Add source_to_raw function

[K-Meech]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?
Currently, atlas example scripts repeat much of the same processing. This PR aims to abstract the main standardisation steps into a re-useable function: source_to_raw

What does this PR do?

Bundles standardisation steps into a re-useable function - see brainglobe/atlas-forge#10 (comment) for an overview of the various steps agreed for the two main processing steps: source_to_raw and raw_to_ready.

The downsampling step is still marked as todo, as I will implement this in a separate PR. See discussion on the source_to_raw issue.

Feedback on any part of this is very welcome!

References

brainglobe/atlas-forge#13

How has this PR been tested?

Automated tests have been added for all parts of source_to_raw, and I have also tested locally on some example Zebrafinch images and masks.

Is this a breaking change?

No

Does this PR require an update to the documentation?

Docstrings have been added for all. We'll add documentation for the overall pipeline once both source_to_raw and raw_to_ready are merged.

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

[K-Meech]

List of changes to be made, before bring out of draft:

• Add downsampling steps (once Allow downsampling to a target resolution #100 is in)
• Add validation of input csv (now Add input csv validation #96 has been merged)
• Add support for downsampling / re-orienting any mask images provided in the input csv. + updating their paths in the output csv
• Add tests for functionality

[K-Meech]

I think this PR is ready to review now - I've implemented the source_to_raw function + corresponding tests. I imagine much of the logic for creating test data / csvs etc. will be shared between this PR and the raw_to_ready one, so once these are in we may have to do a follow-up PR to refactor common/similar functions into a shared location.