New label transformations

[efirdc]

Implements #400.

Description
This implements new label transformations RemapLabels, SequentialLabels, RemoveLabels. Documentation and basic tests are included as well. Please let me know if anything should be improved or changed.

Some extra methods were added to TorchioTestCase for easier testing of these new transformations.

• get_subject_with_labels(self, labels): returns a subject with a LabelMap which has the desired set of labels.
• get_unique_labels(self, label_map): returns the set of unique labels in a LabelMap, not including 0.

A small fix to Subject.apply_inverse_transform. Just applied .clear_history() to the subject after the inverse transformation.

Moved everything related to TypeBounds, and TypeMaskingMethod up to the Transform class so they can be reused in the label transformations.

Demonstration

Original labels:

Apply tio.RemoveLabels([1, 2, 17, 23, 24])

Apply tio.RemapLabels({4:3, 6:5, 10:9, 20:19, 22:21}, masking_method="Right")

Apply tio.SequentialLabels()

Apply subject = subject.apply_inverse_transform()

Checklist

• I have read the CONTRIBUTING docs and have a developer setup (especially important are pre-commitand pytest)
• Non-breaking change (would not break existing functionality)
• Breaking change (would cause existing functionality to change)
• Tests added or modified to cover the changes
• Integration tests passed locally by running pytest
• In-line docstrings updated
• Documentation updated, tested running make html inside the docs/ folder
• This pull request is ready to be reviewed
• If the PR is ready and there are multiple commits, I have squashed them and force-pushed

[codecov]

Codecov Report

Merging #402 (4c1be6e) into master (b9ac52d) will decrease coverage by 0.14%.
The diff coverage is 87.96%.

@@            Coverage Diff             @@
##           master     #402      +/-   ##
==========================================
- Coverage   92.42%   92.28%   -0.15%     
==========================================
  Files         117      124       +7     
  Lines        5942     6103     +161     
==========================================
+ Hits         5492     5632     +140     
- Misses        450      471      +21     

Impacted Files	Coverage Δ
torchio/transforms/augmentation/composition.py	89.02% <50.00%> (+1.37%)	⬆️
torchio/transforms/transform.py	86.12% <70.00%> (-7.89%)	⬇️
tests/utils.py	95.72% <93.33%> (-0.40%)	⬇️
tests/transforms/label/test_remap_labels.py	100.00% <100.00%> (ø)
tests/transforms/label/test_remove_labels.py	100.00% <100.00%> (ø)
tests/transforms/label/test_sequential_labels.py	100.00% <100.00%> (ø)
tests/transforms/test_transforms.py	100.00% <100.00%> (ø)
torchio/data/subject.py	96.15% <100.00%> (+1.62%)	⬆️
torchio/transforms/__init__.py	100.00% <100.00%> (ø)
torchio/transforms/preprocessing/__init__.py	100.00% <100.00%> (ø)
... and 15 more

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[fepegar]

Nice! I really appreciate the effort into the docs and the examples.

Why did you move the bounds stuff into Transform? I haven't seen it in the new transforms.

[efirdc]

No worries, glad to contribute.

The bounds code was moved to Transform so that TypeBounds can be supported as a masking method. You can see where that happens on line 402 of transform.py

[fepegar]

Ok, thanks. I've added some minor edits, will squash and merge once the tests are done.

[fepegar]

Available in v0.18.13. Thanks again for your contribution!

[efirdc]

Great! Thanks for your edits and continued support of this project.