Cython for NumPy users¶
This tutorial is aimed at NumPy users who have no experience with Cython at all. If you have some knowledge of Cython you may want to skip to the ‘’Efficient indexing’’ section which explains the new improvements made in summer 2008.
The main scenario considered is NumPy end-use rather than NumPy/SciPy development. The reason is that Cython is not (yet) able to support functions that are generic with respect to datatype and the number of dimensions in a high-level fashion. This restriction is much more severe for SciPy development than more specific, “end-user” functions. See the last section for more information on this.
The style of this tutorial will not fit everybody, so you can also consider:
- Robert Bradshaw’s slides on cython for SciPy2008 (a higher-level and quicker introduction)
- Basic Cython documentation (see Cython front page).
[:enhancements/buffer:Spec for the efficient indexing]
The fast array access documented below is a completely new feature, and there may be bugs waiting to be discovered. It might be a good idea to do a manual sanity check on the C code Cython generates before using this for serious purposes, at least until some months have passed.
Cython at a glance¶
Cython is a compiler which compiles Python-like code files to C code. Still, ‘’Cython is not a Python to C translator’‘. That is, it doesn’t take your full program and “turns it into C” – rather, the result makes full use of the Python runtime environment. A way of looking at it may be that your code is still Python in that it runs within the Python runtime environment, but rather than compiling to interpreted Python bytecode one compiles to native machine code (but with the addition of extra syntax for easy embedding of faster C-like code).
This has two important consequences:
- Speed. How much depends very much on the program involved though. Typical Python numerical programs would tend to gain very little as most time is spent in lower-level C that is used in a high-level fashion. However for-loop-style programs can gain many orders of magnitude, when typing information is added (and is so made possible as a realistic alternative).
- Easy calling into C code. One of Cython’s purposes is to allow easy wrapping of C libraries. When writing code in Cython you can call into C code as easily as into Python code.
Some Python constructs are not yet supported, though making Cython compile all Python code is a stated goal (among the more important omissions are inner functions and generator functions).
Your Cython environment¶
Using Cython consists of these steps:
- Write a
- Run the Cython compiler to generate a C file
- Run a C compiler to generate a compiled library
- Run the Python interpreter and ask it to import the module
However there are several options to automate these steps:
- The SAGE mathematics software system provides excellent support for using Cython and NumPy from an interactive command line (like IPython) or through a notebook interface (like Maple/Mathematica). See this documentation.
- A version of pyximport is shipped with Cython, so that you can import pyx-files dynamically into Python and have them compiled automatically (See Pyximport).
- Cython supports distutils so that you can very easily create build scripts which automate the process, this is the preferred method for full programs.
- Manual compilation (see below)
If using another interactive command line environment than SAGE, like IPython or Python itself, it is important that you restart the process when you recompile the module. It is not enough to issue an “import” statement again.
Unless you are used to some other automatic method:
download Cython (0.9.8.1.1 or later), unpack it,
and run the usual
`python setup.py install. This will install a
cython executable on your system. It is also possible to use Cython from
the source directory without installing (simply launch
cython.py in the
As of this writing SAGE comes with an older release of Cython than required for this tutorial. So if using SAGE you should download the newest Cython and then execute
$ cd path/to/cython-distro $ path-to-sage/sage -python setup.py install
This will install the newest Cython into SAGE.
As it is always important to know what is going on, I’ll describe the manual method here. First Cython is run:
$ cython yourmod.pyx
yourmod.c which is the C source for a Python extension
module. A useful additional switch is
-a which will generate a document
yourmod.html) that shows which Cython code translates to which C code
line by line.
Then we compile the C file. This may vary according to your system, but the C file should be built like Python was built. Python documentation for writing extensions should have some details. On Linux this often means something like:
$ gcc -shared -pthread -fPIC -fwrapv -O2 -Wall -fno-strict-aliasing -I/usr/include/python2.7 -o yourmod.so yourmod.c
gcc should have access to the NumPy C header files so if they are not
/usr/include/numpy or similar you may need to pass another
option for those.
yourmod.so in the same directory, which is importable by
Python by using a normal
import yourmod statement.
The first Cython program¶
The code below does 2D discrete convolution of an image with a filter (and I’m
sure you can do better!, let it serve for demonstration purposes). It is both
valid Python and valid Cython code. I’ll refer to it as both
convolve_py.py for the Python version and
convolve1.pyx for the
Cython version – Cython uses ”.pyx” as its file suffix.
from __future__ import division import numpy as np def naive_convolve(f, g): # f is an image and is indexed by (v, w) # g is a filter kernel and is indexed by (s, t), # it needs odd dimensions # h is the output image and is indexed by (x, y), # it is not cropped if g.shape % 2 != 1 or g.shape % 2 != 1: raise ValueError("Only odd dimensions on filter supported") # smid and tmid are number of pixels between the center pixel # and the edge, ie for a 5x5 filter they will be 2. # # The output size is calculated by adding smid, tmid to each # side of the dimensions of the input image. vmax = f.shape wmax = f.shape smax = g.shape tmax = g.shape smid = smax // 2 tmid = tmax // 2 xmax = vmax + 2*smid ymax = wmax + 2*tmid # Allocate result image. h = np.zeros([xmax, ymax], dtype=f.dtype) # Do convolution for x in range(xmax): for y in range(ymax): # Calculate pixel value for h at (x,y). Sum one component # for each pixel (s, t) of the filter g. s_from = max(smid - x, -smid) s_to = min((xmax - x) - smid, smid + 1) t_from = max(tmid - y, -tmid) t_to = min((ymax - y) - tmid, tmid + 1) value = 0 for s in range(s_from, s_to): for t in range(t_from, t_to): v = x - smid + s w = y - tmid + t value += g[smid - s, tmid - t] * f[v, w] h[x, y] = value return h
This should be compiled to produce
yourmod.so (for Linux systems). We
run a Python session to test both the Python version (imported from
.py-file) and the compiled Cython module.
In : import numpy as np In : import convolve_py In : convolve_py.naive_convolve(np.array([[1, 1, 1]], dtype=np.int), ... np.array([,,], dtype=np.int)) Out : array([[1, 1, 1], [2, 2, 2], [1, 1, 1]]) In : import convolve1 In : convolve1.naive_convolve(np.array([[1, 1, 1]], dtype=np.int), ... np.array([,,], dtype=np.int)) Out : array([[1, 1, 1], [2, 2, 2], [1, 1, 1]]) In : N = 100 In : f = np.arange(N*N, dtype=np.int).reshape((N,N)) In : g = np.arange(81, dtype=np.int).reshape((9, 9)) In : %timeit -n2 -r3 convolve_py.naive_convolve(f, g) 2 loops, best of 3: 1.86 s per loop In : %timeit -n2 -r3 convolve1.naive_convolve(f, g) 2 loops, best of 3: 1.41 s per loop
There’s not such a huge difference yet; because the C code still does exactly what the Python interpreter does (meaning, for instance, that a new object is allocated for each number used). Look at the generated html file and see what is needed for even the simplest statements you get the point quickly. We need to give Cython more information; we need to add types.
To add types we use custom Cython syntax, so we are now breaking Python source
convolve2.pyx. Read the comments!
from __future__ import division import numpy as np # "cimport" is used to import special compile-time information # about the numpy module (this is stored in a file numpy.pxd which is # currently part of the Cython distribution). cimport numpy as np # We now need to fix a datatype for our arrays. I've used the variable # DTYPE for this, which is assigned to the usual NumPy runtime # type info object. DTYPE = np.int # "ctypedef" assigns a corresponding compile-time type to DTYPE_t. For # every type in the numpy module there's a corresponding compile-time # type with a _t-suffix. ctypedef np.int_t DTYPE_t # The builtin min and max functions works with Python objects, and are # so very slow. So we create our own. # - "cdef" declares a function which has much less overhead than a normal # def function (but it is not Python-callable) # - "inline" is passed on to the C compiler which may inline the functions # - The C type "int" is chosen as return type and argument types # - Cython allows some newer Python constructs like "a if x else b", but # the resulting C file compiles with Python 2.3 through to Python 3.0 beta. cdef inline int int_max(int a, int b): return a if a >= b else b cdef inline int int_min(int a, int b): return a if a <= b else b # "def" can type its arguments but not have a return type. The type of the # arguments for a "def" function is checked at run-time when entering the # function. # # The arrays f, g and h is typed as "np.ndarray" instances. The only effect # this has is to a) insert checks that the function arguments really are # NumPy arrays, and b) make some attribute access like f.shape much # more efficient. (In this example this doesn't matter though.) def naive_convolve(np.ndarray f, np.ndarray g): if g.shape % 2 != 1 or g.shape % 2 != 1: raise ValueError("Only odd dimensions on filter supported") assert f.dtype == DTYPE and g.dtype == DTYPE # The "cdef" keyword is also used within functions to type variables. It # can only be used at the top indentation level (there are non-trivial # problems with allowing them in other places, though we'd love to see # good and thought out proposals for it). # # For the indices, the "int" type is used. This corresponds to a C int, # other C types (like "unsigned int") could have been used instead. # Purists could use "Py_ssize_t" which is the proper Python type for # array indices. cdef int vmax = f.shape cdef int wmax = f.shape cdef int smax = g.shape cdef int tmax = g.shape cdef int smid = smax // 2 cdef int tmid = tmax // 2 cdef int xmax = vmax + 2*smid cdef int ymax = wmax + 2*tmid cdef np.ndarray h = np.zeros([xmax, ymax], dtype=DTYPE) cdef int x, y, s, t, v, w # It is very important to type ALL your variables. You do not get any # warnings if not, only much slower code (they are implicitly typed as # Python objects). cdef int s_from, s_to, t_from, t_to # For the value variable, we want to use the same data type as is # stored in the array, so we use "DTYPE_t" as defined above. # NB! An important side-effect of this is that if "value" overflows its # datatype size, it will simply wrap around like in C, rather than raise # an error like in Python. cdef DTYPE_t value for x in range(xmax): for y in range(ymax): s_from = int_max(smid - x, -smid) s_to = int_min((xmax - x) - smid, smid + 1) t_from = int_max(tmid - y, -tmid) t_to = int_min((ymax - y) - tmid, tmid + 1) value = 0 for s in range(s_from, s_to): for t in range(t_from, t_to): v = x - smid + s w = y - tmid + t value += g[smid - s, tmid - t] * f[v, w] h[x, y] = value return h
At this point, have a look at the generated C code for
convolve2.pyx. Click on the lines to expand them and see corresponding C.
(Note that this code annotation is currently experimental and especially
“trailing” cleanup code for a block may stick to the last expression in the
block and make it look worse than it is – use some common sense).
Especially have a look at the for loops: In
convolve1.c, these are ~20 lines
of C code to set up while in
convolve2.c a normal C for loop is used.
After building this and continuing my (very informal) benchmarks, I get:
In : import convolve2 In : %timeit -n2 -r3 convolve2.naive_convolve(f, g) 2 loops, best of 3: 828 ms per loop
There’s still a bottleneck killing performance, and that is the array lookups
and assignments. The
-operator still uses full Python operations –
what we would like to do instead is to access the data buffer directly at C
What we need to do then is to type the contents of the
We do this with a special “buffer” syntax which must be told the datatype
(first argument) and number of dimensions (“ndim” keyword-only argument, if
not provided then one-dimensional is assumed).
More information on this syntax [:enhancements/buffer:can be found here].
Showing the changes needed to produce
... def naive_convolve(np.ndarray[DTYPE_t, ndim=2] f, np.ndarray[DTYPE_t, ndim=2] g): ... cdef np.ndarray[DTYPE_t, ndim=2] h = ...
In : import convolve3 In : %timeit -n3 -r100 convolve3.naive_convolve(f, g) 3 loops, best of 100: 11.6 ms per loop
Note the importance of this change.
Gotcha: This efficient indexing only affects certain index operations,
namely those with exactly
ndim number of typed integer indices. So if
v for instance isn’t typed, then the lookup
f[v, w] isn’t
optimized. On the other hand this means that you can continue using Python
objects for sophisticated dynamic slicing etc. just as when the array is not
Tuning indexing further¶
The array lookups are still slowed down by two factors:
Bounds checking is performed.
Negative indices are checked for and handled correctly. The code above is explicitly coded so that it doesn’t use negative indices, and it (hopefully) always access within bounds. We can add a decorator to disable bounds checking:
... cimport cython @cython.boundscheck(False) # turn off bounds-checking for entire function def naive_convolve(np.ndarray[DTYPE_t, ndim=2] f, np.ndarray[DTYPE_t, ndim=2] g): ...
Now bounds checking is not performed (and, as a side-effect, if you ‘’do’’ happen to access out of bounds you will in the best case crash your program and in the worst case corrupt data). It is possible to switch bounds-checking mode in many ways, see Compiler directives for more information.
Negative indices are dealt with by ensuring Cython that the indices will be
positive, by casting the variables to unsigned integer types (if you do have
negative values, then this casting will create a very large positive value
instead and you will attempt to access out-of-bounds values). Casting is done
with a special
<>-syntax. The code below is changed to use either
unsigned ints or casting as appropriate:
... cdef int s, t # changed cdef unsigned int x, y, v, w # changed cdef int s_from, s_to, t_from, t_to cdef DTYPE_t value for x in range(xmax): for y in range(ymax): s_from = max(smid - x, -smid) s_to = min((xmax - x) - smid, smid + 1) t_from = max(tmid - y, -tmid) t_to = min((ymax - y) - tmid, tmid + 1) value = 0 for s in range(s_from, s_to): for t in range(t_from, t_to): v = <unsigned int>(x - smid + s) # changed w = <unsigned int>(y - tmid + t) # changed value += g[<unsigned int>(smid - s), <unsigned int>(tmid - t)] * f[v, w] # changed h[x, y] = value ...
(In the next Cython release we will likely add a compiler directive or
argument to the
np.ndarray-type specifier to disable negative indexing
so that casting so much isn’t necessary; feedback on this is welcome.)
The function call overhead now starts to play a role, so we compare the latter two examples with larger N:
In : %timeit -n3 -r100 convolve4.naive_convolve(f, g) 3 loops, best of 100: 5.97 ms per loop In : N = 1000 In : f = np.arange(N*N, dtype=np.int).reshape((N,N)) In : g = np.arange(81, dtype=np.int).reshape((9, 9)) In : %timeit -n1 -r10 convolve3.naive_convolve(f, g) 1 loops, best of 10: 1.16 s per loop In : %timeit -n1 -r10 convolve4.naive_convolve(f, g) 1 loops, best of 10: 597 ms per loop
(Also this is a mixed benchmark as the result array is allocated within the function call.)
Speed comes with some cost. Especially it can be dangerous to set typed
h in our sample code) to
Setting such objects to
None is entirely legal, but all you can do with them
is check whether they are None. All other use (attribute lookup or indexing)
can potentially segfault or corrupt data (rather than raising exceptions as
they would in Python).
The actual rules are a bit more complicated but the main message is clear: Do
not use typed objects without knowing that they are not set to
More generic code¶
It would be possible to do:
def naive_convolve(object[DTYPE_t, ndim=2] f, ...):
object rather than
np.ndarray. Under Python 3.0 this
can allow your algorithm to work with any libraries supporting the buffer
interface; and support for e.g. the Python Imaging Library may easily be added
if someone is interested also under Python 2.x.
There is some speed penalty to this though (as one makes more assumptions
compile-time if the type is set to
np.ndarray, specifically it is
assumed that the data is stored in pure strided mode and not in indirect
These are some points to consider for further development. All points listed here has gone through a lot of thinking and planning already; still they may or may not happen depending on available developer time and resources for Cython.
- Support for efficient access to structs/records stored in arrays; currently only primitive types are allowed.
- Support for efficient access to complex floating point types in arrays. The main obstacle here is getting support for efficient complex datatypes in Cython.
- Calling NumPy/SciPy functions currently has a Python call overhead; it would be possible to take a short-cut from Cython directly to C. (This does however require some isolated and incremental changes to those libraries; mail the Cython mailing list for details).
- Efficient code that is generic with respect to the number of dimensions.
This can probably be done today by calling the NumPy C multi-dimensional
iterator API directly; however it would be nice to have for-loops over
ndenumerate()on NumPy arrays create efficient code.
- A high-level construct for writing type-generic code, so that one can write functions that work simultaneously with many datatypes. Note however that a macro preprocessor language can help with doing this for now.