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@wyli wyli released this 19 Dec 21:05
· 736 commits to dev since this release
a2ec375

Added

  • Hover-Net based digital pathology workflows including new network, loss, postprocessing, metric, training, and inference modules
  • Various enhancements for Auto3dSeg AutoRunner including template caching, selection, and a dry-run mode nni_dry_run
  • Various enhancements for Auto3dSeg algo templates including new state-of-the-art configurations, optimized GPU memory utilization
  • New bundle API and configurations to support experiment management including MLFlowHandler
  • New bundle.script API to support model zoo query and download
  • LossMetric metric to compute loss as cumulative metric measurement
  • Transforms and base transform APIs including RandomizableTrait and MedianSmooth
  • runtime_cache option for CacheDataset and the derived classes to allow for shared caching on the fly
  • Flexible name formatter for SaveImage transform
  • pending_operations MetaTensor property and basic APIs for lazy image resampling
  • Contrastive sensitivity for SSIM metric
  • Extensible backbones for FlexibleUNet
  • Generalize SobelGradients to 3D and any spatial axes
  • warmup_multiplier option for WarmupCosineSchedule
  • F beta score metric based on confusion matrix metric
  • Support of key overwriting in LambdaD
  • Basic premerge tests for Python 3.11
  • Unit and integration tests for CUDA 11.6, 11.7 and A100 GPU
  • DataAnalyzer handles minor image-label shape inconsistencies

Fixed

  • Review and enhance previously untyped APIs with additional type annotations and casts
  • switch_endianness in LoadImage now supports tensor input
  • Reduced memory footprint for various Auto3dSeg tests
  • Issue of @ in monai.bundle.ReferenceResolver
  • Compatibility issue with ITK-Python 5.3 (converting itkMatrixF44 for default collate)
  • Inconsistent of sform and qform when using different backends for SaveImage
  • MetaTensor.shape call now returns a torch.Size instead of tuple
  • Issue of channel reduction in GeneralizedDiceLoss
  • Issue of background handling before softmax in DiceFocalLoss
  • Numerical issue of LocalNormalizedCrossCorrelationLoss
  • Issue of incompatible view size in ConfusionMatrixMetric
  • NetAdapter compatibility with Torchscript
  • Issue of extract_levels in RegUNet
  • Optional bias_downsample in ResNet
  • dtype overflow for ShiftIntensity transform
  • Randomized transforms such as RandCuCIM now inherit RandomizableTrait
  • fg_indices.size compatibility issue in generate_pos_neg_label_crop_centers
  • Issue when inverting ToTensor
  • Issue of capital letters in filename suffixes check in LoadImage
  • Minor tensor compatibility issues in apps.nuclick.transforms
  • Issue of float16 in verify_net_in_out
  • std variable type issue for RandRicianNoise
  • DataAnalyzer accepts None as label key and checks empty labels
  • iter_patch_position now has a smaller memory footprint
  • CumulativeAverage has been refactored and enhanced to allow for simple tracking of metric running stats.
  • Multi-threading issue for MLFlowHandler

Changed

  • Printing a MetaTensor now generates a less verbose representation
  • DistributedSampler raises a ValueError if there are too few devices
  • OpenCV and VideoDataset modules are loaded lazily to avoid dependency issues
  • device in monai.engines.Workflow supports string values
  • Activations and AsDiscrete take kwargs as additional arguments
  • DataAnalyzer is now more efficient and writes summary stats before detailed all case stats
  • Base Docker image upgraded to nvcr.io/nvidia/pytorch:22.10-py3 from nvcr.io/nvidia/pytorch:22.09-py3
  • Simplified Conda environment file environment-dev.yml
  • Versioneer dependency upgraded to 0.23 from 0.19

Deprecated

  • NibabelReader input argument dtype is deprecated, the reader will use the original dtype of the image

Removed

  • Support for PyTorch 1.7