├── .clang-format ├── .coderabbit.yaml ├── .deepsource.toml ├── .dockerignore ├── .gitattributes ├── .github ├── CODEOWNERS ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── question.md ├── codecov.yml ├── dco.yml ├── dependabot.yml ├── pull_request_template.md └── workflows │ ├── blossom-ci.yml │ ├── chatops.yml │ ├── codeql-analysis.yml │ ├── conda.yml │ ├── cron-ngc-bundle.yml │ ├── cron.yml │ ├── docker.yml │ ├── integration.yml │ ├── pythonapp-gpu.yml │ ├── pythonapp-min.yml │ ├── pythonapp.yml │ ├── release.yml │ ├── setupapp.yml │ └── weekly-preview.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── SECURITY.md ├── docs ├── .readthedocs.yaml ├── Makefile ├── _static │ └── custom.css ├── images │ ├── 3d_paired.png │ ├── BTCV_organs.png │ ├── MONAI-logo-color.png │ ├── MONAI_arch.png │ ├── MONAI_bundle_cloud.png │ ├── MONAI_clouds.png │ ├── MONAI_map_cloud.png │ ├── UNETR.png │ ├── affine.png │ ├── amp_training_a100.png │ ├── amp_training_v100.png │ ├── arch_modules.png │ ├── auto3dseg.png │ ├── blend.png │ ├── blend_images.png │ ├── brats_distributed.png │ ├── cache_dataset.png │ ├── cam.png │ ├── coplenet.png │ ├── dataset_progress.png │ ├── datasets_speed.png │ ├── decollate_batch.png │ ├── deepedit.png │ ├── deepgrow.png │ ├── deepgrow_scheme.png │ ├── detection.png │ ├── dints-overview.png │ ├── exp_mgmt.png │ ├── fast_training.png │ ├── favicon.ico │ ├── federated.svg │ ├── gmm_feature_set_comparison_s.png │ ├── hovernet_diagram.png │ ├── invert_transforms.png │ ├── lazy_resampling_apply_pending_example.svg │ ├── lazy_resampling_homogeneous_matrices.svg │ ├── lazy_resampling_lazy_example_1.svg │ ├── lazy_resampling_none_example.svg │ ├── lazy_resampling_trad_example_1.svg │ ├── lr_finder.png │ ├── maisi_infer.png │ ├── maisi_train.png │ ├── matshow3d.png │ ├── medical_transforms.png │ ├── metrics_report.png │ ├── mil-patches.jpg │ ├── models_ensemble.png │ ├── mri_recon.png │ ├── nsight_comparison.png │ ├── nuclick.png │ ├── pathology-meta.png │ ├── pathology.png │ ├── postprocessing_transforms.png │ ├── precision_options.png │ ├── python.svg │ ├── sliding_window.png │ ├── ssl_overview.png │ ├── swin_unetr.png │ ├── threaddataloader.png │ ├── transfer_mmar.png │ ├── tta.png │ ├── unet-pipe.png │ ├── vista2d.png │ ├── vista3d.png │ └── workflows.png ├── requirements.txt └── source │ ├── MONAI-logo-color.png │ ├── api.rst │ ├── apidocs │ ├── modules.rst │ └── monai.rst │ ├── applications.md │ ├── apps.rst │ ├── auto3dseg.rst │ ├── bundle.rst │ ├── bundle_intro.rst │ ├── conf.py │ ├── config_syntax.md │ ├── contrib.rst │ ├── data.rst │ ├── engines.rst │ ├── fl.rst │ ├── handlers.rst │ ├── highlights.rst │ ├── index.rst │ ├── inferers.rst │ ├── installation.md │ ├── lazy_resampling.rst │ ├── losses.rst │ ├── mb_properties.rst │ ├── mb_specification.rst │ ├── metrics.rst │ ├── modules.md │ ├── networks.rst │ ├── optimizers.rst │ ├── precision_accelerating.md │ ├── transforms.rst │ ├── transforms_idx.rst │ ├── utils.rst │ ├── visualize.rst │ ├── whatsnew.rst │ ├── whatsnew_0_5.md │ ├── whatsnew_0_6.md │ ├── whatsnew_0_7.md │ ├── whatsnew_0_8.md │ ├── whatsnew_0_9.md │ ├── whatsnew_1_0.md │ ├── whatsnew_1_1.md │ ├── whatsnew_1_2.md │ ├── whatsnew_1_3.md │ ├── whatsnew_1_4.md │ ├── whatsnew_1_5.md │ └── whatsnew_1_5_1.md ├── environment-dev.yml ├── monai ├── README.md ├── __init__.py ├── _extensions │ ├── __init__.py │ ├── gmm │ │ ├── gmm.cpp │ │ ├── gmm.h │ │ ├── gmm_cpu.cpp │ │ ├── gmm_cuda.cu │ │ └── gmm_cuda_linalg.cuh │ └── loader.py ├── _version.py ├── apps │ ├── __init__.py │ ├── auto3dseg │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── auto_runner.py │ │ ├── bundle_gen.py │ │ ├── data_analyzer.py │ │ ├── ensemble_builder.py │ │ ├── hpo_gen.py │ │ ├── transforms.py │ │ └── utils.py │ ├── datasets.py │ ├── deepedit │ │ ├── __init__.py │ │ ├── interaction.py │ │ └── transforms.py │ ├── deepgrow │ │ ├── __init__.py │ │ ├── dataset.py │ │ ├── interaction.py │ │ └── transforms.py │ ├── detection │ │ ├── __init__.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ ├── coco.py │ │ │ └── matching.py │ │ ├── networks │ │ │ ├── __init__.py │ │ │ ├── retinanet_detector.py │ │ │ └── retinanet_network.py │ │ ├── transforms │ │ │ ├── __init__.py │ │ │ ├── array.py │ │ │ ├── box_ops.py │ │ │ └── dictionary.py │ │ └── utils │ │ │ ├── ATSS_matcher.py │ │ │ ├── __init__.py │ │ │ ├── anchor_utils.py │ │ │ ├── box_coder.py │ │ │ ├── box_selector.py │ │ │ ├── detector_utils.py │ │ │ ├── hard_negative_sampler.py │ │ │ └── predict_utils.py │ ├── generation │ │ ├── __init__.py │ │ └── maisi │ │ │ ├── __init__.py │ │ │ └── networks │ │ │ ├── __init__.py │ │ │ ├── autoencoderkl_maisi.py │ │ │ ├── controlnet_maisi.py │ │ │ └── diffusion_model_unet_maisi.py │ ├── mmars │ │ ├── __init__.py │ │ ├── mmars.py │ │ └── model_desc.py │ ├── nnunet │ │ ├── __init__.py │ │ ├── __main__.py │ │ ├── nnunet_bundle.py │ │ ├── nnunetv2_runner.py │ │ └── utils.py │ ├── nuclick │ │ ├── __init__.py │ │ └── transforms.py │ ├── pathology │ │ ├── __init__.py │ │ ├── engines │ │ │ ├── __init__.py │ │ │ └── utils.py │ │ ├── handlers │ │ │ ├── __init__.py │ │ │ └── utils.py │ │ ├── inferers │ │ │ ├── __init__.py │ │ │ └── inferer.py │ │ ├── losses │ │ │ ├── __init__.py │ │ │ └── hovernet_loss.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ └── lesion_froc.py │ │ ├── transforms │ │ │ ├── __init__.py │ │ │ ├── post │ │ │ │ ├── __init__.py │ │ │ │ ├── array.py │ │ │ │ └── dictionary.py │ │ │ └── stain │ │ │ │ ├── __init__.py │ │ │ │ ├── array.py │ │ │ │ └── dictionary.py │ │ └── utils.py │ ├── reconstruction │ │ ├── __init__.py │ │ ├── complex_utils.py │ │ ├── fastmri_reader.py │ │ ├── mri_utils.py │ │ ├── networks │ │ │ ├── __init__.py │ │ │ ├── blocks │ │ │ │ ├── __init__.py │ │ │ │ └── varnetblock.py │ │ │ └── nets │ │ │ │ ├── __init__.py │ │ │ │ ├── coil_sensitivity_model.py │ │ │ │ ├── complex_unet.py │ │ │ │ ├── utils.py │ │ │ │ └── varnet.py │ │ └── transforms │ │ │ ├── __init__.py │ │ │ ├── array.py │ │ │ └── dictionary.py │ ├── tcia │ │ ├── __init__.py │ │ ├── label_desc.py │ │ └── utils.py │ ├── utils.py │ └── vista3d │ │ ├── __init__.py │ │ ├── inferer.py │ │ ├── sampler.py │ │ └── transforms.py ├── auto3dseg │ ├── __init__.py │ ├── algo_gen.py │ ├── analyzer.py │ ├── operations.py │ ├── seg_summarizer.py │ └── utils.py ├── bundle │ ├── __init__.py │ ├── __main__.py │ ├── config_item.py │ ├── config_parser.py │ ├── properties.py │ ├── reference_resolver.py │ ├── scripts.py │ ├── utils.py │ └── workflows.py ├── config │ ├── __init__.py │ ├── deviceconfig.py │ └── type_definitions.py ├── csrc │ ├── ext.cpp │ ├── filtering │ │ ├── bilateral │ │ │ ├── bilateral.cpp │ │ │ ├── bilateral.h │ │ │ ├── bilateralfilter_cpu.cpp │ │ │ ├── bilateralfilter_cpu_phl.cpp │ │ │ ├── bilateralfilter_cuda.cu │ │ │ └── bilateralfilter_cuda_phl.cu │ │ ├── filtering.h │ │ ├── permutohedral │ │ │ ├── hash_table.cuh │ │ │ ├── permutohedral.cpp │ │ │ ├── permutohedral.h │ │ │ ├── permutohedral_cpu.cpp │ │ │ └── permutohedral_cuda.cu │ │ ├── trainable_bilateral │ │ │ ├── bf_layer_cpu_backward.cpp │ │ │ ├── bf_layer_cpu_forward.cpp │ │ │ ├── bf_layer_gpu_backward.cu │ │ │ ├── bf_layer_gpu_forward.cu │ │ │ ├── trainable_bilateral.cpp │ │ │ └── trainable_bilateral.h │ │ └── trainable_joint_bilateral │ │ │ ├── jbf_layer_cpu_backward.cpp │ │ │ ├── jbf_layer_cpu_forward.cpp │ │ │ ├── jbf_layer_gpu_backward.cu │ │ │ ├── jbf_layer_gpu_forward.cu │ │ │ ├── trainable_joint_bilateral.cpp │ │ │ └── trainable_joint_bilateral.h │ ├── lltm │ │ ├── lltm.h │ │ ├── lltm_cpu.cpp │ │ └── lltm_cuda.cu │ ├── resample │ │ ├── bounds_common.h │ │ ├── interpolation_common.h │ │ ├── pushpull.h │ │ ├── pushpull_cpu.cpp │ │ └── pushpull_cuda.cu │ └── utils │ │ ├── common_utils.h │ │ ├── meta_macros.h │ │ ├── resample_utils.h │ │ ├── tensor_description.h │ │ └── tensor_indexing.h ├── data │ ├── __init__.py │ ├── box_utils.py │ ├── csv_saver.py │ ├── dataloader.py │ ├── dataset.py │ ├── dataset_summary.py │ ├── decathlon_datalist.py │ ├── fft_utils.py │ ├── folder_layout.py │ ├── grid_dataset.py │ ├── image_dataset.py │ ├── image_reader.py │ ├── image_writer.py │ ├── iterable_dataset.py │ ├── itk_torch_bridge.py │ ├── meta_obj.py │ ├── meta_tensor.py │ ├── samplers.py │ ├── synthetic.py │ ├── test_time_augmentation.py │ ├── thread_buffer.py │ ├── torchscript_utils.py │ ├── ultrasound_confidence_map.py │ ├── utils.py │ ├── video_dataset.py │ ├── wsi_datasets.py │ └── wsi_reader.py ├── engines │ ├── __init__.py │ ├── evaluator.py │ ├── trainer.py │ ├── utils.py │ └── workflow.py ├── fl │ ├── __init__.py │ ├── client │ │ ├── __init__.py │ │ ├── client_algo.py │ │ └── monai_algo.py │ └── utils │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── exchange_object.py │ │ └── filters.py ├── handlers │ ├── __init__.py │ ├── average_precision.py │ ├── checkpoint_loader.py │ ├── checkpoint_saver.py │ ├── classification_saver.py │ ├── clearml_handlers.py │ ├── confusion_matrix.py │ ├── decollate_batch.py │ ├── earlystop_handler.py │ ├── garbage_collector.py │ ├── hausdorff_distance.py │ ├── ignite_metric.py │ ├── logfile_handler.py │ ├── lr_schedule_handler.py │ ├── mean_dice.py │ ├── mean_iou.py │ ├── metric_logger.py │ ├── metrics_reloaded_handler.py │ ├── metrics_saver.py │ ├── mlflow_handler.py │ ├── nvtx_handlers.py │ ├── panoptic_quality.py │ ├── parameter_scheduler.py │ ├── postprocessing.py │ ├── probability_maps.py │ ├── regression_metrics.py │ ├── roc_auc.py │ ├── smartcache_handler.py │ ├── stats_handler.py │ ├── surface_distance.py │ ├── tensorboard_handlers.py │ ├── trt_handler.py │ ├── utils.py │ └── validation_handler.py ├── inferers │ ├── __init__.py │ ├── inferer.py │ ├── merger.py │ ├── splitter.py │ └── utils.py ├── losses │ ├── __init__.py │ ├── adversarial_loss.py │ ├── barlow_twins.py │ ├── cldice.py │ ├── contrastive.py │ ├── deform.py │ ├── dice.py │ ├── ds_loss.py │ ├── focal_loss.py │ ├── giou_loss.py │ ├── hausdorff_loss.py │ ├── image_dissimilarity.py │ ├── multi_scale.py │ ├── nacl_loss.py │ ├── perceptual.py │ ├── spatial_mask.py │ ├── spectral_loss.py │ ├── ssim_loss.py │ ├── sure_loss.py │ ├── tversky.py │ ├── unified_focal_loss.py │ └── utils.py ├── metrics │ ├── __init__.py │ ├── active_learning_metrics.py │ ├── average_precision.py │ ├── confusion_matrix.py │ ├── cumulative_average.py │ ├── f_beta_score.py │ ├── fid.py │ ├── froc.py │ ├── generalized_dice.py │ ├── hausdorff_distance.py │ ├── loss_metric.py │ ├── meandice.py │ ├── meaniou.py │ ├── metric.py │ ├── mmd.py │ ├── panoptic_quality.py │ ├── regression.py │ ├── rocauc.py │ ├── surface_dice.py │ ├── surface_distance.py │ ├── utils.py │ └── wrapper.py ├── networks │ ├── __init__.py │ ├── blocks │ │ ├── __init__.py │ │ ├── acti_norm.py │ │ ├── activation.py │ │ ├── activation_checkpointing.py │ │ ├── aspp.py │ │ ├── attention_utils.py │ │ ├── backbone_fpn_utils.py │ │ ├── cablock.py │ │ ├── convolutions.py │ │ ├── crf.py │ │ ├── crossattention.py │ │ ├── denseblock.py │ │ ├── dints_block.py │ │ ├── downsample.py │ │ ├── dynunet_block.py │ │ ├── encoder.py │ │ ├── fcn.py │ │ ├── feature_pyramid_network.py │ │ ├── fft_utils_t.py │ │ ├── localnet_block.py │ │ ├── mednext_block.py │ │ ├── mlp.py │ │ ├── patchembedding.py │ │ ├── pos_embed_utils.py │ │ ├── regunet_block.py │ │ ├── rel_pos_embedding.py │ │ ├── segresnet_block.py │ │ ├── selfattention.py │ │ ├── spade_norm.py │ │ ├── spatialattention.py │ │ ├── squeeze_and_excitation.py │ │ ├── text_embedding.py │ │ ├── transformerblock.py │ │ ├── unetr_block.py │ │ ├── upsample.py │ │ └── warp.py │ ├── layers │ │ ├── __init__.py │ │ ├── conjugate_gradient.py │ │ ├── convutils.py │ │ ├── drop_path.py │ │ ├── factories.py │ │ ├── filtering.py │ │ ├── gmm.py │ │ ├── simplelayers.py │ │ ├── spatial_transforms.py │ │ ├── utils.py │ │ ├── vector_quantizer.py │ │ └── weight_init.py │ ├── nets │ │ ├── __init__.py │ │ ├── ahnet.py │ │ ├── attentionunet.py │ │ ├── autoencoder.py │ │ ├── autoencoderkl.py │ │ ├── basic_unet.py │ │ ├── basic_unetplusplus.py │ │ ├── cell_sam_wrapper.py │ │ ├── classifier.py │ │ ├── controlnet.py │ │ ├── daf3d.py │ │ ├── densenet.py │ │ ├── diffusion_model_unet.py │ │ ├── dints.py │ │ ├── dynunet.py │ │ ├── efficientnet.py │ │ ├── flexible_unet.py │ │ ├── fullyconnectednet.py │ │ ├── generator.py │ │ ├── highresnet.py │ │ ├── hovernet.py │ │ ├── masked_autoencoder_vit.py │ │ ├── mednext.py │ │ ├── milmodel.py │ │ ├── netadapter.py │ │ ├── patchgan_discriminator.py │ │ ├── quicknat.py │ │ ├── regressor.py │ │ ├── regunet.py │ │ ├── resnet.py │ │ ├── restormer.py │ │ ├── segresnet.py │ │ ├── segresnet_ds.py │ │ ├── senet.py │ │ ├── spade_autoencoderkl.py │ │ ├── spade_diffusion_model_unet.py │ │ ├── spade_network.py │ │ ├── swin_unetr.py │ │ ├── torchvision_fc.py │ │ ├── transchex.py │ │ ├── transformer.py │ │ ├── unet.py │ │ ├── unetr.py │ │ ├── varautoencoder.py │ │ ├── vista3d.py │ │ ├── vit.py │ │ ├── vitautoenc.py │ │ ├── vnet.py │ │ ├── voxelmorph.py │ │ └── vqvae.py │ ├── schedulers │ │ ├── __init__.py │ │ ├── ddim.py │ │ ├── ddpm.py │ │ ├── pndm.py │ │ ├── rectified_flow.py │ │ └── scheduler.py │ ├── trt_compiler.py │ └── utils.py ├── optimizers │ ├── __init__.py │ ├── lr_finder.py │ ├── lr_scheduler.py │ ├── novograd.py │ └── utils.py ├── py.typed ├── torch.patch ├── transforms │ ├── __init__.py │ ├── adaptors.py │ ├── compose.py │ ├── croppad │ │ ├── __init__.py │ │ ├── array.py │ │ ├── batch.py │ │ ├── dictionary.py │ │ └── functional.py │ ├── intensity │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── inverse.py │ ├── inverse_batch_transform.py │ ├── io │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── lazy │ │ ├── __init__.py │ │ ├── array.py │ │ ├── dictionary.py │ │ ├── functional.py │ │ └── utils.py │ ├── meta_utility │ │ ├── __init__.py │ │ └── dictionary.py │ ├── nvtx.py │ ├── post │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── regularization │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── signal │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── smooth_field │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── spatial │ │ ├── __init__.py │ │ ├── array.py │ │ ├── dictionary.py │ │ └── functional.py │ ├── traits.py │ ├── transform.py │ ├── utility │ │ ├── __init__.py │ │ ├── array.py │ │ └── dictionary.py │ ├── utils.py │ ├── utils_create_transform_ims.py │ ├── utils_morphological_ops.py │ └── utils_pytorch_numpy_unification.py ├── utils │ ├── __init__.py │ ├── component_store.py │ ├── decorators.py │ ├── deprecate_utils.py │ ├── dist.py │ ├── enums.py │ ├── jupyter_utils.py │ ├── misc.py │ ├── module.py │ ├── nvtx.py │ ├── ordering.py │ ├── profiling.py │ ├── state_cacher.py │ ├── tf32.py │ └── type_conversion.py └── visualize │ ├── __init__.py │ ├── class_activation_maps.py │ ├── gradient_based.py │ ├── img2tensorboard.py │ ├── occlusion_sensitivity.py │ ├── utils.py │ └── visualizer.py ├── pyproject.toml ├── requirements-dev.txt ├── requirements-min.txt ├── requirements.txt ├── runtests.sh ├── setup.cfg ├── setup.py ├── tests ├── __init__.py ├── apps │ ├── __init__.py │ ├── deepedit │ │ ├── __init__.py │ │ └── test_deepedit_transforms.py │ ├── deepgrow │ │ ├── __init__.py │ │ ├── test_deepgrow_dataset.py │ │ └── transforms │ │ │ ├── __init__.py │ │ │ ├── test_deepgrow_interaction.py │ │ │ └── test_deepgrow_transforms.py │ ├── detection │ │ ├── __init__.py │ │ ├── metrics │ │ │ ├── __init__.py │ │ │ └── test_detection_coco_metrics.py │ │ ├── networks │ │ │ ├── __init__.py │ │ │ ├── test_retinanet.py │ │ │ └── test_retinanet_detector.py │ │ ├── test_box_transform.py │ │ └── utils │ │ │ ├── __init__.py │ │ │ ├── test_anchor_box.py │ │ │ ├── test_atss_box_matcher.py │ │ │ ├── test_box_coder.py │ │ │ ├── test_detector_boxselector.py │ │ │ ├── test_detector_utils.py │ │ │ └── test_hardnegsampler.py │ ├── maisi │ │ └── networks │ │ │ ├── __init__.py │ │ │ ├── test_autoencoderkl_maisi.py │ │ │ ├── test_controlnet_maisi.py │ │ │ └── test_diffusion_model_unet_maisi.py │ ├── nuclick │ │ ├── __init__.py │ │ └── test_nuclick_transforms.py │ ├── pathology │ │ ├── __init__.py │ │ ├── handlers │ │ │ ├── __init__.py │ │ │ └── test_from_engine_hovernet.py │ │ ├── test_lesion_froc.py │ │ ├── test_pathology_prob_nms.py │ │ ├── test_prepare_batch_hovernet.py │ │ ├── test_sliding_window_hovernet_inference.py │ │ └── transforms │ │ │ ├── __init__.py │ │ │ ├── post │ │ │ ├── __init__.py │ │ │ ├── test_generate_distance_map.py │ │ │ ├── test_generate_distance_mapd.py │ │ │ ├── test_generate_instance_border.py │ │ │ ├── test_generate_instance_borderd.py │ │ │ ├── test_generate_instance_centroid.py │ │ │ ├── test_generate_instance_centroidd.py │ │ │ ├── test_generate_instance_contour.py │ │ │ ├── test_generate_instance_contourd.py │ │ │ ├── test_generate_instance_type.py │ │ │ ├── test_generate_instance_typed.py │ │ │ ├── test_generate_succinct_contour.py │ │ │ ├── test_generate_succinct_contourd.py │ │ │ ├── test_generate_watershed_markers.py │ │ │ ├── test_generate_watershed_markersd.py │ │ │ ├── test_generate_watershed_mask.py │ │ │ ├── test_generate_watershed_maskd.py │ │ │ ├── test_hovernet_instance_map_post_processing.py │ │ │ ├── test_hovernet_instance_map_post_processingd.py │ │ │ ├── test_hovernet_nuclear_type_post_processing.py │ │ │ ├── test_watershed.py │ │ │ └── test_watershedd.py │ │ │ ├── test_pathology_he_stain.py │ │ │ └── test_pathology_he_stain_dict.py │ ├── reconstruction │ │ ├── __init__.py │ │ ├── nets │ │ │ ├── __init__.py │ │ │ └── test_recon_net_utils.py │ │ ├── test_complex_utils.py │ │ ├── test_fastmri_reader.py │ │ ├── test_mri_utils.py │ │ └── transforms │ │ │ ├── __init__.py │ │ │ ├── test_kspace_mask.py │ │ │ ├── test_reference_based_normalize_intensity.py │ │ │ └── test_reference_based_spatial_cropd.py │ ├── test_auto3dseg.py │ ├── test_auto3dseg_bundlegen.py │ ├── test_check_hash.py │ ├── test_cross_validation.py │ ├── test_decathlondataset.py │ ├── test_download_and_extract.py │ ├── test_download_url_yandex.py │ ├── test_mednistdataset.py │ ├── test_mmar_download.py │ ├── test_tciadataset.py │ └── vista3d │ │ ├── __init__.py │ │ ├── test_point_based_window_inferer.py │ │ ├── test_vista3d_sampler.py │ │ └── test_vista3d_transforms.py ├── bundle │ ├── __init__.py │ ├── test_bundle_ckpt_export.py │ ├── test_bundle_download.py │ ├── test_bundle_get_data.py │ ├── test_bundle_push_to_hf_hub.py │ ├── test_bundle_trt_export.py │ ├── test_bundle_utils.py │ ├── test_bundle_verify_metadata.py │ ├── test_bundle_verify_net.py │ ├── test_bundle_workflow.py │ ├── test_component_locator.py │ ├── test_config_item.py │ ├── test_config_parser.py │ └── test_reference_resolver.py ├── clang_format_utils.py ├── config │ ├── __init__.py │ ├── test_cv2_dist.py │ └── test_print_info.py ├── croppers.py ├── data │ ├── meta_tensor │ │ ├── test_meta_tensor.py │ │ └── test_to_from_meta_tensord.py │ ├── test_arraydataset.py │ ├── test_box_utils.py │ ├── test_cachedataset.py │ ├── test_cachedataset_parallel.py │ ├── test_cachedataset_persistent_workers.py │ ├── test_cachentransdataset.py │ ├── test_check_missing_files.py │ ├── test_create_cross_validation_datalist.py │ ├── test_csv_dataset.py │ ├── test_csv_iterable_dataset.py │ ├── test_csv_saver.py │ ├── test_dataloader.py │ ├── test_dataset.py │ ├── test_dataset_func.py │ ├── test_dataset_summary.py │ ├── test_fft_utils.py │ ├── test_folder_layout.py │ ├── test_gdsdataset.py │ ├── test_grid_dataset.py │ ├── test_handler_smartcache.py │ ├── test_hashing.py │ ├── test_header_correct.py │ ├── test_image_dataset.py │ ├── test_image_rw.py │ ├── test_init_reader.py │ ├── test_is_supported_format.py │ ├── test_iterable_dataset.py │ ├── test_itk_torch_bridge.py │ ├── test_itk_writer.py │ ├── test_list_data_collate.py │ ├── test_lmdbdataset.py │ ├── test_lmdbdataset_dist.py │ ├── test_load_decathlon_datalist.py │ ├── test_make_nifti.py │ ├── test_mapping_file.py │ ├── test_masked_patch_wsi_dataset.py │ ├── test_nifti_header_revise.py │ ├── test_nifti_rw.py │ ├── test_npzdictitemdataset.py │ ├── test_nrrd_reader.py │ ├── test_numpy_reader.py │ ├── test_partition_dataset.py │ ├── test_partition_dataset_classes.py │ ├── test_patch_dataset.py │ ├── test_patch_wsi_dataset.py │ ├── test_persistentdataset.py │ ├── test_persistentdataset_dist.py │ ├── test_pil_reader.py │ ├── test_png_rw.py │ ├── test_resample_datalist.py │ ├── test_sampler_dist.py │ ├── test_select_cross_validation_folds.py │ ├── test_shuffle_buffer.py │ ├── test_sliding_patch_wsi_dataset.py │ ├── test_smartcachedataset.py │ ├── test_synthetic.py │ ├── test_thread_buffer.py │ ├── test_threadcontainer.py │ ├── test_video_datasets.py │ ├── test_weighted_random_sampler_dist.py │ ├── test_zipdataset.py │ └── utils │ │ ├── test_decollate.py │ │ ├── test_dev_collate.py │ │ ├── test_file_basename.py │ │ ├── test_ori_ras_lps.py │ │ └── test_zoom_affine.py ├── engines │ ├── __init__.py │ ├── test_ensemble_evaluator.py │ ├── test_prepare_batch_default.py │ ├── test_prepare_batch_default_dist.py │ ├── test_prepare_batch_diffusion.py │ └── test_prepare_batch_extra_input.py ├── fl │ ├── __init__.py │ ├── monai_algo │ │ ├── __init__.py │ │ ├── test_fl_monai_algo.py │ │ └── test_fl_monai_algo_dist.py │ ├── test_fl_monai_algo_stats.py │ └── utils │ │ ├── __init__.py │ │ └── test_fl_exchange_object.py ├── handlers │ ├── __init__.py │ ├── test_handler_average_precision.py │ ├── test_handler_checkpoint_loader.py │ ├── test_handler_checkpoint_saver.py │ ├── test_handler_classification_saver.py │ ├── test_handler_classification_saver_dist.py │ ├── test_handler_clearml_image.py │ ├── test_handler_clearml_stats.py │ ├── test_handler_confusion_matrix.py │ ├── test_handler_confusion_matrix_dist.py │ ├── test_handler_decollate_batch.py │ ├── test_handler_early_stop.py │ ├── test_handler_garbage_collector.py │ ├── test_handler_hausdorff_distance.py │ ├── test_handler_ignite_metric.py │ ├── test_handler_lr_scheduler.py │ ├── test_handler_mean_dice.py │ ├── test_handler_mean_iou.py │ ├── test_handler_metrics_reloaded.py │ ├── test_handler_metrics_saver.py │ ├── test_handler_metrics_saver_dist.py │ ├── test_handler_mlflow.py │ ├── test_handler_nvtx.py │ ├── test_handler_panoptic_quality.py │ ├── test_handler_parameter_scheduler.py │ ├── test_handler_post_processing.py │ ├── test_handler_prob_map_producer.py │ ├── test_handler_regression_metrics.py │ ├── test_handler_regression_metrics_dist.py │ ├── test_handler_rocauc.py │ ├── test_handler_rocauc_dist.py │ ├── test_handler_stats.py │ ├── test_handler_surface_distance.py │ ├── test_handler_tb_image.py │ ├── test_handler_tb_stats.py │ ├── test_handler_validation.py │ ├── test_trt_compile.py │ └── test_write_metrics_reports.py ├── hvd_evenly_divisible_all_gather.py ├── inferers │ ├── __init__.py │ ├── test_avg_merger.py │ ├── test_controlnet_inferers.py │ ├── test_diffusion_inferer.py │ ├── test_latent_diffusion_inferer.py │ ├── test_patch_inferer.py │ ├── test_saliency_inferer.py │ ├── test_slice_inferer.py │ ├── test_sliding_window_inference.py │ ├── test_sliding_window_splitter.py │ ├── test_wsi_sliding_window_splitter.py │ └── test_zarr_avg_merger.py ├── integration │ ├── __init__.py │ ├── test_auto3dseg_ensemble.py │ ├── test_auto3dseg_hpo.py │ ├── test_deepedit_interaction.py │ ├── test_hovernet_nuclear_type_post_processingd.py │ ├── test_integration_autorunner.py │ ├── test_integration_bundle_run.py │ ├── test_integration_classification_2d.py │ ├── test_integration_determinism.py │ ├── test_integration_fast_train.py │ ├── test_integration_gpu_customization.py │ ├── test_integration_lazy_samples.py │ ├── test_integration_nnunet_bundle.py │ ├── test_integration_nnunetv2_runner.py │ ├── test_integration_segmentation_3d.py │ ├── test_integration_sliding_window.py │ ├── test_integration_stn.py │ ├── test_integration_unet_2d.py │ ├── test_integration_workers.py │ ├── test_integration_workflows.py │ ├── test_integration_workflows_adversarial.py │ ├── test_integration_workflows_gan.py │ ├── test_loader_semaphore.py │ ├── test_mapping_filed.py │ ├── test_meta_affine.py │ ├── test_metatensor_integration.py │ ├── test_module_list.py │ ├── test_one_of.py │ ├── test_pad_collation.py │ ├── test_reg_loss_integration.py │ ├── test_retinanet_predict_utils.py │ ├── test_seg_loss_integration.py │ ├── test_spatial_combine_transforms.py │ ├── test_testtimeaugmentation.py │ ├── test_vis_gradbased.py │ └── test_vista3d_utils.py ├── lazy_transforms_utils.py ├── losses │ ├── __init__.py │ ├── deform │ │ ├── __init__.py │ │ ├── test_bending_energy.py │ │ └── test_diffusion_loss.py │ ├── image_dissimilarity │ │ ├── __init__.py │ │ ├── test_global_mutual_information_loss.py │ │ └── test_local_normalized_cross_correlation_loss.py │ ├── test_adversarial_loss.py │ ├── test_barlow_twins_loss.py │ ├── test_cldice_loss.py │ ├── test_contrastive_loss.py │ ├── test_dice_ce_loss.py │ ├── test_dice_focal_loss.py │ ├── test_dice_loss.py │ ├── test_ds_loss.py │ ├── test_focal_loss.py │ ├── test_generalized_dice_focal_loss.py │ ├── test_generalized_dice_loss.py │ ├── test_generalized_wasserstein_dice_loss.py │ ├── test_giou_loss.py │ ├── test_hausdorff_loss.py │ ├── test_masked_dice_loss.py │ ├── test_masked_loss.py │ ├── test_multi_scale.py │ ├── test_nacl_loss.py │ ├── test_perceptual_loss.py │ ├── test_spectral_loss.py │ ├── test_ssim_loss.py │ ├── test_sure_loss.py │ ├── test_tversky_loss.py │ └── test_unified_focal_loss.py ├── metrics │ ├── __init__.py │ ├── test_compute_average_precision.py │ ├── test_compute_confusion_matrix.py │ ├── test_compute_f_beta.py │ ├── test_compute_fid_metric.py │ ├── test_compute_froc.py │ ├── test_compute_generalized_dice.py │ ├── test_compute_meandice.py │ ├── test_compute_meaniou.py │ ├── test_compute_mmd_metric.py │ ├── test_compute_multiscalessim_metric.py │ ├── test_compute_panoptic_quality.py │ ├── test_compute_regression_metrics.py │ ├── test_compute_roc_auc.py │ ├── test_compute_variance.py │ ├── test_cumulative.py │ ├── test_cumulative_average.py │ ├── test_cumulative_average_dist.py │ ├── test_hausdorff_distance.py │ ├── test_label_quality_score.py │ ├── test_loss_metric.py │ ├── test_metrics_reloaded.py │ ├── test_ssim_metric.py │ ├── test_surface_dice.py │ └── test_surface_distance.py ├── min_tests.py ├── networks │ ├── __init__.py │ ├── blocks │ │ ├── __init__.py │ │ ├── dints_block │ │ │ ├── __init__.py │ │ │ ├── test_acn_block.py │ │ │ ├── test_factorized_increase.py │ │ │ ├── test_factorized_reduce.py │ │ │ └── test_p3d_block.py │ │ ├── test_CABlock.py │ │ ├── test_adn.py │ │ ├── test_convolutions.py │ │ ├── test_crf_cpu.py │ │ ├── test_crf_cuda.py │ │ ├── test_crossattention.py │ │ ├── test_denseblock.py │ │ ├── test_downsample_block.py │ │ ├── test_dynunet_block.py │ │ ├── test_fpn_block.py │ │ ├── test_localnet_block.py │ │ ├── test_mlp.py │ │ ├── test_patchembedding.py │ │ ├── test_regunet_block.py │ │ ├── test_se_block.py │ │ ├── test_se_blocks.py │ │ ├── test_segresnet_block.py │ │ ├── test_selfattention.py │ │ ├── test_simple_aspp.py │ │ ├── test_spatialattention.py │ │ ├── test_subpixel_upsample.py │ │ ├── test_text_encoding.py │ │ ├── test_transformerblock.py │ │ ├── test_unetr_block.py │ │ ├── test_upsample_block.py │ │ └── warp │ │ │ ├── __init__.py │ │ │ ├── test_dvf2ddf.py │ │ │ └── test_warp.py │ ├── layers │ │ ├── __init__.py │ │ ├── filtering │ │ │ ├── __init__.py │ │ │ ├── test_bilateral_approx_cpu.py │ │ │ ├── test_bilateral_approx_cuda.py │ │ │ ├── test_bilateral_precise.py │ │ │ ├── test_phl_cpu.py │ │ │ ├── test_phl_cuda.py │ │ │ ├── test_trainable_bilateral.py │ │ │ └── test_trainable_joint_bilateral.py │ │ ├── test_affine_transform.py │ │ ├── test_apply_filter.py │ │ ├── test_channel_pad.py │ │ ├── test_conjugate_gradient.py │ │ ├── test_drop_path.py │ │ ├── test_gaussian.py │ │ ├── test_gaussian_filter.py │ │ ├── test_get_layers.py │ │ ├── test_gmm.py │ │ ├── test_grid_pull.py │ │ ├── test_hilbert_transform.py │ │ ├── test_lltm.py │ │ ├── test_median_filter.py │ │ ├── test_polyval.py │ │ ├── test_preset_filters.py │ │ ├── test_savitzky_golay_filter.py │ │ ├── test_separable_filter.py │ │ ├── test_skip_connection.py │ │ ├── test_vector_quantizer.py │ │ └── test_weight_init.py │ ├── nets │ │ ├── __init__.py │ │ ├── dints │ │ │ ├── __init__.py │ │ │ ├── test_dints_cell.py │ │ │ └── test_dints_mixop.py │ │ ├── regunet │ │ │ ├── __init__.py │ │ │ ├── test_localnet.py │ │ │ └── test_regunet.py │ │ ├── test_ahnet.py │ │ ├── test_attentionunet.py │ │ ├── test_autoencoder.py │ │ ├── test_autoencoderkl.py │ │ ├── test_basic_unet.py │ │ ├── test_basic_unetplusplus.py │ │ ├── test_bundle_init_bundle.py │ │ ├── test_cell_sam_wrapper.py │ │ ├── test_checkpointunet.py │ │ ├── test_controlnet.py │ │ ├── test_daf3d.py │ │ ├── test_densenet.py │ │ ├── test_diffusion_model_unet.py │ │ ├── test_dints_network.py │ │ ├── test_discriminator.py │ │ ├── test_dynunet.py │ │ ├── test_efficientnet.py │ │ ├── test_flexible_unet.py │ │ ├── test_fullyconnectednet.py │ │ ├── test_generator.py │ │ ├── test_globalnet.py │ │ ├── test_highresnet.py │ │ ├── test_hovernet.py │ │ ├── test_masked_autoencoder_vit.py │ │ ├── test_mednext.py │ │ ├── test_milmodel.py │ │ ├── test_net_adapter.py │ │ ├── test_network_consistency.py │ │ ├── test_patch_gan_dicriminator.py │ │ ├── test_quicknat.py │ │ ├── test_resnet.py │ │ ├── test_restormer.py │ │ ├── test_segresnet.py │ │ ├── test_segresnet_ds.py │ │ ├── test_senet.py │ │ ├── test_spade_autoencoderkl.py │ │ ├── test_spade_diffusion_model_unet.py │ │ ├── test_spade_vaegan.py │ │ ├── test_swin_unetr.py │ │ ├── test_torchvision_fc_model.py │ │ ├── test_transchex.py │ │ ├── test_transformer.py │ │ ├── test_unet.py │ │ ├── test_unetr.py │ │ ├── test_varautoencoder.py │ │ ├── test_vista3d.py │ │ ├── test_vit.py │ │ ├── test_vitautoenc.py │ │ ├── test_vnet.py │ │ ├── test_voxelmorph.py │ │ ├── test_vqvae.py │ │ └── test_vqvaetransformer_inferer.py │ ├── schedulers │ │ ├── __init__.py │ │ ├── test_scheduler_ddim.py │ │ ├── test_scheduler_ddpm.py │ │ ├── test_scheduler_pndm.py │ │ └── test_scheduler_rflow.py │ ├── test_bundle_onnx_export.py │ ├── test_convert_to_onnx.py │ ├── test_convert_to_torchscript.py │ ├── test_convert_to_trt.py │ ├── test_save_state.py │ ├── test_to_onehot.py │ ├── test_varnet.py │ └── utils │ │ ├── __init__.py │ │ ├── test_copy_model_state.py │ │ ├── test_eval_mode.py │ │ ├── test_freeze_layers.py │ │ ├── test_pixelunshuffle.py │ │ ├── test_replace_module.py │ │ └── test_train_mode.py ├── nonconfig_workflow.py ├── optimizers │ ├── __init__.py │ ├── test_generate_param_groups.py │ ├── test_lr_finder.py │ ├── test_lr_scheduler.py │ └── test_optim_novograd.py ├── padders.py ├── profile_subclass │ ├── README.md │ ├── __init__.py │ ├── cprofile_profiling.py │ ├── min_classes.py │ ├── profiling.py │ └── pyspy_profiling.py ├── runner.py ├── test_call_dist.py ├── test_query_memory.py ├── test_timedcall_dist.py ├── test_utils.py ├── testing_data │ ├── 1D_BP_bwd.txt │ ├── 1D_BP_fwd.txt │ ├── CT_DICOM │ │ ├── 7106 │ │ ├── 7136 │ │ ├── 7166 │ │ └── 7196 │ ├── anatomical.nii │ ├── anatomical_label.nii.gz │ ├── bundle_test_network.py │ ├── config_fl_evaluate.json │ ├── config_fl_filters.json │ ├── config_fl_stats_1.json │ ├── config_fl_stats_2.json │ ├── config_fl_train.json │ ├── cpp_resample_answers.py │ ├── data_config.json │ ├── fl_infer_properties.json │ ├── image0.jpeg │ ├── image1.jpeg │ ├── inference.json │ ├── inference.yaml │ ├── integration_answers.py │ ├── kitty_test.jpg │ ├── logging.conf │ ├── matshow3d_patch_test.png │ ├── matshow3d_rgb_test.png │ ├── matshow3d_test.png │ ├── metadata.json │ ├── multi_gpu_evaluate.json │ ├── multi_gpu_train.json │ ├── python_workflow_properties.json │ ├── reoriented_anat_moved.nii │ ├── reoriented_anat_moved_label.nii.gz │ ├── responsive_inference.json │ ├── signal.npy │ ├── threadcontainer_plot_test.png │ ├── transform_metatensor_cases.yaml │ └── ultrasound_confidence_map │ │ ├── femur_input.png │ │ ├── femur_result.npy │ │ ├── neck_input.png │ │ └── neck_result.npy ├── transforms │ ├── __init__.py │ ├── compose │ │ ├── __init__.py │ │ ├── test_compose.py │ │ └── test_some_of.py │ ├── croppad │ │ ├── __init__.py │ │ ├── test_rand_weighted_crop.py │ │ └── test_rand_weighted_cropd.py │ ├── functional │ │ ├── __init__.py │ │ ├── test_apply.py │ │ └── test_resample.py │ ├── intensity │ │ ├── __init__.py │ │ ├── test_compute_ho_ver_maps.py │ │ ├── test_compute_ho_ver_maps_d.py │ │ ├── test_foreground_mask.py │ │ ├── test_foreground_maskd.py │ │ ├── test_rand_histogram_shiftd.py │ │ ├── test_scale_intensity_range_percentiles.py │ │ └── test_scale_intensity_range_percentilesd.py │ ├── inverse │ │ ├── __init__.py │ │ ├── test_inverse.py │ │ ├── test_inverse_array.py │ │ ├── test_inverse_dict.py │ │ ├── test_invert.py │ │ ├── test_invertd.py │ │ └── test_traceable_transform.py │ ├── post │ │ ├── __init__.py │ │ ├── test_label_filterd.py │ │ ├── test_probnms.py │ │ ├── test_probnmsd.py │ │ └── test_remove_small_objects.py │ ├── spatial │ │ ├── __init__.py │ │ ├── test_convert_box_points.py │ │ ├── test_grid_patch.py │ │ ├── test_grid_patchd.py │ │ ├── test_rand_grid_patch.py │ │ ├── test_rand_grid_patchd.py │ │ └── test_spatial_resampled.py │ ├── test_activations.py │ ├── test_activationsd.py │ ├── test_adaptors.py │ ├── test_add_coordinate_channels.py │ ├── test_add_coordinate_channelsd.py │ ├── test_add_extreme_points_channel.py │ ├── test_add_extreme_points_channeld.py │ ├── test_adjust_contrast.py │ ├── test_adjust_contrastd.py │ ├── test_affine.py │ ├── test_affine_grid.py │ ├── test_affined.py │ ├── test_as_channel_last.py │ ├── test_as_channel_lastd.py │ ├── test_as_discrete.py │ ├── test_as_discreted.py │ ├── test_border_pad.py │ ├── test_border_padd.py │ ├── test_bounding_rect.py │ ├── test_bounding_rectd.py │ ├── test_cast_to_type.py │ ├── test_cast_to_typed.py │ ├── test_center_scale_crop.py │ ├── test_center_scale_cropd.py │ ├── test_center_spatial_crop.py │ ├── test_center_spatial_cropd.py │ ├── test_classes_to_indices.py │ ├── test_classes_to_indicesd.py │ ├── test_clip_intensity_percentiles.py │ ├── test_clip_intensity_percentilesd.py │ ├── test_compose_get_number_conversions.py │ ├── test_concat_itemsd.py │ ├── test_convert_to_multi_channel.py │ ├── test_convert_to_multi_channeld.py │ ├── test_copy_itemsd.py │ ├── test_create_grid_and_affine.py │ ├── test_crop_foreground.py │ ├── test_crop_foregroundd.py │ ├── test_cucim_dict_transform.py │ ├── test_cucim_transform.py │ ├── test_data_stats.py │ ├── test_data_statsd.py │ ├── test_delete_itemsd.py │ ├── test_detect_envelope.py │ ├── test_distance_transform_edt.py │ ├── test_divisible_pad.py │ ├── test_divisible_padd.py │ ├── test_ensure_channel_first.py │ ├── test_ensure_channel_firstd.py │ ├── test_ensure_type.py │ ├── test_ensure_typed.py │ ├── test_fg_bg_to_indices.py │ ├── test_fg_bg_to_indicesd.py │ ├── test_fill_holes.py │ ├── test_fill_holesd.py │ ├── test_flatten_sub_keysd.py │ ├── test_flip.py │ ├── test_flipd.py │ ├── test_fourier.py │ ├── test_gaussian_sharpen.py │ ├── test_gaussian_sharpend.py │ ├── test_gaussian_smooth.py │ ├── test_gaussian_smoothd.py │ ├── test_generate_heatmap.py │ ├── test_generate_heatmapd.py │ ├── test_generate_label_classes_crop_centers.py │ ├── test_generate_pos_neg_label_crop_centers.py │ ├── test_generate_spatial_bounding_box.py │ ├── test_get_extreme_points.py │ ├── test_gibbs_noise.py │ ├── test_gibbs_noised.py │ ├── test_grid_distortion.py │ ├── test_grid_distortiond.py │ ├── test_grid_split.py │ ├── test_grid_splitd.py │ ├── test_histogram_normalize.py │ ├── test_histogram_normalized.py │ ├── test_image_filter.py │ ├── test_intensity_stats.py │ ├── test_intensity_statsd.py │ ├── test_inverse_collation.py │ ├── test_k_space_spike_noise.py │ ├── test_k_space_spike_noised.py │ ├── test_keep_largest_connected_component.py │ ├── test_keep_largest_connected_componentd.py │ ├── test_label_filter.py │ ├── test_label_to_contour.py │ ├── test_label_to_contourd.py │ ├── test_label_to_mask.py │ ├── test_label_to_maskd.py │ ├── test_load_image.py │ ├── test_load_imaged.py │ ├── test_load_spacing_orientation.py │ ├── test_map_and_generate_sampling_centers.py │ ├── test_map_binary_to_indices.py │ ├── test_map_classes_to_indices.py │ ├── test_map_label_value.py │ ├── test_map_label_valued.py │ ├── test_map_transform.py │ ├── test_mask_intensity.py │ ├── test_mask_intensityd.py │ ├── test_mean_ensemble.py │ ├── test_mean_ensembled.py │ ├── test_median_smooth.py │ ├── test_median_smoothd.py │ ├── test_morphological_ops.py │ ├── test_nifti_endianness.py │ ├── test_normalize_intensity.py │ ├── test_normalize_intensityd.py │ ├── test_nvtx_decorator.py │ ├── test_nvtx_transform.py │ ├── test_orientation.py │ ├── test_orientationd.py │ ├── test_rand_adjust_contrast.py │ ├── test_rand_adjust_contrastd.py │ ├── test_rand_affine.py │ ├── test_rand_affine_grid.py │ ├── test_rand_affined.py │ ├── test_rand_axis_flip.py │ ├── test_rand_axis_flipd.py │ ├── test_rand_bias_field.py │ ├── test_rand_bias_fieldd.py │ ├── test_rand_coarse_dropout.py │ ├── test_rand_coarse_dropoutd.py │ ├── test_rand_coarse_shuffle.py │ ├── test_rand_coarse_shuffled.py │ ├── test_rand_crop_by_label_classes.py │ ├── test_rand_crop_by_label_classesd.py │ ├── test_rand_crop_by_pos_neg_label.py │ ├── test_rand_crop_by_pos_neg_labeld.py │ ├── test_rand_cucim_dict_transform.py │ ├── test_rand_cucim_transform.py │ ├── test_rand_deform_grid.py │ ├── test_rand_elastic_2d.py │ ├── test_rand_elastic_3d.py │ ├── test_rand_elasticd_2d.py │ ├── test_rand_elasticd_3d.py │ ├── test_rand_flip.py │ ├── test_rand_flipd.py │ ├── test_rand_gaussian_noise.py │ ├── test_rand_gaussian_noised.py │ ├── test_rand_gaussian_sharpen.py │ ├── test_rand_gaussian_sharpend.py │ ├── test_rand_gaussian_smooth.py │ ├── test_rand_gaussian_smoothd.py │ ├── test_rand_gibbs_noise.py │ ├── test_rand_gibbs_noised.py │ ├── test_rand_grid_distortion.py │ ├── test_rand_grid_distortiond.py │ ├── test_rand_histogram_shift.py │ ├── test_rand_k_space_spike_noise.py │ ├── test_rand_k_space_spike_noised.py │ ├── test_rand_rician_noise.py │ ├── test_rand_rician_noised.py │ ├── test_rand_rotate.py │ ├── test_rand_rotate90.py │ ├── test_rand_rotate90d.py │ ├── test_rand_rotated.py │ ├── test_rand_scale_crop.py │ ├── test_rand_scale_cropd.py │ ├── test_rand_scale_intensity.py │ ├── test_rand_scale_intensity_fixed_mean.py │ ├── test_rand_scale_intensity_fixed_meand.py │ ├── test_rand_scale_intensityd.py │ ├── test_rand_shift_intensity.py │ ├── test_rand_shift_intensityd.py │ ├── test_rand_simulate_low_resolution.py │ ├── test_rand_simulate_low_resolutiond.py │ ├── test_rand_spatial_crop.py │ ├── test_rand_spatial_crop_samples.py │ ├── test_rand_spatial_crop_samplesd.py │ ├── test_rand_spatial_cropd.py │ ├── test_rand_std_shift_intensity.py │ ├── test_rand_std_shift_intensityd.py │ ├── test_rand_torchio.py │ ├── test_rand_torchiod.py │ ├── test_rand_zoom.py │ ├── test_rand_zoomd.py │ ├── test_randidentity.py │ ├── test_random_order.py │ ├── test_randtorchvisiond.py │ ├── test_regularization.py │ ├── test_remove_repeated_channel.py │ ├── test_remove_repeated_channeld.py │ ├── test_repeat_channel.py │ ├── test_repeat_channeld.py │ ├── test_resample_backends.py │ ├── test_resample_to_match.py │ ├── test_resample_to_matchd.py │ ├── test_resampler.py │ ├── test_resize.py │ ├── test_resize_with_pad_or_crop.py │ ├── test_resize_with_pad_or_cropd.py │ ├── test_resized.py │ ├── test_rotate.py │ ├── test_rotate90.py │ ├── test_rotate90d.py │ ├── test_rotated.py │ ├── test_save_classificationd.py │ ├── test_save_image.py │ ├── test_save_imaged.py │ ├── test_savitzky_golay_smooth.py │ ├── test_savitzky_golay_smoothd.py │ ├── test_scale_intensity.py │ ├── test_scale_intensity_fixed_mean.py │ ├── test_scale_intensity_range.py │ ├── test_scale_intensity_ranged.py │ ├── test_scale_intensityd.py │ ├── test_select_itemsd.py │ ├── test_shift_intensity.py │ ├── test_shift_intensityd.py │ ├── test_signal_continuouswavelet.py │ ├── test_signal_fillempty.py │ ├── test_signal_fillemptyd.py │ ├── test_signal_rand_add_gaussiannoise.py │ ├── test_signal_rand_add_sine.py │ ├── test_signal_rand_add_sine_partial.py │ ├── test_signal_rand_add_squarepulse.py │ ├── test_signal_rand_add_squarepulse_partial.py │ ├── test_signal_rand_drop.py │ ├── test_signal_rand_scale.py │ ├── test_signal_rand_shift.py │ ├── test_signal_remove_frequency.py │ ├── test_smooth_field.py │ ├── test_sobel_gradient.py │ ├── test_sobel_gradientd.py │ ├── test_spacing.py │ ├── test_spacingd.py │ ├── test_spatial_crop.py │ ├── test_spatial_cropd.py │ ├── test_spatial_pad.py │ ├── test_spatial_padd.py │ ├── test_spatial_resample.py │ ├── test_squeezedim.py │ ├── test_squeezedimd.py │ ├── test_std_shift_intensity.py │ ├── test_std_shift_intensityd.py │ ├── test_threshold_intensity.py │ ├── test_threshold_intensityd.py │ ├── test_to_contiguous.py │ ├── test_to_cupy.py │ ├── test_to_cupyd.py │ ├── test_to_device.py │ ├── test_to_deviced.py │ ├── test_to_numpy.py │ ├── test_to_numpyd.py │ ├── test_to_pil.py │ ├── test_to_pild.py │ ├── test_to_tensor.py │ ├── test_to_tensord.py │ ├── test_torchio.py │ ├── test_torchiod.py │ ├── test_torchvision.py │ ├── test_torchvisiond.py │ ├── test_transform.py │ ├── test_transpose.py │ ├── test_transposed.py │ ├── test_ultrasound_confidence_map_transform.py │ ├── test_utils_pytorch_numpy_unification.py │ ├── test_vote_ensemble.py │ ├── test_vote_ensembled.py │ ├── test_with_allow_missing_keys.py │ ├── test_zoom.py │ ├── test_zoomd.py │ ├── transform │ │ ├── __init__.py │ │ ├── test_randomizable.py │ │ └── test_randomizable_transform_type.py │ ├── utility │ │ ├── __init__.py │ │ ├── test_apply_transform_to_points.py │ │ ├── test_apply_transform_to_pointsd.py │ │ ├── test_identity.py │ │ ├── test_identityd.py │ │ ├── test_lambda.py │ │ ├── test_lambdad.py │ │ ├── test_rand_lambda.py │ │ ├── test_rand_lambdad.py │ │ ├── test_simulatedelay.py │ │ ├── test_simulatedelayd.py │ │ ├── test_splitdim.py │ │ └── test_splitdimd.py │ └── utils │ │ ├── __init__.py │ │ ├── test_correct_crop_centers.py │ │ ├── test_get_unique_labels.py │ │ ├── test_print_transform_backends.py │ │ └── test_soft_clip.py ├── utils │ ├── __init__.py │ ├── enums │ │ ├── __init__.py │ │ ├── test_hovernet_loss.py │ │ ├── test_ordering.py │ │ └── test_wsireader.py │ ├── misc │ │ ├── __init__.py │ │ ├── test_ensure_tuple.py │ │ ├── test_monai_env_vars.py │ │ ├── test_monai_utils_misc.py │ │ ├── test_str2bool.py │ │ └── test_str2list.py │ ├── test_alias.py │ ├── test_component_store.py │ ├── test_deprecated.py │ ├── test_enum_bound_interp.py │ ├── test_evenly_divisible_all_gather_dist.py │ ├── test_get_package_version.py │ ├── test_handler_logfile.py │ ├── test_handler_metric_logger.py │ ├── test_list_to_dict.py │ ├── test_look_up_option.py │ ├── test_optional_import.py │ ├── test_pad_mode.py │ ├── test_profiling.py │ ├── test_rankfilter_dist.py │ ├── test_require_pkg.py │ ├── test_sample_slices.py │ ├── test_set_determinism.py │ ├── test_squeeze_unsqueeze.py │ ├── test_state_cacher.py │ ├── test_torchscript_utils.py │ ├── test_version.py │ ├── test_version_after.py │ └── type_conversion │ │ ├── __init__.py │ │ ├── test_convert_data_type.py │ │ ├── test_get_equivalent_dtype.py │ │ └── test_safe_dtype_range.py └── visualize │ ├── __init__.py │ ├── test_img2tensorboard.py │ ├── test_occlusion_sensitivity.py │ ├── test_plot_2d_or_3d_image.py │ ├── test_vis_cam.py │ ├── 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