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arrayterator.py
""" A buffered iterator for big arrays. This module solves the problem of iterating over a big file-based array without having to read it into memory. The `Arrayterator` class wraps an array object, and when iterated it will return sub-arrays with at most a user-specified number of elements. """ from operator import mul from functools import reduce __all__ = ['Arrayterator'] class Arrayterator: """ Buffered iterator for big arrays. `Arrayterator` creates a buffered iterator for reading big arrays in small contiguous blocks. The class is useful for objects stored in the file system. It allows iteration over the object *without* reading everything in memory; instead, small blocks are read and iterated over. `Arrayterator` can be used with any object that supports multidimensional slices. This includes NumPy arrays, but also variables from Scientific.IO.NetCDF or pynetcdf for example. Parameters ---------- var : array_like The object to iterate over. buf_size : int, optional The buffer size. If `buf_size` is supplied, the maximum amount of data that will be read into memory is `buf_size` elements. Default is None, which will read as many element as possible into memory. Attributes ---------- var buf_size start stop step shape flat See Also -------- ndenumerate : Multidimensional array iterator. flatiter : Flat array iterator. memmap : Create a memory-map to an array stored in a binary file on disk. Notes ----- The algorithm works by first finding a "running dimension", along which the blocks will be extracted. Given an array of dimensions ``(d1, d2, ..., dn)``, e.g. if `buf_size` is smaller than ``d1``, the first dimension will be used. If, on the other hand, ``d1 < buf_size < d1*d2`` the second dimension will be used, and so on. Blocks are extracted along this dimension, and when the last block is returned the process continues from the next dimension, until all elements have been read. Examples -------- >>> a = np.arange(3 * 4 * 5 * 6).reshape(3, 4, 5, 6) >>> a_itor = np.lib.Arrayterator(a, 2) >>> a_itor.shape (3, 4, 5, 6) Now we can iterate over ``a_itor``, and it will return arrays of size two. Since `buf_size` was smaller than any dimension, the first dimension will be iterated over first: >>> for subarr in a_itor: ... if not subarr.all(): ... print(subarr, subarr.shape) # doctest: +SKIP >>> # [[[[0 1]]]] (1, 1, 1, 2) """ def __init__(self, var, buf_size=None): self.var = var self.buf_size = buf_size self.start = [0 for dim in var.shape] self.stop = [dim for dim in var.shape] self.step = [1 for dim in var.shape] def __getattr__(self, attr): return getattr(self.var, attr) def __getitem__(self, index): """ Return a new arrayterator. """ # Fix index, handling ellipsis and incomplete slices. if not isinstance(index, tuple): index = (index,) fixed = [] length, dims = len(index), self.ndim for slice_ in index: if slice_ is Ellipsis: fixed.extend([slice(None)] * (dims-length+1)) length = len(fixed) elif isinstance(slice_, int): fixed.append(slice(slice_, slice_+1, 1)) else: fixed.append(slice_) index = tuple(fixed) if len(index) < dims: index += (slice(None),) * (dims-len(index)) # Return a new arrayterator object. out = self.__class__(self.var, self.buf_size) for i, (start, stop, step, slice_) in enumerate( zip(self.start, self.stop, self.step, index)): out.start[i] = start + (slice_.start or 0) out.step[i] = step * (slice_.step or 1) out.stop[i] = start + (slice_.stop or stop-start) out.stop[i] = min(stop, out.stop[i]) return out def __array__(self): """ Return corresponding data. """ slice_ = tuple(slice(*t) for t in zip( self.start, self.stop, self.step)) return self.var[slice_] @property def flat(self): """ A 1-D flat iterator for Arrayterator objects. This iterator returns elements of the array to be iterated over in `Arrayterator` one by one. It is similar to `flatiter`. See Also -------- Arrayterator flatiter Examples -------- >>> a = np.arange(3 * 4 * 5 * 6).reshape(3, 4, 5, 6) >>> a_itor = np.lib.Arrayterator(a, 2) >>> for subarr in a_itor.flat: ... if not subarr: ... print(subarr, type(subarr)) ... 0 <class 'numpy.int64'> """ for block in self: yield from block.flat @property def shape(self): """ The shape of the array to be iterated over. For an example, see `Arrayterator`. """ return tuple(((stop-start-1)//step+1) for start, stop, step in zip(self.start, self.stop, self.step)) def __iter__(self): # Skip arrays with degenerate dimensions if [dim for dim in self.shape if dim <= 0]: return start = self.start[:] stop = self.stop[:] step = self.step[:] ndims = self.var.ndim while True: count = self.buf_size or reduce(mul, self.shape) # iterate over each dimension, looking for the # running dimension (ie, the dimension along which # the blocks will be built from) rundim = 0 for i in range(ndims-1, -1, -1): # if count is zero we ran out of elements to read # along higher dimensions, so we read only a single position if count == 0: stop[i] = start[i]+1 elif count <= self.shape[i]: # limit along this dimension stop[i] = start[i] + count*step[i] rundim = i else: # read everything along this dimension stop[i] = self.stop[i] stop[i] = min(self.stop[i], stop[i]) count = count//self.shape[i] # yield a block slice_ = tuple(slice(*t) for t in zip(start, stop, step)) yield self.var[slice_] # Update start position, taking care of overflow to # other dimensions start[rundim] = stop[rundim] # start where we stopped for i in range(ndims-1, 0, -1): if start[i] >= self.stop[i]: start[i] = self.start[i] start[i-1] += self.step[i-1] if start[0] >= self.stop[0]: return
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