Some values of matrix do not appear in the plot by Matplotlib

Question

I created an empty reference matrix from CSV, located (x,y) as a position on matrix (and printed them out), and designated 100 to that position on matrix. Each x is the valu

Answer 1

Every pixel in the final image represents 3 or more data points. The renderer then has to decide which color out of 2 times blue, 1 time white to map to that pixel. Statistically, this will be blue twice as often as white, such that 66% of the data points are not shown.

The number of 3 pixels comes from a rough calculation: You image has 480 pixels (which you can either find out in an picture program or by calculating figuresize*dpi). You have 1200 datapoints (seen from the axes). You have margin of ~10% at both ends; so you have roughly 1200/(0.8*480) = 3.1 datapoints per pixel in the final image.

imshow interpolation

You can use an interpolation on the image to make those pixels appear, e.g.

plt.imshow(..., interpolation="sinc")

The result may however not be very appealing visually.

change resolution

You can also make sure your final plot comprises exactly one pixel per datapoint. I.e. for 1200 pixels with a dpi of 100 you can do

m = 0.1
plt.figure(figsize=(8, (1+2.*m)*1200./dpi ))
plt.subplots_adjust(bottom=m, top=1.-m)
plt.imshow(...)

filter data

Another option is to change the data, such that one pixel becomes three pixels along the y direction.

import matplotlib.pyplot as plt
import numpy as np; np.random.seed(1)
import scipy.ndimage.filters as filters

a = np.zeros((1200, 16))
for i in range(16):
    a[i*70+21, i] = 1

kernel = np.array([[0.,1.,0.],
                   [0.,1.,0.],
                   [0.,1.,0.]])
anew = filters.convolve(a,kernel,mode='constant', cval=0)

im = plt.imshow(anew, aspect="auto")
plt.colorbar(im)

plt.show()

drawing lines

import matplotlib.pyplot as plt
import numpy as np

a = np.zeros((1200, 16))

im = plt.imshow(a, aspect="auto", vmin=0, vmax=1)
plt.colorbar(im)

for i in range(16):
    plt.plot([i-.5, i+.5], [i*70+21,i*70+21], color=im.cmap(1.))

plt.show()