from math import ceil from multiprocessing import cpu_count import dask.array as da __all__ = ['process_chunks'] def _get_chunks(shape, ncpu): """ Split the array into equal sized chunks based on the number of available processors. The last chunk in each dimension absorbs the remainder array elements if the number of cpus does not divide evenly into the number of array elements. >>> _get_chunks((4, 4), 4) ((2, 2), (2, 2)) >>> _get_chunks((4, 4), 2) ((2, 2), (4,)) >>> _get_chunks((5, 5), 2) ((2, 3), (5,)) >>> _get_chunks((2, 4), 2) ((1, 1), (4,)) """ chunks = [] nchunks_per_dim = int(ceil(ncpu ** (1./len(shape)))) used_chunks = 1 for i in shape: if used_chunks < ncpu: regular_chunk = i // nchunks_per_dim remainder_chunk = regular_chunk + (i % nchunks_per_dim) if regular_chunk == 0: chunk_lens = (remainder_chunk,) else: chunk_lens = ((regular_chunk,) * (nchunks_per_dim - 1) + (remainder_chunk,)) else: chunk_lens = (i,) chunks.append(chunk_lens) used_chunks *= nchunks_per_dim return tuple(chunks) def process_chunks(function, array, chunks=None, depth=0, mode=None, extra_arguments=(), extra_keywords={}): """Map a function in parallel across an array. Split an array into possibly overlapping chunks of a given depth and boundary type, call the given function in parallel on the chunks, combine the chunks and return the resulting array. Parameters ---------- function : function Function to be mapped which takes an array as an argument. array : numpy array array which the function will be applied to. chunks : int, tuple, or tuple of tuples One tuple of length array.ndim or a list of tuples of length ndim. Where each subtuple adds to the size of the array in the corresponding dimension. If None, the array is broken up into chunks based on the number of available cpus. depth : int integer equal to the depth of the internal external padding mode : 'reflect', 'periodic', 'wrap', 'nearest' type of external boundary padding extra_arguments : tuple Tuple of arguments to be passed to the function. extra_keywords : dictionary Dictionary of keyword arguments to be passed to the function. Notes ----- Be careful choosing the depth so that it is never larger than the length of a chunk. """ if chunks is None: shape = array.shape ncpu = cpu_count() chunks = _get_chunks(shape, ncpu) if mode == 'wrap': mode = 'periodic' def wrapped_func(arr): return function(arr, *extra_arguments, **extra_keywords) darr = da.from_array(array, chunks=chunks) return darr.map_overlap(wrapped_func, depth, boundary=mode).compute()