diff --git a/CHANGELOG.md b/CHANGELOG.md index 804508c262..53f1049449 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,98 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/). ## [Unreleased] +## [1.4.0] - 2024-10-15 +## What's Changed +### Added +* Implemented Conjugate Gradient Solver to generate confidence maps. (#7876) +* Added norm parameter to `ResNet` (#7752, #7805) +* Introduced alpha parameter to `DiceFocalLoss` for improved flexibility (#7841) +* Integrated Tailored ControlNet Implementations (#7875) +* Integrated Tailored Auto-Encoder Model (#7861) +* Integrated Tailored Diffusion U-Net Model (7867) +* Added Maisi morphological functions (#7893) +* Added support for downloading bundles from NGC private registry (#7907, #7929, #8076) +* Integrated generative refactor into the core (#7886, #7962) +* Made `ViT` and `UNETR` models compatible with TorchScript (#7937) +* Implemented post-download checks for MONAI bundles and compatibility warnings (#7938) +* Added NGC prefix argument when downloading bundles (#7974) +* Added flash attention support in the attention block for improved performance (#7977) +* Enhanced `MLPBlock` for compatibility with VISTA-3D (#7995) +* Added support for Neighbor-Aware Calibration Loss (NACL) for calibrated models in segmentation tasks (#7819) +* Added label_smoothing parameter to `DiceCELoss` for enhanced model calibration (#8000) +* Add `include_fc` and `use_combined_linear` argument in the `SABlock` (#7996) +* Added utilities, networks, and an inferer specific to VISTA-3D (#7999, #7987, #8047, #8059, #8021) +* Integrated a new network, `CellSamWrapper`, for cell-based applications (#7981) +* Introduced `WriteFileMapping` transform to map between input image paths and their corresponding output paths (#7769) +* Added `TrtHandler` to accelerate models using TensorRT (#7990, #8064) +* Added box and points conversion transforms for more flexible spatial manipulation (#8053) +* Enhanced `RandSimulateLowResolutiond` transform with deterministic support (#8057) +* Added a contiguous argument to the `Fourier` class to facilitate contiguous tensor outputs (#7969) +* Allowed `ApplyTransformToPointsd` to receive a sequence of reference keys for more versatile point manipulation (#8063) +* Made `MetaTensor` an optional print in `DataStats` and `DataStatsd` for more concise logging (#7814) +#### misc. +* Refactored Dataset to utilize Compose for handling transforms. (#7784) +* Combined `map_classes_to_indices` and `generate_label_classes_crop_centers` into a unified function (#7712) +* Introduced metadata schema directly into the codebase for improved structure and validation (#7409) +* Renamed `optional_packages_version` to `required_packages_version` for clearer package dependency management. (#7253) +* Replaced `pkg_resources` with the more modern packaging module for package handling (#7953) +* Refactored MAISI-related networks to align with the new generative components (#7989, #7993, #8005) +* Added a badge displaying monthly download statistics to enhance project visibility (#7891) +### Fixed +#### transforms +* Ensured deterministic behavior in `MixUp`, `CutMix`, and `CutOut` transforms (#7813) +* Applied a minor correction to `AsDiscrete` transform (#7984) +* Fixed handling of integer weightmaps in `RandomWeightedCrop` (#8097) +* Resolved data type bug in `ScaleIntensityRangePercentile` (#8109) +#### data +* Fixed negative strides issue in the `NrrdReader` (#7809) +* Addressed wsireader issue with retrieving MPP (7921) +* Ensured location is returned as a tuple in wsireader (#8007) +* Corrected interpretation of space directions in nrrd reader (#8091) +#### metrics and losses +* Improved memory management for `NACLLoss` (#8020) +* Fixed reduction logic in `GeneralizedDiceScore` (#7970) +#### networks +* Resolved issue with loading pre-trained weights in `ResNet` (#7924) +* Fixed error where `torch.device` object had no attribute gpu_id during TensorRT export (#8019) +* Corrected function for loading older weights in `DiffusionModelUNet` (#8031) +* Switched to `torch_tensorrt.Device` instead of `torch.device` during TensorRT compilation (#8051) +#### engines and handlers +* Attempted to resolve the "experiment already exists" issue in `MLFlowHandler` (#7916) +* Refactored the model export process for conversion and saving (#7934) +#### misc. +* Adjusted requirements to exclude Numpy version 2.0 (#7859) +* Updated deprecated `scipy.ndimage` namespaces in optional imports (#7847, #7897) +* Resolved `load_module()` deprecation in Python 3.12 (#7881) +* Fixed Ruff type check issues (#7885) +* Cleaned disk space in the conda test pipeline (#7902) +* Replaced deprecated `pkgutil.find_loader` usage (#7906) +* Enhanced docstrings in various modules (#7913, #8055) +* Test cases fixing (#7905, #7794, #7808) +* Fix mypy issue introduced in 1.11.0 (#7941) +* Cleaned up warnings during test collection (#7914) +* Fix incompatible types in assignment issue (#7950) +* Fix outdated link in the docs (#7971) +* Addressed CI issues (#7983, #8013) +* Fix module can not import correctly issue (#8015) +* Fix AttributeError when using torch.min and max (#8041) +* Ensure synchronization by adding `cuda.synchronize` (#8058) +* Ignore warning from nptyping as workaround (#8062) +* Suppress deprecated warning when importing monai (#8067) +* Fix link in test bundle under MONAI-extra-test-data (#8092) +### Changed +* Base Docker image upgraded to `nvcr.io/nvidia/pytorch:24.08-py3` from `nvcr.io/nvidia/pytorch:23.08-py3` +* Change blossom-ci to ACL security format (#7843) +* Move PyType test to weekly test (#8025) +* Adjusted to meet Numpy 2.0 requirements (#7857) +### Deprecated +* Dropped support for Python 3.8 (#7909) +* Remove deprecated arguments and class for v1.4 (#8079) +### Removed +* Remove use of deprecated python 3.12 strtobool (#7900) +* Removed the pipeline for publishing to testpypi (#8086) +* Cleaning up some very old and now obsolete infrastructure (#8113, #8118, #8121) + ## [1.3.2] - 2024-06-25 ### Fixed #### misc. @@ -1040,7 +1132,8 @@ 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/1.3.2...HEAD +[Unreleased]: https://github.com/Project-MONAI/MONAI/compare/1.4.0...HEAD +[1.4.0]: https://github.com/Project-MONAI/MONAI/compare/1.3.2...1.4.0 [1.3.2]: https://github.com/Project-MONAI/MONAI/compare/1.3.1...1.3.2 [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 diff --git a/docs/source/installation.md b/docs/source/installation.md index 70a8b6f1d4..4308a07647 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -254,10 +254,10 @@ Since MONAI v0.2.0, the extras syntax such as `pip install 'monai[nibabel]'` is - The options are ``` -[nibabel, skimage, scipy, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna, onnx, onnxruntime, zarr, lpips, pynvml, huggingface_hub, segment-anything] +[nibabel, skimage, scipy, pillow, tensorboard, gdown, ignite, torchvision, itk, tqdm, lmdb, psutil, cucim, openslide, pandas, einops, transformers, mlflow, clearml, matplotlib, tensorboardX, tifffile, imagecodecs, pyyaml, fire, jsonschema, ninja, pynrrd, pydicom, h5py, nni, optuna, onnx, onnxruntime, zarr, lpips, pynvml, huggingface_hub] ``` which correspond to `nibabel`, `scikit-image`,`scipy`, `pillow`, `tensorboard`, -`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, `onnx`, `onnxruntime`, `zarr`, `lpips`, `nvidia-ml-py`, `huggingface_hub`, `pyamg` and `segment-anything` respectively. +`gdown`, `pytorch-ignite`, `torchvision`, `itk`, `tqdm`, `lmdb`, `psutil`, `cucim`, `openslide-python`, `pandas`, `einops`, `transformers`, `mlflow`, `clearml`, `matplotlib`, `tensorboardX`, `tifffile`, `imagecodecs`, `pyyaml`, `fire`, `jsonschema`, `ninja`, `pynrrd`, `pydicom`, `h5py`, `nni`, `optuna`, `onnx`, `onnxruntime`, `zarr`, `lpips`, `nvidia-ml-py`, `huggingface_hub` and `pyamg` respectively. - `pip install 'monai[all]'` installs all the optional dependencies.