2D histogram with Python

Question

I'm trying to plot a 2D histogram in Python using these code

from math import *
import pylab as p
import matplotlib.pyplot as plt
import numpy as np

x=part.points[:,0]
y=part.points[:,1]
z=part.points[:,2]

H, xedges, yedges = np.histogram2d(x, y, bins=(128,128))
H.shape, xedges.shape, yedges.shape

extent = [yedges[0], yedges[-1], xedges[-1], xedges[0]]

plt.imshow(H, extent=extent, interpolation='nearest')

plt.colorbar()
plt.xlabel("x")
plt.ylabel("y")
plt.show()

Every thing works fine: I have a color bar which represent the counts in each cells. The thing is that I would like to have the log of the count but the function histrogram2d does not have any option for that.

Solution 1

I guess that you could simply do

H_log = np.log(H)
…
plt.imshow(H_log,…)

(assuming that you don't have null counts).

If you want a 3D bar chart instead, you can adapt the example provided in the Matplotlib documentation.

More generally, I heartily recommend that you check the very useful Matplotlib gallery, when you are looking for some specific graphing capabilities.

Solution 2

In this answer there is a solution for 2D and 3D Scatter and Bubble Histograms.

points, sub = hist2d_scatter( radius, density, bins=4 )

points, sub = hist3d_scatter( temperature, density, radius, bins=4 )

Where sub is a matplotlib "Subplot" instance (3D or not) and pointscontains the points used for the scatter plot.

Comments

[Brian]

Thanks, I'm really new with Python. Can I ask you if it is possible to have a 3d histogram? Also including the z coordinate?

[Bruno Feroleto]

@Matteo: I added a note on how to create a "3D histogram". Please mark this answer as accepted (on the left) if it answered your original question. :)