from __future__ import division, absolute_import, print_function # missing Numarray defined names (in from numarray import *) __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 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 else: import 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 = list(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 = int(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 # this function is referenced in the code above but not defined. adding # it back. - phensley def _resizebuf(buf,newsize): "Return a copy of BUF of size NEWSIZE." newbuf = np.newbuffer(newsize) if newsize > len(buf): newbuf[:len(buf)]=buf else: newbuf[:]=buf[:len(newbuf)] return newbuf 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("class: ", nm, file=output) print("shape: ", obj.shape, file=output) strides = obj.strides print("strides: ", strides, file=output) if not numpy: print("byteoffset: 0", file=output) if len(strides) > 0: bs = obj.strides[0] else: bs = obj.itemsize print("bytestride: ", bs, file=output) print("itemsize: ", obj.itemsize, file=output) print("aligned: ", bp(obj.flags.aligned), file=output) print("contiguous: ", bp(obj.flags.contiguous), file=output) if numpy: print("fortran: ", obj.flags.fortran, file=output) if not numpy: print("buffer: ", repr(obj.data), file=output) if not numpy: extra = " (DEBUG ONLY)" tic = "'" else: extra = "" tic = "" print("data pointer: %s%s" % (hex(obj.ctypes._as_parameter_.value), extra), file=output) print("byteorder: ", end=' ', file=output) endian = obj.dtype.byteorder if endian in ['|','=']: print("%s%s%s" % (tic, sys.byteorder, tic), file=output) byteswap = False elif endian == '>': print("%sbig%s" % (tic, tic), file=output) byteswap = sys.byteorder != "big" else: print("%slittle%s" % (tic, tic), file=output) byteswap = sys.byteorder != "little" print("byteswap: ", bp(byteswap), file=output) if not numpy: print("type: ", typefrom(obj).name, file=output) else: print("type: %s" % obj.dtype, file=output) #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 = list(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 = list(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)