Ivadomed

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.6.1...v2.7.0)

**BUG**

- Fix structure wise uncertainty computation. [View pull request](https://github.com/ivadomed/ivadomed/pull/664)
- Fix bugs in plot film params. [View pull request](https://github.com/ivadomed/ivadomed/pull/646)
- Change condition to save FiLM parameters . [View pull request](https://github.com/ivadomed/ivadomed/pull/645)
- Fix store film params. [View pull request](https://github.com/ivadomed/ivadomed/pull/642)
- soft_gt param: only active after Data Augmentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/624)
- AnimatedGIf import and documentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/623)
- Fix pandas typecast issue in test_split_dataset.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/606)
- Make sure test_HeMIS runs tests in order. [View pull request](https://github.com/ivadomed/ivadomed/pull/602)
- Fix loader/adaptative.py code with reading/writing HDF5 files. [View pull request](https://github.com/ivadomed/ivadomed/pull/592)
- Automate_training: fix bug for multiple parameters. [View pull request](https://github.com/ivadomed/ivadomed/pull/586)
- Load 2D GT slice as uint if not soft training. [View pull request](https://github.com/ivadomed/ivadomed/pull/582)

**DOCUMENTATION**

- Updated affiliations, Added Marie-Helene. [View pull request](https://github.com/ivadomed/ivadomed/pull/674)
- Fix missing dilate-gt.png. [View pull request](https://github.com/ivadomed/ivadomed/pull/653)
- Reformat configuration_file.rst for docs. [View pull request](https://github.com/ivadomed/ivadomed/pull/650)
- Add metavar to parser. [View pull request](https://github.com/ivadomed/ivadomed/pull/641)
- Add a README for the Sphinx docs. [View pull request](https://github.com/ivadomed/ivadomed/pull/626)
- Add documentation on packaged model format. [View pull request](https://github.com/ivadomed/ivadomed/pull/625)
- Add the Twitter badge. [View pull request](https://github.com/ivadomed/ivadomed/pull/622)
- Add new custom css rule for table in purpose section (617). [View pull request](https://github.com/ivadomed/ivadomed/pull/619)
- Add DeepReg to comparison table. [View pull request](https://github.com/ivadomed/ivadomed/pull/618)
- Update PyTorch Ref. [View pull request](https://github.com/ivadomed/ivadomed/pull/616)
- Small clarifications and typos fixes in the Unet tutorial. [View pull request](https://github.com/ivadomed/ivadomed/pull/610)
- Added warning on installation to make sure proper Python version is installed. [View pull request](https://github.com/ivadomed/ivadomed/pull/607)
- Made the BIDS example more general for the audience. [View pull request](https://github.com/ivadomed/ivadomed/pull/597)

**ENHANCEMENT**

- Add new keys config manager. [View pull request](https://github.com/ivadomed/ivadomed/pull/668)
- Store FiLM parameters during testing instead of training. [View pull request](https://github.com/ivadomed/ivadomed/pull/663)
- Externalize command, log_directory, and bids_path fields from JSON config files to CLI. [View pull request](https://github.com/ivadomed/ivadomed/pull/652)
- New loader: BidsDataframe class. [View pull request](https://github.com/ivadomed/ivadomed/pull/648)
- version_info.log added in the log directory. [View pull request](https://github.com/ivadomed/ivadomed/pull/639)
- Indicate folder created after running ivadomed_download_data. [View pull request](https://github.com/ivadomed/ivadomed/pull/609)
- Add explanation for Windows incompatibility in installation docs. [View pull request](https://github.com/ivadomed/ivadomed/pull/605)
- Specify Python version in setup.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/603)
- Add new filter to SliceFilter class. [View pull request](https://github.com/ivadomed/ivadomed/pull/594)
- New loader: Adapt splitting methods. [View pull request](https://github.com/ivadomed/ivadomed/pull/591)

**TESTING**

- Add functional test for automate_training run_test flag. [View pull request](https://github.com/ivadomed/ivadomed/pull/647)
- Add test template files. [View pull request](https://github.com/ivadomed/ivadomed/pull/638)
- Remove the testing_data folder from ivadomed. [View pull request](https://github.com/ivadomed/ivadomed/pull/631)
- Bug in Coveralls release 3.0.0. [View pull request](https://github.com/ivadomed/ivadomed/pull/628)
- Add tests for create_bids_dataframe function. [View pull request](https://github.com/ivadomed/ivadomed/pull/584)

**REFACTORING**

- Reformat configuration_file.rst for docs. [View pull request](https://github.com/ivadomed/ivadomed/pull/650)
- New loader: BidsDataframe class. [View pull request](https://github.com/ivadomed/ivadomed/pull/648)
- Standardize the gpu ID argument. [View pull request](https://github.com/ivadomed/ivadomed/pull/644)
- Unit Test cleanup. [View pull request](https://github.com/ivadomed/ivadomed/pull/636)
- Remove test_script and ivado_functional_test files. [View pull request](https://github.com/ivadomed/ivadomed/pull/634)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.6.0...v2.6.1)

**BUG**

- Fix missing attribute softmax. [View pull request](https://github.com/ivadomed/ivadomed/pull/547)
- Split_dataset: consider center_list when per_patient is used. [View pull request](https://github.com/ivadomed/ivadomed/pull/537)

**DOCUMENTATION**

- Make usage clearer. [View pull request](https://github.com/ivadomed/ivadomed/pull/578)
- Removing support for Python 3.9 (for now). [View pull request](https://github.com/ivadomed/ivadomed/pull/562)
- Updating comparison table after review. [View pull request](https://github.com/ivadomed/ivadomed/pull/560)

**ENHANCEMENT**

- Remove small for multiclass. [View pull request](https://github.com/ivadomed/ivadomed/pull/570)
- Save config file before training. [View pull request](https://github.com/ivadomed/ivadomed/pull/569)
- Apply bounding box safety factor in segment volume. [View pull request](https://github.com/ivadomed/ivadomed/pull/549)
- Multichannel support for convert_to_onnx script. [View pull request](https://github.com/ivadomed/ivadomed/pull/544)

**FEATURE**

- Select subjects for training based on metadata. [View pull request](https://github.com/ivadomed/ivadomed/pull/534)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.5.0...v2.6.0)

**BUG**

- Make is_2d retrocompatibility. [View pull request](https://github.com/ivadomed/ivadomed/pull/535)
- Support multiclass if first class missing. [View pull request](https://github.com/ivadomed/ivadomed/pull/522)

**DOCUMENTATION**

- AdapWing 3D: fix comment. [View pull request](https://github.com/ivadomed/ivadomed/pull/531)
- paper.md: overview_title.png path. [View pull request](https://github.com/ivadomed/ivadomed/pull/529)
- paper.bib: correct typo. [View pull request](https://github.com/ivadomed/ivadomed/pull/528)
- Fix DOIs in paper.bib. [View pull request](https://github.com/ivadomed/ivadomed/pull/527)
- Redirect to DokuWiki/GitHub from the contributing guidelines. [View pull request](https://github.com/ivadomed/ivadomed/pull/523)
- Change path for images. [View pull request](https://github.com/ivadomed/ivadomed/pull/521)

**ENHANCEMENT**

- automate_training: add new parameter to change multiple params. [View pull request](https://github.com/ivadomed/ivadomed/pull/533)
- Softseg multiclass. [View pull request](https://github.com/ivadomed/ivadomed/pull/530)
- Multiclass and multichannel support for segment volume. [View pull request](https://github.com/ivadomed/ivadomed/pull/524)

**FEATURE**

- Create sample to balance metadata. [View pull request](https://github.com/ivadomed/ivadomed/pull/503)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.4.0...v2.5.0)

**BUG**

- paper.md: Fixed broken link. [View pull request](https://github.com/ivadomed/ivadomed/pull/517)
- Change default value of config.json. [View pull request](https://github.com/ivadomed/ivadomed/pull/514)

**DEPENDENCIES**

- Requirements.txt: force onnxruntime version. [View pull request](https://github.com/ivadomed/ivadomed/pull/505)
- set h5py version in requirements.txt. [View pull request](https://github.com/ivadomed/ivadomed/pull/500)

**DOCUMENTATION**

- JOSS submission. [View pull request](https://github.com/ivadomed/ivadomed/pull/502)

**ENHANCEMENT**

- Some fixes to logging. [View pull request](https://github.com/ivadomed/ivadomed/pull/509)

**FEATURE**

- Training without test set. [View pull request](https://github.com/ivadomed/ivadomed/pull/498)
- FiLM for 3D Unet. [View pull request](https://github.com/ivadomed/ivadomed/pull/491)

**REFACTORING**

- Refactor utils.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/497)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.3.1...v2.4.0)

**BUG**

- Fix missing version.txt in wheels package. [View pull request](https://github.com/ivadomed/ivadomed/pull/488)

**DOCUMENTATION**

- Added reference to arXiv citation. [View pull request](https://github.com/ivadomed/ivadomed/pull/485)
- Documenting release workflow. [View pull request](https://github.com/ivadomed/ivadomed/pull/483)

**ENHANCEMENT**

- Option to override postprocessing in segment volume. [View pull request](https://github.com/ivadomed/ivadomed/pull/486)
- Configuration File Manager. [View pull request](https://github.com/ivadomed/ivadomed/pull/484)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.3.0...v2.3.1)

**BUG**

- Version format. [View pull request](https://github.com/ivadomed/ivadomed/pull/481)