Ivadomed

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.8.0...release)

**ENHANCEMENT**

- Make ivadomed be compatible with python 3.9 and PyTorch 1.8. [View pull request](https://github.com/ivadomed/ivadomed/pull/819)

**DEPENDENCIES**

- Pin to CUDA-11. [View pull request](https://github.com/ivadomed/ivadomed/pull/951)

**BUG FIXES**

- Pin PyParsing version to be compatible with pip 20. [View pull request](https://github.com/ivadomed/ivadomed/pull/987)
- Fix pytest test_download_data_no_dataset_specified fail bug. [View pull request](https://github.com/ivadomed/ivadomed/pull/968)
- Fix GeneralizedDiceLoss with `include_background=true` and `batch_size>1` . [View pull request](https://github.com/ivadomed/ivadomed/pull/962)
- Fix undo_transforms in volume reconstruction. [View pull request](https://github.com/ivadomed/ivadomed/pull/957)
- Fix undo_transforms in image reconstruction. [View pull request](https://github.com/ivadomed/ivadomed/pull/956)
- add metadata to create_metadata_dict. [View pull request](https://github.com/ivadomed/ivadomed/pull/954)
- Update scripts in `dev/prepare_data` to use new SCT config syntax (`.yml`). [View pull request](https://github.com/ivadomed/ivadomed/pull/949)
- Fix config loading errors. [View pull request](https://github.com/ivadomed/ivadomed/pull/944)
- Fix dropout_rate key in models.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/937)
- Add additional check for incorrect final_activation value. [View pull request](https://github.com/ivadomed/ivadomed/pull/933)
- Make ivadomed be compatible with python3.9 and PyTorch 1.8. [View pull request](https://github.com/ivadomed/ivadomed/pull/819)

**DOCUMENTATION**

- Minor modifications to the documentation for tutorial 3. [View pull request](https://github.com/ivadomed/ivadomed/pull/988)
- Fix resample axis order in documentation. [View pull request](https://github.com/ivadomed/ivadomed/pull/978)
- Update help.rst. [View pull request](https://github.com/ivadomed/ivadomed/pull/967)
- Fixing issues in estimate uncertainty tutorial. [View pull request](https://github.com/ivadomed/ivadomed/pull/936)
- Fix link to data file in ivadomed instructions. [View pull request](https://github.com/ivadomed/ivadomed/pull/929)
- Fixes object detection path in cascaded architecture tutorial. [View pull request](https://github.com/ivadomed/ivadomed/pull/922)
- Make ivadomed be compatible with python3.9 and PyTorch 1.8. [View pull request](https://github.com/ivadomed/ivadomed/pull/819)

**REFACTORING**

- Fully Remove HeMIS model, Adaptive and h5py/HDF5. [View pull request](https://github.com/ivadomed/ivadomed/pull/984)
- Fix path_output in automated training. [View pull request](https://github.com/ivadomed/ivadomed/pull/914)
- Using keywords for ivadomed/scripts folder. [View pull request](https://github.com/ivadomed/ivadomed/pull/934)
- Keywords refactoring Phase II: loader focus. [View pull request](https://github.com/ivadomed/ivadomed/pull/909)
- Adopting pathllib for loader/bids_dataframe. [View pull request](https://github.com/ivadomed/ivadomed/pull/947)
- Adopting pathlib for tests. [View pull request](https://github.com/ivadomed/ivadomed/pull/901)
- Adopting pathlib training.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/897)
- Adopting pathlib for main.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/892)
- Adopting pathlib for loader/utils.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/879)

**TESTING**

- Fix pytest test_download_data_no_dataset_specified fail bug. [View pull request](https://github.com/ivadomed/ivadomed/pull/968)

**CI**

- Update Sphinx dependency version and check RTD.org performance. [View pull request](https://github.com/ivadomed/ivadomed/pull/974)
- Fix pytest problem. [View pull request](https://github.com/ivadomed/ivadomed/pull/968)
- Update to GitHub Action to use `setup-pythonv2`. [View pull request](https://github.com/ivadomed/ivadomed/pull/959)
- Make ivadomed be compatible with python3.9 and PyTorch 1.8. [View pull request](https://github.com/ivadomed/ivadomed/pull/819)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.7.4...v.2.8.0)

**FEATURE**

- Add image reconstruction from 2D patches. [View pull request](https://github.com/ivadomed/ivadomed/pull/782)
- Add sha256 for training data. [View pull request](https://github.com/ivadomed/ivadomed/pull/760)

**CI**

- Exclude testing directory in coveralls. [View pull request](https://github.com/ivadomed/ivadomed/pull/776)
- Improve current GitHub Action CI with multi OS support. [View pull request](https://github.com/ivadomed/ivadomed/pull/757)

**BUG**

- Fix training_curve.py output. [View pull request](https://github.com/ivadomed/ivadomed/pull/923)
- Fix inverted dimensions in microscopy pixelsize. [View pull request](https://github.com/ivadomed/ivadomed/pull/916)
- Fix segment functions for models without pre-processing transforms. [View pull request](https://github.com/ivadomed/ivadomed/pull/874)
- Fix microscopy ground-truth range of values. [View pull request](https://github.com/ivadomed/ivadomed/pull/870)
- `utils.py`: Only raise ArgParseException for non-zero SystemExits. [View pull request](https://github.com/ivadomed/ivadomed/pull/854)
- Remove `anaconda` from explicit dependencies. [View pull request](https://github.com/ivadomed/ivadomed/pull/845)
- Fix multiclass evaluation bug. [View pull request](https://github.com/ivadomed/ivadomed/pull/837)
- Fix last slice missing in testing bug. [View pull request](https://github.com/ivadomed/ivadomed/pull/835)
- Skip all NumpyToTensor transformation for retrocompatibility. [View pull request](https://github.com/ivadomed/ivadomed/pull/830)
- Remove all NumpyToTensor configs keys. [View pull request](https://github.com/ivadomed/ivadomed/pull/826)
- Add missing "-r" flags to installation.rst. [View pull request](https://github.com/ivadomed/ivadomed/pull/820)
- Call NumpyToTensor last. [View pull request](https://github.com/ivadomed/ivadomed/pull/818)
- Fix bug in loader for multiple raters. [View pull request](https://github.com/ivadomed/ivadomed/pull/806)
- Hot patch to address Inference issue 803. [View pull request](https://github.com/ivadomed/ivadomed/pull/804)
- Add tmp and log file to gitignore. [View pull request](https://github.com/ivadomed/ivadomed/pull/794)

**INSTALLATION**

- Remove `anaconda` from explicit dependencies. [View pull request](https://github.com/ivadomed/ivadomed/pull/845)

**DOCUMENTATION**

- Fix neuropoly guidelines link in ivadomed contribution guidelines document. [View pull request](https://github.com/ivadomed/ivadomed/pull/924)
- Change readme to point to the latest build version. [View pull request](https://github.com/ivadomed/ivadomed/pull/875)
- Installation instruction steps explicity recommended for MacOS but not Linux. [View pull request](https://github.com/ivadomed/ivadomed/pull/847)
- Clarified step 2 for pytorch/torchvision. [View pull request](https://github.com/ivadomed/ivadomed/pull/842)
- Add missing "-r" flags to installation.rst. [View pull request](https://github.com/ivadomed/ivadomed/pull/820)
- Update one class segmentation tutorial's output and segmentation image. [View pull request](https://github.com/ivadomed/ivadomed/pull/779)
- Update documentation with the solution to failing test_adaptive.py on MacOS. [View pull request](https://github.com/ivadomed/ivadomed/pull/771)
- Added link to JOSS paper. [View pull request](https://github.com/ivadomed/ivadomed/pull/748)

**DEPENDENCIES**

- Remove `anaconda` from explicit dependencies. [View pull request](https://github.com/ivadomed/ivadomed/pull/845)

**ENHANCEMENT**

- Fix training_curve.py output. [View pull request](https://github.com/ivadomed/ivadomed/pull/923)
- Fix microscopy ground-truth range of values. [View pull request](https://github.com/ivadomed/ivadomed/pull/870)
- Fix generate_sha_256 for joblib files. [View pull request](https://github.com/ivadomed/ivadomed/pull/866)
- Add microscopy config file. [View pull request](https://github.com/ivadomed/ivadomed/pull/850)
- Add the inference steps for PNG/TIF microscopy data. [View pull request](https://github.com/ivadomed/ivadomed/pull/834)
- New loader: Load PNG/TIF/JPG microscopy files as Nibabel objects. [View pull request](https://github.com/ivadomed/ivadomed/pull/813)
- Speed up IvadoMed Import Speed. [View pull request](https://github.com/ivadomed/ivadomed/pull/793)
- Remove data dependencies from `if` statements in the `Decoder()` forward pass. [View pull request](https://github.com/ivadomed/ivadomed/pull/752)

**TESTING**

- Unsilence test_rbg. [View pull request](https://github.com/ivadomed/ivadomed/pull/832)
- Fix test_sampler. [View pull request](https://github.com/ivadomed/ivadomed/pull/831)
- Fix bug in loader for multiple raters. [View pull request](https://github.com/ivadomed/ivadomed/pull/806)
- Exclude testing directory in coveralls. [View pull request](https://github.com/ivadomed/ivadomed/pull/776)
- Update documentation with the solution to failing test_adaptive.py on MacOS. [View pull request](https://github.com/ivadomed/ivadomed/pull/771)
- Migrate test_segment_volume.py from unit_tests to functional_tests. [View pull request](https://github.com/ivadomed/ivadomed/pull/767)
- Improve current GitHub Action CI with multi OS support. [View pull request](https://github.com/ivadomed/ivadomed/pull/757)

**REFACTORING**

- Extract class SliceFilter, BalancedSample and SampleMetaData from loader.util. [View pull request](https://github.com/ivadomed/ivadomed/pull/928)
- Extracted BidsDataFrame class outside of loader/utils.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/917)
- Initialize the adoption of centralized management of keywords via keywords.py (Phase I: compilation of all keywords). [View pull request](https://github.com/ivadomed/ivadomed/pull/904)
- Fix empty list default parameter antipattern.. [View pull request](https://github.com/ivadomed/ivadomed/pull/903)
- Pathlib adoption for visualize.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/900)
- Pathlib adoption for utils.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/899)
- Pathlib adoption for uncertainty.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/898)
- Pathlib adoption for testing.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/896)
- Pathlib adoption for postprocessing.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/895)
- Pathlib adoption for models.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/894)
- Pathlib adoption for mixup.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/893)
- Pathlib adoption for inference.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/891)
- Pathlib adoption for evaluation.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/890)
- pathlib config_manager.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/889)
- Pathlib adoption for visualize_transform. [View pull request](https://github.com/ivadomed/ivadomed/pull/888)
- Pathlib adoption for visualize_and_compare_testing_models.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/887)
- Pathlib adoption for script/training_curve.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/886)
- Pathlib adoption for script/prepare_dataset_vertibral_labeling.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/885)
- Pathlib adoption for extract_small_dataset. [View pull request](https://github.com/ivadomed/ivadomed/pull/884)
- pathlib for download_data. [View pull request](https://github.com/ivadomed/ivadomed/pull/883)
- pathlib for script/automate_training.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/881)
- pathlib change for object_detection/utils.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/880)
- Pathlib adoption for loader/segmentation_pair.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/878)
- Pathlib adoption for loader/film.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/877)
- Pathlib adoption for adaptative.py. [View pull request](https://github.com/ivadomed/ivadomed/pull/876)
- Update config_bids.json following changes in microscopy BEP. [View pull request](https://github.com/ivadomed/ivadomed/pull/838)
- Extracted Loader Classes into separate files. [View pull request](https://github.com/ivadomed/ivadomed/pull/828)
- Refactor segment_volume to reduce complexity. [View pull request](https://github.com/ivadomed/ivadomed/pull/791)
- Refactoring: BidsDataset __init__ reduce complexity . [View pull request](https://github.com/ivadomed/ivadomed/pull/765)
- Refactoring: reduce complexity of BIDStoHDF5 _load_filenames. [View pull request](https://github.com/ivadomed/ivadomed/pull/737)

See `2.7.3`. We had to re-release because the GitHub Action didn't get triggered to push the release
to `PyPI` as it started as a draft. See here for more details:

[GitHub Actions Bug](https://github.community/t/workflow-set-for-on-release-not-triggering-not-showing-up/16286)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.7.2...release)

**BUG**

- Copy nibabel header when creating output prediction. [View pull request](https://github.com/ivadomed/ivadomed/pull/714)
- Dynamically write dataset_description.json file to suppress pybids warning. [View pull request](https://github.com/ivadomed/ivadomed/pull/690)

**DOCUMENTATION**

- Change archive links to repository links for pre-trained models. [View pull request](https://github.com/ivadomed/ivadomed/pull/700)

**ENHANCEMENT**

- New loader: Refactor BidsDataset classes. [View pull request](https://github.com/ivadomed/ivadomed/pull/691)

[View detailed changelog](https://github.com/ivadomed/ivadomed/compare/v2.7.1...v2.7.2)

**BUG**

- Multiclass ignored during inference if n_input and n_output are different. [View pull request](https://github.com/ivadomed/ivadomed/pull/688)
- Merged participants.tsv file saving bug correction. [View pull request](https://github.com/ivadomed/ivadomed/pull/684)
- Make change_keys method from ConfigurationManager compatible with python3.8. [View pull request](https://github.com/ivadomed/ivadomed/pull/681)

**DOCUMENTATION**

- Add DOI JOSS. [View pull request](https://github.com/ivadomed/ivadomed/pull/683)
- Adding Zenodo DOI. [View pull request](https://github.com/ivadomed/ivadomed/pull/677)

**ENHANCEMENT**

- New loader: input from multiple BIDS datasets. [View pull request](https://github.com/ivadomed/ivadomed/pull/687)
- Add pre-commit hooks to limit file size to 500KB . [View pull request](https://github.com/ivadomed/ivadomed/pull/682)
- Shared weights for the two first FiLM generator layers. [View pull request](https://github.com/ivadomed/ivadomed/pull/679)
- Allow for non-dictionary hyperparameters in automate_training. [View pull request](https://github.com/ivadomed/ivadomed/pull/661)

**FEATURE**

- Enable the pipeline to run with inputs from multiple BIDS datasets. [View pull request](https://github.com/ivadomed/ivadomed/pull/588)

[View change](https://github.com/ivadomed/ivadomed/pull/676)