Ivadomed

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.9.5...release)

**Installation**

- unify installation (attempt 2). [View pull request](https://github.com/ivadomed/ivadomed/pull/1129)

**DOCUMENTATION**

- Update documentation and config files to add WandB details. [View pull request](https://github.com/ivadomed/ivadomed/pull/1120)

**ENHANCEMENT**

- Support for WandB Experimental Tracking . [View pull request](https://github.com/ivadomed/ivadomed/pull/1069)

**CONTINUOUS INTEGRATION**

- Adds various CI and testing improvement not impacting end users.

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.9.4...release)

**BUG**

- Fix TSV metadata indexation and remove unused lines from bids_dataframe based on split_method. [View pull request](https://github.com/ivadomed/ivadomed/pull/1112)
- Fix loading of TIF 16bits grayscale files. [View pull request](https://github.com/ivadomed/ivadomed/pull/1107)
- Fix loading when names of multiple target_suffix overlap. [View pull request](https://github.com/ivadomed/ivadomed/pull/1100)

**ENHANCEMENT**

- Add type hintings to fields inside all keywords(KW) dataclasses. [View pull request](https://github.com/ivadomed/ivadomed/pull/1109)

**DOCUMENTATION**

- Clarify data and loading documentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/1103)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.9.3...release)

**FEATURE**

- Segment with ONNX or PT model based on CPU/GPU availability. [View pull request](https://github.com/ivadomed/ivadomed/pull/1086)

**ENHANCEMENT**

- Update microscopy following BEP release. [View pull request](https://github.com/ivadomed/ivadomed/pull/1025)

**BUG**

- Fixing mix-up for GPU training. [View pull request](https://github.com/ivadomed/ivadomed/pull/1063)

- **REFACTORING**

- Refactor missing print statements to be using logger. [View pull request](https://github.com/ivadomed/ivadomed/pull/1085)
- Convert print to logger format for much more granular unified control.. [View pull request](https://github.com/ivadomed/ivadomed/pull/1040)
- Update pybids to 0.14.0. [View pull request](https://github.com/ivadomed/ivadomed/pull/994)

**DOCUMENTATION**

- Add ADS use case in documentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/1080)
- Updated documentation for SoftSeg training. [View pull request](https://github.com/ivadomed/ivadomed/pull/1064)
- Rewrite tutorial 2 with sphinx tab. [View pull request](https://github.com/ivadomed/ivadomed/pull/1045)
- Format revamped Tutorial 1 to highlight the CLI vs JSON approaches. [View pull request](https://github.com/ivadomed/ivadomed/pull/1039)
- Improve Installation Doc Readability based for Step 3 relating to GPU setup. [View pull request](https://github.com/ivadomed/ivadomed/pull/1037)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.9.2...release)

**FEATURE**

- Apply filter parameters on 2D patches to remove empty patches. [View pull request](https://github.com/ivadomed/ivadomed/pull/980)

**REFACTORING**

- Update pred_to_png prediction filenames for ADS integration. [View pull request](https://github.com/ivadomed/ivadomed/pull/1050)

**DOCUMENTATION**

- Instruction to update `"bids_config"` key in microscopy tutorial. [View pull request](https://github.com/ivadomed/ivadomed/pull/1053)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.9.1...release)

**FEATURE**

- Implementation of Random Blur Augmentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/1034)
- Implementation of Random Bias Field Augmentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/1033)
- Implementation of Random Gamma Contrast Augmentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/1015)

**DEPENDENCIES**

- Unpin `tensorboard` to avoid conflict with downstream SCT requirements. [View pull request](https://github.com/ivadomed/ivadomed/pull/1048)

**BUG**

- Rename prediction filenames: add class index and compat. for multi-rater. [View pull request](https://github.com/ivadomed/ivadomed/pull/1043)
- Fix pixel size keyword in run_segment_command. [View pull request](https://github.com/ivadomed/ivadomed/pull/1024)
- Replaced flip_axes with the correct bool element at index.. [View pull request](https://github.com/ivadomed/ivadomed/pull/1013)

**DOCUMENTATION**

- Add microscopy tutorial. [View pull request](https://github.com/ivadomed/ivadomed/pull/1036)
- Removed one child-headings for clarity. [View pull request](https://github.com/ivadomed/ivadomed/pull/1028)
- Typo fix for URL that is bricking the Colab link. [View pull request](https://github.com/ivadomed/ivadomed/pull/1021)
- Experimental incorporation of tutorial jupyter notebooks open in Colab path. [View pull request](https://github.com/ivadomed/ivadomed/pull/998)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.9.0...release)

**ENHANCEMENT**

- Add forced indexation of "micr" datatype. [View pull request](https://github.com/ivadomed/ivadomed/pull/995)
- Apply transforms on 2D patches. [View pull request](https://github.com/ivadomed/ivadomed/pull/982)

**DOCUMENTATION**

- Update Tutorial 1/2/3 and readme.md to fix minor display issues. [View pull request](https://github.com/ivadomed/ivadomed/pull/992)
- Update installation instruction to fit recent CUDA11 and torch 1.8+ push. [View pull request](https://github.com/ivadomed/ivadomed/pull/969)

**REFACTORING**

- Fully Remove HeMIS model, Adaptive and h5py/HDF5. [View pull request](https://github.com/ivadomed/ivadomed/pull/984)
- Use keywords for the rest of the files. [View pull request](https://github.com/ivadomed/ivadomed/pull/946)