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