Using Python as glue¶
Many people like to say that Python is a fantastic glue language. Hopefully, this Chapter will convince you that this is true. The first adopters of Python for science were typically people who used it to glue together large application codes running on super-computers. Not only was it much nicer to code in Python than in a shell script or Perl, in addition, the ability to easily extend Python made it relatively easy to create new classes and types specifically adapted to the problems being solved. From the interactions of these early contributors, Numeric emerged as an array-like object that could be used to pass data between these applications.
As Numeric has matured and developed into NumPy, people have been able to write more code directly in NumPy. Often this code is fast-enough for production use, but there are still times that there is a need to access compiled code. Either to get that last bit of efficiency out of the algorithm or to make it easier to access widely-available codes written in C/C++ or Fortran.
This chapter will review many of the tools that are available for the purpose of accessing code written in other compiled languages. There are many resources available for learning to call other compiled libraries from Python and the purpose of this Chapter is not to make you an expert. The main goal is to make you aware of some of the possibilities so that you will know what to “Google” in order to learn more.
Calling other compiled libraries from Python¶
While Python is a great language and a pleasure to code in, its dynamic nature results in overhead that can cause some code ( i.e. raw computations inside of for loops) to be up 10-100 times slower than equivalent code written in a static compiled language. In addition, it can cause memory usage to be larger than necessary as temporary arrays are created and destroyed during computation. For many types of computing needs, the extra slow-down and memory consumption can often not be spared (at least for time- or memory- critical portions of your code). Therefore one of the most common needs is to call out from Python code to a fast, machine-code routine (e.g. compiled using C/C++ or Fortran). The fact that this is relatively easy to do is a big reason why Python is such an excellent high-level language for scientific and engineering programming.
Their are two basic approaches to calling compiled code: writing an extension module that is then imported to Python using the import command, or calling a shared-library subroutine directly from Python using the ctypes module. Writing an extension module is the most common method.
Warning
Calling C-code from Python can result in Python crashes if you are not careful. None of the approaches in this chapter are immune. You have to know something about the way data is handled by both NumPy and by the third-party library being used.
Hand-generated wrappers¶
Extension modules were discussed in Writing an extension module.
The most basic way to interface with compiled code is to write
an extension module and construct a module method that calls
the compiled code. For improved readability, your method should
take advantage of the PyArg_ParseTuple call to convert between
Python objects and C data-types. For standard C data-types there
is probably already a built-in converter. For others you may need
to write your own converter and use the "O&" format string which
allows you to specify a function that will be used to perform the
conversion from the Python object to whatever C-structures are needed.
Once the conversions to the appropriate C-structures and C data-types have been performed, the next step in the wrapper is to call the underlying function. This is straightforward if the underlying function is in C or C++. However, in order to call Fortran code you must be familiar with how Fortran subroutines are called from C/C++ using your compiler and platform. This can vary somewhat platforms and compilers (which is another reason f2py makes life much simpler for interfacing Fortran code) but generally involves underscore mangling of the name and the fact that all variables are passed by reference (i.e. all arguments are pointers).
The advantage of the hand-generated wrapper is that you have complete control over how the C-library gets used and called which can lead to a lean and tight interface with minimal over-head. The disadvantage is that you have to write, debug, and maintain C-code, although most of it can be adapted using the time-honored technique of “cutting-pasting-and-modifying” from other extension modules. Because, the procedure of calling out to additional C-code is fairly regimented, code-generation procedures have been developed to make this process easier. One of these code-generation techniques is distributed with NumPy and allows easy integration with Fortran and (simple) C code. This package, f2py, will be covered briefly in the next section.
f2py¶
F2py allows you to automatically construct an extension module that interfaces to routines in Fortran 77/90/95 code. It has the ability to parse Fortran 77/90/95 code and automatically generate Python signatures for the subroutines it encounters, or you can guide how the subroutine interfaces with Python by constructing an interface-definition-file (or modifying the f2py-produced one).
Creating source for a basic extension module¶
Probably the easiest way to introduce f2py is to offer a simple
example. Here is one of the subroutines contained in a file named
add.f:
C
SUBROUTINE ZADD(A,B,C,N)
C
DOUBLE COMPLEX A(*)
DOUBLE COMPLEX B(*)
DOUBLE COMPLEX C(*)
INTEGER N
DO 20 J = 1, N
C(J) = A(J)+B(J)
20 CONTINUE
END
This routine simply adds the elements in two contiguous arrays and places the result in a third. The memory for all three arrays must be provided by the calling routine. A very basic interface to this routine can be automatically generated by f2py:
f2py -m add add.f
You should be able to run this command assuming your search-path is set-up properly. This command will produce an extension module named addmodule.c in the current directory. This extension module can now be compiled and used from Python just like any other extension module.
Creating a compiled extension module¶
You can also get f2py to compile add.f and also compile its produced extension module leaving only a shared-library extension file that can be imported from Python:
f2py -c -m add add.f
This command leaves a file named add.{ext} in the current directory (where {ext} is the appropriate extension for a python extension module on your platform — so, pyd, etc. ). This module may then be imported from Python. It will contain a method for each subroutine in add (zadd, cadd, dadd, sadd). The docstring of each method contains information about how the module method may be called:
>>> import add
>>> print add.zadd.__doc__
zadd - Function signature:
zadd(a,b,c,n)
Required arguments:
a : input rank-1 array('D') with bounds (*)
b : input rank-1 array('D') with bounds (*)
c : input rank-1 array('D') with bounds (*)
n : input int
Improving the basic interface¶
The default interface is a very literal translation of the fortran code into Python. The Fortran array arguments must now be NumPy arrays and the integer argument should be an integer. The interface will attempt to convert all arguments to their required types (and shapes) and issue an error if unsuccessful. However, because it knows nothing about the semantics of the arguments (such that C is an output and n should really match the array sizes), it is possible to abuse this function in ways that can cause Python to crash. For example:
>>> add.zadd([1,2,3], [1,2], [3,4], 1000)
will cause a program crash on most systems. Under the covers, the lists are being converted to proper arrays but then the underlying add loop is told to cycle way beyond the borders of the allocated memory.
In order to improve the interface, directives should be provided. This is accomplished by constructing an interface definition file. It is usually best to start from the interface file that f2py can produce (where it gets its default behavior from). To get f2py to generate the interface file use the -h option:
f2py -h add.pyf -m add add.f
This command leaves the file add.pyf in the current directory. The section of this file corresponding to zadd is:
subroutine zadd(a,b,c,n) ! in :add:add.f
double complex dimension(*) :: a
double complex dimension(*) :: b
double complex dimension(*) :: c
integer :: n
end subroutine zadd
By placing intent directives and checking code, the interface can be cleaned up quite a bit until the Python module method is both easier to use and more robust.
subroutine zadd(a,b,c,n) ! in :add:add.f
double complex dimension(n) :: a
double complex dimension(n) :: b
double complex intent(out),dimension(n) :: c
integer intent(hide),depend(a) :: n=len(a)
end subroutine zadd
The intent directive, intent(out) is used to tell f2py that c is
an output variable and should be created by the interface before being
passed to the underlying code. The intent(hide) directive tells f2py
to not allow the user to specify the variable, n, but instead to
get it from the size of a. The depend( a ) directive is
necessary to tell f2py that the value of n depends on the input a (so
that it won’t try to create the variable n until the variable a is
created).
After modifying add.pyf, the new python module file can be generated
by compiling both add.f95 and add.pyf:
f2py -c add.pyf add.f95
The new interface has docstring:
>>> import add
>>> print add.zadd.__doc__
zadd - Function signature:
c = zadd(a,b)
Required arguments:
a : input rank-1 array('D') with bounds (n)
b : input rank-1 array('D') with bounds (n)
Return objects:
c : rank-1 array('D') with bounds (n)
Now, the function can be called in a much more robust way:
>>> add.zadd([1,2,3],[4,5,6])
array([ 5.+0.j, 7.+0.j, 9.+0.j])
Notice the automatic conversion to the correct format that occurred.
Inserting directives in Fortran source¶
The nice interface can also be generated automatically by placing the variable directives as special comments in the original fortran code. Thus, if I modify the source code to contain:
C
SUBROUTINE ZADD(A,B,C,N)
C
CF2PY INTENT(OUT) :: C
CF2PY INTENT(HIDE) :: N
CF2PY DOUBLE COMPLEX :: A(N)
CF2PY DOUBLE COMPLEX :: B(N)
CF2PY DOUBLE COMPLEX :: C(N)
DOUBLE COMPLEX A(*)
DOUBLE COMPLEX B(*)
DOUBLE COMPLEX C(*)
INTEGER N
DO 20 J = 1, N
C(J) = A(J) + B(J)
20 CONTINUE
END
Then, I can compile the extension module using:
f2py -c -m add add.f
The resulting signature for the function add.zadd is exactly the same
one that was created previously. If the original source code had
contained A(N) instead of A(*) and so forth with B and C,
then I could obtain (nearly) the same interface simply by placing the
INTENT(OUT) :: C comment line in the source code. The only difference
is that N would be an optional input that would default to the length
of A.
A filtering example¶
For comparison with the other methods to be discussed. Here is another example of a function that filters a two-dimensional array of double precision floating-point numbers using a fixed averaging filter. The advantage of using Fortran to index into multi-dimensional arrays should be clear from this example.
SUBROUTINE DFILTER2D(A,B,M,N)
C
DOUBLE PRECISION A(M,N)
DOUBLE PRECISION B(M,N)
INTEGER N, M
CF2PY INTENT(OUT) :: B
CF2PY INTENT(HIDE) :: N
CF2PY INTENT(HIDE) :: M
DO 20 I = 2,M-1
DO 40 J=2,N-1
B(I,J) = A(I,J) +
$ (A(I-1,J)+A(I+1,J) +
$ A(I,J-1)+A(I,J+1) )*0.5D0 +
$ (A(I-1,J-1) + A(I-1,J+1) +
$ A(I+1,J-1) + A(I+1,J+1))*0.25D0
40 CONTINUE
20 CONTINUE
END
This code can be compiled and linked into an extension module named filter using:
f2py -c -m filter filter.f
This will produce an extension module named filter.so in the current directory with a method named dfilter2d that returns a filtered version of the input.
Calling f2py from Python¶
The f2py program is written in Python and can be run from inside your code to compile Fortran code at runtime, as follows:
from numpy import f2py
with open("add.f") as sourcefile:
sourcecode = sourcefile.read()
f2py.compile(sourcecode, modulename='add')
import add
The source string can be any valid Fortran code. If you want to save
the extension-module source code then a suitable file-name can be
provided by the source_fn keyword to the compile function.
Automatic extension module generation¶
If you want to distribute your f2py extension module, then you only
need to include the .pyf file and the Fortran code. The distutils
extensions in NumPy allow you to define an extension module entirely
in terms of this interface file. A valid setup.py file allowing
distribution of the add.f module (as part of the package
f2py_examples so that it would be loaded as f2py_examples.add) is:
def configuration(parent_package='', top_path=None)
from numpy.distutils.misc_util import Configuration
config = Configuration('f2py_examples',parent_package, top_path)
config.add_extension('add', sources=['add.pyf','add.f'])
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())
Installation of the new package is easy using:
pip install .
assuming you have the proper permissions to write to the main site-
packages directory for the version of Python you are using. For the
resulting package to work, you need to create a file named __init__.py
(in the same directory as add.pyf). Notice the extension module is
defined entirely in terms of the add.pyf and add.f files. The
conversion of the .pyf file to a .c file is handled by numpy.disutils.
Conclusion¶
The interface definition file (.pyf) is how you can fine-tune the interface between Python and Fortran. There is decent documentation for f2py found in the numpy/f2py/docs directory where-ever NumPy is installed on your system (usually under site-packages). There is also more information on using f2py (including how to use it to wrap C codes) at https://scipy-cookbook.readthedocs.io under the “Interfacing With Other Languages” heading.
The f2py method of linking compiled code is currently the most sophisticated and integrated approach. It allows clean separation of Python with compiled code while still allowing for separate distribution of the extension module. The only draw-back is that it requires the existence of a Fortran compiler in order for a user to install the code. However, with the existence of the free-compilers g77, gfortran, and g95, as well as high-quality commercial compilers, this restriction is not particularly onerous. In my opinion, Fortran is still the easiest way to write fast and clear code for scientific computing. It handles complex numbers, and multi-dimensional indexing in the most straightforward way. Be aware, however, that some Fortran compilers will not be able to optimize code as well as good hand- written C-code.
Cython¶
Cython is a compiler for a Python dialect that adds (optional) static typing for speed, and allows mixing C or C++ code into your modules. It produces C or C++ extensions that can be compiled and imported in Python code.
If you are writing an extension module that will include quite a bit of your own algorithmic code as well, then Cython is a good match. Among its features is the ability to easily and quickly work with multidimensional arrays.
Notice that Cython is an extension-module generator only. Unlike f2py,
it includes no automatic facility for compiling and linking
the extension module (which must be done in the usual fashion). It
does provide a modified distutils class called build_ext which lets
you build an extension module from a .pyx source. Thus, you could
write in a setup.py file:
from Cython.Distutils import build_ext
from distutils.extension import Extension
from distutils.core import setup
import numpy
setup(name='mine', description='Nothing',
ext_modules=[Extension('filter', ['filter.pyx'],
include_dirs=[numpy.get_include()])],
cmdclass = {'build_ext':build_ext})
Adding the NumPy include directory is, of course, only necessary if
you are using NumPy arrays in the extension module (which is what we
assume you are using Cython for). The distutils extensions in NumPy
also include support for automatically producing the extension-module
and linking it from a .pyx file. It works so that if the user does
not have Cython installed, then it looks for a file with the same
file-name but a .c extension which it then uses instead of trying
to produce the .c file again.
If you just use Cython to compile a standard Python module, then you
will get a C extension module that typically runs a bit faster than the
equivalent Python module. Further speed increases can be gained by using
the cdef keyword to statically define C variables.
Let’s look at two examples we’ve seen before to see how they might be implemented using Cython. These examples were compiled into extension modules using Cython 0.21.1.
Complex addition in Cython¶
Here is part of a Cython module named add.pyx which implements the
complex addition functions we previously implemented using f2py:
cimport cython
cimport numpy as np
import numpy as np
# We need to initialize NumPy.
np.import_array()
#@cython.boundscheck(False)
def zadd(in1, in2):
cdef double complex[:] a = in1.ravel()
cdef double complex[:] b = in2.ravel()
out = np.empty(a.shape[0], np.complex64)
cdef double complex[:] c = out.ravel()
for i in range(c.shape[0]):
c[i].real = a[i].real + b[i].real
c[i].imag = a[i].imag + b[i].imag
return out
This module shows use of the cimport statement to load the definitions
from the numpy.pxd header that ships with Cython. It looks like NumPy is
imported twice; cimport only makes the NumPy C-API available, while the
regular import causes a Python-style import at runtime and makes it
possible to call into the familiar NumPy Python API.
The example also demonstrates Cython’s “typed memoryviews”, which are like
NumPy arrays at the C level, in the sense that they are shaped and strided
arrays that know their own extent (unlike a C array addressed through a bare
pointer). The syntax double complex[:] denotes a one-dimensional array
(vector) of doubles, with arbitrary strides. A contiguous array of ints would
be int[::1], while a matrix of floats would be float[:, :].
Shown commented is the cython.boundscheck decorator, which turns
bounds-checking for memory view accesses on or off on a per-function basis.
We can use this to further speed up our code, at the expense of safety
(or a manual check prior to entering the loop).
Other than the view syntax, the function is immediately readable to a Python
programmer. Static typing of the variable i is implicit. Instead of the
view syntax, we could also have used Cython’s special NumPy array syntax,
but the view syntax is preferred.
Image filter in Cython¶
The two-dimensional example we created using Fortran is just as easy to write in Cython:
cimport numpy as np
import numpy as np
np.import_array()
def filter(img):
cdef double[:, :] a = np.asarray(img, dtype=np.double)
out = np.zeros(img.shape, dtype=np.double)
cdef double[:, ::1] b = out
cdef np.npy_intp i, j
for i in range(1, a.shape[0] - 1):
for j in range(1, a.shape[1] - 1):
b[i, j] = (a[i, j]
+ .5 * ( a[i-1, j] + a[i+1, j]
+ a[i, j-1] + a[i, j+1])
+ .25 * ( a[i-1, j-1] + a[i-1, j+1]
+ a[i+1, j-1] + a[i+1, j+1]))
return out
This 2-d averaging filter runs quickly because the loop is in C and
the pointer computations are done only as needed. If the code above is
compiled as a module image, then a 2-d image, img, can be filtered
using this code very quickly using:
import image
out = image.filter(img)
Regarding the code, two things are of note: firstly, it is impossible to
return a memory view to Python. Instead, a NumPy array out is first
created, and then a view b onto this array is used for the computation.
Secondly, the view b is typed double[:, ::1]. This means 2-d array
with contiguous rows, i.e., C matrix order. Specifying the order explicitly
can speed up some algorithms since they can skip stride computations.
Conclusion¶
Cython is the extension mechanism of choice for several scientific Python libraries, including Scipy, Pandas, SAGE, scikit-image and scikit-learn, as well as the XML processing library LXML. The language and compiler are well-maintained.
There are several disadvantages of using Cython:
When coding custom algorithms, and sometimes when wrapping existing C libraries, some familiarity with C is required. In particular, when using C memory management (
mallocand friends), it’s easy to introduce memory leaks. However, just compiling a Python module renamed to.pyxcan already speed it up, and adding a few type declarations can give dramatic speedups in some code.It is easy to lose a clean separation between Python and C which makes re-using your C-code for other non-Python-related projects more difficult.
The C-code generated by Cython is hard to read and modify (and typically compiles with annoying but harmless warnings).
One big advantage of Cython-generated extension modules is that they are easy to distribute. In summary, Cython is a very capable tool for either gluing C code or generating an extension module quickly and should not be over-looked. It is especially useful for people that can’t or won’t write C or Fortran code.
ctypes¶
Ctypes is a Python extension module, included in the stdlib, that allows you to call an arbitrary function in a shared library directly from Python. This approach allows you to interface with C-code directly from Python. This opens up an enormous number of libraries for use from Python. The drawback, however, is that coding mistakes can lead to ugly program crashes very easily (just as can happen in C) because there is little type or bounds checking done on the parameters. This is especially true when array data is passed in as a pointer to a raw memory location. The responsibility is then on you that the subroutine will not access memory outside the actual array area. But, if you don’t mind living a little dangerously ctypes can be an effective tool for quickly taking advantage of a large shared library (or writing extended functionality in your own shared library).
Because the ctypes approach exposes a raw interface to the compiled code it is not always tolerant of user mistakes. Robust use of the ctypes module typically involves an additional layer of Python code in order to check the data types and array bounds of objects passed to the underlying subroutine. This additional layer of checking (not to mention the conversion from ctypes objects to C-data-types that ctypes itself performs), will make the interface slower than a hand-written extension-module interface. However, this overhead should be negligible if the C-routine being called is doing any significant amount of work. If you are a great Python programmer with weak C skills, ctypes is an easy way to write a useful interface to a (shared) library of compiled code.
To use ctypes you must
Have a shared library.
Load the shared library.
Convert the python objects to ctypes-understood arguments.
Call the function from the library with the ctypes arguments.
Converting arguments¶
Python ints/longs, strings, and unicode objects are automatically converted as needed to equivalent ctypes arguments The None object is also converted automatically to a NULL pointer. All other Python objects must be converted to ctypes-specific types. There are two ways around this restriction that allow ctypes to integrate with other objects.
Don’t set the argtypes attribute of the function object and define an
_as_parameter_method for the object you want to pass in. The_as_parameter_method must return a Python int which will be passed directly to the function.Set the argtypes attribute to a list whose entries contain objects with a classmethod named from_param that knows how to convert your object to an object that ctypes can understand (an int/long, string, unicode, or object with the
_as_parameter_attribute).
NumPy uses both methods with a preference for the second method
because it can be safer. The ctypes attribute of the ndarray returns
an object that has an _as_parameter_ attribute which returns an
integer representing the address of the ndarray to which it is
associated. As a result, one can pass this ctypes attribute object
directly to a function expecting a pointer to the data in your
ndarray. The caller must be sure that the ndarray object is of the
correct type, shape, and has the correct flags set or risk nasty
crashes if the data-pointer to inappropriate arrays are passed in.
To implement the second method, NumPy provides the class-factory
function ndpointer in the numpy.ctypeslib module. This
class-factory function produces an appropriate class that can be
placed in an argtypes attribute entry of a ctypes function. The class
will contain a from_param method which ctypes will use to convert any
ndarray passed in to the function to a ctypes-recognized object. In
the process, the conversion will perform checking on any properties of
the ndarray that were specified by the user in the call to ndpointer.
Aspects of the ndarray that can be checked include the data-type, the
number-of-dimensions, the shape, and/or the state of the flags on any
array passed. The return value of the from_param method is the ctypes
attribute of the array which (because it contains the _as_parameter_
attribute pointing to the array data area) can be used by ctypes
directly.
The ctypes attribute of an ndarray is also endowed with additional
attributes that may be convenient when passing additional information
about the array into a ctypes function. The attributes data,
shape, and strides can provide ctypes compatible types
corresponding to the data-area, the shape, and the strides of the
array. The data attribute returns a c_void_p representing a
pointer to the data area. The shape and strides attributes each return
an array of ctypes integers (or None representing a NULL pointer, if a
0-d array). The base ctype of the array is a ctype integer of the same
size as a pointer on the platform. There are also methods
data_as({ctype}), shape_as(<base ctype>), and strides_as(<base
ctype>). These return the data as a ctype object of your choice and
the shape/strides arrays using an underlying base type of your choice.
For convenience, the ctypeslib module also contains c_intp as
a ctypes integer data-type whose size is the same as the size of
c_void_p on the platform (its value is None if ctypes is not
installed).
Calling the function¶
The function is accessed as an attribute of or an item from the loaded
shared-library. Thus, if ./mylib.so has a function named
cool_function1 , I could access this function either as:
lib = numpy.ctypeslib.load_library('mylib','.')
func1 = lib.cool_function1 # or equivalently
func1 = lib['cool_function1']
In ctypes, the return-value of a function is set to be ‘int’ by default. This behavior can be changed by setting the restype attribute of the function. Use None for the restype if the function has no return value (‘void’):
func1.restype = None
As previously discussed, you can also set the argtypes attribute of
the function in order to have ctypes check the types of the input
arguments when the function is called. Use the ndpointer factory
function to generate a ready-made class for data-type, shape, and
flags checking on your new function. The ndpointer function has the
signature
-
ndpointer(dtype=None, ndim=None, shape=None, flags=None)¶ Keyword arguments with the value
Noneare not checked. Specifying a keyword enforces checking of that aspect of the ndarray on conversion to a ctypes-compatible object. The dtype keyword can be any object understood as a data-type object. The ndim keyword should be an integer, and the shape keyword should be an integer or a sequence of integers. The flags keyword specifies the minimal flags that are required on any array passed in. This can be specified as a string of comma separated requirements, an integer indicating the requirement bits OR’d together, or a flags object returned from the flags attribute of an array with the necessary requirements.
Using an ndpointer class in the argtypes method can make it
significantly safer to call a C function using ctypes and the data-
area of an ndarray. You may still want to wrap the function in an
additional Python wrapper to make it user-friendly (hiding some
obvious arguments and making some arguments output arguments). In this
process, the requires function in NumPy may be useful to return the right
kind of array from a given input.
Complete example¶
In this example, I will show how the addition function and the filter
function implemented previously using the other approaches can be
implemented using ctypes. First, the C code which implements the
algorithms contains the functions zadd, dadd, sadd, cadd,
and dfilter2d. The zadd function is:
/* Add arrays of contiguous data */
typedef struct {double real; double imag;} cdouble;
typedef struct {float real; float imag;} cfloat;
void zadd(cdouble *a, cdouble *b, cdouble *c, long n)
{
while (n--) {
c->real = a->real + b->real;
c->imag = a->imag + b->imag;
a++; b++; c++;
}
}
with similar code for cadd, dadd, and sadd that handles complex
float, double, and float data-types, respectively:
void cadd(cfloat *a, cfloat *b, cfloat *c, long n)
{
while (n--) {
c->real = a->real + b->real;
c->imag = a->imag + b->imag;
a++; b++; c++;
}
}
void dadd(double *a, double *b, double *c, long n)
{
while (n--) {
*c++ = *a++ + *b++;
}
}
void sadd(float *a, float *b, float *c, long n)
{
while (n--) {
*c++ = *a++ + *b++;
}
}
The code.c file also contains the function dfilter2d:
/*
* Assumes b is contiguous and has strides that are multiples of
* sizeof(double)
*/
void
dfilter2d(double *a, double *b, ssize_t *astrides, ssize_t *dims)
{
ssize_t i, j, M, N, S0, S1;
ssize_t r, c, rm1, rp1, cp1, cm1;
M = dims[0]; N = dims[1];
S0 = astrides[0]/sizeof(double);
S1 = astrides[1]/sizeof(double);
for (i = 1; i < M - 1; i++) {
r = i*S0;
rp1 = r + S0;
rm1 = r - S0;
for (j = 1; j < N - 1; j++) {
c = j*S1;
cp1 = j + S1;
cm1 = j - S1;
b[i*N + j] = a[r + c] +
(a[rp1 + c] + a[rm1 + c] +
a[r + cp1] + a[r + cm1])*0.5 +
(a[rp1 + cp1] + a[rp1 + cm1] +
a[rm1 + cp1] + a[rm1 + cp1])*0.25;
}
}
}
A possible advantage this code has over the Fortran-equivalent code is
that it takes arbitrarily strided (i.e. non-contiguous arrays) and may
also run faster depending on the optimization capability of your
compiler. But, it is an obviously more complicated than the simple code
in filter.f. This code must be compiled into a shared library. On my
Linux system this is accomplished using:
gcc -o code.so -shared code.c
Which creates a shared_library named code.so in the current directory.
On Windows don’t forget to either add __declspec(dllexport) in front
of void on the line preceding each function definition, or write a
code.def file that lists the names of the functions to be exported.
A suitable Python interface to this shared library should be constructed. To do this create a file named interface.py with the following lines at the top:
__all__ = ['add', 'filter2d']
import numpy as np
import os
_path = os.path.dirname('__file__')
lib = np.ctypeslib.load_library('code', _path)
_typedict = {'zadd' : complex, 'sadd' : np.single,
'cadd' : np.csingle, 'dadd' : float}
for name in _typedict.keys():
val = getattr(lib, name)
val.restype = None
_type = _typedict[name]
val.argtypes = [np.ctypeslib.ndpointer(_type,
flags='aligned, contiguous'),
np.ctypeslib.ndpointer(_type,
flags='aligned, contiguous'),
np.ctypeslib.ndpointer(_type,
flags='aligned, contiguous,'\
'writeable'),
np.ctypeslib.c_intp]
This code loads the shared library named code.{ext} located in the
same path as this file. It then adds a return type of void to the
functions contained in the library. It also adds argument checking to
the functions in the library so that ndarrays can be passed as the
first three arguments along with an integer (large enough to hold a
pointer on the platform) as the fourth argument.
Setting up the filtering function is similar and allows the filtering function to be called with ndarray arguments as the first two arguments and with pointers to integers (large enough to handle the strides and shape of an ndarray) as the last two arguments.:
lib.dfilter2d.restype=None
lib.dfilter2d.argtypes = [np.ctypeslib.ndpointer(float, ndim=2,
flags='aligned'),
np.ctypeslib.ndpointer(float, ndim=2,
flags='aligned, contiguous,'\
'writeable'),
ctypes.POINTER(np.ctypeslib.c_intp),
ctypes.POINTER(np.ctypeslib.c_intp)]
Next, define a simple selection function that chooses which addition function to call in the shared library based on the data-type:
def select(dtype):
if dtype.char in ['?bBhHf']:
return lib.sadd, single
elif dtype.char in ['F']:
return lib.cadd, csingle
elif dtype.char in ['DG']:
return lib.zadd, complex
else:
return lib.dadd, float
return func, ntype
Finally, the two functions to be exported by the interface can be written simply as:
def add(a, b):
requires = ['CONTIGUOUS', 'ALIGNED']
a = np.asanyarray(a)
func, dtype = select(a.dtype)
a = np.require(a, dtype, requires)
b = np.require(b, dtype, requires)
c = np.empty_like(a)
func(a,b,c,a.size)
return c
and:
def filter2d(a):
a = np.require(a, float, ['ALIGNED'])
b = np.zeros_like(a)
lib.dfilter2d(a, b, a.ctypes.strides, a.ctypes.shape)
return b
Conclusion¶
Using ctypes is a powerful way to connect Python with arbitrary C-code. Its advantages for extending Python include
clean separation of C code from Python code
no need to learn a new syntax except Python and C
allows re-use of C code
functionality in shared libraries written for other purposes can be obtained with a simple Python wrapper and search for the library.
easy integration with NumPy through the ctypes attribute
full argument checking with the ndpointer class factory
Its disadvantages include
It is difficult to distribute an extension module made using ctypes because of a lack of support for building shared libraries in distutils (but I suspect this will change in time).
You must have shared-libraries of your code (no static libraries).
Very little support for C++ code and its different library-calling conventions. You will probably need a C wrapper around C++ code to use with ctypes (or just use Boost.Python instead).
Because of the difficulty in distributing an extension module made using ctypes, f2py and Cython are still the easiest ways to extend Python for package creation. However, ctypes is in some cases a useful alternative. This should bring more features to ctypes that should eliminate the difficulty in extending Python and distributing the extension using ctypes.
Additional tools you may find useful¶
These tools have been found useful by others using Python and so are included here. They are discussed separately because they are either older ways to do things now handled by f2py, Cython, or ctypes (SWIG, PyFort) or because I don’t know much about them (SIP, Boost). I have not added links to these methods because my experience is that you can find the most relevant link faster using Google or some other search engine, and any links provided here would be quickly dated. Do not assume that just because it is included in this list, I don’t think the package deserves your attention. I’m including information about these packages because many people have found them useful and I’d like to give you as many options as possible for tackling the problem of easily integrating your code.
SWIG¶
Simplified Wrapper and Interface Generator (SWIG) is an old and fairly
stable method for wrapping C/C++-libraries to a large variety of other
languages. It does not specifically understand NumPy arrays but can be
made useable with NumPy through the use of typemaps. There are some
sample typemaps in the numpy/tools/swig directory under numpy.i together
with an example module that makes use of them. SWIG excels at wrapping
large C/C++ libraries because it can (almost) parse their headers and
auto-produce an interface. Technically, you need to generate a .i
file that defines the interface. Often, however, this .i file can
be parts of the header itself. The interface usually needs a bit of
tweaking to be very useful. This ability to parse C/C++ headers and
auto-generate the interface still makes SWIG a useful approach to
adding functionalilty from C/C++ into Python, despite the other
methods that have emerged that are more targeted to Python. SWIG can
actually target extensions for several languages, but the typemaps
usually have to be language-specific. Nonetheless, with modifications
to the Python-specific typemaps, SWIG can be used to interface a
library with other languages such as Perl, Tcl, and Ruby.
My experience with SWIG has been generally positive in that it is relatively easy to use and quite powerful. I used to use it quite often before becoming more proficient at writing C-extensions. However, I struggled writing custom interfaces with SWIG because it must be done using the concept of typemaps which are not Python specific and are written in a C-like syntax. Therefore, I tend to prefer other gluing strategies and would only attempt to use SWIG to wrap a very-large C/C++ library. Nonetheless, there are others who use SWIG quite happily.
SIP¶
SIP is another tool for wrapping C/C++ libraries that is Python specific and appears to have very good support for C++. Riverbank Computing developed SIP in order to create Python bindings to the QT library. An interface file must be written to generate the binding, but the interface file looks a lot like a C/C++ header file. While SIP is not a full C++ parser, it understands quite a bit of C++ syntax as well as its own special directives that allow modification of how the Python binding is accomplished. It also allows the user to define mappings between Python types and C/C++ structures and classes.
Boost Python¶
Boost is a repository of C++ libraries and Boost.Python is one of those libraries which provides a concise interface for binding C++ classes and functions to Python. The amazing part of the Boost.Python approach is that it works entirely in pure C++ without introducing a new syntax. Many users of C++ report that Boost.Python makes it possible to combine the best of both worlds in a seamless fashion. I have not used Boost.Python because I am not a big user of C++ and using Boost to wrap simple C-subroutines is usually over-kill. It’s primary purpose is to make C++ classes available in Python. So, if you have a set of C++ classes that need to be integrated cleanly into Python, consider learning about and using Boost.Python.
PyFort¶
PyFort is a nice tool for wrapping Fortran and Fortran-like C-code into Python with support for Numeric arrays. It was written by Paul Dubois, a distinguished computer scientist and the very first maintainer of Numeric (now retired). It is worth mentioning in the hopes that somebody will update PyFort to work with NumPy arrays as well which now support either Fortran or C-style contiguous arrays.