improve read_with_dask docs, ignore OME metadata

brainglobe / brainglobe-utils

Shared general purpose tools for the BrainGlobe project

MIT License

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Description

What is this PR

[x] Bug fix
[ ] Addition of a new feature
[ ] Other

Why is this PR needed?

We currently read certain OME tiff files wrongly in read_with_dask, when the metadata for all tiffs is specified in a single tiff's metadata.
read_with_dask lack return value and parameters in docs
read_with_dask ignores .tiff files (only finds .tif files).

What does this PR do?

Ignores the OME metadata, so we can correctly read OME tiff files with dask. Also improvements to docs and ability to read .tiff files lazily, and better error handling.

References

Closes #79

How has this PR been tested?

Locally by @niksirbi and me

Is this a breaking change?

I don't think so.

Does this PR require an update to the documentation?

Docstrings updated.

Checklist:

[x] The code has been tested locally
[ ] Tests have been added to cover all new functionality (unit & integration)

we would need to make, or download, suitable data to test this on. I tried but only got so far, this will be addressed separately later (ignore-ome-test branch in #99 )- so we can use read_with_dask for more urgent work. I did add a negative test for a new error that is now being raised.

[x] The documentation has been updated to reflect any changes
[x] The code has been formatted with pre-commit

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.73%. Comparing base (0d463f6) to head (f2a5f21). Report is 6 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #98 +/- ## ======================================= Coverage 92.72% 92.73% ======================================= Files 37 37 Lines 1855 1857 +2 ======================================= + Hits 1720 1722 +2 Misses 135 135 ``` | [Flag](https://app.codecov.io/gh/brainglobe/brainglobe-utils/pull/98/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=brainglobe) | Coverage Δ | | |---|---|---| | [numba](https://app.codecov.io/gh/brainglobe/brainglobe-utils/pull/98/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=brainglobe) | `92.67% <100.00%> (+<0.01%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=brainglobe#carryforward-flags-in-the-pull-request-comment) to find out more.

brainglobe / brainglobe-utils