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6151 update changelog for v1.2 (#6570)
part of #6151 ### Types of changes <!--- Put an `x` in all the boxes that apply, and remove the not applicable items --> - [x] Non-breaking change (fix or new feature that would not break existing functionality). - [ ] Breaking change (fix or new feature that would cause existing functionality to change). - [ ] New tests added to cover the changes. - [ ] Integration tests passed locally by running `./runtests.sh -f -u --net --coverage`. - [ ] Quick tests passed locally by running `./runtests.sh --quick --unittests --disttests`. - [ ] In-line docstrings updated. - [ ] Documentation updated, tested `make html` command in the `docs/` folder. --------- Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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CHANGELOG.md

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## [Unreleased]
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## [1.2.0] - 2023-06-06
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### Added
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* Various Auto3DSeg enhancements and integration tests including multi-node multi-GPU optimization, major usability improvements
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* TensorRT and ONNX support for `monai.bundle` API and the relevant models
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* nnU-Net V2 integration `monai.apps.nnunet`
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* Binary and categorical metrics and event handlers using `MetricsReloaded`
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* Python module and CLI entry point for bundle workflows in `monai.bundle.workflows` and `monai.fl.client`
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* Modular patch inference API including `PatchInferer`, `merger`, and `splitter`
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* Initial release of lazy resampling including transforms and MetaTensor implementations
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* Bridge for ITK Image object and MetaTensor `monai.data.itk_torch_bridge`
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* Sliding window inference memory efficiency optimization including `SlidingWindowInfererAdapt`
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* Generic kernel filtering transforms `ImageFiltered` and `RandImageFiltered`
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* Trainable bilateral filters and joint bilateral filters
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* ClearML stats and image handlers for experiment tracking
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#### misc.
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* Utility functions to warn API default value changes (#5738)
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* Support of dot notation to access content of `ConfigParser` (#5813)
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* Softmax version to focal loss (#6544)
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* FROC metric for N-dimensional (#6528)
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* Extend SurfaceDiceMetric for 3D images (#6549)
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* A `track_meta` option for Lambda and derived transforms (#6385)
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* CLIP pre-trained text-to-vision embedding (#6282)
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* Optional spacing to surface distances calculations (#6144)
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* `WSIReader` read by power and mpp (#6244)
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* Support GPU tensor for `GridPatch` and `GridPatchDataset` (#6246)
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* `SomeOf` transform composer (#6143)
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* GridPatch with both count and threshold filtering (#6055)
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### Fixed
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#### transforms
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* `map_classes_to_indices` efficiency issue (#6468)
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* Adaptive resampling mode based on backends (#6429)
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* Improve Compose encapsulation (#6224)
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* User-provided `FolderLayout` in `SaveImage` and `SaveImaged` transforms (#6213)
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* `SpacingD` output shape compute stability (#6126)
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* No mutate ratio /user inputs `croppad` (#6127)
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* A `warn` flag to RandCropByLabelClasses (#6121)
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* `nan` to indicate `no_channel`, split dim singleton (#6090)
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* Compatible padding mode (#6076)
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* Allow for missing `filename_or_obj` key (#5980)
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* `Spacing` pixdim in-place change (#5950)
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* Add warning in `RandHistogramShift` (#5877)
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* Exclude `cuCIM` wrappers from `get_transform_backends` (#5838)
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#### data
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* `__format__` implementation of MetaTensor (#6523)
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* `channel_dim` in `TiffFileWSIReader` and `CuCIMWSIReader` (#6514)
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* Prepend `"meta"` to `MetaTensor.__repr__` and `MetaTensor.__str__` for easier identification (#6214)
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* MetaTensor slicing issue (#5845)
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* Default writer flags (#6147)
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* `WSIReader` defaults and tensor conversion (#6058)
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* Remove redundant array copy for WSITiffFileReader (#6089)
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* Fix unused arg in `SlidingPatchWSIDataset` (#6047)
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* `reverse_indexing` for PILReader (#6008)
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* Use `np.linalg` for the small affine inverse (#5967)
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#### metrics and losses
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* Removing L2-norm in contrastive loss (L2-norm already present in CosSim) (#6550)
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* Fixes the SSIM metric (#6250)
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* Efficiency issues of Dice metrics (#6412)
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* Generalized Dice issue (#5929)
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* Unify output tensor devices for multiple metrics (#5924)
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#### networks
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* Make `RetinaNet` throw errors for NaN only when training (#6479)
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* Replace deprecated arg in torchvision models (#6401)
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* Improves NVFuser import check (#6399)
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* Add `device` in `HoVerNetNuclearTypePostProcessing` and `HoVerNetInstanceMapPostProcessing` (#6333)
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* Enhance hovernet load pretrained function (#6269)
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* Access to the `att_mat` in self-attention modules (#6493)
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* Optional swinunetr-v2 (#6203)
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* Add transform to handle empty box as training data for `retinanet_detector` (#6170)
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* GPU utilization of DiNTS network (#6050)
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* A pixelshuffle upsample shape mismatch problem (#5982)
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* GEGLU activation function for the MLP Block (#5856)
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* Constructors for `DenseNet` derived classes (#5846)
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* Flexible interpolation modes in `regunet` (#5807)
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#### bundle
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* Optimized the `deepcopy` logic in `ConfigParser` (#6464)
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* Improve check and error message of bundle run (#6400)
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* Warn or raise ValueError on duplicated key in json/yaml config (#6252)
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* Default metadata and logging values for bundle run (#6072)
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* `pprint` head and tail in bundle script (#5969)
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* Config parsing issue for substring reference (#5932)
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* Fix instantiate for object instantiation with attribute `path` (#5866)
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* Fix `_get_latest_bundle_version` issue on Windows (#5787)
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#### engines and handlers
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* MLflow handler run bug (#6446)
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* `monai.engine` training attribute check (#6132)
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* Update StatsHandler logging message (#6051)
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* Added callable options for `iteration_log` and `epoch_log` in TensorBoard and MLFlow (#5976)
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* `CheckpointSaver` logging error (#6026)
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* Callable options for `iteration_log` and `epoch_log` in StatsHandler (#5965)
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#### misc.
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* Avoid creating cufile.log when `import monai` (#6106)
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* `monai._extensions` module compatibility with rocm (#6161)
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* Issue of repeated UserWarning: "TypedStorage is deprecated" (#6105)
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* Use logging config at module level (#5960)
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* Add ITK to the list of optional dependencies (#5858)
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* `RankFilter` to skip logging when the rank is not meeting criteria (#6243)
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* Various documentation issues
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### Changed
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* Overall more precise and consistent type annotations
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* Optionally depend on PyTorch-Ignite v0.4.11 instead of v0.4.10
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* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:23.03-py3` from `nvcr.io/nvidia/pytorch:22.10-py3`
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### Deprecated
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* `resample=True`; `resample=False` will be the new default in `SaveImage`
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* `random_size=True`; `random_size=False` will be the new default for the random cropping transforms
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* `image_only=False`; `image_only=True` will be the new default in `LoadImage`
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### Removed
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* Deprecated APIs since v0.9, including WSIReader from `monai.apps`, `NiftiSaver` and `PNGSaver` from `monai.data`
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* Support for PyTorch 1.8
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* Support for Python 3.7
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## [1.1.0] - 2022-12-19
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### Added
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* Hover-Net based digital pathology workflows including new network, loss, postprocessing, metric, training, and inference modules
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[highlights]: https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md
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[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.1.0...HEAD
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[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.2.0...HEAD
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[1.2.0]: https://github.com/Project-MONAI/MONAI/compare/1.1.0...1.2.0
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[1.1.0]: https://github.com/Project-MONAI/MONAI/compare/1.0.1...1.1.0
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[1.0.1]: https://github.com/Project-MONAI/MONAI/compare/1.0.0...1.0.1
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[1.0.0]: https://github.com/Project-MONAI/MONAI/compare/0.9.1...1.0.0

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