def tap_histogram(index, x_range, y_range):
(x0, x1), (y0, y1) = x_range, y_range
# if nothing is selected
if index == list():
# select all
index = list(self.df_extracted.index)
return self.polys.iloc[index].opts(opts.Polygons(xlim=(x0, x1), ylim=(y0, y1)))
def __post_init__(self):
"""
:return:
"""
data = self.spectral_cube.data
self.ds = hv.Dataset((np.arange(data.shape[2]), np.arange(
data.shape[1]), np.arange(data.shape[0]), data),
[self.spectral_axis_name, 'x', 'y'], 'Cube')
# maybe PolyEdit as well
# polys = hv.Polygons([hv.Box(int(self.image_width / 2), int(self.image_height / 2), int(self.image_height / 2))])
# self.box_stream = streams.PolyEdit(source=polys)
polys = hv.Polygons([])
self.box_stream = streams.BoxEdit(source=polys)
hlines = hv.HoloMap({i: hv.VLine(i)
for i in range(data.shape[2])}, 'wavelengths')
dmap = hv.DynamicMap(self.roi_curves, streams=[self.box_stream])
im = self.ds.to(hv.Image, ['x', 'y'], dynamic=True)
self.layout = (im * polys + dmap * hlines).opts(
opts.Image(cmap=self.color_map,
width=self.image_width,
height=self.image_height),
opts.Curve(width=650, height=450, framewise=True),
opts.Polygons(fill_alpha=0.2, line_color='white'),
opts.VLine(color='black'))
def index():
mystates = States.query.order_by(States.state)
states_list = pickle.load(open(f'data/states_geo.pkl', "rb"))
choropleth = hv.Polygons(states_list, ['lons', 'lats'],
['state', 'tot', 'unemployed'])
choropleth.opts(
opts.Polygons(logz=True,
tools=['hover'],
xaxis=None,
yaxis=None,
show_grid=False,
show_frame=False,
width=830,
height=500,
color_index='tot',
cmap='Oranges',
colorbar=True,
toolbar='above',
line_color='white'))
return render_template('index.html',
title='Health Care by the Numbers',
mystates=mystates)
def get_plot(path, poly):
return (path * poly).opts(
opts.Polygons(fill_alpha=0.3, active_tools=["poly_draw"]),
opts.Path(color=LINE, height=400, line_width=5, width=400),
)
imgs_pv = ds_sel['p_values'].hvplot.contour(**hvc_opts)
temp = xr.apply_ufunc(combine_pvalues_ufunc, ds_sel['p_values'], input_core_dims=[['ens']], \
output_core_dims = [[]], vectorize = True, dask = 'allowed')
hvc_opts = dict(width=300, dynamic=True, \
x = 'x', y = 'y', colorbar = False, \
logy = True, cmap = ['black', 'gray'], \
levels=[0.01,0.05])
imgs_pv2 = temp.hvplot.contour(**hvc_opts)
# -
# ## Layout
# By combining every panel in a layout, we get clear interactive dashboard
hl = hv.HLine(0).opts(color='gray', line_dash='dotted')
dmap = dmap.opts(xticks=[(i, ens_name) for i, ens_name in enumerate(ens_ls)])
first_panel = im * imgs_pv * polys
second_panel = (dmap * hl * hlines).relabel('ROI drawer')
hv_div = hv.Div(
f"""<h1>{invar} response to {sel_reg} for {month_names[sel_month-1]}</h1>"""
)
second_row = (
(im2 * imgs_pv2).relabel('Model average (p-values combined using Z-score)')
+ hv_div)
layout = ((first_panel + second_panel).opts(
opts.Curve(width=400, framewise=True),
opts.Polygons(fill_alpha=0.2, line_color='green', fill_color='green'),
opts.VLine(color='black')) + second_row).cols(2)
layout
from os.path import abspath
import webbrowser
import holoviews as hv
from holoviews import opts
hv.extension('bokeh')
from bokeh.sampledata.us_counties import data as counties
from bokeh.sampledata.unemployment import data as unemployment
counties = [dict(county, Unemployment=unemployment[cid])
for cid, county in counties.items()
if county["state"] == "tx"]
choropleth = hv.Polygons(counties, ['lons', 'lats'],
[('detailed name', 'County'), 'Unemployment'])
choropleth.opts(opts.Polygons(logz=True,
tools=['hover'],
xaxis=None, yaxis=None,
show_grid=False,
show_frame=False,
width=500, height=500,
color_index='Unemployment',
colorbar=True, toolbar='above',
line_color='white'))
hv.save(choropleth, 'texas.html', backend='bokeh')
url = abspath('texas.html')
webbrowser.open(url)
def plot(self):
"""plot pane"""
# get the tract list
tract_list = self.tracts_in_widget()
# extract the filter from the original data
self.df_filter = self.df[self.df['filter'] == self.filter_]
# extract only the provided metric
self.df_extracted = self.df_filter[['tract','geometry', self.metric, 'x0','x1','y0','y1']]
# rename the metric column (necessary abstraction for plotting)
self.df_extracted = self.df_extracted.rename(columns={self.metric: 'metric'})
if self.df.empty:
return pn.Spacer()
else:
if self.geoviews:
self.polys = gv.Polygons(gpd.GeoDataFrame(self.df_extracted).set_geometry('geometry'), vdims=['metric', 'tract']).opts(
tools=['hover', 'tap'], width=self.plot_width, height=self.plot_height,
line_width=0, active_tools=['wheel_zoom', 'tap'],
colorbar=True, title=self.metric, color='metric')
else:
def create_dict(row):
"""create a dictionary representation of a df row"""
d = {('x','y'): np.array(row.geometry.exterior.coords),
'tract': row['tract'],
'metric': row['metric']
}
return d
# create a dictionary reprresentation of the dataframe
data = list(self.df_extracted.apply(create_dict, axis=1))
# declare polygons
self.polys = hv.Polygons(data, vdims=['metric', 'tract']).opts(
tools=['hover', 'tap'],
line_width=0, active_tools=['wheel_zoom', 'tap'],
colorbar=True, title=self.metric, color='metric')
# Declare Tap stream with polys as source and initial values
self.stream.source = self.polys
# Define a RangeXY stream linked to the image (preserving ranges from the previous image)
self.rangexy = hv.streams.RangeXY(
source=self.polys,
x_range=self.rangexy.x_range,
y_range=self.rangexy.y_range,
)
# set padding (degrees)
padding = 0
# get the limits of the selected filter/metric data
xmin = self.df_extracted.x0.min() - padding
xmax = self.df_extracted.x1.max() + padding
ymin = self.df_extracted.y0.min() - padding
ymax = self.df_extracted.y1.max() + padding
# convert to google mercator if using geoviews
# TODO this produces reasonable, but incorrect results
if self.geoviews:
xmin, ymin = ccrs.GOOGLE_MERCATOR.transform_point(xmin, ymin, ccrs.PlateCarree())
xmax, ymax = ccrs.GOOGLE_MERCATOR.transform_point(xmax, ymax, ccrs.PlateCarree())
# create hook for reseting to full extent
def reset_range_hook(plot, element):
plot.handles['x_range'].reset_start = xmin
plot.handles['x_range'].reset_end = xmax
plot.handles['y_range'].reset_start = ymin
plot.handles['y_range'].reset_end = ymax
# Define function to compute selection based on tap location
def tap_histogram(index, x_range, y_range):
(x0, x1), (y0, y1) = x_range, y_range
# if nothing is selected
if index == list():
# select all
index = list(self.df_extracted.index)
return self.polys.iloc[index].opts(opts.Polygons(xlim=(x0, x1), ylim=(y0, y1)))
tap_dmap = hv.DynamicMap(tap_histogram, streams=[self.stream, self.rangexy])
# set up the plot to match the range stream
if not self.rangexy.x_range and not self.rangexy.y_range:
(x0, x1, y0, y1) = (None, None, None, None)
else:
(x0, x1), (y0, y1) = self.rangexy.x_range, self.rangexy.y_range
return self.polys.opts(opts.Polygons(xlim=(x0, x1),
ylim=(y0, y1),
hooks=[reset_range_hook],
responsive=True,
bgcolor='black')) # TODO: responsive=True isn't changing the width
from holoviews.element.tiles import StamenTerrain
from mednum.loaders import *
from pygal.style import Style
from mednum import tools
from mednum.config import *
import mednum as mind
gv.extension("bokeh")
opts.defaults(
opts.Polygons(
width=800,
height=600,
toolbar="above",
colorbar=True,
tools=["hover", "tap"],
aspect="equal",
)
)
class OverallParameters(param.Parameterized):
localisation = param.String(default="Jegun", label="")
score = param.Range(default=(0, 250), bounds=(0, 250),)
tout_axes = param.Boolean(False, label="")
interfaces_num = param.ListSelector(label="")
infos_num = param.ListSelector(label="")
comp_admin = param.ListSelector(label="")
comp_usage_num = param.ListSelector(label="")
polys = hv.Polygons([])
box_stream = streams.BoxEdit(source=polys)
def roi_curves(data):
if not data or not any(len(d) for d in data.values()):
return hv.NdOverlay({0: hv.Curve([], 'Time', 'Fluorescence')})
curves = {}
data = zip(data['x0'], data['x1'], data['y0'], data['y1'])
for i, (x0, x1, y0, y1) in enumerate(data):
selection = ds.select(x=(x0, x1), y=(y0, y1))
curves[i] = hv.Curve(selection.aggregate('Time', np.mean))
return hv.NdOverlay(curves)
hlines = hv.HoloMap({i: hv.VLine(i) for i in range(50)}, 'Time')
dmap = hv.DynamicMap(roi_curves, streams=[box_stream])
im = ds.to(hv.Image, ['x', 'y'], dynamic=True)
layout = (im * polys + dmap * hlines).opts(
opts.Curve(width=400, framewise=True),
opts.Polygons(fill_alpha=0.2, line_color='white'),
opts.VLine(color='black'))
#hv.renderer('bokeh').server_doc(layout)
#pn.panel(layout).servable(title='babla')
server = pn.serve(layout, start=False, show=False)
server.start()
def plot(self):
debug("OverviewApp.plot()")
"""plot pane"""
# get the tract list
tract_list = self.tracts_in_widget()
# extract the filter from the original data
self.df_filter = self.df[self.df["filter"] == self.filter_]
# extract only the provided metric
self.df_extracted = self.df_filter[["tract", "geometry", self.metric, "x0", "x1", "y0", "y1"]]
# filter down tracts
self.df_extracted = self.df_extracted.loc[self.df_extracted.tract.isin(self.active_tracts)]
debug("OverviewApp.plot() --> Number of Tracts to Plot {}".format(len(self.df_extracted)))
# rename the metric column (necessary abstraction for plotting)
self.df_extracted = self.df_extracted.rename(columns={self.metric: "metric"})
if self.df.empty:
return pn.Spacer()
else:
def create_dict(row):
"""create a dictionary representation of a df row"""
d = {
("x", "y"): np.array(row.geometry.exterior.coords),
"tract": row["tract"],
"metric": row["metric"],
}
return d
# create a dictionary reprresentation of the dataframe
data = list(self.df_extracted.apply(create_dict, axis=1))
# declare polygons
self.polys = hv.Polygons(data, vdims=["metric", "tract"]).opts(
tools=["hover", "tap", "box_select"],
line_width=0,
active_tools=["wheel_zoom", "tap"],
colorbar=True,
title=self.metric,
color="metric",
)
# Declare Tap stream with polys as source and initial values
self.stream.source = self.polys
# Define a RangeXY stream linked to the image (preserving ranges from the previous image)
self.rangexy = hv.streams.RangeXY(
source=self.polys, x_range=self.rangexy.x_range, y_range=self.rangexy.y_range,
)
# set padding (degrees)
padding = 0
# get the limits of the selected filter/metric data
xmin = self.df_extracted.x0.min() - padding
xmax = self.df_extracted.x1.max() + padding
ymin = self.df_extracted.y0.min() - padding
ymax = self.df_extracted.y1.max() + padding
# create hook for reseting to full extent
def reset_range_hook(plot, element):
plot.handles["x_range"].reset_start = xmin
plot.handles["x_range"].reset_end = xmax
plot.handles["y_range"].reset_start = ymin
plot.handles["y_range"].reset_end = ymax
# Define function to compute selection based on tap location
def tap_histogram(index, x_range, y_range):
(x0, x1), (y0, y1) = x_range, y_range
# if nothing is selected
if index == list():
# select all
index = list(self.df_extracted.index)
return self.polys.iloc[index].opts(opts.Polygons(xlim=(x0, x1), ylim=(y0, y1)))
tap_dmap = hv.DynamicMap(tap_histogram, streams=[self.stream, self.rangexy])
# set up the plot to match the range stream
if not self.rangexy.x_range and not self.rangexy.y_range:
(x0, x1, y0, y1) = (None, None, None, None)
else:
(x0, x1), (y0, y1) = self.rangexy.x_range, self.rangexy.y_range
return self.polys.opts(
opts.Polygons(
xlim=(x0, x1), ylim=(y0, y1), hooks=[reset_range_hook], responsive=True, bgcolor="black"
)
) # TODO: responsive=True isn't changing the width
EXCLUDED = ('ak', 'hi', 'pr', 'gu', 'vi', 'mp', 'as')
counties = [
dict(county, Density=popl_dens_dict[cid])
for cid, county in counties.items() if county["state"] not in EXCLUDED
]
choropleth = hv.Polygons(counties, ['lons', 'lats'],
[('detailed name', 'County'), 'Density'])
choropleth.opts(
opts.Polygons(
logz=True,
tools=['hover'],
xaxis=None,
yaxis=None,
show_grid=False,
show_frame=False,
width=1100,
height=700,
colorbar=True,
toolbar='above',
color_index='Density',
cmap='Greys',
line_color=None,
title='2010 Population Density per Square Mile of Land Area'))
hv.save(choropleth, 'choropleth.html', backend='bokeh')
url = abspath('choropleth.html')
webbrowser.open(url)
