python - Plotting Isolines/contours in matplotlib from (x, y, z) data set

Question

Hi I'm new to programming and I'm trying to do something that's probably really obvious but for the life of me I can't figure it out. I have a series of x, y, z data (in my case, corresponding to distance, depth, and pH). I would like to plot isolines of the z data (pH) on an xy (distance, depth) grid using matplotlib. Is there any way to do this? Thanks.

Answer 1

The solution will depend on how the data is organized.

Data on regular grid

If the x and y data already define a grid, they can be easily reshaped to a quadrilateral grid. E.g.

#x  y  z
 4  1  3
 6  1  8
 8  1 -9
 4  2 10
 6  2 -1
 8  2 -8
 4  3  8
 6  3 -9
 8  3  0
 4  4 -1
 6  4 -8
 8  4  8 

can plotted as a contour using

import matplotlib.pyplot as plt
import numpy as np
x,y,z = np.loadtxt("data.txt", unpack=True)
plt.contour(x.reshape(4,3), y.reshape(4,3), z.reshape(4,3))

Arbitrary data

(a) In case the data is not living on a quadrilateral grid, one can interpolate the data on a grid. One method to do so is provided by matplotlib itself, using matplotlib.mlab.griddata.

import matplotlib.mlab
xi = np.linspace(4, 8, 10)
yi = np.linspace(1, 4, 10)
zi = matplotlib.mlab.griddata(x, y, z, xi, yi, interp='linear')
plt.contour(xi, yi, zi)

(b) Finally, one can plot a contour completely without the use of a quadrilateral grid. This can be done using tricontour.

plt.tricontour(x,y,z)

An example comparing the latter two methods is found on the matplotlib page.