Source code for dask_image.imread

# -*- coding: utf-8 -*-

__author__ = """John Kirkham"""
__email__ = ""

import itertools
import numbers
import warnings

import dask
import dask.array
import dask.delayed
import numpy
import pims

from . import _utils

[docs]def imread(fname, nframes=1, *, arraytype="numpy"): """ Read image data into a Dask Array. Provides a simple, fast mechanism to ingest image data into a Dask Array. Parameters ---------- fname : str A glob like string that may match one or multiple filenames. nframes : int, optional Number of the frames to include in each chunk (default: 1). arraytype : str, optional Array type for dask chunks. Available options: "numpy", "cupy". Returns ------- array : dask.array.Array A Dask Array representing the contents of all image files. """ if not isinstance(nframes, numbers.Integral): raise ValueError("`nframes` must be an integer.") if (nframes != -1) and not (nframes > 0): raise ValueError("`nframes` must be greater than zero.") if arraytype == "numpy": arrayfunc = numpy.asanyarray elif arraytype == "cupy": # pragma: no cover import cupy arrayfunc = cupy.asanyarray with as imgs: shape = (len(imgs),) + imgs.frame_shape dtype = numpy.dtype(imgs.pixel_type) if nframes == -1: nframes = shape[0] if nframes > shape[0]: warnings.warn( "`nframes` larger than number of frames in file." " Will truncate to number of frames in file.", RuntimeWarning ) elif shape[0] % nframes != 0: warnings.warn( "`nframes` does not nicely divide number of frames in file." " Last chunk will contain the remainder.", RuntimeWarning ) lower_iter, upper_iter = itertools.tee(itertools.chain( range(0, shape[0], nframes), [shape[0]] )) next(upper_iter) a = [] for i, j in zip(lower_iter, upper_iter): a.append(dask.array.from_delayed( dask.delayed(_utils._read_frame)(fname, slice(i, j), arrayfunc=arrayfunc), (j - i,) + shape[1:], dtype, meta=arrayfunc([]) )) a = dask.array.concatenate(a) return a