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ValueError when trying to display a netCDF file with the explorer
The file is the first made available on this website https://www.unidata.ucar.edu/software/netcdf/examples/files.html. I attached it to the issue: sresa1b_ncar_ccsm3-example.nc.zip
import hvplot.xarray
import xarray as xr
ds = xr.open_dataset("sresa1b_ncar_ccsm3-example.nc")
ds.hvplot.explorer()
ValueError: cannot select an axis to squeeze out which has size not equal to one
Full traceback
WARNING:param.Image02227: Image dimension lat is not evenly sampled to relative tolerance of 0.001. Please use the QuadMesh element for irregularly sampled data or set a higher tolerance on hv.config.image_rtol or the rtol parameter in the Image constructor.
WARNING:param.Image02227: Image dimension lat is not evenly sampled to relative tolerance of 0.001. Please use the QuadMesh element for irregularly sampled data or set a higher tolerance on hv.config.image_rtol or the rtol parameter in the Image constructor.
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/IPython/core/formatters.py:974, in MimeBundleFormatter.__call__(self, obj, include, exclude)
971 method = get_real_method(obj, self.print_method)
973 if method is not None:
--> 974 return method(include=include, exclude=exclude)
975 return None
976 else:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/viewable.py:1096, in Viewer._repr_mimebundle_(self, include, exclude)
1095 def _repr_mimebundle_(self, include=None, exclude=None):
-> 1096 return self._create_view()._repr_mimebundle_(include, exclude)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/viewable.py:820, in Viewable._repr_mimebundle_(self, include, exclude)
818 doc = Document()
819 comm = state._comm_manager.get_server_comm()
--> 820 model = self._render_model(doc, comm)
821 if config.embed:
822 return render_model(model)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/viewable.py:738, in Viewable._render_model(self, doc, comm)
736 if comm is None:
737 comm = state._comm_manager.get_server_comm()
--> 738 model = self.get_root(doc, comm)
740 if self._design and self._design.theme.bokeh_theme:
741 doc.theme = self._design.theme.bokeh_theme
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:306, in Panel.get_root(self, doc, comm, preprocess)
302 def get_root(
303 self, doc: Optional[Document] = None, comm: Optional[Comm] = None,
304 preprocess: bool = True
305 ) -> Model:
--> 306 root = super().get_root(doc, comm, preprocess)
307 # ALERT: Find a better way to handle this
308 if hasattr(root, 'styles') and 'overflow-x' in root.styles:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/viewable.py:660, in Renderable.get_root(self, doc, comm, preprocess)
658 wrapper = self._design._wrapper(self)
659 if wrapper is self:
--> 660 root = self._get_model(doc, comm=comm)
661 if preprocess:
662 self._preprocess(root)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:174, in Panel._get_model(self, doc, root, parent, comm)
172 root = root or model
173 self._models[root.ref['id']] = (model, parent)
--> 174 objects, _ = self._get_objects(model, [], doc, root, comm)
175 props = self._get_properties(doc)
176 props[self._property_mapping['objects']] = objects
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:156, in Panel._get_objects(self, model, old_objects, doc, root, comm)
154 else:
155 try:
--> 156 child = pane._get_model(doc, root, model, comm)
157 except RerenderError as e:
158 if e.layout is not None and e.layout is not self:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:174, in Panel._get_model(self, doc, root, parent, comm)
172 root = root or model
173 self._models[root.ref['id']] = (model, parent)
--> 174 objects, _ = self._get_objects(model, [], doc, root, comm)
175 props = self._get_properties(doc)
176 props[self._property_mapping['objects']] = objects
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:156, in Panel._get_objects(self, model, old_objects, doc, root, comm)
154 else:
155 try:
--> 156 child = pane._get_model(doc, root, model, comm)
157 except RerenderError as e:
158 if e.layout is not None and e.layout is not self:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:174, in Panel._get_model(self, doc, root, parent, comm)
172 root = root or model
173 self._models[root.ref['id']] = (model, parent)
--> 174 objects, _ = self._get_objects(model, [], doc, root, comm)
175 props = self._get_properties(doc)
176 props[self._property_mapping['objects']] = objects
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/tabs.py:211, in Tabs._get_objects(self, model, old_objects, doc, root, comm)
209 else:
210 try:
--> 211 rendered[pref] = child = pane._get_model(doc, root, model, comm)
212 except RerenderError as e:
213 if e.layout is not None and e.layout is not self:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:174, in Panel._get_model(self, doc, root, parent, comm)
172 root = root or model
173 self._models[root.ref['id']] = (model, parent)
--> 174 objects, _ = self._get_objects(model, [], doc, root, comm)
175 props = self._get_properties(doc)
176 props[self._property_mapping['objects']] = objects
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:156, in Panel._get_objects(self, model, old_objects, doc, root, comm)
154 else:
155 try:
--> 156 child = pane._get_model(doc, root, model, comm)
157 except RerenderError as e:
158 if e.layout is not None and e.layout is not self:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:174, in Panel._get_model(self, doc, root, parent, comm)
172 root = root or model
173 self._models[root.ref['id']] = (model, parent)
--> 174 objects, _ = self._get_objects(model, [], doc, root, comm)
175 props = self._get_properties(doc)
176 props[self._property_mapping['objects']] = objects
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/layout/base.py:156, in Panel._get_objects(self, model, old_objects, doc, root, comm)
154 else:
155 try:
--> 156 child = pane._get_model(doc, root, model, comm)
157 except RerenderError as e:
158 if e.layout is not None and e.layout is not self:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/pane/holoviews.py:413, in HoloViews._get_model(self, doc, root, parent, comm)
411 plot = self.object
412 else:
--> 413 plot = self._render(doc, comm, root)
415 plot.pane = self
416 backend = plot.renderer.backend
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/panel/pane/holoviews.py:508, in HoloViews._render(self, doc, comm, root)
505 if comm:
506 kwargs['comm'] = comm
--> 508 return renderer.get_plot(self.object, **kwargs)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/plotting/bokeh/renderer.py:68, in BokehRenderer.get_plot(self_or_cls, obj, doc, renderer, **kwargs)
61 @bothmethod
62 def get_plot(self_or_cls, obj, doc=None, renderer=None, **kwargs):
63 """
64 Given a HoloViews Viewable return a corresponding plot instance.
65 Allows supplying a document attach the plot to, useful when
66 combining the bokeh model with another plot.
67 """
---> 68 plot = super().get_plot(obj, doc, renderer, **kwargs)
69 if plot.document is None:
70 plot.document = Document() if self_or_cls.notebook_context else curdoc()
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/plotting/renderer.py:240, in Renderer.get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
237 defaults = [kd.default for kd in plot.dimensions]
238 init_key = tuple(v if d is None else d for v, d in
239 zip(plot.keys[0], defaults))
--> 240 plot.update(init_key)
241 else:
242 plot = obj
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/plotting/plot.py:955, in DimensionedPlot.update(self, key)
953 def update(self, key):
954 if len(self) == 1 and key in (0, self.keys[0]) and not self.drawn:
--> 955 return self.initialize_plot()
956 item = self.__getitem__(key)
957 self.traverse(lambda x: setattr(x, '_updated', True))
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/plotting/bokeh/element.py:1887, in ElementPlot.initialize_plot(self, ranges, plot, plots, source)
1885 if self.autorange:
1886 self._setup_autorange()
-> 1887 self._init_glyphs(plot, element, ranges, source)
1888 if not self.overlaid:
1889 self._update_plot(key, plot, style_element)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/plotting/bokeh/element.py:1806, in ElementPlot._init_glyphs(self, plot, element, ranges, source)
1804 else:
1805 style = self.style[self.cyclic_index]
-> 1806 data, mapping, style = self.get_data(element, ranges, style)
1807 current_id = element._plot_id
1809 with abbreviated_exception():
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/plotting/bokeh/raster.py:109, in RasterPlot.get_data(self, element, ranges, style)
107 if i > 2 and 'hover' not in self.handles:
108 break
--> 109 img = element.dimension_values(i, flat=False)
110 if img.dtype.kind == 'b':
111 img = img.astype(np.int8)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/core/data/__init__.py:196, in PipelineMeta.pipelined.<locals>.pipelined_fn(*args, **kwargs)
193 inst._in_method = True
195 try:
--> 196 result = method_fn(*args, **kwargs)
197 if PipelineMeta.disable:
198 return result
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/core/data/__init__.py:1099, in Dataset.dimension_values(self, dimension, expanded, flat)
1083 """Return the values along the requested dimension.
1084
1085 Args:
(...)
1096 NumPy array of values along the requested dimension
1097 """
1098 dim = self.get_dimension(dimension, strict=True)
-> 1099 values = self.interface.values(self, dim, expanded, flat)
1100 if dim.nodata is not None:
1101 # Ensure nodata applies to boolean data in py2
1102 values = np.where(values==dim.nodata, np.nan, values)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/core/data/xarray.py:423, in XArrayInterface.values(cls, dataset, dim, expanded, flat, compute, keep_index)
421 data = cupy.asnumpy(data)
422 if not keep_index:
--> 423 data = cls.canonicalize(dataset, data, data_coords=data_coords,
424 virtual_coords=virtual_coords)
425 return data.T.flatten() if flat and not keep_index else data
426 elif expanded:
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/holoviews/core/data/grid.py:329, in GridInterface.canonicalize(cls, dataset, data, data_coords, virtual_coords)
327 data = data.flatten()
328 else:
--> 329 data = np.squeeze(data, axis=tuple(dropped))
331 if not any(cls.irregular(dataset, d) for d in dataset.kdims):
332 inds = [dims.index(kd.name) for kd in dataset.kdims]
File <__array_function__ internals>:200, in squeeze(*args, **kwargs)
File ~/miniconda3/envs/hvplot310/lib/python3.10/site-packages/numpy/core/fromnumeric.py:1571, in squeeze(a, axis)
1569 return squeeze()
1570 else:
-> 1571 return squeeze(axis=axis)
ValueError: cannot select an axis to squeeze out which has size not equal to one
Issue observed when trying https://github.com/holoviz/hvplot/pull/1256
