I'm getting and error trying to use ColumnDataSource in Bokeh

Question

I'm getting this error:

TypeError: Object of type Interval is not JSON serializable

Here is my code.

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import math

from bokeh.io import output_file, show
from bokeh.plotting import figure
from bokeh.models import ColumnDataSource
from bokeh.models import NumeralTickFormatter


def construct_labels(start, end):
    labels = []
    for index, x in enumerate(start):
        y = end[index]
        labels.append('({}, {}]'.format(x, y))
    return labels


values = {'Length': np.random.uniform(0, 4, 10)}

df = pd.DataFrame(values, columns=['Length'])

bin_step_size = 0.5

# List of bin points.
p_bins = np.arange(0, (df['Length'].max() + bin_step_size), bin_step_size)

# Reduce the tail to create the left side bounds.
p_left_limits = p_bins[:-1].copy()

# Cut the head to create the right side bounds.
p_right_limits = np.delete(p_bins, 0)

# Create the bins.
p_range_bins = pd.IntervalIndex.from_arrays(p_left_limits, p_right_limits)

# Create labels.
p_range_labels = construct_labels(p_left_limits, p_right_limits)

p_ranges_binned = pd.cut(
    df['Length'],
    p_range_bins,
    labels=p_range_labels,
    precision=0,
    include_lowest=True)

out = p_ranges_binned
counts = out.value_counts(sort=False)

total_element_count = len(df.index)
foo = pd.DataFrame({'bins': counts.index, 'counts': counts})
foo.reset_index(drop=True, inplace=True)
foo['percent'] = foo['counts'].apply(lambda x: x / total_element_count)
foo['percent_full'] = foo['counts'].apply(lambda x: x / total_element_count * 100)

bin_labels = p_range_labels

# Data Container
source = ColumnDataSource(dict(
    bins=foo['bins'],
    percent=foo['percent'],
    count=foo['counts'],
    labels=pd.DataFrame({'labels': bin_labels})
))

p = figure(x_range=bin_labels, plot_height=600, plot_width=1200, title="Range Counts",
           toolbar_location=None, tools="")

p.vbar(x='labels', top='percent', width=0.9, source=source)

p.yaxis[0].formatter = NumeralTickFormatter(format="0.0%")
p.xaxis.major_label_orientation = math.pi / 2
p.xgrid.grid_line_color = None
p.y_range.start = 0

output_file("bars.html")
show(p)

Answer 1

The error comes from here:

source = ColumnDataSource(dict(
    bins=foo['bins'],
    percent=foo['percent'],
    count=foo['counts'],
    labels=pd.DataFrame({'labels': bin_labels})
))

The bins you passed in is a interval type that cannot be JSON serialized.

After review your code, this bins variable is not used in your plotting, so you can change it to:

source = ColumnDataSource(dict(
    percent=foo['percent'],
    count=foo['counts'],
    labels=bin_labels
))

Notice that I also changed your labels to bin_labels, which is a list and ColumnDataSource can use list as input. But you may want to further format these labels, as right now they are just like

['(0.0, 0.5]',
 '(0.5, 1.0]',
 '(1.0, 1.5]',
 '(1.5, 2.0]',
 '(2.0, 2.5]',
 '(2.5, 3.0]',
 '(3.0, 3.5]',
 '(3.5, 4.0]']

You might want to format them to something prettier.

After this small change you should be able to see your bar graph: