Stop copying whole image before cropping

[StijnvWijn]

Fixes #1305.

Description

A slowdown while sampling patches that are much smaller than the image in Torchio >= 0.20.4

Checklist

• I have read the CONTRIBUTING docs and have a developer setup ready
• Changes are
  • Non-breaking (would not break existing functionality)
  • Breaking (would cause existing functionality to change)
• Tests added or modified to cover the changes
• In-line docstrings updated
• Documentation updated
• This pull request is ready to be reviewed

[fepegar]

@nicoloesch could you please comment on the general design? I can then fix formatting etc.

[nicoloesch]

Really like the changes @StijnvWijn and this is exactly how I would have done it. Some changes are purely stylistic, others require some feedback from @fepegar about formatting and docstring description to make it as clear as possible.
Most of my comments are suggestions instead of requirements.

[StijnvWijn]

So I was building the docs and I encountered an issue I am not sure how to solve:
The Colin27 dataset is a subclass of Subject, but does not allow the same init parameters as the Subject class and has some private attributes that we can't access with .items(). I tried copying using the __dict__ attribute as suggested here, but I can't seem to initialize a Subject without arguments and i need to initialize the Colin27 without arguments, so I am unsure how to generalize the copy behaviour so that every class gets handled correctly.

I fixed it, but now the apply_transform function has some less beautiful code to make a new subject, copy it and all its attributes, it uses the dict and class attributes, but I added some comments, so hopefully it is clear why.

[StijnvWijn]

@nicoloesch Do you have any comments on the new copy mechanism?

[nicoloesch]

All my comments have been addressed! Thank you @StijnvWijn

[fepegar]

@allcontributors please add @nicoloesch for design, maintenance, question, review

[allcontributors]

@fepegar

I've put up a pull request to add @nicoloesch! 🎉

[fepegar]

@allcontributors please add @StijnvWijn for code

[allcontributors]

@fepegar

I've put up a pull request to add @StijnvWijn! 🎉

[fepegar]

Thank you both for your contribution!