Question

I am trying to make a contour plot of the following data using matplotlib in python. The data is of this form –

# x       y      height
  77.23  22.34     56
  77.53  22.87     63
  77.37  22.54     72
  77.29  22.44     88

The data actually consists of nearly 10,000 points, which I am reading from an input file. However the set of distinct possible values of z is small (within 50-90, integers), and I wish to have a contour lines for every such distinct z.

Here is my code –

import matplotlib
import numpy as np
import matplotlib.cm as cm
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import csv
import sys

# read data from file
data = csv.reader(open(sys.argv[1], 'rb'), delimiter='|', quotechar='"')
x = []
y = []
z = []

for row in data:
    try:
        x.append(float(row[0]))
        y.append(float(row[1]))
        z.append(float(row[2]))
    except Exception as e:
        pass
        #print e

X, Y = np.meshgrid(x, y)        # (I don't understand why is this required)

# creating a 2D array of z whose leading diagonal elements
# are the z values from the data set and the off-diagonal
# elements are 0, as I don't care about them.
z_2d = []
default = 0
for i, no in enumerate(z):
    z_temp = []
    for j in xrange(i): z_temp.append(default)
    z_temp.append(no)
    for j in xrange(i+1,  len(x)): z_temp.append(default)
    z_2d.append(z_temp)
Z = z_2d

CS = plt.contour(X, Y, Z, list(set(z)))
plt.figure()
CB = plt.colorbar(CS, shrink=0.8, extend='both')
plt.show()

Here is the plot of a small sample of data –

Here is a close look to one of the regions of the above plot (note the overlapping/intersecting lines) –

I don’t understand why it doesn’t look like a contour plot. The lines are intersecting, which shouldn’t happen. What can be possibly wrong? Please help.

Answer 1

Try to use the following code. This might help you — it’s the same thing which was in the Cookbook:

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.mlab import griddata

# with this way you can load your csv-file really easy -- maybe you should change
# the last 'dtype' to 'int', because you said you have int for the last column
data = np.genfromtxt('output.csv', dtype=[('x',float),('y',float),('z',float)],
                     comments='"', delimiter='|')

# just an assigning for better look in the plot routines
x = data['x']
y = data['y']
z = data['z']

# just an arbitrary number for grid point
ngrid = 500

# create an array with same difference between the entries
# you could use x.min()/x.max() for creating xi and y.min()/y.max() for yi
xi = np.linspace(-1,1,ngrid)
yi = np.linspace(-1,1,ngrid)

# create the grid data for the contour plot
zi = griddata(x,y,z,xi,yi)

# plot the contour and a scatter plot for checking if everything went right
plt.contour(xi,yi,zi,20,linewidths=1)
plt.scatter(x,y,c=z,s=20)
plt.xlim(-1,1)
plt.ylim(-1,1)
plt.show()

I created a sample output file with an Gaussian distribution in 2D. My result with using the code from above:

NOTE:

Maybe you noticed that the edges are kind of cropped. This is due to the fact that the griddata-function create masked arrays. I mean the border of the plot is created by the outer points. Everything outside the border is not there. If your points would be on a line then you will not have any contour for plotting. This is kind of logical. I mention it, cause of your four posted data points. It seems likely that you have this case. Maybe you don’t have it =)

UPDATE

I edited the code a bit. Your problem was probably that you didn’t resolve the dependencies of your input-file correctly. With the following code the plot should work correctly.

import numpy as np
import matplotlib.pyplot as plt
from matplotlib.mlab import griddata
import csv

data = np.genfromtxt('example.csv', dtype=[('x',float),('y',float),('z',float)],
                     comments='"', delimiter=',')

sample_pts = 500
con_levels = 20

x = data['x']
xmin = x.min()
xmax = x.max()

y = data['y']
ymin = y.min()
ymax = y.max()

z = data['z']

xi = np.linspace(xmin,xmax,sample_pts)
yi = np.linspace(ymin,ymax,sample_pts)

zi = griddata(x,y,z,xi,yi)

plt.contour(xi,yi,zi,con_levels,linewidths=1)
plt.scatter(x,y,c=z,s=20)
plt.xlim(xmin,xmax)
plt.ylim(ymin,ymax)
plt.show()

With this code and your small sample I get the following plot:

Try to use my snippet and just change it a bit. For example, I had to change for the given sample csv-file the delimitter from | to ,. The code I wrote for you is not really nice, but it’s written straight foreword.

Sorry for the late response.