Matplotlib fleet optimization: plotting for many small sites

Question

I want to make a movie with some built-in points moving for elementary traffic modeling. Building takes forever, although - ~ 10 frames takes 7 s! What's up with that?

Python Code:

import numpy as np import matplotlib.pyplot as plt import cProfile def slowww_plot(): for i in range(10): plt.plot(0, 0, 'bo') plt.savefig('%03i.png' % i) plt.clf() plt.plot(0, 0, 'ro') plt.savefig('%03i.png' % (i+1)) plt.clf() cProfile.run('slowww_plot()', sort = 'cumulative' 

produces

 In [35]: %run test.py 2035814 function calls (2011194 primitive calls) in 7.322 seconds Ordered by: cumulative time ncalls tottime percall cumtime percall filename:lineno(function) 1 0.000 0.000 7.322 7.322 <string>:1(<module>) 1 0.000 0.000 7.322 7.322 test.py:5(slowww_plot) 40 0.006 0.000 3.615 0.090 axes.py:821(cla) 1440/1120 0.044 0.000 3.278 0.003 axis.py:62(__init__) 20 0.000 0.000 3.049 0.152 pyplot.py:468(savefig) 20 0.000 0.000 3.049 0.152 figure.py:1077(savefig) 20 0.001 0.000 3.048 0.152 backend_bases.py:1892(print_figure) 520/360 0.015 0.000 2.523 0.007 axis.py:697(cla) 20 0.010 0.001 2.506 0.125 backend_bases.py:1791(print_png) 20 0.003 0.000 2.495 0.125 backend_agg.py:444(print_png) 520/360 0.006 0.000 2.475 0.007 axis.py:732(reset_ticks) 4340 0.172 0.000 2.373 0.001 lines.py:128(__init__) 20 0.000 0.000 2.198 0.110 pyplot.py:2449(plot) 20 0.000 0.000 2.149 0.107 pyplot.py:683(gca) 20 0.000 0.000 2.149 0.107 figure.py:1030(gca) 20 0.001 0.000 2.149 0.107 figure.py:710(add_subplot) 20 0.000 0.000 2.146 0.107 axes.py:8327(__init__) 20 0.002 0.000 2.139 0.107 axes.py:359(__init__) 20 0.000 0.000 2.075 0.104 pyplot.py:439(clf) 20 0.001 0.000 2.074 0.104 figure.py:782(clf) 20240 0.189 0.000 1.941 0.000 markers.py:114(_recache) 720/560 0.003 0.000 1.720 0.003 axis.py:1803(_get_tick) 80 0.002 0.000 1.600 0.020 axis.py:830(set_clip_path) 160 0.000 0.000 1.592 0.010 spines.py:153(cla) 720/560 0.003 0.000 1.564 0.003 axis.py:1543(_get_tick) 120 0.004 0.000 1.278 0.011 axis.py:1183(get_major_ticks) 20 1.267 0.063 1.267 0.063 {built-in method write_png} 20 0.000 0.000 1.224 0.061 backend_agg.py:394(draw) 1520/20 0.013 0.000 1.200 0.060 artist.py:53(draw_wrapper) 20 0.002 0.000 1.199 0.060 figure.py:815(draw) 20 0.002 0.000 1.175 0.059 axes.py:1866(draw) 40 0.002 0.000 1.100 0.028 axis.py:1029(draw) 10120 0.017 0.000 1.078 0.000 markers.py:132(set_fillstyle) 5780 0.013 0.000 1.032 0.000 markers.py:109(__init__) 

How can I optimize this? I tried using the PdfPages backend and switching from a PdfPages shell to using Axis.plot , but still slowly.

Answer 1

You do this very inefficiently if you want animation.

Instead of making a new drawing every time, just set up new data and redraw the existing number.

For instance:

 import matplotlib.pyplot as plt import numpy as np xy = 100 * np.random.random((2,10)) x, y = xy fig, ax = plt.subplots() points, = ax.plot(x, y, 'bo') for i in range(10): xy += np.random.random(xy.shape) - 0.5 points.set_data(xy) fig.savefig('%03i.png' % i) 

Answer 2

You might be interested in the matplotlib (1.1.0) new animation function. Here is an example from their site that shows how to make simple animations:

 import numpy as np import matplotlib.pyplot as plt import matplotlib.animation as animation def update_line(num, data, line): line.set_data(data[...,:num]) return line, fig1 = plt.figure() data = np.random.rand(2, 25) l, = plt.plot([], [], 'r-') plt.xlim(0, 1) plt.ylim(0, 1) plt.xlabel('x') plt.title('test') line_ani = animation.FuncAnimation(fig1, update_line, 25, fargs=(data, l), interval=50, blit=True) line_ani.save('lines.mp4')