Plotting many datapoints with matplotlib in Python

Question

I recently switched from MATLAB to Python for data analysis and I am using matplotlib for visualization of the data. This works fine if the number of data points I would like to visualise are low. However, if I would like to visualize e.g.

import matplotlib.pyplot as plt
signal = [round(random.random() * 100) for i in xrange(0, 1000000)]
plt.plot(signal)
plt.show()

I am getting an error:

Exception in Tkinter callback
Traceback (most recent call last):
  File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1489, in __call__
    return self.func(*args)
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 276, in resize
    self.show()
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line 348, in draw
    FigureCanvasAgg.draw(self)
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 451, in draw
    self.figure.draw(self.renderer)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 1034, in draw
    func(*args)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 2086, in draw
    a.draw(renderer)
  File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in draw_wrapper
    draw(artist, renderer, *args, **kwargs)
  File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 562, in draw
    drawFunc(renderer, gc, tpath, affine.frozen())
  File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 938, in _draw_lines
    self._lineFunc(renderer, gc, path, trans)
  File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 978, in _draw_solid
    renderer.draw_path(gc, path, trans)
  File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py", line 145, in draw_path
    self._renderer.draw_path(gc, path, transform, rgbFace)
OverflowError: Allocated too many blocks

Can you give me an advise what you would do in this case? Are you down sampling your data? If I perform the same plot in MATLAB even with more data points, I haven't had this problem before.

Padraic Cunningham · Accepted Answer · 2014-05-26 14:13:57Z

2

Not sure exactly what you are trying to show but you can change the plot to '.' and it will work.

import random
import pylab as plt
signal = [round(random.random() * 100) for i in xrange(0, 1000000)]
plt.plot(signal, '.')
plt.show()

You may be able to get what you want by customising using the matlotlibrc file, the docs are here

edited May 26, 2014 at 14:13

answered May 26, 2014 at 14:06

Padraic Cunningham

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1 Comment

xaneon Over a year ago

Thanks for your reply. Your suggestion works but it is still quite slow (e.g. in comparison to MATLAB). The reason why I want to visualize so many data points is that I have a recording for about an hour acquired with a high sampling rate. I would like to have a quick look at the overall data to see whether the overall signal looks ok, before I zoom in at certain positions for a closer inspection of parts of the signal. Thanks for the link to the matplotlibrc.

G.S · Accepted Answer · 2015-08-20 17:47:42Z

1

I think scatter plot is faster

import matplotlib.pyplot as plt
x=np.random.normal(0,1,1000000)
y=np.random.normal(0,1,1000000)
plt.scatter(x,y)

answered Aug 20, 2015 at 17:47

G.S

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