1.3.0

Added

• Intensity transforms ScaleIntensityFixedMean and RandScaleIntensityFixedMean (#6542)
• UltrasoundConfidenceMapTransform used for computing confidence map from an ultrasound image (#6709)
• channel_wise support in RandScaleIntensity and RandShiftIntensity (#6793, #7025)
• RandSimulateLowResolution and RandSimulateLowResolutiond (#6806)
• SignalFillEmptyd (#7011)
• Euclidean distance transform DistanceTransformEDT with GPU support (#6981)
• Port loss and metrics from monai-generative (#6729, #6836)
• Support invert_image and retain_stats in AdjustContrast and RandAdjustContrast (#6542)
• New network DAF3D and Quicknat (#6306)
• Support sincos position embedding (#6986)
• ZarrAvgMerger used for patch inference (#6633)
• Dataset tracking support to MLFlowHandler (#6616)
• Considering spacing and subvoxel borders in SurfaceDiceMetric (#6681)
• CUCIM support for surface-related metrics (#7008)
• loss_fn support in IgniteMetric and renamed it to IgniteMetricHandler (#6695)
• CallableEventWithFilter and Events options for trigger_event in GarbageCollector (#6663)
• Support random sorting option to GridPatch, RandGridPatch, GridPatchd and RandGridPatchd (#6701)
• Support multi-threaded batch sampling in PatchInferer (#6139)
• SoftclDiceLoss and SoftDiceclDiceLoss (#6763)
• HausdorffDTLoss and LogHausdorffDTLoss (#6994)
• Documentation for TensorFloat-32 (#6770)
• Docstring format guide (#6780)
• GDSDataset support for GDS (#6778)
• PyTorch backend support for MapLabelValue (#6872)
• filter_func in copy_model_state to filter the weights to be loaded and filter_swinunetr (#6917)
• stats_sender to MonaiAlgo for FL stats (#6984)
• freeze_layers to help freeze specific layers (#6970)

misc.

• Refactor multi-node running command used in Auto3DSeg into dedicated functions (#6623)
• Support str type annotation to device in ToTensorD (#6737)
• Improve logging message and file name extenstion in DataAnalyzer for Auto3DSeg (#6758)
• Set data_range as a property in SSIMLoss (#6788)
• Unify environment variable access (#7084)
• end_lr support in WarmupCosineSchedule (#6662)
• Add ClearML as optional dependency (#6827)
• yandex.disk support in download_url (#6667)
• Improve config expression error message (#6977)

Fixed

transforms

• Make convert_box_to_mask throw errors when box size larger than the image (#6637)
• Fix lazy mode in RandAffine (#6774)
• Raise ValueError when map_items is bool in Compose (#6882)
• Improve performance for NormalizeIntensity (#6887)
• Fix mismatched shape in Spacing (#6912)
• Avoid FutureWarning in CropForeground (#6934)
• Fix Lazy=True ignored when using Dataset call (#6975)
• Shape check for arbitrary types for DataStats (#7082)

data

• Fix wrong spacing checking logic in PydicomReader and broken link in ITKReader (#6660)
• Fix boolean indexing of batched MetaTensor (#6781)
• Raise warning when multiprocessing in DataLoader (#6830)
• Remove shuffle in DistributedWeightedRandomSampler (#6886)
• Fix missing SegmentDescription in PydicomReader (#6937)
• Fix reading dicom series error in ITKReader (#6943)
• Fix KeyError in PydicomReader (#6946)
• Update metatensor_to_itk_image to accept RAS MetaTensor and update default 'space' in NrrdReader to SpaceKeys.LPS (#7000)
• Collate common meta dictionary keys (#7054)

metrics and losses

• Fixed bug in GeneralizedDiceLoss when batch=True (#6775)
• Support for BCEWithLogitsLoss in DiceCELoss (#6924)
• Support for weight in Dice and related losses (#7098)

networks

• Use np.prod instead of np.product (#6639)
• Fix dimension issue in MBConvBlock (#6672)
• Fix hard-coded up_kernel_size in ViTAutoEnc (#6735)
• Remove hard-coded bias_downsample in resnet (#6848)
• Fix unused kernel_size in ResBlock (#6999)
• Allow for defining reference grid on non-integer coordinates (#7032)
• Padding option for autoencoder (#7068)
• Lower peak memory usage for SegResNetDS (#7066)

bundle

• Set train_dataset_data and dataset_data to unrequired in BundleProperty (#6607)
• Set None to properties that do not have REF_ID (#6607)
• Fix AttributeError for default value in get_parsed_content for ConfigParser (#6756)
• Update monai.bundle.scripts to support NGC hosting (#6828, #6997)
• Add MetaProperties (#6835)
• Add create_workflow and update load function (#6835)
• Add bundle root directory to Python search directories automatically (#6910)
• Generate properties for bundle docs automatically (#6918)
• Move download_large_files from model zoo to core (#6958)
• Bundle syntax # as alias of :: (#6955)
• Fix bundle download naming issue (#6969, #6963)
• Simplify the usage of ckpt_export (#6965)
• update_kwargs in monai.bundle.script for merging multiple configs (#7109)

engines and handlers

• Added int options for iteration_log and epoch_log in TensorBoardStatsHandler (#7027)
• Support to run validator at training start (#7108)

misc.

• Fix device fallback error in DataAnalyzer (#6658)
• Add int check for current_mode in convert_applied_interp_mode (#6719)
• Consistent type in convert_to_contiguous (#6849)
• Label argmax in DataAnalyzer when retry on CPU (#6852)
• Fix DataAnalyzer with histogram_only=True (#6874)
• Fix AttributeError in RankFilter in single GPU environment (#6895)
• Remove the default warning on TORCH_ALLOW_TF32_CUBLAS_OVERRIDE and add debug print info (#6909)
• Hide user information in print_config (#6913, #6922)
• Optionally pass coordinates to predictor during sliding window (#6795)
• Proper ensembling when trained with a sigmoid in AutoRunner (#6588)
• Fixed test_retinanet by increasing absolute differences (#6615)
• Add type check to avoid comparing a np.array with a string in _check_kwargs_are_present (#6624)
• Fix md5 hashing with FIPS mode (#6635)
• Capture failures from Auto3DSeg related subprocess calls (#6596)
• Code formatting tool for user-specified directory (#7106)
• Various docstring fixes

Changed

• Base Docker image upgraded to nvcr.io/nvidia/pytorch:23.08-py3 from nvcr.io/nvidia/pytorch:23.03-py3

Deprecated

• allow_smaller=True; allow_smaller=False will be the new default in CropForeground and generate_spatial_bounding_box (#6736)
• dropout_prob in VNet in favor of dropout_prob_down and dropout_prob_up (#6768)
• workflow in BundleWorkflow in favor of workflow_type(#6768)
• pos_embed in PatchEmbeddingBlock in favor of proj_type(#6986)
• net_name and net_kwargs in download in favor of model(#7016)
• img_size parameter in SwinUNETR (#7093)

Removed

• pad_val, stride, per_channel and upsampler in OcclusionSensitivity (#6642)
• compute_meaniou (#7019)
• AsChannelFirst, AddChanneland SplitChannel (#7019)
• create_multigpu_supervised_trainer and create_multigpu_supervised_evaluator (#7019)
• runner_id in run (#7019)
• data_src_cfg_filename in AlgoEnsembleBuilder (#7019)
• get_validation_stats in Evaluator and get_train_stats in Trainer (#7019)
• epoch_interval and iteration_interval in TensorBoardStatsHandler (#7019)
• some self-hosted test (#7041)