Harmonise napari plugin and CLI entry points

[adamltyson]

Description

This PR makes sure the outputs of the napari plugin and CLI are equal. Previously, as highlighted in #192 by @AdrianAriasAbreu, there were differences when running the same data in the napari plugin and CLI. +

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?
The plugin and CLI should be two ways of achieving the same thing.

What does this PR do?

1. It ensures that the default parameters in the GUI are the same, are are displayed the same as the defaults in the CLI. Previously, some were made negative under the hood. This PR corrects this so everything matches.
2. It downsamples data in the exact same way as brainglobe_utils.image_io.load.load_any() (as used by the CLI).

References

Closes #192 (I think)

How has this PR been tested?

The same data has been registered with the plugin and CLI and results confirmed to be the same. Existing tests pass.

Is this a breaking change?

No

Does this PR require an update to the documentation?

No, but I noticed some errors in the docs, updated in brainglobe/brainglobe.github.io#170

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[adamltyson]

I assume the tests are failing on macOS as those runners have recently been updated to ARM. #191 should fix this.

[IgorTatarnikov]

Is there a sensible minimum for the smoothing parameters? As it stands right now I can't go below -1.0, or -10. Could be worth adding a min=-99.0 or something similar to the appropriate entries of DEFAULT_PARAMETERS.

[adamltyson]

Good catch, thanks. I've set these to -99 which seems about right.

[IgorTatarnikov]

Looks good! Should we merge now or wait for #191?

[adamltyson]

I think merge. This shouldn't (famous last words) affect only one OS.

[adamltyson]

Will hold off releasing until #191 though.