Normal distribution appears too dense when plotted in matplotlib

Question

I am trying to estimate the probability density function of my data. IN my case, the data is a satellite image with a shape 8200 x 8100. Below, I present you the code of PDF

Answer 1

The issue is that the x values in the PDF plot are not sorted, so the plotted line is going back and forwards between random points, creating the mess you see.

Two options:

1. Don't plot the line, just plot points (not great if you have lots of points, but will confirm if what I said above is right or not):

   plt.plot(lst_flat_filtered, fit, 'bo')
   

2. Sort the lst_flat_filtered array before calculating the PDF and plotting it:

   lst_flat = np.r_[lst_flat]
   lst_flat_filtered = np.sort(lst_flat[~is_outlier(lst_flat)])  # Changed this line
   fit = stats.norm.pdf(lst_flat_filtered, np.mean(lst_flat_filtered), np.std(lst_flat_filtered))
   
   plt.plot(lst_flat_filtered, fit)
   

Here's some minimal examples showing these behaviours:

Reproducing your problem:

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

lst_flat_filtered = np.random.normal(7, 5, 1000)

fit = stats.norm.pdf(lst_flat_filtered, np.mean(lst_flat_filtered), np.std(lst_flat_filtered))

plt.hist(lst_flat_filtered, bins=30, normed=True)

plt.plot(lst_flat_filtered, fit)

plt.show()

Plotting points

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

lst_flat_filtered = np.random.normal(7, 5, 1000)

fit = stats.norm.pdf(lst_flat_filtered, np.mean(lst_flat_filtered), np.std(lst_flat_filtered))

plt.hist(lst_flat_filtered, bins=30, normed=True)

plt.plot(lst_flat_filtered, fit, 'bo')

plt.show()

Sorting the data

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

lst_flat_filtered = np.sort(np.random.normal(7, 5, 1000))

fit = stats.norm.pdf(lst_flat_filtered, np.mean(lst_flat_filtered), np.std(lst_flat_filtered))

plt.hist(lst_flat_filtered, bins=30, normed=True)

plt.plot(lst_flat_filtered, fit)

plt.show()