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@wyli wyli released this 12 Oct 17:37
· 185 commits to dev since this release
1.3.0
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Learn about vigilant mode.

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)
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