New loss functions, refactored engines to only implement forward_method, quality fixes

[georgeyiasemis]

Implements:

• New loss functions (NMSE, NRMSE, NMAE, SobelGradL1Loss, SobelGradL2Loss)
• mri_models performs _do_iteration method, child engines perform forward_function which returns output_image and/or output_kspace
• Changes/Additions in mri_transforms
  • Padding computed as a Tensor with ComputePadding transform (this is helpful when cropping image and tranforming to kspace)
  • ApplyPadding transform
  • ComputeImage transform choices of mod output or not
  • RenameKeys transform
  • Normalize split to ComputeScalingFactor and Normalize
  • Some quality changes
  • Some documentation changes

[codecov[bot]]

Codecov Report

Base: 82.02% // Head: 81.91% // Decreases project coverage by -0.10% :warning:

Coverage data is based on head (09e1ba6) compared to base (1a8ddf5). Patch coverage: 92.57% of modified lines in pull request are covered.

:exclamation: Current head 09e1ba6 differs from pull request most recent head 8220124. Consider uploading reports for the commit 8220124 to get more accurate results

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #224 +/- ## ========================================== - Coverage 82.02% 81.91% -0.11% ========================================== Files 74 77 +3 Lines 5585 5590 +5 ========================================== - Hits 4581 4579 -2 - Misses 1004 1011 +7 ``` | [Impacted Files](https://codecov.io/gh/NKI-AI/direct/pull/224?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI) | Coverage Δ | | |---|---|---| | [direct/nn/cirim/cirim.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L25uL2NpcmltL2NpcmltLnB5) | `98.27% <ø> (ø)` | | | [direct/nn/cirim/cirim\_engine.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L25uL2NpcmltL2NpcmltX2VuZ2luZS5weQ==) | `95.45% <50.00%> (ø)` | | | [direct/exceptions.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2V4Y2VwdGlvbnMucHk=) | `62.50% <85.71%> (+21.32%)` | :arrow_up: | | [direct/nn/mri\_models.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L25uL21yaV9tb2RlbHMucHk=) | `91.30% <85.98%> (-2.31%)` | :arrow_down: | | [direct/data/mri\_transforms.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2RhdGEvbXJpX3RyYW5zZm9ybXMucHk=) | `97.00% <89.47%> (-2.29%)` | :arrow_down: | | [direct/functionals/grad.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2Z1bmN0aW9uYWxzL2dyYWQucHk=) | `97.95% <97.95%> (ø)` | | | [direct/common/subsample.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2NvbW1vbi9zdWJzYW1wbGUucHk=) | `84.63% <100.00%> (ø)` | | | [direct/data/datasets.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2RhdGEvZGF0YXNldHMucHk=) | `87.46% <100.00%> (-0.99%)` | :arrow_down: | | [direct/data/datasets\_config.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2RhdGEvZGF0YXNldHNfY29uZmlnLnB5) | `100.00% <100.00%> (ø)` | | | [direct/data/h5\_data.py](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI#diff-ZGlyZWN0L2RhdGEvaDVfZGF0YS5weQ==) | `65.06% <100.00%> (+0.24%)` | :arrow_up: | | ... and [20 more](https://codecov.io/gh/NKI-AI/direct/pull/224/diff?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI) | | Help us with your feedback. Take ten seconds to tell us [how you rate us](https://about.codecov.io/nps?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI). Have a feature suggestion? [Share it here.](https://app.codecov.io/gh/feedback/?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=NKI-AI)

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