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- """
- =============
- Miscellaneous
- =============
- IEEE 754 Floating Point Special Values
- --------------------------------------
- Special values defined in numpy: nan, inf,
- NaNs can be used as a poor-man's mask (if you don't care what the
- original value was)
- Note: cannot use equality to test NaNs. E.g.: ::
- >>> myarr = np.array([1., 0., np.nan, 3.])
- >>> np.nonzero(myarr == np.nan)
- (array([], dtype=int64),)
- >>> np.nan == np.nan # is always False! Use special numpy functions instead.
- False
- >>> myarr[myarr == np.nan] = 0. # doesn't work
- >>> myarr
- array([ 1., 0., NaN, 3.])
- >>> myarr[np.isnan(myarr)] = 0. # use this instead find
- >>> myarr
- array([ 1., 0., 0., 3.])
- Other related special value functions: ::
- isinf(): True if value is inf
- isfinite(): True if not nan or inf
- nan_to_num(): Map nan to 0, inf to max float, -inf to min float
- The following corresponds to the usual functions except that nans are excluded
- from the results: ::
- nansum()
- nanmax()
- nanmin()
- nanargmax()
- nanargmin()
- >>> x = np.arange(10.)
- >>> x[3] = np.nan
- >>> x.sum()
- nan
- >>> np.nansum(x)
- 42.0
- How numpy handles numerical exceptions
- --------------------------------------
- The default is to ``'warn'`` for ``invalid``, ``divide``, and ``overflow``
- and ``'ignore'`` for ``underflow``. But this can be changed, and it can be
- set individually for different kinds of exceptions. The different behaviors
- are:
- - 'ignore' : Take no action when the exception occurs.
- - 'warn' : Print a `RuntimeWarning` (via the Python `warnings` module).
- - 'raise' : Raise a `FloatingPointError`.
- - 'call' : Call a function specified using the `seterrcall` function.
- - 'print' : Print a warning directly to ``stdout``.
- - 'log' : Record error in a Log object specified by `seterrcall`.
- These behaviors can be set for all kinds of errors or specific ones:
- - all : apply to all numeric exceptions
- - invalid : when NaNs are generated
- - divide : divide by zero (for integers as well!)
- - overflow : floating point overflows
- - underflow : floating point underflows
- Note that integer divide-by-zero is handled by the same machinery.
- These behaviors are set on a per-thread basis.
- Examples
- --------
- ::
- >>> oldsettings = np.seterr(all='warn')
- >>> np.zeros(5,dtype=np.float32)/0.
- invalid value encountered in divide
- >>> j = np.seterr(under='ignore')
- >>> np.array([1.e-100])**10
- >>> j = np.seterr(invalid='raise')
- >>> np.sqrt(np.array([-1.]))
- FloatingPointError: invalid value encountered in sqrt
- >>> def errorhandler(errstr, errflag):
- ... print("saw stupid error!")
- >>> np.seterrcall(errorhandler)
- <function err_handler at 0x...>
- >>> j = np.seterr(all='call')
- >>> np.zeros(5, dtype=np.int32)/0
- FloatingPointError: invalid value encountered in divide
- saw stupid error!
- >>> j = np.seterr(**oldsettings) # restore previous
- ... # error-handling settings
- Interfacing to C
- ----------------
- Only a survey of the choices. Little detail on how each works.
- 1) Bare metal, wrap your own C-code manually.
- - Plusses:
- - Efficient
- - No dependencies on other tools
- - Minuses:
- - Lots of learning overhead:
- - need to learn basics of Python C API
- - need to learn basics of numpy C API
- - need to learn how to handle reference counting and love it.
- - Reference counting often difficult to get right.
- - getting it wrong leads to memory leaks, and worse, segfaults
- - API will change for Python 3.0!
- 2) Cython
- - Plusses:
- - avoid learning C API's
- - no dealing with reference counting
- - can code in pseudo python and generate C code
- - can also interface to existing C code
- - should shield you from changes to Python C api
- - has become the de-facto standard within the scientific Python community
- - fast indexing support for arrays
- - Minuses:
- - Can write code in non-standard form which may become obsolete
- - Not as flexible as manual wrapping
- 3) ctypes
- - Plusses:
- - part of Python standard library
- - good for interfacing to existing sharable libraries, particularly
- Windows DLLs
- - avoids API/reference counting issues
- - good numpy support: arrays have all these in their ctypes
- attribute: ::
- a.ctypes.data a.ctypes.get_strides
- a.ctypes.data_as a.ctypes.shape
- a.ctypes.get_as_parameter a.ctypes.shape_as
- a.ctypes.get_data a.ctypes.strides
- a.ctypes.get_shape a.ctypes.strides_as
- - Minuses:
- - can't use for writing code to be turned into C extensions, only a wrapper
- tool.
- 4) SWIG (automatic wrapper generator)
- - Plusses:
- - around a long time
- - multiple scripting language support
- - C++ support
- - Good for wrapping large (many functions) existing C libraries
- - Minuses:
- - generates lots of code between Python and the C code
- - can cause performance problems that are nearly impossible to optimize
- out
- - interface files can be hard to write
- - doesn't necessarily avoid reference counting issues or needing to know
- API's
- 5) scipy.weave
- - Plusses:
- - can turn many numpy expressions into C code
- - dynamic compiling and loading of generated C code
- - can embed pure C code in Python module and have weave extract, generate
- interfaces and compile, etc.
- - Minuses:
- - Future very uncertain: it's the only part of Scipy not ported to Python 3
- and is effectively deprecated in favor of Cython.
- 6) Psyco
- - Plusses:
- - Turns pure python into efficient machine code through jit-like
- optimizations
- - very fast when it optimizes well
- - Minuses:
- - Only on intel (windows?)
- - Doesn't do much for numpy?
- Interfacing to Fortran:
- -----------------------
- The clear choice to wrap Fortran code is
- `f2py <https://docs.scipy.org/doc/numpy/f2py/>`_.
- Pyfort is an older alternative, but not supported any longer.
- Fwrap is a newer project that looked promising but isn't being developed any
- longer.
- Interfacing to C++:
- -------------------
- 1) Cython
- 2) CXX
- 3) Boost.python
- 4) SWIG
- 5) SIP (used mainly in PyQT)
- """
- from __future__ import division, absolute_import, print_function
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