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7753 update changelog for v1.3.1 #7773

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merged 8 commits into from
May 17, 2024
Merged

7753 update changelog for v1.3.1 #7773

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5892a4c
Add changelog for 1.3.1
KumoLiu May 15, 2024
425897e
polish changelog
KumoLiu May 16, 2024
578e977
Merge branch 'dev' into changelog
KumoLiu May 16, 2024
40a6926
minor update
KumoLiu May 17, 2024
7f8b391
Merge remote-tracking branch 'origin/dev' into changelog
KumoLiu May 17, 2024
0e97cb0
Merge branch 'dev' into changelog
KumoLiu May 17, 2024
5ef1b34
minor fix
KumoLiu May 17, 2024
3ba61c7
Merge branch 'changelog' of https://github.com/KumoLiu/MONAI into cha…
KumoLiu May 17, 2024
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95 changes: 94 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -5,6 +5,98 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/).

## [Unreleased]

## [1.3.1] - 2024-05-17
### Added
* Support for `by_measure` argument in `RemoveSmallObjects` (#7137)
* Support for `pretrained` flag in `ResNet` (#7095)
* Support for uploading and downloading bundles to and from the Hugging Face Hub (#6454)
* Added weight parameter in DiceLoss to apply weight to voxels of each class (#7158)
* Support for returning dice for each class in `DiceMetric` (#7163)
* Introduced `ComponentStore` for storage purposes (#7159)
* Added utilities used in MONAI Generative (#7134)
* Enabled Python 3.11 support for `convert_to_torchscript` and `convert_to_onnx` (#7182)
* Support for MLflow in `AutoRunner` (#7176)
* `fname_regex` option in PydicomReader (#7181)
* Allowed setting AutoRunner parameters from config (#7175)
* `VoxelMorphUNet` and `VoxelMorph` (#7178)
* Enabled `cache` option in `GridPatchDataset` (#7180)
* Introduced `class_labels` option in `write_metrics_reports` for improved readability (#7249)
* `DiffusionLoss` for image registration task (#7272)
* Supported specifying `filename` in `Saveimage` (#7318)
* Compile support in `SupervisedTrainer` and `SupervisedEvaluator` (#7375)
* `mlflow_experiment_name` support in `Auto3DSeg` (#7442)
* Arm support (#7500)
* `BarlowTwinsLoss` for representation learning (#7530)
* `SURELoss` and `ConjugateGradient` for diffusion models (#7308)
* Support for `CutMix`, `CutOut`, and `MixUp` augmentation techniques (#7198)
* `meta_file` and `logging_file` options to `BundleWorkflow` (#7549)
* `properties_path` option to `BundleWorkflow` for customized properties (#7542)
* Support for both soft and hard clipping in `ClipIntensityPercentiles` (#7535)
* Support for not saving artifacts in `MLFlowHandler` (#7604)
* Support for multi-channel images in `PerceptualLoss` (#7568)
* Added ResNet backbone for `FlexibleUNet` (#7571)
* Introduced `dim_head` option in `SABlock` to set dimensions for each head (#7664)
* Direct links to github source code to docs (#7738, #7779)
#### misc.
* Refactored `list_data_collate` and `collate_meta_tensor` to utilize the latest PyTorch API (#7165)
* Added __str__ method in `Metric` base class (#7487)
* Made enhancements for testing files (#7662, #7670, #7663, #7671, #7672)
* Improved documentation for bundles (#7116)
### Fixed
#### transforms
* Addressed issue where lazy mode was ignored in `SpatialPadd` (#7316)
* Tracked applied operations in `ImageFilter` (#7395)
* Warnings are now given only if missing class is not set to 0 in `generate_label_classes_crop_centers` (#7602)
* Input is now always converted to C-order in `distance_transform_edt` to ensure consistent behavior (#7675)
#### data
* Modified .npz file behavior to use keys in `NumpyReader` (#7148)
* Handled corrupted cached files in `PersistentDataset` (#7244)
* Corrected affine update in `NrrdReader` (#7415)
#### metrics and losses
* Addressed precision issue in `get_confusion_matrix` (#7187)
* Harmonized and clarified documentation and tests for dice losses variants (#7587)
#### networks
* Removed hard-coded `spatial_dims` in `SwinTransformer` (#7302)
* Fixed learnable `position_embeddings` in `PatchEmbeddingBlock` (#7564, #7605)
* Removed `memory_pool_limit` in TRT config (#7647)
* Propagated `kernel_size` to `ConvBlocks` within `AttentionUnet` (#7734)
* Addressed hard-coded activation layer in `ResNet` (#7749)
#### bundle
* Resolved bundle download issue (#7280)
* Updated `bundle_root` directory for `NNIGen` (#7586)
* Checked for `num_fold` and failed early if incorrect (#7634)
* Enhanced logging logic in `ConfigWorkflow` (#7745)
#### misc.
* Enabled chaining in `Auto3DSeg` CLI (#7168)
* Addressed useless error message in `nnUNetV2Runner` (#7217)
* Resolved typing and deprecation issues in Mypy (#7231)
* Quoted `$PY_EXE` variable to handle Python path that contains spaces in Bash (#7268)
* Improved documentation, code examples, and warning messages in various modules (#7234, #7213, #7271, #7326, #7569, #7584)
* Fixed typos in various modules (#7321, #7322, #7458, #7595, #7612)
* Enhanced docstrings in various modules (#7245, #7381, #7746)
* Handled error when data is on CPU in `DataAnalyzer` (#7310)
* Updated version requirements for third-party packages (#7343, #7344, #7384, #7448, #7659, #7704, #7744, #7742, #7780)
* Addressed incorrect slice compute in `ImageStats` (#7374)
* Avoided editing a loop's mutable iterable to address B308 (#7397)
* Fixed issue with `CUDA_VISIBLE_DEVICES` setting being ignored (#7408, #7581)
* Avoided changing Python version in CICD (#7424)
* Renamed partial to callable in instantiate mode (#7413)
* Imported AttributeError for Python 3.12 compatibility (#7482)
* Updated `nnUNetV2Runner` to support nnunetv2 2.2 (#7483)
* Used uint8 instead of int8 in `LabelStats` (#7489)
* Utilized subprocess for nnUNet training (#7576)
* Addressed deprecated warning in ruff (#7625)
* Fixed downloading failure on FIPS machine (#7698)
* Updated `torch_tensorrt` compile parameters to avoid warning (#7714)
* Restrict `Auto3DSeg` fold input based on datalist (#7778)
### Changed
* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:24.03-py3` from `nvcr.io/nvidia/pytorch:23.08-py3`
### Removed
* Removed unrecommended star-arg unpacking after a keyword argument, addressed B026 (#7262)
* Skipped old PyTorch version test for `SwinUNETR` (#7266)
* Dropped docker build workflow and migrated to Nvidia Blossom system (#7450)
* Dropped Python 3.8 test on quick-py3 workflow (#7719)

## [1.3.0] - 2023-10-12
### Added
* Intensity transforms `ScaleIntensityFixedMean` and `RandScaleIntensityFixedMean` (#6542)
Expand Down Expand Up @@ -943,7 +1035,8 @@ the postprocessing steps should be used before calling the metrics methods

[highlights]: https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md

[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...HEAD
[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.3.1...HEAD
[1.3.1]: https://github.com/Project-MONAI/MONAI/compare/1.3.0...1.3.1
[1.3.0]: https://github.com/Project-MONAI/MONAI/compare/1.2.0...1.3.0
[1.2.0]: https://github.com/Project-MONAI/MONAI/compare/1.1.0...1.2.0
[1.1.0]: https://github.com/Project-MONAI/MONAI/compare/1.0.1...1.1.0
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