Using Cython with NumPy
=======================
-Cython has support for fast access to NumPy arrays. To optimize code
-using such arrays one must ``cimport`` the NumPy pxd file (which ships
-with Cython), and declare any arrays as having the ``ndarray``
-type. The data type and number of dimensions should be fixed at
-compile-time and passed. For instance::
-
- import numpy as np
- cimport numpy as np
- def myfunc(np.ndarray[np.float64_t, ndim=2] A):
- <...>
-
-``myfunc`` can now only be passed two-dimensional arrays containing
-double precision floats, but array indexing operation is much, much faster,
-making it suitable for numerical loops. Expect speed increases well
-over 100 times over a pure Python loop; in some cases the speed
-increase can be as high as 700 times or more. [Seljebotn09]_
-contains detailed examples and benchmarks.
-
-Fast array declarations can currently only be used with function
-local variables and arguments to ``def``-style functions (not with
-arguments to ``cpdef`` or ``cdef``, and neither with fields in cdef
-classes or as global variables). These limitations are considered
-known defects and we hope to remove them eventually. In most
-circumstances it is possible to work around these limitations rather
-easily and without a significant speed penalty, as all NumPy arrays
-can also be passed as untyped objects.
-
-Array indexing is only optimized if exactly as many indices are
-provided as the number of array dimensions. Furthermore, all indices
-must have a native integer type. Slices and NumPy "fancy indexing" is
-not optimized. Examples::
-
- def myfunc(np.ndarray[np.float64_t, ndim=1] A):
- cdef Py_ssize_t i, j
- for i in range(A.shape[0]):
- print A[i, 0] # fast
- j = 2*i
- print A[i, j] # fast
- k = 2*i
- print A[i, k] # slow, k is not typed
- print A[i][j] # slow
- print A[i,:] # slow
-
-``Py_ssize_t`` is a signed integer type provided by Python which
-covers the same range of values as is supported as NumPy array
-indices. It is the preferred type to use for loops over arrays.
-
-Any Cython primitive type (float, complex float and integer types) can
-be passed as the array data type. For each valid dtype in the ``numpy``
-module (such as ``np.uint8``, ``np.complex128``) there is a
-corresponding Cython compile-time definition in the cimport-ed NumPy
-pxd file with a ``_t`` suffix [#]_. Cython structs are also allowed
-and corresponds to NumPy record arrays. Examples::
-
- cdef packed struct Point:
- np.float64_t x, y
-
- def f():
- cdef np.ndarray[np.complex128_t, ndim=3] a = \
- np.zeros((3,3,3), dtype=np.complex128)
- cdef np.ndarray[Point] b = np.zeros(10,
- dtype=np.dtype([('x', np.float64),
- ('y', np.float64)]))
- <...>
-
-Note that ``ndim`` defaults to 1. Also note that NumPy record arrays
-are by default unaligned, meaning data is packed as tightly as
-possible without considering the alignment preferences of the
-CPU. Such unaligned record arrays corresponds to a Cython ``packed``
-struct. If one uses an aligned dtype, by passing ``align=True`` to the
-``dtype`` constructor, one must drop the ``packed`` keyword on the
-struct definition.
-
-Some data types are not yet supported, like boolean arrays and string
-arrays. Also data types describing data which is not in the native
-endian will likely never be supported. It is however possible to
-access such arrays on a lower level by casting the arrays::
-
- cdef np.ndarray[np.uint8, cast=True] boolarr = (x < y)
- cdef np.ndarray[np.uint32, cast=True] values = \
- np.arange(10, dtype='>i4')
-
-Assuming one is on a little-endian system, the ``values`` array
-can still access the raw bit content of the array (which must then
-be reinterpreted to yield valid results on a little-endian system).
-
-Finally, note that typed NumPy array variables in some respects behave
-a little differently from untyped arrays. ``arr.shape`` is no longer a
-tuple. ``arr.shape[0]`` is valid but to e.g. print the shape one must
-do ``print (<object>arr).shape`` in order to "untype" the variable
-first. The same is true for ``arr.data`` (which in typed mode is a C
-data pointer).
-
-There are many more options for optimizations to consider for Cython
-and NumPy arrays. We again refer the interested reader to [Seljebotn09]_.
-
-.. [#] In Cython 0.11.2, ``np.complex64_t`` and ``np.complex128_t``
- does not work and one must write ``complex`` or
- ``double complex`` instead. This is fixed in 0.11.3. Cython
- 0.11.1 and earlier does not support complex numbers.
-
-.. [Seljebotn09] D. S. Seljebotn, Fast numerical computations with Cython,
- Proceedings of the 8th Python in Science Conference, 2009.
+Cython has support for fast access to NumPy arrays. Let's see how this
+works with a simple example.
+
+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
+:file:`convolve_py.py` for the Python version and :file:`convolve1.pyx` for the
+Cython version -- Cython uses ".pyx" as its file suffix.
+
+.. code-block:: python
+
+ 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[0] % 2 != 1 or g.shape[1] % 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[0]
+ wmax = f.shape[1]
+ smax = g.shape[0]
+ tmax = g.shape[1]
+ 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 :file:`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.
+
+.. sourcecode:: ipython
+
+ In [1]: import numpy as np
+ In [2]: import convolve_py
+ In [3]: convolve_py.naive_convolve(np.array([[1, 1, 1]], dtype=np.int),
+ ... np.array([[1],[2],[1]], dtype=np.int))
+ Out [3]:
+ array([[1, 1, 1],
+ [2, 2, 2],
+ [1, 1, 1]])
+ In [4]: import convolve1
+ In [4]: convolve1.naive_convolve(np.array([[1, 1, 1]], dtype=np.int),
+ ... np.array([[1],[2],[1]], dtype=np.int))
+ Out [4]:
+ array([[1, 1, 1],
+ [2, 2, 2],
+ [1, 1, 1]])
+ In [11]: N = 100
+ In [12]: f = np.arange(N*N, dtype=np.int).reshape((N,N))
+ In [13]: g = np.arange(81, dtype=np.int).reshape((9, 9))
+ In [19]: %timeit -n2 -r3 convolve_py.naive_convolve(f, g)
+ 2 loops, best of 3: 1.86 s per loop
+ In [20]: %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.
+
+Adding types
+=============
+
+To add types we use custom Cython syntax, so we are now breaking Python source
+compatibility. Here's :file:`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[0] much
+ # more efficient. (In this example this doesn't matter though.)
+ def naive_convolve(np.ndarray f, np.ndarray g):
+ if g.shape[0] % 2 != 1 or g.shape[1] % 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 indendation 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[0]
+ cdef int wmax = f.shape[1]
+ cdef int smax = g.shape[0]
+ cdef int tmax = g.shape[1]
+ 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
+
+After building this and continuing my (very informal) benchmarks, I get:
+
+.. sourcecode:: ipython
+
+ In [21]: import convolve2
+ In [22]: %timeit -n2 -r3 convolve2.naive_convolve(f, g)
+ 2 loops, best of 3: 828 ms per loop
+
+Efficient indexing
+====================
+
+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
+speed.
+
+What we need to do then is to type the contents of the :obj:`ndarray` objects.
+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 :file:`convolve3.pyx` only::
+
+ ...
+ 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 = ...
+
+Usage:
+
+.. sourcecode:: ipython
+
+ In [18]: import convolve3
+ In [19]: %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
+typed.
+
+Tuning indexing further
+========================
+
+The array lookups are still slowed down by two factors:
+
+1. Bounds checking is performed.
+2. 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 of 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 [:docs/compilerdirectives: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
+ ...
+
+The function call overhead now starts to play a role, so we compare the latter
+two examples with larger N:
+
+.. sourcecode:: ipython
+
+ In [11]: %timeit -n3 -r100 convolve4.naive_convolve(f, g)
+ 3 loops, best of 100: 5.97 ms per loop
+ In [12]: N = 1000
+ In [13]: f = np.arange(N*N, dtype=np.int).reshape((N,N))
+ In [14]: g = np.arange(81, dtype=np.int).reshape((9, 9))
+ In [17]: %timeit -n1 -r10 convolve3.naive_convolve(f, g)
+ 1 loops, best of 10: 1.16 s per loop
+ In [18]: %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.)
+
+.. Warning::
+
+ Speed comes with some cost. Especially it can be dangerous to set typed
+ objects (like ``f``, ``g`` and ``h`` in our sample code) to
+ :keyword:`None`. Setting such objects to :keyword:`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 None.
+
+More generic code
+==================
+
+It would be possible to do::
+
+ def naive_convolve(object[DTYPE_t, ndim=2] f, ...):
+
+i.e. use :obj:`object` rather than :obj:`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 :obj:`np.ndarray`, specifically it is
+assumed that the data is stored in pure strided more and not in indirect
+mode).
+
+++ /dev/null
-.. highlight:: cython
-
-.. _numpy_tutorial:
-
-**************************
-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
- <http://wiki.sagemath.org/scipy08?action=AttachFile&do=get&target=scipy-cython.tgz>`_
- (a higher-level and quicker introduction)
-* Basic Cython documentation (see `Cython front page <http://cython.org>`_).
-* ``[:enhancements/buffer:Spec for the efficient indexing]``
-
-.. Note::
- 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:
-
-1. Write a :file:`.pyx` source file
-2. Run the Cython compiler to generate a C file
-3. Run a C compiler to generate a compiled library
-4. Run the Python interpreter and ask it to import the module
-
-However there are several options to automate these steps:
-
-1. The `SAGE <http://sagemath.org>`_ 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
- <http://www.sagemath.org/doc/prog/node40.html>`_.
-2. A version of `pyximport <http://www.prescod.net/pyximport/>`_ is shipped
- with Cython, so that you can import pyx-files dynamically into Python and
- have them compiled automatically (See :ref:`pyximport`).
-3. Cython supports distutils so that you can very easily create build scripts
- which automate the process, this is the preferred method for full programs.
-4. Manual compilation (see below)
-
-.. Note::
- 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.
-
-Installation
-=============
-
-Unless you are used to some other automatic method:
-`download Cython <http://cython.org/#download>`_ (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 :file:`cython.py` in the
-root directory).
-
-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.
-
-Manual compilation
-====================
-
-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
-
-This creates :file:`yourmod.c` which is the C source for a Python extension
-module. A useful additional switch is ``-a`` which will generate a document
-:file:`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/python2.5 -o yourmod.so yourmod.c
-
-``gcc`` should have access to the NumPy C header files so if they are not
-installed at :file:`/usr/include/numpy` or similar you may need to pass another
-option for those.
-
-This creates :file:`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
-:file:`convolve_py.py` for the Python version and :file:`convolve1.pyx` for the
-Cython version -- Cython uses ".pyx" as its file suffix.
-
-.. code-block:: python
-
- 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[0] % 2 != 1 or g.shape[1] % 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[0]
- wmax = f.shape[1]
- smax = g.shape[0]
- tmax = g.shape[1]
- 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 :file:`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.
-
-.. sourcecode:: ipython
-
- In [1]: import numpy as np
- In [2]: import convolve_py
- In [3]: convolve_py.naive_convolve(np.array([[1, 1, 1]], dtype=np.int),
- ... np.array([[1],[2],[1]], dtype=np.int))
- Out [3]:
- array([[1, 1, 1],
- [2, 2, 2],
- [1, 1, 1]])
- In [4]: import convolve1
- In [4]: convolve1.naive_convolve(np.array([[1, 1, 1]], dtype=np.int),
- ... np.array([[1],[2],[1]], dtype=np.int))
- Out [4]:
- array([[1, 1, 1],
- [2, 2, 2],
- [1, 1, 1]])
- In [11]: N = 100
- In [12]: f = np.arange(N*N, dtype=np.int).reshape((N,N))
- In [13]: g = np.arange(81, dtype=np.int).reshape((9, 9))
- In [19]: %timeit -n2 -r3 convolve_py.naive_convolve(f, g)
- 2 loops, best of 3: 1.86 s per loop
- In [20]: %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.
-
-Adding types
-=============
-
-To add types we use custom Cython syntax, so we are now breaking Python source
-compatibility. Here's :file:`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[0] much
- # more efficient. (In this example this doesn't matter though.)
- def naive_convolve(np.ndarray f, np.ndarray g):
- if g.shape[0] % 2 != 1 or g.shape[1] % 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 indendation 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[0]
- cdef int wmax = f.shape[1]
- cdef int smax = g.shape[0]
- cdef int tmax = g.shape[1]
- 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 :file:`convolve1.pyx` and
-:file:`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).
-
-* .. literalinclude: convolve1.html
-* .. literalinclude: convolve2.html
-
-Especially have a look at the for loops: In :file:`convolve1.c`, these are ~20 lines
-of C code to set up while in :file:`convolve2.c` a normal C for loop is used.
-
-After building this and continuing my (very informal) benchmarks, I get:
-
-.. sourcecode:: ipython
-
- In [21]: import convolve2
- In [22]: %timeit -n2 -r3 convolve2.naive_convolve(f, g)
- 2 loops, best of 3: 828 ms per loop
-
-Efficient indexing
-====================
-
-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
-speed.
-
-What we need to do then is to type the contents of the :obj:`ndarray` objects.
-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 :file:`convolve3.pyx` only::
-
- ...
- 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 = ...
-
-Usage:
-
-.. sourcecode:: ipython
-
- In [18]: import convolve3
- In [19]: %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
-typed.
-
-Tuning indexing further
-========================
-
-The array lookups are still slowed down by two factors:
-
-1. Bounds checking is performed.
-2. 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 of 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 [:docs/compilerdirectives: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:
-
-.. sourcecode:: ipython
-
- In [11]: %timeit -n3 -r100 convolve4.naive_convolve(f, g)
- 3 loops, best of 100: 5.97 ms per loop
- In [12]: N = 1000
- In [13]: f = np.arange(N*N, dtype=np.int).reshape((N,N))
- In [14]: g = np.arange(81, dtype=np.int).reshape((9, 9))
- In [17]: %timeit -n1 -r10 convolve3.naive_convolve(f, g)
- 1 loops, best of 10: 1.16 s per loop
- In [18]: %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.)
-
-.. Warning::
-
- Speed comes with some cost. Especially it can be dangerous to set typed
- objects (like ``f``, ``g`` and ``h`` in our sample code) to :keyword:`None`.
- Setting such objects to :keyword:`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 None.
-
-More generic code
-==================
-
-It would be possible to do::
-
- def naive_convolve(object[DTYPE_t, ndim=2] f, ...):
-
-i.e. use :obj:`object` rather than :obj:`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 :obj:`np.ndarray`, specifically it is
-assumed that the data is stored in pure strided more and not in indirect
-mode).
-
-[:enhancements/buffer:More information]
-
-The future
-============
-
-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.
-
-1. Support for efficient access to structs/records stored in arrays; currently
- only primitive types are allowed.
-2. Support for efficient access to complex floating point types in arrays. The
- main obstacle here is getting support for efficient complex datatypes in
- Cython.
-3. 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).
-4. 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
- :func:`enumerate` and :func:`ndenumerate` on NumPy arrays create efficient
- code.
-5. 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.
-
projects / cython.git / commitdiff