monai-weekly 1.5.dev2505__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/meta_tensor.py +5 -0
- 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/jupyter_utils.py +1 -1
- monai/utils/tf32.py +0 -10
- monai/visualize/class_activation_maps.py +5 -8
- monai/visualize/img2tensorboard.py +2 -2
- {monai_weekly-1.5.dev2505.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.dev2505.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
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- 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.dev2505.dist-info/RECORD +0 -427
- {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
- {monai_weekly-1.5.dev2505.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 os
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import unittest
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from pathlib import Path
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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 parameterized import parameterized
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from monai.data import DataLoader, Dataset, MetaTensor
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from monai.engines import Evaluator
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from monai.handlers import ProbMapProducer, ValidationHandler
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from monai.utils.enums import ProbMapKeys
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TEST_CASE_0 = ["temp_image_inference_output_1", 1]
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TEST_CASE_1 = ["temp_image_inference_output_2", 9]
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TEST_CASE_2 = ["temp_image_inference_output_3", 100]
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class TestDataset(Dataset):
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__test__ = False # indicate to pytest that this class is not intended for collection
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def __init__(self, name, size):
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super().__init__(
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data=[
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{
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"image": name,
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ProbMapKeys.COUNT.value: size,
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ProbMapKeys.SIZE.value: np.array([size + 1, size + 1]),
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ProbMapKeys.LOCATION.value: np.array([i, i + 1]),
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}
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for i in range(size)
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]
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)
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self.image_data = [
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{
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ProbMapKeys.NAME.value: name,
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ProbMapKeys.COUNT.value: size,
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ProbMapKeys.SIZE.value: np.array([size + 1, size + 1]),
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}
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]
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def __getitem__(self, index):
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image = np.ones((3, 2, 2)) * index
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metadata = {
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ProbMapKeys.COUNT.value: self.data[index][ProbMapKeys.COUNT.value],
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ProbMapKeys.NAME.value: self.data[index]["image"],
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ProbMapKeys.SIZE.value: self.data[index][ProbMapKeys.SIZE.value],
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ProbMapKeys.LOCATION.value: self.data[index][ProbMapKeys.LOCATION.value],
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}
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return {"image": MetaTensor(x=image, meta=metadata), "pred": index + 1}
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class TestEvaluator(Evaluator):
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__test__ = False # indicate to pytest that this class is not intended for collection
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def _iteration(self, engine, batchdata):
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return batchdata
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class TestHandlerProbMapGenerator(unittest.TestCase):
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@parameterized.expand([TEST_CASE_0, TEST_CASE_1, TEST_CASE_2])
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def test_prob_map_generator(self, name, size):
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# set up dataset
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dataset = TestDataset(name, size)
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batch_size = 2
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data_loader = DataLoader(dataset, batch_size=batch_size)
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# set up engine
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def inference(engine, batch):
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pass
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engine = Engine(inference)
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tests_path = Path(__file__).parents[1].as_posix()
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# add ProbMapGenerator() to evaluator
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output_dir = os.path.join(tests_path, "testing_data")
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prob_map_gen = ProbMapProducer(output_dir=output_dir)
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evaluator = TestEvaluator(
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torch.device("cpu:0"), data_loader, np.ceil(size / batch_size), val_handlers=[prob_map_gen]
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)
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# set up validation handler
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validation = ValidationHandler(interval=1, validator=None)
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validation.attach(engine)
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validation.set_validator(validator=evaluator)
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engine.run(data_loader)
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prob_map = np.load(os.path.join(output_dir, name + ".npy"))
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self.assertListEqual(np.vstack(prob_map.nonzero()).T.tolist(), [[i, i + 1] for i in range(size)])
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self.assertListEqual(prob_map[prob_map.nonzero()].tolist(), [i + 1 for i in range(size)])
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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 functools import partial
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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 MeanAbsoluteError, MeanSquaredError, PeakSignalToNoiseRatio, RootMeanSquaredError
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from monai.utils import set_determinism
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# define a numpy flatten function that only preserves batch dimension
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def flatten(data):
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return np.reshape(data, [data.shape[0], -1])
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# define metrics computation truth functions to check our monai metrics against
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def msemetric_np(y_pred, y):
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return np.mean((flatten(y_pred) - flatten(y)) ** 2)
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def maemetric_np(y_pred, y):
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return np.mean(np.abs(flatten(y_pred) - flatten(y)))
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def rmsemetric_np(y_pred, y):
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return np.mean(np.sqrt(np.mean((flatten(y_pred) - flatten(y)) ** 2, axis=1)))
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def psnrmetric_np(max_val, y_pred, y):
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mse = np.mean((flatten(y_pred) - flatten(y)) ** 2, axis=1)
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return np.mean(20 * np.log10(max_val) - 10 * np.log10(mse))
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class TestHandlerRegressionMetrics(unittest.TestCase):
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def test_compute(self):
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set_determinism(seed=123)
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device = "cuda" if torch.cuda.is_available() else "cpu"
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# regression metrics to check + truth metric function in numpy
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metrics = [
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MeanSquaredError,
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MeanAbsoluteError,
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RootMeanSquaredError,
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partial(PeakSignalToNoiseRatio, max_val=1.0),
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]
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metrics_np = [msemetric_np, maemetric_np, rmsemetric_np, partial(psnrmetric_np, max_val=1.0)]
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# define variations in batch/base_dims/spatial_dims
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batch_dims = [1, 2, 4, 16]
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base_dims = [16, 32, 64]
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spatial_dims = [2, 3, 4]
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# iterate over all variations and check shapes for different reduction functions
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for mt_fn, mt_fn_np in zip(metrics, metrics_np):
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for batch in batch_dims:
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for spatial in spatial_dims:
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for base in base_dims:
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mt_fn_obj = mt_fn(**{"save_details": False})
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# create random tensor
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in_tensor_a1 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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in_tensor_b1 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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mt_fn_obj.update([in_tensor_a1, in_tensor_b1])
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out_tensor_np1 = mt_fn_np(y_pred=in_tensor_a1.cpu().numpy(), y=in_tensor_b1.cpu().numpy())
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in_tensor_a2 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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in_tensor_b2 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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mt_fn_obj.update([in_tensor_a2, in_tensor_b2])
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out_tensor_np2 = mt_fn_np(y_pred=in_tensor_a2.cpu().numpy(), y=in_tensor_b2.cpu().numpy())
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out_tensor = mt_fn_obj.compute()
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out_tensor_np = (out_tensor_np1 + out_tensor_np2) / 2.0
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np.testing.assert_allclose(out_tensor, out_tensor_np, atol=1e-4)
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def test_compute_engine(self):
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set_determinism(seed=123)
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device = "cuda" if torch.cuda.is_available() else "cpu"
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# regression metrics to check + truth metric function in numpy
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metrics_names = ["MSE", "MAE", "RMSE", "PSNR"]
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metrics = [
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MeanSquaredError,
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MeanAbsoluteError,
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RootMeanSquaredError,
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partial(PeakSignalToNoiseRatio, max_val=1.0),
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]
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metrics_np = [msemetric_np, maemetric_np, rmsemetric_np, partial(psnrmetric_np, max_val=1.0)]
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def _val_func(engine, batch):
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pass
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# define variations in batch/base_dims/spatial_dims
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batch_dims = [1, 2, 4, 16]
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base_dims = [16, 32, 64]
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spatial_dims = [2, 3, 4]
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# iterate over all variations and check shapes for different reduction functions
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for mt_fn_name, mt_fn, mt_fn_np in zip(metrics_names, metrics, metrics_np):
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for batch in batch_dims:
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for spatial in spatial_dims:
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for base in base_dims:
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mt_fn_obj = mt_fn() # 'save_details' == True
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engine = Engine(_val_func)
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mt_fn_obj.attach(engine, mt_fn_name)
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# create random tensor
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in_tensor_a1 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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in_tensor_b1 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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mt_fn_obj.update([in_tensor_a1, in_tensor_b1])
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out_tensor_np1 = mt_fn_np(y_pred=in_tensor_a1.cpu().numpy(), y=in_tensor_b1.cpu().numpy())
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in_tensor_a2 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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in_tensor_b2 = torch.rand((batch,) + (base,) * (spatial - 1)).to(device)
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mt_fn_obj.update([in_tensor_a2, in_tensor_b2])
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out_tensor_np2 = mt_fn_np(y_pred=in_tensor_a2.cpu().numpy(), y=in_tensor_b2.cpu().numpy())
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out_tensor = mt_fn_obj.compute()
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out_tensor_np = (out_tensor_np1 + out_tensor_np2) / 2.0
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np.testing.assert_allclose(out_tensor, out_tensor_np, atol=1e-4)
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def test_ill_shape(self):
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set_determinism(seed=123)
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device = "cuda" if torch.cuda.is_available() else "cpu"
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# regression metrics to check + truth metric function in numpy
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metrics = [
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MeanSquaredError,
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MeanAbsoluteError,
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RootMeanSquaredError,
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partial(PeakSignalToNoiseRatio, max_val=1.0),
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]
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basedim = 10
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# different shape for pred/target
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with self.assertRaises((AssertionError, ValueError)):
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in_tensor_a = torch.rand((basedim,)).to(device)
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in_tensor_b = torch.rand((basedim, basedim)).to(device)
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for mt_fn in metrics:
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mt_fn().update([in_tensor_a, in_tensor_b])
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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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import torch.distributed as dist
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from ignite.engine import Engine
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from monai.handlers import MeanAbsoluteError, MeanSquaredError, PeakSignalToNoiseRatio, RootMeanSquaredError
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from monai.utils import set_determinism
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from tests.test_utils import DistCall, DistTestCase
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# define a numpy flatten function that only preserves batch dimension
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def flatten(data):
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return np.reshape(data, [data.shape[0], -1])
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# define metrics computation truth functions to check our monai metrics against
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def msemetric_np(y_pred, y):
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return np.mean((flatten(y_pred) - flatten(y)) ** 2)
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def maemetric_np(y_pred, y):
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return np.mean(np.abs(flatten(y_pred) - flatten(y)))
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def rmsemetric_np(y_pred, y):
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return np.mean(np.sqrt(np.mean((flatten(y_pred) - flatten(y)) ** 2, axis=1)))
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+
|
43
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+
|
44
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+
def psnrmetric_np(max_val, y_pred, y):
|
45
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+
mse = np.mean((flatten(y_pred) - flatten(y)) ** 2, axis=1)
|
46
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+
return np.mean(20 * np.log10(max_val) - 10 * np.log10(mse))
|
47
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+
|
48
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+
|
49
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+
# define tensor size as (BATCH_SIZE, (BASE_DIM_SIZE,) * SPATIAL_DIM)
|
50
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+
# One tensor with following shape takes 4*32*32*32*32/(8*1000) = 512 MB on a single GPU
|
51
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+
# We have total of 2 tensors each on one GPU for following tests, so required GPU memory is 1024 MB on each GPU
|
52
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+
# The required GPU memory can be lowered by changing BASE_DIM_SIZE to another value e.g. BASE_DIM_SIZE=16 will
|
53
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+
# require 128 MB on each GPU
|
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+
BATCH_SIZE = 4
|
55
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+
BASE_DIM_SIZE = 32
|
56
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+
SPATIAL_DIM = 3
|
57
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+
|
58
|
+
|
59
|
+
class DistributedMeanSquaredError(DistTestCase):
|
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+
@DistCall(nnodes=1, nproc_per_node=2)
|
61
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def test_compute(self):
|
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set_determinism(123)
|
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self._compute()
|
64
|
+
|
65
|
+
def _compute(self):
|
66
|
+
device = f"cuda:{dist.get_rank()}" if torch.cuda.is_available() else "cpu"
|
67
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+
metric = MeanSquaredError()
|
68
|
+
|
69
|
+
def _val_func(engine, batch):
|
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pass
|
71
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+
|
72
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+
engine = Engine(_val_func)
|
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+
metric.attach(engine, "MSE")
|
74
|
+
|
75
|
+
# get testing data
|
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|
+
batch = BATCH_SIZE
|
77
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+
base = BASE_DIM_SIZE
|
78
|
+
spatial = SPATIAL_DIM
|
79
|
+
in_tensor_a1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
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+
in_tensor_b1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
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|
+
|
82
|
+
in_tensor_a2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
83
|
+
in_tensor_b2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
84
|
+
|
85
|
+
if dist.get_rank() == 0:
|
86
|
+
y_pred = in_tensor_a1.to(device)
|
87
|
+
y = in_tensor_b1.to(device)
|
88
|
+
metric.update([y_pred, y])
|
89
|
+
|
90
|
+
if dist.get_rank() == 1:
|
91
|
+
y_pred = in_tensor_a2.to(device)
|
92
|
+
y = in_tensor_b2.to(device)
|
93
|
+
metric.update([y_pred, y])
|
94
|
+
|
95
|
+
out_tensor = metric.compute()
|
96
|
+
|
97
|
+
# do numpy functions to get ground truth referece
|
98
|
+
out_tensor_np1 = msemetric_np(y_pred=in_tensor_a1.cpu().numpy(), y=in_tensor_b1.cpu().numpy())
|
99
|
+
out_tensor_np2 = msemetric_np(y_pred=in_tensor_a2.cpu().numpy(), y=in_tensor_b2.cpu().numpy())
|
100
|
+
out_tensor_np = (out_tensor_np1 + out_tensor_np2) / 2.0
|
101
|
+
|
102
|
+
np.testing.assert_allclose(out_tensor, out_tensor_np, rtol=1e-04, atol=1e-04)
|
103
|
+
|
104
|
+
|
105
|
+
class DistributedMeanAbsoluteError(DistTestCase):
|
106
|
+
@DistCall(nnodes=1, nproc_per_node=2)
|
107
|
+
def test_compute(self):
|
108
|
+
set_determinism(123)
|
109
|
+
self._compute()
|
110
|
+
|
111
|
+
def _compute(self):
|
112
|
+
device = f"cuda:{dist.get_rank()}" if torch.cuda.is_available() else "cpu"
|
113
|
+
metric = MeanAbsoluteError()
|
114
|
+
|
115
|
+
def _val_func(engine, batch):
|
116
|
+
pass
|
117
|
+
|
118
|
+
engine = Engine(_val_func)
|
119
|
+
metric.attach(engine, "MAE")
|
120
|
+
|
121
|
+
# get testing data
|
122
|
+
batch = BATCH_SIZE
|
123
|
+
base = BASE_DIM_SIZE
|
124
|
+
spatial = SPATIAL_DIM
|
125
|
+
in_tensor_a1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
126
|
+
in_tensor_b1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
127
|
+
|
128
|
+
in_tensor_a2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
129
|
+
in_tensor_b2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
130
|
+
|
131
|
+
if dist.get_rank() == 0:
|
132
|
+
y_pred = in_tensor_a1.to(device)
|
133
|
+
y = in_tensor_b1.to(device)
|
134
|
+
metric.update([y_pred, y])
|
135
|
+
|
136
|
+
if dist.get_rank() == 1:
|
137
|
+
y_pred = in_tensor_a2.to(device)
|
138
|
+
y = in_tensor_b2.to(device)
|
139
|
+
metric.update([y_pred, y])
|
140
|
+
|
141
|
+
out_tensor = metric.compute()
|
142
|
+
|
143
|
+
# do numpy functions to get ground truth referece
|
144
|
+
out_tensor_np1 = maemetric_np(y_pred=in_tensor_a1.cpu().numpy(), y=in_tensor_b1.cpu().numpy())
|
145
|
+
out_tensor_np2 = maemetric_np(y_pred=in_tensor_a2.cpu().numpy(), y=in_tensor_b2.cpu().numpy())
|
146
|
+
out_tensor_np = (out_tensor_np1 + out_tensor_np2) / 2.0
|
147
|
+
|
148
|
+
np.testing.assert_allclose(out_tensor, out_tensor_np, rtol=1e-04, atol=1e-04)
|
149
|
+
|
150
|
+
|
151
|
+
class DistributedRootMeanSquaredError(DistTestCase):
|
152
|
+
@DistCall(nnodes=1, nproc_per_node=2)
|
153
|
+
def test_compute(self):
|
154
|
+
set_determinism(123)
|
155
|
+
self._compute()
|
156
|
+
|
157
|
+
def _compute(self):
|
158
|
+
device = f"cuda:{dist.get_rank()}" if torch.cuda.is_available() else "cpu"
|
159
|
+
metric = RootMeanSquaredError()
|
160
|
+
|
161
|
+
def _val_func(engine, batch):
|
162
|
+
pass
|
163
|
+
|
164
|
+
engine = Engine(_val_func)
|
165
|
+
metric.attach(engine, "RMSE")
|
166
|
+
|
167
|
+
# get testing data
|
168
|
+
batch = BATCH_SIZE
|
169
|
+
base = BASE_DIM_SIZE
|
170
|
+
spatial = SPATIAL_DIM
|
171
|
+
in_tensor_a1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
172
|
+
in_tensor_b1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
173
|
+
|
174
|
+
in_tensor_a2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
175
|
+
in_tensor_b2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
176
|
+
|
177
|
+
if dist.get_rank() == 0:
|
178
|
+
y_pred = in_tensor_a1.to(device)
|
179
|
+
y = in_tensor_b1.to(device)
|
180
|
+
metric.update([y_pred, y])
|
181
|
+
|
182
|
+
if dist.get_rank() == 1:
|
183
|
+
y_pred = in_tensor_a2.to(device)
|
184
|
+
y = in_tensor_b2.to(device)
|
185
|
+
metric.update([y_pred, y])
|
186
|
+
|
187
|
+
out_tensor = metric.compute()
|
188
|
+
|
189
|
+
# do numpy functions to get ground truth referece
|
190
|
+
out_tensor_np1 = rmsemetric_np(y_pred=in_tensor_a1.cpu().numpy(), y=in_tensor_b1.cpu().numpy())
|
191
|
+
out_tensor_np2 = rmsemetric_np(y_pred=in_tensor_a2.cpu().numpy(), y=in_tensor_b2.cpu().numpy())
|
192
|
+
out_tensor_np = (out_tensor_np1 + out_tensor_np2) / 2.0
|
193
|
+
|
194
|
+
np.testing.assert_allclose(out_tensor, out_tensor_np, rtol=1e-04, atol=1e-04)
|
195
|
+
|
196
|
+
|
197
|
+
class DistributedPeakSignalToNoiseRatio(DistTestCase):
|
198
|
+
@DistCall(nnodes=1, nproc_per_node=2)
|
199
|
+
def test_compute(self):
|
200
|
+
set_determinism(123)
|
201
|
+
self._compute()
|
202
|
+
|
203
|
+
def _compute(self):
|
204
|
+
device = f"cuda:{dist.get_rank()}" if torch.cuda.is_available() else "cpu"
|
205
|
+
max_val = 1.0
|
206
|
+
metric = PeakSignalToNoiseRatio(max_val=max_val)
|
207
|
+
|
208
|
+
def _val_func(engine, batch):
|
209
|
+
pass
|
210
|
+
|
211
|
+
engine = Engine(_val_func)
|
212
|
+
metric.attach(engine, "PSNR")
|
213
|
+
|
214
|
+
# get testing data
|
215
|
+
batch = BATCH_SIZE
|
216
|
+
base = BASE_DIM_SIZE
|
217
|
+
spatial = SPATIAL_DIM
|
218
|
+
in_tensor_a1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
219
|
+
in_tensor_b1 = torch.rand((batch,) + (base,) * (spatial - 1))
|
220
|
+
|
221
|
+
in_tensor_a2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
222
|
+
in_tensor_b2 = torch.rand((batch,) + (base,) * (spatial - 1))
|
223
|
+
|
224
|
+
if dist.get_rank() == 0:
|
225
|
+
y_pred = in_tensor_a1.to(device)
|
226
|
+
y = in_tensor_b1.to(device)
|
227
|
+
metric.update([y_pred, y])
|
228
|
+
|
229
|
+
if dist.get_rank() == 1:
|
230
|
+
y_pred = in_tensor_a2.to(device)
|
231
|
+
y = in_tensor_b2.to(device)
|
232
|
+
metric.update([y_pred, y])
|
233
|
+
|
234
|
+
out_tensor = metric.compute()
|
235
|
+
|
236
|
+
# do numpy functions to get ground truth referece
|
237
|
+
out_tensor_np1 = psnrmetric_np(max_val=max_val, y_pred=in_tensor_a1.cpu().numpy(), y=in_tensor_b1.cpu().numpy())
|
238
|
+
out_tensor_np2 = psnrmetric_np(max_val=max_val, y_pred=in_tensor_a2.cpu().numpy(), y=in_tensor_b2.cpu().numpy())
|
239
|
+
out_tensor_np = (out_tensor_np1 + out_tensor_np2) / 2.0
|
240
|
+
|
241
|
+
np.testing.assert_allclose(out_tensor, out_tensor_np, rtol=1e-04, atol=1e-04)
|
242
|
+
|
243
|
+
|
244
|
+
if __name__ == "__main__":
|
245
|
+
unittest.main()
|
@@ -0,0 +1,48 @@
|
|
1
|
+
# Copyright (c) MONAI Consortium
|
2
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
3
|
+
# you may not use this file except in compliance with the License.
|
4
|
+
# You may obtain a copy of the License at
|
5
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
6
|
+
# Unless required by applicable law or agreed to in writing, software
|
7
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
8
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
9
|
+
# See the License for the specific language governing permissions and
|
10
|
+
# limitations under the License.
|
11
|
+
|
12
|
+
from __future__ import annotations
|
13
|
+
|
14
|
+
import unittest
|
15
|
+
|
16
|
+
import numpy as np
|
17
|
+
import torch
|
18
|
+
|
19
|
+
from monai.handlers import ROCAUC
|
20
|
+
from monai.transforms import Activations, AsDiscrete
|
21
|
+
|
22
|
+
|
23
|
+
class TestHandlerROCAUC(unittest.TestCase):
|
24
|
+
|
25
|
+
def test_compute(self):
|
26
|
+
auc_metric = ROCAUC()
|
27
|
+
act = Activations(softmax=True)
|
28
|
+
to_onehot = AsDiscrete(to_onehot=2)
|
29
|
+
|
30
|
+
y_pred = [torch.Tensor([0.1, 0.9]), torch.Tensor([0.3, 1.4])]
|
31
|
+
y = [torch.Tensor([0]), torch.Tensor([1])]
|
32
|
+
y_pred = [act(p) for p in y_pred]
|
33
|
+
y = [to_onehot(y_) for y_ in y]
|
34
|
+
auc_metric.update([y_pred, y])
|
35
|
+
|
36
|
+
y_pred = [torch.Tensor([0.2, 0.1]), torch.Tensor([0.1, 0.5])]
|
37
|
+
y = [torch.Tensor([0]), torch.Tensor([1])]
|
38
|
+
y_pred = [act(p) for p in y_pred]
|
39
|
+
y = [to_onehot(y_) for y_ in y]
|
40
|
+
|
41
|
+
auc_metric.update([y_pred, y])
|
42
|
+
|
43
|
+
auc = auc_metric.compute()
|
44
|
+
np.testing.assert_allclose(0.75, auc)
|
45
|
+
|
46
|
+
|
47
|
+
if __name__ == "__main__":
|
48
|
+
unittest.main()
|
@@ -0,0 +1,54 @@
|
|
1
|
+
# Copyright (c) MONAI Consortium
|
2
|
+
# Licensed under the Apache License, Version 2.0 (the "License");
|
3
|
+
# you may not use this file except in compliance with the License.
|
4
|
+
# You may obtain a copy of the License at
|
5
|
+
# http://www.apache.org/licenses/LICENSE-2.0
|
6
|
+
# Unless required by applicable law or agreed to in writing, software
|
7
|
+
# distributed under the License is distributed on an "AS IS" BASIS,
|
8
|
+
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
9
|
+
# See the License for the specific language governing permissions and
|
10
|
+
# limitations under the License.
|
11
|
+
|
12
|
+
from __future__ import annotations
|
13
|
+
|
14
|
+
import unittest
|
15
|
+
|
16
|
+
import numpy as np
|
17
|
+
import torch
|
18
|
+
import torch.distributed as dist
|
19
|
+
|
20
|
+
from monai.handlers import ROCAUC
|
21
|
+
from monai.transforms import Activations, AsDiscrete
|
22
|
+
from tests.test_utils import DistCall, DistTestCase
|
23
|
+
|
24
|
+
|
25
|
+
class DistributedROCAUC(DistTestCase):
|
26
|
+
@DistCall(nnodes=1, nproc_per_node=2, node_rank=0)
|
27
|
+
def test_compute(self):
|
28
|
+
auc_metric = ROCAUC()
|
29
|
+
act = Activations(softmax=True)
|
30
|
+
to_onehot = AsDiscrete(to_onehot=2)
|
31
|
+
|
32
|
+
device = f"cuda:{dist.get_rank()}" if torch.cuda.is_available() else "cpu"
|
33
|
+
if dist.get_rank() == 0:
|
34
|
+
y_pred = [torch.tensor([0.1, 0.9], device=device), torch.tensor([0.3, 1.4], device=device)]
|
35
|
+
y = [torch.tensor([0], device=device), torch.tensor([1], device=device)]
|
36
|
+
|
37
|
+
if dist.get_rank() == 1:
|
38
|
+
y_pred = [
|
39
|
+
torch.tensor([0.2, 0.1], device=device),
|
40
|
+
torch.tensor([0.1, 0.5], device=device),
|
41
|
+
torch.tensor([0.3, 0.4], device=device),
|
42
|
+
]
|
43
|
+
y = [torch.tensor([0], device=device), torch.tensor([1], device=device), torch.tensor([1], device=device)]
|
44
|
+
|
45
|
+
y_pred = [act(p) for p in y_pred]
|
46
|
+
y = [to_onehot(y_) for y_ in y]
|
47
|
+
auc_metric.update([y_pred, y])
|
48
|
+
|
49
|
+
result = auc_metric.compute()
|
50
|
+
np.testing.assert_allclose(0.66667, result, rtol=1e-4)
|
51
|
+
|
52
|
+
|
53
|
+
if __name__ == "__main__":
|
54
|
+
unittest.main()
|