Image Geometry get_slice returns IG with offset centre

[lauramurgatroyd]

Description

Closes #2217

• Adds get_centre_slice method to ImageData, ImageGeometry, AcquisitionGeometry
• Allows passing vertical='centre' to ImageGeometry.get_slice
• Sets center_x, center_y, center_z appropriately for ImageGeometry returned by get_slice

Example Usage

Contribution Notes

• The content of this Pull Request (the Contribution) is intentionally submitted for inclusion in CIL (the Work) under the terms and conditions of the Apache-2.0 License
• I confirm that the contribution does not violate any intellectual property rights of third parties

Changes

Testing you performed

Please add any demo scripts to https://github.com/TomographicImaging/CIL-Demos/tree/main/misc

Added unit tests for:

• Image Geometry get_slice
• New get_centre_slice methods

Related issues/links

Checklist

• I have performed a self-review of my code
• I have added docstrings in line with the guidance in the developer guide
• I have updated the relevant documentation
• I have implemented unit tests that cover any new or modified functionality
• CHANGELOG.md has been updated with any functionality change
• Request review from all relevant developers

[hrobarts]

Hi Laura, this looks really useful. Just a couple of questions.

[gfardell]

Can we have a meeting about this, maybe we could discuss it in a dev meeting. I remember lots of discussions about axis lengths or 0 vs 1 and what it meant, but I don't remember what we landed on or what the implications were.

[lauramurgatroyd]

@gfardell - this is what we decided on previously - to raise a warning if they set vertical=0

[lauramurgatroyd]

Note this does not mean the shape is 1 in this dimension:

CIL/Wrappers/Python/cil/framework/image_geometry.py

Lines 101 to 107 in 8ad816b

	for i, x in enumerate(shape_default):
	if x == 0 or x==1:
	try:
	labels.remove(labels_default[i])
	except ValueError:
	pass #if not in custom list carry on
	return tuple(labels)

[lauramurgatroyd]

Not clear where index 0 sits

[lauramurgatroyd]

make really clear, single 2D slice in 3D space with offset calculated from where it was in 3D original object

Puts one slice at location where it was requested
offset is height of slice from centre

Add example - if used with vertical this is what you'd get

[lauramurgatroyd]

After discussion with @gfardell and @paskino today, updating ImageGeometry and ImageData significantly.

• ImageData and ImageGeometry should always be 3D, so always have at least size 1 on vertical, horizontal_x, horizontal_y
  • This means number of voxels can't be 0 on any of these axes, and should default to 1.
  • Need check on if all dims > 1 have labels, if not add these in. Prepend dimension if needed.
  • Consider having a 'None' dimension for e.g. channels or true 2D slice