Plot 3 columns matrix with pyplot

Question

I have a (numpy) matrix with three columns, the first two being the position and the third the value. I would like to plot this matrix. I tried to use plt.imshow(...) but the axis are then the indexes of my matrix and not the position.

How can I do that?

EDIT : my matrix is like that :

array([[ -0.00000000e+00,   0.00000000e+00,   9.72157349e+01],
       [ -2.50000000e-02,   0.00000000e+00,   9.72157349e+01],
       [ -5.00000000e-02,   0.00000000e+00,   9.72157349e+01],
       ..., 
       [ -2.42500000e+00,   8.28630000e-05,   9.72157349e+01],
       [ -2.45000000e+00,   8.28630000e-05,   9.72157349e+01],
       [ -2.47500000e+00,   8.28630000e-05,   9.72157349e+01]])

with the first column beiing the x-position, the second one being the y-position and the third the value at the point.

I rolled back the edit that included the answer. The answer only needs to be in one place, as an answer. — David
– David, Commented May 29, 2014 at 22:53

score 1 · Accepted Answer · 2014-05-29 22:42:28Z

1

Imshow requires you to recalculate the third column into a 2D matrix and extract the x and y axis first. Then you can use imshow. For imshow you also need to specify the boundaries (extent) like so:

plt.imshow(matrix, cmap=plt.cm.jet, aspect='auto', origin='lower', alpha=1,interpolation='none', extent=(xAxis[0],xAxis[-1], yAxis[0], yAxis[-1]))

plt.colorbar()
plt.show()

Then you should see the correct "positions"

edited May 29, 2014 at 22:42

answered May 29, 2014 at 22:04

user3413108

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6 Comments

cphyc Over a year ago

I supposed that xAxis is my first column and yAxis my second. However, when I use your command, I get the right extent, but I still don't get the colormap that corresponds to my data (the third column).

user3413108 Over a year ago

Ok, for that you have to use plt.colorbar() in addition. I have included it in the code.

cphyc Over a year ago

What I wanted to say is that with your solution I get !this. What I want is !that but with the correct extent (those of the first image).

user3413108 Over a year ago

are the axis values equally spaced?

cphyc Over a year ago

Yes, that's why it works. How could I do it with non-equally spaced values?

|

JLT · Accepted Answer · 2016-09-28 07:48:12Z

0

Best to use a scatter plot and use the third column for the color value:

 A = your_matrix_as_numpy_array
 X,Y,Z = A.T # with Z the values at points x,y
 import matplotlib.pyplot as plt
 plt.scatter(X,Y,c=Z) 
 plt.colorbar()
 plt.show

Note that you can still make the points larger/smaller and change the shape etcetera

answered Sep 28, 2016 at 7:48

JLT

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