1.3.1

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)