monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2507__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- monai/__init__.py +1 -1
- monai/_version.py +3 -3
- monai/apps/auto3dseg/transforms.py +1 -4
- monai/data/utils.py +6 -13
- monai/inferers/utils.py +1 -2
- monai/losses/dice.py +2 -14
- monai/losses/ds_loss.py +1 -3
- monai/networks/layers/simplelayers.py +2 -14
- monai/networks/utils.py +4 -16
- monai/transforms/compose.py +28 -11
- monai/transforms/croppad/array.py +1 -6
- monai/transforms/io/array.py +0 -1
- monai/transforms/transform.py +15 -6
- monai/transforms/utils.py +1 -2
- monai/utils/tf32.py +0 -10
- monai/visualize/class_activation_maps.py +5 -8
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
- monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
- tests/apps/__init__.py +10 -0
- tests/apps/deepedit/__init__.py +10 -0
- tests/apps/deepedit/test_deepedit_transforms.py +314 -0
- tests/apps/deepgrow/__init__.py +10 -0
- tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
- tests/apps/deepgrow/transforms/__init__.py +10 -0
- tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
- tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
- tests/apps/detection/__init__.py +10 -0
- tests/apps/detection/metrics/__init__.py +10 -0
- tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
- tests/apps/detection/networks/__init__.py +10 -0
- tests/apps/detection/networks/test_retinanet.py +210 -0
- tests/apps/detection/networks/test_retinanet_detector.py +203 -0
- tests/apps/detection/test_box_transform.py +370 -0
- tests/apps/detection/utils/__init__.py +10 -0
- tests/apps/detection/utils/test_anchor_box.py +88 -0
- tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
- tests/apps/detection/utils/test_box_coder.py +43 -0
- tests/apps/detection/utils/test_detector_boxselector.py +67 -0
- tests/apps/detection/utils/test_detector_utils.py +96 -0
- tests/apps/detection/utils/test_hardnegsampler.py +54 -0
- tests/apps/nuclick/__init__.py +10 -0
- tests/apps/nuclick/test_nuclick_transforms.py +259 -0
- tests/apps/pathology/__init__.py +10 -0
- tests/apps/pathology/handlers/__init__.py +10 -0
- tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
- tests/apps/pathology/test_lesion_froc.py +333 -0
- tests/apps/pathology/test_pathology_prob_nms.py +55 -0
- tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
- tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
- tests/apps/pathology/transforms/__init__.py +10 -0
- tests/apps/pathology/transforms/post/__init__.py +10 -0
- tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
- tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
- tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
- tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
- tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
- tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
- tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
- tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
- tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
- tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
- tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
- tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
- tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
- tests/apps/pathology/transforms/post/test_watershed.py +60 -0
- tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
- tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
- tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
- tests/apps/reconstruction/__init__.py +10 -0
- tests/apps/reconstruction/nets/__init__.py +10 -0
- tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
- tests/apps/reconstruction/test_complex_utils.py +77 -0
- tests/apps/reconstruction/test_fastmri_reader.py +82 -0
- tests/apps/reconstruction/test_mri_utils.py +37 -0
- tests/apps/reconstruction/transforms/__init__.py +10 -0
- tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
- tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
- tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
- tests/apps/test_auto3dseg_bundlegen.py +156 -0
- tests/apps/test_check_hash.py +53 -0
- tests/apps/test_cross_validation.py +74 -0
- tests/apps/test_decathlondataset.py +93 -0
- tests/apps/test_download_and_extract.py +70 -0
- tests/apps/test_download_url_yandex.py +45 -0
- tests/apps/test_mednistdataset.py +72 -0
- tests/apps/test_mmar_download.py +154 -0
- tests/apps/test_tciadataset.py +123 -0
- tests/apps/vista3d/__init__.py +10 -0
- tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
- tests/apps/vista3d/test_vista3d_sampler.py +100 -0
- tests/apps/vista3d/test_vista3d_transforms.py +94 -0
- tests/bundle/__init__.py +10 -0
- tests/bundle/test_bundle_ckpt_export.py +107 -0
- tests/bundle/test_bundle_download.py +435 -0
- tests/bundle/test_bundle_get_data.py +94 -0
- tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
- tests/bundle/test_bundle_trt_export.py +147 -0
- tests/bundle/test_bundle_utils.py +149 -0
- tests/bundle/test_bundle_verify_metadata.py +66 -0
- tests/bundle/test_bundle_verify_net.py +76 -0
- tests/bundle/test_bundle_workflow.py +272 -0
- tests/bundle/test_component_locator.py +38 -0
- tests/bundle/test_config_item.py +138 -0
- tests/bundle/test_config_parser.py +392 -0
- tests/bundle/test_reference_resolver.py +114 -0
- tests/config/__init__.py +10 -0
- tests/config/test_cv2_dist.py +53 -0
- tests/engines/__init__.py +10 -0
- tests/engines/test_ensemble_evaluator.py +94 -0
- tests/engines/test_prepare_batch_default.py +76 -0
- tests/engines/test_prepare_batch_default_dist.py +76 -0
- tests/engines/test_prepare_batch_diffusion.py +104 -0
- tests/engines/test_prepare_batch_extra_input.py +80 -0
- tests/fl/__init__.py +10 -0
- tests/fl/monai_algo/__init__.py +10 -0
- tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
- tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
- tests/fl/test_fl_monai_algo_stats.py +81 -0
- tests/fl/utils/__init__.py +10 -0
- tests/fl/utils/test_fl_exchange_object.py +63 -0
- tests/handlers/__init__.py +10 -0
- tests/handlers/test_handler_checkpoint_loader.py +182 -0
- tests/handlers/test_handler_checkpoint_saver.py +233 -0
- tests/handlers/test_handler_classification_saver.py +64 -0
- tests/handlers/test_handler_classification_saver_dist.py +77 -0
- tests/handlers/test_handler_clearml_image.py +65 -0
- tests/handlers/test_handler_clearml_stats.py +65 -0
- tests/handlers/test_handler_confusion_matrix.py +104 -0
- tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
- tests/handlers/test_handler_decollate_batch.py +66 -0
- tests/handlers/test_handler_early_stop.py +68 -0
- tests/handlers/test_handler_garbage_collector.py +73 -0
- tests/handlers/test_handler_hausdorff_distance.py +111 -0
- tests/handlers/test_handler_ignite_metric.py +191 -0
- tests/handlers/test_handler_lr_scheduler.py +94 -0
- tests/handlers/test_handler_mean_dice.py +98 -0
- tests/handlers/test_handler_mean_iou.py +76 -0
- tests/handlers/test_handler_metrics_reloaded.py +149 -0
- tests/handlers/test_handler_metrics_saver.py +89 -0
- tests/handlers/test_handler_metrics_saver_dist.py +120 -0
- tests/handlers/test_handler_mlflow.py +296 -0
- tests/handlers/test_handler_nvtx.py +93 -0
- tests/handlers/test_handler_panoptic_quality.py +89 -0
- tests/handlers/test_handler_parameter_scheduler.py +136 -0
- tests/handlers/test_handler_post_processing.py +74 -0
- tests/handlers/test_handler_prob_map_producer.py +111 -0
- tests/handlers/test_handler_regression_metrics.py +160 -0
- tests/handlers/test_handler_regression_metrics_dist.py +245 -0
- tests/handlers/test_handler_rocauc.py +48 -0
- tests/handlers/test_handler_rocauc_dist.py +54 -0
- tests/handlers/test_handler_stats.py +281 -0
- tests/handlers/test_handler_surface_distance.py +113 -0
- tests/handlers/test_handler_tb_image.py +61 -0
- tests/handlers/test_handler_tb_stats.py +166 -0
- tests/handlers/test_handler_validation.py +59 -0
- tests/handlers/test_trt_compile.py +145 -0
- tests/handlers/test_write_metrics_reports.py +68 -0
- tests/inferers/__init__.py +10 -0
- tests/inferers/test_avg_merger.py +179 -0
- tests/inferers/test_controlnet_inferers.py +1310 -0
- tests/inferers/test_diffusion_inferer.py +236 -0
- tests/inferers/test_latent_diffusion_inferer.py +824 -0
- tests/inferers/test_patch_inferer.py +309 -0
- tests/inferers/test_saliency_inferer.py +55 -0
- tests/inferers/test_slice_inferer.py +57 -0
- tests/inferers/test_sliding_window_inference.py +377 -0
- tests/inferers/test_sliding_window_splitter.py +284 -0
- tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
- tests/inferers/test_zarr_avg_merger.py +326 -0
- tests/integration/__init__.py +10 -0
- tests/integration/test_auto3dseg_ensemble.py +211 -0
- tests/integration/test_auto3dseg_hpo.py +189 -0
- tests/integration/test_deepedit_interaction.py +122 -0
- tests/integration/test_downsample_block.py +50 -0
- tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
- tests/integration/test_integration_autorunner.py +201 -0
- tests/integration/test_integration_bundle_run.py +240 -0
- tests/integration/test_integration_classification_2d.py +282 -0
- tests/integration/test_integration_determinism.py +95 -0
- tests/integration/test_integration_fast_train.py +231 -0
- tests/integration/test_integration_gpu_customization.py +159 -0
- tests/integration/test_integration_lazy_samples.py +219 -0
- tests/integration/test_integration_nnunetv2_runner.py +96 -0
- tests/integration/test_integration_segmentation_3d.py +304 -0
- tests/integration/test_integration_sliding_window.py +100 -0
- tests/integration/test_integration_stn.py +133 -0
- tests/integration/test_integration_unet_2d.py +67 -0
- tests/integration/test_integration_workers.py +61 -0
- tests/integration/test_integration_workflows.py +365 -0
- tests/integration/test_integration_workflows_adversarial.py +173 -0
- tests/integration/test_integration_workflows_gan.py +158 -0
- tests/integration/test_loader_semaphore.py +48 -0
- tests/integration/test_mapping_filed.py +122 -0
- tests/integration/test_meta_affine.py +183 -0
- tests/integration/test_metatensor_integration.py +114 -0
- tests/integration/test_module_list.py +76 -0
- tests/integration/test_one_of.py +283 -0
- tests/integration/test_pad_collation.py +124 -0
- tests/integration/test_reg_loss_integration.py +107 -0
- tests/integration/test_retinanet_predict_utils.py +154 -0
- tests/integration/test_seg_loss_integration.py +159 -0
- tests/integration/test_spatial_combine_transforms.py +185 -0
- tests/integration/test_testtimeaugmentation.py +186 -0
- tests/integration/test_vis_gradbased.py +69 -0
- tests/integration/test_vista3d_utils.py +159 -0
- tests/losses/__init__.py +10 -0
- tests/losses/deform/__init__.py +10 -0
- tests/losses/deform/test_bending_energy.py +88 -0
- tests/losses/deform/test_diffusion_loss.py +117 -0
- tests/losses/image_dissimilarity/__init__.py +10 -0
- tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
- tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
- tests/losses/test_adversarial_loss.py +94 -0
- tests/losses/test_barlow_twins_loss.py +109 -0
- tests/losses/test_cldice_loss.py +51 -0
- tests/losses/test_contrastive_loss.py +86 -0
- tests/losses/test_dice_ce_loss.py +123 -0
- tests/losses/test_dice_focal_loss.py +124 -0
- tests/losses/test_dice_loss.py +227 -0
- tests/losses/test_ds_loss.py +189 -0
- tests/losses/test_focal_loss.py +379 -0
- tests/losses/test_generalized_dice_focal_loss.py +85 -0
- tests/losses/test_generalized_dice_loss.py +221 -0
- tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
- tests/losses/test_giou_loss.py +62 -0
- tests/losses/test_hausdorff_loss.py +264 -0
- tests/losses/test_masked_dice_loss.py +152 -0
- tests/losses/test_masked_loss.py +87 -0
- tests/losses/test_multi_scale.py +86 -0
- tests/losses/test_nacl_loss.py +167 -0
- tests/losses/test_perceptual_loss.py +122 -0
- tests/losses/test_spectral_loss.py +86 -0
- tests/losses/test_ssim_loss.py +59 -0
- tests/losses/test_sure_loss.py +72 -0
- tests/losses/test_tversky_loss.py +198 -0
- tests/losses/test_unified_focal_loss.py +66 -0
- tests/metrics/__init__.py +10 -0
- tests/metrics/test_compute_confusion_matrix.py +294 -0
- tests/metrics/test_compute_f_beta.py +80 -0
- tests/metrics/test_compute_fid_metric.py +40 -0
- tests/metrics/test_compute_froc.py +143 -0
- tests/metrics/test_compute_generalized_dice.py +240 -0
- tests/metrics/test_compute_meandice.py +306 -0
- tests/metrics/test_compute_meaniou.py +223 -0
- tests/metrics/test_compute_mmd_metric.py +56 -0
- tests/metrics/test_compute_multiscalessim_metric.py +83 -0
- tests/metrics/test_compute_panoptic_quality.py +113 -0
- tests/metrics/test_compute_regression_metrics.py +196 -0
- tests/metrics/test_compute_roc_auc.py +155 -0
- tests/metrics/test_compute_variance.py +147 -0
- tests/metrics/test_cumulative.py +63 -0
- tests/metrics/test_cumulative_average.py +74 -0
- tests/metrics/test_cumulative_average_dist.py +48 -0
- tests/metrics/test_hausdorff_distance.py +209 -0
- tests/metrics/test_label_quality_score.py +134 -0
- tests/metrics/test_loss_metric.py +57 -0
- tests/metrics/test_metrics_reloaded.py +96 -0
- tests/metrics/test_ssim_metric.py +78 -0
- tests/metrics/test_surface_dice.py +416 -0
- tests/metrics/test_surface_distance.py +186 -0
- tests/networks/__init__.py +10 -0
- tests/networks/blocks/__init__.py +10 -0
- tests/networks/blocks/dints_block/__init__.py +10 -0
- tests/networks/blocks/dints_block/test_acn_block.py +41 -0
- tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
- tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
- tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
- tests/networks/blocks/test_adn.py +86 -0
- tests/networks/blocks/test_convolutions.py +156 -0
- tests/networks/blocks/test_crf_cpu.py +513 -0
- tests/networks/blocks/test_crf_cuda.py +528 -0
- tests/networks/blocks/test_crossattention.py +185 -0
- tests/networks/blocks/test_denseblock.py +105 -0
- tests/networks/blocks/test_dynunet_block.py +116 -0
- tests/networks/blocks/test_fpn_block.py +88 -0
- tests/networks/blocks/test_localnet_block.py +121 -0
- tests/networks/blocks/test_mlp.py +78 -0
- tests/networks/blocks/test_patchembedding.py +212 -0
- tests/networks/blocks/test_regunet_block.py +103 -0
- tests/networks/blocks/test_se_block.py +85 -0
- tests/networks/blocks/test_se_blocks.py +78 -0
- tests/networks/blocks/test_segresnet_block.py +57 -0
- tests/networks/blocks/test_selfattention.py +232 -0
- tests/networks/blocks/test_simple_aspp.py +87 -0
- tests/networks/blocks/test_spatialattention.py +55 -0
- tests/networks/blocks/test_subpixel_upsample.py +87 -0
- tests/networks/blocks/test_text_encoding.py +49 -0
- tests/networks/blocks/test_transformerblock.py +90 -0
- tests/networks/blocks/test_unetr_block.py +158 -0
- tests/networks/blocks/test_upsample_block.py +134 -0
- tests/networks/blocks/warp/__init__.py +10 -0
- tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
- tests/networks/blocks/warp/test_warp.py +250 -0
- tests/networks/layers/__init__.py +10 -0
- tests/networks/layers/filtering/__init__.py +10 -0
- tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
- tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
- tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
- tests/networks/layers/filtering/test_phl_cpu.py +259 -0
- tests/networks/layers/filtering/test_phl_cuda.py +167 -0
- tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
- tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
- tests/networks/layers/test_affine_transform.py +385 -0
- tests/networks/layers/test_apply_filter.py +89 -0
- tests/networks/layers/test_channel_pad.py +51 -0
- tests/networks/layers/test_conjugate_gradient.py +56 -0
- tests/networks/layers/test_drop_path.py +46 -0
- tests/networks/layers/test_gaussian.py +317 -0
- tests/networks/layers/test_gaussian_filter.py +206 -0
- tests/networks/layers/test_get_layers.py +65 -0
- tests/networks/layers/test_gmm.py +314 -0
- tests/networks/layers/test_grid_pull.py +93 -0
- tests/networks/layers/test_hilbert_transform.py +131 -0
- tests/networks/layers/test_lltm.py +62 -0
- tests/networks/layers/test_median_filter.py +52 -0
- tests/networks/layers/test_polyval.py +55 -0
- tests/networks/layers/test_preset_filters.py +136 -0
- tests/networks/layers/test_savitzky_golay_filter.py +141 -0
- tests/networks/layers/test_separable_filter.py +87 -0
- tests/networks/layers/test_skip_connection.py +48 -0
- tests/networks/layers/test_vector_quantizer.py +89 -0
- tests/networks/layers/test_weight_init.py +50 -0
- tests/networks/nets/__init__.py +10 -0
- tests/networks/nets/dints/__init__.py +10 -0
- tests/networks/nets/dints/test_dints_cell.py +110 -0
- tests/networks/nets/dints/test_dints_mixop.py +84 -0
- tests/networks/nets/regunet/__init__.py +10 -0
- tests/networks/nets/regunet/test_localnet.py +86 -0
- tests/networks/nets/regunet/test_regunet.py +88 -0
- tests/networks/nets/test_ahnet.py +224 -0
- tests/networks/nets/test_attentionunet.py +88 -0
- tests/networks/nets/test_autoencoder.py +95 -0
- tests/networks/nets/test_autoencoderkl.py +337 -0
- tests/networks/nets/test_basic_unet.py +102 -0
- tests/networks/nets/test_basic_unetplusplus.py +109 -0
- tests/networks/nets/test_bundle_init_bundle.py +55 -0
- tests/networks/nets/test_cell_sam_wrapper.py +58 -0
- tests/networks/nets/test_controlnet.py +215 -0
- tests/networks/nets/test_daf3d.py +62 -0
- tests/networks/nets/test_densenet.py +121 -0
- tests/networks/nets/test_diffusion_model_unet.py +585 -0
- tests/networks/nets/test_dints_network.py +168 -0
- tests/networks/nets/test_discriminator.py +59 -0
- tests/networks/nets/test_dynunet.py +181 -0
- tests/networks/nets/test_efficientnet.py +400 -0
- tests/networks/nets/test_flexible_unet.py +341 -0
- tests/networks/nets/test_fullyconnectednet.py +69 -0
- tests/networks/nets/test_generator.py +59 -0
- tests/networks/nets/test_globalnet.py +103 -0
- tests/networks/nets/test_highresnet.py +67 -0
- tests/networks/nets/test_hovernet.py +218 -0
- tests/networks/nets/test_mednext.py +122 -0
- tests/networks/nets/test_milmodel.py +92 -0
- tests/networks/nets/test_net_adapter.py +68 -0
- tests/networks/nets/test_network_consistency.py +86 -0
- tests/networks/nets/test_patch_gan_dicriminator.py +179 -0
- tests/networks/nets/test_quicknat.py +57 -0
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- tests/utils/test_handler_metric_logger.py +62 -0
- tests/utils/test_list_to_dict.py +43 -0
- tests/utils/test_look_up_option.py +87 -0
- tests/utils/test_optional_import.py +80 -0
- tests/utils/test_pad_mode.py +39 -0
- tests/utils/test_profiling.py +208 -0
- tests/utils/test_rankfilter_dist.py +77 -0
- tests/utils/test_require_pkg.py +83 -0
- tests/utils/test_sample_slices.py +43 -0
- tests/utils/test_set_determinism.py +74 -0
- tests/utils/test_squeeze_unsqueeze.py +71 -0
- tests/utils/test_state_cacher.py +67 -0
- tests/utils/test_torchscript_utils.py +113 -0
- tests/utils/test_version.py +91 -0
- tests/utils/test_version_after.py +65 -0
- tests/utils/type_conversion/__init__.py +10 -0
- tests/utils/type_conversion/test_convert_data_type.py +152 -0
- tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
- tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
- tests/visualize/__init__.py +10 -0
- tests/visualize/test_img2tensorboard.py +46 -0
- tests/visualize/test_occlusion_sensitivity.py +128 -0
- tests/visualize/test_plot_2d_or_3d_image.py +74 -0
- tests/visualize/test_vis_cam.py +98 -0
- tests/visualize/test_vis_gradcam.py +211 -0
- tests/visualize/utils/__init__.py +10 -0
- tests/visualize/utils/test_blend_images.py +63 -0
- tests/visualize/utils/test_matshow3d.py +133 -0
- monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from __future__ import annotations
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import unittest
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import numpy as np
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from parameterized import parameterized
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from monai.transforms import RandShiftIntensity
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from tests.test_utils import TEST_NDARRAYS, NumpyImageTestCase2D, assert_allclose
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class TestRandShiftIntensity(NumpyImageTestCase2D):
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@parameterized.expand([[p] for p in TEST_NDARRAYS])
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def test_value(self, p):
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shifter = RandShiftIntensity(offsets=1.0, prob=1.0)
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shifter.set_random_state(seed=0)
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im = p(self.imt)
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result = shifter(im, factor=1.0)
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np.random.seed(0)
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# simulate the randomize() of transform
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np.random.random()
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expected = self.imt + np.random.uniform(low=-1.0, high=1.0)
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assert_allclose(result, expected, type_test="tensor")
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@parameterized.expand([[p] for p in TEST_NDARRAYS])
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def test_channel_wise(self, p):
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scaler = RandShiftIntensity(offsets=3.0, channel_wise=True, prob=1.0)
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scaler.set_random_state(seed=0)
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im = p(self.imt)
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result = scaler(im)
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np.random.seed(0)
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# simulate the randomize() of transform
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np.random.random()
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channel_num = self.imt.shape[0]
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factor = [np.random.uniform(low=-3.0, high=3.0) for _ in range(channel_num)]
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expected = p(np.stack([np.asarray((self.imt[i]) + factor[i]) for i in range(channel_num)]).astype(np.float32))
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assert_allclose(result, expected, atol=0, rtol=1e-5, type_test=False)
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if __name__ == "__main__":
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unittest.main()
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from __future__ import annotations
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import unittest
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import numpy as np
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from monai.transforms import IntensityStatsd, RandShiftIntensityd
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from monai.utils.enums import PostFix
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from tests.test_utils import TEST_NDARRAYS, NumpyImageTestCase2D, assert_allclose
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class TestRandShiftIntensityd(NumpyImageTestCase2D):
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def test_value(self):
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key = "img"
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for p in TEST_NDARRAYS:
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shifter = RandShiftIntensityd(keys=[key], offsets=1.0, prob=1.0)
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shifter.set_random_state(seed=0)
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result = shifter({key: p(self.imt)})
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np.random.seed(0)
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# simulate the randomize() of transform
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np.random.random()
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expected = self.imt + np.random.uniform(low=-1.0, high=1.0)
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assert_allclose(result[key], p(expected), type_test="tensor")
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def test_factor(self):
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key = "img"
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stats = IntensityStatsd(keys=key, ops="max", key_prefix="orig")
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shifter = RandShiftIntensityd(keys=[key], offsets=1.0, factor_key=["orig_max"], prob=1.0)
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data = {key: self.imt, PostFix.meta(key): {"affine": None}}
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shifter.set_random_state(seed=0)
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result = shifter(stats(data))
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np.random.seed(0)
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# simulate the randomize() of transform
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np.random.random()
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expected = self.imt + np.random.uniform(low=-1.0, high=1.0) * np.nanmax(self.imt)
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np.testing.assert_allclose(result[key], expected)
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def test_channel_wise(self):
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key = "img"
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for p in TEST_NDARRAYS:
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scaler = RandShiftIntensityd(keys=[key], offsets=3.0, prob=1.0, channel_wise=True)
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scaler.set_random_state(seed=0)
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result = scaler({key: p(self.imt)})
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np.random.seed(0)
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# simulate the randomize function of transform
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np.random.random()
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channel_num = self.imt.shape[0]
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factor = [np.random.uniform(low=-3.0, high=3.0) for _ in range(channel_num)]
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expected = p(
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np.stack([np.asarray((self.imt[i]) + factor[i]) for i in range(channel_num)]).astype(np.float32)
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)
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assert_allclose(result[key], p(expected), type_test="tensor")
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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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from parameterized import parameterized
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from monai.transforms import RandSimulateLowResolution
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from tests.test_utils import TEST_NDARRAYS, assert_allclose
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TESTS = []
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for p in TEST_NDARRAYS:
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TESTS.append(
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[
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dict(prob=1.0, zoom_range=(0.8, 0.81)),
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p(
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np.array(
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[
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[
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[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11], [12, 13, 14, 15]],
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[[16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27], [28, 29, 30, 31]],
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[[32, 33, 34, 35], [36, 37, 38, 39], [40, 41, 42, 43], [44, 45, 46, 47]],
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[[48, 49, 50, 51], [52, 53, 54, 55], [56, 57, 58, 59], [60, 61, 62, 63]],
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]
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]
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)
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),
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np.array(
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[
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[
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[
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[0.0000, 0.6250, 1.3750, 2.0000],
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[2.5000, 3.1250, 3.8750, 4.5000],
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[5.5000, 6.1250, 6.8750, 7.5000],
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[8.0000, 8.6250, 9.3750, 10.0000],
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],
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[
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[10.0000, 10.6250, 11.3750, 12.0000],
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[12.5000, 13.1250, 13.8750, 14.5000],
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[15.5000, 16.1250, 16.8750, 17.5000],
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[18.0000, 18.6250, 19.3750, 20.0000],
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],
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[
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[22.0000, 22.6250, 23.3750, 24.0000],
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[24.5000, 25.1250, 25.8750, 26.5000],
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[27.5000, 28.1250, 28.8750, 29.5000],
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[30.0000, 30.6250, 31.3750, 32.0000],
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],
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[
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[32.0000, 32.6250, 33.3750, 34.0000],
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[34.5000, 35.1250, 35.8750, 36.5000],
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[37.5000, 38.1250, 38.8750, 39.5000],
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[40.0000, 40.6250, 41.3750, 42.0000],
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],
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]
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]
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),
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]
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)
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class TestRandGaussianSmooth(unittest.TestCase):
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@parameterized.expand(TESTS)
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def test_value(self, arguments, image, expected_data):
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randsimlowres = RandSimulateLowResolution(**arguments)
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randsimlowres.set_random_state(seed=0)
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result = randsimlowres(image)
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assert_allclose(result, expected_data, rtol=1e-4, type_test="tensor")
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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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from parameterized import parameterized
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from monai.transforms import RandSimulateLowResolutiond
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from tests.test_utils import TEST_NDARRAYS, assert_allclose
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TESTS = []
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for p in TEST_NDARRAYS:
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TESTS.append(
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[
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dict(keys=["img", "seg"], prob=1.0, zoom_range=(0.8, 0.81)),
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{"img": p(np.arange(64).reshape(1, 4, 4, 4)), "seg": p(np.arange(64).reshape(1, 4, 4, 4))},
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np.array(
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[
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[
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[
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[0.0000, 0.6250, 1.3750, 2.0000],
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[2.5000, 3.1250, 3.8750, 4.5000],
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[5.5000, 6.1250, 6.8750, 7.5000],
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[8.0000, 8.6250, 9.3750, 10.0000],
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],
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[
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[10.0000, 10.6250, 11.3750, 12.0000],
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[12.5000, 13.1250, 13.8750, 14.5000],
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[15.5000, 16.1250, 16.8750, 17.5000],
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[18.0000, 18.6250, 19.3750, 20.0000],
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],
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[
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[22.0000, 22.6250, 23.3750, 24.0000],
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[24.5000, 25.1250, 25.8750, 26.5000],
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[27.5000, 28.1250, 28.8750, 29.5000],
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[30.0000, 30.6250, 31.3750, 32.0000],
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],
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[
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[32.0000, 32.6250, 33.3750, 34.0000],
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[34.5000, 35.1250, 35.8750, 36.5000],
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[37.5000, 38.1250, 38.8750, 39.5000],
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[40.0000, 40.6250, 41.3750, 42.0000],
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],
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]
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]
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),
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]
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)
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class TestRandGaussianSmoothd(unittest.TestCase):
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@parameterized.expand(TESTS)
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def test_value(self, arguments, image, expected_data):
|
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converter = RandSimulateLowResolutiond(**arguments)
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converter.set_random_state(seed=0)
|
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result = converter(image)
|
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assert_allclose(result["img"], expected_data, rtol=1e-4, type_test=False)
|
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assert_allclose(result["seg"], expected_data, rtol=1e-4, type_test=False)
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if __name__ == "__main__":
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unittest.main()
|
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
|
3
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# you may not use this file except in compliance with the License.
|
4
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# You may obtain a copy of the License at
|
5
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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
|
7
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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.
|
9
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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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from parameterized import parameterized
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from monai.data.meta_tensor import MetaTensor
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from monai.transforms import RandScaleCrop, RandSpatialCrop
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from monai.transforms.lazy.functional import apply_pending
|
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from tests.croppers import CropTest
|
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from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
|
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|
25
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TEST_SHAPES = [
|
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[{"roi_size": [3, 3, -1], "random_center": True}, (3, 3, 3, 4), (3, 3, 3, 4)],
|
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[{"roi_size": [3, 3, 3], "random_center": True}, (3, 3, 3, 3), (3, 3, 3, 3)],
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[{"roi_size": [3, 3, 3], "random_center": False}, (3, 3, 3, 3), (3, 3, 3, 3)],
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[{"roi_size": [3, 3, 2], "random_center": False, "random_size": False}, (3, 3, 3, 3), (3, 3, 3, 2)],
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+
]
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+
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+
TEST_VALUES = [
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+
[
|
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+
{"roi_size": [3, 3], "random_center": False},
|
35
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+
np.array([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 1, 2, 1, 0], [0, 0, 0, 0, 0]]]),
|
36
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+
]
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37
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+
]
|
38
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+
|
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+
TEST_RANDOM_SHAPES = [
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40
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+
[
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+
{"roi_size": [3, 3, 3], "max_roi_size": [5, -1, 4], "random_center": True, "random_size": True},
|
42
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+
(1, 4, 5, 6),
|
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+
(1, 4, 4, 3),
|
44
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+
],
|
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+
[{"roi_size": 3, "max_roi_size": 4, "random_center": True, "random_size": True}, (1, 4, 5, 6), (1, 3, 4, 3)],
|
46
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+
]
|
47
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+
|
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+
func1 = {RandSpatialCrop: {"roi_size": [8, 7, -1], "random_center": True, "random_size": False}}
|
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+
func2 = {RandScaleCrop: {"roi_scale": [0.5, 0.6, -1.0], "random_center": True, "random_size": True}}
|
50
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+
func3 = {RandScaleCrop: {"roi_scale": [1.0, 0.5, -1.0], "random_center": False, "random_size": False}}
|
51
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+
|
52
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+
TESTS_COMBINE = []
|
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+
TESTS_COMBINE.append([[func1, func2, func3], (3, 10, 10, 8)])
|
54
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+
TESTS_COMBINE.append([[func1, func2], (3, 8, 8, 4)])
|
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+
TESTS_COMBINE.append([[func2, func2], (3, 8, 8, 4)])
|
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+
|
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+
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+
class TestRandSpatialCrop(CropTest):
|
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+
Cropper = RandSpatialCrop
|
60
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+
|
61
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+
@parameterized.expand(TEST_SHAPES)
|
62
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+
def test_shape(self, input_param, input_shape, expected_shape):
|
63
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+
self.crop_test(input_param, input_shape, expected_shape)
|
64
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+
|
65
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+
@parameterized.expand(TEST_VALUES)
|
66
|
+
def test_value(self, input_param, input_data):
|
67
|
+
for im_type in TEST_NDARRAYS_ALL:
|
68
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+
with self.subTest(im_type=im_type):
|
69
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+
cropper = RandSpatialCrop(**input_param)
|
70
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+
result = cropper(im_type(input_data))
|
71
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+
roi = [(2 - i // 2, 2 + i - i // 2) for i in cropper._size]
|
72
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+
assert_allclose(result, input_data[:, roi[0][0] : roi[0][1], roi[1][0] : roi[1][1]], type_test="tensor")
|
73
|
+
|
74
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+
@parameterized.expand(TEST_RANDOM_SHAPES)
|
75
|
+
def test_random_shape(self, input_param, input_shape, expected_shape):
|
76
|
+
for im_type in TEST_NDARRAYS_ALL:
|
77
|
+
with self.subTest(im_type=im_type):
|
78
|
+
cropper = RandSpatialCrop(**input_param)
|
79
|
+
cropper.set_random_state(seed=123)
|
80
|
+
input_data = im_type(np.random.randint(0, 2, input_shape))
|
81
|
+
expected = cropper(input_data)
|
82
|
+
self.assertTupleEqual(expected.shape, expected_shape)
|
83
|
+
|
84
|
+
# lazy
|
85
|
+
# reset random seed to ensure the same results
|
86
|
+
cropper.set_random_state(seed=123)
|
87
|
+
cropper.lazy = True
|
88
|
+
pending_result = cropper(input_data)
|
89
|
+
self.assertIsInstance(pending_result, MetaTensor)
|
90
|
+
assert_allclose(pending_result.peek_pending_affine(), expected.affine)
|
91
|
+
assert_allclose(pending_result.peek_pending_shape(), expected.shape[1:])
|
92
|
+
# only support nearest
|
93
|
+
result = apply_pending(pending_result, overrides={"mode": "nearest", "align_corners": False})[0]
|
94
|
+
# compare
|
95
|
+
assert_allclose(result, expected, rtol=1e-5)
|
96
|
+
|
97
|
+
@parameterized.expand(TEST_SHAPES)
|
98
|
+
def test_pending_ops(self, input_param, input_shape, _):
|
99
|
+
self.crop_test_pending_ops(input_param, input_shape)
|
100
|
+
|
101
|
+
@parameterized.expand(TESTS_COMBINE)
|
102
|
+
def test_combine_ops(self, funcs, input_shape):
|
103
|
+
self.crop_test_combine_ops(funcs, input_shape)
|
104
|
+
|
105
|
+
|
106
|
+
if __name__ == "__main__":
|
107
|
+
unittest.main()
|
@@ -0,0 +1,128 @@
|
|
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
|
+
from parameterized import parameterized
|
18
|
+
|
19
|
+
from monai.data.meta_tensor import MetaTensor
|
20
|
+
from monai.transforms import RandSpatialCropSamples
|
21
|
+
from monai.transforms.lazy.functional import apply_pending
|
22
|
+
from tests.croppers import CropTest
|
23
|
+
from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
|
24
|
+
|
25
|
+
TEST_CASE_1 = [
|
26
|
+
{"roi_size": [3, 3, 3], "num_samples": 4, "random_center": True, "random_size": False},
|
27
|
+
(3, 4, 4, 4),
|
28
|
+
[(3, 3, 3, 3), (3, 3, 3, 3), (3, 3, 3, 3), (3, 3, 3, 3)],
|
29
|
+
np.array(
|
30
|
+
[
|
31
|
+
[
|
32
|
+
[[21, 22, 23], [25, 26, 27], [29, 30, 31]],
|
33
|
+
[[37, 38, 39], [41, 42, 43], [45, 46, 47]],
|
34
|
+
[[53, 54, 55], [57, 58, 59], [61, 62, 63]],
|
35
|
+
],
|
36
|
+
[
|
37
|
+
[[85, 86, 87], [89, 90, 91], [93, 94, 95]],
|
38
|
+
[[101, 102, 103], [105, 106, 107], [109, 110, 111]],
|
39
|
+
[[117, 118, 119], [121, 122, 123], [125, 126, 127]],
|
40
|
+
],
|
41
|
+
[
|
42
|
+
[[149, 150, 151], [153, 154, 155], [157, 158, 159]],
|
43
|
+
[[165, 166, 167], [169, 170, 171], [173, 174, 175]],
|
44
|
+
[[181, 182, 183], [185, 186, 187], [189, 190, 191]],
|
45
|
+
],
|
46
|
+
]
|
47
|
+
),
|
48
|
+
]
|
49
|
+
|
50
|
+
TEST_CASE_2 = [
|
51
|
+
{"roi_size": [3, 3, 3], "num_samples": 8, "random_center": False, "random_size": True},
|
52
|
+
(3, 4, 4, 4),
|
53
|
+
[(3, 4, 4, 3), (3, 4, 3, 3), (3, 3, 4, 4), (3, 4, 4, 4), (3, 3, 3, 4), (3, 3, 3, 3), (3, 3, 3, 3), (3, 3, 3, 3)],
|
54
|
+
np.array(
|
55
|
+
[
|
56
|
+
[
|
57
|
+
[[21, 22, 23], [25, 26, 27], [29, 30, 31]],
|
58
|
+
[[37, 38, 39], [41, 42, 43], [45, 46, 47]],
|
59
|
+
[[53, 54, 55], [57, 58, 59], [61, 62, 63]],
|
60
|
+
],
|
61
|
+
[
|
62
|
+
[[85, 86, 87], [89, 90, 91], [93, 94, 95]],
|
63
|
+
[[101, 102, 103], [105, 106, 107], [109, 110, 111]],
|
64
|
+
[[117, 118, 119], [121, 122, 123], [125, 126, 127]],
|
65
|
+
],
|
66
|
+
[
|
67
|
+
[[149, 150, 151], [153, 154, 155], [157, 158, 159]],
|
68
|
+
[[165, 166, 167], [169, 170, 171], [173, 174, 175]],
|
69
|
+
[[181, 182, 183], [185, 186, 187], [189, 190, 191]],
|
70
|
+
],
|
71
|
+
]
|
72
|
+
),
|
73
|
+
]
|
74
|
+
|
75
|
+
TEST_INVERSE_LIST = [
|
76
|
+
[(1, 2, 2), {"roi_size": (1, 1), "num_samples": 4, "random_size": False}],
|
77
|
+
[(1, 3, 2), {"roi_size": (1, 1), "num_samples": 100, "random_size": False}],
|
78
|
+
[(3, 10, 11, 12), {"roi_size": (3, 5, 4), "num_samples": 7, "random_size": False}],
|
79
|
+
[(3, 10, 11, 12), {"roi_size": (10, 11, 12), "num_samples": 3, "random_size": False}],
|
80
|
+
[(3, 10, 11, 12), {"roi_size": (3, 4, 5), "num_samples": 100, "random_size": False}],
|
81
|
+
]
|
82
|
+
|
83
|
+
|
84
|
+
class TestRandSpatialCropSamples(CropTest):
|
85
|
+
Cropper = RandSpatialCropSamples
|
86
|
+
|
87
|
+
@parameterized.expand([TEST_CASE_1, TEST_CASE_2])
|
88
|
+
def test_shape(self, input_param, input_shape, expected_shape, expected_last_item):
|
89
|
+
input_data = np.arange(192).reshape(*input_shape)
|
90
|
+
|
91
|
+
for p in TEST_NDARRAYS_ALL:
|
92
|
+
xform = RandSpatialCropSamples(**input_param)
|
93
|
+
xform.set_random_state(1234)
|
94
|
+
result = xform(p(input_data))
|
95
|
+
|
96
|
+
np.testing.assert_equal(len(result), input_param["num_samples"])
|
97
|
+
for i, (item, expected) in enumerate(zip(result, expected_shape)):
|
98
|
+
self.assertTupleEqual(item.shape, expected)
|
99
|
+
self.assertEqual(item.meta["patch_index"], i)
|
100
|
+
assert_allclose(result[-1], expected_last_item, type_test="tensor")
|
101
|
+
|
102
|
+
@parameterized.expand([TEST_CASE_1, TEST_CASE_2])
|
103
|
+
def test_pending_ops(self, input_param, input_shape, _expected_shape, _expected_last_item):
|
104
|
+
input_data = np.arange(192).reshape(*input_shape)
|
105
|
+
|
106
|
+
for p in TEST_NDARRAYS_ALL:
|
107
|
+
xform = RandSpatialCropSamples(**input_param)
|
108
|
+
image = p(input_data)
|
109
|
+
# non-lazy
|
110
|
+
xform.set_random_state(1234)
|
111
|
+
expected = xform(image)
|
112
|
+
self.assertIsInstance(expected[0], MetaTensor)
|
113
|
+
# lazy
|
114
|
+
xform.set_random_state(1234)
|
115
|
+
xform.lazy = True
|
116
|
+
pending_result = xform(image)
|
117
|
+
for i, _pending_result in enumerate(pending_result):
|
118
|
+
self.assertIsInstance(_pending_result, MetaTensor)
|
119
|
+
assert_allclose(_pending_result.peek_pending_affine(), expected[i].affine)
|
120
|
+
assert_allclose(_pending_result.peek_pending_shape(), expected[i].shape[1:])
|
121
|
+
# only support nearest
|
122
|
+
result = apply_pending(_pending_result, overrides={"mode": "nearest", "align_corners": False})[0]
|
123
|
+
# compare
|
124
|
+
assert_allclose(result, expected[i], rtol=1e-5)
|
125
|
+
|
126
|
+
|
127
|
+
if __name__ == "__main__":
|
128
|
+
unittest.main()
|
@@ -0,0 +1,147 @@
|
|
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
|
+
from parameterized import parameterized
|
18
|
+
|
19
|
+
from monai.data.meta_tensor import MetaTensor
|
20
|
+
from monai.transforms import Compose, DivisiblePadd, RandSpatialCropSamplesd
|
21
|
+
from monai.transforms.lazy.functional import apply_pending
|
22
|
+
from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
|
23
|
+
|
24
|
+
TEST_CASE_1 = [
|
25
|
+
{"keys": ["img", "seg"], "num_samples": 4, "roi_size": [2, 2, 2], "random_center": True, "random_size": True},
|
26
|
+
{"img": np.arange(81).reshape(3, 3, 3, 3), "seg": np.arange(81, 0, -1).reshape(3, 3, 3, 3)},
|
27
|
+
[(3, 2, 2, 2), (3, 2, 3, 3), (3, 2, 3, 2), (3, 2, 3, 2)],
|
28
|
+
{
|
29
|
+
"img": np.array(
|
30
|
+
[
|
31
|
+
[[[1, 2], [4, 5], [7, 8]], [[10, 11], [13, 14], [16, 17]]],
|
32
|
+
[[[28, 29], [31, 32], [34, 35]], [[37, 38], [40, 41], [43, 44]]],
|
33
|
+
[[[55, 56], [58, 59], [61, 62]], [[64, 65], [67, 68], [70, 71]]],
|
34
|
+
]
|
35
|
+
),
|
36
|
+
"seg": np.array(
|
37
|
+
[
|
38
|
+
[[[80, 79], [77, 76], [74, 73]], [[71, 70], [68, 67], [65, 64]]],
|
39
|
+
[[[53, 52], [50, 49], [47, 46]], [[44, 43], [41, 40], [38, 37]]],
|
40
|
+
[[[26, 25], [23, 22], [20, 19]], [[17, 16], [14, 13], [11, 10]]],
|
41
|
+
]
|
42
|
+
),
|
43
|
+
},
|
44
|
+
]
|
45
|
+
|
46
|
+
TEST_CASE_2 = []
|
47
|
+
for p in TEST_NDARRAYS_ALL:
|
48
|
+
TEST_CASE_2.append(
|
49
|
+
[
|
50
|
+
{
|
51
|
+
"keys": ["img", "seg"],
|
52
|
+
"num_samples": 8,
|
53
|
+
"roi_size": [2, 2, 3],
|
54
|
+
"random_center": False,
|
55
|
+
"random_size": True,
|
56
|
+
},
|
57
|
+
{"img": p(np.arange(81).reshape(3, 3, 3, 3)), "seg": p(np.arange(81, 0, -1).reshape(3, 3, 3, 3))},
|
58
|
+
[
|
59
|
+
(3, 2, 2, 3),
|
60
|
+
(3, 2, 2, 3),
|
61
|
+
(3, 3, 3, 3),
|
62
|
+
(3, 2, 3, 3),
|
63
|
+
(3, 3, 3, 3),
|
64
|
+
(3, 2, 3, 3),
|
65
|
+
(3, 2, 3, 3),
|
66
|
+
(3, 3, 2, 3),
|
67
|
+
],
|
68
|
+
{
|
69
|
+
"img": p(
|
70
|
+
np.array(
|
71
|
+
[
|
72
|
+
[[[0, 1, 2], [3, 4, 5]], [[9, 10, 11], [12, 13, 14]], [[18, 19, 20], [21, 22, 23]]],
|
73
|
+
[[[27, 28, 29], [30, 31, 32]], [[36, 37, 38], [39, 40, 41]], [[45, 46, 47], [48, 49, 50]]],
|
74
|
+
[[[54, 55, 56], [57, 58, 59]], [[63, 64, 65], [66, 67, 68]], [[72, 73, 74], [75, 76, 77]]],
|
75
|
+
]
|
76
|
+
)
|
77
|
+
),
|
78
|
+
"seg": p(
|
79
|
+
np.array(
|
80
|
+
[
|
81
|
+
[[[81, 80, 79], [78, 77, 76]], [[72, 71, 70], [69, 68, 67]], [[63, 62, 61], [60, 59, 58]]],
|
82
|
+
[[[54, 53, 52], [51, 50, 49]], [[45, 44, 43], [42, 41, 40]], [[36, 35, 34], [33, 32, 31]]],
|
83
|
+
[[[27, 26, 25], [24, 23, 22]], [[18, 17, 16], [15, 14, 13]], [[9, 8, 7], [6, 5, 4]]],
|
84
|
+
]
|
85
|
+
)
|
86
|
+
),
|
87
|
+
},
|
88
|
+
]
|
89
|
+
)
|
90
|
+
|
91
|
+
|
92
|
+
class TestRandSpatialCropSamplesd(unittest.TestCase):
|
93
|
+
@parameterized.expand([TEST_CASE_1, *TEST_CASE_2])
|
94
|
+
def test_shape(self, input_param, input_data, expected_shape, expected_last):
|
95
|
+
xform = RandSpatialCropSamplesd(**input_param)
|
96
|
+
xform.set_random_state(1234)
|
97
|
+
result = xform(input_data)
|
98
|
+
_len = len(tuple(input_data.keys()))
|
99
|
+
self.assertTupleEqual(tuple(result[0].keys())[:_len], tuple(input_data.keys()))
|
100
|
+
for item, expected in zip(result, expected_shape):
|
101
|
+
self.assertTupleEqual(item["img"].shape, expected)
|
102
|
+
self.assertTupleEqual(item["seg"].shape, expected)
|
103
|
+
for i, item in enumerate(result):
|
104
|
+
self.assertEqual(item["img"].meta["patch_index"], i)
|
105
|
+
self.assertEqual(item["seg"].meta["patch_index"], i)
|
106
|
+
assert_allclose(item["img"], expected_last["img"], type_test=False)
|
107
|
+
assert_allclose(item["seg"], expected_last["seg"], type_test=False)
|
108
|
+
|
109
|
+
def test_deep_copy(self):
|
110
|
+
data = {"img": np.ones((1, 10, 11, 12))}
|
111
|
+
num_samples = 3
|
112
|
+
sampler = RandSpatialCropSamplesd(
|
113
|
+
keys=["img"], roi_size=(3, 3, 3), num_samples=num_samples, random_center=True, random_size=False
|
114
|
+
)
|
115
|
+
transform = Compose([DivisiblePadd(keys="img", k=5), sampler])
|
116
|
+
samples = transform(data)
|
117
|
+
self.assertEqual(len(samples), num_samples)
|
118
|
+
for sample in samples:
|
119
|
+
self.assertEqual(len(sample["img"].applied_operations), len(transform))
|
120
|
+
|
121
|
+
@parameterized.expand([TEST_CASE_1, *TEST_CASE_2])
|
122
|
+
def test_pending_ops(self, input_param, input_data, _expected_shape, _expected_last):
|
123
|
+
xform = RandSpatialCropSamplesd(**input_param)
|
124
|
+
# non-lazy
|
125
|
+
xform.set_random_state(1234)
|
126
|
+
expected = xform(input_data)
|
127
|
+
self.assertIsInstance(expected[0]["img"], MetaTensor)
|
128
|
+
|
129
|
+
# lazy
|
130
|
+
xform.set_random_state(1234)
|
131
|
+
xform.lazy = True
|
132
|
+
pending_result = xform(input_data)
|
133
|
+
for i, _pending_result in enumerate(pending_result):
|
134
|
+
self.assertIsInstance(_pending_result["img"], MetaTensor)
|
135
|
+
assert_allclose(_pending_result["img"].peek_pending_affine(), expected[i]["img"].affine)
|
136
|
+
assert_allclose(_pending_result["img"].peek_pending_shape(), expected[i]["img"].shape[1:])
|
137
|
+
# only support nearest
|
138
|
+
overrides = {"mode": "nearest", "align_corners": False}
|
139
|
+
result_img = apply_pending(_pending_result["img"], overrides=overrides)[0]
|
140
|
+
result_seg = apply_pending(_pending_result["seg"], overrides=overrides)[0]
|
141
|
+
# compare
|
142
|
+
assert_allclose(result_img, expected[i]["img"], rtol=1e-5)
|
143
|
+
assert_allclose(result_seg, expected[i]["seg"], rtol=1e-5)
|
144
|
+
|
145
|
+
|
146
|
+
if __name__ == "__main__":
|
147
|
+
unittest.main()
|