Plotting at full resolution with matplotlib.pyplot, imshow() and savefig()?

Question

I have a medium-sized array (e.g. 1500x3000) that I want to plot at scale since it is an image. However, the vertical and horizontal scales are very different. For simplification let say that there is one meter/row and 10/column. The plot should then produce an image which is c. 1500x30000. I use the kwarg extent for the scales and aspect = 1 to avoid deformation. Either by using the plotting windows (QT4) and imshow() or by using savefig(), I never succeeded in producing the image at scale and at full resolution.

I have looked to many proposed solutions as indicated in here, here, or here and there or there in case it was a bug. I have altered my matplotlibrc and placed it in ~/.config/matplotlib to try forcing the my display / savefig options but to no avail. I also tried with pcolormesh() but without success. I use python 2.7 and matplotlib 1.3 from the repo of Ubuntu 14.04 and QT4Agg as a backend. I tried TkAgg too but it is slow and gives the same results. I have the impression that in the x axis the resolution is right but it is definitely downsampled in the vertical direction. Here is a piece of code which should simulate my issue.

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

R, C = 1500, 3000
DATA = np.random.random((R, C))
DATA[::2, :] *= -1  # make every other line negative
Yi, Xi = 1, 10 # increment
CMP = 'seismic'
ImageFormat ='pdf'
Name = 'Image'


DataRange = (np.absolute(DATA)).max() # I want my data centred on 0
EXTENT = [0, Xi*C, 0 ,Yi*R]
NORM = matplotlib.colors.Normalize(vmin =-DataRange, vmax= DataRange, clip =True)

for i in range(1,4):
    Fig=plt.figure(figsize=(45, 10), dpi = 100*i, tight_layout=True)
    Fig.suptitle(Name+str(i)+'00DPI')
    ax = Fig.add_subplot(1, 1, 1)
    Plot = ax.imshow(DATA, cmap=plt.get_cmap(CMP), norm = NORM, extent = EXTENT, aspect = 1, interpolation='none') 
    ax.set_xlabel('metres')
    ax.set_ylabel('metres')
    Fig.savefig(Name+str(i)+'00DPI.'+ImageFormat,  format = ImageFormat, dpi = Fig.dpi)
plt.close()

In imshow(), interpolation = 'none' or 'nearest' or 'bilinear' does not change the resolution for some reason although I think it is supposed to at least in the Qt4 window if I do show() instead of savefig(). Notice that the resolution is the same in the figures saved whatever you setup in the plt.figure(dpi=).

I am out of idea and at the limit of my understanding on how things work with this system. Any help is very welcome.

Thanks in advance.

Answer 1

Running your example, everything looks good in matplotlib after zooming: no matter the resolution, results are the same and I see one pixel per axis unit. Also, trying with smaller arrays, pdfs (or other formats) work well.

This is my explanation: when you set figure dpi, you are setting the dpi of the entire figure (not only the data area). On my system, this results in the plot area occupying vertically about 20% of the entire figure. If you set 300 dpi and 10 in height, you get for vertical data axis a total of 300x10x0.2=600 pixels, that are not enough to represent 1500 points, this explains to me why output must be resampled. Note that reducing the width sometimes incidentally works because it changes the fraction of figure occupied by the data plot.

Then you have to increase the dpi and also set interpolation='none' (it shouldn't matter if resolution is perfectly set, but it matters if it is just close enough). Also you can adjust the plot position and size to take a larger part of the figure, but going back to the optimal resolution settings, ideally you want to have a number of pixel on the axis that is a multiple of your data points, otherwise some kind of interpolation must happen (think how you can plot two points on three pixels, or viceversa).

I don't know if the following is the best way to do it, there might be more suitable methods and properties in matplotlib, but I would try something like this to calculate the optimal dpi:

vsize=ax.get_position().size[1]  #fraction of figure occupied by axes
axesdpi= int((Fig.get_size_inches()[1]*vsize)/R)  #(or Yi*R according to what you want to do)

Then your code (reduced to the first loop), becomes:

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

R, C = 1500, 3000
DATA = np.random.random((R, C))
DATA[::2, :] *= -1  # make every other line negative
Yi, Xi = 1, 10 # increment
CMP = 'seismic'
ImageFormat ='pdf'
Name = 'Image'


DataRange = (np.absolute(DATA)).max() # I want my data centred on 0
EXTENT = [0, Xi*C, 0 ,Yi*R]
NORM = matplotlib.colors.Normalize(vmin =-DataRange, vmax= DataRange, clip =True)

for i in (1,):
    print i 
    Fig=plt.figure(figsize=(45, 10), dpi = 100*i, tight_layout=True)
    Fig.suptitle(Name+str(i)+'00DPI')
    ax = Fig.add_subplot(1, 1, 1)
    Plot = ax.imshow(DATA, cmap=plt.get_cmap(CMP), norm = NORM, extent = EXTENT, aspect = 1, interpolation='none') 
    ax.set_xlabel('metres')
    ax.set_ylabel('metres')
    vsize=ax.get_position().size[1]  #fraction of figure occupied by axes
    axesdpi= int((Fig.get_size_inches()[1]*vsize)/R)  #(or Yi*R according to what you want to do)
    Fig.savefig(Name+str(axesdpi)+'DPI.'+ImageFormat,  format = ImageFormat, dpi = axesdpi)
    #plt.close()

This works reasonably for me.