover])
p.circle(x="x", y="y", source=source, size=7, color="color", line_color=None, fill_alpha="alpha")
def select_movies():
genre_val = genre.value
director_val = director.value.strip()
cast_val = cast.value.strip()
selected = movies[
(movies.Reviews >= reviews.value) &
(movies.BoxOffice >= (boxoffice.value * 1e6)) &
(movies.Year >= min_year.value) &
(movies.Year <= max_year.value) &
(movies.Oscars >= oscars.value)
]
if (genre_val != "All"):
selected = selected[selected.Genre.str.contains(genre_val)==True]
if (director_val != ""):
def create_component_hst(result_dict):
"""Generate front end plots HST
Function that is responsible for generating the front-end spectra plots for HST.
Parameters
----------
result_dict : dict
The dictionary returned from a PandExo (HST) run
Returns
-------
tuple
A tuple containing `(script, div)`, where the `script` is the
front-end javascript required, and `div` is a dictionary of plot
objects.
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
#plot planet spectrum
mwave = result_dict['planet_spec']['model_wave']
mspec = result_dict['planet_spec']['model_spec']
binwave = result_dict['planet_spec']['binwave']
binspec = result_dict['planet_spec']['binspec']
error = result_dict['planet_spec']['error']
error = np.zeros(len(binspec))+ error
xlims = [result_dict['planet_spec']['wmin'], result_dict['planet_spec']['wmax']]
ylims = [np.min(binspec)-2.0*error[0], np.max(binspec)+2.0*error[0]]
eventType = result_dict['calc_start_window']['eventType']
if eventType=='tranist':
y_axis = '(Rp/R*)^2'
elif eventType =='eclipse':
y_axis='Fp/F*'
plot_spectrum = Figure(plot_width=800, plot_height=300, x_range=xlims,
y_range=ylims, tools=TOOLS,#responsive=True,
x_axis_label='Wavelength [microns]',
y_axis_label=y_axis,
title="Original Model with Observation")
y_err = []
x_err = []
for px, py, yerr in zip(binwave, binspec, error):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
plot_spectrum.line(mwave,mspec, color= "black", alpha = 0.5, line_width = 4)
plot_spectrum.circle(binwave,binspec, line_width=3, line_alpha=0.6)
plot_spectrum.multi_line(x_err, y_err)
#earliest and latest start times
obsphase1 = result_dict['calc_start_window']['obsphase1']
obstr1 = result_dict['calc_start_window']['obstr1']
rms = result_dict['calc_start_window']['light_curve_rms']
obsphase2 = result_dict['calc_start_window']['obsphase2']
obstr2 = result_dict['calc_start_window']['obstr2']
phase1 = result_dict['calc_start_window']['phase1']
phase2 = result_dict['calc_start_window']['phase2']
trmodel1 = result_dict['calc_start_window']['trmodel1']
trmodel2 = result_dict['calc_start_window']['trmodel2']
if isinstance(rms, float):
rms = np.zeros(len(obsphase1))+rms
y_err1 = []
x_err1 = []
for px, py, yerr in zip(obsphase1, obstr1, rms):
np.array(x_err1.append((px, px)))
np.array(y_err1.append((py - yerr, py + yerr)))
y_err2 = []
x_err2 = []
for px, py, yerr in zip(obsphase2, obstr2, rms):
np.array(x_err2.append((px, px)))
np.array(y_err2.append((py - yerr, py + yerr)))
early = Figure(plot_width=400, plot_height=300,
tools=TOOLS,#responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Earliest Start Time")
early.line(phase1, trmodel1, color='black',alpha=0.5, line_width = 4)
early.circle(obsphase1, obstr1, line_width=3, line_alpha=0.6)
early.multi_line(x_err1, y_err1)
late = Figure(plot_width=400, plot_height=300,
tools=TOOLS,#responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Latest Start Time")
late.line(phase2, trmodel2, color='black',alpha=0.5, line_width = 3)
late.circle(obsphase2, obstr2, line_width=3, line_alpha=0.6)
late.multi_line(x_err2, y_err2)
start_time = row(early, late)
result_comp = components({'plot_spectrum':plot_spectrum,
'start_time':start_time})
return result_comp
class DynamicPlotHandler(Handler):
def __init__(self, network):
self._network = weakref.ref(network)
self.sources = {}
self._last_time_list = None
self._update_complete = False
self._recurring_update = RecurringTask(self.plan_update_data, delay=5)
self._pcb = None # Periodic callback
self._ntcb = None # Next Tick callback
super().__init__()
@property
def network(self):
return self._network()
def organize_data(self):
self._log.debug("Organize Data")
self.s = {}
for point in self.network.trends:
self.s[point.history.name] = (point.history, point.history.units)
self.lst_of_trends = [his[0] for name, his in self.s.items()]
def build_data_sources(self):
sources = {}
self.organize_data()
for each in self.lst_of_trends:
df = pd.DataFrame(each)
df = df.reset_index()
df["name"] = each.name
df["units"] = str(each.units)
df["time_s"] = df["index"].apply(str)
df.states = each.states
try:
df = (
df.fillna(method="ffill")
.fillna(method="bfill")
.replace(["inactive", "active"], [0, 1])
)
except TypeError:
df = df.fillna(method="ffill").fillna(method="bfill")
sources[each.name] = ColumnDataSource(
data=dict(
x=df["index"],
y=df[each.name],
time=df["time_s"],
name=df["name"],
units=df["units"],
)
)
return sources
def build_plot(self):
self._log.debug("Build Plot")
self.stop_update_data()
self.sources = self.build_data_sources()
TOOLS = "pan,box_zoom,wheel_zoom,save,reset"
self.p = Figure(
x_axis_type="datetime",
x_axis_label="Time",
y_axis_label="Numeric Value",
title="BAC0 Trends",
tools=TOOLS,
plot_width=800,
plot_height=600,
toolbar_location="above",
)
self.p.background_fill_color = "#f4f3ef"
self.p.border_fill_color = "#f4f3ef"
self.p.extra_y_ranges = {
"bool": Range1d(start=0, end=1.1),
"enum": Range1d(start=0, end=10),
}
self.p.add_layout(LinearAxis(y_range_name="bool", axis_label="Binary"), "left")
self.p.add_layout(
LinearAxis(y_range_name="enum", axis_label="Enumerated"), "right"
)
hover = HoverTool(
tooltips=[
("name", "@name"),
("value", "@y"),
("units", "@units"),
("time", "@time"),
]
)
self.p.add_tools(hover)
self.legends_list = []
length = len(self.s.keys())
if length <= 10:
if length < 3:
length = 3
color_mapper = dict(zip(self.s.keys(), d3["Category10"][length]))
else:
# This would be a very loaded trend...
color_mapper = dict(zip(self.s.keys(), Spectral6[:length]))
for each in self.lst_of_trends:
if each.states == "binary":
self.p.circle(
"x",
"y",
source=self.sources[each.name],
name=each.name,
color=color_mapper[each.name],
legend=("{} | {} (OFF-ON)".format(each.name, each.description)),
y_range_name="bool",
size=10,
)
# self.legends_list.append(
# (("{} | {} (OFF-ON)".format(each.name, each.description)), [c])
# )
elif each.states == "multistates":
self.p.diamond(
"x",
"y",
source=self.sources[each.name],
name=each.name,
color=color_mapper[each.name],
legend=(
"{} | {} ({})".format(each.name, each.description, each.units)
),
y_range_name="enum",
size=20,
)
else:
self.p.line(
"x",
"y",
source=self.sources[each.name],
name=each.name,
color=color_mapper[each.name],
legend=(
"{} | {} ({})".format(each.name, each.description, each.units)
),
line_width=2,
)
self.p.legend.location = "top_left"
# legend = Legend(items=self.legends_list, location=(0, -60))
self.p.legend.click_policy = "hide"
# self.p.add_layout(legend, "right")
self.plots = [self.p]
def update_data(self):
self._log.debug("Update Data")
doc = curdoc()
# self.organize_data()
if self._last_time_list:
if self._last_time_list != self.s.keys():
self._list_have_changed = True
self.stop_update_data()
# doc.add_next_tick_callback(self.modify_document)
self.modify_document(doc)
else:
self._list_have_changed = False
l = []
for each in self.p.renderers:
l.append(each.name)
# for each in self.lst_of_trends:
# df = pd.DataFrame(each)
# df = df.reset_index()
# df['name'] = each.name
# df['units'] = str(each.units)
# df['time_s'] = df['index'].apply(str)
# try:
# df = df.fillna(method='ffill').fillna(
# method='bfill').replace(['inactive', 'active'], [0, 1])
# except TypeError:
# df = df.fillna(method='ffill').fillna(method='bfill')
index = l.index(each.name)
# renderer = self.p.renderers[index]
# new_data = {}
# new_data['name'] = df['name']
# new_data['x'] = df['index']
# new_data['y'] = df[each.name]
# if each.states == 'binary':
# new_data['units'] = [each.units[int(x)] for x in df[each.name]]
# elif each.states == 'multistates':
# new_data['units'] = [
# each.units[int(math.fabs(x-1))] for x in df[each.name]]
# else:
# new_data['units'] = df['units']
# new_data['time'] = df['time_s']
# renderer.data_source.data = new_data
try:
new_data = self.build_data_sources()
for each in self.lst_of_trends:
self.sources[each.name].data = new_data[each.name].data
except KeyError:
self._log.warning(
"Problem updating {} on chart, will try again next time.".format(
each.name
)
)
else:
self._last_time_list = self.s.keys()
# self.start_update_data()
self._update_complete = True
def modify_document(self, doc):
doc.clear()
self.build_plot()
layout = gridplot(self.plots, ncols=2)
doc.add_root(layout)
self._pcb = doc.add_periodic_callback(self.update_data, 10000)
return doc
def plan_update_data(self):
doc = curdoc()
if self._update_complete == True:
self._update_complete = False
self._ntcb = doc.add_next_tick_callback(self.update_data)
def stop_update_data(self):
doc = curdoc()
try:
doc.remove_periodic_callback(self._pcb)
except:
pass
if self._recurring_update.is_running:
self._recurring_update.stop()
while self._recurring_update.is_running:
pass
try:
doc.remove_next_tick_callback(self._ntcb)
except (ValueError, RuntimeError):
pass # Already gone
def start_update_data(self):
if not self._recurring_update.is_running:
try:
self._recurring_update.start()
while not self._recurring_update.is_running:
pass
except RuntimeError:
pass
def create_component_jwst(result_dict):
"""Generate front end plots JWST
Function that is responsible for generating the front-end interactive plots for JWST.
Parameters
----------
result_dict : dict
the dictionary returned from a PandExo run
Returns
-------
tuple
A tuple containing `(script, div)`, where the `script` is the
front-end javascript required, and `div` is a dictionary of plot
objects.
"""
timing = result_dict['timing']
noccultations = result_dict['timing']['Number of Transits']
out = result_dict['PandeiaOutTrans']
# select the tools we want
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
#Define units for x and y axis
punit = result_dict['input']['Primary/Secondary']
p=1.0
if punit == 'fp/f*': p = -1.0
else: punit = punit
if result_dict['input']['Calculation Type'] =='phase_spec':
x_axis_label='Time (secs)'
frac = 1.0
else:
x_axis_label='Wavelength [microns]'
frac = result_dict['timing']['Num Integrations Out of Transit']/result_dict['timing']['Num Integrations In Transit']
electrons_out = result_dict['RawData']['electrons_out']
electrons_in = result_dict['RawData']['electrons_in']
var_in = result_dict['RawData']['var_in']
var_out = result_dict['RawData']['var_out']
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['spectrum_w_rand']
err = result_dict['FinalSpectrum']['error_w_floor']
y_err = []
x_err = []
for px, py, yerr in zip(x, y, err):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
source = ColumnDataSource(data=dict(x=x, y=y, y_err=y_err, x_err=x_err, err=err,
electrons_out=electrons_out, electrons_in=electrons_in, var_in=var_in, var_out=var_out,
p=var_in*0+p,nocc=var_in*0+noccultations, frac = var_in*0+frac))
original = ColumnDataSource(data=dict(x=x, y=y, y_err=y_err, x_err=x_err, err=err, electrons_out=electrons_out, electrons_in=electrons_in, var_in=var_in, var_out=var_out))
ylims = [min(result_dict['OriginalInput']['model_spec'])- 0.1*min(result_dict['OriginalInput']['model_spec']),
0.1*max(result_dict['OriginalInput']['model_spec'])+max(result_dict['OriginalInput']['model_spec'])]
xlims = [min(result_dict['FinalSpectrum']['wave']), max(result_dict['FinalSpectrum']['wave'])]
plot_spectrum = Figure(plot_width=800, plot_height=300, x_range=xlims,
y_range=ylims, tools=TOOLS,#responsive=True,
x_axis_label=x_axis_label,
y_axis_label=punit,
title="Original Model with Observation")
plot_spectrum.line(result_dict['OriginalInput']['model_wave'],result_dict['OriginalInput']['model_spec'], color= "black", alpha = 0.5, line_width = 4)
plot_spectrum.circle('x', 'y', source=source, line_width=3, line_alpha=0.6)
plot_spectrum.multi_line('x_err', 'y_err', source=source)
callback = CustomJS(args=dict(source=source, original=original), code="""
// Grab some references to the data
var sdata = source.get('data');
var odata = original.get('data');
// Create copies of the original data, store them as the source data
sdata['x'] = odata['x'].slice(0);
sdata['y'] = odata['y'].slice(0);
sdata['y_err'] = odata['y_err'].slice(0);
sdata['x_err'] = odata['x_err'].slice(0);
sdata['err'] = odata['err'].slice(0);
sdata['electrons_out'] = odata['electrons_out'].slice(0);
sdata['electrons_in'] = odata['electrons_in'].slice(0);
sdata['var_in'] = odata['var_in'].slice(0);
sdata['var_out'] = odata['var_out'].slice(0);
// Create some variables referencing the source data
var x = sdata['x'];
var y = sdata['y'];
var y_err = sdata['y_err'];
var x_err = sdata['x_err'];
var err = sdata['err'];
var p = sdata['p'];
var frac = sdata['frac'];
var og_ntran = sdata['nocc'];
var electrons_out = sdata['electrons_out'];
var electrons_in = sdata['electrons_in'];
var var_in = sdata['var_in'];
var var_out = sdata['var_out'];
var f = wbin.get('value');
var ntran = ntran.get('value');
var wlength = Math.pow(10.0,f);
var ind = [];
ind.push(0);
var start = 0;
for (i = 0; i < x.length-1; i++) {
if (x[i+1] - x[start] >= wlength) {
ind.push(i+1);
start = i;
}
}
if (ind[ind.length-1] != x.length) {
ind.push(x.length);
}
var xout = [];
var foutout = [];
var finout = [];
var varinout = [];
var varoutout = [];
var xslice = [];
var foutslice = [];
var finslice = [];
var varoutslice = [];
var varinslice = [];
function add(a, b) {
return a+b;
}
for (i = 0; i < ind.length-1; i++) {
xslice = x.slice(ind[i],ind[i+1]);
foutslice = electrons_out.slice(ind[i],ind[i+1]);
finslice = electrons_in.slice(ind[i],ind[i+1]);
varinslice = var_in.slice(ind[i],ind[i+1]);
varoutslice = var_out.slice(ind[i],ind[i+1]);
xout.push(xslice.reduce(add, 0)/xslice.length);
foutout.push(foutslice.reduce(add, 0));
finout.push(finslice.reduce(add, 0));
varinout.push(varinslice.reduce(add, 0));
varoutout.push(varoutslice.reduce(add, 0));
xslice = [];
foutslice = [];
finslice = [];
varinslice = [];
varoutslice = [];
}
var new_err = 1.0;
var rand = 1.0;
for (i = 0; i < x.length; i++) {
new_err = Math.pow((frac[i]/foutout[i]),2)*varinout[i] + Math.pow((finout[i]*frac[i]/Math.pow(foutout[i],2)),2)*varoutout[i];
new_err = Math.sqrt(new_err)*Math.sqrt(og_ntran[i]/ntran);
rand = new_err*(Math.random()-Math.random());
y[i] = p[i]*((1.0 - frac[i]*finout[i]/foutout[i]) + rand);
x[i] = xout[i];
x_err[i][0] = xout[i];
x_err[i][1] = xout[i];
y_err[i][0] = y[i] + new_err;
y_err[i][1] = y[i] - new_err;
}
source.trigger('change');
""")
#var_tot = (frac/electrons_out)**2.0 * var_in + (electrons_in*frac/electrons_out**2.0)**2.0 * var_out
sliderWbin = Slider(title="binning", value=np.log10(x[1]-x[0]), start=np.log10(x[1]-x[0]), end=np.log10(max(x)/2.0), step= .05, callback=callback)
callback.args["wbin"] = sliderWbin
sliderTrans = Slider(title="Num Trans", value=noccultations, start=1, end=50, step= 1, callback=callback)
callback.args["ntran"] = sliderTrans
layout = column(row(sliderWbin,sliderTrans), plot_spectrum)
#out of transit 2d output
raw = result_dict['RawData']
# Flux 1d
x, y = raw['wave'], raw['e_rate_out']*result_dict['timing']['Seconds per Frame']*(timing["APT: Num Groups per Integration"]-1)
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
plot_flux_1d1 = Figure(tools=TOOLS,
x_axis_label='Wavelength [microns]',
y_axis_label='e-/integration', title="Flux Per Integration",
plot_width=800, plot_height=300)
plot_flux_1d1.line(x, y, line_width = 4, alpha = .7)
tab1 = Panel(child=plot_flux_1d1, title="Flux per Int")
# BG 1d
#x, y = out['1d']['extracted_bg_only']
#y = y[~np.isnan(y)]
#x = x[~np.isnan(y)]
#plot_bg_1d1 = Figure(tools=TOOLS,
# x_axis_label='Wavelength [microns]',
# y_axis_label='Flux (e/s)', title="Background",
# plot_width=800, plot_height=300)
#plot_bg_1d1.line(x, y, line_width = 4, alpha = .7)
#tab2 = Panel(child=plot_bg_1d1, title="Background Flux")
# SNR
y = np.sqrt(y) #this is computing the SNR (sqrt of photons in a single integration)
plot_snr_1d1 = Figure(tools=TOOLS,
x_axis_label=x_axis_label,
y_axis_label='sqrt(e-)/integration', title="SNR per integration",
plot_width=800, plot_height=300)
plot_snr_1d1.line(x, y, line_width = 4, alpha = .7)
tab3 = Panel(child=plot_snr_1d1, title="SNR per Int")
# Error bars (ppm)
x = result_dict['FinalSpectrum']['wave']
y = result_dict['FinalSpectrum']['error_w_floor']*1e6
x = x[~np.isnan(y)]
y = y[~np.isnan(y)]
ymed = np.median(y)
plot_noise_1d1 = Figure(tools=TOOLS,#responsive=True,
x_axis_label=x_axis_label,
y_axis_label='Spectral Precision (ppm)', title="Spectral Precision",
plot_width=800, plot_height=300, y_range = [0,2.0*ymed])
ymed = np.median(y)
plot_noise_1d1.circle(x, y, line_width = 4, alpha = .7)
tab4 = Panel(child=plot_noise_1d1, title="Precision")
#Not happy? Need help picking a different mode?
plot_spectrum2 = Figure(plot_width=800, plot_height=300, x_range=xlims,y_range=ylims, tools=TOOLS,
x_axis_label=x_axis_label,
y_axis_label=punit, title="Original Model",y_axis_type="log")
plot_spectrum2.line(result_dict['OriginalInput']['model_wave'],result_dict['OriginalInput']['model_spec'],
line_width = 4,alpha = .7)
tab5 = Panel(child=plot_spectrum2, title="Original Model")
#create set of five tabs
tabs1d = Tabs(tabs=[ tab1,tab3, tab4, tab5])
# Detector 2d
data = out['2d']['detector']
xr, yr = data.shape
plot_detector_2d = Figure(tools="pan,wheel_zoom,box_zoom,resize,reset,hover,save",
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="2D Detector Image",
plot_width=800, plot_height=300)
plot_detector_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
#2d tabs
#2d snr
data = out['2d']['snr']
data[np.isinf(data)] = 0.0
xr, yr = data.shape
plot_snr_2d = Figure(tools=TOOLS,
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="Signal-to-Noise Ratio",
plot_width=800, plot_height=300)
plot_snr_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
tab1b = Panel(child=plot_snr_2d, title="SNR")
#saturation
data = out['2d']['saturation']
xr, yr = data.shape
plot_sat_2d = Figure(tools=TOOLS,
x_range=[0, yr], y_range=[0, xr],
x_axis_label='Pixel', y_axis_label='Spatial',
title="Saturation",
plot_width=800, plot_height=300)
plot_sat_2d.image(image=[data], x=[0], y=[0], dh=[xr], dw=[yr],
palette="Spectral11")
tab2b = Panel(child=plot_sat_2d, title="Saturation")
tabs2d = Tabs(tabs=[ tab1b, tab2b])
result_comp = components({'plot_spectrum':layout,
'tabs1d': tabs1d, 'det_2d': plot_detector_2d,
'tabs2d': tabs2d})
return result_comp
indne = set(indb).intersection(indt).intersection(indne)
indye = set(indb).intersection(indt).intersection(indye)
noerrorlegend = bandname if len(indne) == 0 else ''
source = ColumnDataSource(
data = dict(
x = [phototime[i] for i in indne],
y = [photoAB[i] for i in indne],
err = [photoerrs[i] for i in indne],
desc = [photoband[i] for i in indne],
instr = [photoinstru[i] for i in indne],
src = [photosource[i] for i in indne]
)
)
p1.circle('x', 'y', source = source, color=bandcolorf(band), fill_color="white", legend=noerrorlegend, size=4)
source = ColumnDataSource(
data = dict(
x = [phototime[i] for i in indye],
y = [photoAB[i] for i in indye],
err = [photoerrs[i] for i in indye],
desc = [photoband[i] for i in indye],
instr = [photoinstru[i] for i in indye],
src = [photosource[i] for i in indye]
)
)
p1.multi_line([err_xs[x] for x in indye], [err_ys[x] for x in indye], color=bandcolorf(band))
p1.circle('x', 'y', source = source, color=bandcolorf(band), legend=bandname, size=4)
upplimlegend = bandname if len(indye) == 0 and len(indne) == 0 else ''
class DynamicPlotHandler(Handler):
def __init__(self, network):
self._network = weakref.ref(network)
self.sources = {}
self._last_time_list = None
self._update_complete = False
self._recurring_update = RecurringTask(self.plan_update_data, delay=5)
self._pcb = None # Periodic callback
self._ntcb = None # Next Tick callback
super().__init__()
@property
def network(self):
return self._network()
def organize_data(self):
self._log.debug("Organize Data")
self.s = {}
for point in self.network.trends:
self.s[point.history.name] = (point.history, point.history.units)
self.lst_of_trends = [his[0] for name, his in self.s.items()]
def build_data_sources(self):
sources = {}
self.organize_data()
for each in self.lst_of_trends:
df = pd.DataFrame(each)
df = df.reset_index()
df["name"] = each.name
df["units"] = str(each.units)
df["time_s"] = df["index"].apply(str)
df.states = each.states
try:
df = (
df.fillna(method="ffill")
.fillna(method="bfill")
.replace(["inactive", "active"], [0, 1])
)
except TypeError:
df = df.fillna(method="ffill").fillna(method="bfill")
sources[each.name] = ColumnDataSource(
data=dict(
x=df["index"],
y=df[each.name],
time=df["time_s"],
name=df["name"],
units=df["units"],
)
)
return sources
def build_plot(self):
self._log.debug("Build Plot")
self.stop_update_data()
self.sources = self.build_data_sources()
TOOLS = "pan,box_zoom,wheel_zoom,save,reset"
self.p = Figure(
x_axis_type="datetime",
x_axis_label="Time",
y_axis_label="Numeric Value",
title="BAC0 Trends",
tools=TOOLS,
plot_width=800,
plot_height=600,
toolbar_location="above",
)
self.p.background_fill_color = "#f4f3ef"
self.p.border_fill_color = "#f4f3ef"
self.p.extra_y_ranges = {
"bool": Range1d(start=0, end=1.1),
"enum": Range1d(start=0, end=10),
}
self.p.add_layout(LinearAxis(y_range_name="bool", axis_label="Binary"), "left")
self.p.add_layout(
LinearAxis(y_range_name="enum", axis_label="Enumerated"), "right"
)
hover = HoverTool(
tooltips=[
("name", "@name"),
("value", "@y"),
("units", "@units"),
("time", "@time"),
]
)
self.p.add_tools(hover)
length = len(self.s.keys())
if length <= 10:
if length < 3:
length = 3
color_mapper = dict(zip(self.s.keys(), d3["Category10"][length]))
else:
# This would be a very loaded trend...
color_mapper = dict(zip(self.s.keys(), Spectral6[:length]))
for each in self.lst_of_trends:
if each.states == "binary":
self.p.circle(
"x",
"y",
source=self.sources[each.name],
name=each.name,
color=color_mapper[each.name],
legend=("%s | %s (OFF-ON)" % (each.name, each.description)),
y_range_name="bool",
size=10,
)
elif each.states == "multistates":
self.p.diamond(
"x",
"y",
source=self.sources[each.name],
name=each.name,
color=color_mapper[each.name],
legend=("%s | %s (%s)" % (each.name, each.description, each.units)),
y_range_name="enum",
size=20,
)
else:
self.p.line(
"x",
"y",
source=self.sources[each.name],
name=each.name,
color=color_mapper[each.name],
legend=("%s | %s (%s)" % (each.name, each.description, each.units)),
line_width=2,
)
self.p.legend.location = "bottom_right"
self.p.legend.click_policy = "hide"
self.plots = [self.p]
def update_data(self):
self._log.debug("Update Data")
doc = curdoc()
# self.organize_data()
if self._last_time_list:
if self._last_time_list != self.s.keys():
self._list_have_changed = True
self.stop_update_data()
# doc.add_next_tick_callback(self.modify_document)
self.modify_document(doc)
else:
self._list_have_changed = False
l = []
for each in self.p.renderers:
l.append(each.name)
# for each in self.lst_of_trends:
# df = pd.DataFrame(each)
# df = df.reset_index()
# df['name'] = each.name
# df['units'] = str(each.units)
# df['time_s'] = df['index'].apply(str)
# try:
# df = df.fillna(method='ffill').fillna(
# method='bfill').replace(['inactive', 'active'], [0, 1])
# except TypeError:
# df = df.fillna(method='ffill').fillna(method='bfill')
index = l.index(each.name)
# renderer = self.p.renderers[index]
# new_data = {}
# new_data['name'] = df['name']
# new_data['x'] = df['index']
# new_data['y'] = df[each.name]
# if each.states == 'binary':
# new_data['units'] = [each.units[int(x)] for x in df[each.name]]
# elif each.states == 'multistates':
# new_data['units'] = [
# each.units[int(math.fabs(x-1))] for x in df[each.name]]
# else:
# new_data['units'] = df['units']
# new_data['time'] = df['time_s']
# renderer.data_source.data = new_data
try:
new_data = self.build_data_sources()
for each in self.lst_of_trends:
self.sources[each.name].data = new_data[each.name].data
except KeyError:
self._log.warning(
"Problem updating {} on chart, will try again next time.".format(
each.name
)
)
else:
self._last_time_list = self.s.keys()
# self.start_update_data()
self._update_complete = True
def modify_document(self, doc):
curdoc().clear()
# doc = curdoc()
try:
curdoc().remove_periodic_callback(self._pcb)
except:
pass
doc.clear()
self.build_plot()
layout = gridplot(self.plots, ncols=2)
doc.add_root(layout)
self._pcb = doc.add_periodic_callback(self.update_data, 10000)
return doc
def plan_update_data(self):
doc = curdoc()
if self._update_complete == True:
self._update_complete = False
self._ntcb = doc.add_next_tick_callback(self.update_data)
def stop_update_data(self):
doc = curdoc()
if self._recurring_update.is_running:
self._recurring_update.stop()
while self._recurring_update.is_running:
pass
try:
doc.remove_next_tick_callback(self._ntcb)
except (ValueError, RuntimeError):
pass # Already gone
def start_update_data(self):
if not self._recurring_update.is_running:
try:
self._recurring_update.start()
while not self._recurring_update.is_running:
pass
except RuntimeError:
pass
def create_component_hst(result_dict):
"""Generate front end plots HST
Function that is responsible for generating the front-end spectra plots for HST.
Parameters
----------
result_dict : dict
The dictionary returned from a PandExo (HST) run
Returns
-------
tuple
A tuple containing `(script, div)`, where the `script` is the
front-end javascript required, and `div` is a dictionary of plot
objects.
"""
TOOLS = "pan,wheel_zoom,box_zoom,resize,reset,save"
#plot planet spectrum
mwave = result_dict['planet_spec']['model_wave']
mspec = result_dict['planet_spec']['model_spec']
binwave = result_dict['planet_spec']['binwave']
binspec = result_dict['planet_spec']['binspec']
error = result_dict['planet_spec']['error']
error = np.zeros(len(binspec))+ error
xlims = [result_dict['planet_spec']['wmin'], result_dict['planet_spec']['wmax']]
ylims = [np.min(binspec)-2.0*error[0], np.max(binspec)+2.0*error[0]]
plot_spectrum = Figure(plot_width=800, plot_height=300, x_range=xlims,
y_range=ylims, tools=TOOLS,#responsive=True,
x_axis_label='Wavelength [microns]',
y_axis_label='(Rp/R*)^2',
title="Original Model with Observation")
y_err = []
x_err = []
for px, py, yerr in zip(binwave, binspec, error):
np.array(x_err.append((px, px)))
np.array(y_err.append((py - yerr, py + yerr)))
plot_spectrum.line(mwave,mspec, color= "black", alpha = 0.5, line_width = 4)
plot_spectrum.circle(binwave,binspec, line_width=3, line_alpha=0.6)
plot_spectrum.multi_line(x_err, y_err)
#earliest and latest start times
obsphase1 = result_dict['calc_start_window']['obsphase1']
obstr1 = result_dict['calc_start_window']['obstr1']
rms = result_dict['calc_start_window']['light_curve_rms']
obsphase2 = result_dict['calc_start_window']['obsphase2']
obstr2 = result_dict['calc_start_window']['obstr2']
phase1 = result_dict['calc_start_window']['phase1']
phase2 = result_dict['calc_start_window']['phase2']
trmodel1 = result_dict['calc_start_window']['trmodel1']
trmodel2 = result_dict['calc_start_window']['trmodel2']
if isinstance(rms, float):
rms = np.zeros(len(obsphase1))+rms
y_err1 = []
x_err1 = []
for px, py, yerr in zip(obsphase1, obstr1, rms):
np.array(x_err1.append((px, px)))
np.array(y_err1.append((py - yerr, py + yerr)))
y_err2 = []
x_err2 = []
for px, py, yerr in zip(obsphase2, obstr2, rms):
np.array(x_err2.append((px, px)))
np.array(y_err2.append((py - yerr, py + yerr)))
early = Figure(plot_width=400, plot_height=300,
tools=TOOLS,#responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Earliest Start Time")
early.line(phase1, trmodel1, color='black',alpha=0.5, line_width = 4)
early.circle(obsphase1, obstr1, line_width=3, line_alpha=0.6)
early.multi_line(x_err1, y_err1)
late = Figure(plot_width=400, plot_height=300,
tools=TOOLS,#responsive=True,
x_axis_label='Orbital Phase',
y_axis_label='Flux',
title="Latest Start Time")
late.line(phase2, trmodel2, color='black',alpha=0.5, line_width = 3)
late.circle(obsphase2, obstr2, line_width=3, line_alpha=0.6)
late.multi_line(x_err2, y_err2)
start_time = row(early, late)
result_comp = components({'plot_spectrum':plot_spectrum,
'start_time':start_time})
return result_comp
plot_width=400,
tools=toolset,
title="Time dependent PDEs",
x_range=[pde_settings.x_min, pde_settings.x_max],
y_range=[-1, 1]
)
# Plot the numerical solution at time=t by the x,u values in the source property
plot.line('x', 'u', source=plot_data_num,
line_width=.5,
line_alpha=.6,
line_dash=[4, 4],
color='red')
plot.line('x', 'u', source=plot_data_ana,
line_width=.5,
line_alpha=.6,
color='blue',
legend='analytical solution')
plot.circle('x', 'u', source=plot_data_num,
color='red',
legend='numerical solution')
# calculate data
init_pde()
# lists all the controls in our app
controls = widgetbox(initial_condition,time_slider,h_slider,k_slider,pde_type, solver_type,width=400)
# make layout
curdoc().add_root(row(plot,controls,width=800))
