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 unittest
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import torch
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from monai.engines import SupervisedEvaluator
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from monai.handlers import DecollateBatch, PostProcessing
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from monai.transforms import Activationsd, AsDiscreted, Compose, CopyItemsd
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from tests.test_utils import assert_allclose
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class TestHandlerDecollateBatch(unittest.TestCase):
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def test_compute(self):
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data = [
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{"image": torch.tensor([[[[2.0], [3.0]]]]), "filename": ["test1"]},
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{"image": torch.tensor([[[[6.0], [8.0]]]]), "filename": ["test2"]},
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]
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handlers = [
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DecollateBatch(event="MODEL_COMPLETED"),
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PostProcessing(
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transform=Compose(
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[
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Activationsd(keys="pred", sigmoid=True),
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CopyItemsd(keys="filename", times=1, names="filename_bak"),
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AsDiscreted(keys="pred", threshold=0.5, to_onehot=2),
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]
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)
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),
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]
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# set up engine, PostProcessing handler works together with postprocessing transforms of engine
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engine = SupervisedEvaluator(
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device=torch.device("cpu:0"),
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val_data_loader=data,
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epoch_length=2,
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network=torch.nn.PReLU(),
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# set decollate=False and execute some postprocessing first, then decollate in handlers
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postprocessing=lambda x: dict(pred=x["pred"] + 1.0),
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decollate=False,
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val_handlers=handlers,
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)
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engine.run()
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expected = torch.tensor([[[[1.0], [1.0]], [[0.0], [0.0]]]])
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for o, e in zip(engine.state.output, expected):
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assert_allclose(o["pred"], e)
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filename = o.get("filename_bak")
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if filename is not None:
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self.assertEqual(filename, "test2")
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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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from ignite.engine import Engine, Events
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from monai.handlers import EarlyStopHandler
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class TestHandlerEarlyStop(unittest.TestCase):
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def test_early_stop_train_loss(self):
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def _train_func(engine, batch):
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return {"loss": 1.5}
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trainer = Engine(_train_func)
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EarlyStopHandler(
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patience=5, score_function=lambda x: x.state.output["loss"], trainer=trainer, epoch_level=False
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).attach(trainer)
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trainer.run(range(4), max_epochs=2)
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self.assertEqual(trainer.state.iteration, 6)
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self.assertEqual(trainer.state.epoch, 2)
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def test_early_stop_val_metric(self):
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def _train_func(engine, batch):
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pass
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trainer = Engine(_train_func)
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validator = Engine(_train_func)
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validator.state.metrics["val_acc"] = 0.90
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@trainer.on(Events.EPOCH_COMPLETED)
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def run_validation(engine):
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validator.state.metrics["val_acc"] += 0.01
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validator.run(range(3))
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handler = EarlyStopHandler(
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patience=3,
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score_function=lambda x: x.state.metrics["val_acc"],
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trainer=None,
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min_delta=0.1,
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cumulative_delta=True,
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epoch_level=True,
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)
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handler.attach(validator)
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handler.set_trainer(trainer=trainer)
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trainer.run(range(3), max_epochs=5)
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self.assertEqual(trainer.state.iteration, 12)
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self.assertEqual(trainer.state.epoch, 4)
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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 gc
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import unittest
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from unittest import skipUnless
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import torch
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from ignite.engine import Engine
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from parameterized import parameterized
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from monai.data import Dataset
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from monai.handlers import GarbageCollector
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from monai.utils import IgniteInfo, min_version, optional_import
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Events, has_ignite = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
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TEST_CASE_0 = [[0, 1, 2], "epoch"]
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TEST_CASE_1 = [[0, 1, 2], "iteration"]
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TEST_CASE_2 = [[0, 1, 2], Events.EPOCH_COMPLETED]
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class TestHandlerGarbageCollector(unittest.TestCase):
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@skipUnless(has_ignite, "Requires ignite")
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@parameterized.expand([TEST_CASE_0, TEST_CASE_1, TEST_CASE_2])
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def test_content(self, data, trigger_event):
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# set up engine
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gb_count_dict = {}
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def _train_func(engine, batch):
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# store garbage collection counts
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if trigger_event == Events.EPOCH_COMPLETED or trigger_event.lower() == "epoch":
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if engine.state.iteration % engine.state.epoch_length == 1:
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gb_count_dict[engine.state.epoch] = gc.get_count()
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elif trigger_event.lower() == "iteration":
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gb_count_dict[engine.state.iteration] = gc.get_count()
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engine = Engine(_train_func)
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# set up testing handler
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dataset = Dataset(data, transform=None)
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data_loader = torch.utils.data.DataLoader(dataset, batch_size=1)
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GarbageCollector(trigger_event=trigger_event, log_level=30).attach(engine)
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engine.run(data_loader, max_epochs=5)
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first_count = 0
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for iter, gb_count in gb_count_dict.items():
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# At least one zero-generation object is collected
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# self.assertGreaterEqual(gb_count[0], 0)
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if iter > 1:
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# Since we are collecting all objects from all generations manually at each call,
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# starting from the second call, there shouldn't be any 1st and 2nd
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# generation objects available to collect.
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self.assertEqual(gb_count[1], first_count)
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self.assertEqual(gb_count[2], first_count)
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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 ignite.engine import Engine
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from monai.handlers import HausdorffDistance
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from tests.test_utils import assert_allclose
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def create_spherical_seg_3d(
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radius: float = 20.0, centre: tuple[int, int, int] = (49, 49, 49), im_shape: tuple[int, int, int] = (99, 99, 99)
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) -> np.ndarray:
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"""
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Return a 3D image with a sphere inside. Voxel values will be
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1 inside the sphere, and 0 elsewhere.
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Args:
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radius: radius of sphere (in terms of number of voxels, can be partial)
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centre: location of sphere centre.
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im_shape: shape of image to create
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See also:
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:py:meth:`~create_test_image_3d`
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"""
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# Create image
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image = np.zeros(im_shape, dtype=np.int32)
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spy, spx, spz = np.ogrid[
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-centre[0] : im_shape[0] - centre[0], -centre[1] : im_shape[1] - centre[1], -centre[2] : im_shape[2] - centre[2]
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]
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circle = (spx * spx + spy * spy + spz * spz) <= radius * radius
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image[circle] = 1
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image[~circle] = 0
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return image
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sampler_sphere = torch.Tensor(create_spherical_seg_3d(radius=20, centre=(20, 20, 20))).unsqueeze(0).unsqueeze(0)
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# test input a list of channel-first tensor
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sampler_sphere_gt = [torch.Tensor(create_spherical_seg_3d(radius=20, centre=(10, 20, 20))).unsqueeze(0)]
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sampler_sphere_zeros = torch.zeros_like(sampler_sphere)
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TEST_SAMPLE_1 = [sampler_sphere, sampler_sphere_gt]
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TEST_SAMPLE_2 = [sampler_sphere_gt, sampler_sphere_gt]
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TEST_SAMPLE_3 = [sampler_sphere_zeros, sampler_sphere_gt]
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TEST_SAMPLE_4 = [sampler_sphere_zeros, sampler_sphere_zeros]
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class TestHandlerHausdorffDistance(unittest.TestCase):
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# TODO test multi node Hausdorff Distance
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def test_compute(self):
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hd_metric = HausdorffDistance(include_background=True)
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def _val_func(engine, batch):
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pass
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engine = Engine(_val_func)
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hd_metric.attach(engine, "hausdorff_distance")
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y_pred, y = TEST_SAMPLE_1
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hd_metric.update([y_pred, y])
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self.assertEqual(hd_metric.compute(), 10)
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y_pred, y = TEST_SAMPLE_2
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hd_metric.update([y_pred, y])
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self.assertEqual(hd_metric.compute(), 5)
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y_pred, y = TEST_SAMPLE_3
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hd_metric.update([y_pred, y])
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self.assertEqual(hd_metric.compute(), float("inf"))
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y_pred, y = TEST_SAMPLE_4
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hd_metric.update([y_pred, y])
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self.assertEqual(hd_metric.compute(), float("inf"))
|
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|
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def test_shape_mismatch(self):
|
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hd_metric = HausdorffDistance(include_background=True)
|
89
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with self.assertRaises((AssertionError, ValueError)):
|
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y_pred = TEST_SAMPLE_1[0]
|
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y = torch.ones((1, 1, 10, 10, 10))
|
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hd_metric.update([y_pred, y])
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|
94
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def test_reduction(self):
|
95
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hd_metric = HausdorffDistance(include_background=True, reduction="mean_channel")
|
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|
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def _val_func(engine, batch):
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pass
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engine = Engine(_val_func)
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hd_metric.attach(engine, "hausdorff_distance")
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|
103
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y_pred, y = TEST_SAMPLE_1
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hd_metric.update([y_pred, y])
|
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y_pred, y = TEST_SAMPLE_2
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hd_metric.update([y_pred, y])
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assert_allclose(hd_metric.compute().float(), torch.tensor([10.0, 0.0]))
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|
109
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|
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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 torch
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from parameterized import parameterized
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from monai.handlers import IgniteMetricHandler, from_engine
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from monai.losses import DiceLoss
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from monai.metrics import LossMetric
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from tests.test_utils import SkipIfNoModule, assert_allclose, optional_import
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try:
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_, has_ignite = optional_import("ignite")
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from ignite.engine import Engine, Events
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except ImportError:
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has_ignite = False
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TEST_CASE_1 = [
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{"reduction": "none", "include_background": True},
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{},
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{"output_transform": from_engine(["pred", "label"])},
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0.25,
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]
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TEST_CASE_2 = [
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{"reduction": "mean", "include_background": False},
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{},
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{"output_transform": from_engine(["pred", "label"])},
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0.5,
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]
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TEST_CASE_3 = [
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{"reduction": "none"},
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{"reduction": "mean_channel"},
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{"output_transform": from_engine(["pred", "label"])},
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torch.Tensor([0.5, 0]),
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]
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TEST_CASES = [
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[
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{"include_background": True, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
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{
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"input": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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},
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0,
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],
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[
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{"include_background": False, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
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{
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"input": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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},
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0,
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],
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[
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{"include_background": True, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
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{
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"input": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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"target": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[0.0, 0.0], [0.0, 0.0]]]]),
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},
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1,
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],
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[
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{"include_background": False, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
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{
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"input": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[0.0, 0.0], [0.0, 0.0]]]]),
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"target": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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},
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1,
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],
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[
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{"include_background": True, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
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{
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"input": torch.tensor([[[[0.0, 1.0], [0.0, 1.0]], [[0.0, 1.0], [0.0, 1.0]]]]),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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},
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0.333333,
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],
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[
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{"include_background": False, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
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{
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"input": torch.tensor([[[[0.0, 1.0], [0.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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"target": torch.tensor([[[[1.0, 0.0], [1.0, 0.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
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},
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0,
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],
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]
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class TestHandlerIgniteMetricHandler(unittest.TestCase):
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@SkipIfNoModule("ignite")
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@parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
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def test_metric_fn(self, loss_params, metric_params, handler_params, expected_avg):
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loss_fn = DiceLoss(**loss_params)
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metric_fn = LossMetric(loss_fn=loss_fn, **metric_params)
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ignite_metric = IgniteMetricHandler(metric_fn=metric_fn, **handler_params)
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def _val_func(engine, batch):
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pass
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engine = Engine(_val_func)
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ignite_metric.attach(engine=engine, name="ignite_dice_loss")
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y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
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y = torch.tensor([[[[0.0, 1.0]], [[0.0, 1.0]]]])
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engine.state.output = {"pred": y_pred, "label": y}
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engine.fire_event(Events.ITERATION_COMPLETED)
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y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
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y = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
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engine.state.output = {"pred": y_pred, "label": y}
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engine.fire_event(Events.ITERATION_COMPLETED)
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engine.fire_event(Events.EPOCH_COMPLETED)
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assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_avg, atol=1e-4, rtol=1e-4, type_test=False)
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@SkipIfNoModule("ignite")
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@parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
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def test_loss_fn(self, loss_params, metric_params, handler_params, expected_avg):
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loss_fn = DiceLoss(**loss_params)
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ignite_metric = IgniteMetricHandler(loss_fn=loss_fn, **handler_params, **metric_params)
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def _val_func(engine, batch):
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pass
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engine = Engine(_val_func)
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ignite_metric.attach(engine=engine, name="ignite_dice_loss")
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y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
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y = torch.tensor([[[[0.0, 1.0]], [[0.0, 1.0]]]])
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engine.state.output = {"pred": y_pred, "label": y}
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engine.fire_event(Events.ITERATION_COMPLETED)
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y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
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y = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
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engine.state.output = {"pred": y_pred, "label": y}
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engine.fire_event(Events.ITERATION_COMPLETED)
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engine.fire_event(Events.EPOCH_COMPLETED)
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assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_avg, atol=1e-4, rtol=1e-4, type_test=False)
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@SkipIfNoModule("ignite")
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@parameterized.expand(TEST_CASES)
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def test_dice_loss(self, input_param, input_data, expected_val):
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loss_fn = DiceLoss(**input_param)
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ignite_metric = IgniteMetricHandler(loss_fn=loss_fn, output_transform=from_engine(["pred", "label"]))
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def _val_func(engine, batch):
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pass
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engine = Engine(_val_func)
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ignite_metric.attach(engine=engine, name="ignite_dice_loss")
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y_pred = input_data["input"]
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y = input_data["target"]
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engine.state.output = {"pred": y_pred, "label": y}
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engine.fire_event(Events.ITERATION_COMPLETED)
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engine.fire_event(Events.EPOCH_COMPLETED)
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assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_val, atol=1e-4, rtol=1e-4, type_test=False)
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@SkipIfNoModule("ignite")
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@parameterized.expand(TEST_CASES[0:2])
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def test_old_ignite_metric(self, input_param, input_data, expected_val):
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loss_fn = DiceLoss(**input_param)
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ignite_metric = IgniteMetricHandler(loss_fn=loss_fn, output_transform=from_engine(["pred", "label"]))
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def _val_func(engine, batch):
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pass
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engine = Engine(_val_func)
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ignite_metric.attach(engine=engine, name="ignite_dice_loss")
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y_pred = input_data["input"]
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y = input_data["target"]
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engine.state.output = {"pred": y_pred, "label": y}
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engine.fire_event(Events.ITERATION_COMPLETED)
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engine.fire_event(Events.EPOCH_COMPLETED)
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assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_val, atol=1e-4, rtol=1e-4, type_test=False)
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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 logging
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import os
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import re
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import tempfile
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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 ignite.engine import Engine, Events
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from monai.handlers import LrScheduleHandler
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class TestHandlerLrSchedule(unittest.TestCase):
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def test_content(self):
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data = [0] * 8
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test_lr = 0.1
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gamma = 0.1
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# set up engine
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def _train_func(engine, batch):
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pass
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val_engine = Engine(_train_func)
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train_engine = Engine(_train_func)
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@train_engine.on(Events.EPOCH_COMPLETED)
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def run_validation(engine):
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val_engine.run(data)
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val_engine.state.metrics["val_loss"] = 1
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# set up testing handler
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net = torch.nn.PReLU()
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def _reduce_lr_on_plateau():
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optimizer = torch.optim.SGD(net.parameters(), test_lr)
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lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, patience=1)
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handler = LrScheduleHandler(lr_scheduler, step_transform=lambda x: val_engine.state.metrics["val_loss"])
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handler.attach(train_engine)
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return handler
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with tempfile.TemporaryDirectory() as tempdir:
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key_to_handler = "test_log_lr"
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key_to_print = "Current learning rate"
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filename = os.path.join(tempdir, "test_lr.log")
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# test with additional logging handler
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file_saver = logging.FileHandler(filename, mode="w")
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file_saver.setLevel(logging.INFO)
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logger = logging.getLogger(key_to_handler)
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logger.setLevel(logging.INFO)
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logger.addHandler(file_saver)
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def _reduce_on_step():
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optimizer = torch.optim.SGD(net.parameters(), test_lr)
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lr_scheduler = torch.optim.lr_scheduler.StepLR(optimizer, step_size=2, gamma=gamma)
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handler = LrScheduleHandler(lr_scheduler, name=key_to_handler)
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handler.attach(train_engine)
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return handler
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schedulers = _reduce_lr_on_plateau(), _reduce_on_step()
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train_engine.run(data, max_epochs=5)
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file_saver.close()
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logger.removeHandler(file_saver)
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with open(filename) as f:
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output_str = f.read()
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has_key_word = re.compile(f".*{key_to_print}.*")
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content_count = 0
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for line in output_str.split("\n"):
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if has_key_word.match(line):
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content_count += 1
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self.assertTrue(content_count > 0)
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for scheduler in schedulers:
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np.testing.assert_allclose(scheduler.lr_scheduler._last_lr[0], 0.001)
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+
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if __name__ == "__main__":
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unittest.main()
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