Extract and replace data in overlapping regions between tiles

[IgorTatarnikov]

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Description

What is this PR

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

Why is this PR needed? In order to correct for brightness differences, and interpolate over the stitches in the final fused images it's important to keep track of which tiles overlap and the coordinates of the overlap in both local (relative to the tile itself) and global (relative to the final fused image) coordinates.

What does this PR do?

• brainglobe_stitch/tile.py: Introduced the Overlap class to store and manage information about the overlap between two tiles, including methods to calculate local overlap coordinates and extract/replace overlap data.

• brainglobe_stitch/image_mosaic.py: Updated the ImageMosaic class to include an overlaps attribute and methods to calculate overlaps between tiles. This involved modifying the constructor, load_mesospim_directory, and stitch methods, and adding the calculate_overlaps method.

• tests/test_unit/test_tile.py: Added new tests for the Overlap class, including tests for initialization, local coordinate calculation, overlap data extraction, and data replacement. These tests ensure that the overlap functionality works correctly.

How has this PR been tested?

Tests added to cover the new functionality.

NOTE: To test the functionality locally you must install Fiji and also add BigStitcher to the update sites. This can be done using the GUI see here or via the command line after installing Fiji.

./ImageJ-linux64 --update add-update-sites "BigStitcherUpdate" "https://sites.imagej.net/BigStitcher/" ./ImageJ-linux64 --update update

Replace ImageJ-linux64 with the path to the local ImageJ executable.

Three different datasets are available for testing:

• Tiny (~28 MB): this is mostly used for automated testing and doesn't work for visual inspection. It can be downloaded here.
• Small (~1.8 GB): this dataset is more useful for visual inspection. It can be downloaded here.
• A full size dataset is available (~130 GB): this dataset works best for testing overall performance, especially when reading or writing data. It's available by request.

Is this a breaking change?

No

Does this PR require an update to the documentation?

Yes, will come in subsequent PR.

Checklist:

• [x] The code has been tested locally
• [x] Tests have been added to cover all new functionality (unit & integration)
• [x] The code has been formatted with pre-commit

[codecov[bot]]

Codecov Report

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

Project coverage is 95.54%. Comparing base (ffa996a) to head (6a2a380). Report is 25 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #20 +/- ## ========================================== + Coverage 95.20% 95.54% +0.33% ========================================== Files 6 6 Lines 626 673 +47 ========================================== + Hits 596 643 +47 Misses 30 30 ```

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