monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2508__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- monai/__init__.py +1 -1
- monai/_version.py +3 -3
- monai/apps/auto3dseg/transforms.py +1 -4
- monai/data/utils.py +6 -13
- monai/handlers/__init__.py +1 -0
- monai/handlers/average_precision.py +53 -0
- monai/inferers/inferer.py +10 -7
- monai/inferers/utils.py +1 -2
- monai/losses/dice.py +2 -14
- monai/losses/ds_loss.py +1 -3
- monai/metrics/__init__.py +1 -0
- monai/metrics/average_precision.py +187 -0
- monai/networks/layers/simplelayers.py +2 -14
- monai/networks/utils.py +4 -16
- monai/transforms/compose.py +28 -11
- monai/transforms/croppad/array.py +1 -6
- monai/transforms/io/array.py +0 -1
- monai/transforms/transform.py +15 -6
- monai/transforms/utility/array.py +2 -12
- monai/transforms/utils.py +1 -2
- monai/transforms/utils_pytorch_numpy_unification.py +2 -4
- monai/utils/enums.py +3 -2
- monai/utils/module.py +6 -6
- monai/utils/tf32.py +0 -10
- monai/visualize/class_activation_maps.py +5 -8
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/METADATA +21 -17
- monai_weekly-1.5.dev2508.dist-info/RECORD +1185 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/top_level.txt +1 -0
- tests/apps/__init__.py +10 -0
- tests/apps/deepedit/__init__.py +10 -0
- tests/apps/deepedit/test_deepedit_transforms.py +314 -0
- tests/apps/deepgrow/__init__.py +10 -0
- tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
- tests/apps/deepgrow/transforms/__init__.py +10 -0
- tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
- tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
- tests/apps/detection/__init__.py +10 -0
- tests/apps/detection/metrics/__init__.py +10 -0
- tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
- tests/apps/detection/networks/__init__.py +10 -0
- tests/apps/detection/networks/test_retinanet.py +210 -0
- tests/apps/detection/networks/test_retinanet_detector.py +203 -0
- tests/apps/detection/test_box_transform.py +370 -0
- tests/apps/detection/utils/__init__.py +10 -0
- tests/apps/detection/utils/test_anchor_box.py +88 -0
- tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
- tests/apps/detection/utils/test_box_coder.py +43 -0
- tests/apps/detection/utils/test_detector_boxselector.py +67 -0
- tests/apps/detection/utils/test_detector_utils.py +96 -0
- tests/apps/detection/utils/test_hardnegsampler.py +54 -0
- tests/apps/nuclick/__init__.py +10 -0
- tests/apps/nuclick/test_nuclick_transforms.py +259 -0
- tests/apps/pathology/__init__.py +10 -0
- tests/apps/pathology/handlers/__init__.py +10 -0
- tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
- tests/apps/pathology/test_lesion_froc.py +333 -0
- tests/apps/pathology/test_pathology_prob_nms.py +55 -0
- tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
- tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
- tests/apps/pathology/transforms/__init__.py +10 -0
- tests/apps/pathology/transforms/post/__init__.py +10 -0
- tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
- tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
- tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
- tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
- tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
- tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
- tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
- tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
- tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
- tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
- tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
- tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
- tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
- tests/apps/pathology/transforms/post/test_watershed.py +60 -0
- tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
- tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
- tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
- tests/apps/reconstruction/__init__.py +10 -0
- tests/apps/reconstruction/nets/__init__.py +10 -0
- tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
- tests/apps/reconstruction/test_complex_utils.py +77 -0
- tests/apps/reconstruction/test_fastmri_reader.py +82 -0
- tests/apps/reconstruction/test_mri_utils.py +37 -0
- tests/apps/reconstruction/transforms/__init__.py +10 -0
- tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
- tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
- tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
- tests/apps/test_auto3dseg_bundlegen.py +156 -0
- tests/apps/test_check_hash.py +53 -0
- tests/apps/test_cross_validation.py +74 -0
- tests/apps/test_decathlondataset.py +93 -0
- tests/apps/test_download_and_extract.py +70 -0
- tests/apps/test_download_url_yandex.py +45 -0
- tests/apps/test_mednistdataset.py +72 -0
- tests/apps/test_mmar_download.py +154 -0
- tests/apps/test_tciadataset.py +123 -0
- tests/apps/vista3d/__init__.py +10 -0
- tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
- tests/apps/vista3d/test_vista3d_sampler.py +100 -0
- tests/apps/vista3d/test_vista3d_transforms.py +94 -0
- tests/bundle/__init__.py +10 -0
- tests/bundle/test_bundle_ckpt_export.py +107 -0
- tests/bundle/test_bundle_download.py +435 -0
- tests/bundle/test_bundle_get_data.py +94 -0
- tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
- tests/bundle/test_bundle_trt_export.py +147 -0
- tests/bundle/test_bundle_utils.py +149 -0
- tests/bundle/test_bundle_verify_metadata.py +66 -0
- tests/bundle/test_bundle_verify_net.py +76 -0
- tests/bundle/test_bundle_workflow.py +272 -0
- tests/bundle/test_component_locator.py +38 -0
- tests/bundle/test_config_item.py +138 -0
- tests/bundle/test_config_parser.py +392 -0
- tests/bundle/test_reference_resolver.py +114 -0
- tests/config/__init__.py +10 -0
- tests/config/test_cv2_dist.py +53 -0
- tests/engines/__init__.py +10 -0
- tests/engines/test_ensemble_evaluator.py +94 -0
- tests/engines/test_prepare_batch_default.py +76 -0
- tests/engines/test_prepare_batch_default_dist.py +76 -0
- tests/engines/test_prepare_batch_diffusion.py +104 -0
- tests/engines/test_prepare_batch_extra_input.py +80 -0
- tests/fl/__init__.py +10 -0
- tests/fl/monai_algo/__init__.py +10 -0
- tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
- tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
- tests/fl/test_fl_monai_algo_stats.py +81 -0
- tests/fl/utils/__init__.py +10 -0
- tests/fl/utils/test_fl_exchange_object.py +63 -0
- tests/handlers/__init__.py +10 -0
- tests/handlers/test_handler_average_precision.py +79 -0
- tests/handlers/test_handler_checkpoint_loader.py +182 -0
- tests/handlers/test_handler_checkpoint_saver.py +233 -0
- tests/handlers/test_handler_classification_saver.py +64 -0
- tests/handlers/test_handler_classification_saver_dist.py +77 -0
- tests/handlers/test_handler_clearml_image.py +65 -0
- tests/handlers/test_handler_clearml_stats.py +65 -0
- tests/handlers/test_handler_confusion_matrix.py +104 -0
- tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
- tests/handlers/test_handler_decollate_batch.py +66 -0
- tests/handlers/test_handler_early_stop.py +68 -0
- tests/handlers/test_handler_garbage_collector.py +73 -0
- tests/handlers/test_handler_hausdorff_distance.py +111 -0
- tests/handlers/test_handler_ignite_metric.py +191 -0
- tests/handlers/test_handler_lr_scheduler.py +94 -0
- tests/handlers/test_handler_mean_dice.py +98 -0
- tests/handlers/test_handler_mean_iou.py +76 -0
- tests/handlers/test_handler_metrics_reloaded.py +149 -0
- tests/handlers/test_handler_metrics_saver.py +89 -0
- tests/handlers/test_handler_metrics_saver_dist.py +120 -0
- tests/handlers/test_handler_mlflow.py +296 -0
- tests/handlers/test_handler_nvtx.py +93 -0
- tests/handlers/test_handler_panoptic_quality.py +89 -0
- tests/handlers/test_handler_parameter_scheduler.py +136 -0
- tests/handlers/test_handler_post_processing.py +74 -0
- tests/handlers/test_handler_prob_map_producer.py +111 -0
- tests/handlers/test_handler_regression_metrics.py +160 -0
- tests/handlers/test_handler_regression_metrics_dist.py +245 -0
- tests/handlers/test_handler_rocauc.py +48 -0
- tests/handlers/test_handler_rocauc_dist.py +54 -0
- tests/handlers/test_handler_stats.py +281 -0
- tests/handlers/test_handler_surface_distance.py +113 -0
- tests/handlers/test_handler_tb_image.py +61 -0
- tests/handlers/test_handler_tb_stats.py +166 -0
- tests/handlers/test_handler_validation.py +59 -0
- tests/handlers/test_trt_compile.py +145 -0
- tests/handlers/test_write_metrics_reports.py +68 -0
- tests/inferers/__init__.py +10 -0
- tests/inferers/test_avg_merger.py +179 -0
- tests/inferers/test_controlnet_inferers.py +1388 -0
- tests/inferers/test_diffusion_inferer.py +236 -0
- tests/inferers/test_latent_diffusion_inferer.py +884 -0
- tests/inferers/test_patch_inferer.py +309 -0
- tests/inferers/test_saliency_inferer.py +55 -0
- tests/inferers/test_slice_inferer.py +57 -0
- tests/inferers/test_sliding_window_inference.py +377 -0
- tests/inferers/test_sliding_window_splitter.py +284 -0
- tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
- tests/inferers/test_zarr_avg_merger.py +326 -0
- tests/integration/__init__.py +10 -0
- tests/integration/test_auto3dseg_ensemble.py +211 -0
- tests/integration/test_auto3dseg_hpo.py +189 -0
- tests/integration/test_deepedit_interaction.py +122 -0
- tests/integration/test_downsample_block.py +50 -0
- tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
- tests/integration/test_integration_autorunner.py +201 -0
- tests/integration/test_integration_bundle_run.py +240 -0
- tests/integration/test_integration_classification_2d.py +282 -0
- tests/integration/test_integration_determinism.py +95 -0
- tests/integration/test_integration_fast_train.py +231 -0
- tests/integration/test_integration_gpu_customization.py +159 -0
- tests/integration/test_integration_lazy_samples.py +219 -0
- tests/integration/test_integration_nnunetv2_runner.py +96 -0
- tests/integration/test_integration_segmentation_3d.py +304 -0
- tests/integration/test_integration_sliding_window.py +100 -0
- tests/integration/test_integration_stn.py +133 -0
- tests/integration/test_integration_unet_2d.py +67 -0
- tests/integration/test_integration_workers.py +61 -0
- tests/integration/test_integration_workflows.py +365 -0
- tests/integration/test_integration_workflows_adversarial.py +173 -0
- tests/integration/test_integration_workflows_gan.py +158 -0
- tests/integration/test_loader_semaphore.py +48 -0
- tests/integration/test_mapping_filed.py +122 -0
- tests/integration/test_meta_affine.py +183 -0
- tests/integration/test_metatensor_integration.py +114 -0
- tests/integration/test_module_list.py +76 -0
- tests/integration/test_one_of.py +283 -0
- tests/integration/test_pad_collation.py +124 -0
- tests/integration/test_reg_loss_integration.py +107 -0
- tests/integration/test_retinanet_predict_utils.py +154 -0
- tests/integration/test_seg_loss_integration.py +159 -0
- tests/integration/test_spatial_combine_transforms.py +185 -0
- tests/integration/test_testtimeaugmentation.py +186 -0
- tests/integration/test_vis_gradbased.py +69 -0
- tests/integration/test_vista3d_utils.py +159 -0
- tests/losses/__init__.py +10 -0
- tests/losses/deform/__init__.py +10 -0
- tests/losses/deform/test_bending_energy.py +88 -0
- tests/losses/deform/test_diffusion_loss.py +117 -0
- tests/losses/image_dissimilarity/__init__.py +10 -0
- tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
- tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
- tests/losses/test_adversarial_loss.py +94 -0
- tests/losses/test_barlow_twins_loss.py +109 -0
- tests/losses/test_cldice_loss.py +51 -0
- tests/losses/test_contrastive_loss.py +86 -0
- tests/losses/test_dice_ce_loss.py +123 -0
- tests/losses/test_dice_focal_loss.py +124 -0
- tests/losses/test_dice_loss.py +227 -0
- tests/losses/test_ds_loss.py +189 -0
- tests/losses/test_focal_loss.py +379 -0
- tests/losses/test_generalized_dice_focal_loss.py +85 -0
- tests/losses/test_generalized_dice_loss.py +221 -0
- tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
- tests/losses/test_giou_loss.py +62 -0
- tests/losses/test_hausdorff_loss.py +264 -0
- tests/losses/test_masked_dice_loss.py +152 -0
- tests/losses/test_masked_loss.py +87 -0
- tests/losses/test_multi_scale.py +86 -0
- tests/losses/test_nacl_loss.py +167 -0
- tests/losses/test_perceptual_loss.py +122 -0
- tests/losses/test_spectral_loss.py +86 -0
- tests/losses/test_ssim_loss.py +59 -0
- tests/losses/test_sure_loss.py +72 -0
- tests/losses/test_tversky_loss.py +198 -0
- tests/losses/test_unified_focal_loss.py +66 -0
- tests/metrics/__init__.py +10 -0
- tests/metrics/test_compute_average_precision.py +162 -0
- tests/metrics/test_compute_confusion_matrix.py +294 -0
- tests/metrics/test_compute_f_beta.py +80 -0
- tests/metrics/test_compute_fid_metric.py +40 -0
- tests/metrics/test_compute_froc.py +143 -0
- tests/metrics/test_compute_generalized_dice.py +240 -0
- tests/metrics/test_compute_meandice.py +306 -0
- tests/metrics/test_compute_meaniou.py +223 -0
- tests/metrics/test_compute_mmd_metric.py +56 -0
- tests/metrics/test_compute_multiscalessim_metric.py +83 -0
- tests/metrics/test_compute_panoptic_quality.py +113 -0
- tests/metrics/test_compute_regression_metrics.py +196 -0
- tests/metrics/test_compute_roc_auc.py +155 -0
- tests/metrics/test_compute_variance.py +147 -0
- tests/metrics/test_cumulative.py +63 -0
- tests/metrics/test_cumulative_average.py +74 -0
- tests/metrics/test_cumulative_average_dist.py +48 -0
- tests/metrics/test_hausdorff_distance.py +209 -0
- tests/metrics/test_label_quality_score.py +134 -0
- tests/metrics/test_loss_metric.py +57 -0
- tests/metrics/test_metrics_reloaded.py +96 -0
- tests/metrics/test_ssim_metric.py +78 -0
- tests/metrics/test_surface_dice.py +416 -0
- tests/metrics/test_surface_distance.py +186 -0
- tests/networks/__init__.py +10 -0
- tests/networks/blocks/__init__.py +10 -0
- tests/networks/blocks/dints_block/__init__.py +10 -0
- tests/networks/blocks/dints_block/test_acn_block.py +41 -0
- tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
- tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
- tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
- tests/networks/blocks/test_adn.py +86 -0
- tests/networks/blocks/test_convolutions.py +156 -0
- tests/networks/blocks/test_crf_cpu.py +513 -0
- tests/networks/blocks/test_crf_cuda.py +528 -0
- tests/networks/blocks/test_crossattention.py +185 -0
- tests/networks/blocks/test_denseblock.py +105 -0
- tests/networks/blocks/test_dynunet_block.py +116 -0
- tests/networks/blocks/test_fpn_block.py +88 -0
- tests/networks/blocks/test_localnet_block.py +121 -0
- tests/networks/blocks/test_mlp.py +78 -0
- tests/networks/blocks/test_patchembedding.py +212 -0
- tests/networks/blocks/test_regunet_block.py +103 -0
- tests/networks/blocks/test_se_block.py +85 -0
- tests/networks/blocks/test_se_blocks.py +78 -0
- tests/networks/blocks/test_segresnet_block.py +57 -0
- tests/networks/blocks/test_selfattention.py +232 -0
- tests/networks/blocks/test_simple_aspp.py +87 -0
- tests/networks/blocks/test_spatialattention.py +55 -0
- tests/networks/blocks/test_subpixel_upsample.py +87 -0
- tests/networks/blocks/test_text_encoding.py +49 -0
- tests/networks/blocks/test_transformerblock.py +90 -0
- tests/networks/blocks/test_unetr_block.py +158 -0
- tests/networks/blocks/test_upsample_block.py +134 -0
- tests/networks/blocks/warp/__init__.py +10 -0
- tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
- tests/networks/blocks/warp/test_warp.py +250 -0
- tests/networks/layers/__init__.py +10 -0
- tests/networks/layers/filtering/__init__.py +10 -0
- tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
- tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
- tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
- tests/networks/layers/filtering/test_phl_cpu.py +259 -0
- tests/networks/layers/filtering/test_phl_cuda.py +167 -0
- tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
- tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
- tests/networks/layers/test_affine_transform.py +385 -0
- tests/networks/layers/test_apply_filter.py +89 -0
- tests/networks/layers/test_channel_pad.py +51 -0
- tests/networks/layers/test_conjugate_gradient.py +56 -0
- tests/networks/layers/test_drop_path.py +46 -0
- tests/networks/layers/test_gaussian.py +317 -0
- tests/networks/layers/test_gaussian_filter.py +206 -0
- tests/networks/layers/test_get_layers.py +65 -0
- tests/networks/layers/test_gmm.py +314 -0
- tests/networks/layers/test_grid_pull.py +93 -0
- tests/networks/layers/test_hilbert_transform.py +131 -0
- tests/networks/layers/test_lltm.py +62 -0
- tests/networks/layers/test_median_filter.py +52 -0
- tests/networks/layers/test_polyval.py +55 -0
- tests/networks/layers/test_preset_filters.py +136 -0
- tests/networks/layers/test_savitzky_golay_filter.py +141 -0
- tests/networks/layers/test_separable_filter.py +87 -0
- tests/networks/layers/test_skip_connection.py +48 -0
- tests/networks/layers/test_vector_quantizer.py +89 -0
- tests/networks/layers/test_weight_init.py +50 -0
- tests/networks/nets/__init__.py +10 -0
- tests/networks/nets/dints/__init__.py +10 -0
- tests/networks/nets/dints/test_dints_cell.py +110 -0
- tests/networks/nets/dints/test_dints_mixop.py +84 -0
- tests/networks/nets/regunet/__init__.py +10 -0
- tests/networks/nets/regunet/test_localnet.py +86 -0
- tests/networks/nets/regunet/test_regunet.py +88 -0
- tests/networks/nets/test_ahnet.py +224 -0
- tests/networks/nets/test_attentionunet.py +88 -0
- tests/networks/nets/test_autoencoder.py +95 -0
- tests/networks/nets/test_autoencoderkl.py +337 -0
- tests/networks/nets/test_basic_unet.py +102 -0
- tests/networks/nets/test_basic_unetplusplus.py +109 -0
- tests/networks/nets/test_bundle_init_bundle.py +55 -0
- tests/networks/nets/test_cell_sam_wrapper.py +58 -0
- tests/networks/nets/test_controlnet.py +215 -0
- tests/networks/nets/test_daf3d.py +62 -0
- tests/networks/nets/test_densenet.py +121 -0
- tests/networks/nets/test_diffusion_model_unet.py +585 -0
- tests/networks/nets/test_dints_network.py +168 -0
- tests/networks/nets/test_discriminator.py +59 -0
- tests/networks/nets/test_dynunet.py +181 -0
- tests/networks/nets/test_efficientnet.py +400 -0
- tests/networks/nets/test_flexible_unet.py +341 -0
- tests/networks/nets/test_fullyconnectednet.py +69 -0
- tests/networks/nets/test_generator.py +59 -0
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- tests/utils/misc/test_monai_utils_misc.py +103 -0
- tests/utils/misc/test_str2bool.py +34 -0
- tests/utils/misc/test_str2list.py +33 -0
- tests/utils/test_alias.py +44 -0
- tests/utils/test_component_store.py +73 -0
- tests/utils/test_deprecated.py +455 -0
- tests/utils/test_enum_bound_interp.py +75 -0
- tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
- tests/utils/test_get_package_version.py +34 -0
- tests/utils/test_handler_logfile.py +84 -0
- tests/utils/test_handler_metric_logger.py +62 -0
- tests/utils/test_list_to_dict.py +43 -0
- tests/utils/test_look_up_option.py +87 -0
- tests/utils/test_optional_import.py +80 -0
- tests/utils/test_pad_mode.py +39 -0
- tests/utils/test_profiling.py +208 -0
- tests/utils/test_rankfilter_dist.py +77 -0
- tests/utils/test_require_pkg.py +83 -0
- tests/utils/test_sample_slices.py +43 -0
- tests/utils/test_set_determinism.py +74 -0
- tests/utils/test_squeeze_unsqueeze.py +71 -0
- tests/utils/test_state_cacher.py +67 -0
- tests/utils/test_torchscript_utils.py +113 -0
- tests/utils/test_version.py +91 -0
- tests/utils/test_version_after.py +65 -0
- tests/utils/type_conversion/__init__.py +10 -0
- tests/utils/type_conversion/test_convert_data_type.py +152 -0
- tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
- tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
- tests/visualize/__init__.py +10 -0
- tests/visualize/test_img2tensorboard.py +46 -0
- tests/visualize/test_occlusion_sensitivity.py +128 -0
- tests/visualize/test_plot_2d_or_3d_image.py +74 -0
- tests/visualize/test_vis_cam.py +98 -0
- tests/visualize/test_vis_gradcam.py +211 -0
- tests/visualize/utils/__init__.py +10 -0
- tests/visualize/utils/test_blend_images.py +63 -0
- tests/visualize/utils/test_matshow3d.py +133 -0
- monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/LICENSE +0 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/WHEEL +0 -0
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from __future__ import annotations
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import os
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import unittest
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import warnings
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import numpy as np
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import torch
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from torch.utils.data import DataLoader
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import monai
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from monai.apps import download_and_extract
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from monai.data import decollate_batch
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from monai.metrics import ROCAUCMetric
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from monai.networks import eval_mode
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from monai.networks.nets import DenseNet121
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from monai.transforms import (
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Activations,
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AsDiscrete,
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Compose,
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EnsureChannelFirst,
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LoadImage,
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RandFlip,
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RandRotate,
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RandZoom,
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ScaleIntensity,
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Transpose,
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)
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from monai.utils import set_determinism
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from tests.test_utils import DistTestCase, TimedCall, skip_if_downloading_fails, skip_if_quick, testing_data_config
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from tests.testing_data.integration_answers import test_integration_value
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TASK = "integration_classification_2d"
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class MedNISTDataset(torch.utils.data.Dataset):
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def __init__(self, image_files, labels, transforms):
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self.image_files = image_files
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self.labels = labels
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self.transforms = transforms
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def __len__(self):
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return len(self.image_files)
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def __getitem__(self, index):
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return self.transforms(self.image_files[index]), self.labels[index]
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def run_training_test(root_dir, train_x, train_y, val_x, val_y, device="cuda:0", num_workers=10):
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monai.config.print_config()
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# define transforms for image and classification
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train_transforms = Compose(
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[
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LoadImage(image_only=True, simple_keys=True),
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EnsureChannelFirst(channel_dim="no_channel"),
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Transpose(indices=[0, 2, 1]),
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ScaleIntensity(),
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RandRotate(range_x=np.pi / 12, prob=0.5, keep_size=True, dtype=np.float64),
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RandFlip(spatial_axis=0, prob=0.5),
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RandZoom(min_zoom=0.9, max_zoom=1.1, prob=0.5),
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]
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)
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train_transforms.set_random_state(1234)
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val_transforms = Compose(
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[
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LoadImage(image_only=True, simple_keys=True),
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EnsureChannelFirst(channel_dim="no_channel"),
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Transpose(indices=[0, 2, 1]),
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ScaleIntensity(),
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]
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)
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y_pred_trans = Compose([Activations(softmax=True)])
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y_trans = AsDiscrete(to_onehot=len(np.unique(train_y)))
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auc_metric = ROCAUCMetric()
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# create train, val data loaders
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train_ds = MedNISTDataset(train_x, train_y, train_transforms)
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train_loader = DataLoader(train_ds, batch_size=300, shuffle=True, num_workers=num_workers)
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val_ds = MedNISTDataset(val_x, val_y, val_transforms)
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val_loader = DataLoader(val_ds, batch_size=300, num_workers=num_workers)
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model = DenseNet121(spatial_dims=2, in_channels=1, out_channels=len(np.unique(train_y))).to(device)
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loss_function = torch.nn.CrossEntropyLoss()
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optimizer = torch.optim.Adam(model.parameters(), 1e-5)
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epoch_num = 1
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val_interval = 1
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# start training validation
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best_metric = -1
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best_metric_epoch = -1
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epoch_loss_values = []
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metric_values = []
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model_filename = os.path.join(root_dir, "best_metric_model.pth")
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for epoch in range(epoch_num):
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print("-" * 10)
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print(f"Epoch {epoch + 1}/{epoch_num}")
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model.train()
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epoch_loss = 0
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step = 0
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for batch_data in train_loader:
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step += 1
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inputs, labels = batch_data[0].to(device), batch_data[1].to(device)
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optimizer.zero_grad()
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outputs = model(inputs)
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loss = loss_function(outputs, labels)
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loss.backward()
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optimizer.step()
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epoch_loss += loss.item()
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epoch_loss /= step
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epoch_loss_values.append(epoch_loss)
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print(f"epoch {epoch + 1} average loss:{epoch_loss:0.4f}")
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if (epoch + 1) % val_interval == 0:
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with eval_mode(model):
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y_pred = torch.tensor([], dtype=torch.float32, device=device)
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y = torch.tensor([], dtype=torch.long, device=device)
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for val_data in val_loader:
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val_images, val_labels = (val_data[0].to(device), val_data[1].to(device))
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y_pred = torch.cat([y_pred, model(val_images)], dim=0)
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y = torch.cat([y, val_labels], dim=0)
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# compute accuracy
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acc_value = torch.eq(y_pred.argmax(dim=1), y)
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acc_metric = acc_value.sum().item() / len(acc_value)
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# decollate prediction and label and execute post processing
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y_pred = [y_pred_trans(i) for i in decollate_batch(y_pred)]
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y = [y_trans(i) for i in decollate_batch(y, detach=False)]
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# compute AUC
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auc_metric(y_pred, y)
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auc_value = auc_metric.aggregate()
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auc_metric.reset()
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metric_values.append(auc_value)
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if auc_value > best_metric:
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best_metric = auc_value
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best_metric_epoch = epoch + 1
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torch.save(model.state_dict(), model_filename)
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print("saved new best metric model")
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print(
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f"current epoch {epoch + 1} current AUC: {auc_value:0.4f} "
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f"current accuracy: {acc_metric:0.4f} best AUC: {best_metric:0.4f} at epoch {best_metric_epoch}"
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)
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print(f"train completed, best_metric: {best_metric:0.4f} at epoch: {best_metric_epoch}")
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return epoch_loss_values, best_metric, best_metric_epoch
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def run_inference_test(root_dir, test_x, test_y, device="cuda:0", num_workers=10):
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# define transforms for image and classification
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val_transforms = Compose(
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[LoadImage(image_only=True), EnsureChannelFirst(channel_dim="no_channel"), ScaleIntensity()]
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)
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val_ds = MedNISTDataset(test_x, test_y, val_transforms)
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val_loader = DataLoader(val_ds, batch_size=300, num_workers=num_workers)
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model = DenseNet121(spatial_dims=2, in_channels=1, out_channels=len(np.unique(test_y))).to(device)
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model_filename = os.path.join(root_dir, "best_metric_model.pth")
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model.load_state_dict(torch.load(model_filename))
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y_true = []
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y_pred = []
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with eval_mode(model):
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for test_data in val_loader:
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test_images, test_labels = test_data[0].to(device), test_data[1].to(device)
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pred = model(test_images).argmax(dim=1)
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for i in range(len(pred)):
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y_true.append(test_labels[i].item())
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y_pred.append(pred[i].item())
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tps = [np.sum((np.asarray(y_true) == idx) & (np.asarray(y_pred) == idx)) for idx in np.unique(test_y)]
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return tps
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@skip_if_quick
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class IntegrationClassification2D(DistTestCase):
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def setUp(self):
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set_determinism(seed=0)
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self.data_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../testing_data")
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data_dir = os.path.join(self.data_dir, "MedNIST")
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dataset_file = os.path.join(self.data_dir, "MedNIST.tar.gz")
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if not os.path.exists(data_dir):
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with skip_if_downloading_fails():
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data_spec = testing_data_config("images", "mednist")
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download_and_extract(
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data_spec["url"],
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dataset_file,
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self.data_dir,
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hash_val=data_spec["hash_val"],
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hash_type=data_spec["hash_type"],
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)
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assert os.path.exists(data_dir)
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class_names = sorted(x for x in os.listdir(data_dir) if os.path.isdir(os.path.join(data_dir, x)))
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image_files = [
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[os.path.join(data_dir, class_name, x) for x in sorted(os.listdir(os.path.join(data_dir, class_name)))]
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for class_name in class_names
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]
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image_file_list, image_classes = [], []
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for i, _ in enumerate(class_names):
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image_file_list.extend(image_files[i])
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image_classes.extend([i] * len(image_files[i]))
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# split train, val, test
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valid_frac, test_frac = 0.1, 0.1
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self.train_x, self.train_y = [], []
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self.val_x, self.val_y = [], []
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self.test_x, self.test_y = [], []
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for i in range(len(image_classes)):
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rann = np.random.random()
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if rann < valid_frac:
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self.val_x.append(image_file_list[i])
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self.val_y.append(image_classes[i])
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elif rann < test_frac + valid_frac:
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self.test_x.append(image_file_list[i])
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self.test_y.append(image_classes[i])
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else:
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self.train_x.append(image_file_list[i])
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self.train_y.append(image_classes[i])
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self.device = "cuda:0" if torch.cuda.is_available() else "cpu:0"
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def tearDown(self):
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set_determinism(seed=None)
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try:
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os.remove(os.path.join(self.data_dir, "best_metric_model.pth"))
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except FileNotFoundError:
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warnings.warn("not found best_metric_model.pth, training skipped?")
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pass
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def train_and_infer(self, idx=0):
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results = []
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if not os.path.exists(os.path.join(self.data_dir, "MedNIST")):
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# skip test if no MedNIST dataset
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return results
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set_determinism(seed=0)
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losses, best_metric, best_metric_epoch = run_training_test(
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self.data_dir, self.train_x, self.train_y, self.val_x, self.val_y, device=self.device
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)
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infer_metric = run_inference_test(self.data_dir, self.test_x, self.test_y, device=self.device)
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print(f"integration_classification_2d {losses}")
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print("best metric", best_metric)
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print("infer metric", infer_metric)
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# check training properties
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self.assertTrue(test_integration_value(TASK, key="losses", data=losses, rtol=1e-2))
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self.assertTrue(test_integration_value(TASK, key="best_metric", data=best_metric, rtol=1e-4))
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np.testing.assert_allclose(best_metric_epoch, 4)
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model_file = os.path.join(self.data_dir, "best_metric_model.pth")
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self.assertTrue(os.path.exists(model_file))
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# check inference properties
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self.assertTrue(test_integration_value(TASK, key="infer_prop", data=np.asarray(infer_metric), rtol=1))
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results.extend(losses)
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results.append(best_metric)
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results.extend(infer_metric)
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return results
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def test_training(self):
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repeated = []
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for i in range(1):
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results = self.train_and_infer(i)
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repeated.append(results)
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np.testing.assert_allclose(repeated[0], repeated[1])
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@TimedCall(seconds=2000, skip_timing=not torch.cuda.is_available(), force_quit=False, daemon=False)
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def test_timing(self):
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self.train_and_infer()
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if __name__ == "__main__":
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unittest.main()
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from __future__ import annotations
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import unittest
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import numpy as np
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import torch
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from torch.utils.data import DataLoader, Dataset
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from monai.data import create_test_image_2d
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from monai.losses import DiceLoss
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from monai.networks.nets import UNet
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from monai.transforms import Compose, EnsureChannelFirst, RandRotate90, RandSpatialCrop, ScaleIntensity
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from monai.utils import set_determinism
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from tests.test_utils import DistTestCase, TimedCall
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def run_test(batch_size=64, train_steps=200, device="cuda:0"):
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class _TestBatch(Dataset):
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def __init__(self, transforms):
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self.transforms = transforms
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def __getitem__(self, _unused_id):
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im, seg = create_test_image_2d(128, 128, noise_max=1, num_objs=4, num_seg_classes=1)
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seed = np.random.randint(2147483647)
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self.transforms.set_random_state(seed=seed)
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im = self.transforms(im)
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self.transforms.set_random_state(seed=seed)
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seg = self.transforms(seg)
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return im, seg
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+
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def __len__(self):
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return train_steps
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net = UNet(
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spatial_dims=2, in_channels=1, out_channels=1, channels=(4, 8, 16, 32), strides=(2, 2, 2), num_res_units=2
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).to(device)
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loss = DiceLoss(sigmoid=True)
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opt = torch.optim.Adam(net.parameters(), 1e-2)
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train_transforms = Compose(
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[
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EnsureChannelFirst(channel_dim="no_channel"),
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ScaleIntensity(),
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RandSpatialCrop((96, 96), random_size=False),
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RandRotate90(),
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]
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)
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src = DataLoader(_TestBatch(train_transforms), batch_size=batch_size, shuffle=True)
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+
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net.train()
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epoch_loss = 0
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step = 0
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for img, seg in src:
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step += 1
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opt.zero_grad()
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output = net(img.to(device))
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step_loss = loss(output, seg.to(device))
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step_loss.backward()
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opt.step()
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epoch_loss += step_loss.item()
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epoch_loss /= step
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+
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return epoch_loss, step
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class TestDeterminism(DistTestCase):
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def setUp(self):
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self.device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu:0")
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+
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def tearDown(self):
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set_determinism(seed=None)
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@TimedCall(seconds=150, skip_timing=not torch.cuda.is_available())
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def test_training(self):
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set_determinism(seed=0)
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loss, step = run_test(device=self.device)
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print(f"Deterministic loss {loss} at training step {step}")
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np.testing.assert_allclose(step, 4)
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np.testing.assert_allclose(loss, 0.536134, rtol=1e-4)
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if __name__ == "__main__":
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unittest.main()
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@@ -0,0 +1,231 @@
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
|
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
|
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# limitations under the License.
|
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from __future__ import annotations
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import math
|
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import os
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+
import shutil
|
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import tempfile
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import time
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import unittest
|
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from glob import glob
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import nibabel as nib
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import numpy as np
|
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+
import torch
|
25
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+
|
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+
import monai
|
27
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+
from monai.data import CacheDataset, ThreadDataLoader, create_test_image_3d, decollate_batch
|
28
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+
from monai.inferers import sliding_window_inference
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29
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+
from monai.losses import DiceCELoss
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30
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from monai.metrics import DiceMetric
|
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from monai.networks.layers import Norm
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32
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+
from monai.networks.nets import UNet
|
33
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+
from monai.optimizers import Novograd
|
34
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+
from monai.transforms import (
|
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AsDiscrete,
|
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Compose,
|
37
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+
CropForegroundd,
|
38
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EnsureChannelFirstd,
|
39
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+
FgBgToIndicesd,
|
40
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+
LoadImaged,
|
41
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+
RandAffined,
|
42
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+
RandAxisFlipd,
|
43
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+
RandCropByPosNegLabeld,
|
44
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+
RandFlipd,
|
45
|
+
RandGaussianNoised,
|
46
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+
RandRotate90d,
|
47
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RandRotated,
|
48
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RandStdShiftIntensityd,
|
49
|
+
RandZoomd,
|
50
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+
ScaleIntensityd,
|
51
|
+
Spacingd,
|
52
|
+
ToDeviced,
|
53
|
+
)
|
54
|
+
from monai.utils import set_determinism
|
55
|
+
from tests.test_utils import DistTestCase, TimedCall, skip_if_no_cuda, skip_if_quick
|
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+
|
57
|
+
|
58
|
+
@skip_if_no_cuda
|
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+
@skip_if_quick
|
60
|
+
class IntegrationFastTrain(DistTestCase):
|
61
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+
def setUp(self):
|
62
|
+
set_determinism(seed=0)
|
63
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+
monai.config.print_config()
|
64
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+
|
65
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+
self.data_dir = tempfile.mkdtemp()
|
66
|
+
for i in range(41):
|
67
|
+
im, seg = create_test_image_3d(128, 128, 128, num_seg_classes=1, channel_dim=-1)
|
68
|
+
n = nib.Nifti1Image(im, np.eye(4))
|
69
|
+
nib.save(n, os.path.join(self.data_dir, f"img{i:d}.nii.gz"))
|
70
|
+
n = nib.Nifti1Image(seg, np.eye(4))
|
71
|
+
nib.save(n, os.path.join(self.data_dir, f"seg{i:d}.nii.gz"))
|
72
|
+
|
73
|
+
def tearDown(self):
|
74
|
+
set_determinism(seed=None)
|
75
|
+
shutil.rmtree(self.data_dir)
|
76
|
+
|
77
|
+
# test the fast training speed is as expected
|
78
|
+
@TimedCall(seconds=100, daemon=False, force_quit=False)
|
79
|
+
def test_train_timing(self):
|
80
|
+
images = sorted(glob(os.path.join(self.data_dir, "img*.nii.gz")))
|
81
|
+
segs = sorted(glob(os.path.join(self.data_dir, "seg*.nii.gz")))
|
82
|
+
train_files = [{"image": img, "label": seg} for img, seg in zip(images[:32], segs[:32])]
|
83
|
+
val_files = [{"image": img, "label": seg} for img, seg in zip(images[-9:], segs[-9:])]
|
84
|
+
|
85
|
+
device = torch.device("cuda:0")
|
86
|
+
# define transforms for train and validation
|
87
|
+
train_transforms = Compose(
|
88
|
+
[
|
89
|
+
LoadImaged(keys=["image", "label"]),
|
90
|
+
EnsureChannelFirstd(keys=["image", "label"]),
|
91
|
+
Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "nearest")),
|
92
|
+
ScaleIntensityd(keys="image"),
|
93
|
+
CropForegroundd(keys=["image", "label"], source_key="image"),
|
94
|
+
# pre-compute foreground and background indexes
|
95
|
+
# and cache them to accelerate training
|
96
|
+
FgBgToIndicesd(keys="label", fg_postfix="_fg", bg_postfix="_bg"),
|
97
|
+
# move the data to GPU and cache to avoid CPU -> GPU sync in every epoch
|
98
|
+
ToDeviced(keys=["image", "label"], device=device),
|
99
|
+
# randomly crop out patch samples from big
|
100
|
+
# image based on pos / neg ratio
|
101
|
+
# the image centers of negative samples
|
102
|
+
# must be in valid image area
|
103
|
+
RandCropByPosNegLabeld(
|
104
|
+
keys=["image", "label"],
|
105
|
+
label_key="label",
|
106
|
+
spatial_size=(64, 64, 64),
|
107
|
+
pos=1,
|
108
|
+
neg=1,
|
109
|
+
num_samples=4,
|
110
|
+
fg_indices_key="label_fg",
|
111
|
+
bg_indices_key="label_bg",
|
112
|
+
),
|
113
|
+
RandFlipd(keys=["image", "label"], prob=0.5, spatial_axis=[1, 2]),
|
114
|
+
RandAxisFlipd(keys=["image", "label"], prob=0.5),
|
115
|
+
RandRotate90d(keys=["image", "label"], prob=0.5, spatial_axes=(1, 2)),
|
116
|
+
RandZoomd(keys=["image", "label"], prob=0.5, min_zoom=0.8, max_zoom=1.2, keep_size=True),
|
117
|
+
RandRotated(
|
118
|
+
keys=["image", "label"],
|
119
|
+
prob=0.5,
|
120
|
+
range_x=np.pi / 4,
|
121
|
+
mode=("bilinear", "nearest"),
|
122
|
+
align_corners=True,
|
123
|
+
dtype=np.float64,
|
124
|
+
),
|
125
|
+
RandAffined(keys=["image", "label"], prob=0.5, rotate_range=np.pi / 2, mode=("bilinear", "nearest")),
|
126
|
+
RandGaussianNoised(keys="image", prob=0.5),
|
127
|
+
RandStdShiftIntensityd(keys="image", prob=0.5, factors=0.05, nonzero=True),
|
128
|
+
]
|
129
|
+
)
|
130
|
+
|
131
|
+
val_transforms = Compose(
|
132
|
+
[
|
133
|
+
LoadImaged(keys=["image", "label"]),
|
134
|
+
EnsureChannelFirstd(keys=["image", "label"]),
|
135
|
+
Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "nearest")),
|
136
|
+
ScaleIntensityd(keys="image"),
|
137
|
+
CropForegroundd(keys=["image", "label"], source_key="image"),
|
138
|
+
# move the data to GPU and cache to avoid CPU -> GPU sync in every epoch
|
139
|
+
ToDeviced(keys=["image", "label"], device=device),
|
140
|
+
]
|
141
|
+
)
|
142
|
+
|
143
|
+
max_epochs = 5
|
144
|
+
learning_rate = 2e-4
|
145
|
+
val_interval = 1 # do validation for every epoch
|
146
|
+
|
147
|
+
# set CacheDataset, ThreadDataLoader and DiceCE loss for MONAI fast training
|
148
|
+
train_ds = CacheDataset(data=train_files, transform=train_transforms, cache_rate=1.0, num_workers=8)
|
149
|
+
val_ds = CacheDataset(data=val_files, transform=val_transforms, cache_rate=1.0, runtime_cache=True)
|
150
|
+
# disable multi-workers because `ThreadDataLoader` works with multi-threads
|
151
|
+
train_loader = ThreadDataLoader(train_ds, num_workers=0, batch_size=4, shuffle=True)
|
152
|
+
val_loader = ThreadDataLoader(val_ds, num_workers=0, batch_size=1)
|
153
|
+
|
154
|
+
loss_function = DiceCELoss(to_onehot_y=True, softmax=True, squared_pred=True, batch=True)
|
155
|
+
model = UNet(
|
156
|
+
spatial_dims=3,
|
157
|
+
in_channels=1,
|
158
|
+
out_channels=2,
|
159
|
+
channels=(16, 32, 64, 128, 256),
|
160
|
+
strides=(2, 2, 2, 2),
|
161
|
+
num_res_units=2,
|
162
|
+
norm=Norm.BATCH,
|
163
|
+
).to(device)
|
164
|
+
|
165
|
+
# Novograd paper suggests to use a bigger LR than Adam,
|
166
|
+
# because Adam does normalization by element-wise second moments
|
167
|
+
optimizer = Novograd(model.parameters(), learning_rate * 10)
|
168
|
+
scaler = torch.cuda.amp.GradScaler()
|
169
|
+
|
170
|
+
post_pred = AsDiscrete(argmax=True, to_onehot=2)
|
171
|
+
post_label = AsDiscrete(to_onehot=2)
|
172
|
+
|
173
|
+
dice_metric = DiceMetric(include_background=True, reduction="mean", get_not_nans=False)
|
174
|
+
|
175
|
+
best_metric = -1
|
176
|
+
total_start = time.time()
|
177
|
+
for epoch in range(max_epochs):
|
178
|
+
epoch_start = time.time()
|
179
|
+
print("-" * 10)
|
180
|
+
print(f"epoch {epoch + 1}/{max_epochs}")
|
181
|
+
model.train()
|
182
|
+
epoch_loss = 0
|
183
|
+
step = 0
|
184
|
+
for batch_data in train_loader:
|
185
|
+
step_start = time.time()
|
186
|
+
step += 1
|
187
|
+
optimizer.zero_grad()
|
188
|
+
# set AMP for training
|
189
|
+
with torch.cuda.amp.autocast():
|
190
|
+
outputs = model(batch_data["image"])
|
191
|
+
loss = loss_function(outputs, batch_data["label"])
|
192
|
+
scaler.scale(loss).backward()
|
193
|
+
scaler.step(optimizer)
|
194
|
+
scaler.update()
|
195
|
+
epoch_loss += loss.item()
|
196
|
+
epoch_len = math.ceil(len(train_ds) / train_loader.batch_size)
|
197
|
+
print(
|
198
|
+
f"{step}/{epoch_len}, train_loss: {loss.item():.4f}" f" step time: {(time.time() - step_start):.4f}"
|
199
|
+
)
|
200
|
+
epoch_loss /= step
|
201
|
+
print(f"epoch {epoch + 1} average loss: {epoch_loss:.4f}")
|
202
|
+
|
203
|
+
if (epoch + 1) % val_interval == 0:
|
204
|
+
model.eval()
|
205
|
+
with torch.no_grad():
|
206
|
+
for val_data in val_loader:
|
207
|
+
roi_size = (96, 96, 96)
|
208
|
+
sw_batch_size = 4
|
209
|
+
# set AMP for validation
|
210
|
+
with torch.cuda.amp.autocast():
|
211
|
+
val_outputs = sliding_window_inference(val_data["image"], roi_size, sw_batch_size, model)
|
212
|
+
|
213
|
+
val_outputs = [post_pred(i) for i in decollate_batch(val_outputs)]
|
214
|
+
val_labels = [post_label(i) for i in decollate_batch(val_data["label"])]
|
215
|
+
dice_metric(y_pred=val_outputs, y=val_labels)
|
216
|
+
|
217
|
+
metric = dice_metric.aggregate().item()
|
218
|
+
dice_metric.reset()
|
219
|
+
if metric > best_metric:
|
220
|
+
best_metric = metric
|
221
|
+
print(f"epoch: {epoch + 1} current mean dice: {metric:.4f}, best mean dice: {best_metric:.4f}")
|
222
|
+
print(f"time consuming of epoch {epoch + 1} is: {(time.time() - epoch_start):.4f}")
|
223
|
+
|
224
|
+
total_time = time.time() - total_start
|
225
|
+
print(f"train completed, best_metric: {best_metric:.4f} total time: {total_time:.4f}")
|
226
|
+
# test expected metrics
|
227
|
+
self.assertGreater(best_metric, 0.95)
|
228
|
+
|
229
|
+
|
230
|
+
if __name__ == "__main__":
|
231
|
+
unittest.main()
|