numpy 1.9.2__zip → 1.10.0__zip

numpy-1.10.0.post2/numpy/core/machar.py

@@ -0,0 +1,342 @@
+"""
+Machine arithmetics - determine the parameters of the
+floating-point arithmetic system
+
+Author: Pearu Peterson, September 2003
+
+"""
+from __future__ import division, absolute_import, print_function
+
+__all__ = ['MachAr']
+
+from numpy.core.fromnumeric import any
+from numpy.core.numeric import errstate
+
+# Need to speed this up...especially for longfloat
+
+class MachAr(object):
+    """
+    Diagnosing machine parameters.
+
+    Attributes
+    ----------
+    ibeta : int
+        Radix in which numbers are represented.
+    it : int
+        Number of base-`ibeta` digits in the floating point mantissa M.
+    machep : int
+        Exponent of the smallest (most negative) power of `ibeta` that,
+        added to 1.0, gives something different from 1.0
+    eps : float
+        Floating-point number ``beta**machep`` (floating point precision)
+    negep : int
+        Exponent of the smallest power of `ibeta` that, substracted
+        from 1.0, gives something different from 1.0.
+    epsneg : float
+        Floating-point number ``beta**negep``.
+    iexp : int
+        Number of bits in the exponent (including its sign and bias).
+    minexp : int
+        Smallest (most negative) power of `ibeta` consistent with there
+        being no leading zeros in the mantissa.
+    xmin : float
+        Floating point number ``beta**minexp`` (the smallest [in
+        magnitude] usable floating value).
+    maxexp : int
+        Smallest (positive) power of `ibeta` that causes overflow.
+    xmax : float
+        ``(1-epsneg) * beta**maxexp`` (the largest [in magnitude]
+        usable floating value).
+    irnd : int
+        In ``range(6)``, information on what kind of rounding is done
+        in addition, and on how underflow is handled.
+    ngrd : int
+        Number of 'guard digits' used when truncating the product
+        of two mantissas to fit the representation.
+    epsilon : float
+        Same as `eps`.
+    tiny : float
+        Same as `xmin`.
+    huge : float
+        Same as `xmax`.
+    precision : float
+        ``- int(-log10(eps))``
+    resolution : float
+        ``- 10**(-precision)``
+
+    Parameters
+    ----------
+    float_conv : function, optional
+        Function that converts an integer or integer array to a float
+        or float array. Default is `float`.
+    int_conv : function, optional
+        Function that converts a float or float array to an integer or
+        integer array. Default is `int`.
+    float_to_float : function, optional
+        Function that converts a float array to float. Default is `float`.
+        Note that this does not seem to do anything useful in the current
+        implementation.
+    float_to_str : function, optional
+        Function that converts a single float to a string. Default is
+        ``lambda v:'%24.16e' %v``.
+    title : str, optional
+        Title that is printed in the string representation of `MachAr`.
+
+    See Also
+    --------
+    finfo : Machine limits for floating point types.
+    iinfo : Machine limits for integer types.
+
+    References
+    ----------
+    .. [1] Press, Teukolsky, Vetterling and Flannery,
+           "Numerical Recipes in C++," 2nd ed,
+           Cambridge University Press, 2002, p. 31.
+
+    """
+
+    def __init__(self, float_conv=float,int_conv=int,
+                 float_to_float=float,
+                 float_to_str=lambda v:'%24.16e' % v,
+                 title='Python floating point number'):
+        """
+
+        float_conv - convert integer to float (array)
+        int_conv   - convert float (array) to integer
+        float_to_float - convert float array to float
+        float_to_str - convert array float to str
+        title        - description of used floating point numbers
+
+        """
+        # We ignore all errors here because we are purposely triggering
+        # underflow to detect the properties of the runninng arch.
+        with errstate(under='ignore'):
+            self._do_init(float_conv, int_conv, float_to_float, float_to_str, title)
+
+    def _do_init(self, float_conv, int_conv, float_to_float, float_to_str, title):
+        max_iterN = 10000
+        msg = "Did not converge after %d tries with %s"
+        one = float_conv(1)
+        two = one + one
+        zero = one - one
+
+        # Do we really need to do this?  Aren't they 2 and 2.0?
+        # Determine ibeta and beta
+        a = one
+        for _ in range(max_iterN):
+            a = a + a
+            temp = a + one
+            temp1 = temp - a
+            if any(temp1 - one != zero):
+                break
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        b = one
+        for _ in range(max_iterN):
+            b = b + b
+            temp = a + b
+            itemp = int_conv(temp-a)
+            if any(itemp != 0):
+                break
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        ibeta = itemp
+        beta = float_conv(ibeta)
+
+        # Determine it and irnd
+        it = -1
+        b = one
+        for _ in range(max_iterN):
+            it = it + 1
+            b = b * beta
+            temp = b + one
+            temp1 = temp - b
+            if any(temp1 - one != zero):
+                break
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+
+        betah = beta / two
+        a = one
+        for _ in range(max_iterN):
+            a = a + a
+            temp = a + one
+            temp1 = temp - a
+            if any(temp1 - one != zero):
+                break
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        temp = a + betah
+        irnd = 0
+        if any(temp-a != zero):
+            irnd = 1
+        tempa = a + beta
+        temp = tempa + betah
+        if irnd == 0 and any(temp-tempa != zero):
+            irnd = 2
+
+        # Determine negep and epsneg
+        negep = it + 3
+        betain = one / beta
+        a = one
+        for i in range(negep):
+            a = a * betain
+        b = a
+        for _ in range(max_iterN):
+            temp = one - a
+            if any(temp-one != zero):
+                break
+            a = a * beta
+            negep = negep - 1
+            # Prevent infinite loop on PPC with gcc 4.0:
+            if negep < 0:
+                raise RuntimeError("could not determine machine tolerance "
+                                   "for 'negep', locals() -> %s" % (locals()))
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        negep = -negep
+        epsneg = a
+
+        # Determine machep and eps
+        machep = - it - 3
+        a = b
+
+        for _ in range(max_iterN):
+            temp = one + a
+            if any(temp-one != zero):
+                break
+            a = a * beta
+            machep = machep + 1
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        eps = a
+
+        # Determine ngrd
+        ngrd = 0
+        temp = one + eps
+        if irnd == 0 and any(temp*one - one != zero):
+            ngrd = 1
+
+        # Determine iexp
+        i = 0
+        k = 1
+        z = betain
+        t = one + eps
+        nxres = 0
+        for _ in range(max_iterN):
+            y = z
+            z = y*y
+            a = z*one  # Check here for underflow
+            temp = z*t
+            if any(a+a == zero) or any(abs(z) >= y):
+                break
+            temp1 = temp * betain
+            if any(temp1*beta == z):
+                break
+            i = i + 1
+            k = k + k
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        if ibeta != 10:
+            iexp = i + 1
+            mx = k + k
+        else:
+            iexp = 2
+            iz = ibeta
+            while k >= iz:
+                iz = iz * ibeta
+                iexp = iexp + 1
+            mx = iz + iz - 1
+
+        # Determine minexp and xmin
+        for _ in range(max_iterN):
+            xmin = y
+            y = y * betain
+            a = y * one
+            temp = y * t
+            if any((a + a) != zero) and any(abs(y) < xmin):
+                k = k + 1
+                temp1 = temp * betain
+                if any(temp1*beta == y) and any(temp != y):
+                    nxres = 3
+                    xmin = y
+                    break
+            else:
+                break
+        else:
+            raise RuntimeError(msg % (_, one.dtype))
+        minexp = -k
+
+        # Determine maxexp, xmax
+        if mx <= k + k - 3 and ibeta != 10:
+            mx = mx + mx
+            iexp = iexp + 1
+        maxexp = mx + minexp
+        irnd = irnd + nxres
+        if irnd >= 2:
+            maxexp = maxexp - 2
+        i = maxexp + minexp
+        if ibeta == 2 and not i:
+            maxexp = maxexp - 1
+        if i > 20:
+            maxexp = maxexp - 1
+        if any(a != y):
+            maxexp = maxexp - 2
+        xmax = one - epsneg
+        if any(xmax*one != xmax):
+            xmax = one - beta*epsneg
+        xmax = xmax / (xmin*beta*beta*beta)
+        i = maxexp + minexp + 3
+        for j in range(i):
+            if ibeta == 2:
+                xmax = xmax + xmax
+            else:
+                xmax = xmax * beta
+
+        self.ibeta = ibeta
+        self.it = it
+        self.negep = negep
+        self.epsneg = float_to_float(epsneg)
+        self._str_epsneg = float_to_str(epsneg)
+        self.machep = machep
+        self.eps = float_to_float(eps)
+        self._str_eps = float_to_str(eps)
+        self.ngrd = ngrd
+        self.iexp = iexp
+        self.minexp = minexp
+        self.xmin = float_to_float(xmin)
+        self._str_xmin = float_to_str(xmin)
+        self.maxexp = maxexp
+        self.xmax = float_to_float(xmax)
+        self._str_xmax = float_to_str(xmax)
+        self.irnd = irnd
+
+        self.title = title
+        # Commonly used parameters
+        self.epsilon = self.eps
+        self.tiny = self.xmin
+        self.huge = self.xmax
+
+        import math
+        self.precision = int(-math.log10(float_to_float(self.eps)))
+        ten = two + two + two + two + two
+        resolution = ten ** (-self.precision)
+        self.resolution = float_to_float(resolution)
+        self._str_resolution = float_to_str(resolution)
+
+    def __str__(self):
+        fmt = (
+           'Machine parameters for %(title)s\n'
+           '---------------------------------------------------------------------\n'
+           'ibeta=%(ibeta)s it=%(it)s iexp=%(iexp)s ngrd=%(ngrd)s irnd=%(irnd)s\n'
+           'machep=%(machep)s     eps=%(_str_eps)s (beta**machep == epsilon)\n'
+           'negep =%(negep)s  epsneg=%(_str_epsneg)s (beta**epsneg)\n'
+           'minexp=%(minexp)s   xmin=%(_str_xmin)s (beta**minexp == tiny)\n'
+           'maxexp=%(maxexp)s    xmax=%(_str_xmax)s ((1-epsneg)*beta**maxexp == huge)\n'
+           '---------------------------------------------------------------------\n'
+           )
+        return fmt % self.__dict__
+
+
+if __name__ == '__main__':
+    print(MachAr())

numpy-1.10.0.post2/numpy/core/memmap.py

@@ -0,0 +1,311 @@
+from __future__ import division, absolute_import, print_function
+
+import numpy as np
+from .numeric import uint8, ndarray, dtype
+from numpy.compat import long, basestring
+
+__all__ = ['memmap']
+
+dtypedescr = dtype
+valid_filemodes = ["r", "c", "r+", "w+"]
+writeable_filemodes = ["r+", "w+"]
+
+mode_equivalents = {
+    "readonly":"r",
+    "copyonwrite":"c",
+    "readwrite":"r+",
+    "write":"w+"
+    }
+
+class memmap(ndarray):
+    """Create a memory-map to an array stored in a *binary* file on disk.
+
+    Memory-mapped files are used for accessing small segments of large files
+    on disk, without reading the entire file into memory.  Numpy's
+    memmap's are array-like objects.  This differs from Python's ``mmap``
+    module, which uses file-like objects.
+
+    This subclass of ndarray has some unpleasant interactions with
+    some operations, because it doesn't quite fit properly as a subclass.
+    An alternative to using this subclass is to create the ``mmap``
+    object yourself, then create an ndarray with ndarray.__new__ directly,
+    passing the object created in its 'buffer=' parameter.
+
+    This class may at some point be turned into a factory function
+    which returns a view into an mmap buffer.
+
+    Delete the memmap instance to close.
+
+
+    Parameters
+    ----------
+    filename : str or file-like object
+        The file name or file object to be used as the array data buffer.
+    dtype : data-type, optional
+        The data-type used to interpret the file contents.
+        Default is `uint8`.
+    mode : {'r+', 'r', 'w+', 'c'}, optional
+        The file is opened in this mode:
+
+        +------+-------------------------------------------------------------+
+        | 'r'  | Open existing file for reading only.                        |
+        +------+-------------------------------------------------------------+
+        | 'r+' | Open existing file for reading and writing.                 |
+        +------+-------------------------------------------------------------+
+        | 'w+' | Create or overwrite existing file for reading and writing.  |
+        +------+-------------------------------------------------------------+
+        | 'c'  | Copy-on-write: assignments affect data in memory, but       |
+        |      | changes are not saved to disk.  The file on disk is         |
+        |      | read-only.                                                  |
+        +------+-------------------------------------------------------------+
+
+        Default is 'r+'.
+    offset : int, optional
+        In the file, array data starts at this offset. Since `offset` is
+        measured in bytes, it should normally be a multiple of the byte-size
+        of `dtype`. When ``mode != 'r'``, even positive offsets beyond end of
+        file are valid; The file will be extended to accommodate the
+        additional data. By default, ``memmap`` will start at the beginning of
+        the file, even if ``filename`` is a file pointer ``fp`` and
+        ``fp.tell() != 0``.
+    shape : tuple, optional
+        The desired shape of the array. If ``mode == 'r'`` and the number
+        of remaining bytes after `offset` is not a multiple of the byte-size
+        of `dtype`, you must specify `shape`. By default, the returned array
+        will be 1-D with the number of elements determined by file size
+        and data-type.
+    order : {'C', 'F'}, optional
+        Specify the order of the ndarray memory layout:
+        :term:`row-major`, C-style or :term:`column-major`,
+        Fortran-style.  This only has an effect if the shape is
+        greater than 1-D.  The default order is 'C'.
+
+    Attributes
+    ----------
+    filename : str
+        Path to the mapped file.
+    offset : int
+        Offset position in the file.
+    mode : str
+        File mode.
+
+    Methods
+    -------
+    flush
+        Flush any changes in memory to file on disk.
+        When you delete a memmap object, flush is called first to write
+        changes to disk before removing the object.
+
+
+    Notes
+    -----
+    The memmap object can be used anywhere an ndarray is accepted.
+    Given a memmap ``fp``, ``isinstance(fp, numpy.ndarray)`` returns
+    ``True``.
+
+    Memory-mapped arrays use the Python memory-map object which
+    (prior to Python 2.5) does not allow files to be larger than a
+    certain size depending on the platform. This size is always < 2GB
+    even on 64-bit systems.
+
+    When a memmap causes a file to be created or extended beyond its
+    current size in the filesystem, the contents of the new part are
+    unspecified. On systems with POSIX filesystem semantics, the extended
+    part will be filled with zero bytes.
+
+    Examples
+    --------
+    >>> data = np.arange(12, dtype='float32')
+    >>> data.resize((3,4))
+
+    This example uses a temporary file so that doctest doesn't write
+    files to your directory. You would use a 'normal' filename.
+
+    >>> from tempfile import mkdtemp
+    >>> import os.path as path
+    >>> filename = path.join(mkdtemp(), 'newfile.dat')
+
+    Create a memmap with dtype and shape that matches our data:
+
+    >>> fp = np.memmap(filename, dtype='float32', mode='w+', shape=(3,4))
+    >>> fp
+    memmap([[ 0.,  0.,  0.,  0.],
+            [ 0.,  0.,  0.,  0.],
+            [ 0.,  0.,  0.,  0.]], dtype=float32)
+
+    Write data to memmap array:
+
+    >>> fp[:] = data[:]
+    >>> fp
+    memmap([[  0.,   1.,   2.,   3.],
+            [  4.,   5.,   6.,   7.],
+            [  8.,   9.,  10.,  11.]], dtype=float32)
+
+    >>> fp.filename == path.abspath(filename)
+    True
+
+    Deletion flushes memory changes to disk before removing the object:
+
+    >>> del fp
+
+    Load the memmap and verify data was stored:
+
+    >>> newfp = np.memmap(filename, dtype='float32', mode='r', shape=(3,4))
+    >>> newfp
+    memmap([[  0.,   1.,   2.,   3.],
+            [  4.,   5.,   6.,   7.],
+            [  8.,   9.,  10.,  11.]], dtype=float32)
+
+    Read-only memmap:
+
+    >>> fpr = np.memmap(filename, dtype='float32', mode='r', shape=(3,4))
+    >>> fpr.flags.writeable
+    False
+
+    Copy-on-write memmap:
+
+    >>> fpc = np.memmap(filename, dtype='float32', mode='c', shape=(3,4))
+    >>> fpc.flags.writeable
+    True
+
+    It's possible to assign to copy-on-write array, but values are only
+    written into the memory copy of the array, and not written to disk:
+
+    >>> fpc
+    memmap([[  0.,   1.,   2.,   3.],
+            [  4.,   5.,   6.,   7.],
+            [  8.,   9.,  10.,  11.]], dtype=float32)
+    >>> fpc[0,:] = 0
+    >>> fpc
+    memmap([[  0.,   0.,   0.,   0.],
+            [  4.,   5.,   6.,   7.],
+            [  8.,   9.,  10.,  11.]], dtype=float32)
+
+    File on disk is unchanged:
+
+    >>> fpr
+    memmap([[  0.,   1.,   2.,   3.],
+            [  4.,   5.,   6.,   7.],
+            [  8.,   9.,  10.,  11.]], dtype=float32)
+
+    Offset into a memmap:
+
+    >>> fpo = np.memmap(filename, dtype='float32', mode='r', offset=16)
+    >>> fpo
+    memmap([  4.,   5.,   6.,   7.,   8.,   9.,  10.,  11.], dtype=float32)
+
+    """
+
+    __array_priority__ = -100.0
+
+    def __new__(subtype, filename, dtype=uint8, mode='r+', offset=0,
+                shape=None, order='C'):
+        # Import here to minimize 'import numpy' overhead
+        import mmap
+        import os.path
+        try:
+            mode = mode_equivalents[mode]
+        except KeyError:
+            if mode not in valid_filemodes:
+                raise ValueError("mode must be one of %s" %
+                                 (valid_filemodes + list(mode_equivalents.keys())))
+
+        if hasattr(filename, 'read'):
+            fid = filename
+            own_file = False
+        else:
+            fid = open(filename, (mode == 'c' and 'r' or mode)+'b')
+            own_file = True
+
+        if (mode == 'w+') and shape is None:
+            raise ValueError("shape must be given")
+
+        fid.seek(0, 2)
+        flen = fid.tell()
+        descr = dtypedescr(dtype)
+        _dbytes = descr.itemsize
+
+        if shape is None:
+            bytes = flen - offset
+            if (bytes % _dbytes):
+                fid.close()
+                raise ValueError("Size of available data is not a "
+                        "multiple of the data-type size.")
+            size = bytes // _dbytes
+            shape = (size,)
+        else:
+            if not isinstance(shape, tuple):
+                shape = (shape,)
+            size = 1
+            for k in shape:
+                size *= k
+
+        bytes = long(offset + size*_dbytes)
+
+        if mode == 'w+' or (mode == 'r+' and flen < bytes):
+            fid.seek(bytes - 1, 0)
+            fid.write(np.compat.asbytes('\0'))
+            fid.flush()
+
+        if mode == 'c':
+            acc = mmap.ACCESS_COPY
+        elif mode == 'r':
+            acc = mmap.ACCESS_READ
+        else:
+            acc = mmap.ACCESS_WRITE
+
+        start = offset - offset % mmap.ALLOCATIONGRANULARITY
+        bytes -= start
+        offset -= start
+        mm = mmap.mmap(fid.fileno(), bytes, access=acc, offset=start)
+
+        self = ndarray.__new__(subtype, shape, dtype=descr, buffer=mm,
+            offset=offset, order=order)
+        self._mmap = mm
+        self.offset = offset
+        self.mode = mode
+
+        if isinstance(filename, basestring):
+            self.filename = os.path.abspath(filename)
+        # py3 returns int for TemporaryFile().name
+        elif (hasattr(filename, "name") and
+              isinstance(filename.name, basestring)):
+            self.filename = os.path.abspath(filename.name)
+        # same as memmap copies (e.g. memmap + 1)
+        else:
+            self.filename = None
+
+        if own_file:
+            fid.close()
+
+        return self
+
+    def __array_finalize__(self, obj):
+        if hasattr(obj, '_mmap') and np.may_share_memory(self, obj):
+            self._mmap = obj._mmap
+            self.filename = obj.filename
+            self.offset = obj.offset
+            self.mode = obj.mode
+        else:
+            self._mmap = None
+            self.filename = None
+            self.offset = None
+            self.mode = None
+
+    def flush(self):
+        """
+        Write any changes in the array to the file on disk.
+
+        For further information, see `memmap`.
+
+        Parameters
+        ----------
+        None
+
+        See Also
+        --------
+        memmap
+
+        """
+        if self.base is not None and hasattr(self.base, 'flush'):
+            self.base.flush()