finalize stitching

[nathanin]

This introduces non-rectangular region handling

Codex objects should be instantiated with a "region" number for experiments imaged with more than 1 ROI. Experiments imaged as a single ROI should have "region" number 0:

• https://github.com/KnottLab/codex/blob/6e532998c5d35cb682197369ada358e345b44f17/model/codex.py#L40

A "real_tiles" metadata field is introduced. real_tiles represents to the enclosing rectangle of the given region as an NxM array of strings holding a formatted integer (i.e. '00', '01', etc.) indicating the coded tile ID for that position. real_tiles will contain an 'x' where that (x,y) tile position was not actually scanned, but is needed to fill out the enclosing rectangle area. These missing regions get filled with 0's during processing:

• https://github.com/KnottLab/codex/blob/6e532998c5d35cb682197369ada358e345b44f17/preprocessing/xml_decoder.py#L28

region loading logic is updated to deal with the different folder structure and file naming used in cases:

• single ROI
• multiple ROI, each ROI with multiple tiles
• multiple ROI, with single tiles (called Position, rather than Region)
• https://github.com/KnottLab/codex/blob/6e532998c5d35cb682197369ada358e345b44f17/utilities/utility.py#L33

[nathanin]

@abs51295 please check how the real_tiles situation interacts with the stitching module. I've so far just inserted the usual check here.

• https://github.com/KnottLab/codex/blob/6e532998c5d35cb682197369ada358e345b44f17/preprocessing/stitching.py#L168-L178

Also the stitching loop condition:

• https://github.com/KnottLab/codex/blob/5fb423da21e69cf63dac84dbbee5ba2d9e1108b0/src/main.py#L114