A lot of folks have time stacks of imagery data (data cubes) and seems like a common use case would be to make a map, click a location on the map and see a time series from that spot.
Our Google Summer of Code student wrote xrviz which does this, but it’s pretty complex, using a SigSlot library, which I’m not sure is the latest best practice for building Panel apps like this.
Does anyone have a simple example of this type of Panel app?
I haven’t learned how to use panel’s latest methods, but this is how I did it:
import panel as pn
import numpy as np
import xarray as xr
import holoviews as hv
import hvplot.xarray
pn.extension()
ds = xr.tutorial.open_dataset('air_temperature')
image = ds.hvplot('lon', 'lat')
stream = hv.streams.Tap(source=image, x=-88 + 360, y=40)
@pn.depends(stream.param.x, stream.param.y)
def timeseries(x, y):
return ds.sel(lon=x, lat=y, method='nearest').hvplot('time')
pn.Column(image, timeseries)
modified from Example of using holoviews TapStream with Panel
Thanks, @ahuang11! If you want to see how it looks using pn.bind from panel 0.10.1 instead of @depends, it’s just:
import panel as pn
import numpy as np
import xarray as xr
import holoviews as hv
import hvplot.xarray
pn.extension()
ds = xr.tutorial.open_dataset('air_temperature')
image = ds.hvplot('lon', 'lat')
stream = hv.streams.Tap(source=image, x=-88 + 360, y=40)
def timeseries(x, y):
return ds.sel(lon=x, lat=y, method='nearest').hvplot('time')
pn.Column(image, pn.bind(timeseries, x=stream.param.x, y=stream.param.y))
I.e., basically the same, but now you can write your callback function as just a regular Python function now, with no decorator, and then later bind its arguments to widgets or to stream parameters when you want to put it in a panel.
[UPDATED with working code; I needed to add .dmap()]
You can also write this even more simply using the new .interactive support in hvPlot, which lets you eliminate the callback entirely:
import panel as pn
import numpy as np
import xarray as xr
import holoviews as hv
import hvplot.xarray
pn.extension()
ds = xr.tutorial.open_dataset('air_temperature')
image = ds.hvplot('lon', 'lat')
stream = hv.streams.Tap(source=image, x=-88+360, y=40)
timeseries = ds.interactive.sel(lon=stream.param.x, lat=stream.param.y,
method="nearest").hvplot('time')
pn.Column(image, timeseries.dmap())
@jbednar, this works great, but if I change the slider widget to “Select” using widgets={'time':pn.widgets.Select} thusly, it bombs:
import panel as pn
import numpy as np
import xarray as xr
import holoviews as hv
import hvplot.xarray
pn.extension()
ds = xr.tutorial.open_dataset('air_temperature')
image = ds.hvplot('lon', 'lat', widgets={'time':pn.widgets.Select})
stream = hv.streams.Tap(source=image, x=-88 + 360, y=40)
def timeseries(x, y):
return ds.sel(lon=x, lat=y, method='nearest').hvplot('time')
pn.Column(image, pn.bind(timeseries, x=stream.param.x, y=stream.param.y))
with the error:
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
968
969 if method is not None:
--> 970 return method(include=include, exclude=exclude)
971 return None
972 else:
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/viewable.py in _repr_mimebundle_(self, include, exclude)
571 doc = _Document()
572 comm = state._comm_manager.get_server_comm()
--> 573 model = self._render_model(doc, comm)
574 ref = model.ref['id']
575 manager = CommManager(comm_id=comm.id, plot_id=ref)
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/viewable.py in _render_model(self, doc, comm)
422 if comm is None:
423 comm = state._comm_manager.get_server_comm()
--> 424 model = self.get_root(doc, comm)
425
426 if config.embed:
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/viewable.py in get_root(self, doc, comm, preprocess)
480 """
481 doc = init_doc(doc)
--> 482 root = self._get_model(doc, comm=comm)
483 if preprocess:
484 self._preprocess(root)
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/layout/base.py in _get_model(self, doc, root, parent, comm)
110 if root is None:
111 root = model
--> 112 objects = self._get_objects(model, [], doc, root, comm)
113 props = dict(self._init_properties(), objects=objects)
114 model.update(**self._process_param_change(props))
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/layout/base.py in _get_objects(self, model, old_objects, doc, root, comm)
100 else:
101 try:
--> 102 child = pane._get_model(doc, root, model, comm)
103 except RerenderError:
104 return self._get_objects(model, current_objects[:i], doc, root, comm)
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/layout/base.py in _get_model(self, doc, root, parent, comm)
110 if root is None:
111 root = model
--> 112 objects = self._get_objects(model, [], doc, root, comm)
113 props = dict(self._init_properties(), objects=objects)
114 model.update(**self._process_param_change(props))
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/layout/base.py in _get_objects(self, model, old_objects, doc, root, comm)
100 else:
101 try:
--> 102 child = pane._get_model(doc, root, model, comm)
103 except RerenderError:
104 return self._get_objects(model, current_objects[:i], doc, root, comm)
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/pane/holoviews.py in _get_model(self, doc, root, parent, comm)
239 plot = self.object
240 else:
--> 241 plot = self._render(doc, comm, root)
242
243 plot.pane = self
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/panel/pane/holoviews.py in _render(self, doc, comm, root)
304 kwargs['comm'] = comm
305
--> 306 return renderer.get_plot(self.object, **kwargs)
307
308 def _cleanup(self, root):
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/holoviews/plotting/bokeh/renderer.py in get_plot(self_or_cls, obj, doc, renderer, **kwargs)
71 combining the bokeh model with another plot.
72 """
---> 73 plot = super(BokehRenderer, self_or_cls).get_plot(obj, doc, renderer, **kwargs)
74 if plot.document is None:
75 plot.document = Document() if self_or_cls.notebook_context else curdoc()
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/holoviews/plotting/renderer.py in get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
234 obj = Layout(obj)
235 plot = self_or_cls.plotting_class(obj)(obj, renderer=renderer,
--> 236 **plot_opts)
237 defaults = [kd.default for kd in plot.dimensions]
238 init_key = tuple(v if d is None else d for v, d in
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/holoviews/plotting/bokeh/raster.py in __init__(self, *args, **kwargs)
72
73 def __init__(self, *args, **kwargs):
---> 74 super(RasterPlot, self).__init__(*args, **kwargs)
75 if self.hmap.type == Raster:
76 self.invert_yaxis = not self.invert_yaxis
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/holoviews/plotting/bokeh/element.py in __init__(self, element, plot, **params)
204 self.handles = {} if plot is None else self.handles['plot']
205 self.static = len(self.hmap) == 1 and len(self.keys) == len(self.hmap)
--> 206 self.callbacks = self._construct_callbacks()
207 self.static_source = False
208 self.streaming = [s for s in self.streams if isinstance(s, Buffer)]
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/holoviews/plotting/plot.py in _construct_callbacks(self)
952 for source in self.link_sources:
953 streams = [
--> 954 s for src, streams in registry for s in streams
955 if src is source or (src._plot_id is not None and
956 src._plot_id == source._plot_id)]
/home/conda/store/5413108540ec5590442f729933018374edec0237f31b6b39bdb179c9e72aa025-pangeo/lib/python3.7/site-packages/holoviews/plotting/plot.py in <listcomp>(.0)
953 streams = [
954 s for src, streams in registry for s in streams
--> 955 if src is source or (src._plot_id is not None and
956 src._plot_id == source._plot_id)]
957 cb_classes |= {(callbacks[type(stream)], stream) for stream in streams
AttributeError: 'Row' object has no attribute '_plot_id'
Column
[0] Row
[0] HoloViews(DynamicMap, widgets={'time': <class '...})
[1] Column
[0] WidgetBox
[0] Select(margin=(20, 20, 20, 20), name='Time', options=OrderedDict([('2013-01-01 ...]), value=numpy.datetime64('2013-01-..., width=250)
[1] VSpacer()
[1] ParamFunction(function)
Am I doing this wrong or is it a bug?
When you set pn.widgets.Select, hvplot becomes a pn.Row object with the first item being a pn.pane.Holoviews and the second item as a pn.pane.Select. With the type changes in mind, this works:
import panel as pn
import numpy as np
import xarray as xr
import holoviews as hv
import hvplot.xarray
pn.extension()
ds = xr.tutorial.open_dataset('air_temperature')
image, select = ds.hvplot('lon', 'lat', widgets={'time':pn.widgets.Select})
stream = hv.streams.Tap(source=image.object, x=-88 + 360, y=40)
def timeseries(x, y):
return ds.sel(lon=x, lat=y, method='nearest').hvplot('time')
pn.Column(image, select, pn.bind(timeseries, x=stream.param.x, y=stream.param.y))
If overlaying with anything, it doesn’t work either.
import panel as pn
import numpy as np
import xarray as xr
import holoviews as hv
import hvplot.xarray
pn.extension()
ds = xr.tutorial.open_dataset('air_temperature')
image, select = ds.hvplot('lon', 'lat', widgets={'time':pn.widgets.Select}, coastline=True)
stream = hv.streams.Tap(source=image.object, x=-88 + 360, y=40)
def timeseries(x, y):
return ds.sel(lon=x, lat=y, method='nearest').hvplot('time')
pn.Column(image, select, pn.bind(timeseries, x=stream.param.x, y=stream.param.y))
The solution is to do image * gv.features.coastline() after calling the bind.
Adding to this discussion. I was trying to embed this into a dashboard. This is the working code:
ds = xr.tutorial.open_dataset('air_temperature')
#create a new variable to have something to change
ds['air_C'] = ds['air']-273
class GliderParams(param.Parameterized):
'''Class containing the methods for dataset and variable selection'''
surface_var = param.Selector(['air','air_C'], default = 'air', label = 'Surface Field')
#@param.depends('surface_var')
def imaging(surface_var):
image,select = ds[surface_var].hvplot(groupby='time',widget_location = 'bottom',
cmap='RdBu_r',ylim=[15,80],xlim = [200,360],
crs=ccrs.PlateCarree(),projection=ccrs.PlateCarree())
#coastline=True,
stream = hv.streams.Tap(source=image.object, x=0, y=0)
timeseries = ds[surface_var].interactive.sel(lon=stream.param.x, lat=stream.param.y, method='nearest').hvplot('time')
return pn.Column(image, select,timeseries.dmap())
gp = GliderParams()
pn.Row(pn.Param(gp, name=''),pn.bind(imaging,gp.param.surface_var))
However, when adding coastline=True, I get an empty plot (not sure why).
The second problem I’m encountering is how to add a dynamic title to the timeseries plot to incorporate the clicked lat/lon?
Thank you!
The solution is to do image * gv.features.coastline() after calling the bind.
And maybe
timeseries = ds[surface_var].interactive.sel(lon=stream.param.x, lat=stream.param.y, method='nearest').hvplot('time').apply.opts(title=f"{stream.param.x}, {stream.param.y}")
Hi @khider
After reading your last comment I am in doubt if you need more help. Could you post your minimum, reproducible example and questions if any to make it very clear what you are looking for? Thanks. 
Working Example:
#To load and manipulate the data
import xarray as xr
import os
import glob
import numpy as np
import math
import pandas as pd
from calendar import monthrange
import xesmf as xe
import dask
#For Viz
import matplotlib.pyplot as plt
import param
import datetime as dt
import panel as pn
import hvplot.xarray # noqa
import holoviews as hv
import panel.widgets as pnw
import cartopy.crs as ccrs
import geoviews as gv
ds = xr.tutorial.open_dataset('air_temperature')
#create a new variable to have something to change
ds['air_C'] = ds['air']-273
class GliderParams(param.Parameterized):
'''Class containing the methods for dataset and variable selection'''
surface_var = param.Selector(['air','air_C'], default = 'air', label = 'Surface Field')
#@param.depends('surface_var')
def imaging(surface_var):
image,select = ds[surface_var].hvplot(groupby='time',widget_location = 'bottom',
cmap='RdBu_r',ylim=[15,80],xlim = [200,360],
crs=ccrs.PlateCarree(),projection=ccrs.PlateCarree())
#coastline=True,
stream = hv.streams.Tap(source=image.object, x=0, y=0)
timeseries = ds[surface_var].interactive.sel(lon=stream.param.x, lat=stream.param.y, method='nearest').hvplot('time')
return pn.Column(image, select,timeseries.dmap())
gp = GliderParams()
pn.Row(pn.Param(gp, name=''),pn.bind(imaging,gp.param.surface_var))
To this, I’m trying to add two things:
def imaging(surface_var):
image,select = ds[surface_var].hvplot(groupby='time',widget_location = 'bottom',
cmap='RdBu_r',ylim=[15,80],xlim = [200,360],
crs=ccrs.PlateCarree(),projection=ccrs.PlateCarree())
#coastline=True,
stream = hv.streams.Tap(source=image.object, x=0, y=0)
timeseries = ds[surface_var].interactive.sel(lon=stream.param.x, lat=stream.param.y, method='nearest').hvplot('time').apply.opts(title=f"{stream.x}, {stream.y}")
return pn.Column(image, select,timeseries.dmap())
Which returns: 0,0 as the title (the default for stream) but doesn’t update.
def imaging(surface_var):
image,select = ds[surface_var].hvplot(groupby='time',widget_location = 'bottom',
cmap='RdBu_r',ylim=[15,80],xlim = [200,360],
crs=ccrs.PlateCarree(),projection=ccrs.PlateCarree())
#coastline=True,
stream = hv.streams.Tap(source=image.object, x=0, y=0)
timeseries = ds[surface_var].interactive.sel(lon=stream.param.x, lat=stream.param.y, method='nearest').hvplot('time').apply.opts(title=f"{stream.x}, {stream.y}")
return pn.Column(image* gv.features.coastline(), select,timeseries.dmap())
And got:
AttributeError Traceback (most recent call last)
in
1 gp = GliderParams()
----> 2 pn.Row(pn.Param(gp, name=‘’),pn.bind(imaging,gp.param.surface_var))
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/layout/base.py in init(self, *objects, **params)
359 "as positional arguments or as a keyword, "
360 “not both.” % type(self).name)
→ 361 params[‘objects’] = [panel(pane) for pane in objects]
362 elif ‘objects’ in params:
363 params[‘objects’] = [panel(pane) for pane in params[‘objects’]]
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/layout/base.py in (.0)
359 "as positional arguments or as a keyword, "
360 “not both.” % type(self).name)
→ 361 params[‘objects’] = [panel(pane) for pane in objects]
362 elif ‘objects’ in params:
363 params[‘objects’] = [panel(pane) for pane in params[‘objects’]]
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/pane/base.py in panel(obj, **kwargs)
49 if kwargs.get(‘name’, False) is None:
50 kwargs.pop(‘name’)
—> 51 pane = PaneBase.get_pane_type(obj, **kwargs)(obj, **kwargs)
52 if len(pane.layout) == 1 and pane._unpack:
53 return pane.layout[0]
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/param.py in init(self, object, **params)
687 if object is not None:
688 self._validate_object()
→ 689 self._replace_pane(not self.lazy)
690
691 @param.depends(‘object’, watch=True)
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/param.py in _replace_pane(self, force, *args)
730 new_object = Spacer()
731 else:
→ 732 new_object = self.eval(self.object)
733 self._update_inner(new_object)
734 finally:
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/param.py in eval(self, function)
720 args = (getattr(dep.owner, dep.name) for dep in arg_deps)
721 kwargs = {n: getattr(dep.owner, dep.name) for n, dep in kw_deps.items()}
→ 722 return function(*args, **kwargs)
723
724 def _replace_pane(self, *args, force=False):
/srv/conda/envs/notebook/lib/python3.8/site-packages/param/parameterized.py in _depends(*args, **kw)
349 @wraps(func)
350 def _depends(*args,**kw):
→ 351 return func(*args,**kw)
352
353 deps = list(dependencies)+list(kw.values())
/srv/conda/envs/notebook/lib/python3.8/site-packages/panel/depends.py in wrapped(*wargs, **wkwargs)
171 combined_kwargs[kw] = arg
172
→ 173 return function(*combined_args, **combined_kwargs)
174 return wrapped
in imaging(surface_var)
17 stream = hv.streams.Tap(source=image.object, x=0, y=0)
18 timeseries = ds[surface_var].interactive.sel(lon=stream.param.x, lat=stream.param.y, method=‘nearest’).hvplot(‘time’).apply.opts(title=f"{stream.x}, {stream.y}")
—> 19 return pn.Column(image* gv.features.coastline(), select,timeseries.dmap())
AttributeError: module ‘geoviews’ has no attribute ‘features’
gv.feature.coastline()
https://geoviews.org/user_guide/Geometries.html
Maybe don’t use interactive since it’s still new. Use the basic .param.watch or depends (see Holoviews to HoloViews — pYdeas 0.0.0 documentation)
Thanks, that actually solved a lot of my problems.
How would I wrap the
gv.tile_sources.CartoDark() * gv.Points([-122.76, 49.555]).opts(alpha=0)
in order to make it responsive (sizing_mode="stretch_width") as it seems if I wrap in pn.pane.Holoviews I get the
AttributeError: 'HoloViews' object has no attribute '_plot_id'
class Example(pn.viewable.Viewer):
def get_map(self):
return (gv.tile_sources.CartoDark() * gv.Points([-122.76, 49.555]).opts(alpha=0)).opts(width=1000)
def tap_series(self, x, y):
lon, lat = to_lon_lat(x, y)
self.figs_col.clear()
self.figs_col.append( lon )
return hv.Div(
"""<hr style="border-top: 1px transparent; height: 1px;">"""
).opts(height=5)
def __init__(self):
self.figs_col = pn.Column()
self.map = self.get_map()
self.tap_stream = hv.streams.Tap(source=self.map, x=-122.76, y=49.555)
self.dynamic_map = hv.DynamicMap(self.tap_series, streams=[self.tap_stream])
super().__init__()
def view(self):
return pn.Column(self.dynamic_map, self.figs_col)
app = Example()
template = pn.template.MaterialTemplate(
logo="https://www.canada.ca/etc/designs/canada/wet-boew/assets/sig-blk-en.svg",
site="CMC",
title="Temperatures for different models",
main=[app.map, app.view],
sidebar_width=200,
).servable()
Hi @StuckDuckF
Please open a new post with a minimum, reproducible example. You are welcome to refer to the old post.
Thanks.