From 087e5cfc59ee7974a72001b96ca1a0bcf2bb511b Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Fri, 2 Apr 2021 14:18:19 +0100 Subject: [PATCH 1/2] changelog for 0.5.0 Signed-off-by: Wenqi Li --- CHANGELOG.md | 81 +++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 80 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 56e65a7d92..b44671becd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,84 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). ## [Unreleased] +## [0.5.0] - 2020-04-09 +### Added +* Overview document for [feature highlights in v0.5.0](https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md) +* Invertible spatial transforms + * `InvertibleTransform` base APIs + * Batch inverse and decollating APIs + * Inverse of `Compose` + * Test-time augmentation as an application +* Initial support of learning-based image registration: + * Bending energy, LNCC, and global mutual information loss + * Fully convolutional architectures + * Dense displacement field, dense velocity field computation + * Warping with high-order interpolation with C++/CUDA implementations +* Deepgrow modules for interactive segmentation: + * Workflows with simulations of clicks + * Distance-based transforms for guidance signals +* Digital pathology support: + * Efficient whole slide imaging IO and sampling with Nvidia cuCIM and SmartCache + * FROC measurements for lesion + * Probabilistic post-processing for lesion detection + * TorchVision classification model adaptor for fully convolutional analysis +* 12 new transforms, grid patch dataset, `ThreadDataLoader` +* 4 iteration events for the engine for finer control of workflows +* New C++/CUDA extensions: + * Conditional random field + * Fast bilateral filtering using the permutohedral lattice +* Metrics summary reporting and saving APIs +* DiceCELoss, DiceFocalLoss, a multi-scale wrapper for segmentation loss computation +* Data loading utilities： + * `decollate_batch` + * `PadListDataCollate` with inverse support +* Support of slicing syntax for `Dataset` +* Initial Torchscript support for the loss modules +* Learning rate finder +* Allow for missing keys in the dictionary-based transforms +* Various summary and plotting utilities for Jupyter notebooks +* Contributor Covenant Code of Conduct +* Major CI/CD enhancements covering the tutorial repository +* Fully compatible with PyTorch 1.8 +* Initial nightly CI/CD pipelines using Nvidia Blossom Infrastructure + +### Changed +* Enhanced `list_data_collate` error handling +* Unified iteration metric APIs +* `densenet*` extensions are renamed to `DenseNet*` +* `se_res*` network extensions are renamed to `SERes*` +* Transform base APIs are rearranged into `compose`, `inverse`, and `transform` +* `_do_transform` flag for the random augmentations is unified via `RandomizableTransform` +* Decoupled post-processing steps, e.g. `softmax`, `to_onehot_y`, from the metrics computations +* Moved the distributed samplers to `monai.data.samplers` from `monai.data.utils` +* Engine's data loaders now accept generic iterables as input +* Various type hints according to Numpy 1.20 +* Refactored testing utility `runtests.sh` to have `--unittest` and `--net` (integration tests) options +* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:21.03-py3` from `nvcr.io/nvidia/pytorch:20.10-py3` +* Docker images are now built with self-hosted environments +* Primary contact email updated to `monai.contact@gmail.com` +* Now using GitHub Discussions as the primary communication forum + +### Removed +* Compatibility tests for PyTorch 1.5.x +* Format specific loaders, e.g. `LoadNifti`, `NiftiDataset` +* Assert statements from non-test files +* `from module import *` statements, addressed flake8 F403 + +### Fixed +* Uses American English spelling for code, as per PyTorch +* Code coverage now takes multiprocessing runs into account +* SmartCache with initial shuffling +* `ConvertToMultiChannelBasedOnBratsClasses` now supports channel-first inputs +* Checkpoint handler to save with non-root permissions +* Fixed an issue for exiting the distributed unit tests +* Unified `DynUNet` to have single tensor output w/o deep supervision +* `SegmentationSaver` now supports user-specified data types, and a `squeeze_end_dims` flag +* Fixed `*Saver` event handlers output filenames with a `data_root_dir` option +* Load image functions now ensures little-endian +* Fixed the test runner to support regex-based test case matching +* Usability issues in the event handlers + ## [0.4.0] - 2020-12-15 ### Added * Overview document for [feature highlights in v0.4.0](https://github.com/Project-MONAI/MONAI/blob/master/docs/source/highlights.md) @@ -173,7 +251,8 @@ 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/0.4.0...HEAD +[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/0.5.0...HEAD +[0.5.0]: https://github.com/Project-MONAI/MONAI/compare/0.4.0...0.5.0 [0.4.0]: https://github.com/Project-MONAI/MONAI/compare/0.3.0...0.4.0 [0.3.0]: https://github.com/Project-MONAI/MONAI/compare/0.2.0...0.3.0 [0.2.0]: https://github.com/Project-MONAI/MONAI/compare/0.1.0...0.2.0 From b369ca736472b20ff340df0da275e15217a8bf07 Mon Sep 17 00:00:00 2001 From: Wenqi Li Date: Fri, 9 Apr 2021 10:44:30 +0100 Subject: [PATCH 2/2] update changelog Signed-off-by: Wenqi Li --- CHANGELOG.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b44671becd..7e1c785aa6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * `InvertibleTransform` base APIs * Batch inverse and decollating APIs * Inverse of `Compose` + * Batch inverse event handling * Test-time augmentation as an application * Initial support of learning-based image registration: * Bending energy, LNCC, and global mutual information loss @@ -26,7 +27,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * FROC measurements for lesion * Probabilistic post-processing for lesion detection * TorchVision classification model adaptor for fully convolutional analysis -* 12 new transforms, grid patch dataset, `ThreadDataLoader` +* 12 new transforms, grid patch dataset, `ThreadDataLoader`, EfficientNets B0-B7 * 4 iteration events for the engine for finer control of workflows * New C++/CUDA extensions: * Conditional random field @@ -40,6 +41,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * Initial Torchscript support for the loss modules * Learning rate finder * Allow for missing keys in the dictionary-based transforms +* Support of checkpoint loading for transfer learning * Various summary and plotting utilities for Jupyter notebooks * Contributor Covenant Code of Conduct * Major CI/CD enhancements covering the tutorial repository @@ -56,6 +58,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * Decoupled post-processing steps, e.g. `softmax`, `to_onehot_y`, from the metrics computations * Moved the distributed samplers to `monai.data.samplers` from `monai.data.utils` * Engine's data loaders now accept generic iterables as input +* Workflows now accept additional custom events and state properties * Various type hints according to Numpy 1.20 * Refactored testing utility `runtests.sh` to have `--unittest` and `--net` (integration tests) options * Base Docker image upgraded to `nvcr.io/nvidia/pytorch:21.03-py3` from `nvcr.io/nvidia/pytorch:20.10-py3` @@ -77,9 +80,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * Checkpoint handler to save with non-root permissions * Fixed an issue for exiting the distributed unit tests * Unified `DynUNet` to have single tensor output w/o deep supervision -* `SegmentationSaver` now supports user-specified data types, and a `squeeze_end_dims` flag +* `SegmentationSaver` now supports user-specified data types and a `squeeze_end_dims` flag * Fixed `*Saver` event handlers output filenames with a `data_root_dir` option -* Load image functions now ensures little-endian +* Load image functions now ensure little-endian * Fixed the test runner to support regex-based test case matching * Usability issues in the event handlers