monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2507__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/inferers/utils.py +1 -2
- monai/losses/dice.py +2 -14
- monai/losses/ds_loss.py +1 -3
- 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/utils.py +1 -2
- 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.dev2507.dist-info}/METADATA +2 -2
- monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.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_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 +1310 -0
- tests/inferers/test_diffusion_inferer.py +236 -0
- tests/inferers/test_latent_diffusion_inferer.py +824 -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_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
- tests/networks/nets/test_globalnet.py +103 -0
- tests/networks/nets/test_highresnet.py +67 -0
- tests/networks/nets/test_hovernet.py +218 -0
- tests/networks/nets/test_mednext.py +122 -0
- tests/networks/nets/test_milmodel.py +92 -0
- tests/networks/nets/test_net_adapter.py +68 -0
- tests/networks/nets/test_network_consistency.py +86 -0
- tests/networks/nets/test_patch_gan_dicriminator.py +179 -0
- tests/networks/nets/test_quicknat.py +57 -0
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- 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.dev2507.dist-info}/LICENSE +0 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.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 numpy as np
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import torch
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import torch.nn as nn
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import torch.nn.functional as F
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import torch.optim as optim
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from monai.losses import GeneralizedWassersteinDiceLoss
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from tests.test_utils import test_script_save
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class TestGeneralizedWassersteinDiceLoss(unittest.TestCase):
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def test_bin_seg_2d(self):
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target = torch.tensor([[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]])
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# add another dimension corresponding to the batch (batch size = 1 here)
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target = target.unsqueeze(0)
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pred_very_good = 1000 * F.one_hot(target, num_classes=2).permute(0, 3, 1, 2).float()
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pred_very_poor = 1000 * F.one_hot(1 - target, num_classes=2).permute(0, 3, 1, 2).float()
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for weight_mode in ["default", "GDL"]:
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# initialize the loss
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loss = GeneralizedWassersteinDiceLoss(
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dist_matrix=np.array([[0.0, 1.0], [1.0, 0.0]]), weighting_mode=weight_mode
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)
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# the loss for pred_very_good should be close to 0
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loss_good = float(loss.forward(pred_very_good, target))
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self.assertAlmostEqual(loss_good, 0.0, places=3)
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# same test, but with target with a class dimension
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target_4dim = target.unsqueeze(1)
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loss_good = float(loss.forward(pred_very_good, target_4dim))
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self.assertAlmostEqual(loss_good, 0.0, places=3)
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# the loss for pred_very_poor should be close to 1
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loss_poor = float(loss.forward(pred_very_poor, target))
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self.assertAlmostEqual(loss_poor, 1.0, places=3)
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def test_different_target_data_type(self):
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"""
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Test if the loss is compatible with all the integer types
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for the target segmentation.
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"""
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# define 2d examples
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target = torch.tensor([[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]])
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# add another dimension corresponding to the batch (batch size = 1 here)
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target = target.unsqueeze(0) # shape (1, H, W)
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pred_very_good = 1000 * F.one_hot(target, num_classes=2).permute(0, 3, 1, 2).float()
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target_uint8 = target.to(torch.uint8)
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target_int8 = target.to(torch.int8)
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target_short = target.short()
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target_int = target.int()
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target_long = target.long()
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target_list = [target_uint8, target_int8, target_short, target_int, target_long]
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for w_mode in ["default", "GDL"]:
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# initialize the loss
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loss = GeneralizedWassersteinDiceLoss(dist_matrix=np.array([[0.0, 1.0], [1.0, 0.0]]), weighting_mode=w_mode)
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# The test should pass irrespectively of the integer type used
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for t in target_list:
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# the loss for pred_very_good should be close to 0
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loss_good = float(loss.forward(pred_very_good, t))
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self.assertAlmostEqual(loss_good, 0.0, places=3)
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def test_empty_class_2d(self):
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num_classes = 2
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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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# add another dimension corresponding to the batch (batch size = 1 here)
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target = target.unsqueeze(0)
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pred_very_good = 1000 * F.one_hot(target, num_classes=num_classes).permute(0, 3, 1, 2).float()
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pred_very_poor = 1000 * F.one_hot(1 - target, num_classes=num_classes).permute(0, 3, 1, 2).float()
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for w_mode in ["default", "GDL"]:
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# initialize the loss
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loss = GeneralizedWassersteinDiceLoss(dist_matrix=np.array([[0.0, 1.0], [1.0, 0.0]]), weighting_mode=w_mode)
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# loss for pred_very_good should be close to 0
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loss_good = float(loss.forward(pred_very_good, target))
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self.assertAlmostEqual(loss_good, 0.0, places=3)
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# loss for pred_very_poor should be close to 1
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loss_poor = float(loss.forward(pred_very_poor, target))
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self.assertAlmostEqual(loss_poor, 1.0, places=3)
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def test_bin_seg_3d(self):
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# define 3d examples
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target = torch.tensor(
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[
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# raw 0
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[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
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# raw 1
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[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
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# raw 2
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[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
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]
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)
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# add another dimension corresponding to the batch (batch size = 1 here)
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target = target.unsqueeze(0) # shape (1, H, W, D)
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pred_very_good = 1000 * F.one_hot(target, num_classes=2).permute(0, 4, 1, 2, 3).float()
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pred_very_poor = 1000 * F.one_hot(1 - target, num_classes=2).permute(0, 4, 1, 2, 3).float()
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for w_mode in ["default", "GDL"]:
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# initialize the loss
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loss = GeneralizedWassersteinDiceLoss(dist_matrix=np.array([[0.0, 1.0], [1.0, 0.0]]), weighting_mode=w_mode)
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# mean dice loss for pred_very_good should be close to 0
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loss_good = float(loss.forward(pred_very_good, target))
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self.assertAlmostEqual(loss_good, 0.0, places=3)
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# mean dice loss for pred_very_poor should be close to 1
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loss_poor = float(loss.forward(pred_very_poor, target))
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self.assertAlmostEqual(loss_poor, 1.0, places=3)
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def test_convergence(self):
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"""
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The goal of this test is to assess if the gradient of the loss function
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is correct by testing if we can train a one layer neural network
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to segment one image.
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We verify that the loss is decreasing in almost all SGD steps.
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"""
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learning_rate = 0.001
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max_iter = 50
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# define a simple 3d example
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target_seg = torch.tensor(
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[
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# raw 0
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[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
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# raw 1
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[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
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# raw 2
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[[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]],
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]
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)
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target_seg = torch.unsqueeze(target_seg, dim=0)
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image = 12 * target_seg + 27 # dummy image to segment
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image = image.float()
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num_classes = 2
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num_voxels = 3 * 4 * 4
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# define a model with one layer
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class OnelayerNet(nn.Module):
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def __init__(self):
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super().__init__()
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self.layer = nn.Linear(num_voxels, num_voxels * num_classes)
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def forward(self, x):
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x = x.view(-1, num_voxels)
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x = self.layer(x)
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x = x.view(-1, num_classes, 3, 4, 4)
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return x
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for w_mode in ["default", "GDL"]:
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# initialise the network
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net = OnelayerNet()
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# initialize the loss
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loss = GeneralizedWassersteinDiceLoss(dist_matrix=np.array([[0.0, 1.0], [1.0, 0.0]]), weighting_mode=w_mode)
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# initialize an optimizer
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optimizer = optim.Adam(net.parameters(), lr=learning_rate)
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# initial difference between pred and target
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pred_start = torch.argmax(net(image), dim=1)
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diff_start = torch.norm(pred_start.float() - target_seg.float())
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loss_history = []
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# train the network
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for _ in range(max_iter):
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# set the gradient to zero
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optimizer.zero_grad()
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# forward pass
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output = net(image)
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loss_val = loss(output, target_seg)
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# backward pass
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loss_val.backward()
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optimizer.step()
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# stats
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loss_history.append(loss_val.item())
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# difference between pred and target after training
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pred_end = torch.argmax(net(image), dim=1)
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diff_end = torch.norm(pred_end.float() - target_seg.float())
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# count the number of SGD steps in which the loss decreases
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num_decreasing_steps = 0
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for i in range(len(loss_history) - 1):
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if loss_history[i] > loss_history[i + 1]:
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num_decreasing_steps += 1
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decreasing_steps_ratio = float(num_decreasing_steps) / (len(loss_history) - 1)
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# verify that the loss is decreasing for sufficiently many SGD steps
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self.assertTrue(decreasing_steps_ratio > 0.75)
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# check that the predicted segmentation has improved
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self.assertGreater(diff_start, diff_end)
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def test_script(self):
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target = torch.tensor([[0, 0, 0, 0], [0, 1, 1, 0], [0, 1, 1, 0], [0, 0, 0, 0]])
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# add another dimension corresponding to the batch (batch size = 1 here)
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target = target.unsqueeze(0)
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pred_very_good = 1000 * F.one_hot(target, num_classes=2).permute(0, 3, 1, 2).float()
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loss = GeneralizedWassersteinDiceLoss(dist_matrix=np.array([[0.0, 1.0], [1.0, 0.0]]), weighting_mode="default")
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test_script_save(loss, pred_very_good, target)
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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 parameterized import parameterized
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from monai.losses import BoxGIoULoss
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TEST_CASES = [
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[ # shape: (1, 4), (1, 4)
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{"input": torch.tensor([[1.0, 1.0, 2.0, 2.0]]), "target": torch.tensor([[1.0, 1.0, 2.0, 2.0]])},
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0.0,
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],
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[ # shape: (1, 6), (1, 6)
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{
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"input": torch.tensor([[1.0, 1.0, 1.0, 2.0, 2.0, 2.0]]),
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"target": torch.tensor([[1.0, 1.0, 1.0, 2.0, 2.0, 2.0]]),
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},
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0.0,
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],
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]
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class TestGIoULoss(unittest.TestCase):
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@parameterized.expand(TEST_CASES)
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def test_result(self, input_data, expected_val):
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loss = BoxGIoULoss()
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result = loss(**input_data)
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np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, atol=1e-4, rtol=1e-4)
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def test_ill_shape(self):
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loss = BoxGIoULoss()
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with self.assertRaisesRegex(ValueError, ""):
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loss(torch.ones((1, 2, 3)), torch.ones((1, 1, 2, 3)))
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def test_with_cuda(self):
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loss = BoxGIoULoss()
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i = torch.tensor([[1.0, 1.0, 2.0, 2.0]])
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j = torch.tensor([[1.0, 1.0, 2.0, 2.0]])
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if torch.cuda.is_available():
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i = i.cuda()
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j = j.cuda()
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output = loss(i, j)
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np.testing.assert_allclose(output.detach().cpu().numpy(), 0.0, atol=1e-4, rtol=1e-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 unittest
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from unittest.case import skipUnless
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import numpy as np
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import torch
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from parameterized import parameterized
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from monai.losses import HausdorffDTLoss, LogHausdorffDTLoss
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from monai.utils import optional_import
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_, has_scipy = optional_import("scipy")
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TEST_CASES = []
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for device in ["cpu", "cuda"] if torch.cuda.is_available() else ["cpu"]:
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TEST_CASES.append(
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[ # shape: (1, 1, 2, 2), (1, 1, 2, 2)
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{"include_background": True, "sigmoid": True},
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{
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"input": torch.tensor([[[[1.0, -1.0], [-1.0, 1.0]]]], device=device),
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"target": torch.tensor([[[[1.0, 0.0], [1.0, 1.0]]]], device=device),
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},
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0.509329,
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]
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)
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TEST_CASES.append(
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[ # shape: (1, 1, 1, 2, 2), (1, 1, 1, 2, 2)
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{"include_background": True, "sigmoid": True},
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{
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"input": torch.tensor([[[[[1.0, -1.0], [-1.0, 1.0]]]]], device=device),
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"target": torch.tensor([[[[[1.0, 0.0], [1.0, 1.0]]]]], device=device),
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},
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0.509329,
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]
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)
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TEST_CASES.append(
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[ # shape: (1, 1, 2, 2, 2), (1, 1, 2, 2, 2)
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{"include_background": True, "sigmoid": True},
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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]]]]], device=device),
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"target": torch.tensor([[[[[1.0, 0.0], [1.0, 0.0]], [[0.0, 0.0], [1.0, 1.0]]]]], device=device),
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},
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0.375718,
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]
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)
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TEST_CASES.append(
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[ # shape: (1, 2, 2, 2), (1, 2, 2, 2)
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{"include_background": True, "sigmoid": True},
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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]]]], device=device),
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"target": torch.tensor([[[[1.0, 0.0], [1.0, 1.0]], [[1.0, 0.0], [0.0, 1.0]]]], device=device),
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},
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0.326994,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 1, 2, 2), (2, 1, 2, 2)
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{"include_background": True, "sigmoid": True},
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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]]]], device=device),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]]], [[[1.0, 0.0], [1.0, 0.0]]]], device=device),
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},
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0.455082,
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]
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)
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TEST_CASES.append(
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[ # shape: (1, 1, 2, 2), (1, 1, 2, 2)
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{"include_background": False, "sigmoid": True},
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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]]]], device=device),
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"target": torch.tensor([[[[1.0, 0.0], [1.0, 1.0]], [[1.0, 0.0], [0.0, 1.0]]]], device=device),
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},
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0.144659,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 2, 3, 1), (2, 1, 3, 1)
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{"include_background": True, "to_onehot_y": True, "sigmoid": True, "reduction": "none"},
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{
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"input": torch.tensor(
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[[[[-1.0], [0.0], [1.0]], [[1.0], [0.0], [-1.0]]], [[[0.0], [0.0], [0.0]], [[0.0], [0.0], [0.0]]]],
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device=device,
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),
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"target": torch.tensor([[[[1.0], [0.0], [0.0]]], [[[1.0], [1.0], [0.0]]]], device=device),
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},
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[[[[0.407765]], [[0.407765]]], [[[0.5000]], [[0.5000]]]],
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 2, 3, 1), (2, 1, 3, 1)
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{"include_background": True, "to_onehot_y": True, "softmax": True},
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{
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"input": torch.tensor(
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[[[[-1.0], [0.0], [1.0]], [[1.0], [0.0], [-1.0]]], [[[0.0], [0.0], [0.0]], [[0.0], [0.0], [0.0]]]],
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device=device,
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),
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"target": torch.tensor([[[[1.0], [0.0], [0.0]]], [[[1.0], [1.0], [0.0]]]], device=device),
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},
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0.357016,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 2, 3, 1), (2, 1, 3, 1)
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{"include_background": True, "to_onehot_y": True, "softmax": True, "reduction": "sum"},
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{
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"input": torch.tensor(
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[[[[-1.0], [0.0], [1.0]], [[1.0], [0.0], [-1.0]]], [[[0.0], [0.0], [0.0]], [[0.0], [0.0], [0.0]]]],
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device=device,
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),
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"target": torch.tensor([[[[1.0], [0.0], [0.0]]], [[[1.0], [1.0], [0.0]]]], device=device),
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},
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1.428062,
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]
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)
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TEST_CASES.append(
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[ # shape: (1, 1, 2, 2), (1, 1, 2, 2)
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{"include_background": True, "sigmoid": True},
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{
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"input": torch.tensor([[[[1.0, -1.0], [-1.0, 1.0]]]], device=device),
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"target": torch.tensor([[[[1.0, 0.0], [1.0, 1.0]]]], device=device),
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},
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0.509329,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 1, 2, 2), (2, 1, 2, 2)
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{"include_background": True, "other_act": torch.tanh},
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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]]]], device=device),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]]], [[[1.0, 0.0], [1.0, 0.0]]]], device=device),
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},
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1.870039,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 2, 3), (2, 1, 3)
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{"include_background": True, "to_onehot_y": True, "other_act": lambda x: torch.log_softmax(x, dim=1)},
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{
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"input": torch.tensor(
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[[[[-1.0], [0.0], [1.0]], [[1.0], [0.0], [-1.0]]], [[[0.0], [0.0], [0.0]], [[0.0], [0.0], [0.0]]]],
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device=device,
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),
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"target": torch.tensor([[[[1.0], [0.0], [0.0]]], [[[1.0], [1.0], [0.0]]]], device=device),
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},
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4.366613,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 1, 2, 2), (2, 1, 2, 2)
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{"include_background": True, "other_act": torch.tanh, "batch": True},
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{
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"input": torch.tensor([[[[1.0, -0.0], [-1.0, 1.0]]], [[[1.0, -1.0], [-1.0, 1.0]]]], device=device),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]]], [[[1.0, 0.0], [1.0, 0.0]]]], device=device),
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},
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1.607137,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 1, 2, 2), (2, 1, 2, 2)
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{"include_background": True, "other_act": torch.tanh, "batch": True},
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{
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"input": torch.tensor([[[[1.0, -0.0], [-1.0, 1.0]]], [[[1.0, -1.0], [-1.0, 1.0]]]], device=device),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]]], [[[1.0, 0.0], [1.0, 0.0]]]], device=device),
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},
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1.607137,
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]
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)
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TEST_CASES.append(
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[ # shape: (2, 1, 2, 2), (2, 1, 2, 2)
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{"include_background": True, "other_act": torch.tanh, "batch": False},
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{
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"input": torch.tensor([[[[1.0, -0.0], [-1.0, 1.0]]], [[[1.0, -1.0], [-1.0, 1.0]]]], device=device),
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"target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]]], [[[1.0, 0.0], [1.0, 0.0]]]], device=device),
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},
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1.607137,
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]
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)
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TEST_CASES_LOG = [[*inputs, np.log(np.array(output) + 1)] for *inputs, output in TEST_CASES]
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def _describe_test_case(test_func, test_number, params):
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input_param, input_data, _ = params.args
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return f"params:{input_param}, shape:{input_data['input'].shape}, device:{input_data['input'].device}"
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@skipUnless(has_scipy, "Scipy required")
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class TestHausdorffDTLoss(unittest.TestCase):
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@parameterized.expand(TEST_CASES, doc_func=_describe_test_case)
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def test_shape(self, input_param, input_data, expected_val):
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result = HausdorffDTLoss(**input_param).forward(**input_data)
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np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5)
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def test_ill_shape(self):
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loss = HausdorffDTLoss()
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with self.assertRaisesRegex(AssertionError, ""):
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loss.forward(torch.ones((1, 1, 2, 3)), torch.ones((1, 4, 5, 6)))
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def test_ill_opts(self):
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with self.assertRaisesRegex(ValueError, ""):
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HausdorffDTLoss(sigmoid=True, softmax=True)
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chn_input = torch.ones((1, 1, 3))
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chn_target = torch.ones((1, 1, 3))
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with self.assertRaisesRegex(ValueError, ""):
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HausdorffDTLoss(reduction="unknown")(chn_input, chn_target)
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with self.assertRaisesRegex(ValueError, ""):
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HausdorffDTLoss(reduction=None)(chn_input, chn_target)
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@parameterized.expand([(False, False, False), (False, True, False), (False, False, True)])
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def test_input_warnings(self, include_background, softmax, to_onehot_y):
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chn_input = torch.ones((1, 1, 1, 3))
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chn_target = torch.ones((1, 1, 1, 3))
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with self.assertWarns(Warning):
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loss = HausdorffDTLoss(include_background=include_background, softmax=softmax, to_onehot_y=to_onehot_y)
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loss.forward(chn_input, chn_target)
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@skipUnless(has_scipy, "Scipy required")
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class TesLogtHausdorffDTLoss(unittest.TestCase):
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@parameterized.expand(TEST_CASES_LOG, doc_func=_describe_test_case)
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def test_shape(self, input_param, input_data, expected_val):
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result = LogHausdorffDTLoss(**input_param).forward(**input_data)
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np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5)
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def test_ill_shape(self):
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loss = LogHausdorffDTLoss()
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with self.assertRaisesRegex(AssertionError, ""):
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loss.forward(torch.ones((1, 1, 2, 3)), torch.ones((1, 4, 5, 6)))
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def test_ill_opts(self):
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with self.assertRaisesRegex(ValueError, ""):
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LogHausdorffDTLoss(sigmoid=True, softmax=True)
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chn_input = torch.ones((1, 1, 3))
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chn_target = torch.ones((1, 1, 3))
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with self.assertRaisesRegex(ValueError, ""):
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LogHausdorffDTLoss(reduction="unknown")(chn_input, chn_target)
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with self.assertRaisesRegex(ValueError, ""):
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LogHausdorffDTLoss(reduction=None)(chn_input, chn_target)
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@parameterized.expand([(False, False, False), (False, True, False), (False, False, True)])
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def test_input_warnings(self, include_background, softmax, to_onehot_y):
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chn_input = torch.ones((1, 1, 1, 3))
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chn_target = torch.ones((1, 1, 1, 3))
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with self.assertWarns(Warning):
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loss = LogHausdorffDTLoss(include_background=include_background, softmax=softmax, to_onehot_y=to_onehot_y)
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loss.forward(chn_input, chn_target)
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+
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262
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263
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+
if __name__ == "__main__":
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unittest.main()
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