EVOLUTION-MANAGER

Edit File: functions.py

# missing Numarray defined names (in from numarray import *)
##__all__ = ['ClassicUnpickler', 'Complex32_fromtype',
##           'Complex64_fromtype', 'ComplexArray', 'Error',
##           'MAX_ALIGN', 'MAX_INT_SIZE', 'MAX_LINE_WIDTH',
##           'NDArray', 'NewArray', 'NumArray',
##           'NumError', 'PRECISION', 'Py2NumType',
##           'PyINT_TYPES', 'PyLevel2Type', 'PyNUMERIC_TYPES', 'PyREAL_TYPES',
##           'SUPPRESS_SMALL',
##           'SuitableBuffer', 'USING_BLAS',
##           'UsesOpPriority',
##           'codegenerator', 'generic', 'libnumarray', 'libnumeric',
##           'make_ufuncs', 'memory',
##           'numarrayall', 'numarraycore', 'numinclude', 'safethread',
##           'typecode', 'typecodes', 'typeconv', 'ufunc', 'ufuncFactory',
##           'ieeemask']

__all__ = ['asarray', 'ones', 'zeros', 'array', 'where']
__all__ += ['vdot', 'dot', 'matrixmultiply', 'ravel', 'indices',
            'arange', 'concatenate', 'all', 'allclose', 'alltrue', 'and_',
            'any', 'argmax', 'argmin', 'argsort', 'around', 'array_equal',
            'array_equiv', 'arrayrange', 'array_str', 'array_repr',
            'array2list', 'average', 'choose', 'CLIP', 'RAISE', 'WRAP',
            'clip', 'compress', 'copy', 'copy_reg',
            'diagonal', 'divide_remainder', 'e', 'explicit_type', 'pi',
            'flush_caches', 'fromfile', 'os', 'sys', 'STRICT',
            'SLOPPY', 'WARN', 'EarlyEOFError', 'SizeMismatchError',
            'SizeMismatchWarning', 'FileSeekWarning', 'fromstring',
            'fromfunction', 'fromlist', 'getShape', 'getTypeObject',
            'identity', 'info', 'innerproduct', 'inputarray',
            'isBigEndian', 'kroneckerproduct', 'lexsort', 'math',
            'operator', 'outerproduct', 'put', 'putmask', 'rank',
            'repeat', 'reshape', 'resize', 'round', 'searchsorted',
            'shape', 'size', 'sometrue', 'sort', 'swapaxes', 'take',
            'tcode', 'tname', 'tensormultiply', 'trace', 'transpose',
            'types', 'value', 'cumsum', 'cumproduct', 'nonzero', 'newobj',
            'togglebyteorder'
            ]

import copy
import copy_reg
import types
import os
import sys
import math
import operator

from numpy import dot as matrixmultiply, dot, vdot, ravel, concatenate, all,\
     allclose, any, argsort, array_equal, array_equiv,\
     array_str, array_repr, CLIP, RAISE, WRAP, clip, concatenate, \
     diagonal, e, pi, inner as innerproduct, nonzero, \
     outer as outerproduct, kron as kroneckerproduct, lexsort, putmask, rank, \
     resize, searchsorted, shape, size, sort, swapaxes, trace, transpose
import numpy as np

from numerictypes import typefrom

if sys.version_info[0] >= 3:
    import copyreg as copy_reg

isBigEndian = sys.byteorder != 'little'
value = tcode = 'f'
tname = 'Float32'

#  If dtype is not None, then it is used
#  If type is not None, then it is used
#  If typecode is not None then it is used
#  If use_default is True, then the default
#   data-type is returned if all are None
def type2dtype(typecode, type, dtype, use_default=True):
    if dtype is None:
        if type is None:
            if use_default or typecode is not None:
                dtype = np.dtype(typecode)
        else:
            dtype = np.dtype(type)
    if use_default and dtype is None:
        dtype = np.dtype('int')
    return dtype

def fromfunction(shape, dimensions, type=None, typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, 1)
    return np.fromfunction(shape, dimensions, dtype=dtype)
def ones(shape, type=None, typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, 1)
    return np.ones(shape, dtype)

def zeros(shape, type=None, typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, 1)
    return np.zeros(shape, dtype)

def where(condition, x=None, y=None, out=None):
    if x is None and y is None:
        arr = np.where(condition)
    else:
        arr = np.where(condition, x, y)
    if out is not None:
        out[...] = arr
        return out
    return arr

def indices(shape, type=None):
    return np.indices(shape, type)

def arange(a1, a2=None, stride=1, type=None, shape=None,
           typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, 0)
    return np.arange(a1, a2, stride, dtype)

arrayrange = arange

def alltrue(x, axis=0):
    return np.alltrue(x, axis)

def and_(a, b):
    """Same as a & b
    """
    return a & b

def divide_remainder(a, b):
    a, b = asarray(a), asarray(b)
    return (a/b,a%b)

def around(array, digits=0, output=None):
    ret = np.around(array, digits, output)
    if output is None:
        return ret
    return

def array2list(arr):
    return arr.tolist()

def choose(selector, population, outarr=None, clipmode=RAISE):
    a = np.asarray(selector)
    ret = a.choose(population, out=outarr, mode=clipmode)
    if outarr is None:
        return ret
    return

def compress(condition, a, axis=0):
    return np.compress(condition, a, axis)

# only returns a view
def explicit_type(a):
    x = a.view()
    return x

# stub
def flush_caches():
    pass

class EarlyEOFError(Exception):
    "Raised in fromfile() if EOF unexpectedly occurs."
    pass

class SizeMismatchError(Exception):
    "Raised in fromfile() if file size does not match shape."
    pass

class SizeMismatchWarning(Warning):
    "Issued in fromfile() if file size does not match shape."
    pass

class FileSeekWarning(Warning):
    "Issued in fromfile() if there is unused data and seek() fails"
    pass

STRICT, SLOPPY, WARN = range(3)

_BLOCKSIZE=1024

# taken and adapted directly from numarray
def fromfile(infile, type=None, shape=None, sizing=STRICT,
             typecode=None, dtype=None):
    if isinstance(infile, (str, unicode)):
        infile = open(infile, 'rb')
    dtype = type2dtype(typecode, type, dtype, True)
    if shape is None:
        shape = (-1,)
    if not isinstance(shape, tuple):
        shape = (shape,)

if (list(shape).count(-1)>1):
        raise ValueError("At most one unspecified dimension in shape")

if -1 not in shape:
        if sizing != STRICT:
            raise ValueError("sizing must be STRICT if size complete")
        arr = np.empty(shape, dtype)
        bytesleft=arr.nbytes
        bytesread=0
        while(bytesleft > _BLOCKSIZE):
            data = infile.read(_BLOCKSIZE)
            if len(data) != _BLOCKSIZE:
                raise EarlyEOFError("Unexpected EOF reading data for size complete array")
            arr.data[bytesread:bytesread+_BLOCKSIZE]=data
            bytesread += _BLOCKSIZE
            bytesleft -= _BLOCKSIZE
        if bytesleft > 0:
            data = infile.read(bytesleft)
            if len(data) != bytesleft:
                raise EarlyEOFError("Unexpected EOF reading data for size complete array")
            arr.data[bytesread:bytesread+bytesleft]=data
        return arr

##shape is incompletely specified
    ##read until EOF
    ##implementation 1: naively use memory blocks
    ##problematic because memory allocation can be double what is
    ##necessary (!)

##the most common case, namely reading in data from an unchanging
    ##file whose size may be determined before allocation, should be
    ##quick -- only one allocation will be needed.

recsize = dtype.itemsize * np.product([i for i in shape if i != -1])
    blocksize = max(_BLOCKSIZE/recsize, 1)*recsize

##try to estimate file size
    try:
        curpos=infile.tell()
        infile.seek(0,2)
        endpos=infile.tell()
        infile.seek(curpos)
    except (AttributeError, IOError):
        initsize=blocksize
    else:
        initsize=max(1,(endpos-curpos)/recsize)*recsize

buf = np.newbuffer(initsize)

bytesread=0
    while 1:
        data=infile.read(blocksize)
        if len(data) != blocksize: ##eof
            break
        ##do we have space?
        if len(buf) < bytesread+blocksize:
            buf=_resizebuf(buf,len(buf)+blocksize)
            ## or rather a=resizebuf(a,2*len(a)) ?
        assert len(buf) >= bytesread+blocksize
        buf[bytesread:bytesread+blocksize]=data
        bytesread += blocksize

if len(data) % recsize != 0:
        if sizing == STRICT:
            raise SizeMismatchError("Filesize does not match specified shape")
        if sizing == WARN:
            _warnings.warn("Filesize does not match specified shape",
                           SizeMismatchWarning)
        try:
            infile.seek(-(len(data) % recsize),1)
        except AttributeError:
            _warnings.warn("Could not rewind (no seek support)",
                           FileSeekWarning)
        except IOError:
            _warnings.warn("Could not rewind (IOError in seek)",
                           FileSeekWarning)
    datasize = (len(data)/recsize) * recsize
    if len(buf) != bytesread+datasize:
        buf=_resizebuf(buf,bytesread+datasize)
    buf[bytesread:bytesread+datasize]=data[:datasize]
    ##deduce shape from len(buf)
    shape = list(shape)
    uidx = shape.index(-1)
    shape[uidx]=len(buf) / recsize

a = np.ndarray(shape=shape, dtype=type, buffer=buf)
    if a.dtype.char == '?':
        np.not_equal(a, 0, a)
    return a

def fromstring(datastring, type=None, shape=None, typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, True)
    if shape is None:
        count = -1
    else:
        count = np.product(shape)
    res = np.fromstring(datastring, dtype=dtype, count=count)
    if shape is not None:
        res.shape = shape
    return res

# check_overflow is ignored
def fromlist(seq, type=None, shape=None, check_overflow=0, typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, False)
    return np.array(seq, dtype)

def array(sequence=None, typecode=None, copy=1, savespace=0,
          type=None, shape=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, 0)
    if sequence is None:
        if shape is None:
            return None
        if dtype is None:
            dtype = 'l'
        return np.empty(shape, dtype)
    if isinstance(sequence, file):
        return fromfile(sequence, dtype=dtype, shape=shape)
    if isinstance(sequence, str):
        return fromstring(sequence, dtype=dtype, shape=shape)
    if isinstance(sequence, buffer):
        arr = np.frombuffer(sequence, dtype=dtype)
    else:
        arr = np.array(sequence, dtype, copy=copy)
    if shape is not None:
        arr.shape = shape
    return arr

def asarray(seq, type=None, typecode=None, dtype=None):
    if isinstance(seq, np.ndarray) and type is None and \
           typecode is None and dtype is None:
        return seq
    return array(seq, type=type, typecode=typecode, copy=0, dtype=dtype)

inputarray = asarray

def getTypeObject(sequence, type):
    if type is not None:
        return type
    try:
        return typefrom(np.array(sequence))
    except:
        raise TypeError("Can't determine a reasonable type from sequence")

def getShape(shape, *args):
    try:
        if shape is () and not args:
            return ()
        if len(args) > 0:
            shape = (shape, ) + args
        else:
            shape = tuple(shape)
        dummy = np.array(shape)
        if not issubclass(dummy.dtype.type, np.integer):
            raise TypeError
        if len(dummy) > np.MAXDIMS:
            raise TypeError
    except:
        raise TypeError("Shape must be a sequence of integers")
    return shape

def identity(n, type=None, typecode=None, dtype=None):
    dtype = type2dtype(typecode, type, dtype, True)
    return np.identity(n, dtype)

def info(obj, output=sys.stdout, numpy=0):
    if numpy:
        bp = lambda x: x
    else:
        bp = lambda x: int(x)
    cls = getattr(obj, '__class__', type(obj))
    if numpy:
        nm = getattr(cls, '__name__', cls)
    else:
        nm = cls
    print >> output, "class: ", nm
    print >> output, "shape: ", obj.shape
    strides = obj.strides
    print >> output, "strides: ", strides
    if not numpy:
        print >> output, "byteoffset: 0"
        if len(strides) > 0:
            bs = obj.strides[0]
        else:
            bs = obj.itemsize
        print >> output, "bytestride: ", bs
    print >> output, "itemsize: ", obj.itemsize
    print >> output, "aligned: ", bp(obj.flags.aligned)
    print >> output, "contiguous: ", bp(obj.flags.contiguous)
    if numpy:
        print >> output, "fortran: ", obj.flags.fortran
    if not numpy:
        print >> output, "buffer: ", repr(obj.data)
    if not numpy:
        extra = " (DEBUG ONLY)"
        tic = "'"
    else:
        extra = ""
        tic = ""
    print >> output, "data pointer: %s%s" % (hex(obj.ctypes._as_parameter_.value), extra)
    print >> output, "byteorder: ",
    endian = obj.dtype.byteorder
    if endian in ['|','=']:
        print >> output, "%s%s%s" % (tic, sys.byteorder, tic)
        byteswap = False
    elif endian == '>':
        print >> output, "%sbig%s" % (tic, tic)
        byteswap = sys.byteorder != "big"
    else:
        print >> output, "%slittle%s" % (tic, tic)
        byteswap = sys.byteorder != "little"
    print >> output, "byteswap: ", bp(byteswap)
    if not numpy:
        print >> output, "type: ", typefrom(obj).name
    else:
        print >> output, "type: %s" % obj.dtype

#clipmode is ignored if axis is not 0 and array is not 1d
def put(array, indices, values, axis=0, clipmode=RAISE):
    if not isinstance(array, np.ndarray):
        raise TypeError("put only works on subclass of ndarray")
    work = asarray(array)
    if axis == 0:
        if array.ndim == 1:
            work.put(indices, values, clipmode)
        else:
            work[indices] = values
    elif isinstance(axis, (int, long, np.integer)):
        work = work.swapaxes(0, axis)
        work[indices] = values
        work = work.swapaxes(0, axis)
    else:
        def_axes = range(work.ndim)
        for x in axis:
            def_axes.remove(x)
        axis = list(axis)+def_axes
        work = work.transpose(axis)
        work[indices] = values
        work = work.transpose(axis)

def repeat(array, repeats, axis=0):
    return np.repeat(array, repeats, axis)

def reshape(array, shape, *args):
    if len(args) > 0:
        shape = (shape,) + args
    return np.reshape(array, shape)

import warnings as _warnings
def round(*args, **keys):
    _warnings.warn("round() is deprecated. Switch to around()",
                   DeprecationWarning)
    return around(*args, **keys)

def sometrue(array, axis=0):
    return np.sometrue(array, axis)

#clipmode is ignored if axis is not an integer
def take(array, indices, axis=0, outarr=None, clipmode=RAISE):
    array = np.asarray(array)
    if isinstance(axis, (int, long, np.integer)):
        res = array.take(indices, axis, outarr, clipmode)
        if outarr is None:
            return res
        return
    else:
        def_axes = range(array.ndim)
        for x in axis:
            def_axes.remove(x)
        axis = list(axis) + def_axes
        work = array.transpose(axis)
        res = work[indices]
        if outarr is None:
            return res
        outarr[...] = res
        return

def tensormultiply(a1, a2):
    a1, a2 = np.asarray(a1), np.asarray(a2)
    if (a1.shape[-1] != a2.shape[0]):
        raise ValueError("Unmatched dimensions")
    shape = a1.shape[:-1] + a2.shape[1:]
    return np.reshape(dot(np.reshape(a1, (-1, a1.shape[-1])),
                          np.reshape(a2, (a2.shape[0],-1))),
                      shape)

def cumsum(a1, axis=0, out=None, type=None, dim=0):
    return np.asarray(a1).cumsum(axis,dtype=type,out=out)

def cumproduct(a1, axis=0, out=None, type=None, dim=0):
    return np.asarray(a1).cumprod(axis,dtype=type,out=out)

def argmax(x, axis=-1):
    return np.argmax(x, axis)

def argmin(x, axis=-1):
    return np.argmin(x, axis)

def newobj(self, type):
    if type is None:
        return np.empty_like(self)
    else:
        return np.empty(self.shape, type)

def togglebyteorder(self):
    self.dtype=self.dtype.newbyteorder()

def average(a, axis=0, weights=None, returned=0):
    return np.average(a, axis, weights, returned)