I am simply trying to plot some values against datetime64[ns] timestamps with holoviews. That is, x-axis = nx1 datetime64[ns] values y-axis = nx1 data.
Here is a screen shot of what I have:
<class 'pandas._libs.tslibs.timestamps.Timestamp'>
and my overall code:
import hvplot.pandas
import pandas as pd
##
Code ommitted at the start to extract data and create dictionary to convert to data frame
##
#create dictionary
temp_dict = dict(sampling_time=time_y_value_is_taken, y_axis_values = y_values)
df = pd.Dataframe.from_dict(temp_dict)
df.sampling_time=df.sampling_time.astype('datetime64[ns]')
df=df.set_index('sampling_time')
##The following code cannot run this line- it throws error
df.hvplot.line()
I keep getting the error code : 'pandas_datetime_types' is not defined. I have also tried importing datetime as datetime - but it does not work.
EDIT: Here is the traceback:
---------------------------------------------------------------------------
NameError Traceback (most recent call last)
~\miniconda3\envs\mpess_visual\lib\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:
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\core\dimension.py in _repr_mimebundle_(self, include, exclude)
1315 combined and returned.
1316 """
-> 1317 return Store.render(self)
1318
1319
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\core\options.py in render(cls, obj)
1403 data, metadata = {}, {}
1404 for hook in hooks:
-> 1405 ret = hook(obj)
1406 if ret is None:
1407 continue
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\ipython\display_hooks.py in pprint_display(obj)
280 if not ip.display_formatter.formatters['text/plain'].pprint:
281 return None
--> 282 return display(obj, raw_output=True)
283
284
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\ipython\display_hooks.py in display(obj, raw_output, **kwargs)
250 elif isinstance(obj, (CompositeOverlay, ViewableElement)):
251 with option_state(obj):
--> 252 output = element_display(obj)
253 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
254 with option_state(obj):
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\ipython\display_hooks.py in wrapped(element)
144 try:
145 max_frames = OutputSettings.options['max_frames']
--> 146 mimebundle = fn(element, max_frames=max_frames)
147 if mimebundle is None:
148 return {}, {}
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\ipython\display_hooks.py in element_display(element, max_frames)
190 return None
191
--> 192 return render(element)
193
194
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\ipython\display_hooks.py in render(obj, **kwargs)
66 renderer = renderer.instance(fig='png')
67
---> 68 return renderer.components(obj, **kwargs)
69
70
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\renderer.py in components(self, obj, fmt, comm, **kwargs)
408 doc = Document()
409 with config.set(embed=embed):
--> 410 model = plot.layout._render_model(doc, comm)
411 if embed:
412 return render_model(model, comm)
~\miniconda3\envs\mpess_visual\lib\site-packages\panel\viewable.py in _render_model(self, doc, comm)
453 if comm is None:
454 comm = state._comm_manager.get_server_comm()
--> 455 model = self.get_root(doc, comm)
456
457 if config.embed:
~\miniconda3\envs\mpess_visual\lib\site-packages\panel\viewable.py in get_root(self, doc, comm, preprocess)
510 """
511 doc = init_doc(doc)
--> 512 root = self._get_model(doc, comm=comm)
513 if preprocess:
514 self._preprocess(root)
~\miniconda3\envs\mpess_visual\lib\site-packages\panel\layout\base.py in _get_model(self, doc, root, parent, comm)
120 if root is None:
121 root = model
--> 122 objects = self._get_objects(model, [], doc, root, comm)
123 props = dict(self._init_params(), objects=objects)
124 model.update(**self._process_param_change(props))
~\miniconda3\envs\mpess_visual\lib\site-packages\panel\layout\base.py in _get_objects(self, model, old_objects, doc, root, comm)
110 else:
111 try:
--> 112 child = pane._get_model(doc, root, model, comm)
113 except RerenderError:
114 return self._get_objects(model, current_objects[:i], doc, root, comm)
~\miniconda3\envs\mpess_visual\lib\site-packages\panel\pane\holoviews.py in _get_model(self, doc, root, parent, comm)
237 plot = self.object
238 else:
--> 239 plot = self._render(doc, comm, root)
240
241 plot.pane = self
~\miniconda3\envs\mpess_visual\lib\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):
~\miniconda3\envs\mpess_visual\lib\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()
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\renderer.py in get_plot(self_or_cls, obj, doc, renderer, comm, **kwargs)
241 init_key = tuple(v if d is None else d for v, d in
242 zip(plot.keys[0], defaults))
--> 243 plot.update(init_key)
244 else:
245 plot = obj
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\plot.py in update(self, key)
980 def update(self, key):
981 if len(self) == 1 and ((key == 0) or (key == self.keys[0])) and not self.drawn:
--> 982 return self.initialize_plot()
983 item = self.__getitem__(key)
984 self.traverse(lambda x: setattr(x, '_updated', True))
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\bokeh\element.py in initialize_plot(self, ranges, plot, plots, source)
1388 element = self.hmap.last
1389 key = util.wrap_tuple(self.hmap.last_key)
-> 1390 ranges = self.compute_ranges(self.hmap, key, ranges)
1391 self.current_ranges = ranges
1392 self.current_frame = element
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\plot.py in compute_ranges(self, obj, key, ranges)
636 if (not (axiswise and not isinstance(obj, HoloMap)) or
637 (not framewise and isinstance(obj, HoloMap))):
--> 638 self._compute_group_range(group, elements, ranges, framewise,
639 axiswise, robust, self.top_level,
640 prev_frame)
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\plot.py in _compute_group_range(cls, group, elements, ranges, framewise, axiswise, robust, top_level, prev_frame)
853 continue
854 matching &= (
--> 855 len({'date' if isinstance(v, util.datetime_types) else 'number'
856 for rng in rs for v in rng if util.isfinite(v)}) < 2
857 )
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\plotting\plot.py in <setcomp>(.0)
854 matching &= (
855 len({'date' if isinstance(v, util.datetime_types) else 'number'
--> 856 for rng in rs for v in rng if util.isfinite(v)}) < 2
857 )
858 if matching:
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\core\util.py in isfinite(val)
902 return finite
903 elif isinstance(val, datetime_types+timedelta_types):
--> 904 return not isnat(val)
905 elif isinstance(val, (basestring, bytes)):
906 return True
~\miniconda3\envs\mpess_visual\lib\site-packages\holoviews\core\util.py in isnat(val)
866 elif pd and val is pd.NaT:
867 return True
--> 868 elif pd and isinstance(val, pandas_datetime_types+pandas_timedelta_types):
869 return pd.isna(val)
870 else:
NameError: name 'pandas_datetime_types' is not defined
Any suggestions? Thank you
Although I couldn't find any official doc to support my statement, it's a compatibility issue (HoloViews 1.14.4 was released before Pandas 1.3.0).
Looking at [gitHub]: holoviz/holoviews - (v1.14.4) holoviews/holoviews/core/util.py (starting with line #83), there are some conditional imports. One of them is ABCIndexClass.
[GitHub]: pandas-dev/pandas - (v1.3.0) pandas/pandas/core/dtypes/dtypes.py on the other hand, does not provide it (as opposed from let's say its v1.2.5 counterpart) yielding (silent) exception, and the behavior you're experiencing.
Ways to go:
Upgrade HoloViews to v1.14.5 which no longer has this problem, (or at least, there's a Pandas 1.3.0 conditional as well - fixed by [GitHub]: holoviz/holoviews - Add support for pandas>=1.3)
You could also downgrade Pandas to (e.g.) v1.2.5, although this is not the way to go