def generate_social_media_comments_table(media_comments_data_source,
sentiment_label="Negative"):
datetime_formatter, title_link_formatter = get_table_formatters()
data_columns = [
TableColumn(field="published",
title="Date Published",
width=105,
formatter=datetime_formatter,
name="time_series"),
TableColumn(
field="extract",
title=f"{sentiment_label} Covid-19 Facebook Comments by Engagement",
formatter=title_link_formatter,
name="extract",
width=380)
]
data_table = DataTable(
source=media_comments_data_source,
columns=data_columns,
fit_columns=False,
selectable=False,
sortable=True,
index_position=None,
width=500,
row_height=100,
)
table_html = file_html(
data_table, CDN,
f"Most Engaged {sentiment_label} Social Media Comments")
return table_html
def transform(self):
print("converting")
for f in self.__selected:
print(".")
f['results'] = self.__extract_observations(f['rdf'])
print("writing")
self.__write_geojson(self.__selected)
print("done converting")
self.__file_list = self.__get_eurostats()
geojson_data = {'id': [], 'lvl': []}
for file in self.__file_list:
if file['geojson']['nuts1']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(1)
if file['geojson']['nuts2']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(2)
if file['geojson']['nuts3']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(3)
self.__geojson_table_source = ColumnDataSource(geojson_data)
geojson_table_columns = [
TableColumn(field='lvl', title='NUTS Level'),
TableColumn(field='id', title='ID')
]
self.geojson_table = DataTable(source=self.__geojson_table_source,
columns=geojson_table_columns,
width=300,
height=500,
selectable=True)
self.__layout.children[2] = column(self.geojson_table)
def generate_most_recent_media_table(most_media_datasource):
datetime_formatter, title_link_formatter = get_table_formatters()
media_data_columns = [
TableColumn(field="published",
title="Date Published",
width=105,
formatter=datetime_formatter),
TableColumn(field="title",
title="Media Links",
formatter=title_link_formatter,
width=1000 - 105),
]
media_data_table = DataTable(source=most_media_datasource,
columns=media_data_columns,
fit_columns=False,
selectable=False,
sortable=True,
index_position=None,
height=300,
width=1000,
sizing_mode="scale_both")
table_html = file_html(media_data_table, CDN, "Most Recent Media Links")
return table_html
def _get_columns(self):
if self.value is None:
return []
indexes = self.indexes
col_names = list(self.value.columns)
if not self.hierarchical or len(indexes) == 1:
col_names = indexes + col_names
else:
col_names = indexes[-1:] + col_names
df = self.value.reset_index() if len(indexes) > 1 else self.value
columns = []
for col in col_names:
if col in df.columns:
data = df[col]
else:
data = df.index
col_kwargs = {}
kind = data.dtype.kind
if kind == 'i':
formatter = NumberFormatter()
editor = IntEditor()
elif kind == 'f':
formatter = NumberFormatter(format='0,0.0[00000]')
editor = NumberEditor()
elif isdatetime(data) or kind == 'M':
formatter = DateFormatter(format='%Y-%m-%d %H:%M:%S')
editor = DateEditor()
else:
formatter = StringFormatter()
editor = StringEditor()
if col in self.editors:
editor = self.editors[col]
if col in indexes or editor is None:
editor = CellEditor()
if col in self.formatters:
formatter = self.formatters[col]
if str(col) != col:
self._renamed_cols[str(col)] = col
if isinstance(self.widths, int):
col_kwargs['width'] = self.widths
elif str(col) in self.widths:
col_kwargs['width'] = self.widths.get(str(col))
title = str(col)
if col in indexes and len(indexes) > 1 and self.hierarchical:
title = 'Index: %s' % ' | '.join(indexes)
column = TableColumn(field=str(col),
title=title,
editor=editor,
formatter=formatter,
**col_kwargs)
columns.append(column)
return columns
def __init__(self, layout):
self.__layout = layout
self.__selected = []
self.__file_list = self.__get_eurostats()
self.__rdf_table_source = ColumnDataSource(
dict(id=[f['id'] for f in self.__file_list]))
self.__rdf_table_source.on_change('selected', self.__on_select)
rdf_table_columns = [TableColumn(field='id', title='RDF ID')]
self.rdf_table = DataTable(source=self.__rdf_table_source,
columns=rdf_table_columns,
width=300,
height=500,
selectable=True)
geojson_data = {'id': [], 'lvl': []}
for file in self.__file_list:
if file['geojson']['nuts1']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(1)
if file['geojson']['nuts2']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(2)
if file['geojson']['nuts3']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(3)
self.__geojson_table_source = ColumnDataSource(geojson_data)
geojson_table_columns = [
TableColumn(field='lvl', title='NUTS Level'),
TableColumn(field='id', title='ID')
]
self.geojson_table = DataTable(source=self.__geojson_table_source,
columns=geojson_table_columns,
width=300,
height=500,
selectable=True)
convert_button = Button(label="Convert to GeoJSON",
button_type="success")
convert_button.on_click(self.transform)
# todo: creates bug - empty table
#self.__layout.children[1] = column(widgetbox(self.rdf_table), convert_button)
self.__layout.children[2] = column(self.geojson_table)
def _init_datatable(self):
columns = [
TableColumn(
width=80,
field="parameter",
title="Parameter",
formatter=self.param_formatter,
editor=CellEditor() # non editable
),
TableColumn(width=50,
field="value",
title="Value",
formatter=self.value_formatter,
editor=CellEditor()),
TableColumn(width=40,
field="flag",
title="Flag",
formatter=self.flag_formatter,
editor=StringEditor()),
]
self.table_df = pd.DataFrame(
dict(
parameter=self.params,
value=[''] * len(self.params),
flag=[''] * len(self.params),
))
table_cds = ColumnDataSource(self.table_df)
self.data_table = DataTable(
width=190,
height=125,
source=table_cds,
columns=columns,
editable=
True, # TODO: check if there is a better way than https://stackoverflow.com/a/49424647/4891717
fit_columns=False, # avoids horizontal scrolls bar
index_position=None, # hides index column
selectable=True, # this is needed to edit cells
reorderable=
False, # NOTE: this needs jquery ui, but it is not needed
scroll_to_selection=False, # not needed
sortable=False, # not needed
)
self.data_table.source.on_change('data', self.on_change_data_source)
def weather_tab(self):
data = pd.DataFrame(columns = ['time','desc','temp','wind','humidity'])
self.weather_source = ColumnDataSource(data)
self.weather_subtitle = Div(text="Weather", css_classes=['subt-style'])
columns = [TableColumn(field='time', title='Time (local)', width=75),
TableColumn(field='desc', title='Description', width=200, editor=StringEditor()),
TableColumn(field='temp', title='Temperature (C)', width=100, editor=NumberEditor()),
TableColumn(field='wind', title='Wind Speed (mph)', width=120, editor=NumberEditor()),
TableColumn(field='humidity', title='Humidity (%)', width=100, editor=PercentEditor())]
self.weather_inst = Div(text="Every hour include a description of the weather and any other relevant information, as well as fill in all the fields below. Click the Update Night Log button after every hour's entry. To update a cell: double click in it, record the information, click out of the cell.", width=1000, css_classes=['inst-style'])
self.weather_time = TextInput(placeholder='17:00', value=None, width=100) #title='Time in Kitt Peak local time',
self.weather_desc = TextInput(title='Description', placeholder='description', value=None)
self.weather_temp = TextInput(title='Temperature (C)', placeholder='50', value=None)
self.weather_wind = TextInput(title='Wind Speed (mph)', placeholder='10', value=None)
self.weather_humidity = TextInput(title='Humidity (%)', placeholder='5', value=None)
self.weather_table = DataTable(source=self.weather_source, columns=columns)
self.weather_btn = Button(label='Add Weather', css_classes=['add_button'])
def __init__(self):
# extend __init__ super class
_DataSource.__init__(self)
# overwrite base class filepath with FileInput widget
self.filepath = FileInput(accept=".xlsx")
self.filepath.on_change('value', self.update_data)
# add columndatasource and table
self.cds = ColumnDataSource(data=dict(values=['']))
self.table = DataTable(source=self.cds, columns=[TableColumn(field='', title='')], editable=True)
def __init__(self, layout):
self.__layout = layout
self.__selected = []
self.__file_list = self.__get_eurostats()
geojson_data = {'id': [], 'lvl': []}
for file in self.__file_list:
if file['geojson']['nuts1']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(1)
if file['geojson']['nuts2']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(2)
if file['geojson']['nuts3']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(3)
self.__geojson_table_source = ColumnDataSource(geojson_data)
geojson_table_columns = [
TableColumn(field='lvl', title='NUTS Level'),
TableColumn(field='id', title='ID')
]
self.geojson_table = DataTable(source=self.__geojson_table_source,
columns=geojson_table_columns,
width=300,
height=500,
selectable=True)
convert_button = Button(label="Convert to GeoJSON",
button_type="success")
convert_button.on_click(self.transform)
self.__endpoint_input = TextInput(placeholder="SPARQL Endpoint")
self.__graph_input = TextInput(placeholder="Graph")
self.__layout.children[1] = column(self.__endpoint_input,
self.__graph_input, convert_button)
self.__layout.children[2] = column(self.geojson_table)
def get_nightlytable(exposures):
'''
Generates a summary table of the exposures from the night observed.
Args:
exposures: Table of exposures with columns...
Returns a bokeh DataTable object.
'''
source = ColumnDataSource(
data=dict(expid=np.array(exposures['EXPID']),
flavor=np.array(exposures['FLAVOR'], dtype='str'),
exptime=np.array(exposures['EXPTIME']),
tileid=np.array(exposures['TILEID']),
airmass=np.array(exposures['AIRMASS']),
seeing=np.array(exposures['SEEING']),
transp=np.array(exposures['TRANSP']),
sky=np.array(exposures['SKY']),
hourangle=np.array(exposures['HOURANGLE'])))
formatter = NumberFormatter(format='0,0.00')
columns = [
TableColumn(field='expid', title='Exposure ID'),
TableColumn(field='flavor', title='Flavor'),
TableColumn(field='exptime', title='Exposure Time'),
TableColumn(field='tileid', title='Tile ID'),
TableColumn(field='airmass', title='Airmass', formatter=formatter),
TableColumn(field='seeing', title='Seeing', formatter=formatter),
TableColumn(field='transp', title='Transparency', formatter=formatter),
TableColumn(field='sky', title='Sky', formatter=formatter),
TableColumn(field='hourangle', title='Hour Angle', formatter=formatter)
]
nightly_table = DataTable(source=source,
columns=columns,
width=1000,
sortable=True)
return nightly_table
def generate_rdf_column_data_source(self, files, column_title="ID"):
"""
Generate data table based on files list with ``id``.
:param List files: List of Dictionaries that contain the key ``id``.
:param string column_title: Title of the data table column.
:return: Data table containing the file IDs.
"""
ids = [tmp_id['id'] for tmp_id in files]
data = dict(id=ids)
table_source = ColumnDataSource(data)
columns = [TableColumn(field="id", title=column_title)]
data_table = DataTable(source=table_source,
columns=columns,
width=500,
height=400,
selectable=True)
return data_table
def import_data(self):
"""
This overrides the base class method
:return:
"""
# # decode file (received as b64 encoded) and write to xlsx locally
decoded = base64.b64decode(self.filepath.value)
# stream data to pandas df without saving locally
toread = io.BytesIO()
toread.write(decoded) # pass your `decrypted` string as the argument here
toread.seek(0) # reset the pointer
self.df = get_one_table(toread, 'quote_table').dropna(axis=0, how='all')
cols = [TableColumn(field=_, title=_) for _ in self.df.columns] # bokeh columns
self.table.columns = cols
self.cds.data = self.df
def get_nl_layout(self):
exp_data = pd.DataFrame(columns = ['date_obs','id','program','sequence','flavor','exptime'])
self.explist_source = ColumnDataSource(exp_data)
columns = [TableColumn(field='date_obs', title='Time (UTC)', width=50, formatter=self.datefmt),
TableColumn(field='id', title='Exposure', width=50),
TableColumn(field='sequence', title='Sequence', width=100),
TableColumn(field='flavor', title='Flavor', width=50),
TableColumn(field='exptime', title='Exptime', width=50),
TableColumn(field='program', title='Program', width=300)]
self.exp_table = DataTable(source=self.explist_source, columns=columns, width=1000)
nl_layout = layout([self.title,
self.nl_subtitle,
self.nl_alert,
self.nl_text,
self.exptable_alert,
self.exp_table], width=1000)
self.nl_tab = Panel(child=nl_layout, title="Current DESI Night Log")
def _get_column_definitions(self, col_names, df):
import pandas as pd
indexes = self.indexes
columns = []
for col in col_names:
if col in df.columns:
data = df[col]
else:
data = df.index
if isinstance(data, pd.DataFrame):
raise ValueError("DataFrame contains duplicate column names.")
col_kwargs = {}
kind = data.dtype.kind
if kind == 'i':
formatter = NumberFormatter()
editor = IntEditor()
elif kind == 'b':
formatter = StringFormatter()
editor = CheckboxEditor()
elif kind == 'f':
formatter = NumberFormatter(format='0,0.0[00000]')
editor = NumberEditor()
elif isdatetime(data) or kind == 'M':
if len(data) and isinstance(data.values[0], dt.date):
date_format = '%Y-%m-%d'
else:
date_format = '%Y-%m-%d %H:%M:%S'
formatter = DateFormatter(format=date_format)
editor = DateEditor()
else:
formatter = StringFormatter()
editor = StringEditor()
if col in self.editors and not isinstance(self.editors[col],
(dict, str)):
editor = self.editors[col]
if col in indexes or editor is None:
editor = CellEditor()
if col in self.formatters and not isinstance(
self.formatters[col], (dict, str)):
formatter = self.formatters[col]
if str(col) != col:
self._renamed_cols[str(col)] = col
if isinstance(self.widths, int):
col_kwargs['width'] = self.widths
elif str(col) in self.widths:
col_kwargs['width'] = self.widths.get(str(col))
title = self.titles.get(col, str(col))
if col in indexes and len(indexes) > 1 and self.hierarchical:
title = 'Index: %s' % ' | '.join(indexes)
column = TableColumn(field=str(col),
title=title,
editor=editor,
formatter=formatter,
**col_kwargs)
columns.append(column)
return columns
def __init__(self):
# app variables
self.active = True
self.playAnimation = None
self.start_epoch = None
self.stop_epoch = None
self.current_epoch = None
# get initial configuration
self.available_models = inspect.getmembers(StandardEphemerisModels,
inspect.isfunction)
self.ephemeris_model = self.available_models[0][1]()
self.spice_provider = SpiceProvider()
self.spice_provider.SPICE_IDS = self.ephemeris_model.objects
self.spice_provider.SPICE_NAMES = {
v: k
for k, v in self.ephemeris_model.objects.items()
}
# init data sources
self.plot_source = self.spice_provider.state_source
self.table_source = self.spice_provider.ephemeris_source
self.cum_source = self.spice_provider.cum_source
# gather options from ephemeris model and spice provider
self.allowed_models = {
model[1]().name: model[1]
for model in self.available_models
}
allowed_objects = [
self.spice_provider.fromId(name)
for name in self.ephemeris_model.objects
]
allowed_frames = self.ephemeris_model.FRAMES
allowed_corrections = [name for name in SpiceProvider.CORRECTIONS]
allowed_durations = [
str(v) for v in self.ephemeris_model.DURATION_DAYS
]
allowed_intervals = [name for name in SpiceProvider.INTERVALS]
# set up widgets
self.model = Select(title="Ephemeris Model",
options=list(self.allowed_models.keys()))
self.center = Select(title="Center",
value=self.ephemeris_model.center,
options=allowed_objects)
self.target = Select(title="Target",
value=self.ephemeris_model.target,
options=allowed_objects)
self.frames = Select(title="Frame",
value=self.ephemeris_model.frame,
options=allowed_frames)
self.planes = RadioButtonGroup(labels=['XY', 'YZ', 'XZ'], active=0)
self.vector = Select(title='Vector Type',
value=self.ephemeris_model.vector_type,
options=allowed_corrections)
self.epoch = DatePicker(title="Select Epoch",
value=datetime.strftime(
self.ephemeris_model.epoch, "%Y-%m-%d"))
self.offset = Slider(title="Days Since Epoch",
value=self.ephemeris_model.offset,
start=0,
end=self.ephemeris_model.duration,
step=1)
self.duration = Select(title="Duration (Days)",
value=str(self.ephemeris_model.duration),
options=allowed_durations)
self.interval = Select(title="Time Step",
value=str(self.ephemeris_model.step_size),
options=allowed_intervals)
# create buttons
self.play_button = Button(label="Play")
self.exportRange = Div(text="Start and Stop Epoch: ")
self.update_button = Button(label="Play")
self.export_button = Button(label="Export")
self.infoDiv = Div(
text=
"<hr>All ephemeris data shown on this website was obtained from publicly available "
"SPICE files located at <a href='https://naif.jpl.nasa.gov/naif/data.html'>"
"https://naif.jpl.nasa.gov/naif/data.html</a>, which is hosted by the "
"Navigation and Ancillary Information Facility (NAIF) at the NASA Jet Propulsion "
"Laboratory. The exception is the SPICE kernel for the Parker Solar Probe, which is "
"available at <a href='https://sppgway.jhuapl.edu/ancil_products'>"
"https://sppgway.jhuapl.edu/ancil_products</a>, hosted by the Johns Hopkins University "
"Applied Physics Laboratory. SpiceyPy is being used to process the SPICE files.",
sizing_mode='stretch_width')
# create plot tab objects
self.plot = figure(match_aspect=True,
sizing_mode="stretch_both",
title="Astropynamics",
tools="hover, pan, reset, save",
tooltips=[("name", "@index")])
self.plot.add_tools(BoxZoomTool(match_aspect=True))
self.plot.circle('px',
'py',
size='radii',
source=self.plot_source,
line_width=3,
line_alpha=0.5,
name='XY')
self.plot.circle('px',
'pz',
size='radii',
source=self.plot_source,
line_width=3,
line_alpha=0.5,
name='XZ').visible = False
self.plot.circle('py',
'pz',
size='radii',
source=self.plot_source,
line_width=3,
line_alpha=0.5,
name='YZ').visible = False
self.plot.line('px',
'py',
source=self.cum_source,
line_width=2,
line_alpha=0.5,
color='red',
name='XYOrbit')
self.plot.line('px',
'pz',
source=self.cum_source,
line_width=2,
line_alpha=0.5,
color='red',
name='XZOrbit').visible = False
self.plot.line('py',
'pz',
source=self.cum_source,
line_width=2,
line_alpha=0.5,
color='red',
name='YZOrbit').visible = False
self.plotLayout = column(self.plot,
self.offset,
sizing_mode="stretch_width")
self.plotTab = Panel(child=self.plotLayout, title="Display")
# create data table tab objects
fmt = NumberFormatter(format='0.000', text_align=TextAlign.right)
columns = [
TableColumn(field="index",
title="Epoch",
formatter=DateFormatter(format="%m/%d/%Y %H:%M:%S")),
TableColumn(field="px", title="PX", formatter=fmt, width=10),
TableColumn(field="py", title="PY", formatter=fmt),
TableColumn(field="pz", title="PZ", formatter=fmt),
TableColumn(field="vx", title="VX", formatter=fmt),
TableColumn(field="vy", title="VY", formatter=fmt),
TableColumn(field="vz", title="VZ", formatter=fmt)
]
self.ephemerisTable = DataTable(source=self.table_source,
columns=columns,
sizing_mode="stretch_both")
self.ephemerisLayout = column(self.exportRange,
self.ephemerisTable,
sizing_mode="stretch_width")
self.dataTab = Panel(child=self.ephemerisLayout, title="Table")
self.kernels = Div()
self.kernelTab = Panel(child=self.kernels, title="Kernels")
self.tabs = Tabs(tabs=[self.plotTab, self.dataTab, self.kernelTab])
# init data
self.model.value = "The Solar System"
self.update_model(None, 0, self.model.value)
self.update_epochs(None, 0, 0)
self.update_states(None, 0, 0)
self.model.on_change('value', self.update_model)
self.frames.on_change('value', self.update_epochs)
self.planes.on_change('active', self.update_plot_view)
self.center.on_change('value', self.update_epochs)
self.target.on_change('value', self.update_epochs)
self.offset.on_change('value', self.update_offset)
self.epoch.on_change('value', self.update_epochs)
self.duration.on_change('value', self.update_epochs)
self.interval.on_change('value', self.update_epochs)
self.update_button.on_click(self.update_onclick)
self.tabs.on_change('active', self.update_button_type)
self.inputs = column(self.model, self.frames, self.planes, self.center,
self.target, self.epoch, self.duration,
self.interval, self.update_button)
def assisted_dijkstras_plot(G, s=0, **kw) -> GridBox:
"""Return a plot in which the user creates a shortest path tree from s.
Args:
G (nx.Graph): Networkx graph.
s (int): The vertex to generate a shortest path tree from.
Returns:
GridBox: Plot in which the user creates a shortest path tree from s.
"""
G = G.copy()
plot = _blank_plot(G, **kw)
_set_edge_positions(G)
_set_graph_colors(G)
nodes_src, nodes_glyph = _add_nodes(G, plot)
nodes_src.data['fill_color'][s] = SECONDARY_COLOR
nodes_src.data['line_color'][s] = SECONDARY_DARK_COLOR
edges_src, edges_glyph = _add_edges(G, plot, show_labels=True)
src_data = _get_blank_src_data(G)
dist = [float('inf')] * len(G)
dist[s] = 0
src_data['dist'] = dist
src_data['prev'] = [float('nan')] * len(G)
src_data['settled'] = []
src_data['frontier'] = [s]
edge_ids, G_matrix = _edge_src_maps(G, edges_src)
src_data['edge_ids'] = edge_ids
cost_matrix = ColumnDataSource(data={'G': G_matrix})
# docs indicate that each value should be of the same length but this works
with warnings.catch_warnings():
warnings.simplefilter("ignore")
source = ColumnDataSource(data=src_data)
error_msg = Div(text='', width=int(plot.plot_width / 3), align='center')
table_data = {str(i): ['inf', '-'] for i in range(len(G))}
table_data['index'] = ['label', 'prev']
table_data[str(s)][1] = '0'
table_src = ColumnDataSource(data=table_data)
columns = [TableColumn(field='index', title='')]
for i in range(len(G)):
columns.append(TableColumn(field=str(i), title=str(i)))
table = DataTable(source=table_src,
columns=columns,
height=80,
width_policy='fit',
max_width=plot.plot_width,
width=plot.plot_width,
background='white',
index_position=None,
editable=False,
reorderable=False,
sortable=False,
selectable=False)
on_click = PLOT_CREATE_JS + 'check_done()\nload_data()\ndijkstras()\n'
_add_tools(plot,
on_click=on_click,
nodes_glyph=nodes_glyph,
renderer=nodes_glyph,
source=source,
nodes_src=nodes_src,
edges_src=edges_src,
cost_matrix=cost_matrix,
error_msg=error_msg,
table_src=table_src)
grid = gridplot([[plot], [table], [row(error_msg)]],
plot_width=plot.plot_width,
plot_height=plot.plot_height,
toolbar_location=None,
toolbar_options={'logo': None})
return grid
def _graph_iterations_plot(G: nx.Graph,
nodes: List[List[int]] = None,
edges: List[List[List[int]]] = None,
costs: List[float] = None,
tables: List[pd.DataFrame] = None,
swaps: List[List[int]] = None,
show_all_edges: bool = True,
show_labels: bool = True,
**kw) -> GridBox:
"""Return a plot of multiple iterations of a graph.
Args:
G (nx.Graph): Networkx graph.
nodes (List[List[int]]): Highlighted nodes at every iteration.
edges (List[List[List[int]]]): Highlighted edges at every iteration.
costs (List[float]): Cost at every iteration.
tables (List[pd.DataFrame]): Table to be shown at every iteration.
swaps (List[List[int]]): Edge swap to highlight at every iteration.
show_all_edges (bool, optional): True iff all edges should be shown.
show_labels (bool, optional): True iff labels should be shown.
Returns:
GridBox: Plot of multiple iterations of a graph.
"""
G = G.copy()
plot = _blank_plot(G, **kw)
_set_edge_positions(G)
_set_graph_colors(G)
args_dict = {} # keep track of objects to pass to JS callback
# nodes and edges
nodes_src, nodes_glyph = _add_nodes(G, plot)
args_dict['nodes_src'] = nodes_src
if nodes is not None:
for i in nodes[0]:
nodes_src.data['line_color'][i] = PRIMARY_DARK_COLOR
nodes_src.data['fill_color'][i] = PRIMARY_DARK_COLOR
if show_all_edges:
edges_src, edges_glyph = _add_edges(G, plot, show_labels=show_labels)
# current iteration
n = Div(text='0', width=plot.plot_width, align='center')
args_dict['n'] = n
# total number of iterations
features = [edges, nodes, costs, tables, swaps]
k = max([0 if feature is None else len(feature) for feature in features])
k = Div(text=str(k), width=plot.plot_width, align='center')
args_dict['k'] = k
# indicate if on final iteration
done = Div(text='', width=int(plot.plot_width / 2), align='center')
args_dict['done'] = done
source_data = {}
if edges is not None:
tmp = list(zip(*[_edge_positions(G, edge) for edge in edges]))
edge_xs, edge_ys = tmp
source_data['edge_xs'] = edge_xs
source_data['edge_ys'] = edge_ys
edge_subset_src = ColumnDataSource(data={
'xs': edge_xs[0],
'ys': edge_ys[0]
})
plot.multi_line('xs',
'ys',
line_color=TERTIARY_DARK_COLOR,
line_width=LINE_WIDTH,
level=EDGE_LEVEL,
line_cap='round',
source=edge_subset_src)
args_dict['edge_subset_src'] = edge_subset_src
if nodes is not None:
source_data['nodes'] = nodes
if costs is not None:
source_data['costs'] = costs
cost = Div(text=str(costs[0]),
width=int(plot.plot_width / 2),
align='center')
args_dict['cost'] = cost
if tables is not None:
tables = [table.to_dict(orient='list') for table in tables]
source_data['tables'] = tables
table_src = ColumnDataSource(data=tables[0])
columns = [TableColumn(field='index', title='')]
for i in range(len(tables[0]) - 1):
columns.append(TableColumn(field=str(i), title=str(i)))
table = DataTable(source=table_src,
columns=columns,
height=80,
width_policy='fit',
max_width=plot.plot_width,
width=plot.plot_width,
background='white',
index_position=None,
editable=False,
reorderable=False,
sortable=False,
selectable=False)
args_dict['table_src'] = table_src
if swaps is not None:
tmp = list(zip(*[_swap_positions(G, swap) for swap in swaps]))
swaps_before_x, swaps_before_y, swaps_after_x, swaps_after_y = tmp
source_data['swaps_before_x'] = swaps_before_x
source_data['swaps_before_y'] = swaps_before_y
source_data['swaps_after_x'] = swaps_after_x
source_data['swaps_after_y'] = swaps_after_y
swaps_src = ColumnDataSource(
data={
'swaps_before_x': swaps_before_x[0],
'swaps_before_y': swaps_before_y[0],
'swaps_after_x': swaps_after_x[0],
'swaps_after_y': swaps_after_y[0]
})
plot.multi_line(xs='swaps_before_x',
ys='swaps_before_y',
line_color=SECONDARY_COLOR,
line_width=LINE_WIDTH,
line_cap='round',
level=EDGE_LEVEL,
source=swaps_src)
plot.multi_line(xs='swaps_after_x',
ys='swaps_after_y',
line_color=SECONDARY_COLOR,
line_width=LINE_WIDTH,
line_cap='round',
level=EDGE_LEVEL,
line_dash=[10, 12],
source=swaps_src)
args_dict['swaps_src'] = swaps_src
source = ColumnDataSource(data=source_data)
args_dict['source'] = source
code = ('done_update()\n' + 'cost_update()\n' * (costs is not None) +
'edge_subset_update()\n' * (edges is not None) +
'table_update()\n' * (tables is not None) + 'nodes_update()\n' *
(nodes is not None) + 'swaps_update()\n' * (swaps is not None))
next_btn_code = PLOT_GRAPH_ITERATIONS_JS + 'increment_iteration()\n' + code
prev_btn_code = PLOT_GRAPH_ITERATIONS_JS + 'decrement_iteration()\n' + code
# buttons
next_button = Button(label="Next",
button_type="primary",
max_width=int(plot.plot_width / 2),
width_policy='fit',
sizing_mode='stretch_width')
next_button.js_on_click(CustomJS(args=args_dict, code=next_btn_code))
prev_button = Button(label="Previous",
button_type="primary",
max_width=int(plot.plot_width / 2),
width_policy='fit',
sizing_mode='stretch_width')
prev_button.js_on_click(CustomJS(args=args_dict, code=prev_btn_code))
plot.add_tools(
HoverTool(tooltips=[("Index", "$index"), ("Name", "@name")],
renderers=[nodes_glyph]))
# create layout
layout = [[plot],
[
row(prev_button,
next_button,
max_width=plot.plot_width,
sizing_mode='stretch_both')
], [row(cost, done) if costs else row(done)]]
if tables is not None:
layout.insert(1, [table])
grid = gridplot(layout,
plot_width=plot.plot_width,
plot_height=plot.plot_height,
toolbar_location=None,
toolbar_options={'logo': None})
return grid
DataTable, TableColumn, SelectEditor, IntEditor, NumberEditor)
from bokeh.layouts import column, layout
import numpy as np
np.seterr(all='raise')
fpa_experts = ['Duan', 'Fanning', 'Fagrelius', 'Schubnell', 'Silber',
'Poppett', 'Kai']
pcm = pm.PosCalManager()
pi = pm.get_positioner_index()
source = ColumnDataSource(data=pcm.table)
source.selected.indices = [pcm.i_selected] # ['1d']['indices'] = [i_selected]
title = Div(text='''
<font size="4">Positioner Calibrations</font> (some columns editable)''',
width=500)
columns = [TableColumn(field='UTC', title='UTC', width=160),
TableColumn(field='expid', title='expid', width=50),
TableColumn(field='test name', title='test name', width=260),
TableColumn(field='exptime', title='exptime/s', width=60,
editor=NumberEditor()),
TableColumn(field='dome', title='dome', width=50,
editor=SelectEditor(options=['open', 'closed', '?'])),
TableColumn(field='zenith angle', title='zenith angle', width=69,
editor=IntEditor()),
TableColumn(field='tracking', title='tracking', width=50,
editor=SelectEditor(options=['on', 'off', '?'])),
TableColumn(field='T ambient', title='T ambient/°C', width=75,
editor=NumberEditor()),
TableColumn(field='T mirror', title='T mirror/°C', width=65,
editor=NumberEditor()),
TableColumn(field='PMTC', title='PMTC', width=50,
def get_summarytable(exposures):
'''
Generates a summary table of key values for each night observed. Uses collections.Counter(), OrderedDict()
Args:
exposures: Table of exposures with columns...
Returns a bokeh DataTable object.
'''
nights = np.unique(exposures['NIGHT'])
isbright = (exposures['PROGRAM'] == 'BRIGHT')
isgray = (exposures['PROGRAM'] == 'GRAY')
isdark = (exposures['PROGRAM'] == 'DARK')
iscalib = (exposures['PROGRAM'] == 'CALIB')
num_nights = len(nights)
brights = list()
grays = list()
darks = list()
calibs = list()
totals = list()
for n in nights:
thisnight = exposures['NIGHT'] == n
totals.append(np.count_nonzero(thisnight))
brights.append(np.count_nonzero(thisnight & isbright))
grays.append(np.count_nonzero(thisnight & isgray))
darks.append(np.count_nonzero(thisnight & isdark))
calibs.append(np.count_nonzero(thisnight & iscalib))
med_air = get_median('AIRMASS', exposures)
med_seeing = get_median('SEEING', exposures)
med_exptime = get_median('EXPTIME', exposures)
med_transp = get_median('TRANSP', exposures)
med_sky = get_median('SKY', exposures)
source = ColumnDataSource(data=dict(
nights=list(nights),
totals=totals,
brights=brights,
grays=grays,
darks=darks,
calibs=calibs,
med_air=med_air,
med_seeing=med_seeing,
med_exptime=med_exptime,
med_transp=med_transp,
med_sky=med_sky,
))
formatter = NumberFormatter(format='0,0.00')
template_str = '<a href="night-<%= nights %>.html"' + ' target="_blank"><%= value%></a>'
columns = [
TableColumn(field='nights',
title='NIGHT',
width=100,
formatter=HTMLTemplateFormatter(template=template_str)),
TableColumn(field='totals', title='Total', width=50),
TableColumn(field='brights', title='Bright', width=50),
TableColumn(field='grays', title='Gray', width=50),
TableColumn(field='darks', title='Dark', width=50),
TableColumn(field='calibs', title='Calibs', width=50),
TableColumn(field='med_exptime', title='Median Exp. Time', width=100),
TableColumn(field='med_air',
title='Median Airmass',
width=100,
formatter=formatter),
TableColumn(field='med_seeing',
title='Median Seeing',
width=100,
formatter=formatter),
TableColumn(field='med_sky',
title='Median Sky',
width=100,
formatter=formatter),
TableColumn(field='med_transp',
title='Median Transparency',
width=115,
formatter=formatter),
]
summary_table = DataTable(source=source,
columns=columns,
width=900,
sortable=True,
fit_columns=False)
return summary_table
def __init__(self, model):
"""
Construct separation dashboard
"""
# Save reference to model
self.model = model
################################
# Process button
################################
self.process = Button(label="Generate",
button_type="primary",
name='process',
sizing_mode='scale_width',
css_classes=['generate'])
self.process.js_on_click(CustomJS(code="toggleLoading()"))
################################
# Widgets
################################
# Data type selection
self.data_type = RadioButtonGroup(
labels=["All Data", "Experimental", "Simulated"],
active=0,
css_classes=['dtypes'])
# Adsorbate drop-down selections
self.g1_sel = Select(title="Adsorbate 1",
options=self.model.ads_list,
value=self.model.g1,
css_classes=['g-selectors'])
self.g2_sel = Select(title="Adsorbate 2",
options=self.model.ads_list,
value=self.model.g2)
# Temperature selection
self.t_absolute = Spinner(value=self.model.t_abs,
title='Temperature:',
css_classes=['t-abs'])
self.t_tolerance = Spinner(value=self.model.t_tol,
title='Tolerance:',
css_classes=['t-tol'])
# Combined in a layout
self.dsel_widgets = layout([
[self.data_type],
[self.g1_sel, self.g2_sel, self.t_absolute, self.t_tolerance],
],
sizing_mode='scale_width',
name="widgets")
################################
# KPI Plots
################################
# Top graph generation
tooltip = load_tooltip()
self.p_henry, rend1 = self.top_graph("K", "Henry coefficient (log)",
self.model.data,
self.model.errors, tooltip)
self.p_loading, rend2 = self.top_graph(
"L", "Uptake at selected pressure (bar)", self.model.data,
self.model.errors, tooltip)
self.p_wc, rend3 = self.top_graph(
"W", "Working capacity in selected range (bar)", self.model.data,
self.model.errors, tooltip)
# Give graphs the same hover and select effect
sel = Circle(fill_alpha=1, fill_color="red", line_color=None)
nonsel = Circle(fill_alpha=0.2, fill_color="blue", line_color=None)
for rend in [rend1, rend2, rend3]:
rend.selection_glyph = sel
rend.nonselection_glyph = nonsel
rend.hover_glyph = sel
# Pressure slider
self.p_slider = Slider(
title="Pressure (bar)",
value=0.5,
start=0,
end=20,
step=0.5,
callback_policy='throttle',
callback_throttle=200,
)
# Working capacity slider
self.wc_slider = RangeSlider(
title="Working capacity (bar)",
value=(0.5, 5),
start=0,
end=20,
step=0.5,
callback_policy='throttle',
callback_throttle=200,
)
# Material datatable
self.mat_list = DataTable(
columns=[
TableColumn(field="labels", title="Material", width=300),
TableColumn(field="sel",
title="KH2/KH1",
width=35,
formatter=NumberFormatter(format='‘0.0a’')),
TableColumn(field="psa_W",
title="PSA-API",
width=35,
formatter=NumberFormatter(format='‘0.0a’')),
],
source=self.model.data,
index_position=None,
selectable='checkbox',
scroll_to_selection=True,
width=400,
fit_columns=True,
)
# Custom css classes for interactors
self.p_henry.css_classes = ['g-henry']
self.p_loading.css_classes = ['g-load']
self.p_wc.css_classes = ['g-wcap']
self.mat_list.css_classes = ['t-details']
# Generate the axis labels
self.top_graph_labels()
self.kpi_plots = layout([
[
gridplot([[self.mat_list, self.p_henry],
[self.p_loading, self.p_wc]],
sizing_mode='scale_width')
],
[self.p_slider, self.wc_slider],
],
sizing_mode='scale_width',
name="kpiplots")
self.kpi_plots.children[0].css_classes = ['kpi']
self.kpi_plots.children[1].css_classes = ['p-selectors']
################################
# Isotherm details explorer
################################
# Isotherm display graphs
self.p_g1iso = self.bottom_graph(self.model.g1_iso_sel, self.model.g1)
self.p_g2iso = self.bottom_graph(self.model.g2_iso_sel, self.model.g2)
# Isotherm display palette
self.c_cyc = cycle(gen_palette(20))
self.detail_plots = layout([
[self.p_g1iso, self.p_g2iso],
],
sizing_mode='scale_width',
name="detailplots")
self.detail_plots.children[0].css_classes = ['isotherms']
'O4: Lieutenant Commander', 'O5: Commander', 'O6: Captain',
'O7: Rear Admiral (lower half)', 'O8: Rear Admiral (upper half)',
'O9: Vice Admiral', 'O10: Admiral'
]
}
dictDT3 = {
'RankNames': [
'CWO2: Chief Warrant Officer', 'CWO3: Chief Warrant Officer',
'CWO4: Chief Warrant Officer', 'CWO5: Chief Warrant Officer'
]
}
sourceDT1 = ColumnDataSource(data=dictDT1)
sourceDT2 = ColumnDataSource(data=dictDT1)
sourceDT3 = ColumnDataSource(data=dictDT1)
columnsDT = [TableColumn(field="RankNames", title="Rank")]
data_table1 = DataTable(source=sourceDT1,
columns=columnsDT,
width=170,
editable=True,
reorderable=False,
index_position=None)
data_table2 = DataTable(source=sourceDT2,
columns=columnsDT,
width=170,
editable=True,
reorderable=False,
index_position=None)
data_table3 = DataTable(source=sourceDT3,
columns=columnsDT,
width=170,
def transform(self):
if self.__graph_input.value and self.__endpoint_input.value:
filename = self.__graph_input.value.split('/')[-1].split('.')[0]
print("converting")
sparql = SPARQLWrapper("https://www.foodie-cloud.org/sparql")
query_a = """
prefix obs: <http://purl.org/linked-data/sdmx/2009/measure#>
prefix prop: <http://eurostat.linked-statistics.org/property#>
prefix qb: <http://purl.org/linked-data/cube#>
prefix sdmx-dimension: <http://purl.org/linked-data/sdmx/2009/dimension#>
select distinct ?designation ?time ?value ?unit
"""
graph = "from <{}>".format(self.__graph_input.value)
query_b = """
where {
?observation a qb:Observation.
?observation prop:geo ?designation.
?observation prop:unit ?unit.
?observation sdmx-dimension:timePeriod ?time.
?observation obs:obsValue ?value.
}
"""
query = "{}\n{}\n{}".format(query_a, graph, query_b)
sparql.setQuery(query)
sparql.setReturnFormat(JSON)
results = sparql.query().convert()
print("writing")
self.__write_geojson(results, filename)
print("done converting")
self.__file_list = self.__get_eurostats()
geojson_data = {'id': [], 'lvl': []}
for file in self.__file_list:
if file['geojson']['nuts1']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(1)
if file['geojson']['nuts2']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(2)
if file['geojson']['nuts3']['exists']:
geojson_data['id'].append(file['id'])
geojson_data['lvl'].append(3)
self.__geojson_table_source = ColumnDataSource(geojson_data)
geojson_table_columns = [
TableColumn(field='lvl', title='NUTS Level'),
TableColumn(field='id', title='ID')
]
self.geojson_table = DataTable(source=self.__geojson_table_source,
columns=geojson_table_columns,
width=300,
height=500,
selectable=True)
self.__layout.children[2] = column(self.geojson_table)
main_scatter_plot = figure(tools='box_select,lasso_select,pan,wheel_zoom,reset,resize,save')
main_scatter_plot.add_tools(hover)
main_scatter_df = df[(df.attr_rank==0) & (df.attr_name==selected_attribute) & (df.attr_rank==0)]
main_scatter_source=ColumnDataSource(main_scatter_df)
color = to_color(main_scatter_df)
r=main_scatter_plot.circle('x','y', source=main_scatter_source, radius=0.25, fill_alpha=0.8, color=color)
# calculate context
context_df = df.groupby(['attr_value']).agg({'id':'count'}).rename(columns={'id':'n'})
# setup attribute table
table_df = df[df.attr_name==selected_attribute].groupby(['attr_value']).agg({'id':'count'})
table_df = table_df.sort_values(by='id', ascending=False).rename(columns={'id':'n'})
joined_df = calculate_ratio(table_df)
table_source = ColumnDataSource(joined_df)
table_source_column = [TableColumn(field="attr_value", title="Attribute Value"),TableColumn(field="n", title="Counts"),TableColumn(field="ratio", title="Ratio"),]
table_data_table = DataTable(source=table_source, columns=table_source_column, width=400, height=800)
# setup dropdowns
main_dropdown = Select(title="Chart Attributes", options=attributes_name, value=selected_attribute)
table_dropdown = Select(title="Histogram Attributes", options=attributes_name, value=selected_attribute)
# setup text input
threshold_input = TextInput(value=str(threshold), title="Threshold:")
# setup layout
layout_left = VBox(main_scatter_plot, main_dropdown)
layout_right = VBox(HBox(table_dropdown,threshold_input), table_data_table)
layout = HBox(layout_left,layout_right)
def update_threshold_callback(attr_name, old, new):
def init_source(self):
self.source = ColumnDataSource(data=data)
self.data_table = DataTable(source=self.source,
columns=[
TableColumn(field='fpid',
title='FPID'),
TableColumn(field='chromophore_name',
title='chromophore_name'),
TableColumn(field='chromophore_class',
title='chromophore_class'),
TableColumn(field='protein_name',
title='Protein name'),
TableColumn(field='excitation_new',
title='Excitation'),
TableColumn(field='emission_new',
title='Emission'),
TableColumn(field='pdb_id',
title='PDB ID'),
TableColumn(field='genbank',
title='Genbank ID'),
TableColumn(field='mutation',
title='Mutation'),
TableColumn(field='quantum_yield',
title='Quantum Yield'),
TableColumn(field='pka', title='pka'),
TableColumn(
field='amino_acid_sequence',
title='Sequence'),
])
self.data_table.width = 1200
fill_color='bar_color')
plot_dc.add_glyph(ColumnDataSource(dc_df), glyph_dc)
plot_dc.add_layout(
LinearAxis(axis_label='Number of articles', **axis_defaults), 'left')
plot_dc.add_layout(
CategoricalAxis(axis_label='Date',
major_label_orientation=pi / 2,
**axis_defaults), 'below')
# most popular table
pop_dt = DataTable(row_headers=False,
selectable=False,
sortable=True,
sizing_mode='scale_both')
pop_dt.columns = [
TableColumn(field='rank', title='Rank', sortable=True, width=50),
TableColumn(field='section_name',
title='Section',
sortable=True,
width=150),
TableColumn(field='pub_date', title='Date', sortable=True, width=150),
TableColumn(field='headline', title='Headline', sortable=True),
TableColumn(field='emails rank',
title='Email rank',
sortable=True,
width=125),
TableColumn(field='shares rank',
title='Share rank',
sortable=True,
width=125),
TableColumn(field='views rank',
