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@wyli wyli released this 08 Jun 17:16
· 474 commits to dev since this release
1.2.0
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Added

  • Various Auto3DSeg enhancements and integration tests including multi-node multi-GPU optimization, major usability improvements
  • TensorRT and ONNX support for monai.bundle API and the relevant models
  • nnU-Net V2 integration monai.apps.nnunet
  • Binary and categorical metrics and event handlers using MetricsReloaded
  • Python module and CLI entry point for bundle workflows in monai.bundle.workflows and monai.fl.client
  • Modular patch inference API including PatchInferer, merger, and splitter
  • Initial release of lazy resampling including transforms and MetaTensor implementations
  • Bridge for ITK Image object and MetaTensor monai.data.itk_torch_bridge
  • Sliding window inference memory efficiency optimization including SlidingWindowInfererAdapt
  • Generic kernel filtering transforms ImageFiltered and RandImageFiltered
  • Trainable bilateral filters and joint bilateral filters
  • ClearML stats and image handlers for experiment tracking

misc.

  • Utility functions to warn API default value changes (#5738)
  • Support of dot notation to access content of ConfigParser (#5813)
  • Softmax version to focal loss (#6544)
  • FROC metric for N-dimensional (#6528)
  • Extend SurfaceDiceMetric for 3D images (#6549)
  • A track_meta option for Lambda and derived transforms (#6385)
  • CLIP pre-trained text-to-vision embedding (#6282)
  • Optional spacing to surface distances calculations (#6144)
  • WSIReader read by power and mpp (#6244)
  • Support GPU tensor for GridPatch and GridPatchDataset (#6246)
  • SomeOf transform composer (#6143)
  • GridPatch with both count and threshold filtering (#6055)

Fixed

transforms

  • map_classes_to_indices efficiency issue (#6468)
  • Adaptive resampling mode based on backends (#6429)
  • Improve Compose encapsulation (#6224)
  • User-provided FolderLayout in SaveImage and SaveImaged transforms (#6213)
  • SpacingD output shape compute stability (#6126)
  • No mutate ratio /user inputs croppad (#6127)
  • A warn flag to RandCropByLabelClasses (#6121)
  • nan to indicate no_channel, split dim singleton (#6090)
  • Compatible padding mode (#6076)
  • Allow for missing filename_or_obj key (#5980)
  • Spacing pixdim in-place change (#5950)
  • Add warning in RandHistogramShift (#5877)
  • Exclude cuCIM wrappers from get_transform_backends (#5838)

data

  • __format__ implementation of MetaTensor (#6523)
  • channel_dim in TiffFileWSIReader and CuCIMWSIReader (#6514)
  • Prepend "meta" to MetaTensor.__repr__ and MetaTensor.__str__ for easier identification (#6214)
  • MetaTensor slicing issue (#5845)
  • Default writer flags (#6147)
  • WSIReader defaults and tensor conversion (#6058)
  • Remove redundant array copy for WSITiffFileReader (#6089)
  • Fix unused arg in SlidingPatchWSIDataset (#6047)
  • reverse_indexing for PILReader (#6008)
  • Use np.linalg for the small affine inverse (#5967)

metrics and losses

  • Removing L2-norm in contrastive loss (L2-norm already present in CosSim) (#6550)
  • Fixes the SSIM metric (#6250)
  • Efficiency issues of Dice metrics (#6412)
  • Generalized Dice issue (#5929)
  • Unify output tensor devices for multiple metrics (#5924)

networks

  • Make RetinaNet throw errors for NaN only when training (#6479)
  • Replace deprecated arg in torchvision models (#6401)
  • Improves NVFuser import check (#6399)
  • Add device in HoVerNetNuclearTypePostProcessing and HoVerNetInstanceMapPostProcessing (#6333)
  • Enhance hovernet load pretrained function (#6269)
  • Access to the att_mat in self-attention modules (#6493)
  • Optional swinunetr-v2 (#6203)
  • Add transform to handle empty box as training data for retinanet_detector (#6170)
  • GPU utilization of DiNTS network (#6050)
  • A pixelshuffle upsample shape mismatch problem (#5982)
  • GEGLU activation function for the MLP Block (#5856)
  • Constructors for DenseNet derived classes (#5846)
  • Flexible interpolation modes in regunet (#5807)

bundle

  • Optimized the deepcopy logic in ConfigParser (#6464)
  • Improve check and error message of bundle run (#6400)
  • Warn or raise ValueError on duplicated key in json/yaml config (#6252)
  • Default metadata and logging values for bundle run (#6072)
  • pprint head and tail in bundle script (#5969)
  • Config parsing issue for substring reference (#5932)
  • Fix instantiate for object instantiation with attribute path (#5866)
  • Fix _get_latest_bundle_version issue on Windows (#5787)

engines and handlers

  • MLflow handler run bug (#6446)
  • monai.engine training attribute check (#6132)
  • Update StatsHandler logging message (#6051)
  • Added callable options for iteration_log and epoch_log in TensorBoard and MLFlow (#5976)
  • CheckpointSaver logging error (#6026)
  • Callable options for iteration_log and epoch_log in StatsHandler (#5965)

misc.

  • Avoid creating cufile.log when import monai (#6106)
  • monai._extensions module compatibility with rocm (#6161)
  • Issue of repeated UserWarning: "TypedStorage is deprecated" (#6105)
  • Use logging config at module level (#5960)
  • Add ITK to the list of optional dependencies (#5858)
  • RankFilter to skip logging when the rank is not meeting criteria (#6243)
  • Various documentation issues

Changed

  • Overall more precise and consistent type annotations
  • Optionally depend on PyTorch-Ignite v0.4.11 instead of v0.4.10
  • Base Docker image upgraded to nvcr.io/nvidia/pytorch:23.03-py3 from nvcr.io/nvidia/pytorch:22.10-py3

Deprecated

  • resample=True; resample=False will be the new default in SaveImage
  • random_size=True; random_size=False will be the new default for the random cropping transforms
  • image_only=False; image_only=True will be the new default in LoadImage
  • AddChannel and AsChannelFirst in favor of EnsureChannelFirst

Removed

  • Deprecated APIs since v0.9, including WSIReader from monai.apps, NiftiSaver and PNGSaver from monai.data
  • Support for PyTorch 1.8
  • Support for Python 3.7
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