Shape.from_record crashes when a dataset is supplied #1248

Guillemdb · 2017-04-07T10:36:26Z

I have found some bugs when trying to use the Shape.from_record function both in bokeh and matplotlib backends.

Here is some information about what is failing and how to reproduce the bug:

Package versions:

Last versions from the holoviews and the geoviews cloned repos.
Jupyter:
jupyter==1.0.0
jupyter-client==5.0.1
jupyter-console==5.1.0
jupyter-core==4.3.0

Bokeh: bokeh==0.12.5

Bug description:

I was trying to replicate the kind of plots used to show the results of the brexit referendum described here: https://www.continuum.io/blog/developer-blog/introducing-geoviews

Matplotlib backend
Works well if no dataset is used to color the plot.

If I create the plot with a supplied dataset I get an error (stacktrace at the bottom)

With the following workaround in the _norm_kwargs function in the /plotting/mpl/element.py file I get the colors to work:

      try:
          if values.dtype.kind not in 'OSUM':
            el_min, el_max = np.nanmin(values), np.nanmax(values)
          else:
            el_min, el_max = -np.inf, np.inf
      except:
          print("error in hv/plotting/mpl/element _norm_kwargs")
          el_min, el_max = np.nanmin(values), np.nanmax(values)

This error is raised due to values being a list and not having the dtype attribute. I didn't go through all your code, but if this is intended to check if all the values are nan/inf maybe using np.isnan or np.isinf would be a good idea.

It works when ignoring the dtype check as long as there is a valid value to plot.

bokeh backend

In this case, with a similar workaround I am able to display the bokeh plot with tooltip information, but I am unable to apply a color mapping to the different patches:

In this case the error is located in the /plotting/bokeh/util.py file in the filter_batched_data function.

The workaround I used:

try:
          if len(np.unique(values)) == 1:
            mapping[k] = values[0]
            del data[v]
except:
          print("error in hv/plotting/bokeh/util filter_batched_data")
``

It fails in the np.unique(values) execution. I am not able to figure out why.

## Stacktraces

- **matplotlib**

AttributeError Traceback (most recent call last)
/home/kalidus/anaconda3/lib/python3.5/site-packages/IPython/core/formatters.py in call(self, obj)
305 pass
306 else:
--> 307 return printer(obj)
308 # Finally look for special method names
309 method = get_real_method(obj, self.print_method)

/home/kalidus/github/holoviews/holoviews/ipython/display_hooks.py in pprint_display(obj)
236 if not ip.display_formatter.formatters['text/plain'].pprint:
237 return None
--> 238 return display(obj, raw=True)
239
240

/home/kalidus/github/holoviews/holoviews/ipython/display_hooks.py in display(obj, raw, **kwargs)
218 html = grid_display(obj)
219 elif isinstance(obj, (CompositeOverlay, ViewableElement)):
--> 220 html = element_display(obj)
221 elif isinstance(obj, (Layout, NdLayout, AdjointLayout)):
222 html = layout_display(obj)

/home/kalidus/github/holoviews/holoviews/ipython/display_hooks.py in wrapped(element)
147 if sys.version_info[0] < 3:
148 raise (t, v, tb)
--> 149 raise v.with_traceback(tb)
150 return wrapped
151

/home/kalidus/github/holoviews/holoviews/ipython/display_hooks.py in wrapped(element)
114 html = fn(element,
115 max_frames=OutputMagic.options['max_frames'],
--> 116 max_branches = OutputMagic.options['max_branches'])
117
118 # Only want to add to the archive for one display hook...

/home/kalidus/github/holoviews/holoviews/ipython/display_hooks.py in element_display(element, max_frames, max_branches)
164 if renderer.fig == 'pdf':
165 renderer = renderer.instance(fig='png')
--> 166 return renderer.html(element, fmt=renderer.fig)
167
168

/home/kalidus/github/holoviews/holoviews/plotting/renderer.py in html(self, obj, fmt, css, comm, **kwargs)
251 code to initialize a Comm, if the plot supplies one.
252 """
--> 253 plot, fmt = self._validate(obj, fmt)
254 figdata, _ = self(plot, fmt, **kwargs)
255 if css is None: css = self.css

/home/kalidus/github/holoviews/holoviews/plotting/renderer.py in _validate(self, obj, fmt)
187 if isinstance(obj, tuple(self.widgets.values())):
188 return obj, 'html'
--> 189 plot = self.get_plot(obj, renderer=self)
190
191 fig_formats = self.mode_formats['fig'][self.mode]

/home/kalidus/github/holoviews/holoviews/plotting/renderer.py in get_plot(self_or_cls, obj, renderer)
174 plot = self_or_cls.plotting_class(obj)(obj, renderer=renderer,
175 **plot_opts)
--> 176 plot.update(0)
177 else:
178 plot = obj

/home/kalidus/github/holoviews/holoviews/plotting/mpl/plot.py in update(self, key)
222 def update(self, key):
223 if len(self) == 1 and key == 0 and not self.drawn:
--> 224 return self.initialize_plot()
225 return self.getitem(key)
226

/home/kalidus/github/holoviews/holoviews/plotting/mpl/plot.py in wrapper(self, *args, **kwargs)
26 def wrapper(self, *args, **kwargs):
27 with mpl.rc_context(rc=self.fig_rcparams):
---> 28 return f(self, *args, **kwargs)
29 return wrapper
30

/home/kalidus/github/holoviews/holoviews/plotting/mpl/element.py in initialize_plot(self, ranges)
827 ranges = self.compute_ranges(self.hmap, key, ranges)
828 for k, subplot in self.subplots.items():
--> 829 subplot.initialize_plot(ranges=ranges)
830 if isinstance(element, CompositeOverlay):
831 frame = element.get(k, None)

/home/kalidus/github/holoviews/holoviews/plotting/mpl/plot.py in wrapper(self, *args, **kwargs)
26 def wrapper(self, *args, **kwargs):
27 with mpl.rc_context(rc=self.fig_rcparams):
---> 28 return f(self, *args, **kwargs)
29 return wrapper
30

/home/kalidus/github/holoviews/holoviews/plotting/mpl/element.py in initialize_plot(self, ranges)
481 style['label'] = element.label
482
--> 483 plot_data, plot_kwargs, axis_kwargs = self.get_data(element, ranges, style)
484
485 with abbreviated_exception():

/home/kalidus/github/geoviews/geoviews/plotting/mpl/init.py in get_data(self, element, ranges, style)
307 value = element.level
308 if vdim is not None and (value is not None and np.isfinite(value)):
--> 309 self._norm_kwargs(element, ranges, style, vdim)
310 style['clim'] = style.pop('vmin'), style.pop('vmax')
311 style['array'] = np.array([value]*len(element.data))

/home/kalidus/github/holoviews/holoviews/plotting/mpl/element.py in _norm_kwargs(self, element, ranges, opts, vdim)
668 #print(values,element)
669
--> 670 if values.dtype.kind not in 'OSUM':
671 el_min, el_max = np.nanmin(values), np.nanmax(values)
672 else:

AttributeError: 'list' object has no attribute 'dtype'


- **bokeh**

ValueError Traceback (most recent call last)
/home/kalidus/anaconda3/lib/python3.5/site-packages/IPython/core/formatters.py in call(self, obj)
305 pass
306 else:
--> 307 return printer(obj)
308 # Finally look for special method names
309 method = get_real_method(obj, self.print_method)