Completes with error

[chourroutm]

(upsample-zarr) linux@DESKTOP-MSM16:~/data_mask/upsample-zarr$ uv run python upsample_zarr.py --upsample-factor 2 "/home/linux/data_mask/132.36um_mask-brain_tmp.ome.zarr/0" "/home/linux/sheep_head_mask/66.18um_mask-brain_tmp2.ome.zarr/0"
👋 Hello from upsample-zarr!

Upsampling zarr at /home/linux/sheep_head_mask/132.36um_mask-brain_tmp.ome.zarr/0
Saving to /home/linux/sheep_head_mask/66.18um_mask-brain_tmp2.ome.zarr/0
Upsampling by 2

Loading input Zarr...
shape: (1132, 1132, 1687)
🎉 Loaded

Setting up output Zarr store...
shape: (2264, 2264, 3374)
chunks: (256, 256, 256)
dtype: int16
fill value: 0
compressor: Blosc(cname='lz4', clevel=5, shuffle=SHUFFLE, blocksize=0)
🎉 Set up Zarr Store

Setting up upsampling jobs
🎉 Set up 175 upsampling jobs

Executing jobs...
[Parallel(n_jobs=-1)]: Using backend LokyBackend with 32 concurrent workers.
[Parallel(n_jobs=-1)]: Done 8 tasks | elapsed: 4.2s
[Parallel(n_jobs=-1)]: Done 21 tasks | elapsed: 6.1s
[Parallel(n_jobs=-1)]: Done 34 tasks | elapsed: 6.3s
[Parallel(n_jobs=-1)]: Done 49 tasks | elapsed: 8.5s
[Parallel(n_jobs=-1)]: Done 64 tasks | elapsed: 9.7s
[Parallel(n_jobs=-1)]: Done 81 tasks | elapsed: 11.6s
[Parallel(n_jobs=-1)]: Done 98 tasks | elapsed: 12.6s
[Parallel(n_jobs=-1)]: Done 130 out of 175 | elapsed: 15.0s remaining: 5.2s
[Parallel(n_jobs=-1)]: Done 148 out of 175 | elapsed: 15.6s remaining: 2.9s
[Parallel(n_jobs=-1)]: Done 166 out of 175 | elapsed: 16.1s remaining: 0.9s
[Parallel(n_jobs=-1)]: Done 175 out of 175 | elapsed: 16.1s finished
🎉 Finished executing jobs

Congratulations, your array has been upsampled.
We hope you enjoyed using upsample-zarr
Please consider leavning us a 5⭐️ review!
Exception ignored in: <function ResourceTracker.del at 0x7f3200002520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7ffb85512520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f346e506520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f0a9c80e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fe5e1e0a520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7feb81f12520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f01ecd0e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f60e2d06520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
Exception ignored in: <function ResourceTracker.del at 0x7ff7f5512520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
ChildProcessError: [Errno 10] No child processes
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fde6d30e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fa6d5706520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f0e1f712520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fd6c7e0e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7ff894602520>
Exception ignored in: <function ResourceTracker.del at 0x7f914d802520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
Traceback (most recent call last):
Exception ignored in: <function ResourceTracker.del at 0x7f0182e02520>
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f0bac10e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f409360e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fb2f8a02520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
Exception ignored in: <function ResourceTracker.del at 0x7f10f6402520>
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f28f4202520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
Exception ignored in: <function ResourceTracker.del at 0x7f0a3250e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
ChildProcessError: [Errno 10] No child processes
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fe3eee0e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f77e320a520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f0e26802520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f5196e02520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7f5bb3512520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
Exception ignored in: <function ResourceTracker.del at 0x7f60fee0a520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fef2d002520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fb190706520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7efdbee0e520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes
Exception ignored in: <function ResourceTracker.del at 0x7fbff3c02520>
Traceback (most recent call last):
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 77, in del
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 86, in _stop
File "/home/linux/.local/share/uv/python/cpython-3.12.10-linux-x86_64-gnu/lib/python3.12/multiprocessing/resource_tracker.py", line 111, in _stop_locked
ChildProcessError: [Errno 10] No child processes

[dstansby]

Thanks for reporting - I'm guessing you got this error on Linux? And am I right in thinking it all worked fine, just there was an error at the end?

[chourroutm]

Yes! But was it supposed to write the .zattrs file at the end?

[dstansby]

I don't think so - this just deals with arrays directly (not OME-Zarr groups), so it wouldn't work with .zattrs files that store non-Zarr user metadata (which includes OME-Zarr metadata).

[chourroutm]

I see!

So I copied the .zattrs that was generated by stack-to-chunk and adapted it (+ .zgroup but as-is), does it seem right?

.zattrs

{
    "multiscales": [
        {
            "axes": [
                {
                    "name": "x",
                    "type": "space",
                    "unit": "micrometer"
                },
                {
                    "name": "y",
                    "type": "space",
                    "unit": "micrometer"
                },
                {
                    "name": "z",
                    "type": "space",
                    "unit": "micrometer"
                }
            ],
            "datasets": [
                {
                    "coordinateTransformations": [
                        {
                            "scale": [
                                16.545
                            ],
                            "type": "scale"
                        },
                        {
                            "translation": [
                                8.2725
                            ],
                            "type": "translation"
                        }
                    ],
                    "path": "0"
                }
            ],
            "metadata": {
                "description": "Downscaled using local mean in 2x2x2 blocks.",
                "kwargs": {
                    "block_size": 2,
                    "func": "np.mean"
                },
                "method": "skimage.measure.block_reduce",
                "version": "0.24.0"
            },
            "name": "my_zarr_group",
            "type": "local mean",
            "version": "0.4"
        }
    ]
}

.zgroup

{
    "zarr_format": 2
}

I'm asking because the tool (neuroscales/ngtools) I'm using to visually inspect it fails to recognize it as Zarr.

[balbasty]

Hiya!

What makes it fail in ngtools is that the scale and translation vectors are of length 1, whereas the number of axes is 3. The OME 0.4 spec says "The length of the scale and translation array MUST be the same as the length of "axes"."

[chourroutm]

Okay, so it's my fault when applying stack-to-chunk:

group = stack_to_chunk.MultiScaleGroup(
    pathlib.Path(".") / "132.36um_mask-brain_tmp.ome.zarr",
    name="my_zarr_group",
    spatial_unit="micrometer",
    voxel_size=(132.36,),
)
print(group.levels)

where it should be:

group = stack_to_chunk.MultiScaleGroup(
    pathlib.Path(".") / "132.36um_mask-brain_tmp.ome.zarr",
    name="my_zarr_group",
    spatial_unit="micrometer",
    voxel_size=(132.36,)*3,
)
print(group.levels)

Should that be enforced? I've opened an issue in HiPCTProject/stack-to-chunk#125

[chourroutm]

So, that part is solved! But I'm keeping the issue open because of the errors in the log.