Python:Speed

Python is a powerful high-level programming language with a clean syntax. However, the flexibility and generality (e.g. dynamic typing) does have an associated performance cost. There are various strategies to improve the speed of execution of Python code:

1. Re-code: As always, the first thing to try is to identify the bottleneck in the code, and rework it. Typically, using the most appropriate algorithm can improve execution by orders-of-magnitude.
2. Libraries: Exploiting Python libraries (which are highly optimized and often written in lower-level languages) can greatly improve performance. In particular, using numpy for matrix-style numerical computations (rather than using expensive for-loops or other iterations) can massively speedup computations. Processing on images can be improved using the Python Image Library (PIL), etc.
3. Externals: Critical code can be written in C/C++, and called as a function within Python. This allows the computational bottleneck to be written in a more specialized and efficient manner.
   • SWIG (official site, Wikipedia) can provide a 50-200× speedup.
   • Cython (official site, [https://en.wikipedia.org/wiki/Cython Wikipedia) is a version of Python with an interface for invoking C/C++ routines.
   • ctypes (documentation) is a function library that provides C-compatible data types, allowing external libraries to be used in Python.
   • Python/C API (documentation, tutorial) is available in Python, allowing C extensions to be directly called in Python without much overhead. This 'manual' method lacks the clean wrapping provided by the previously-enumerated methods, but is the most direct method and works well for calling small bits of code.
4. JIT: Just-in-time compilation (JIT) involves compiling Python code as it is needed. The compiling adds a speed penalty as code is first run, but improves overall execution speed if the code iterates over a large dataset.
   • Psycho (official site, Wikipedia) provides a 2-4× speedup (100× in some cases). It is only 32-bit.
   • PyPy (official site, Wikipedia) is an alternative Python interpretation, which features JIT. It provides a 2-25× speedup. Unfortunately, modules/libraries have to be re-installed/re-compiled into the PyPy environment (separate from the usual Python environment).
   • Numba (official site) uses decorators to allow ultra-easy speedups. (CUDA extension also available.)
5. Translation: There are some attempts to automatically translate Python code into optimized lower-level code.
   • shedskin (official site 1, official site 2, Wikipedia) translates Python into C++, providing a 2-200× speedup. Most extensions/libraries are not currently supported. On the other hand, one can isolate some critical code and convert this to an optimized external that is called from conventional Python code.

Matplotlib

The Matplotlib plotting package is popular and powerful. The plotting can sometimes be too slow for rapid animation-style plots. Refer to Speeding up Matplotlib for some hints about improving plotting performance. Here is one example that compares two methods for refreshing a plot:

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

plt.ion()

imgs = np.random.random((100,100,100))
fig = plt.figure(0)
plt.imshow(imgs[0])


ax = plt.gca()
ch = ax.get_children()

plt.cla()
plt.show()

#slow method
tstart = time.time()
for i in np.arange(100):
    print("iteration {}".format(i))
    plt.cla()
    plt.imshow(imgs[0])
    plt.draw()
    time.sleep(0.1)
    plt.pause(.0001)
tend = time.time()
totslow = tend-tstart

plt.cla()

#fast method
tstart = time.time()
for i in np.arange(100):
    print("iteration {}".format(i))
    ch[2].set_data(imgs[i]) #ch[2] is the member of axes that stores the image, AxesImage object
    ax.draw_artist(ch[2])
    fig.canvas.blit()
    fig.canvas.flush_events()
tend = time.time()
totfast = tend-tstart

print("Slow method timing: {} seconds".format(totslow))
print("Fast method timing: {} seconds".format(totfast))