diff options
author | Pauli Virtanen <pav@iki.fi> | 2009-03-21 21:19:53 +0000 |
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committer | Pauli Virtanen <pav@iki.fi> | 2009-03-21 21:19:53 +0000 |
commit | bab64b897064cfdf8cf86fcc62b44e21df1153ee (patch) | |
tree | 6e1cee5b837bbccdfb2c78f12f3f6205ed40953a /doc/source/user | |
parent | b2634ff922176acd12ddd3725434d3dfaaf25422 (diff) | |
download | numpy-bab64b897064cfdf8cf86fcc62b44e21df1153ee.tar.gz |
docs: strip trailing whitespace from RST files
Diffstat (limited to 'doc/source/user')
-rw-r--r-- | doc/source/user/basics.indexing.rst | 4 | ||||
-rw-r--r-- | doc/source/user/basics.types.rst | 2 | ||||
-rw-r--r-- | doc/source/user/c-info.beyond-basics.rst | 162 | ||||
-rw-r--r-- | doc/source/user/c-info.how-to-extend.rst | 104 | ||||
-rw-r--r-- | doc/source/user/c-info.python-as-glue.rst | 324 | ||||
-rw-r--r-- | doc/source/user/index.rst | 2 |
6 files changed, 299 insertions, 299 deletions
diff --git a/doc/source/user/basics.indexing.rst b/doc/source/user/basics.indexing.rst index 7427874a5..f218fd060 100644 --- a/doc/source/user/basics.indexing.rst +++ b/doc/source/user/basics.indexing.rst @@ -6,9 +6,9 @@ Indexing .. seealso:: :ref:`Indexing routines <routines.indexing>` -.. note:: +.. note:: - XXX: Combine ``numpy.doc.indexing`` with material + XXX: Combine ``numpy.doc.indexing`` with material section 2.2 Basic indexing? Or incorporate the material directly here? diff --git a/doc/source/user/basics.types.rst b/doc/source/user/basics.types.rst index 1a95dc6b4..4982045a2 100644 --- a/doc/source/user/basics.types.rst +++ b/doc/source/user/basics.types.rst @@ -4,7 +4,7 @@ Data types .. seealso:: :ref:`Data type objects <arrays.dtypes>` -.. note:: +.. note:: XXX: Combine ``numpy.doc.indexing`` with material from "Guide to Numpy" (section 2.1 Data-Type descriptors)? diff --git a/doc/source/user/c-info.beyond-basics.rst b/doc/source/user/c-info.beyond-basics.rst index 905ab67eb..491c2c9ae 100644 --- a/doc/source/user/c-info.beyond-basics.rst +++ b/doc/source/user/c-info.beyond-basics.rst @@ -3,12 +3,12 @@ Beyond the Basics ***************** | The voyage of discovery is not in seeking new landscapes but in having -| new eyes. -| --- *Marcel Proust* +| new eyes. +| --- *Marcel Proust* | Discovery is seeing what everyone else has seen and thinking what no -| one else has thought. -| --- *Albert Szent-Gyorgi* +| one else has thought. +| --- *Albert Szent-Gyorgi* Iterating over elements in the array @@ -27,7 +27,7 @@ using, then you can always write nested for loops to accomplish the iteration. If, however, you want to write code that works with any number of dimensions, then you can make use of the array iterator. An array iterator object is returned when accessing the .flat attribute -of an array. +of an array. .. index:: single: array iterator @@ -42,7 +42,7 @@ size of the array, ``iter->index``, which contains the current 1-d index into the array, and ``iter->dataptr`` which is a pointer to the data for the current element of the array. Sometimes it is also useful to access ``iter->ao`` which is a pointer to the underlying -ndarray object. +ndarray object. After processing data at the current element of the array, the next element of the array can be obtained using the macro @@ -54,7 +54,7 @@ array of npy_intp data-type with space to handle at least the number of dimensions in the underlying array. Occasionally it is useful to use :cfunc:`PyArray_ITER_GOTO1D` ( ``iter``, ``index`` ) which will jump to the 1-d index given by the value of ``index``. The most common -usage, however, is given in the following example. +usage, however, is given in the following example. .. code-block:: c @@ -71,7 +71,7 @@ usage, however, is given in the following example. You can also use :cfunc:`PyArrayIter_Check` ( ``obj`` ) to ensure you have an iterator object and :cfunc:`PyArray_ITER_RESET` ( ``iter`` ) to reset an -iterator object back to the beginning of the array. +iterator object back to the beginning of the array. It should be emphasized at this point that you may not need the array iterator if your array is already contiguous (using an array iterator @@ -82,7 +82,7 @@ many places in the NumPy source code itself. If you already know your array is contiguous (Fortran or C), then simply adding the element- size to a running pointer variable will step you through the array very efficiently. In other words, code like this will probably be -faster for you in the contiguous case (assuming doubles). +faster for you in the contiguous case (assuming doubles). .. code-block:: c @@ -110,7 +110,7 @@ to a small(er) fraction of the total time. Even if the interior of the loop is performed without a function call it can be advantageous to perform the inner loop over the dimension with the highest number of elements to take advantage of speed enhancements available on micro- -processors that use pipelining to enhance fundmental operations. +processors that use pipelining to enhance fundmental operations. The :cfunc:`PyArray_IterAllButAxis` ( ``array``, ``&dim`` ) constructs an iterator object that is modified so that it will not iterate over the @@ -123,7 +123,7 @@ PyArrayIterObject \*. All that's been done is to modify the strides and dimensions of the returned iterator to simulate iterating over array[...,0,...] where 0 is placed on the :math:`\textrm{dim}^{\textrm{th}}` dimension. If dim is negative, then -the dimension with the largest axis is found and used. +the dimension with the largest axis is found and used. Iterating over multiple arrays @@ -135,7 +135,7 @@ behavior. If all you want to do is iterate over arrays with the same shape, then simply creating several iterator objects is the standard procedure. For example, the following code iterates over two arrays assumed to be the same shape and size (actually obj1 just has to have -at least as many total elements as does obj2): +at least as many total elements as does obj2): .. code-block:: c @@ -175,7 +175,7 @@ multiterator ``obj`` as either a :ctype:`PyArrayMultiObject *` or a :ctype:`PyObject *`). The data from input number ``i`` is available using :cfunc:`PyArray_MultiIter_DATA` ( ``obj``, ``i`` ) and the total (broadcasted) size as :cfunc:`PyArray_MultiIter_SIZE` ( ``obj``). An example of using this -feature follows. +feature follows. .. code-block:: c @@ -194,14 +194,14 @@ iteration does not take place over the largest dimension (it makes that dimension of size 1). The code being looped over that makes use of the pointers will very-likely also need the strides data for each of the iterators. This information is stored in -multi->iters[i]->strides. +multi->iters[i]->strides. .. index:: single: array iterator There are several examples of using the multi-iterator in the NumPy source code as it makes N-dimensional broadcasting-code very simple to -write. Browse the source for more examples. +write. Browse the source for more examples. .. _`sec:Creating-a-new`: @@ -216,7 +216,7 @@ ufuncs. It provides a great many examples of how to create a universal function. Creating your own ufunc that will make use of the ufunc machinery is not difficult either. Suppose you have a function that you want to operate element-by-element over its inputs. By creating a -new ufunc you will obtain a function that handles +new ufunc you will obtain a function that handles - broadcasting @@ -231,7 +231,7 @@ a 1-d loop for each data-type you want to support. Each 1-d loop must have a specific signature, and only ufuncs for fixed-size data-types can be used. The function call used to create a new ufunc to work on built-in data-types is given below. A different mechanism is used to -register ufuncs for user-defined data-types. +register ufuncs for user-defined data-types. .. cfunction:: PyObject *PyUFunc_FromFuncAndData( PyUFuncGenericFunction* func, void** data, char* types, int ntypes, int nin, int nout, int identity, char* name, char* doc, int check_return) @@ -240,34 +240,34 @@ register ufuncs for user-defined data-types. A pointer to an array of 1-d functions to use. This array must be at least ntypes long. Each entry in the array must be a ``PyUFuncGenericFunction`` function. This function has the following signature. An example of a valid 1d loop function is also given. - + .. cfunction:: void loop1d(char** args, npy_intp* dimensions, npy_intp* steps, void* data) - + *args* An array of pointers to the actual data for the input and output arrays. The input arguments are given first followed by the output arguments. - + *dimensions* A pointer to the size of the dimension over which this function is looping. - + *steps* A pointer to the number of bytes to jump to get to the next element in this dimension for each of the input and output arguments. - + *data* Arbitrary data (extra arguments, function names, *etc.* ) that can be stored with the ufunc and will be passed in when it is called. - + .. code-block:: c - + static void double_add(char *args, npy_intp *dimensions, npy_intp *steps, void *extra) { @@ -281,7 +281,7 @@ register ufuncs for user-defined data-types. i1 += is1; i2 += is2; op += os; } } - + *data* An array of data. There should be ntypes entries (or NULL) --- one for @@ -289,7 +289,7 @@ register ufuncs for user-defined data-types. in to the 1-d loop. One common use of this data variable is to pass in an actual function to call to compute the result when a generic 1-d loop (e.g. :cfunc:`PyUFunc_d_d`) is being used. - + *types* An array of type-number signatures (type ``char`` ). This @@ -300,46 +300,46 @@ register ufuncs for user-defined data-types. (length-2 func and data arrays) that takes 2 inputs and returns 1 output that is always a complex double, then the types array would be - - + + The bit-width names can also be used (e.g. :cdata:`NPY_INT32`, :cdata:`NPY_COMPLEX128` ) if desired. - + *ntypes* The number of data-types supported. This is equal to the number of 1-d loops provided. - + *nin* The number of input arguments. - + *nout* The number of output arguments. - + *identity* Either :cdata:`PyUFunc_One`, :cdata:`PyUFunc_Zero`, :cdata:`PyUFunc_None`. This specifies what should be returned when an empty array is passed to the reduce method of the ufunc. - + *name* A ``NULL`` -terminated string providing the name of this ufunc (should be the Python name it will be called). - + *doc* A documentation string for this ufunc (will be used in generating the response to ``{ufunc_name}.__doc__``). Do not include the function signature or the name as this is generated automatically. - + *check_return* Not presently used, but this integer value does get set in the structure-member of similar name. - + .. index:: pair: ufunc; adding new @@ -347,13 +347,13 @@ register ufuncs for user-defined data-types. placed in a (module) dictionary under the same name as was used in the name argument to the ufunc-creation routine. The following example is adapted from the umath module - + .. code-block:: c static PyUFuncGenericFunction atan2_functions[]=\ {PyUFunc_ff_f, PyUFunc_dd_d, PyUFunc_gg_g, PyUFunc_OO_O_method}; - static void* atan2_data[]=\ + static void* atan2_data[]=\ {(void *)atan2f,(void *) atan2, (void *)atan2l,(void *)"arctan2"}; static char atan2_signatures[]=\ @@ -361,7 +361,7 @@ register ufuncs for user-defined data-types. NPY_DOUBLE, NPY_DOUBLE, NPY_DOUBLE, NPY_LONGDOUBLE, NPY_LONGDOUBLE, NPY_LONGDOUBLE - NPY_OBJECT, NPY_OBJECT, + NPY_OBJECT, NPY_OBJECT, NPY_OBJECT}; ... /* in the module initialization code */ @@ -369,9 +369,9 @@ register ufuncs for user-defined data-types. ... dict = PyModule_GetDict(module); ... - f = PyUFunc_FromFuncAndData(atan2_functions, - atan2_data, atan2_signatures, 4, 2, 1, - PyUFunc_None, "arctan2", + f = PyUFunc_FromFuncAndData(atan2_functions, + atan2_data, atan2_signatures, 4, 2, 1, + PyUFunc_None, "arctan2", "a safe and correct arctan(x1/x2)", 0); PyDict_SetItemString(dict, "arctan2", f); Py_DECREF(f); @@ -396,7 +396,7 @@ if you can't do what you want to do using the OBJECT or VOID data-types that are already available. As an example of what I consider a useful application of the ability to add data-types is the possibility of adding a data-type of arbitrary precision floats to -NumPy. +NumPy. .. index:: pair: dtype; adding new @@ -421,7 +421,7 @@ type. For example, a suitable structure for the new Python type is: typedef struct { PyObject_HEAD; - some_data_type obval; + some_data_type obval; /* the name can be whatever you want */ } PySomeDataTypeObject; @@ -432,7 +432,7 @@ required functions in the ".f" member must be defined: nonzero, copyswap, copyswapn, setitem, getitem, and cast. The more functions in the ".f" member you define, however, the more useful the new data-type will be. It is very important to intialize unused functions to NULL. -This can be achieved using :cfunc:`PyArray_InitArrFuncs` (f). +This can be achieved using :cfunc:`PyArray_InitArrFuncs` (f). Once a new :ctype:`PyArray_Descr` structure is created and filled with the needed information and useful functions you call @@ -442,7 +442,7 @@ specifies your data-type. This type number should be stored and made available by your module so that other modules can use it to recognize your data-type (the other mechanism for finding a user-defined data-type number is to search based on the name of the type-object -associated with the data-type using :cfunc:`PyArray_TypeNumFromName` ). +associated with the data-type using :cfunc:`PyArray_TypeNumFromName` ). Registering a casting function @@ -454,7 +454,7 @@ possible, you must register a casting function with the data-type you want to be able to cast from. This requires writing low-level casting functions for each conversion you want to support and then registering these functions with the data-type descriptor. A low-level casting -function has the signature. +function has the signature. .. cfunction:: void castfunc( void* from, void* to, npy_intp n, void* fromarr, void* toarr) @@ -501,7 +501,7 @@ function :cfunc:`PyArray_RegisterCanCast` (from_descr, totype_number, scalarkind) should be used to specify that the data-type object from_descr can be cast to the data-type with type number totype_number. If you are not trying to alter scalar coercion rules, -then use :cdata:`PyArray_NOSCALAR` for the scalarkind argument. +then use :cdata:`PyArray_NOSCALAR` for the scalarkind argument. If you want to allow your new data-type to also be able to share in the scalar coercion rules, then you need to specify the scalarkind @@ -511,7 +511,7 @@ available to that function). Then, you can register data-types that can be cast to separately for each scalar kind that may be returned from your user-defined data-type. If you don't register scalar coercion handling, then all of your user-defined data-types will be -seen as :cdata:`PyArray_NOSCALAR`. +seen as :cdata:`PyArray_NOSCALAR`. Registering a ufunc loop @@ -521,30 +521,30 @@ You may also want to register low-level ufunc loops for your data-type so that an ndarray of your data-type can have math applied to it seamlessly. Registering a new loop with exactly the same arg_types signature, silently replaces any previously registered loops for that -data-type. +data-type. Before you can register a 1-d loop for a ufunc, the ufunc must be previously created. Then you call :cfunc:`PyUFunc_RegisterLoopForType` (...) with the information needed for the loop. The return value of this function is ``0`` if the process was successful and ``-1`` with -an error condition set if it was not successful. +an error condition set if it was not successful. .. cfunction:: int PyUFunc_RegisterLoopForType( PyUFuncObject* ufunc, int usertype, PyUFuncGenericFunction function, int* arg_types, void* data) *ufunc* The ufunc to attach this loop to. - + *usertype* The user-defined type this loop should be indexed under. This number must be a user-defined type or an error occurs. - + *function* The ufunc inner 1-d loop. This function must have the signature as explained in Section `3 <#sec-creating-a-new>`__ . - + *arg_types* (optional) If given, this should contain an array of integers of at @@ -553,15 +553,15 @@ an error condition set if it was not successful. the memory for this argument should be deleted after calling this function. If this is NULL, then it will be assumed that all data-types are of type usertype. - + *data* (optional) Specify any optional data needed by the function which will - be passed when the function is called. - + be passed when the function is called. + .. index:: pair: dtype; adding new - + Subtyping the ndarray in C ========================== @@ -577,7 +577,7 @@ type, sub-typing from multiple parent types is also possible. Multiple inheritence in C is generally less useful than it is in Python because a restriction on Python sub-types is that they have a binary compatible memory layout. Perhaps for this reason, it is somewhat -easier to sub-type from a single parent type. +easier to sub-type from a single parent type. .. index:: pair: ndarray; subtyping @@ -592,7 +592,7 @@ the parent structure ( *i.e.* it will cast a given pointer to a pointer to the parent structure and then dereference one of it's members). If the memory layouts are not compatible, then this attempt will cause unpredictable behavior (eventually leading to a memory -violation and program crash). +violation and program crash). One of the elements in :cmacro:`PyObject_HEAD` is a pointer to a type-object structure. A new Python type is created by creating a new @@ -605,7 +605,7 @@ while a :ctype:`PyArrayObject *` variable is a pointer to a particular instance of an ndarray (one of the members of the ndarray structure is, in turn, a pointer to the type- object table :cdata:`&PyArray_Type`). Finally :cfunc:`PyType_Ready` (<pointer_to_type_object>) must be called for -every new Python type. +every new Python type. Creating sub-types @@ -615,22 +615,22 @@ To create a sub-type, a similar proceedure must be followed except only behaviors that are different require new entries in the type- object structure. All other entires can be NULL and will be filled in by :cfunc:`PyType_Ready` with appropriate functions from the parent -type(s). In particular, to create a sub-type in C follow these steps: +type(s). In particular, to create a sub-type in C follow these steps: 1. If needed create a new C-structure to handle each instance of your type. A typical C-structure would be: - + .. code-block:: c - + typedef _new_struct { PyArrayObject base; /* new things here */ } NewArrayObject; - + Notice that the full PyArrayObject is used as the first entry in order to ensure that the binary layout of instances of the new type is - identical to the PyArrayObject. - + identical to the PyArrayObject. + 2. Fill in a new Python type-object structure with pointers to new functions that will over-ride the default behavior while leaving any function that should remain the same unfilled (or NULL). The tp_name @@ -650,14 +650,14 @@ type(s). In particular, to create a sub-type in C follow these steps: module dictionary so it can be accessed from Python. More information on creating sub-types in C can be learned by reading -PEP 253 (available at http://www.python.org/dev/peps/pep-0253). +PEP 253 (available at http://www.python.org/dev/peps/pep-0253). Specific features of ndarray sub-typing --------------------------------------- Some special methods and attributes are used by arrays in order to -facilitate the interoperation of sub-types with the base ndarray type. +facilitate the interoperation of sub-types with the base ndarray type. .. note:: XXX: some of the documentation below needs to be moved to the reference guide. @@ -667,7 +667,7 @@ The __array_finalize\__ method ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. attribute:: ndarray.__array_finalize__ - + Several array-creation functions of the ndarray allow specification of a particular sub-type to be created. This allows sub-types to be handled seamlessly in many routines. When a @@ -678,25 +678,25 @@ The __array_finalize\__ method attribute is looked-up in the object dictionary. If it is present and not None, then it can be either a CObject containing a pointer to a :cfunc:`PyArray_FinalizeFunc` or it can be a method taking a - single argument (which could be None). - + single argument (which could be None). + If the :obj:`__array_finalize__` attribute is a CObject, then the pointer must be a pointer to a function with the signature: - + .. code-block:: c - + (int) (PyArrayObject *, PyObject *) - + The first argument is the newly created sub-type. The second argument (if not NULL) is the "parent" array (if the array was created using slicing or some other operation where a clearly-distinguishable parent is present). This routine can do anything it wants to. It should - return a -1 on error and 0 otherwise. - + return a -1 on error and 0 otherwise. + If the :obj:`__array_finalize__` attribute is not None nor a CObject, then it must be a Python method that takes the parent array as an argument (which could be None if there is no parent), and returns - nothing. Errors in this method will be caught and handled. + nothing. Errors in this method will be caught and handled. The __array_priority\__ attribute @@ -715,7 +715,7 @@ The __array_priority\__ attribute ndarray type and 1.0 for a sub-type. This attribute can also be defined by objects that are not sub-types of the ndarray and can be used to determine which :obj:`__array_wrap__` method should be called for - the return output. + the return output. The __array_wrap\__ method ^^^^^^^^^^^^^^^^^^^^^^^^^^ @@ -728,7 +728,7 @@ The __array_wrap\__ method ufuncs (and other NumPy functions) to allow other objects to pass through. For Python >2.4, it can also be used to write a decorator that converts a function that works only with ndarrays to one that - works with any type with :obj:`__array__` and :obj:`__array_wrap__` methods. - + works with any type with :obj:`__array__` and :obj:`__array_wrap__` methods. + .. index:: pair: ndarray; subtyping diff --git a/doc/source/user/c-info.how-to-extend.rst b/doc/source/user/c-info.how-to-extend.rst index 56f3c99f1..b2921239e 100644 --- a/doc/source/user/c-info.how-to-extend.rst +++ b/doc/source/user/c-info.how-to-extend.rst @@ -3,11 +3,11 @@ How to extend NumPy ******************* | That which is static and repetitive is boring. That which is dynamic -| and random is confusing. In between lies art. -| --- *John A. Locke* +| and random is confusing. In between lies art. +| --- *John A. Locke* -| Science is a differential equation. Religion is a boundary condition. -| --- *Alan Turing* +| Science is a differential equation. Religion is a boundary condition. +| --- *Alan Turing* .. _`sec:Writing-an-extension`: @@ -25,7 +25,7 @@ that numpy includes f2py so that an easy-to-use mechanisms for linking available. You are encouraged to use and improve this mechanism. The purpose of this section is not to document this tool but to document the more basic steps to writing an extension module that this tool -depends on. +depends on. .. index:: single: extension module @@ -36,7 +36,7 @@ into Python as if it were a standard python file. It will contain objects and methods that have been defined and compiled in C code. The basic steps for doing this in Python are well-documented and you can find more information in the documentation for Python itself available -online at `www.python.org <http://www.python.org>`_ . +online at `www.python.org <http://www.python.org>`_ . In addition to the Python C-API, there is a full and rich C-API for NumPy allowing sophisticated manipulations on a C-level. However, for @@ -45,7 +45,7 @@ you need to do is extract a pointer to memory along with some shape information to pass to another calculation routine, then you will use very different calls, then if you are trying to create a new array- like type or add a new data type for ndarrays. This chapter documents -the API calls and macros that are most commonly used. +the API calls and macros that are most commonly used. Required subroutine @@ -63,7 +63,7 @@ to place these commands will show itself as an ugly segmentation fault actually possible to have multiple init{name} functions in a single file in which case multiple modules will be defined by that file. However, there are some tricks to get that to work correctly and it is -not covered here. +not covered here. A minimal ``init{name}`` method looks like: @@ -71,7 +71,7 @@ A minimal ``init{name}`` method looks like: PyMODINIT_FUNC init{name}(void) - { + { (void)Py_InitModule({name}, mymethods); import_array(); } @@ -88,7 +88,7 @@ whatever you like to the module manually. An easier way to add objects to the module is to use one of three additional Python C-API calls that do not require a separate extraction of the module dictionary. These are documented in the Python documentation, but repeated here -for convenience: +for convenience: .. cfunction:: int PyModule_AddObject(PyObject* module, char* name, PyObject* value) @@ -132,12 +132,12 @@ this function, and 4) The docstring for the function. Any number of functions may be defined for a single module by adding more entries to this table. The last entry must be all NULL as shown to act as a sentinel. Python looks for this entry to know that all of the -functions for the module have been defined. +functions for the module have been defined. The last thing that must be done to finish the extension module is to actually write the code that performs the desired functions. There are two kinds of functions: those that don't accept keyword arguments, and -those that do. +those that do. Functions without keyword arguments @@ -172,7 +172,7 @@ that may be of use. In particular, the :cfunc:`PyArray_DescrConverter` function is very useful to support arbitrary data-type specification. This function transforms any valid data-type Python object into a :ctype:`PyArray_Descr *` object. Remember to pass in the address of the -C-variables that should be filled in. +C-variables that should be filled in. There are lots of examples of how to use :cfunc:`PyArg_ParseTuple` throughout the NumPy source code. The standard usage is like this: @@ -196,7 +196,7 @@ was successful but the integer conversion failed, then you would need to release the reference count to the data-type object before returning. A typical way to do this is to set *dtype* to ``NULL`` before calling :cfunc:`PyArg_ParseTuple` and then use :cfunc:`Py_XDECREF` -on *dtype* before returning. +on *dtype* before returning. After the input arguments are processed, the code that actually does the work is written (likely calling other functions as needed). The @@ -216,7 +216,7 @@ corresponding :ctype:`PyObject *` C-variable. You should use 'N' if you ave already created a reference for the object and just want to give that reference to the tuple. You should use 'O' if you only have a borrowed reference to an object and need to create one to provide for the -tuple. +tuple. Functions with keyword arguments @@ -243,11 +243,11 @@ char \*kwlist[], addresses...). The kwlist parameter to this function is a ``NULL`` -terminated array of strings providing the expected keyword arguments. There should be one string for each entry in the format_string. Using this function will raise a TypeError if invalid -keyword arguments are passed in. +keyword arguments are passed in. For more help on this function please see section 1.8 (Keyword Paramters for Extension Functions) of the Extending and Embedding -tutorial in the Python documentation. +tutorial in the Python documentation. Reference counting @@ -269,7 +269,7 @@ being not using DECREF on objects before exiting early from a routine due to some error. In second place, is the common error of not owning the reference on an object that is passed to a function or macro that is going to steal the reference ( *e.g.* :cfunc:`PyTuple_SET_ITEM`, and -most functions that take :ctype:`PyArray_Descr` objects). +most functions that take :ctype:`PyArray_Descr` objects). .. index:: single: reference counting @@ -304,7 +304,7 @@ variable is deleted and the reference count decremented by one, there will still be that extra reference count, and the array will never be deallocated. You will have a reference-counting induced memory leak. Using the 'N' character will avoid this situation as it will return to -the caller an object (inside the tuple) with a single reference count. +the caller an object (inside the tuple) with a single reference count. .. index:: single: reference counting @@ -318,7 +318,7 @@ Dealing with array objects Most extension modules for NumPy will need to access the memory for an ndarray object (or one of it's sub-classes). The easiest way to do this doesn't require you to know much about the internals of NumPy. -The method is to +The method is to 1. Ensure you are dealing with a well-behaved array (aligned, in machine byte-order and single-segment) of the correct type and number of @@ -326,12 +326,12 @@ The method is to 1. By converting it from some Python object using :cfunc:`PyArray_FromAny` or a macro built on it. - + 2. By constructing a new ndarray of your desired shape and type using :cfunc:`PyArray_NewFromDescr` or a simpler macro or function based on it. - - + + 2. Get the shape of the array and a pointer to its actual data. 3. Pass the data and shape information on to a subroutine or other @@ -343,7 +343,7 @@ The method is to you can relax your requirements so as not to force a single-segment array and the data-copying that might result. -Each of these sub-topics is covered in the following sub-sections. +Each of these sub-topics is covered in the following sub-sections. Converting an arbitrary sequence object @@ -389,35 +389,35 @@ writeable). The syntax is requirements flag. A copy is made only if necessary. If you want to guarantee a copy, then pass in :cdata:`NPY_ENSURECOPY` to the requirements flag. - + *typenum* One of the enumerated types or :cdata:`NPY_NOTYPE` if the data-type should be determined from the object itself. The C-based names can be used: - + :cdata:`NPY_BOOL`, :cdata:`NPY_BYTE`, :cdata:`NPY_UBYTE`, :cdata:`NPY_SHORT`, :cdata:`NPY_USHORT`, :cdata:`NPY_INT`, :cdata:`NPY_UINT`, :cdata:`NPY_LONG`, :cdata:`NPY_ULONG`, :cdata:`NPY_LONGLONG`, :cdata:`NPY_ULONGLONG`, :cdata:`NPY_DOUBLE`, :cdata:`NPY_LONGDOUBLE`, :cdata:`NPY_CFLOAT`, :cdata:`NPY_CDOUBLE`, - :cdata:`NPY_CLONGDOUBLE`, :cdata:`NPY_OBJECT`. - + :cdata:`NPY_CLONGDOUBLE`, :cdata:`NPY_OBJECT`. + Alternatively, the bit-width names can be used as supported on the platform. For example: - + :cdata:`NPY_INT8`, :cdata:`NPY_INT16`, :cdata:`NPY_INT32`, :cdata:`NPY_INT64`, :cdata:`NPY_UINT8`, :cdata:`NPY_UINT16`, :cdata:`NPY_UINT32`, :cdata:`NPY_UINT64`, :cdata:`NPY_FLOAT32`, :cdata:`NPY_FLOAT64`, :cdata:`NPY_COMPLEX64`, :cdata:`NPY_COMPLEX128`. - + The object will be converted to the desired type only if it can be done without losing precision. Otherwise ``NULL`` will be returned and an error raised. Use :cdata:`NPY_FORCECAST` in the requirements flag to override this behavior. - + *requirements* The memory model for an ndarray admits arbitrary strides in @@ -431,7 +431,7 @@ writeable). The syntax is the array data. Both of these problems can be solved by converting the Python object into an array that is more "well-behaved" for your specific usage. - + The requirements flag allows specification of what kind of array is acceptable. If the object passed in does not satisfy this requirements then a copy is made so that thre returned object will satisfy the @@ -440,7 +440,7 @@ writeable). The syntax is returned array object. All of the flags are explained in the detailed API chapter. The flags most commonly needed are :cdata:`NPY_IN_ARRAY`, :cdata:`NPY_OUT_ARRAY`, and :cdata:`NPY_INOUT_ARRAY`: - + .. cvar:: NPY_IN_ARRAY Equivalent to :cdata:`NPY_CONTIGUOUS` \| @@ -448,7 +448,7 @@ writeable). The syntax is for arrays that must be in C-contiguous order and aligned. These kinds of arrays are usually input arrays for some algorithm. - + .. cvar:: NPY_OUT_ARRAY Equivalent to :cdata:`NPY_CONTIGUOUS` \| @@ -458,7 +458,7 @@ writeable). The syntax is as well. Such an array is usually returned as output (although normally such output arrays are created from scratch). - + .. cvar:: NPY_INOUT_ARRAY Equivalent to :cdata:`NPY_CONTIGUOUS` \| @@ -476,19 +476,19 @@ writeable). The syntax is with the :cdata:`NPY_UPDATEIFCOPY` flag set. This will delete the array without causing the contents to be copied back into the original array. - - + + Other useful flags that can be OR'd as additional requirements are: - + .. cvar:: NPY_FORCECAST Cast to the desired type, even if it can't be done without losing information. - + .. cvar:: NPY_ENSURECOPY Make sure the resulting array is a copy of the original. - + .. cvar:: NPY_ENSUREARRAY Make sure the resulting object is an actual ndarray and not a sub- @@ -514,7 +514,7 @@ to get an ndarray object of whatever data-type is needed. The most general function for doing this is :cfunc:`PyArray_NewFromDescr`. All array creation functions go through this heavily re-used code. Because of its flexibility, it can be somewhat confusing to use. As a result, -simpler forms exist that are easier to use. +simpler forms exist that are easier to use. .. cfunction:: PyObject *PyArray_SimpleNew(int nd, npy_intp* dims, int typenum) @@ -570,7 +570,7 @@ For arrays less than 4-dimensions there are :cfunc:`PyArray_GETPTR{k}` using the array strides easier. The arguments .... represent {k} non- negative integer indices into the array. For example, suppose ``E`` is a 3-dimensional ndarray. A (void*) pointer to the element ``E[i,j,k]`` -is obtained as :cfunc:`PyArray_GETPTR3` (E, i, j, k). +is obtained as :cfunc:`PyArray_GETPTR3` (E, i, j, k). As explained previously, C-style contiguous arrays and Fortran-style contiguous arrays have particular striding patterns. Two array flags @@ -597,7 +597,7 @@ Example The following example shows how you might write a wrapper that accepts two input arguments (that will be converted to an array) and an output argument (that must be an array). The function returns None and -updates the output array. +updates the output array. .. code-block:: c @@ -606,33 +606,33 @@ updates the output array. { PyObject *arg1=NULL, *arg2=NULL, *out=NULL; PyObject *arr1=NULL, *arr2=NULL, *oarr=NULL; - + if (!PyArg_ParseTuple(args, OOO&, &arg1, *arg2, &PyArrayType, *out)) return NULL; - + arr1 = PyArray_FROM_OTF(arg1, NPY_DOUBLE, NPY_IN_ARRAY); if (arr1 == NULL) return NULL; - arr2 = PyArray_FROM_OTF(arg2, NPY_DOUBLE, NPY_IN_ARRAY); + arr2 = PyArray_FROM_OTF(arg2, NPY_DOUBLE, NPY_IN_ARRAY); if (arr2 == NULL) goto fail; oarr = PyArray_FROM_OTF(out, NPY_DOUBLE, NPY_INOUT_ARRAY); if (oarr == NULL) goto fail; - + /* code that makes use of arguments */ - /* You will probably need at least + /* You will probably need at least nd = PyArray_NDIM(<..>) -- number of dimensions - dims = PyArray_DIMS(<..>) -- npy_intp array of length nd + dims = PyArray_DIMS(<..>) -- npy_intp array of length nd showing length in each dim. dptr = (double *)PyArray_DATA(<..>) -- pointer to data. - + If an error occurs goto fail. */ - + Py_DECREF(arr1); Py_DECREF(arr2); Py_DECREF(oarr); Py_INCREF(Py_None); return Py_None; - + fail: Py_XDECREF(arr1); Py_XDECREF(arr2); diff --git a/doc/source/user/c-info.python-as-glue.rst b/doc/source/user/c-info.python-as-glue.rst index 0e0c73cd8..4fb337821 100644 --- a/doc/source/user/c-info.python-as-glue.rst +++ b/doc/source/user/c-info.python-as-glue.rst @@ -3,12 +3,12 @@ Using Python as glue ******************** | There is no conversation more boring than the one where everybody -| agrees. -| --- *Michel de Montaigne* +| agrees. +| --- *Michel de Montaigne* | Duct tape is like the force. It has a light side, and a dark side, and -| it holds the universe together. -| --- *Carl Zwanzig* +| it holds the universe together. +| --- *Carl Zwanzig* Many people like to say that Python is a fantastic glue language. Hopefully, this Chapter will convince you that this is true. The first @@ -19,21 +19,21 @@ 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. +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. +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. +possibilities so that you will know what to "Google" in order to learn more. The http://www.scipy.org website also contains a great deal of useful information about many of these tools. For example, there is a nice @@ -42,7 +42,7 @@ http://www.scipy.org/PerformancePython. This link provides several ways to solve the same problem showing how to use and connect with compiled code to get the best performance. In the process you can get a taste for several of the approaches that will be discussed in this -chapter. +chapter. Calling other compiled libraries from Python @@ -60,21 +60,21 @@ 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. +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 (included in the standard distribution with Python 2.5). The first method is the most common (but with the -inclusion of ctypes into Python 2.5 this status may change). +inclusion of ctypes into Python 2.5 this status may change). .. 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. + the third-party library being used. Hand-generated wrappers @@ -89,7 +89,7 @@ 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. +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 @@ -100,7 +100,7 @@ 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). +(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 @@ -113,7 +113,7 @@ 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 session. +next session. f2py @@ -124,7 +124,7 @@ 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- -defintion-file (or modifying the f2py-produced one). +defintion-file (or modifying the f2py-produced one). .. index:: single: f2py @@ -148,7 +148,7 @@ example. Here is one of the subroutines contained in a file named DO 20 J = 1, N C(J) = A(J)+B(J) 20 CONTINUE - END + 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 @@ -160,7 +160,7 @@ routine can be automatically generated by f2py:: 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. +compiled and used from Python just like any other extension module. Creating a compiled extension module @@ -181,13 +181,13 @@ information about how the module method may be called: >>> import add >>> print add.zadd.__doc__ - zadd - Function signature: + zadd - Function signature: zadd(a,b,c,n) - Required arguments: + 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 + n : input int Improving the basic interface @@ -200,13 +200,13 @@ 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: +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. +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 @@ -221,11 +221,11 @@ section of this file corresponding to zadd is: .. code-block:: none - subroutine zadd(a,b,c,n) ! in :add:add.f - double complex dimension(*) :: a - double complex dimension(*) :: b - double complex dimension(*) :: c - integer :: n + 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 @@ -234,11 +234,11 @@ to use and more robust. .. code-block:: none - 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) + 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 @@ -248,25 +248,25 @@ 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). +created). The new interface has docstring: >>> 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) + 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: +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. +Notice the automatic conversion to the correct format that occurred. Inserting directives in Fortran source @@ -305,7 +305,7 @@ 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. +of A. A filtering example @@ -315,7 +315,7 @@ 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. +should be clear from this example. .. code-block:: none @@ -329,7 +329,7 @@ should be clear from this example. CF2PY INTENT(HIDE) :: M DO 20 I = 2,M-1 DO 40 J=2,N-1 - B(I,J) = A(I,J) + + 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) + @@ -345,7 +345,7 @@ filter using:: 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. +version of the input. Calling f2py from Python @@ -367,7 +367,7 @@ executed using Python code is: 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. +provided by the source_fn keyword to the compile function. Automatic extension module generation @@ -387,7 +387,7 @@ so that it would be loaded as f2py_examples.add) is: 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()) @@ -401,7 +401,7 @@ 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. +conversion of the .pyf file to a .c file is handled by numpy.disutils. Conclusion @@ -413,7 +413,7 @@ 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 http://www.scipy.org/Cookbook under the "Using NumPy with -Other Languages" heading. +Other Languages" heading. The f2py method of linking compiled code is currently the most sophisticated and integrated approach. It allows clean separation of @@ -427,7 +427,7 @@ 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. +written C-code. .. index:: single: f2py @@ -443,7 +443,7 @@ temporary variables, to directly "inline" C/C++ code into Python, or to create a fully-named extension module. You must either install scipy or get the weave package separately and install it using the standard python setup.py install. You must also have a C/C++-compiler -installed and useable by Python distutils in order to use weave. +installed and useable by Python distutils in order to use weave. .. index:: single: weave @@ -451,7 +451,7 @@ installed and useable by Python distutils in order to use weave. Somewhat dated, but still useful documentation for weave can be found at the link http://www.scipy/Weave. There are also many examples found in the examples directory which is installed under the weave directory -in the place where weave is installed on your system. +in the place where weave is installed on your system. Speed up code involving arrays (also see scipy.numexpr) @@ -470,7 +470,7 @@ quickly than the equivalent NumPy expression. This is especially true if your array sizes are large and the expression would require NumPy to create several temporaries. Only expressions involving basic arithmetic operations and basic array slicing can be converted to -Blitz C++ code. +Blitz C++ code. For example, consider the expression:: @@ -489,12 +489,12 @@ execution time is only about 0.20 seconds (about 0.14 seconds spent in weave and the rest in allocating space for d). Thus, we've sped up the code by a factor of 2 using only a simnple command (weave.blitz). Your mileage may vary, but factors of 2-8 speed-ups are possible with this -very simple technique. +very simple technique. If you are interested in using weave in this way, then you should also look at scipy.numexpr which is another similar way to speed up expressions by eliminating the need for temporary variables. Using -numexpr does not require a C/C++ compiler. +numexpr does not require a C/C++ compiler. Inline C-code @@ -514,24 +514,24 @@ following example shows how to use weave on basic Python objects: .. code-block:: python - code = r""" - int i; - py::tuple results(2); - for (i=0; i<a.length(); i++) { + code = r""" + int i; + py::tuple results(2); + for (i=0; i<a.length(); i++) { a[i] = i; - } - results[0] = 3.0; - results[1] = 4.0; + } + results[0] = 3.0; + results[1] = 4.0; return_val = results; - """ - a = [None]*10 + """ + a = [None]*10 res = weave.inline(code,['a']) The C++ code shown in the code string uses the name 'a' to refer to the Python list that is passed in. Because the Python List is a mutable type, the elements of the list itself are modified by the C++ code. A set of C++ classes are used to access Python objects using -simple syntax. +simple syntax. The main advantage of using C-code, however, is to speed up processing on an array of data. Accessing a NumPy array in C++ code using weave, @@ -540,16 +540,16 @@ arrays to C++ code. The default converter creates 5 variables for the C-code for every NumPy array passed in to weave.inline. The following table shows these variables which can all be used in the C++ code. The table assumes that ``myvar`` is the name of the array in Python with -data-type {dtype} (i.e. float64, float32, int8, etc.) +data-type {dtype} (i.e. float64, float32, int8, etc.) =========== ============== ========================================= -Variable Type Contents +Variable Type Contents =========== ============== ========================================= -myvar {dtype}* Pointer to the first element of the array -Nmyvar npy_intp* A pointer to the dimensions array -Smyvar npy_intp* A pointer to the strides array -Dmyvar int The number of dimensions -myvar_array PyArrayObject* The entire structure for the array +myvar {dtype}* Pointer to the first element of the array +Nmyvar npy_intp* A pointer to the dimensions array +Smyvar npy_intp* A pointer to the strides array +Dmyvar int The number of dimensions +myvar_array PyArrayObject* The entire structure for the array =========== ============== ========================================= The in-lined code can contain references to any of these variables as @@ -561,7 +561,7 @@ checking (be-sure to use the correct macro and ensure the array is aligned and in correct byte-swap order in order to get useful results). The following code shows how you might use these variables and macros to code a loop in C that computes a simple 2-d weighted -averaging filter. +averaging filter. .. code-block:: c++ @@ -582,7 +582,7 @@ The above code doesn't have any error checking and so could fail with a Python crash if, ``a`` had the wrong number of dimensions, or ``b`` did not have the same shape as ``a``. However, it could be placed inside a standard Python function with the necessary error checking to -produce a robust but fast subroutine. +produce a robust but fast subroutine. One final note about weave.inline: if you have additional code you want to include in the final extension module such as supporting @@ -592,7 +592,7 @@ support_code=support)``. If you need the extension module to link against an additional library then you can also pass in distutils-style keyword arguments such as library_dirs, libraries, and/or runtime_library_dirs which point to the appropriate libraries -and directories. +and directories. Simplify creation of an extension module ---------------------------------------- @@ -604,9 +604,9 @@ codes to execute in C, it would be better to make them all separate functions in a single extension module with multiple functions. You can also use the tools weave provides to produce this larger extension module. In fact, the weave.inline function just uses these more -general tools to do its work. +general tools to do its work. -The approach is to: +The approach is to: 1. construct a extension module object using ext_tools.ext_module(``module_name``); @@ -626,7 +626,7 @@ The approach is to: Several examples are available in the examples directory where weave is installed on your system. Look particularly at ramp2.py, -increment_example.py and fibonacii.py +increment_example.py and fibonacii.py Conclusion @@ -643,7 +643,7 @@ normal way *(* using a setup.py file). While you can use weave to build larger extension modules with many methods, creating methods with a variable- number of arguments is not possible. Thus, for a more sophisticated module, you will still probably want a Python-layer that -calls the weave-produced extension. +calls the weave-produced extension. .. index:: single: weave @@ -661,7 +661,7 @@ to interface to a large library of code. However, if you are writing an extension module that will include quite a bit of your own algorithmic code, as well, then Pyrex is a good match. A big weakness perhaps is the inability to easily and quickly access the elements of -a multidimensional array. +a multidimensional array. .. index:: single: pyrex @@ -678,12 +678,12 @@ write in a setup.py file: from Pyrex.Distutils import build_ext from distutils.extension import Extension from distutils.core import setup - + import numpy py_ext = Extension('mine', ['mine.pyx'], include_dirs=[numpy.get_include()]) - - setup(name='mine', description='Nothing', + + setup(name='mine', description='Nothing', ext_modules=[pyx_ext], cmdclass = {'build_ext':build_ext}) @@ -694,7 +694,7 @@ 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 Pyrex 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. +to produce the ``.c`` file again. Pyrex does not natively understand NumPy arrays. However, it is not difficult to include information that lets Pyrex deal with them @@ -709,7 +709,7 @@ located in the .../site-packages/numpy/doc/pyrex directory where you have Python installed. There is also an example in that directory of using Pyrex to construct a simple extension module. It shows that Pyrex looks a lot like Python but also contains some new syntax that -is necessary in order to get C-like speed. +is necessary in order to get C-like speed. If you just use Pyrex to compile a standard Python module, then you will get a C-extension module that runs either as fast or, possibly, @@ -724,7 +724,7 @@ use a special construct to create for loops: Let's look at two examples we've seen before to see how they might be implemented using Pyrex. These examples were compiled into extension -modules using Pyrex-0.9.3.1. +modules using Pyrex-0.9.3.1. Pyrex-add @@ -739,16 +739,16 @@ functions we previously implemented using f2py: from c_numpy cimport import_array, ndarray, npy_intp, npy_cdouble, \ npy_cfloat, NPY_DOUBLE, NPY_CDOUBLE, NPY_FLOAT, \ NPY_CFLOAT - + #We need to initialize NumPy import_array() - + def zadd(object ao, object bo): cdef ndarray c, a, b cdef npy_intp i - a = c_numpy.PyArray_ContiguousFromAny(ao, + a = c_numpy.PyArray_ContiguousFromAny(ao, NPY_CDOUBLE, 1, 1) - b = c_numpy.PyArray_ContiguousFromAny(bo, + b = c_numpy.PyArray_ContiguousFromAny(bo, NPY_CDOUBLE, 1, 1) c = c_numpy.PyArray_SimpleNew(a.nd, a.dimensions, a.descr.type_num) @@ -778,7 +778,7 @@ Python objects, Pyrex inserts the checks for NULL into the C-code for you and returns with failure if need be. There is also a way to get Pyrex to automatically check for exceptions when you call functions that don't return Python objects. See the documentation of Pyrex for -details. +details. Pyrex-filter @@ -787,15 +787,15 @@ Pyrex-filter The two-dimensional example we created using weave is a bit uglierto implement in Pyrex because two-dimensional indexing using Pyrex is not as simple. But, it is straightforward (and possibly faster because of -pre-computed indices). Here is the Pyrex-file I named image.pyx. +pre-computed indices). Here is the Pyrex-file I named image.pyx. .. code-block:: none cimport c_numpy - from c_numpy cimport import_array, ndarray, npy_intp,\ + from c_numpy cimport import_array, ndarray, npy_intp,\ NPY_DOUBLE, NPY_CDOUBLE, \ NPY_FLOAT, NPY_CFLOAT, NPY_ALIGNED \ - + #We need to initialize NumPy import_array() def filter(object ao): @@ -803,7 +803,7 @@ pre-computed indices). Here is the Pyrex-file I named image.pyx. cdef npy_intp i, j, M, N, oS cdef npy_intp r,rm1,rp1,c,cm1,cp1 cdef double value - # Require an ALIGNED array + # Require an ALIGNED array # (but not necessarily contiguous) # We will use strides to access the elements. a = c_numpy.PyArray_FROMANY(ao, NPY_DOUBLE, \ @@ -829,7 +829,7 @@ pre-computed indices). Here is the Pyrex-file I named image.pyx. (<double *>(a.data+rp1+c))[0] + \ (<double *>(a.data+r+cm1))[0] + \ (<double *>(a.data+r+cp1))[0])*0.5 + \ - ((<double *>(a.data+rm1+cm1))[0] + \ + ((<double *>(a.data+rm1+cm1))[0] + \ (<double *>(a.data+rp1+cm1))[0] + \ (<double *>(a.data+rp1+cp1))[0] + \ (<double *>(a.data+rm1+cp1))[0])*0.25 @@ -849,7 +849,7 @@ particularly easy to understand what is happening. A 2-d image, ``in`` Conclusion ---------- -There are several disadvantages of using Pyrex: +There are several disadvantages of using Pyrex: 1. The syntax for Pyrex can get a bit bulky, and it can be confusing at first to understand what kind of objects you are getting and how to @@ -859,13 +859,13 @@ There are several disadvantages of using Pyrex: mismatches can result in failures such as 1. Pyrex failing to generate the extension module source code, - + 2. Compiler failure while generating the extension module binary due to incorrect C syntax, - + 3. Python failure when trying to use the module. - - + + 3. 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. @@ -886,7 +886,7 @@ be over-looked. It is especially useful for people that can't or won't write C-code or Fortran code. But, if you are already able to write simple subroutines in C or Fortran, then I would use one of the other approaches such as f2py (for Fortran), ctypes (for C shared- -libraries), or weave (for inline C-code). +libraries), or weave (for inline C-code). .. index:: single: pyrex @@ -910,7 +910,7 @@ 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). +extended functionality in your own shared library). .. index:: single: ctypes @@ -926,9 +926,9 @@ extension-module interface. However, this overhead should be neglible 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. +code. -To use c-types you must +To use c-types you must 1. Have a shared library. @@ -945,7 +945,7 @@ Having a shared library There are several requirements for a shared library that can be used with c-types that are platform specific. This guide assumes you have some familiarity with making a shared library on your system (or -simply have a shared library available to you). Items to remember are: +simply have a shared library available to you). Items to remember are: - A shared library must be compiled in a special way ( *e.g.* using the -shared flag with gcc). @@ -953,25 +953,25 @@ simply have a shared library available to you). Items to remember are: - On some platforms (*e.g.* Windows) , a shared library requires a .def file that specifies the functions to be exported. For example a mylib.def file might contain. - + :: - + LIBRARY mylib.dll EXPORTS cool_function1 cool_function2 - + Alternatively, you may be able to use the storage-class specifier __declspec(dllexport) in the C-definition of the function to avoid the - need for this .def file. - + need for this .def file. + There is no standard way in Python distutils to create a standard shared library (an extension module is a "special" shared library Python understands) in a cross-platform manner. Thus, a big disadvantage of ctypes at the time of writing this book is that it is difficult to distribute in a cross-platform manner a Python extension that uses c-types and includes your own code which should be compiled -as a shared library on the users system. +as a shared library on the users system. Loading the shared library @@ -994,7 +994,7 @@ foolproof. Complicating matters, different platforms have different default extensions used by shared libraries (e.g. .dll -- Windows, .so -- Linux, .dylib -- Mac OS X). This must also be taken into account if you are using c-types to wrap code that needs to work on several -platforms. +platforms. NumPy provides a convenience function called :func:`ctypeslib.load_library` (name, path). This function takes the name @@ -1005,13 +1005,13 @@ cannot be found or raises an ImportError if the ctypes module is not available. (Windows users: the ctypes library object loaded using :func:`load_library` is always loaded assuming cdecl calling convention. See the ctypes documentation under ctypes.windll and/or ctypes.oledll -for ways to load libraries under other calling conventions). +for ways to load libraries under other calling conventions). The functions in the shared library are available as attributes of the ctypes library object (returned from :func:`ctypeslib.load_library`) or as items using ``lib['func_name']`` syntax. The latter method for retrieving a function name is particularly useful if the function name -contains characters that are not allowable in Python variable names. +contains characters that are not allowable in Python variable names. Converting arguments @@ -1022,7 +1022,7 @@ converted as needed to equivalent c-types 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 c-types to integrate with other -objects. +objects. 1. Don't set the argtypes attribute of the function object and define an :obj:`_as_parameter_` method for the object you want to pass in. The @@ -1042,7 +1042,7 @@ 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 passsed in. +crashes if the data-pointer to inappropriate arrays are passsed in. To implement the second method, NumPy provides the class-factory function :func:`ndpointer` in the :mod:`ctypeslib` module. This @@ -1057,7 +1057,7 @@ 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. +directly. The ctypes attribute of an ndarray is also endowed with additional attributes that may be convenient when passing additional information @@ -1075,7 +1075,7 @@ 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 (it's value is None if ctypes is not -installed). +installed). Calling the function @@ -1105,7 +1105,7 @@ the function in order to have ctypes check the types of the input arguments when the function is called. Use the :func:`ndpointer` factory function to generate a ready-made class for data-type, shape, and flags checking on your new function. The :func:`ndpointer` function has the -signature +signature .. function:: ndpointer(dtype=None, ndim=None, shape=None, flags=None) @@ -1127,7 +1127,7 @@ 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. +a given input. Complete example @@ -1149,8 +1149,8 @@ dfilter2d. The zadd function is: while (n--) { c->real = a->real + b->real; c->imag = a->imag + b->imag; - a++; b++; c++; - } + a++; b++; c++; + } } with similar code for cadd, dadd, and sadd that handles complex float, @@ -1163,16 +1163,16 @@ double, and float data-types, respectively: while (n--) { c->real = a->real + b->real; c->imag = a->imag + b->imag; - a++; b++; c++; - } + a++; b++; c++; + } } - void dadd(double *a, double *b, double *c, long n) + 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) + void sadd(float *a, float *b, float *c, long n) { while (n--) { *c++ = *a++ + *b++; @@ -1183,17 +1183,17 @@ The code.c file also contains the function dfilter2d: .. code-block:: c - /* Assumes b is contiguous and + /* Assumes b is contiguous and a has strides that are multiples of sizeof(double) */ - void + void dfilter2d(double *a, double *b, int *astrides, int *dims) { int i, j, M, N, S0, S1; int r, c, rm1, rp1, cp1, cm1; - + M = dims[0]; N = dims[1]; - S0 = astrides[0]/sizeof(double); + 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; @@ -1220,7 +1220,7 @@ Linux system this is accomplished using:: 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 preceeding each function definition, or write a -code.def file that lists the names of the functions to be exported. +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 @@ -1229,10 +1229,10 @@ following lines at the top: .. code-block:: python __all__ = ['add', 'filter2d'] - + import numpy as N import os - + _path = os.path.dirname('__file__') lib = N.ctypeslib.load_library('code', _path) _typedict = {'zadd' : complex, 'sadd' : N.single, @@ -1241,11 +1241,11 @@ following lines at the top: val = getattr(lib, name) val.restype = None _type = _typedict[name] - val.argtypes = [N.ctypeslib.ndpointer(_type, + val.argtypes = [N.ctypeslib.ndpointer(_type, flags='aligned, contiguous'), - N.ctypeslib.ndpointer(_type, + N.ctypeslib.ndpointer(_type, flags='aligned, contiguous'), - N.ctypeslib.ndpointer(_type, + N.ctypeslib.ndpointer(_type, flags='aligned, contiguous,'\ 'writeable'), N.ctypeslib.c_intp] @@ -1255,7 +1255,7 @@ 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. +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 @@ -1269,9 +1269,9 @@ strides and shape of an ndarray) as the last two arguments.: flags='aligned'), N.ctypeslib.ndpointer(float, ndim=2, flags='aligned, contiguous,'\ - 'writeable'), - ctypes.POINTER(N.ctypeslib.c_intp), - ctypes.POINTER(N.ctypeslib.c_intp)] + 'writeable'), + ctypes.POINTER(N.ctypeslib.c_intp), + ctypes.POINTER(N.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: @@ -1322,23 +1322,23 @@ Conclusion single: ctypes Using ctypes is a powerful way to connect Python with arbitrary -C-code. It's advantages for extending Python include +C-code. It's 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 -It's disadvantages include +It's disadvantages include - It is difficult to distribute an extension module made using ctypes because of a lack of support for building shared libraries in @@ -1356,7 +1356,7 @@ package creation. However, ctypes is a close second and will probably be growing in popularity now that it is part of the Python distribution. This should bring more features to ctypes that should eliminate the difficulty in extending Python and distributing the -extension using ctypes. +extension using ctypes. Additional tools you may find useful @@ -1373,7 +1373,7 @@ 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. +as possible for tackling the problem of easily integrating your code. SWIG @@ -1399,7 +1399,7 @@ 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. +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 @@ -1409,7 +1409,7 @@ 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. +SWIG quite happily. SIP @@ -1426,7 +1426,7 @@ 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++ structrues and classes. +mappings between Python types and C/C++ structrues and classes. Boost Python @@ -1445,7 +1445,7 @@ 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. +Python, consider learning about and using Boost.Python. Instant @@ -1469,18 +1469,18 @@ arrays (adapted from the test2 included in the Instant distribution): PyObject* add(PyObject* a_, PyObject* b_){ /* various checks - */ + */ PyArrayObject* a=(PyArrayObject*) a_; PyArrayObject* b=(PyArrayObject*) b_; int n = a->dimensions[0]; int dims[1]; - dims[0] = n; + dims[0] = n; PyArrayObject* ret; - ret = (PyArrayObject*) PyArray_FromDims(1, dims, NPY_DOUBLE); + ret = (PyArrayObject*) PyArray_FromDims(1, dims, NPY_DOUBLE); int i; char *aj=a->data; char *bj=b->data; - double *retj = (double *)ret->data; + double *retj = (double *)ret->data; for (i=0; i < n; i++) { *retj++ = *((double *)aj) + *((double *)bj); aj += a->strides[0]; @@ -1500,7 +1500,7 @@ arrays (adapted from the test2 included in the Instant distribution): d = test2b_ext.add(a,b) Except perhaps for the dependence on SWIG, Instant is a -straightforward utility for writing extension modules. +straightforward utility for writing extension modules. PyInline @@ -1509,7 +1509,7 @@ PyInline This is a much older module that allows automatic building of extension modules so that C-code can be included with Python code. It's latest release (version 0.03) was in 2001, and it appears that it -is not being updated. +is not being updated. PyFort @@ -1520,4 +1520,4 @@ 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. +well which now support either Fortran or C-style contiguous arrays. diff --git a/doc/source/user/index.rst b/doc/source/user/index.rst index 750062d50..8d8812c80 100644 --- a/doc/source/user/index.rst +++ b/doc/source/user/index.rst @@ -18,7 +18,7 @@ and classes, see :ref:`reference`. .. toctree:: :maxdepth: 2 - + howtofind basics performance |