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 sys
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import unittest
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import numpy as np
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import torch.multiprocessing as mp
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from parameterized import parameterized
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from monai.data import DataLoader, Dataset
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from monai.transforms import IntensityStatsd
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from monai.utils.enums import PostFix
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TEST_CASE_1 = [
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{"keys": "img", "ops": ["max", "mean"], "key_prefix": "orig", "meta_keys": "test_meta"},
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{"img": np.array([[[0.0, 1.0], [2.0, 3.0]]]), "test_meta": {"affine": None}},
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"test_meta",
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{"orig_max": 3.0, "orig_mean": 1.5},
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]
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TEST_CASE_2 = [
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{"keys": "img", "ops": "std", "key_prefix": "orig"},
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{"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])},
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PostFix.meta("img"),
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{"orig_std": 1.118034},
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]
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TEST_CASE_3 = [
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{"keys": "img", "ops": [np.mean, "max", np.min], "key_prefix": "orig"},
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{"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])},
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PostFix.meta("img"),
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{"orig_custom_0": 1.5, "orig_max": 3.0, "orig_custom_1": 0.0},
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]
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TEST_CASE_4 = [
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{"keys": "img", "ops": ["max", "mean"], "key_prefix": "orig", "channel_wise": True, "meta_key_postfix": "meta"},
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{"img": np.array([[[0.0, 1.0], [2.0, 3.0]], [[4.0, 5.0], [6.0, 7.0]]]), "img_meta": {"affine": None}},
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"img_meta",
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{"orig_max": [3.0, 7.0], "orig_mean": [1.5, 5.5]},
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]
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class TestIntensityStatsd(unittest.TestCase):
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@parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4])
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def test_value(self, input_param, data, meta_key, expected):
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meta = IntensityStatsd(**input_param)(data)[meta_key]
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for k, v in expected.items():
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self.assertTrue(k in meta)
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np.testing.assert_allclose(v, meta[k], atol=1e-3)
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def test_dataloader(self):
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dataset = Dataset(
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data=[{"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])}, {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])}],
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transform=IntensityStatsd(keys="img", ops=["max", "mean"], key_prefix="orig"),
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)
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# set num workers = 0 for mac / win
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num_workers = 2 if sys.platform == "linux" else 0
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dataloader = DataLoader(dataset=dataset, num_workers=num_workers, batch_size=2)
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orig_method = mp.get_start_method()
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mp.set_start_method("spawn", force=True)
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for d in dataloader:
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meta = d[PostFix.meta("img")]
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np.testing.assert_allclose(meta["orig_max"], [3.0, 3.0], atol=1e-3)
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np.testing.assert_allclose(meta["orig_mean"], [1.5, 1.5], atol=1e-3)
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# restore the mp method
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mp.set_start_method(orig_method, force=True)
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def test_mask(self):
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data = {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]]), "img_mask": np.array([[[1, 0], [1, 0]]], dtype=bool)}
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stats = IntensityStatsd(keys="img", ops=["max", "mean"], mask_keys="img_mask", key_prefix="orig")
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meta = stats(data)[PostFix.meta("img")]
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np.testing.assert_allclose(meta["orig_max"], 2.0, atol=1e-3)
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np.testing.assert_allclose(meta["orig_mean"], 1.0, atol=1e-3)
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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 random
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import sys
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import unittest
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from copy import deepcopy
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from functools import partial
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from typing import TYPE_CHECKING
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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.data import CacheDataset, DataLoader, MetaTensor, create_test_image_2d, create_test_image_3d, decollate_batch
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from monai.networks.nets import UNet
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from monai.transforms import (
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Affined,
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BorderPadd,
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CenterScaleCropd,
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CenterSpatialCropd,
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Compose,
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CropForegroundd,
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DivisiblePadd,
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EnsureChannelFirstd,
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Flipd,
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FromMetaTensord,
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InvertibleTransform,
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Lambdad,
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LoadImaged,
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Orientationd,
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RandAffined,
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RandAxisFlipd,
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RandCropByLabelClassesd,
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RandCropByPosNegLabeld,
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RandFlipd,
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RandLambdad,
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Randomizable,
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RandRotate90d,
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RandRotated,
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RandSpatialCropd,
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RandSpatialCropSamplesd,
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RandWeightedCropd,
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RandZoomd,
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Resized,
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ResizeWithPadOrCrop,
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ResizeWithPadOrCropd,
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Rotate90d,
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Rotated,
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Spacingd,
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SpatialCropd,
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SpatialPadd,
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ToMetaTensord,
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Transposed,
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Zoomd,
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allow_missing_keys_mode,
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convert_applied_interp_mode,
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reset_ops_id,
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)
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from monai.utils import first, get_seed, optional_import, set_determinism
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from tests.test_utils import make_nifti_image, make_rand_affine
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if TYPE_CHECKING:
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has_nib = True
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else:
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_, has_nib = optional_import("nibabel")
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KEYS = ["image", "label"]
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TESTS: list[tuple] = []
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# For pad, start with odd/even images and add odd/even amounts
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for name in ("1D even", "1D odd"):
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for val in (3, 4):
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for t in (
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partial(SpatialPadd, spatial_size=val, method="symmetric"),
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partial(SpatialPadd, spatial_size=val, method="end"),
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partial(BorderPadd, spatial_border=[val, val + 1]),
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partial(DivisiblePadd, k=val),
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partial(ResizeWithPadOrCropd, spatial_size=20 + val),
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partial(CenterSpatialCropd, roi_size=10 + val),
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partial(CenterScaleCropd, roi_scale=0.8),
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partial(CropForegroundd, source_key="label"),
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partial(SpatialCropd, roi_center=10, roi_size=10 + val),
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partial(SpatialCropd, roi_center=11, roi_size=10 + val),
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partial(SpatialCropd, roi_start=val, roi_end=17),
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partial(SpatialCropd, roi_start=val, roi_end=16),
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partial(RandSpatialCropd, roi_size=12 + val),
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partial(ResizeWithPadOrCropd, spatial_size=21 - val),
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):
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TESTS.append((t.func.__name__ + name, name, 0, True, t(KEYS))) # type: ignore
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# non-sensical tests: crop bigger or pad smaller or -ve values
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for t in (
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partial(DivisiblePadd, k=-3),
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partial(CenterSpatialCropd, roi_size=-3),
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partial(RandSpatialCropd, roi_size=-3),
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partial(SpatialPadd, spatial_size=15),
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partial(BorderPadd, spatial_border=[15, 16]),
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partial(CenterSpatialCropd, roi_size=30),
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partial(SpatialCropd, roi_center=10, roi_size=100),
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partial(SpatialCropd, roi_start=3, roi_end=100),
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):
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TESTS.append((t.func.__name__ + "bad 1D even", "1D even", 0, True, t(KEYS))) # type: ignore
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TESTS.append(
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(
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"SpatialPadd (x2) 2d",
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"2D",
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0,
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True,
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SpatialPadd(KEYS, spatial_size=[111, 113], method="end"),
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SpatialPadd(KEYS, spatial_size=[118, 117]),
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)
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)
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TESTS.append(("SpatialPadd 3d", "3D", 0, True, SpatialPadd(KEYS, spatial_size=[112, 113, 116])))
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TESTS.append(("SpatialCropd 2d", "2D", 0, True, SpatialCropd(KEYS, [49, 51], [90, 89])))
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TESTS.append(
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(
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"SpatialCropd 3d",
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"3D",
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0,
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True,
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SpatialCropd(KEYS, roi_slices=[slice(s, e) for s, e in zip([None, None, -99], [None, -2, None])]),
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)
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)
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TESTS.append(("SpatialCropd 2d", "2D", 0, True, SpatialCropd(KEYS, [49, 51], [390, 89])))
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TESTS.append(("SpatialCropd 3d", "3D", 0, True, SpatialCropd(KEYS, [49, 51, 44], [90, 89, 93])))
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TESTS.append(("RandSpatialCropd 2d", "2D", 0, True, RandSpatialCropd(KEYS, [96, 93], None, True, False)))
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TESTS.append(("RandSpatialCropd 3d", "3D", 0, True, RandSpatialCropd(KEYS, [96, 93, 92], None, False, False)))
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TESTS.append(("BorderPadd 2d", "2D", 0, True, BorderPadd(KEYS, [3, 7, 2, 5])))
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TESTS.append(("BorderPadd 2d", "2D", 0, True, BorderPadd(KEYS, [3, 7])))
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TESTS.append(("BorderPadd 3d", "3D", 0, True, BorderPadd(KEYS, [4])))
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TESTS.append(("DivisiblePadd 2d", "2D", 0, True, DivisiblePadd(KEYS, k=4)))
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TESTS.append(("DivisiblePadd 3d", "3D", 0, True, DivisiblePadd(KEYS, k=[4, 8, 11])))
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TESTS.append(("CenterSpatialCropd 2d", "2D", 0, True, CenterSpatialCropd(KEYS, roi_size=95)))
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TESTS.append(("CenterSpatialCropd 3d", "3D", 0, True, CenterSpatialCropd(KEYS, roi_size=[95, 97, 98])))
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TESTS.append(("CropForegroundd 2d", "2D", 0, True, CropForegroundd(KEYS, source_key="label", margin=2)))
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TESTS.append(("CropForegroundd 3d", "3D", 0, True, CropForegroundd(KEYS, source_key="label", k_divisible=[5, 101, 2])))
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TESTS.append(("ResizeWithPadOrCropd 3d", "3D", 0, True, ResizeWithPadOrCropd(KEYS, [201, 150, 105])))
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TESTS.append(("Flipd 3d", "3D", 0, True, Flipd(KEYS, [1, 2])))
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TESTS.append(("Flipd 3d", "3D", 0, True, Flipd(KEYS, [1, 2])))
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TESTS.append(("RandFlipd 3d", "3D", 0, True, RandFlipd(KEYS, 1, [1, 2])))
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TESTS.append(("RandAxisFlipd 3d", "3D", 0, True, RandAxisFlipd(KEYS, 1)))
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TESTS.append(("RandAxisFlipd 3d", "3D", 0, True, RandAxisFlipd(KEYS, 1)))
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for acc in [True, False]:
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TESTS.append(("Orientationd 3d", "3D", 0, True, Orientationd(KEYS, "RAS", as_closest_canonical=acc)))
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TESTS.append(("Rotate90d 2d", "2D", 0, True, Rotate90d(KEYS)))
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TESTS.append(("Rotate90d 3d", "3D", 0, True, Rotate90d(KEYS, k=2, spatial_axes=(1, 2))))
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TESTS.append(("RandRotate90d 3d", "3D", 0, True, RandRotate90d(KEYS, prob=1, spatial_axes=(1, 2))))
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TESTS.append(("Spacingd 3d", "3D", 3e-2, True, Spacingd(KEYS, [0.5, 0.7, 0.9], diagonal=False)))
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TESTS.append(("Resized 2d", "2D", 2e-1, True, Resized(KEYS, [50, 47])))
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TESTS.append(("Resized 3d", "3D", 5e-2, True, Resized(KEYS, [201, 150, 78])))
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TESTS.append(("Resized longest 2d", "2D", 2e-1, True, Resized(KEYS, 47, "longest", "area")))
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TESTS.append(("Resized longest 3d", "3D", 5e-2, True, Resized(KEYS, 201, "longest", "trilinear", True)))
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+
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TESTS.append(
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("Lambdad 2d", "2D", 5e-2, False, Lambdad(KEYS, func=lambda x: x + 5, inv_func=lambda x: x - 5, overwrite=True))
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)
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+
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TESTS.append(
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(
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"RandLambdad 3d",
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"3D",
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5e-2,
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False,
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RandLambdad(KEYS, func=lambda x: x * 10, inv_func=lambda x: x / 10, overwrite=True, prob=0.5),
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)
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)
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+
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TESTS.append(("Zoomd 1d", "1D odd", 0, True, Zoomd(KEYS, zoom=2, keep_size=False)))
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+
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TESTS.append(("Zoomd 2d", "2D", 2e-1, True, Zoomd(KEYS, zoom=0.9)))
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+
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TESTS.append(("Zoomd 3d", "3D", 3e-2, True, Zoomd(KEYS, zoom=[2.5, 1, 3], keep_size=False)))
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+
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+
TESTS.append(("RandZoom 3d", "3D", 9e-2, True, RandZoomd(KEYS, 1, [0.5, 0.6, 0.9], [1.1, 1, 1.05], keep_size=True)))
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+
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+
TESTS.append(("RandRotated, prob 0", "2D", 0, True, RandRotated(KEYS, prob=0, dtype=np.float64)))
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+
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TESTS.append(
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(
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"Rotated 2d",
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"2D",
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+
8e-2,
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True,
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Rotated(KEYS, random.uniform(np.pi / 6, np.pi), keep_size=True, align_corners=False, dtype=np.float64),
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)
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)
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TESTS.append(
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(
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"Rotated 3d",
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"3D",
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1e-1,
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True,
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Rotated(KEYS, [random.uniform(np.pi / 6, np.pi) for _ in range(3)], True, dtype=np.float64),
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)
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)
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+
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TESTS.append(
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(
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"RandRotated 3d",
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"3D",
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1e-1,
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+
True,
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+
RandRotated(KEYS, *[random.uniform(np.pi / 6, np.pi) for _ in range(3)], 1, dtype=np.float64), # type: ignore
|
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+
)
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+
)
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+
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TESTS.append(("Transposed 2d", "2D", 0, False, Transposed(KEYS, [0, 2, 1]))) # channel=0
|
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+
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+
TESTS.append(("Transposed 3d", "3D", 0, False, Transposed(KEYS, [0, 3, 1, 2]))) # channel=0
|
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+
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+
TESTS.append(
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+
(
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+
"Affine 3d",
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+
"3D",
|
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+
1e-1,
|
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+
True,
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+
Affined(
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+
KEYS,
|
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+
spatial_size=[155, 179, 192],
|
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+
rotate_params=[np.pi / 6, -np.pi / 5, np.pi / 7],
|
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+
shear_params=[0.5, 0.5],
|
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+
translate_params=[10, 5, -4],
|
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+
scale_params=[0.8, 1.3],
|
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+
),
|
269
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+
)
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+
)
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+
|
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+
TESTS.append(
|
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+
(
|
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+
"RandAffine 3d",
|
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|
+
"3D",
|
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|
+
1e-1,
|
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|
+
True,
|
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|
+
RandAffined(
|
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|
+
KEYS,
|
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+
[155, 179, 192],
|
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|
+
prob=1,
|
282
|
+
padding_mode="zeros",
|
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|
+
rotate_range=[np.pi / 6, -np.pi / 5, np.pi / 7],
|
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|
+
shear_range=[(0.5, 0.5)],
|
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|
+
translate_range=[10, 5, -4],
|
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|
+
scale_range=[(0.8, 1.2), (0.9, 1.3)],
|
287
|
+
),
|
288
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+
)
|
289
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+
)
|
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+
|
291
|
+
TESTS.append(("RandAffine 3d", "3D", 0, True, RandAffined(KEYS, spatial_size=None, prob=0)))
|
292
|
+
|
293
|
+
TESTS.append(
|
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|
+
(
|
295
|
+
"RandCropByLabelClassesd 2d",
|
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|
+
"2D",
|
297
|
+
1e-7,
|
298
|
+
True,
|
299
|
+
RandCropByLabelClassesd(KEYS, "label", (99, 96), ratios=[1, 2, 3, 4, 5], num_classes=5, num_samples=10),
|
300
|
+
)
|
301
|
+
)
|
302
|
+
|
303
|
+
TESTS.append(
|
304
|
+
("RandCropByPosNegLabeld 2d", "2D", 1e-7, True, RandCropByPosNegLabeld(KEYS, "label", (99, 96), num_samples=10))
|
305
|
+
)
|
306
|
+
|
307
|
+
TESTS.append(("RandSpatialCropSamplesd 2d", "2D", 1e-7, True, RandSpatialCropSamplesd(KEYS, (90, 91), num_samples=10)))
|
308
|
+
|
309
|
+
TESTS.append(("RandWeightedCropd 2d", "2D", 1e-7, True, RandWeightedCropd(KEYS, "label", (90, 91), num_samples=10)))
|
310
|
+
|
311
|
+
TESTS_COMPOSE_X2 = [(t[0] + " Compose", t[1], t[2], t[3], Compose(Compose(t[4:]))) for t in TESTS]
|
312
|
+
|
313
|
+
TESTS = TESTS + TESTS_COMPOSE_X2
|
314
|
+
|
315
|
+
NUM_SAMPLES = 5
|
316
|
+
N_SAMPLES_TESTS = [
|
317
|
+
[RandCropByLabelClassesd(KEYS, "label", (110, 99), [1, 2, 3, 4, 5], num_classes=5, num_samples=NUM_SAMPLES)],
|
318
|
+
[RandCropByPosNegLabeld(KEYS, "label", (110, 99), num_samples=NUM_SAMPLES)],
|
319
|
+
[RandSpatialCropSamplesd(KEYS, (90, 91), num_samples=NUM_SAMPLES, random_size=False)],
|
320
|
+
[RandWeightedCropd(KEYS, "label", (90, 91), num_samples=NUM_SAMPLES)],
|
321
|
+
]
|
322
|
+
|
323
|
+
|
324
|
+
def no_collation(x):
|
325
|
+
return x
|
326
|
+
|
327
|
+
|
328
|
+
class TestInverse(unittest.TestCase):
|
329
|
+
"""Test inverse methods.
|
330
|
+
|
331
|
+
If tests are failing, the following function might be useful for displaying
|
332
|
+
`x`, `fx`, `f⁻¹fx` and `x - f⁻¹fx`.
|
333
|
+
|
334
|
+
.. code-block:: python
|
335
|
+
|
336
|
+
def plot_im(orig, fwd_bck, fwd):
|
337
|
+
import matplotlib.pyplot as plt
|
338
|
+
diff_orig_fwd_bck = orig - fwd_bck
|
339
|
+
ims_to_show = [orig, fwd, fwd_bck, diff_orig_fwd_bck]
|
340
|
+
titles = ["x", "fx", "f⁻¹fx", "x - f⁻¹fx"]
|
341
|
+
fig, axes = plt.subplots(1, 4, gridspec_kw={"width_ratios": [i.shape[1] for i in ims_to_show]})
|
342
|
+
vmin = min(np.array(i).min() for i in [orig, fwd_bck, fwd])
|
343
|
+
vmax = max(np.array(i).max() for i in [orig, fwd_bck, fwd])
|
344
|
+
for im, title, ax in zip(ims_to_show, titles, axes):
|
345
|
+
_vmin, _vmax = (vmin, vmax) if id(im) != id(diff_orig_fwd_bck) else (None, None)
|
346
|
+
im = np.squeeze(np.array(im))
|
347
|
+
while im.ndim > 2:
|
348
|
+
im = im[..., im.shape[-1] // 2]
|
349
|
+
im_show = ax.imshow(np.squeeze(im), vmin=_vmin, vmax=_vmax)
|
350
|
+
ax.set_title(title, fontsize=25)
|
351
|
+
ax.axis("off")
|
352
|
+
fig.colorbar(im_show, ax=ax)
|
353
|
+
plt.show()
|
354
|
+
|
355
|
+
This can then be added to the exception:
|
356
|
+
|
357
|
+
.. code-block:: python
|
358
|
+
|
359
|
+
except AssertionError:
|
360
|
+
print(
|
361
|
+
f"Failed: {name}. Mean diff = {mean_diff} (expected <= {acceptable_diff}), unmodified diff: {unmodded_diff}"
|
362
|
+
)
|
363
|
+
if orig[0].ndim > 1:
|
364
|
+
plot_im(orig, fwd_bck, unmodified)
|
365
|
+
"""
|
366
|
+
|
367
|
+
def setUp(self):
|
368
|
+
if not has_nib:
|
369
|
+
self.skipTest("nibabel required for test_inverse")
|
370
|
+
|
371
|
+
set_determinism(seed=0)
|
372
|
+
|
373
|
+
self.all_data = {}
|
374
|
+
|
375
|
+
affine = make_rand_affine()
|
376
|
+
affine[0] *= 2
|
377
|
+
|
378
|
+
for size in [10, 11]:
|
379
|
+
# pad 5 onto both ends so that cropping can be lossless
|
380
|
+
im_1d = np.pad(np.arange(size), 5)[None]
|
381
|
+
name = "1D even" if size % 2 == 0 else "1D odd"
|
382
|
+
self.all_data[name] = {
|
383
|
+
"image": torch.as_tensor(np.array(im_1d, copy=True)),
|
384
|
+
"label": torch.as_tensor(np.array(im_1d, copy=True)),
|
385
|
+
"other": torch.as_tensor(np.array(im_1d, copy=True)),
|
386
|
+
}
|
387
|
+
|
388
|
+
im_2d_fname, seg_2d_fname = (make_nifti_image(i) for i in create_test_image_2d(101, 100))
|
389
|
+
im_3d_fname, seg_3d_fname = (make_nifti_image(i, affine) for i in create_test_image_3d(100, 101, 107))
|
390
|
+
|
391
|
+
load_ims = Compose(
|
392
|
+
[LoadImaged(KEYS), EnsureChannelFirstd(KEYS, channel_dim="no_channel"), FromMetaTensord(KEYS)]
|
393
|
+
)
|
394
|
+
self.all_data["2D"] = load_ims({"image": im_2d_fname, "label": seg_2d_fname})
|
395
|
+
self.all_data["3D"] = load_ims({"image": im_3d_fname, "label": seg_3d_fname})
|
396
|
+
|
397
|
+
def tearDown(self):
|
398
|
+
set_determinism(seed=None)
|
399
|
+
|
400
|
+
def check_inverse(self, name, keys, orig_d, fwd_bck_d, unmodified_d, acceptable_diff):
|
401
|
+
for key in keys:
|
402
|
+
orig = orig_d[key]
|
403
|
+
fwd_bck = fwd_bck_d[key]
|
404
|
+
if isinstance(fwd_bck, torch.Tensor):
|
405
|
+
fwd_bck = fwd_bck.cpu().numpy()
|
406
|
+
unmodified = unmodified_d[key]
|
407
|
+
if isinstance(orig, np.ndarray):
|
408
|
+
mean_diff = np.mean(np.abs(orig - fwd_bck))
|
409
|
+
resized = ResizeWithPadOrCrop(orig.shape[1:])(unmodified)
|
410
|
+
if isinstance(resized, torch.Tensor):
|
411
|
+
resized = resized.detach().cpu().numpy()
|
412
|
+
unmodded_diff = np.mean(np.abs(orig - resized))
|
413
|
+
try:
|
414
|
+
self.assertLessEqual(mean_diff, acceptable_diff)
|
415
|
+
except AssertionError:
|
416
|
+
print(
|
417
|
+
f"Failed: {name}. Mean diff = {mean_diff} (expected <= {acceptable_diff}), unmodified diff: {unmodded_diff}"
|
418
|
+
)
|
419
|
+
if orig[0].ndim == 1:
|
420
|
+
print("orig", orig[0])
|
421
|
+
print("fwd_bck", fwd_bck[0])
|
422
|
+
print("unmod", unmodified[0])
|
423
|
+
raise
|
424
|
+
|
425
|
+
@parameterized.expand(TESTS)
|
426
|
+
def test_inverse(self, _, data_name, acceptable_diff, is_meta, *transforms):
|
427
|
+
name = _
|
428
|
+
|
429
|
+
data = self.all_data[data_name]
|
430
|
+
if is_meta:
|
431
|
+
data = ToMetaTensord(KEYS)(data)
|
432
|
+
|
433
|
+
forwards = [data.copy()]
|
434
|
+
|
435
|
+
# Apply forwards
|
436
|
+
for t in transforms:
|
437
|
+
if isinstance(t, Randomizable):
|
438
|
+
t.set_random_state(seed=get_seed())
|
439
|
+
forwards.append(t(forwards[-1]))
|
440
|
+
|
441
|
+
# Apply inverses
|
442
|
+
fwd_bck = forwards[-1].copy()
|
443
|
+
for i, t in enumerate(reversed(transforms)):
|
444
|
+
if isinstance(t, InvertibleTransform):
|
445
|
+
if isinstance(fwd_bck, list):
|
446
|
+
for j, _fwd_bck in enumerate(fwd_bck):
|
447
|
+
fwd_bck = t.inverse(_fwd_bck)
|
448
|
+
self.check_inverse(
|
449
|
+
name, data.keys(), forwards[-i - 2], fwd_bck, forwards[-1][j], acceptable_diff
|
450
|
+
)
|
451
|
+
else:
|
452
|
+
fwd_bck = t.inverse(fwd_bck)
|
453
|
+
self.check_inverse(name, data.keys(), forwards[-i - 2], fwd_bck, forwards[-1], acceptable_diff)
|
454
|
+
|
455
|
+
# skip this test if multiprocessing uses 'spawn', as the check is only basic anyway
|
456
|
+
@skipUnless(torch.multiprocessing.get_start_method() == "spawn", "requires spawn")
|
457
|
+
def test_fail(self):
|
458
|
+
t1 = SpatialPadd("image", [10, 5])
|
459
|
+
data = t1(self.all_data["2D"])
|
460
|
+
|
461
|
+
# Check that error is thrown when inverse are used out of order.
|
462
|
+
t2 = ResizeWithPadOrCropd("image", [10, 5])
|
463
|
+
with self.assertRaises(RuntimeError):
|
464
|
+
t2.inverse(data)
|
465
|
+
|
466
|
+
@parameterized.expand(N_SAMPLES_TESTS)
|
467
|
+
def test_inverse_inferred_seg(self, extra_transform):
|
468
|
+
test_data = []
|
469
|
+
for _ in range(20):
|
470
|
+
image, label = create_test_image_2d(100, 101)
|
471
|
+
test_data.append({"image": image, "label": label.astype(np.float32)})
|
472
|
+
|
473
|
+
batch_size = 10
|
474
|
+
# num workers = 0 for mac
|
475
|
+
num_workers = 2 if sys.platform == "linux" else 0
|
476
|
+
transforms = Compose(
|
477
|
+
[EnsureChannelFirstd(KEYS, channel_dim="no_channel"), SpatialPadd(KEYS, (150, 153)), extra_transform]
|
478
|
+
)
|
479
|
+
|
480
|
+
dataset = CacheDataset(test_data, transform=transforms, progress=False)
|
481
|
+
loader = DataLoader(dataset, batch_size=batch_size, shuffle=False, num_workers=num_workers)
|
482
|
+
|
483
|
+
device = "cuda" if torch.cuda.is_available() else "cpu"
|
484
|
+
model = UNet(spatial_dims=2, in_channels=1, out_channels=1, channels=(2, 4), strides=(1,)).to(device)
|
485
|
+
|
486
|
+
data = first(loader)
|
487
|
+
self.assertEqual(data["image"].shape[0], batch_size * NUM_SAMPLES)
|
488
|
+
|
489
|
+
labels = data["label"].to(device)
|
490
|
+
self.assertIsInstance(labels, MetaTensor)
|
491
|
+
segs = model(labels).detach().cpu()
|
492
|
+
segs_decollated = decollate_batch(segs)
|
493
|
+
self.assertIsInstance(segs_decollated[0], MetaTensor)
|
494
|
+
# inverse of individual segmentation
|
495
|
+
seg_metatensor = first(segs_decollated)
|
496
|
+
# test to convert interpolation mode for 1 data of model output batch
|
497
|
+
convert_applied_interp_mode(seg_metatensor.applied_operations, mode="nearest", align_corners=None)
|
498
|
+
|
499
|
+
# manually invert the last crop samples
|
500
|
+
xform = seg_metatensor.applied_operations.pop(-1)
|
501
|
+
shape_before_extra_xform = xform["orig_size"]
|
502
|
+
resizer = ResizeWithPadOrCrop(spatial_size=shape_before_extra_xform)
|
503
|
+
with resizer.trace_transform(False):
|
504
|
+
seg_metatensor = resizer(seg_metatensor)
|
505
|
+
no_ops_id_tensor = reset_ops_id(deepcopy(seg_metatensor))
|
506
|
+
|
507
|
+
with allow_missing_keys_mode(transforms):
|
508
|
+
inv_seg = transforms.inverse({"label": seg_metatensor})["label"]
|
509
|
+
inv_seg_1 = transforms.inverse({"label": no_ops_id_tensor})["label"]
|
510
|
+
self.assertEqual(inv_seg.shape[1:], test_data[0]["label"].shape)
|
511
|
+
self.assertEqual(inv_seg_1.shape[1:], test_data[0]["label"].shape)
|
512
|
+
|
513
|
+
# # Inverse of batch
|
514
|
+
# batch_inverter = BatchInverseTransform(transforms, loader, collate_fn=no_collation, detach=True)
|
515
|
+
# with allow_missing_keys_mode(transforms):
|
516
|
+
# inv_batch = batch_inverter(first(loader))
|
517
|
+
# self.assertEqual(inv_batch[0]["label"].shape[1:], test_data[0]["label"].shape)
|
518
|
+
|
519
|
+
|
520
|
+
if __name__ == "__main__":
|
521
|
+
unittest.main()
|