Ome ngff pattonw #361
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Ome ngff pattonw #361
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Thanks for this test. I found a couple problems:
1) `funlib.persistence` uses `voxel_size` instead of `resolution` by
default. (fixed)
2) The `funlib.persistence` `open_ome_ds` function had a bug in it
resulting in an "Attribute does not exist" error (fixed)
3) The metadata provided in the test is apparently invalid. `iohub`
throws this error: "WARNING root:ngff.py:291 Zarr group at does not have
valid metadata for <class 'iohub.ngff.Position'>". ( not yet fixed )
Probably not worth doing for the test, but this can be configured in
multiple ways (using python function `set_default_metadata_format` from
`funlib.persistence.arrays.metadata`, or using config files. One of :
```
LOCAL_PATHS = [Path("pyproject.toml"), Path("funlib_persistence.toml")]
USER_PATHS = [
Path.home() / ".config" / "funlib_persistence" / "funlib_persistence.toml"
]
GLOBAL_PATHS = [Path("/etc/funlib_persistence/funlib_persistence.toml")]
```
mzouink
commented
Jan 20, 2025
|
@pattonw can you please check the tests.py file so we can merge |
|
Yes, I don't remember adding those tests. I'm not sure where they came from. I'll check it out and see if we need them |
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@pattonw i added some tests
Still getting error resolution is not correct, expected (1, 2, 4), got (1, 1, 1)