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