Bokeh heatmap usage

Question

I have an array of certain events with time stamp and want to create a heatmap:

• x axis should represent the date, fe '2016-02-03',
• y axis should represent the hour of occurrence, fe 13 (if 13:32),
• the color should depend on the count of occurred event.

My data (as pandas dataframe z.head() ):

         date hour  i
0  2016-01-15   13  1
1  2016-01-15   13  1
2  2016-01-15   12  1
3  2016-01-15   10  1
4  2016-01-15   10  1

My failed attempt:

from bokeh._legacy_charts import HeatMap, output_file, show
hm = HeatMap(z.head(), x='date', y='hour', values='i', stat='count')

And the exception:

AttributeError                            Traceback (most recent call last)
<ipython-input-98-83c7e9319496> in <module>()
----> 1 hm = HeatMap(z.head(), x='date', y='hour', values='i', stat='count')

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/builders/heatmap_builder.py in HeatMap(data, x, y, values, stat, xgrid, ygrid, hover_tool, hover_text, **kw)
     90     kw['values'] = values
     91     kw['stat'] = stat
---> 92     chart = create_and_build(HeatMapBuilder, data, xgrid=xgrid, ygrid=ygrid, **kw)
     93 
     94     if hover_tool:

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/builder.py in create_and_build(builder_class, *data, **kws)
     65     chart_kws = { k:v for k,v in kws.items() if k not in builder_props}
     66     chart = Chart(**chart_kws)
---> 67     chart.add_builder(builder)
     68     chart.start_plot()
     69 

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/chart.py in add_builder(self, builder)
    150     def add_builder(self, builder):
    151         self._builders.append(builder)
--> 152         builder.create(self)
    153 
    154     def add_ranges(self, dim, range):

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/builder.
    510         # call methods that allow customized setup by subc
    511         self.setup()
--> 512         self.process_data()
    513 
    514         # create and add renderers to chart

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/builders
    169         # color by the values selection
    170         self.attributes['color'].setup(data=self._data.sou
--> 171                                        columns=self.values
    172         self.attributes['color'].add_bin_labels(self._data
    173 

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/attribut
    187 
    188         if self.columns is not None and self.data is not N
--> 189             self.attr_map = self._create_attr_map(self.dat
    190 
    191     def update_data(self, data):

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/attribut
    158         """Creates map between unique values and available
    159 
--> 160         self._generate_items(df, columns)
    161         iterable = self._setup_iterable()
    162 

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/attribut
    230 
    231                 self.bins = Bins(source=ColumnDataSource(d
--> 232                                  bin_count=len(self.iterab
    233 
    234                 if self.sort:

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/stats.py
    309         properties['source'] = source
    310 
--> 311         super(Bins, self).__init__(**properties)
    312 
    313     def _get_stat(self):

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/stats.py
     54 
     55         super(Stat, self).__init__(**properties)
---> 56         self._refresh()
     57 
     58     def _refresh(self):

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/stats.py
     60         if self.get_data() is not None:
     61             self.update()
---> 62             self.calculate()
     63 
     64     def set_data(self, data, column=None):

/home/user/.local/lib/python3.4/site-packages/bokeh/charts/stats.py
    342         if self.source is not None:
    343             # add bin column to data source
--> 344             self.source.add(binned.tolist(), name=self.bin
    345             df = self.source.to_df()
    346         else:

AttributeError: 'Categorical' object has no attribute 'tolist'

Bokeh is in the version 0.11, installed with pip3. What am I doing wrong? Thank you.

UPDATED:

• My bad on the legacy_charts (copied wrong line).
• I have reinstalled bokeh pip3 install --user --force-reinstall --upgrade bokeh . Still no joy.

The whole code:

import pandas as pd
from bokeh.charts import HeatMap, output_file, show

z = pd.DataFrame()
z['date'] = ['2016-01-15', '2016-01-13', '2016-01-11', '2016-01-14', '2016-01-15']
z['hour'] = [12, 10, 11, 3, 0]
z['i'] = [1, 1, 1, 1, 1]

output_file('/tmp/test.html')
hm = HeatMap(z, x='date', y='hour', stat='count')
show(hm)

And running using python3:

Traceback (most recent call last):
  File "so.py", line 10, in <module>
    hm = HeatMap(z, x='date', y='hour', stat='count')
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/builders/heatmap_builder.py", line 92, in HeatMap
    chart = create_and_build(HeatMapBuilder, data, xgrid=xgrid, ygrid=ygrid, **kw)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/builder.py", line 67, in create_and_build
    chart.add_builder(builder)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/chart.py", line 152, in add_builder
    builder.create(self)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/builder.py", line 512, in create
    self.process_data()
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/builders/heatmap_builder.py", line 171, in process_data
    columns=self.values.selection)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/attributes.py", line 189, in setup
    self.attr_map = self._create_attr_map(self.data.to_df(), self.columns)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/attributes.py", line 160, in _create_attr_map
    self._generate_items(df, columns)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/attributes.py", line 232, in _generate_items
    bin_count=len(self.iterable), aggregate=False)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/stats.py", line 311, in __init__
    super(Bins, self).__init__(**properties)
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/stats.py", line 56, in __init__
    self._refresh()
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/stats.py", line 62, in _refresh
    self.calculate()
  File "/home/ktx/.local/lib/python3.4/site-packages/bokeh/charts/stats.py", line 344, in calculate
    self.source.add(binned.tolist(), name=self.bin_column)
AttributeError: 'Categorical' object has no attribute 'tolist'

Answer 1

bigreddot is right. If you have 0.11, you shouldn't have legacy_charts . Once you properly update Bokeh, this should work:

from bokeh.charts import HeatMap, output_file, show
import pandas as pd

output_file('test.html')

hm = HeatMap(z, x='date', y='hour',  values='i', stat='count')

show(hm)

Answer 2

1. On bigreddot pointers I reinstalled bokeh, didn't work even then. I got several times errors in pip3 (some bug on the linux distribution level).
2. Then the python3-pip package, pandas and few others got purged.
3. Afterwards rm -rf ~/.local/lib/python* was executed to cleanup the user-install direcotries.
4. Then get-pip.py got downloaded.
5. I reinstalled pip3 (+ ln -s ~/.local/bin/pip3 ~/bin ) and reinstalled bokeh & pandas from the PyPi repositories.

Now everything works nicely. Thank you bigreddot for pointing in the right direction.