contourf() plots white space over finite data

问题

I'm attempting to plot a 3D chart using matplotlib.pyplot.contourf() with the following program:

import numpy as np
import matplotlib.pyplot as plt
import scipy

# calculates Fast Fourier transforms for each value in the 1D array "Altitude"
# and stacks them vertically to form a 2D array of fft values called "Fourier"
Fourier = np.array([])
for i in range(len(Altitude)):
    Ne_fft = Ne_lowpass[i,:]/np.average(Ne_lowpass[i,:])
    Ne_fft = Ne_fft - Ne_fft.mean()
    W = scipy.fftpack.fftfreq(10*Ne_fft.size, d=(Time[-1]-Time[0])/len(Ne_fft))
    P = 1/abs(W)
    FFT = abs(scipy.fftpack.fft(Ne_fft, n=10*len(Ne_fft)))
    FFT = FFT**2
    if len(Fourier) == 0:
        Fourier = FFT
    else:
        Fourier = np.vstack((Fourier,FFT))

# plots the 2D contourf plot of "Fourier", with respect to "Altitude" and period "P"
plt.figure(5)
C = plt.contourf(P,Altitude,Fourier,100,cmap='jet')
plt.xscale('log')
plt.xlim([1,P[np.argmax(P)+1]])
plt.ylim([59,687])
plt.ylabel("Altitude")
plt.xlabel("Period")
plt.title("Power spectrum of Ne")
cbar = plt.colorbar(C)
cbar.set_label("Power", fontsize = 16)

For the most part it is working fine; however, in some places useless white space is plotted. the plot produced can be found here (sorry, I don't have enough reputation points to attach images directly)

The purpose of this program is to calculate a series of Fast Fourier Transforms across 1 axis of a 2 dimensional numpy array, and stack them up to display a contour plot depicting which periodicities are most prominent in the data.

I checked the parts of the plotted quantity that appear white, and finite values are still present, although much smaller than noticable quantities elsewhere in the plot:

print(Fourier[100:,14000:])
[[  2.41147887e-03   1.50783490e-02   4.82620482e-02 ...,   1.49769976e+03
    5.88859945e+02   1.31930217e+02]
 [  2.12684922e-03   1.44076962e-02   4.65881565e-02 ...,   1.54719976e+03
    6.14086374e+02   1.38727145e+02]
 [  1.84414615e-03   1.38162140e-02   4.51940720e-02 ...,   1.56478339e+03
    6.23619105e+02   1.41367042e+02]
 ..., 
 [  3.51539440e-03   3.20182148e-03   2.38117665e-03 ...,   2.43824864e+03
    1.18676851e+03   3.13067945e+02]
 [  3.51256439e-03   3.19924000e-03   2.37923875e-03 ...,   2.43805298e+03
    1.18667139e+03   3.13042038e+02]
 [  3.50985146e-03   3.19677302e-03   2.37741084e-03 ...,   2.43790243e+03
    1.18659640e+03   3.13021994e+02]]

print(np.isfinite(Fourier.all()))
True
print(np.isnan(Fourier.any()))
False

Is the white space present because the values are so small compared to the rest of the plot? I'm not sure at all how to fix this.

回答1:

In the line plt.contourf(P,Altitude,Fourier,100,cmap='jet') you are taking 100 automatically chosen levels for the contour plot. "Automatic" in this case does not guarantee that those levels include all data.

If you want to make sure they all data is included you may define you own levels to use

plt.contourf(x, y, Z, np.linspace(Z.min(), Z.max(), 100))

回答2:

You can fix this problem by adding option extend='both'. Eg. C = plt.contourf(P,Altitude,Fourier,100,cmap='jet',extend='both')

Ref: https://matplotlib.org/examples/pylab_examples/contourf_demo.html

来源：https://stackoverflow.com/questions/51386947/contourf-plots-white-space-over-finite-data

标签

python

matplotlib

scipy

contourf