Automatically shrink reconstruction volume

[hrobarts]

Changes

Code to reduce the reconstruction volume

• Performs a quick binned reconstruction and applies a circular mask (maybe this should be optional)
• If auto=True, tries to automatically find the limits for the reduced reconstruction
• Set a threshold between data and background or use an Otsu filter
• Plots the maximum pixel intensity along each direction, finds pixels above the threshold, identifies large connected components and calculates limits around them
• Can apply a buffer around the automatically calculated limits
• If manual_limits are set these over-ride the automatically calculated limits

vs = VolumeShrinker()
ig_reduced = vs.run(data, auto=True)

ig_reduced = vs.run(data, auto=True, buffer=10)

Use manual limits in specified direction

Don't reduce in specified directions
vs = VolumeShrinker()
ig_reduced = vs.run(data, auto=True, buffer=10, manual_limits={'horizontal_x':None, 'horizontal_y':None})

If logging is enabled, plot a histogram with the threshold and reduced box

Testing you performed

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

Related issues/links

May close #1998

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]

For discussion:

Could this be a method on image_data

• The user would have to reconstruct their data themselves before calling the get reduced image geometry method
• Once they have reconstructed the full thing they might not be interested in reducing the volume
• If they bin the data they will have to convert the binned reduced geometry to their unbinned reduced geometry

Could this be a method on acquisition_geometry

• The method needs access to the data so would have to pass the data as an argument?
• Similar to the ag.get_ImageGeometry() method we could have ag.get_reduced_ImageGeometry(data)

Could this be a method on acqusition_data

• Makes the most sense, but confusing get_ImageGeometry is a method on acquisition_geometry and this would be a method on acqusition_data. Could allow both?

[hrobarts]

What should the name be

• get_reduced_ImageGeometry()
• get_optimal_ImageGeometry() - makes more sense if we also do rotation at some point
• get_shrunk_ImageGeometry()
  or
  get_ImageGeometry() with argument method=auto (or rotate in future?) or enums like in labels