monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2508__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- monai/__init__.py +1 -1
- monai/_version.py +3 -3
- monai/apps/auto3dseg/transforms.py +1 -4
- monai/data/utils.py +6 -13
- monai/handlers/__init__.py +1 -0
- monai/handlers/average_precision.py +53 -0
- monai/inferers/inferer.py +10 -7
- monai/inferers/utils.py +1 -2
- monai/losses/dice.py +2 -14
- monai/losses/ds_loss.py +1 -3
- monai/metrics/__init__.py +1 -0
- monai/metrics/average_precision.py +187 -0
- monai/networks/layers/simplelayers.py +2 -14
- monai/networks/utils.py +4 -16
- monai/transforms/compose.py +28 -11
- monai/transforms/croppad/array.py +1 -6
- monai/transforms/io/array.py +0 -1
- monai/transforms/transform.py +15 -6
- monai/transforms/utility/array.py +2 -12
- monai/transforms/utils.py +1 -2
- monai/transforms/utils_pytorch_numpy_unification.py +2 -4
- monai/utils/enums.py +3 -2
- monai/utils/module.py +6 -6
- monai/utils/tf32.py +0 -10
- monai/visualize/class_activation_maps.py +5 -8
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/METADATA +21 -17
- monai_weekly-1.5.dev2508.dist-info/RECORD +1185 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/top_level.txt +1 -0
- tests/apps/__init__.py +10 -0
- tests/apps/deepedit/__init__.py +10 -0
- tests/apps/deepedit/test_deepedit_transforms.py +314 -0
- tests/apps/deepgrow/__init__.py +10 -0
- tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
- tests/apps/deepgrow/transforms/__init__.py +10 -0
- tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
- tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
- tests/apps/detection/__init__.py +10 -0
- tests/apps/detection/metrics/__init__.py +10 -0
- tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
- tests/apps/detection/networks/__init__.py +10 -0
- tests/apps/detection/networks/test_retinanet.py +210 -0
- tests/apps/detection/networks/test_retinanet_detector.py +203 -0
- tests/apps/detection/test_box_transform.py +370 -0
- tests/apps/detection/utils/__init__.py +10 -0
- tests/apps/detection/utils/test_anchor_box.py +88 -0
- tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
- tests/apps/detection/utils/test_box_coder.py +43 -0
- tests/apps/detection/utils/test_detector_boxselector.py +67 -0
- tests/apps/detection/utils/test_detector_utils.py +96 -0
- tests/apps/detection/utils/test_hardnegsampler.py +54 -0
- tests/apps/nuclick/__init__.py +10 -0
- tests/apps/nuclick/test_nuclick_transforms.py +259 -0
- tests/apps/pathology/__init__.py +10 -0
- tests/apps/pathology/handlers/__init__.py +10 -0
- tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
- tests/apps/pathology/test_lesion_froc.py +333 -0
- tests/apps/pathology/test_pathology_prob_nms.py +55 -0
- tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
- tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
- tests/apps/pathology/transforms/__init__.py +10 -0
- tests/apps/pathology/transforms/post/__init__.py +10 -0
- tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
- tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
- tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
- tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
- tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
- tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
- tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
- tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
- tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
- tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
- tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
- tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
- tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
- tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
- tests/apps/pathology/transforms/post/test_watershed.py +60 -0
- tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
- tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
- tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
- tests/apps/reconstruction/__init__.py +10 -0
- tests/apps/reconstruction/nets/__init__.py +10 -0
- tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
- tests/apps/reconstruction/test_complex_utils.py +77 -0
- tests/apps/reconstruction/test_fastmri_reader.py +82 -0
- tests/apps/reconstruction/test_mri_utils.py +37 -0
- tests/apps/reconstruction/transforms/__init__.py +10 -0
- tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
- tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
- tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
- tests/apps/test_auto3dseg_bundlegen.py +156 -0
- tests/apps/test_check_hash.py +53 -0
- tests/apps/test_cross_validation.py +74 -0
- tests/apps/test_decathlondataset.py +93 -0
- tests/apps/test_download_and_extract.py +70 -0
- tests/apps/test_download_url_yandex.py +45 -0
- tests/apps/test_mednistdataset.py +72 -0
- tests/apps/test_mmar_download.py +154 -0
- tests/apps/test_tciadataset.py +123 -0
- tests/apps/vista3d/__init__.py +10 -0
- tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
- tests/apps/vista3d/test_vista3d_sampler.py +100 -0
- tests/apps/vista3d/test_vista3d_transforms.py +94 -0
- tests/bundle/__init__.py +10 -0
- tests/bundle/test_bundle_ckpt_export.py +107 -0
- tests/bundle/test_bundle_download.py +435 -0
- tests/bundle/test_bundle_get_data.py +94 -0
- tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
- tests/bundle/test_bundle_trt_export.py +147 -0
- tests/bundle/test_bundle_utils.py +149 -0
- tests/bundle/test_bundle_verify_metadata.py +66 -0
- tests/bundle/test_bundle_verify_net.py +76 -0
- tests/bundle/test_bundle_workflow.py +272 -0
- tests/bundle/test_component_locator.py +38 -0
- tests/bundle/test_config_item.py +138 -0
- tests/bundle/test_config_parser.py +392 -0
- tests/bundle/test_reference_resolver.py +114 -0
- tests/config/__init__.py +10 -0
- tests/config/test_cv2_dist.py +53 -0
- tests/engines/__init__.py +10 -0
- tests/engines/test_ensemble_evaluator.py +94 -0
- tests/engines/test_prepare_batch_default.py +76 -0
- tests/engines/test_prepare_batch_default_dist.py +76 -0
- tests/engines/test_prepare_batch_diffusion.py +104 -0
- tests/engines/test_prepare_batch_extra_input.py +80 -0
- tests/fl/__init__.py +10 -0
- tests/fl/monai_algo/__init__.py +10 -0
- tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
- tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
- tests/fl/test_fl_monai_algo_stats.py +81 -0
- tests/fl/utils/__init__.py +10 -0
- tests/fl/utils/test_fl_exchange_object.py +63 -0
- tests/handlers/__init__.py +10 -0
- tests/handlers/test_handler_average_precision.py +79 -0
- tests/handlers/test_handler_checkpoint_loader.py +182 -0
- tests/handlers/test_handler_checkpoint_saver.py +233 -0
- tests/handlers/test_handler_classification_saver.py +64 -0
- tests/handlers/test_handler_classification_saver_dist.py +77 -0
- tests/handlers/test_handler_clearml_image.py +65 -0
- tests/handlers/test_handler_clearml_stats.py +65 -0
- tests/handlers/test_handler_confusion_matrix.py +104 -0
- tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
- tests/handlers/test_handler_decollate_batch.py +66 -0
- tests/handlers/test_handler_early_stop.py +68 -0
- tests/handlers/test_handler_garbage_collector.py +73 -0
- tests/handlers/test_handler_hausdorff_distance.py +111 -0
- tests/handlers/test_handler_ignite_metric.py +191 -0
- tests/handlers/test_handler_lr_scheduler.py +94 -0
- tests/handlers/test_handler_mean_dice.py +98 -0
- tests/handlers/test_handler_mean_iou.py +76 -0
- tests/handlers/test_handler_metrics_reloaded.py +149 -0
- tests/handlers/test_handler_metrics_saver.py +89 -0
- tests/handlers/test_handler_metrics_saver_dist.py +120 -0
- tests/handlers/test_handler_mlflow.py +296 -0
- tests/handlers/test_handler_nvtx.py +93 -0
- tests/handlers/test_handler_panoptic_quality.py +89 -0
- tests/handlers/test_handler_parameter_scheduler.py +136 -0
- tests/handlers/test_handler_post_processing.py +74 -0
- tests/handlers/test_handler_prob_map_producer.py +111 -0
- tests/handlers/test_handler_regression_metrics.py +160 -0
- tests/handlers/test_handler_regression_metrics_dist.py +245 -0
- tests/handlers/test_handler_rocauc.py +48 -0
- tests/handlers/test_handler_rocauc_dist.py +54 -0
- tests/handlers/test_handler_stats.py +281 -0
- tests/handlers/test_handler_surface_distance.py +113 -0
- tests/handlers/test_handler_tb_image.py +61 -0
- tests/handlers/test_handler_tb_stats.py +166 -0
- tests/handlers/test_handler_validation.py +59 -0
- tests/handlers/test_trt_compile.py +145 -0
- tests/handlers/test_write_metrics_reports.py +68 -0
- tests/inferers/__init__.py +10 -0
- tests/inferers/test_avg_merger.py +179 -0
- tests/inferers/test_controlnet_inferers.py +1388 -0
- tests/inferers/test_diffusion_inferer.py +236 -0
- tests/inferers/test_latent_diffusion_inferer.py +884 -0
- tests/inferers/test_patch_inferer.py +309 -0
- tests/inferers/test_saliency_inferer.py +55 -0
- tests/inferers/test_slice_inferer.py +57 -0
- tests/inferers/test_sliding_window_inference.py +377 -0
- tests/inferers/test_sliding_window_splitter.py +284 -0
- tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
- tests/inferers/test_zarr_avg_merger.py +326 -0
- tests/integration/__init__.py +10 -0
- tests/integration/test_auto3dseg_ensemble.py +211 -0
- tests/integration/test_auto3dseg_hpo.py +189 -0
- tests/integration/test_deepedit_interaction.py +122 -0
- tests/integration/test_downsample_block.py +50 -0
- tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
- tests/integration/test_integration_autorunner.py +201 -0
- tests/integration/test_integration_bundle_run.py +240 -0
- tests/integration/test_integration_classification_2d.py +282 -0
- tests/integration/test_integration_determinism.py +95 -0
- tests/integration/test_integration_fast_train.py +231 -0
- tests/integration/test_integration_gpu_customization.py +159 -0
- tests/integration/test_integration_lazy_samples.py +219 -0
- tests/integration/test_integration_nnunetv2_runner.py +96 -0
- tests/integration/test_integration_segmentation_3d.py +304 -0
- tests/integration/test_integration_sliding_window.py +100 -0
- tests/integration/test_integration_stn.py +133 -0
- tests/integration/test_integration_unet_2d.py +67 -0
- tests/integration/test_integration_workers.py +61 -0
- tests/integration/test_integration_workflows.py +365 -0
- tests/integration/test_integration_workflows_adversarial.py +173 -0
- tests/integration/test_integration_workflows_gan.py +158 -0
- tests/integration/test_loader_semaphore.py +48 -0
- tests/integration/test_mapping_filed.py +122 -0
- tests/integration/test_meta_affine.py +183 -0
- tests/integration/test_metatensor_integration.py +114 -0
- tests/integration/test_module_list.py +76 -0
- tests/integration/test_one_of.py +283 -0
- tests/integration/test_pad_collation.py +124 -0
- tests/integration/test_reg_loss_integration.py +107 -0
- tests/integration/test_retinanet_predict_utils.py +154 -0
- tests/integration/test_seg_loss_integration.py +159 -0
- tests/integration/test_spatial_combine_transforms.py +185 -0
- tests/integration/test_testtimeaugmentation.py +186 -0
- tests/integration/test_vis_gradbased.py +69 -0
- tests/integration/test_vista3d_utils.py +159 -0
- tests/losses/__init__.py +10 -0
- tests/losses/deform/__init__.py +10 -0
- tests/losses/deform/test_bending_energy.py +88 -0
- tests/losses/deform/test_diffusion_loss.py +117 -0
- tests/losses/image_dissimilarity/__init__.py +10 -0
- tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
- tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
- tests/losses/test_adversarial_loss.py +94 -0
- tests/losses/test_barlow_twins_loss.py +109 -0
- tests/losses/test_cldice_loss.py +51 -0
- tests/losses/test_contrastive_loss.py +86 -0
- tests/losses/test_dice_ce_loss.py +123 -0
- tests/losses/test_dice_focal_loss.py +124 -0
- tests/losses/test_dice_loss.py +227 -0
- tests/losses/test_ds_loss.py +189 -0
- tests/losses/test_focal_loss.py +379 -0
- tests/losses/test_generalized_dice_focal_loss.py +85 -0
- tests/losses/test_generalized_dice_loss.py +221 -0
- tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
- tests/losses/test_giou_loss.py +62 -0
- tests/losses/test_hausdorff_loss.py +264 -0
- tests/losses/test_masked_dice_loss.py +152 -0
- tests/losses/test_masked_loss.py +87 -0
- tests/losses/test_multi_scale.py +86 -0
- tests/losses/test_nacl_loss.py +167 -0
- tests/losses/test_perceptual_loss.py +122 -0
- tests/losses/test_spectral_loss.py +86 -0
- tests/losses/test_ssim_loss.py +59 -0
- tests/losses/test_sure_loss.py +72 -0
- tests/losses/test_tversky_loss.py +198 -0
- tests/losses/test_unified_focal_loss.py +66 -0
- tests/metrics/__init__.py +10 -0
- tests/metrics/test_compute_average_precision.py +162 -0
- tests/metrics/test_compute_confusion_matrix.py +294 -0
- tests/metrics/test_compute_f_beta.py +80 -0
- tests/metrics/test_compute_fid_metric.py +40 -0
- tests/metrics/test_compute_froc.py +143 -0
- tests/metrics/test_compute_generalized_dice.py +240 -0
- tests/metrics/test_compute_meandice.py +306 -0
- tests/metrics/test_compute_meaniou.py +223 -0
- tests/metrics/test_compute_mmd_metric.py +56 -0
- tests/metrics/test_compute_multiscalessim_metric.py +83 -0
- tests/metrics/test_compute_panoptic_quality.py +113 -0
- tests/metrics/test_compute_regression_metrics.py +196 -0
- tests/metrics/test_compute_roc_auc.py +155 -0
- tests/metrics/test_compute_variance.py +147 -0
- tests/metrics/test_cumulative.py +63 -0
- tests/metrics/test_cumulative_average.py +74 -0
- tests/metrics/test_cumulative_average_dist.py +48 -0
- tests/metrics/test_hausdorff_distance.py +209 -0
- tests/metrics/test_label_quality_score.py +134 -0
- tests/metrics/test_loss_metric.py +57 -0
- tests/metrics/test_metrics_reloaded.py +96 -0
- tests/metrics/test_ssim_metric.py +78 -0
- tests/metrics/test_surface_dice.py +416 -0
- tests/metrics/test_surface_distance.py +186 -0
- tests/networks/__init__.py +10 -0
- tests/networks/blocks/__init__.py +10 -0
- tests/networks/blocks/dints_block/__init__.py +10 -0
- tests/networks/blocks/dints_block/test_acn_block.py +41 -0
- tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
- tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
- tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
- tests/networks/blocks/test_adn.py +86 -0
- tests/networks/blocks/test_convolutions.py +156 -0
- tests/networks/blocks/test_crf_cpu.py +513 -0
- tests/networks/blocks/test_crf_cuda.py +528 -0
- tests/networks/blocks/test_crossattention.py +185 -0
- tests/networks/blocks/test_denseblock.py +105 -0
- tests/networks/blocks/test_dynunet_block.py +116 -0
- tests/networks/blocks/test_fpn_block.py +88 -0
- tests/networks/blocks/test_localnet_block.py +121 -0
- tests/networks/blocks/test_mlp.py +78 -0
- tests/networks/blocks/test_patchembedding.py +212 -0
- tests/networks/blocks/test_regunet_block.py +103 -0
- tests/networks/blocks/test_se_block.py +85 -0
- tests/networks/blocks/test_se_blocks.py +78 -0
- tests/networks/blocks/test_segresnet_block.py +57 -0
- tests/networks/blocks/test_selfattention.py +232 -0
- tests/networks/blocks/test_simple_aspp.py +87 -0
- tests/networks/blocks/test_spatialattention.py +55 -0
- tests/networks/blocks/test_subpixel_upsample.py +87 -0
- tests/networks/blocks/test_text_encoding.py +49 -0
- tests/networks/blocks/test_transformerblock.py +90 -0
- tests/networks/blocks/test_unetr_block.py +158 -0
- tests/networks/blocks/test_upsample_block.py +134 -0
- tests/networks/blocks/warp/__init__.py +10 -0
- tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
- tests/networks/blocks/warp/test_warp.py +250 -0
- tests/networks/layers/__init__.py +10 -0
- tests/networks/layers/filtering/__init__.py +10 -0
- tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
- tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
- tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
- tests/networks/layers/filtering/test_phl_cpu.py +259 -0
- tests/networks/layers/filtering/test_phl_cuda.py +167 -0
- tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
- tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
- tests/networks/layers/test_affine_transform.py +385 -0
- tests/networks/layers/test_apply_filter.py +89 -0
- tests/networks/layers/test_channel_pad.py +51 -0
- tests/networks/layers/test_conjugate_gradient.py +56 -0
- tests/networks/layers/test_drop_path.py +46 -0
- tests/networks/layers/test_gaussian.py +317 -0
- tests/networks/layers/test_gaussian_filter.py +206 -0
- tests/networks/layers/test_get_layers.py +65 -0
- tests/networks/layers/test_gmm.py +314 -0
- tests/networks/layers/test_grid_pull.py +93 -0
- tests/networks/layers/test_hilbert_transform.py +131 -0
- tests/networks/layers/test_lltm.py +62 -0
- tests/networks/layers/test_median_filter.py +52 -0
- tests/networks/layers/test_polyval.py +55 -0
- tests/networks/layers/test_preset_filters.py +136 -0
- tests/networks/layers/test_savitzky_golay_filter.py +141 -0
- tests/networks/layers/test_separable_filter.py +87 -0
- tests/networks/layers/test_skip_connection.py +48 -0
- tests/networks/layers/test_vector_quantizer.py +89 -0
- tests/networks/layers/test_weight_init.py +50 -0
- tests/networks/nets/__init__.py +10 -0
- tests/networks/nets/dints/__init__.py +10 -0
- tests/networks/nets/dints/test_dints_cell.py +110 -0
- tests/networks/nets/dints/test_dints_mixop.py +84 -0
- tests/networks/nets/regunet/__init__.py +10 -0
- tests/networks/nets/regunet/test_localnet.py +86 -0
- tests/networks/nets/regunet/test_regunet.py +88 -0
- tests/networks/nets/test_ahnet.py +224 -0
- tests/networks/nets/test_attentionunet.py +88 -0
- tests/networks/nets/test_autoencoder.py +95 -0
- tests/networks/nets/test_autoencoderkl.py +337 -0
- tests/networks/nets/test_basic_unet.py +102 -0
- tests/networks/nets/test_basic_unetplusplus.py +109 -0
- tests/networks/nets/test_bundle_init_bundle.py +55 -0
- tests/networks/nets/test_cell_sam_wrapper.py +58 -0
- tests/networks/nets/test_controlnet.py +215 -0
- tests/networks/nets/test_daf3d.py +62 -0
- tests/networks/nets/test_densenet.py +121 -0
- tests/networks/nets/test_diffusion_model_unet.py +585 -0
- tests/networks/nets/test_dints_network.py +168 -0
- tests/networks/nets/test_discriminator.py +59 -0
- tests/networks/nets/test_dynunet.py +181 -0
- tests/networks/nets/test_efficientnet.py +400 -0
- tests/networks/nets/test_flexible_unet.py +341 -0
- tests/networks/nets/test_fullyconnectednet.py +69 -0
- tests/networks/nets/test_generator.py +59 -0
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- tests/utils/misc/test_str2bool.py +34 -0
- tests/utils/misc/test_str2list.py +33 -0
- tests/utils/test_alias.py +44 -0
- tests/utils/test_component_store.py +73 -0
- tests/utils/test_deprecated.py +455 -0
- tests/utils/test_enum_bound_interp.py +75 -0
- tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
- tests/utils/test_get_package_version.py +34 -0
- tests/utils/test_handler_logfile.py +84 -0
- tests/utils/test_handler_metric_logger.py +62 -0
- tests/utils/test_list_to_dict.py +43 -0
- tests/utils/test_look_up_option.py +87 -0
- tests/utils/test_optional_import.py +80 -0
- tests/utils/test_pad_mode.py +39 -0
- tests/utils/test_profiling.py +208 -0
- tests/utils/test_rankfilter_dist.py +77 -0
- tests/utils/test_require_pkg.py +83 -0
- tests/utils/test_sample_slices.py +43 -0
- tests/utils/test_set_determinism.py +74 -0
- tests/utils/test_squeeze_unsqueeze.py +71 -0
- tests/utils/test_state_cacher.py +67 -0
- tests/utils/test_torchscript_utils.py +113 -0
- tests/utils/test_version.py +91 -0
- tests/utils/test_version_after.py +65 -0
- tests/utils/type_conversion/__init__.py +10 -0
- tests/utils/type_conversion/test_convert_data_type.py +152 -0
- tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
- tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
- tests/visualize/__init__.py +10 -0
- tests/visualize/test_img2tensorboard.py +46 -0
- tests/visualize/test_occlusion_sensitivity.py +128 -0
- tests/visualize/test_plot_2d_or_3d_image.py +74 -0
- tests/visualize/test_vis_cam.py +98 -0
- tests/visualize/test_vis_gradcam.py +211 -0
- tests/visualize/utils/__init__.py +10 -0
- tests/visualize/utils/test_blend_images.py +63 -0
- tests/visualize/utils/test_matshow3d.py +133 -0
- monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/LICENSE +0 -0
- {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/WHEEL +0 -0
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from __future__ import annotations
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import unittest
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import numpy as np
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import torch
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from parameterized import parameterized
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from monai.transforms import (
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Compose,
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CuCIM,
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Flip,
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Flipd,
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OneOf,
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RandAdjustContrast,
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RandCuCIM,
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RandFlip,
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RandomizableTrait,
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Rotate90,
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ToCupy,
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ToNumpy,
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TorchVision,
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ToTensor,
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ToTensord,
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)
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from monai.utils import Range, optional_import
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from tests.test_utils import HAS_CUPY
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_, has_nvtx = optional_import("torch._C._nvtx", descriptor="NVTX is not installed. Are you sure you have a CUDA build?")
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_, has_tvt = optional_import("torchvision.transforms")
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_, has_cut = optional_import("cucim.core.operations.expose.transform")
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TEST_CASE_ARRAY_0 = [np.random.randn(3, 3)]
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TEST_CASE_ARRAY_1 = [np.random.randn(3, 10, 10)]
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TEST_CASE_DICT_0 = [{"image": np.random.randn(3, 3)}]
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TEST_CASE_DICT_1 = [{"image": np.random.randn(3, 10, 10)}]
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TEST_CASE_TORCH_0 = [torch.randn(3, 3)]
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TEST_CASE_TORCH_1 = [torch.randn(3, 10, 10)]
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TEST_CASE_WRAPPER = [np.random.randn(3, 10, 10)]
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TEST_CASE_RECURSIVE_0 = [
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torch.randn(3, 3),
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Compose([ToNumpy(), Flip(), RandAdjustContrast(prob=0.0), RandFlip(prob=1.0), ToTensor()]),
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]
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TEST_CASE_RECURSIVE_1 = [
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torch.randn(3, 3),
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Compose([ToNumpy(), Flip(), Compose([RandAdjustContrast(prob=0.0), RandFlip(prob=1.0)]), ToTensor()]),
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]
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TEST_CASE_RECURSIVE_2 = [
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torch.randn(3, 3),
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Compose([ToNumpy(), Flip(), OneOf([RandAdjustContrast(prob=0.0), RandFlip(prob=1.0)], weights=[0, 1]), ToTensor()]),
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]
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TEST_CASE_RECURSIVE_LIST = [
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torch.randn(3, 3),
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[ToNumpy(), Flip(), RandAdjustContrast(prob=0.0), RandFlip(prob=1.0), ToTensor()],
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]
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@unittest.skipUnless(has_nvtx, "Required torch._C._nvtx for NVTX Range!")
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class TestNVTXRangeDecorator(unittest.TestCase):
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@parameterized.expand([TEST_CASE_ARRAY_0, TEST_CASE_ARRAY_1])
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def test_tranform_array(self, input):
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transforms = Compose([Range("random flip")(Flip()), Range()(ToTensor())])
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# Apply transforms
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output = transforms(input)
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# Decorate with NVTX Range
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transforms1 = Range()(transforms)
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transforms2 = Range("Transforms2")(transforms)
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transforms3 = Range(name="Transforms3", methods="__call__")(transforms)
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# Apply transforms with Range
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output1 = transforms1(input)
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output2 = transforms2(input)
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output3 = transforms3(input)
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# Check the outputs
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self.assertIsInstance(output, torch.Tensor)
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self.assertIsInstance(output1, torch.Tensor)
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self.assertIsInstance(output2, torch.Tensor)
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self.assertIsInstance(output3, torch.Tensor)
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np.testing.assert_equal(output.numpy(), output1.numpy())
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np.testing.assert_equal(output.numpy(), output2.numpy())
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np.testing.assert_equal(output.numpy(), output3.numpy())
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@parameterized.expand([TEST_CASE_DICT_0, TEST_CASE_DICT_1])
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def test_tranform_dict(self, input):
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transforms = Compose([Range("random flip dict")(Flipd(keys="image")), Range()(ToTensord("image"))])
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# Apply transforms
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output = transforms(input)["image"]
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# Decorate with NVTX Range
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transforms1 = Range()(transforms)
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transforms2 = Range("Transforms2")(transforms)
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transforms3 = Range(name="Transforms3", methods="__call__")(transforms)
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# Apply transforms with Range
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output1 = transforms1(input)["image"]
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output2 = transforms2(input)["image"]
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output3 = transforms3(input)["image"]
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# Check the outputs
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self.assertIsInstance(output, torch.Tensor)
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self.assertIsInstance(output1, torch.Tensor)
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self.assertIsInstance(output2, torch.Tensor)
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self.assertIsInstance(output3, torch.Tensor)
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np.testing.assert_equal(output.numpy(), output1.numpy())
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np.testing.assert_equal(output.numpy(), output2.numpy())
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np.testing.assert_equal(output.numpy(), output3.numpy())
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@parameterized.expand([TEST_CASE_WRAPPER])
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@unittest.skipUnless(HAS_CUPY, "Requires CuPy.")
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@unittest.skipUnless(has_cut, "Requires cuCIM transforms.")
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@unittest.skipUnless(has_tvt, "Requires torchvision transforms.")
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def test_wrapper_tranforms(self, input):
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transform_list = [
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ToTensor(),
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TorchVision(name="RandomHorizontalFlip", p=1.0),
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ToCupy(),
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CuCIM(name="image_flip", spatial_axis=-1),
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RandCuCIM(name="rand_image_rotate_90", prob=1.0, max_k=1, spatial_axis=(-2, -1)),
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]
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transforms = Compose(transform_list)
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transforms_range = Compose([Range()(t) for t in transform_list])
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# Apply transforms
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output = transforms(input)
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# Apply transforms with Range
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output_r = transforms_range(input)
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# Check the outputs
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np.testing.assert_equal(output.get(), output_r.get())
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@parameterized.expand([TEST_CASE_RECURSIVE_0, TEST_CASE_RECURSIVE_1, TEST_CASE_RECURSIVE_2])
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def test_recursive_tranforms(self, input, transforms):
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transforms_range = Range(name="Recursive Compose", recursive=True)(transforms)
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# Apply transforms
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output = transforms(input)
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# Apply transforms with Range
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output_r = transforms_range(input)
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# Check the outputs
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self.assertEqual(transforms.map_items, transforms_range.map_items)
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self.assertEqual(transforms.unpack_items, transforms_range.unpack_items)
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np.testing.assert_equal(output.numpy(), output_r.numpy())
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@parameterized.expand([TEST_CASE_RECURSIVE_LIST])
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def test_recursive_list_tranforms(self, input, transform_list):
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transforms_list_range = Range(recursive=True)(transform_list)
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# Apply transforms
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output = Compose(transform_list)(input)
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# Apply transforms with Range
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output_r = Compose(transforms_list_range)(input)
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# Check the outputs
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np.testing.assert_equal(output.numpy(), output_r.numpy())
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@parameterized.expand([TEST_CASE_ARRAY_1])
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def test_tranform_randomized(self, input):
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# Compose deterministic and randomized transforms
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transforms = Compose(
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[
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Range("flip")(Flip()),
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Rotate90(),
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Range()(RandAdjustContrast(prob=0.0)),
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Range("random flip")(RandFlip(prob=1.0)),
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ToTensor(),
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]
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)
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# Apply transforms
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output = transforms(input)
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# Decorate with NVTX Range
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transforms1 = Range()(transforms)
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transforms2 = Range("Transforms2")(transforms)
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transforms3 = Range(name="Transforms3", methods="__call__")(transforms)
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# Apply transforms with Range
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output1 = transforms1(input)
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output2 = transforms2(input)
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output3 = transforms3(input)
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# Check if the outputs are equal
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self.assertIsInstance(output, torch.Tensor)
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self.assertIsInstance(output1, torch.Tensor)
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self.assertIsInstance(output2, torch.Tensor)
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self.assertIsInstance(output3, torch.Tensor)
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np.testing.assert_equal(output.numpy(), output1.numpy())
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np.testing.assert_equal(output.numpy(), output2.numpy())
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np.testing.assert_equal(output.numpy(), output3.numpy())
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# Check if the first randomized is RandAdjustContrast
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for tran in transforms.transforms:
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if isinstance(tran, RandomizableTrait):
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self.assertIsInstance(tran, RandAdjustContrast)
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break
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@parameterized.expand([TEST_CASE_TORCH_0, TEST_CASE_TORCH_1])
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def test_network(self, input):
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# Create a network
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model = torch.nn.Sequential(torch.nn.ReLU(), torch.nn.Sigmoid())
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# Forward
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output = model(input)
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# Decorate with NVTX Range
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model1 = Range()(model)
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model2 = Range("Model2")(model)
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model3 = Range(name="Model3", methods="forward")(model)
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# Forward with Range
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output1 = model1(input)
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output2 = model2(input)
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output3 = model3(input)
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# Check the outputs
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self.assertIsInstance(output, torch.Tensor)
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self.assertIsInstance(output1, torch.Tensor)
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self.assertIsInstance(output2, torch.Tensor)
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self.assertIsInstance(output3, torch.Tensor)
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np.testing.assert_equal(output.numpy(), output1.numpy())
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np.testing.assert_equal(output.numpy(), output2.numpy())
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np.testing.assert_equal(output.numpy(), output3.numpy())
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@parameterized.expand([TEST_CASE_TORCH_0, TEST_CASE_TORCH_1])
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def test_loss(self, input):
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# Create a network and loss
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model = torch.nn.Sigmoid()
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loss = torch.nn.BCELoss()
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pred = model(input)
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target = torch.empty_like(input).random_(2)
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# Loss evaluation
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output = loss(pred, target)
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# Decorate with NVTX Range
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loss1 = Range()(loss)
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loss2 = Range("Loss2")(loss)
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loss3 = Range(name="Loss3", methods="forward")(loss)
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# Loss evaluation with Range
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output1 = loss1(pred, target)
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output2 = loss2(pred, target)
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output3 = loss3(pred, target)
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# Check the outputs
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self.assertIsInstance(output, torch.Tensor)
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self.assertIsInstance(output1, torch.Tensor)
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self.assertIsInstance(output2, torch.Tensor)
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self.assertIsInstance(output3, torch.Tensor)
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np.testing.assert_equal(output.numpy(), output1.numpy())
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np.testing.assert_equal(output.numpy(), output2.numpy())
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np.testing.assert_equal(output.numpy(), output3.numpy())
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def test_context_manager(self):
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model = torch.nn.Sigmoid()
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loss = torch.nn.BCELoss()
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with Range():
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input = torch.randn(3, requires_grad=True)
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target = torch.empty(3).random_(2)
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with Range("Model"):
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output = loss(model(input), target)
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output.backward()
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if __name__ == "__main__":
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unittest.main()
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# Copyright (c) MONAI Consortium
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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# http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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from __future__ import annotations
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import unittest
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import numpy as np
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import torch
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from parameterized import parameterized
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from monai.transforms import Compose, Flip, RandFlip, RandFlipD, RandomizableTrait, ToTensor, ToTensorD
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from monai.transforms.nvtx import (
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Mark,
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MarkD,
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RandMark,
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RandMarkD,
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RandRangePop,
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RandRangePopD,
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RandRangePush,
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RandRangePushD,
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RangePop,
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RangePopD,
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RangePush,
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RangePushD,
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)
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from monai.utils import optional_import
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+
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+
_, has_nvtx = optional_import("torch._C._nvtx", descriptor="NVTX is not installed. Are you sure you have a CUDA build?")
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+
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+
TEST_CASE_ARRAY_0 = [np.random.randn(3, 3)]
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+
TEST_CASE_ARRAY_1 = [np.random.randn(3, 10, 10)]
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TEST_CASE_DICT_0 = [{"image": np.random.randn(3, 3)}]
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TEST_CASE_DICT_1 = [{"image": np.random.randn(3, 10, 10)}]
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+
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class TestNVTXTransforms(unittest.TestCase):
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@parameterized.expand([TEST_CASE_ARRAY_0, TEST_CASE_ARRAY_1, TEST_CASE_DICT_0, TEST_CASE_DICT_1])
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+
@unittest.skipUnless(has_nvtx, "CUDA is required for NVTX!")
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def test_nvtx_transfroms_alone(self, input):
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transforms = Compose(
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[
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Mark("Mark: Transforms Start!"),
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+
RangePush("Range: RandFlipD"),
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+
RangePop(),
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RandRangePush("Range: ToTensorD"),
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RandRangePop(),
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RandMark("Mark: Transforms End!"),
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+
]
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)
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output = transforms(input)
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self.assertEqual(id(input), id(output))
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+
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# Check if chain of randomizable/non-randomizable transforms is not broken
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for tran in transforms.transforms:
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+
if isinstance(tran, RandomizableTrait):
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self.assertIsInstance(tran, RangePush)
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break
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+
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+
@parameterized.expand([TEST_CASE_ARRAY_0, TEST_CASE_ARRAY_1])
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+
@unittest.skipUnless(has_nvtx, "CUDA is required for NVTX!")
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+
def test_nvtx_transfroms_array(self, input):
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# with prob == 0.0
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transforms = Compose(
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[
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RandMark("Mark: Transforms Start!"),
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RandRangePush("Range: RandFlip"),
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+
RandFlip(prob=0.0),
|
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+
RandRangePop(),
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+
RangePush("Range: ToTensor"),
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+
ToTensor(),
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+
RangePop(),
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+
Mark("Mark: Transforms End!"),
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+
]
|
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+
)
|
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output = transforms(input)
|
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+
self.assertIsInstance(output, torch.Tensor)
|
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+
np.testing.assert_array_equal(input, output)
|
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+
# with prob == 1.0
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+
transforms = Compose(
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[
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RandMark("Mark: Transforms Start!"),
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RandRangePush("Range: RandFlip"),
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RandFlip(prob=1.0),
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+
RandRangePop(),
|
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+
RangePush("Range: ToTensor"),
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ToTensor(),
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RangePop(),
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Mark("Mark: Transforms End!"),
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]
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)
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output = transforms(input)
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self.assertIsInstance(output, torch.Tensor)
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np.testing.assert_array_equal(input, Flip()(output.numpy()))
|
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+
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+
@parameterized.expand([TEST_CASE_DICT_0, TEST_CASE_DICT_1])
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@unittest.skipUnless(has_nvtx, "CUDA is required for NVTX!")
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+
def test_nvtx_transfroms_dict(self, input):
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# with prob == 0.0
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transforms = Compose(
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[
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RandMarkD("Mark: Transforms (p=0) Start!"),
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RandRangePushD("Range: RandFlipD"),
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+
RandFlipD(keys="image", prob=0.0),
|
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RandRangePopD(),
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RangePushD("Range: ToTensorD"),
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+
ToTensorD(keys=("image")),
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+
RangePopD(),
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+
MarkD("Mark: Transforms (p=0) End!"),
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+
]
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+
)
|
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+
output = transforms(input)
|
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+
self.assertIsInstance(output["image"], torch.Tensor)
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np.testing.assert_array_equal(input["image"], output["image"])
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# with prob == 1.0
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transforms = Compose(
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[
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RandMarkD("Mark: Transforms (p=1) Start!"),
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+
RandRangePushD("Range: RandFlipD"),
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+
RandFlipD(keys="image", prob=1.0),
|
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+
RandRangePopD(),
|
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RangePushD("Range: ToTensorD"),
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ToTensorD(keys=("image")),
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+
RangePopD(),
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MarkD("Mark: Transforms (p=1) End!"),
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]
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+
)
|
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+
output = transforms(input)
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self.assertIsInstance(output["image"], torch.Tensor)
|
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np.testing.assert_array_equal(input["image"], Flip()(output["image"].numpy()))
|
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+
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+
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+
if __name__ == "__main__":
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unittest.main()
|
@@ -0,0 +1,247 @@
|
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1
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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.
|
4
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+
# You may obtain a copy of the License at
|
5
|
+
# 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.
|
9
|
+
# See the License for the specific language governing permissions and
|
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|
+
# limitations under the License.
|
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+
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|
+
from __future__ import annotations
|
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import unittest
|
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+
|
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+
import nibabel as nib
|
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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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+
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+
from monai.data.meta_obj import set_track_meta
|
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+
from monai.data.meta_tensor import MetaTensor
|
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+
from monai.transforms import Orientation, create_rotate, create_translate
|
24
|
+
from tests.lazy_transforms_utils import test_resampler_lazy
|
25
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+
from tests.test_utils import TEST_DEVICES, assert_allclose
|
26
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+
|
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+
TESTS = []
|
28
|
+
for device in TEST_DEVICES:
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+
TESTS.append(
|
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+
[
|
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+
{"axcodes": "RAS"},
|
32
|
+
torch.arange(12).reshape((2, 1, 2, 3)),
|
33
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+
torch.eye(4),
|
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+
torch.arange(12).reshape((2, 1, 2, 3)),
|
35
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+
"RAS",
|
36
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+
*device,
|
37
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+
]
|
38
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+
)
|
39
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+
TESTS.append(
|
40
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+
[
|
41
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+
{"axcodes": "ALS"},
|
42
|
+
torch.arange(12).reshape((2, 1, 2, 3)),
|
43
|
+
torch.as_tensor(np.diag([-1, -1, 1, 1])),
|
44
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+
torch.tensor([[[[3, 4, 5]], [[0, 1, 2]]], [[[9, 10, 11]], [[6, 7, 8]]]]),
|
45
|
+
"ALS",
|
46
|
+
*device,
|
47
|
+
]
|
48
|
+
)
|
49
|
+
TESTS.append(
|
50
|
+
[
|
51
|
+
{"axcodes": "RAS"},
|
52
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+
torch.arange(12).reshape((2, 1, 2, 3)),
|
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+
torch.as_tensor(np.diag([-1, -1, 1, 1])),
|
54
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+
torch.tensor([[[[3, 4, 5], [0, 1, 2]]], [[[9, 10, 11], [6, 7, 8]]]]),
|
55
|
+
"RAS",
|
56
|
+
*device,
|
57
|
+
]
|
58
|
+
)
|
59
|
+
TESTS.append(
|
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|
+
[
|
61
|
+
{"axcodes": "AL"},
|
62
|
+
torch.arange(6).reshape((2, 1, 3)),
|
63
|
+
torch.eye(3),
|
64
|
+
torch.tensor([[[0], [1], [2]], [[3], [4], [5]]]),
|
65
|
+
"AL",
|
66
|
+
*device,
|
67
|
+
]
|
68
|
+
)
|
69
|
+
TESTS.append(
|
70
|
+
[
|
71
|
+
{"axcodes": "L"},
|
72
|
+
torch.arange(6).reshape((2, 3)),
|
73
|
+
torch.eye(2),
|
74
|
+
torch.tensor([[2, 1, 0], [5, 4, 3]]),
|
75
|
+
"L",
|
76
|
+
*device,
|
77
|
+
]
|
78
|
+
)
|
79
|
+
TESTS.append(
|
80
|
+
[
|
81
|
+
{"axcodes": "L"},
|
82
|
+
torch.arange(6).reshape((2, 3)),
|
83
|
+
torch.eye(2),
|
84
|
+
torch.tensor([[2, 1, 0], [5, 4, 3]]),
|
85
|
+
"L",
|
86
|
+
*device,
|
87
|
+
]
|
88
|
+
)
|
89
|
+
TESTS.append(
|
90
|
+
[
|
91
|
+
{"axcodes": "L"},
|
92
|
+
torch.arange(6).reshape((2, 3)),
|
93
|
+
torch.as_tensor(np.diag([-1, 1])),
|
94
|
+
torch.arange(6).reshape((2, 3)),
|
95
|
+
"L",
|
96
|
+
*device,
|
97
|
+
]
|
98
|
+
)
|
99
|
+
TESTS.append(
|
100
|
+
[
|
101
|
+
{"axcodes": "LPS"},
|
102
|
+
torch.arange(12).reshape((2, 1, 2, 3)),
|
103
|
+
torch.as_tensor(
|
104
|
+
create_translate(3, (10, 20, 30))
|
105
|
+
@ create_rotate(3, (np.pi / 2, np.pi / 2, np.pi / 4))
|
106
|
+
@ np.diag([-1, 1, 1, 1])
|
107
|
+
),
|
108
|
+
torch.tensor([[[[2, 5]], [[1, 4]], [[0, 3]]], [[[8, 11]], [[7, 10]], [[6, 9]]]]),
|
109
|
+
"LPS",
|
110
|
+
*device,
|
111
|
+
]
|
112
|
+
)
|
113
|
+
TESTS.append(
|
114
|
+
[
|
115
|
+
{"as_closest_canonical": True},
|
116
|
+
torch.arange(12).reshape((2, 1, 2, 3)),
|
117
|
+
torch.as_tensor(
|
118
|
+
create_translate(3, (10, 20, 30))
|
119
|
+
@ create_rotate(3, (np.pi / 2, np.pi / 2, np.pi / 4))
|
120
|
+
@ np.diag([-1, 1, 1, 1])
|
121
|
+
),
|
122
|
+
torch.tensor([[[[0, 3]], [[1, 4]], [[2, 5]]], [[[6, 9]], [[7, 10]], [[8, 11]]]]),
|
123
|
+
"RAS",
|
124
|
+
*device,
|
125
|
+
]
|
126
|
+
)
|
127
|
+
TESTS.append(
|
128
|
+
[
|
129
|
+
{"as_closest_canonical": True},
|
130
|
+
torch.arange(6).reshape((1, 2, 3)),
|
131
|
+
torch.as_tensor(create_translate(2, (10, 20)) @ create_rotate(2, (np.pi / 3)) @ np.diag([-1, -0.2, 1])),
|
132
|
+
torch.tensor([[[3, 0], [4, 1], [5, 2]]]),
|
133
|
+
"RA",
|
134
|
+
*device,
|
135
|
+
]
|
136
|
+
)
|
137
|
+
TESTS.append(
|
138
|
+
[
|
139
|
+
{"axcodes": "LP"},
|
140
|
+
torch.arange(6).reshape((1, 2, 3)),
|
141
|
+
torch.as_tensor(create_translate(2, (10, 20)) @ create_rotate(2, (np.pi / 3)) @ np.diag([-1, -0.2, 1])),
|
142
|
+
torch.tensor([[[2, 5], [1, 4], [0, 3]]]),
|
143
|
+
"LP",
|
144
|
+
*device,
|
145
|
+
]
|
146
|
+
)
|
147
|
+
TESTS.append(
|
148
|
+
[
|
149
|
+
{"axcodes": "LPID", "labels": tuple(zip("LPIC", "RASD"))},
|
150
|
+
torch.zeros((1, 2, 3, 4, 5)),
|
151
|
+
torch.as_tensor(np.diag([-1, -0.2, -1, 1, 1])),
|
152
|
+
torch.zeros((1, 2, 3, 4, 5)),
|
153
|
+
"LPID",
|
154
|
+
*device,
|
155
|
+
]
|
156
|
+
)
|
157
|
+
TESTS.append(
|
158
|
+
[
|
159
|
+
{"as_closest_canonical": True, "labels": tuple(zip("LPIC", "RASD"))},
|
160
|
+
torch.zeros((1, 2, 3, 4, 5)),
|
161
|
+
torch.as_tensor(np.diag([-1, -0.2, -1, 1, 1])),
|
162
|
+
torch.zeros((1, 2, 3, 4, 5)),
|
163
|
+
"RASD",
|
164
|
+
*device,
|
165
|
+
]
|
166
|
+
)
|
167
|
+
|
168
|
+
TESTS_TORCH = []
|
169
|
+
for track_meta in (False, True):
|
170
|
+
for device in TEST_DEVICES:
|
171
|
+
TESTS_TORCH.append([{"axcodes": "LPS"}, torch.zeros((1, 3, 4, 5)), track_meta, *device])
|
172
|
+
|
173
|
+
ILL_CASES = [
|
174
|
+
# too short axcodes
|
175
|
+
[{"axcodes": "RA"}, torch.arange(12).reshape((2, 1, 2, 3)), torch.eye(4)]
|
176
|
+
]
|
177
|
+
|
178
|
+
|
179
|
+
class TestOrientationCase(unittest.TestCase):
|
180
|
+
@parameterized.expand(TESTS)
|
181
|
+
def test_ornt_meta(
|
182
|
+
self,
|
183
|
+
init_param,
|
184
|
+
img: torch.Tensor,
|
185
|
+
affine: torch.Tensor,
|
186
|
+
expected_data: torch.Tensor,
|
187
|
+
expected_code: str,
|
188
|
+
device,
|
189
|
+
):
|
190
|
+
img = MetaTensor(img, affine=affine).to(device)
|
191
|
+
ornt = Orientation(**init_param)
|
192
|
+
call_param = {"data_array": img}
|
193
|
+
res = ornt(**call_param) # type: ignore[arg-type]
|
194
|
+
if img.ndim in (3, 4):
|
195
|
+
test_resampler_lazy(ornt, res, init_param, call_param)
|
196
|
+
|
197
|
+
assert_allclose(res, expected_data.to(device))
|
198
|
+
new_code = nib.orientations.aff2axcodes(res.affine.cpu(), labels=ornt.labels) # type: ignore
|
199
|
+
self.assertEqual("".join(new_code), expected_code)
|
200
|
+
|
201
|
+
@parameterized.expand(TESTS_TORCH)
|
202
|
+
def test_ornt_torch(self, init_param, img: torch.Tensor, track_meta: bool, device):
|
203
|
+
set_track_meta(track_meta)
|
204
|
+
ornt = Orientation(**init_param)
|
205
|
+
|
206
|
+
img = img.to(device)
|
207
|
+
expected_data = img.clone()
|
208
|
+
expected_code = ornt.axcodes
|
209
|
+
|
210
|
+
res = ornt(img)
|
211
|
+
assert_allclose(res, expected_data)
|
212
|
+
if track_meta:
|
213
|
+
self.assertIsInstance(res, MetaTensor)
|
214
|
+
assert isinstance(res, MetaTensor) # for mypy type narrowing
|
215
|
+
new_code = nib.orientations.aff2axcodes(res.affine.cpu(), labels=ornt.labels)
|
216
|
+
self.assertEqual("".join(new_code), expected_code)
|
217
|
+
else:
|
218
|
+
self.assertIsInstance(res, torch.Tensor)
|
219
|
+
self.assertNotIsInstance(res, MetaTensor)
|
220
|
+
|
221
|
+
@parameterized.expand(ILL_CASES)
|
222
|
+
def test_bad_params(self, init_param, img: torch.Tensor, affine: torch.Tensor):
|
223
|
+
img = MetaTensor(img, affine=affine)
|
224
|
+
with self.assertRaises(ValueError):
|
225
|
+
Orientation(**init_param)(img)
|
226
|
+
|
227
|
+
@parameterized.expand(TEST_DEVICES)
|
228
|
+
def test_inverse(self, device):
|
229
|
+
img_t = torch.rand((1, 10, 9, 8), dtype=torch.float32, device=device)
|
230
|
+
affine = torch.tensor(
|
231
|
+
[[0, 0, -1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]], dtype=torch.float32, device="cpu"
|
232
|
+
)
|
233
|
+
meta = {"fname": "somewhere"}
|
234
|
+
img = MetaTensor(img_t, affine=affine, meta=meta)
|
235
|
+
tr = Orientation("LPS")
|
236
|
+
# check that image and affine have changed
|
237
|
+
img = tr(img)
|
238
|
+
self.assertNotEqual(img.shape, img_t.shape)
|
239
|
+
self.assertGreater((affine - img.affine).max(), 0.5)
|
240
|
+
# check that with inverse, image affine are back to how they were
|
241
|
+
img = tr.inverse(img)
|
242
|
+
self.assertEqual(img.shape, img_t.shape)
|
243
|
+
self.assertLess((affine - img.affine).max(), 1e-2)
|
244
|
+
|
245
|
+
|
246
|
+
if __name__ == "__main__":
|
247
|
+
unittest.main()
|