✨ Add on-the-fly Registered Slide Visualization

[measty]

This PR is a rough draft of code to allow a registration transform to be loaded as an 'overlay', which will allow the slide to be viewed as if that registration transform had been applied to it. This will work with either an affine transformation saved as a .npy, or a non-rigid one represented by a SimpleITK displacement field saved as a .mha (such as what would be output by DeeperHistoReg, for example).

It introduces a new WSIReader subclass called TransformedWSIReader, which when initialized with a slide and transformation will apply the transformation on the fly when regions are requested.

It also adds '.npy' and '.mha' to the overlay types the visualization tool picks up; upon loading one of these types, the current slide will be opened as a TransformedWSIReader with that transform, allowing it to be visualized on the fly as a registered slide.

still to do:

• Implement read_bounds (currently only done read_rect)
• Correctly handle coord_space argument
• Check affine capabilities of read_bounds
• Add unit tests

[codecov]

Codecov Report

Attention: Patch coverage is 98.93048% with 2 lines in your changes missing coverage. Please review.

Project coverage is 99.63%. Comparing base (b6eefcf) to head (45f3477).

Files with missing lines	Patch %	Lines
tiatoolbox/visualization/tileserver.py	94.73%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #875      +/-   ##
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- Coverage    99.70%   99.63%   -0.08%     
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  Files           71       71              
  Lines         8851     9024     +173     
  Branches      1154     1171      +17     
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+ Hits          8825     8991     +166     
- Misses          23       28       +5     
- Partials         3        5       +2     

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[shaneahmed]

Can we also test the values or just shape is enough?

[adamshephard]

Here, we haven't performed the test with the correct MHA files as didn't want to add lots of new slides to the server. So think shape alone is reasonable.