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Check Well exists before trying to load data #296

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merged 2 commits into from
Sep 29, 2023

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Fixes #263.

For sparse Plates with empty Wells, we shouldn't try to load empty Wells.
Here, we check if the Well exists first - and return zeros.

To test, try to open a sparse plate in napari, e.g.

$ napari https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0072B/9512.zarr

Should see no errors in the terminal.
Without this PR you get lots of errors like this...

Traceback (most recent call last):
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/bin/napari", line 8, in <module>
    sys.exit(main())
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/napari/__main__.py", line 551, in main
    _maybe_rerun_with_macos_fixes()
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/napari/__main__.py", line 539, in _maybe_rerun_with_macos_fixes
    result = subprocess.run(cmd, env=env, cwd=cwd)
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/subprocess.py", line 507, in run
    stdout, stderr = process.communicate(input, timeout=timeout)
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/subprocess.py", line 1126, in communicate
    self.wait()
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/subprocess.py", line 1189, in wait
    return self._wait(timeout=timeout)
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/subprocess.py", line 1917, in _wait
    (pid, sts) = self._try_wait(0)
  File "/Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/subprocess.py", line 1875, in _try_wait
    (pid, sts) = os.waitpid(self.pid, wait_flags)
KeyboardInterrupt

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codecov bot commented Aug 18, 2023

Codecov Report

All modified lines are covered by tests ✅

Files Coverage Δ
ome_zarr/reader.py 90.66% <100.00%> (-0.71%) ⬇️

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This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/strange-behavior-of-ome-zarr-created-by-bioformats2raw-from-a-czi-image/85177/4

@will-moore will-moore added this to the 0.8.1 milestone Sep 13, 2023
@will-moore will-moore merged commit 2739e55 into ome:master Sep 29, 2023
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Successfully merging this pull request may close these issues.

Sparse plate, with "missing" Wells shouldn't throw exceptions
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