Dask数组到zarr，形状未知

Question

我正在尝试将dask数组存储在zarr文件中。

当dask数组具有定义的形状时，我成功地做到了这一点。

import dask
import dask.array as da
import numpy as np
from tempfile import TemporaryDirectory
import zarr


np_array = np.random.randint(1, 10, size=1000)
array = da.from_array(np_array)

with TemporaryDirectory() as tmpdir:
    delayed = da.to_zarr(array, url=tmpdir,
                         compute=False, component='/data')
    dask.compute(delayed)

     z_object = zarr.open_group(tmpdir, mode='r')

     assert np.all(np_array == z_object.data[:])

但是，如果我对dask数组执行了任何操作，形状就会丢失，并且zarr会抱怨形状中的Nans。

# this will fail

np_array = np.random.randint(1, 10, size=1000)
array = da.from_array(np_array)

array = array[array > 5]

with TemporaryDirectory() as tmpdir:
    delayed = da.to_zarr(array, url=tmpdir,
                         compute=False, component='/data')
    dask.compute(delayed)

    z_object = zarr.open_group(tmpdir, mode='r')

    assert np.all(np_array[np_array > 5] == z_object.data[:])

这是引发的错误：

Traceback (most recent call last):
  File "/home/peio/devel/variation/variation6/variation6/tests/test_zarr.py", line 38, in <module>
    without_shape()
  File "/home/peio/devel/variation/variation6/variation6/tests/test_zarr.py", line 29, in without_shape
    compute=False, component='/data')
  File "/home/peio/devel/variation/pyenv3/lib/python3.7/site-packages/dask/array/core.py", line 2808, in to_zarr
    **kwargs
  File "/home/peio/devel/variation/pyenv3/lib/python3.7/site-packages/zarr/creation.py", line 120, in create
    chunk_store=chunk_store, filters=filters, object_codec=object_codec)
  File "/home/peio/devel/variation/pyenv3/lib/python3.7/site-packages/zarr/storage.py", line 323, in init_array
    object_codec=object_codec)
  File "/home/peio/devel/variation/pyenv3/lib/python3.7/site-packages/zarr/storage.py", line 343, in _init_array_metadata
    shape = normalize_shape(shape) + dtype.shape
  File "/home/peio/devel/variation/pyenv3/lib/python3.7/site-packages/zarr/util.py", line 58, in normalize_shape
    shape = tuple(int(s) for s in shape)
  File "/home/peio/devel/variation/pyenv3/lib/python3.7/site-packages/zarr/util.py", line 58, in <genexpr>
    shape = tuple(int(s) for s in shape)
ValueError: cannot convert float NaN to integer

有没有办法将不知道形状的dask数组存储到zarr文件中？

提前感谢！

Answer 1

Zarr希望块的形状是统一的，并且事先就知道了。目前，Dask通过将数组重新分块为均匀数组来促进这一点。然而，array[array > 5]创建了一个具有未知块形状的Dask数组。因此，由于不存在所需的信息，因此无法预先将其重新分块为统一的。也就是说，我们可以使用explain this better。

可以通过使用返回已知块形状的Dask操作来解决此问题(如David所建议的)。或者，可以在存储之前确定块形状(at the cost of computing)。我们也可以讨论extending Zarr to handle this case，但这是一个长期的解决方案。