Date: 01/2019

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.

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.

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:

```
sum=0
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.

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.

`ctypes`

to call functions from a native libraryTo 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`

.

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 = A.ascontiguousarray(A)
```

- https://docs.python.org/3/library/ctypes.html
- https://stackoverflow.com/questions/5862915/passing-numpy-arrays-to-a-c-function-for-input-and-output
- https://stackoverflow.com/questions/29947639/cheapest-way-to-get-a-numpy-array-into-c-contiguous-order

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