dask.array.overlap.map_overlap
dask.array.overlap.map_overlap¶
- dask.array.overlap.map_overlap(func, *args, depth=None, boundary=None, trim=True, align_arrays=True, allow_rechunk=True, **kwargs)[source]¶
Map a function over blocks of arrays with some overlap
We share neighboring zones between blocks of the array, map a function, and then trim away the neighboring strips. If depth is larger than any chunk along a particular axis, then the array is rechunked.
Note that this function will attempt to automatically determine the output array type before computing it, please refer to the
meta
keyword argument inmap_blocks
if you expect that the function will not succeed when operating on 0-d arrays.- Parameters
- func: function
The function to apply to each extended block. If multiple arrays are provided, then the function should expect to receive chunks of each array in the same order.
- argsdask arrays
- depth: int, tuple, dict or list, keyword only
The number of elements that each block should share with its neighbors If a tuple or dict then this can be different per axis. If a list then each element of that list must be an int, tuple or dict defining depth for the corresponding array in args. Asymmetric depths may be specified using a dict value of (-/+) tuples. Note that asymmetric depths are currently only supported when
boundary
is ‘none’. The default value is 0.- boundary: str, tuple, dict or list, keyword only
How to handle the boundaries. Values include ‘reflect’, ‘periodic’, ‘nearest’, ‘none’, or any constant value like 0 or np.nan. If a list then each element must be a str, tuple or dict defining the boundary for the corresponding array in args. The default value is ‘reflect’.
- trim: bool, keyword only
Whether or not to trim
depth
elements from each block after calling the map function. Set this to False if your mapping function already does this for you- align_arrays: bool, keyword only
Whether or not to align chunks along equally sized dimensions when multiple arrays are provided. This allows for larger chunks in some arrays to be broken into smaller ones that match chunk sizes in other arrays such that they are compatible for block function mapping. If this is false, then an error will be thrown if arrays do not already have the same number of blocks in each dimension.
- allow_rechunk: bool, keyword only
Allows rechunking, otherwise chunk sizes need to match and core dimensions are to consist only of one chunk.
- **kwargs:
Other keyword arguments valid in
map_blocks
Examples
>>> import numpy as np >>> import dask.array as da
>>> x = np.array([1, 1, 2, 3, 3, 3, 2, 1, 1]) >>> x = da.from_array(x, chunks=5) >>> def derivative(x): ... return x - np.roll(x, 1)
>>> y = x.map_overlap(derivative, depth=1, boundary=0) >>> y.compute() array([ 1, 0, 1, 1, 0, 0, -1, -1, 0])
>>> x = np.arange(16).reshape((4, 4)) >>> d = da.from_array(x, chunks=(2, 2)) >>> d.map_overlap(lambda x: x + x.size, depth=1, boundary='reflect').compute() array([[16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27], [28, 29, 30, 31]])
>>> func = lambda x: x + x.size >>> depth = {0: 1, 1: 1} >>> boundary = {0: 'reflect', 1: 'none'} >>> d.map_overlap(func, depth, boundary).compute() array([[12, 13, 14, 15], [16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27]])
The
da.map_overlap
function can also accept multiple arrays.>>> func = lambda x, y: x + y >>> x = da.arange(8).reshape(2, 4).rechunk((1, 2)) >>> y = da.arange(4).rechunk(2) >>> da.map_overlap(func, x, y, depth=1, boundary='reflect').compute() array([[ 0, 2, 4, 6], [ 4, 6, 8, 10]])
When multiple arrays are given, they do not need to have the same number of dimensions but they must broadcast together. Arrays are aligned block by block (just as in
da.map_blocks
) so the blocks must have a common chunk size. This common chunking is determined automatically as long asalign_arrays
is True.>>> x = da.arange(8, chunks=4) >>> y = da.arange(8, chunks=2) >>> r = da.map_overlap(func, x, y, depth=1, boundary='reflect', align_arrays=True) >>> len(r.to_delayed()) 4
>>> da.map_overlap(func, x, y, depth=1, boundary='reflect', align_arrays=False).compute() Traceback (most recent call last): ... ValueError: Shapes do not align {'.0': {2, 4}}
Note also that this function is equivalent to
map_blocks
by default. A non-zerodepth
must be defined for any overlap to appear in the arrays provided tofunc
.>>> func = lambda x: x.sum() >>> x = da.ones(10, dtype='int') >>> block_args = dict(chunks=(), drop_axis=0) >>> da.map_blocks(func, x, **block_args).compute() 10 >>> da.map_overlap(func, x, **block_args, boundary='reflect').compute() 10 >>> da.map_overlap(func, x, **block_args, depth=1, boundary='reflect').compute() 12
For functions that may not handle 0-d arrays, it’s also possible to specify
meta
with an empty array matching the type of the expected result. In the example below,func
will result in anIndexError
when computingmeta
:>>> x = np.arange(16).reshape((4, 4)) >>> d = da.from_array(x, chunks=(2, 2)) >>> y = d.map_overlap(lambda x: x + x[2], depth=1, boundary='reflect', meta=np.array(())) >>> y dask.array<_trim, shape=(4, 4), dtype=float64, chunksize=(2, 2), chunktype=numpy.ndarray> >>> y.compute() array([[ 4, 6, 8, 10], [ 8, 10, 12, 14], [20, 22, 24, 26], [24, 26, 28, 30]])
Similarly, it’s possible to specify a non-NumPy array to
meta
:>>> import cupy >>> x = cupy.arange(16).reshape((4, 4)) >>> d = da.from_array(x, chunks=(2, 2)) >>> y = d.map_overlap(lambda x: x + x[2], depth=1, boundary='reflect', meta=cupy.array(())) >>> y dask.array<_trim, shape=(4, 4), dtype=float64, chunksize=(2, 2), chunktype=cupy.ndarray> >>> y.compute() array([[ 4, 6, 8, 10], [ 8, 10, 12, 14], [20, 22, 24, 26], [24, 26, 28, 30]])