Matplotlib 2D Image Plotting with pcolormesh

Introduction

In this tutorial, we will learn how to use the pcolormesh function in the Matplotlib library to generate 2D image-style plots. We will cover the basic usage of pcolormesh, non-rectilinear pcolormesh, centered coordinates, and making levels using norms.

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Skills Graph

Basic pcolormesh

We usually specify a pcolormesh by defining the edge of quadrilaterals and the value of the quadrilateral. Note that here x and y each have one extra element than Z in the respective dimension.

import matplotlib.pyplot as plt
import numpy as np

np.random.seed(19680801)
Z = np.random.rand(6, 10)
x = np.arange(-0.5, 10, 1)  ## len = 11
y = np.arange(4.5, 11, 1)  ## len = 7

fig, ax = plt.subplots()
ax.pcolormesh(x, y, Z)

Non-rectilinear pcolormesh

Note that we can also specify matrices for X and Y and have non-rectilinear quadrilaterals.

import matplotlib.pyplot as plt
import numpy as np

np.random.seed(19680801)
Z = np.random.rand(6, 10)
x = np.arange(-0.5, 10, 1)  ## len = 11
y = np.arange(4.5, 11, 1)  ## len = 7
X, Y = np.meshgrid(x, y)
X = X + 0.2 * Y  ## tilt the coordinates.
Y = Y + 0.3 * X

fig, ax = plt.subplots()
ax.pcolormesh(X, Y, Z)

Centered coordinates

Often a user wants to pass X and Y with the same sizes as Z to .axes.Axes.pcolormesh. This is also allowed if shading='auto' is passed (default set by :rc:pcolor.shading). Pre Matplotlib 3.3, shading='flat' would drop the last column and row of Z, but now gives an error. If this is really what you want, then simply drop the last row and column of Z manually:

import matplotlib.pyplot as plt
import numpy as np

np.random.seed(19680801)
Z = np.random.rand(6, 10)
x = np.arange(10)  ## len = 10
y = np.arange(6)  ## len = 6
X, Y = np.meshgrid(x, y)

fig, axs = plt.subplots(2, 1, sharex=True, sharey=True)
axs[0].pcolormesh(X, Y, Z, vmin=np.min(Z), vmax=np.max(Z), shading='auto')
axs[0].set_title("shading='auto' = 'nearest'")
axs[1].pcolormesh(X, Y, Z[:-1, :-1], vmin=np.min(Z), vmax=np.max(Z),
                  shading='flat')
axs[1].set_title("shading='flat'")

Making levels using norms

Shows how to combine Normalization and Colormap instances to draw "levels" in .axes.Axes.pcolor, .axes.Axes.pcolormesh and .axes.Axes.imshow type plots in a similar way to the levels keyword argument to contour/contourf.

import matplotlib.pyplot as plt
import numpy as np

from matplotlib.colors import BoundaryNorm
from matplotlib.ticker import MaxNLocator

## make these smaller to increase the resolution
dx, dy = 0.05, 0.05

## generate 2 2d grids for the x & y bounds
y, x = np.mgrid[slice(1, 5 + dy, dy),
                slice(1, 5 + dx, dx)]

z = np.sin(x)**10 + np.cos(10 + y*x) * np.cos(x)

## x and y are bounds, so z should be the value *inside* those bounds.
## Therefore, remove the last value from the z array.
z = z[:-1, :-1]
levels = MaxNLocator(nbins=15).tick_values(z.min(), z.max())


## pick the desired colormap, sensible levels, and define a normalization
## instance which takes data values and translates those into levels.
cmap = plt.colormaps['PiYG']
norm = BoundaryNorm(levels, ncolors=cmap.N, clip=True)

fig, (ax0, ax1) = plt.subplots(nrows=2)

im = ax0.pcolormesh(x, y, z, cmap=cmap, norm=norm)
fig.colorbar(im, ax=ax0)
ax0.set_title('pcolormesh with levels')


## contours are *point* based plots, so convert our bound into point
## centers
cf = ax1.contourf(x[:-1, :-1] + dx/2.,
                  y[:-1, :-1] + dy/2., z, levels=levels,
                  cmap=cmap)
fig.colorbar(cf, ax=ax1)
ax1.set_title('contourf with levels')

## adjust spacing between subplots so `ax1` title and `ax0` tick labels
## don't overlap
fig.tight_layout()

plt.show()

Summary

In this tutorial, we learned how to use the pcolormesh function in the Matplotlib library. We covered the basic usage of pcolormesh, non-rectilinear pcolormesh, centered coordinates, and making levels using norms. These techniques can be used to generate different types of 2D image-style plots in Matplotlib.