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Processing a numpy array in native code

Date: 2019-01-14, Author: Nenad Markuš

In this post, we show how to process a numpy array with native code written in C. A self-contained example is available here.

If you prefer a more verbose explanation than going through Python code, please read on.

Introduction and motivation

The Python programming language is nowadays a de facto standard for prototyping/research in data science, computer vision, machine learning, etc. However, writing algorithms in pure Python is computationally inefficient as it is an interpreted language. Thus, most scientific programs written in it use libraries like numpy to perform numeric computations.

While numpy is a great library, some algorithms are difficult (or impossible) to express with its built-in functionalities. Thus, for awesome performance, it might be desirable to pass an array to native code for processing. To achieve this, we use ctypes, a foreign function library for Python. This library provides C compatible data types and allows to wrap functions in DLLs or shared libraries in pure Python.

Let us first formulate a dummy problem through which we will illustrate all the important points.

Our dummy problem

Let A be an array consisting of n 32-bit floating point numbers. Our task is to find the mean value of this array, i.e.,

\[\mu= \frac{1}{n}\sum_{i=0}^{n-1} A_i\]

Using pure Python, this can be computed as:

for i in range(0, n):
	sum += A[i]
mean = sum/n

Trivial, of course. However, it is even simpler using numpy:

mean = numpy.mean(A)

In the next section, we express this computation in native code.

Native code for computing the mean of an array

The following C function will do the job:

float compute_mean(float* A, int n)
	int i;
	float sum = 0.0f;
	for(i=0; i<n; ++i)
		sum += A[i];
	return sum/n;

If we assume that the above code is in a file lib.c, we can compile a shared library as follows:

cc lib.c -fPIC -shared -o lib.so

The following section shows how to invoke this function from Python.

Using ctypes to call functions from a native library

To load lib.so as a Python object, execute the following commands:

import ctypes
lib = ctypes.cdll.LoadLibrary('./lib.so')

The compute_mean function expects a pointer to the array and the number of elements within this array as parameters. The first parameter can be obtained with ctypes.c_void_p(A.ctypes.data) and the second as ctypes.c_int(n).

Next, we indicate that we expect a float as a return value and call the desired function on our array:

lib.compute_mean.restype = ctypes.c_float
mean = lib.compute_mean(ctypes.c_void_p(A.ctypes.data), ctypes.c_int(n))

The default restype is c_int, so we do not have to set this flag in the case when the native function returns a C int.

Additional remarks

A self-contained code for this tutorial is available here.

A possible pitfall of this approach is forgetting that a numpy array can be stored in a non-continuous block of memory (e.g., if we perform a slicing operation on a 2D array). We can examine whether an array is contiguous by checking its C_CONTIGUOUS flag and, if required, react accordingly:

if not A.flags['C_CONTIGUOUS']:
	A = numpy.ascontiguousarray(A)