Closed
Description
Zarr version
v2.13.3
Numcodecs version
v0.10.2
Python Version
3.10.8
Operating System
tested on Linux, Mac
Installation
poetry
Description
I was trying
6B94
to upgrade zarr-python in our webKnossos libs and noticed failing tests. The tests essentially write some data, reopen the array, read the data back, and compare before/after.
We use F-order to write our data. I tried to replace F with C order and the tests succeeded. Interestingly, the issue does not occur when writing with compression (tested with Blosc). I didn't check whether the writing or reading part is the cause for this problem.
Steps to reproduce
from pathlib import Path
from shutil import rmtree
import numpy as np
import zarr
def get_multichanneled_data(dtype: type) -> np.ndarray:
data: np.ndarray = np.zeros((3, 250, 200, 10), dtype=dtype)
for h in range(10):
for i in range(250):
for j in range(200):
data[0, i, j, h] = i * 256
data[1, i, j, h] = j * 256
data[2, i, j, h] = 100 * 256
return data
def main():
ds_path = Path("testoutput") / "test_zarr"
rmtree(ds_path, ignore_errors=True)
data = get_multichanneled_data(np.uint16)
ds = zarr.create(
shape=data.shape,
chunks=(3, 32, 32, 32),
dtype=data.dtype,
compressor=(None),
store=zarr.storage.FSStore(url=str(ds_path), mode="a"),
order="F",
)
ds[:, :, :, :] = data
ds_reopened = zarr.open_array(
store=zarr.storage.FSStore(url=str(ds_path), mode="r")
)
written_data = ds_reopened[:, :, :, :]
assert data.shape == written_data.shape
assert np.array_equal(data, written_data)
if __name__ == "__main__":
main()Additional output
No response