[Bug]: Large crops using a U-Net aren't cropped correctly

[MaxGamill-Sheffield]

Checklist

• Re-run analysis with topostats process --core 1.
• Describe the bug.
• Include the configuration file.
• Copy of the output.
• The exact command that failed. This is what you typed at the command line, including any options.
• TopoStats version, this is reported by topostats --version
• Operating System and Python Version

Describe the bug

When the crop size is large there may be a chance that the squared bbox clips the edge. This is fine as we can then expand in one direction, unless the crop is too large that the expansion is then also beyond the array limits.

Similarly, it seems that PIL loads images with inverted array axes, and as such, if the resized array is not square for whatever reason, it cannot be mapped back into the image.

Copy of the output

e.g using the current square bbox func with:
bbox = (117, 20, 521, 603)
image_shape = (608, 608)

Include the configuration file

N/A

To Reproduce

use square bbox func with:
bbox = (117, 20, 521, 603)
image_shape = (608, 608)

TopoStats Version

2.1.2

Python Version

3.9

Operating System

MacOS M1/M2 (post-2021)

Python Packages

No response