monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2508__py3-none-any.whl

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Files changed (787) hide show
  1. monai/__init__.py +1 -1
  2. monai/_version.py +3 -3
  3. monai/apps/auto3dseg/transforms.py +1 -4
  4. monai/data/utils.py +6 -13
  5. monai/handlers/__init__.py +1 -0
  6. monai/handlers/average_precision.py +53 -0
  7. monai/inferers/inferer.py +10 -7
  8. monai/inferers/utils.py +1 -2
  9. monai/losses/dice.py +2 -14
  10. monai/losses/ds_loss.py +1 -3
  11. monai/metrics/__init__.py +1 -0
  12. monai/metrics/average_precision.py +187 -0
  13. monai/networks/layers/simplelayers.py +2 -14
  14. monai/networks/utils.py +4 -16
  15. monai/transforms/compose.py +28 -11
  16. monai/transforms/croppad/array.py +1 -6
  17. monai/transforms/io/array.py +0 -1
  18. monai/transforms/transform.py +15 -6
  19. monai/transforms/utility/array.py +2 -12
  20. monai/transforms/utils.py +1 -2
  21. monai/transforms/utils_pytorch_numpy_unification.py +2 -4
  22. monai/utils/enums.py +3 -2
  23. monai/utils/module.py +6 -6
  24. monai/utils/tf32.py +0 -10
  25. monai/visualize/class_activation_maps.py +5 -8
  26. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/METADATA +21 -17
  27. monai_weekly-1.5.dev2508.dist-info/RECORD +1185 -0
  28. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/top_level.txt +1 -0
  29. tests/apps/__init__.py +10 -0
  30. tests/apps/deepedit/__init__.py +10 -0
  31. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  32. tests/apps/deepgrow/__init__.py +10 -0
  33. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  34. tests/apps/deepgrow/transforms/__init__.py +10 -0
  35. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  36. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  37. tests/apps/detection/__init__.py +10 -0
  38. tests/apps/detection/metrics/__init__.py +10 -0
  39. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  40. tests/apps/detection/networks/__init__.py +10 -0
  41. tests/apps/detection/networks/test_retinanet.py +210 -0
  42. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  43. tests/apps/detection/test_box_transform.py +370 -0
  44. tests/apps/detection/utils/__init__.py +10 -0
  45. tests/apps/detection/utils/test_anchor_box.py +88 -0
  46. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  47. tests/apps/detection/utils/test_box_coder.py +43 -0
  48. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  49. tests/apps/detection/utils/test_detector_utils.py +96 -0
  50. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  51. tests/apps/nuclick/__init__.py +10 -0
  52. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  53. tests/apps/pathology/__init__.py +10 -0
  54. tests/apps/pathology/handlers/__init__.py +10 -0
  55. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  56. tests/apps/pathology/test_lesion_froc.py +333 -0
  57. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  58. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  59. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  60. tests/apps/pathology/transforms/__init__.py +10 -0
  61. tests/apps/pathology/transforms/post/__init__.py +10 -0
  62. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  63. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  64. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  65. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  66. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  67. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  68. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  69. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  70. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  71. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  72. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  73. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  74. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  75. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  76. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  77. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  78. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  79. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  80. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  81. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  82. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  83. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  84. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  85. tests/apps/reconstruction/__init__.py +10 -0
  86. tests/apps/reconstruction/nets/__init__.py +10 -0
  87. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  88. tests/apps/reconstruction/test_complex_utils.py +77 -0
  89. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  90. tests/apps/reconstruction/test_mri_utils.py +37 -0
  91. tests/apps/reconstruction/transforms/__init__.py +10 -0
  92. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  93. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  94. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  95. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  96. tests/apps/test_check_hash.py +53 -0
  97. tests/apps/test_cross_validation.py +74 -0
  98. tests/apps/test_decathlondataset.py +93 -0
  99. tests/apps/test_download_and_extract.py +70 -0
  100. tests/apps/test_download_url_yandex.py +45 -0
  101. tests/apps/test_mednistdataset.py +72 -0
  102. tests/apps/test_mmar_download.py +154 -0
  103. tests/apps/test_tciadataset.py +123 -0
  104. tests/apps/vista3d/__init__.py +10 -0
  105. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  106. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  107. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  108. tests/bundle/__init__.py +10 -0
  109. tests/bundle/test_bundle_ckpt_export.py +107 -0
  110. tests/bundle/test_bundle_download.py +435 -0
  111. tests/bundle/test_bundle_get_data.py +94 -0
  112. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  113. tests/bundle/test_bundle_trt_export.py +147 -0
  114. tests/bundle/test_bundle_utils.py +149 -0
  115. tests/bundle/test_bundle_verify_metadata.py +66 -0
  116. tests/bundle/test_bundle_verify_net.py +76 -0
  117. tests/bundle/test_bundle_workflow.py +272 -0
  118. tests/bundle/test_component_locator.py +38 -0
  119. tests/bundle/test_config_item.py +138 -0
  120. tests/bundle/test_config_parser.py +392 -0
  121. tests/bundle/test_reference_resolver.py +114 -0
  122. tests/config/__init__.py +10 -0
  123. tests/config/test_cv2_dist.py +53 -0
  124. tests/engines/__init__.py +10 -0
  125. tests/engines/test_ensemble_evaluator.py +94 -0
  126. tests/engines/test_prepare_batch_default.py +76 -0
  127. tests/engines/test_prepare_batch_default_dist.py +76 -0
  128. tests/engines/test_prepare_batch_diffusion.py +104 -0
  129. tests/engines/test_prepare_batch_extra_input.py +80 -0
  130. tests/fl/__init__.py +10 -0
  131. tests/fl/monai_algo/__init__.py +10 -0
  132. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  133. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  134. tests/fl/test_fl_monai_algo_stats.py +81 -0
  135. tests/fl/utils/__init__.py +10 -0
  136. tests/fl/utils/test_fl_exchange_object.py +63 -0
  137. tests/handlers/__init__.py +10 -0
  138. tests/handlers/test_handler_average_precision.py +79 -0
  139. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  140. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  141. tests/handlers/test_handler_classification_saver.py +64 -0
  142. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  143. tests/handlers/test_handler_clearml_image.py +65 -0
  144. tests/handlers/test_handler_clearml_stats.py +65 -0
  145. tests/handlers/test_handler_confusion_matrix.py +104 -0
  146. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  147. tests/handlers/test_handler_decollate_batch.py +66 -0
  148. tests/handlers/test_handler_early_stop.py +68 -0
  149. tests/handlers/test_handler_garbage_collector.py +73 -0
  150. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  151. tests/handlers/test_handler_ignite_metric.py +191 -0
  152. tests/handlers/test_handler_lr_scheduler.py +94 -0
  153. tests/handlers/test_handler_mean_dice.py +98 -0
  154. tests/handlers/test_handler_mean_iou.py +76 -0
  155. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  156. tests/handlers/test_handler_metrics_saver.py +89 -0
  157. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  158. tests/handlers/test_handler_mlflow.py +296 -0
  159. tests/handlers/test_handler_nvtx.py +93 -0
  160. tests/handlers/test_handler_panoptic_quality.py +89 -0
  161. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  162. tests/handlers/test_handler_post_processing.py +74 -0
  163. tests/handlers/test_handler_prob_map_producer.py +111 -0
  164. tests/handlers/test_handler_regression_metrics.py +160 -0
  165. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  166. tests/handlers/test_handler_rocauc.py +48 -0
  167. tests/handlers/test_handler_rocauc_dist.py +54 -0
  168. tests/handlers/test_handler_stats.py +281 -0
  169. tests/handlers/test_handler_surface_distance.py +113 -0
  170. tests/handlers/test_handler_tb_image.py +61 -0
  171. tests/handlers/test_handler_tb_stats.py +166 -0
  172. tests/handlers/test_handler_validation.py +59 -0
  173. tests/handlers/test_trt_compile.py +145 -0
  174. tests/handlers/test_write_metrics_reports.py +68 -0
  175. tests/inferers/__init__.py +10 -0
  176. tests/inferers/test_avg_merger.py +179 -0
  177. tests/inferers/test_controlnet_inferers.py +1388 -0
  178. tests/inferers/test_diffusion_inferer.py +236 -0
  179. tests/inferers/test_latent_diffusion_inferer.py +884 -0
  180. tests/inferers/test_patch_inferer.py +309 -0
  181. tests/inferers/test_saliency_inferer.py +55 -0
  182. tests/inferers/test_slice_inferer.py +57 -0
  183. tests/inferers/test_sliding_window_inference.py +377 -0
  184. tests/inferers/test_sliding_window_splitter.py +284 -0
  185. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  186. tests/inferers/test_zarr_avg_merger.py +326 -0
  187. tests/integration/__init__.py +10 -0
  188. tests/integration/test_auto3dseg_ensemble.py +211 -0
  189. tests/integration/test_auto3dseg_hpo.py +189 -0
  190. tests/integration/test_deepedit_interaction.py +122 -0
  191. tests/integration/test_downsample_block.py +50 -0
  192. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  193. tests/integration/test_integration_autorunner.py +201 -0
  194. tests/integration/test_integration_bundle_run.py +240 -0
  195. tests/integration/test_integration_classification_2d.py +282 -0
  196. tests/integration/test_integration_determinism.py +95 -0
  197. tests/integration/test_integration_fast_train.py +231 -0
  198. tests/integration/test_integration_gpu_customization.py +159 -0
  199. tests/integration/test_integration_lazy_samples.py +219 -0
  200. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  201. tests/integration/test_integration_segmentation_3d.py +304 -0
  202. tests/integration/test_integration_sliding_window.py +100 -0
  203. tests/integration/test_integration_stn.py +133 -0
  204. tests/integration/test_integration_unet_2d.py +67 -0
  205. tests/integration/test_integration_workers.py +61 -0
  206. tests/integration/test_integration_workflows.py +365 -0
  207. tests/integration/test_integration_workflows_adversarial.py +173 -0
  208. tests/integration/test_integration_workflows_gan.py +158 -0
  209. tests/integration/test_loader_semaphore.py +48 -0
  210. tests/integration/test_mapping_filed.py +122 -0
  211. tests/integration/test_meta_affine.py +183 -0
  212. tests/integration/test_metatensor_integration.py +114 -0
  213. tests/integration/test_module_list.py +76 -0
  214. tests/integration/test_one_of.py +283 -0
  215. tests/integration/test_pad_collation.py +124 -0
  216. tests/integration/test_reg_loss_integration.py +107 -0
  217. tests/integration/test_retinanet_predict_utils.py +154 -0
  218. tests/integration/test_seg_loss_integration.py +159 -0
  219. tests/integration/test_spatial_combine_transforms.py +185 -0
  220. tests/integration/test_testtimeaugmentation.py +186 -0
  221. tests/integration/test_vis_gradbased.py +69 -0
  222. tests/integration/test_vista3d_utils.py +159 -0
  223. tests/losses/__init__.py +10 -0
  224. tests/losses/deform/__init__.py +10 -0
  225. tests/losses/deform/test_bending_energy.py +88 -0
  226. tests/losses/deform/test_diffusion_loss.py +117 -0
  227. tests/losses/image_dissimilarity/__init__.py +10 -0
  228. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  229. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  230. tests/losses/test_adversarial_loss.py +94 -0
  231. tests/losses/test_barlow_twins_loss.py +109 -0
  232. tests/losses/test_cldice_loss.py +51 -0
  233. tests/losses/test_contrastive_loss.py +86 -0
  234. tests/losses/test_dice_ce_loss.py +123 -0
  235. tests/losses/test_dice_focal_loss.py +124 -0
  236. tests/losses/test_dice_loss.py +227 -0
  237. tests/losses/test_ds_loss.py +189 -0
  238. tests/losses/test_focal_loss.py +379 -0
  239. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  240. tests/losses/test_generalized_dice_loss.py +221 -0
  241. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  242. tests/losses/test_giou_loss.py +62 -0
  243. tests/losses/test_hausdorff_loss.py +264 -0
  244. tests/losses/test_masked_dice_loss.py +152 -0
  245. tests/losses/test_masked_loss.py +87 -0
  246. tests/losses/test_multi_scale.py +86 -0
  247. tests/losses/test_nacl_loss.py +167 -0
  248. tests/losses/test_perceptual_loss.py +122 -0
  249. tests/losses/test_spectral_loss.py +86 -0
  250. tests/losses/test_ssim_loss.py +59 -0
  251. tests/losses/test_sure_loss.py +72 -0
  252. tests/losses/test_tversky_loss.py +198 -0
  253. tests/losses/test_unified_focal_loss.py +66 -0
  254. tests/metrics/__init__.py +10 -0
  255. tests/metrics/test_compute_average_precision.py +162 -0
  256. tests/metrics/test_compute_confusion_matrix.py +294 -0
  257. tests/metrics/test_compute_f_beta.py +80 -0
  258. tests/metrics/test_compute_fid_metric.py +40 -0
  259. tests/metrics/test_compute_froc.py +143 -0
  260. tests/metrics/test_compute_generalized_dice.py +240 -0
  261. tests/metrics/test_compute_meandice.py +306 -0
  262. tests/metrics/test_compute_meaniou.py +223 -0
  263. tests/metrics/test_compute_mmd_metric.py +56 -0
  264. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  265. tests/metrics/test_compute_panoptic_quality.py +113 -0
  266. tests/metrics/test_compute_regression_metrics.py +196 -0
  267. tests/metrics/test_compute_roc_auc.py +155 -0
  268. tests/metrics/test_compute_variance.py +147 -0
  269. tests/metrics/test_cumulative.py +63 -0
  270. tests/metrics/test_cumulative_average.py +74 -0
  271. tests/metrics/test_cumulative_average_dist.py +48 -0
  272. tests/metrics/test_hausdorff_distance.py +209 -0
  273. tests/metrics/test_label_quality_score.py +134 -0
  274. tests/metrics/test_loss_metric.py +57 -0
  275. tests/metrics/test_metrics_reloaded.py +96 -0
  276. tests/metrics/test_ssim_metric.py +78 -0
  277. tests/metrics/test_surface_dice.py +416 -0
  278. tests/metrics/test_surface_distance.py +186 -0
  279. tests/networks/__init__.py +10 -0
  280. tests/networks/blocks/__init__.py +10 -0
  281. tests/networks/blocks/dints_block/__init__.py +10 -0
  282. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  283. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  284. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  285. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  286. tests/networks/blocks/test_adn.py +86 -0
  287. tests/networks/blocks/test_convolutions.py +156 -0
  288. tests/networks/blocks/test_crf_cpu.py +513 -0
  289. tests/networks/blocks/test_crf_cuda.py +528 -0
  290. tests/networks/blocks/test_crossattention.py +185 -0
  291. tests/networks/blocks/test_denseblock.py +105 -0
  292. tests/networks/blocks/test_dynunet_block.py +116 -0
  293. tests/networks/blocks/test_fpn_block.py +88 -0
  294. tests/networks/blocks/test_localnet_block.py +121 -0
  295. tests/networks/blocks/test_mlp.py +78 -0
  296. tests/networks/blocks/test_patchembedding.py +212 -0
  297. tests/networks/blocks/test_regunet_block.py +103 -0
  298. tests/networks/blocks/test_se_block.py +85 -0
  299. tests/networks/blocks/test_se_blocks.py +78 -0
  300. tests/networks/blocks/test_segresnet_block.py +57 -0
  301. tests/networks/blocks/test_selfattention.py +232 -0
  302. tests/networks/blocks/test_simple_aspp.py +87 -0
  303. tests/networks/blocks/test_spatialattention.py +55 -0
  304. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  305. tests/networks/blocks/test_text_encoding.py +49 -0
  306. tests/networks/blocks/test_transformerblock.py +90 -0
  307. tests/networks/blocks/test_unetr_block.py +158 -0
  308. tests/networks/blocks/test_upsample_block.py +134 -0
  309. tests/networks/blocks/warp/__init__.py +10 -0
  310. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  311. tests/networks/blocks/warp/test_warp.py +250 -0
  312. tests/networks/layers/__init__.py +10 -0
  313. tests/networks/layers/filtering/__init__.py +10 -0
  314. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  315. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  316. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  317. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  318. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  319. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  320. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  321. tests/networks/layers/test_affine_transform.py +385 -0
  322. tests/networks/layers/test_apply_filter.py +89 -0
  323. tests/networks/layers/test_channel_pad.py +51 -0
  324. tests/networks/layers/test_conjugate_gradient.py +56 -0
  325. tests/networks/layers/test_drop_path.py +46 -0
  326. tests/networks/layers/test_gaussian.py +317 -0
  327. tests/networks/layers/test_gaussian_filter.py +206 -0
  328. tests/networks/layers/test_get_layers.py +65 -0
  329. tests/networks/layers/test_gmm.py +314 -0
  330. tests/networks/layers/test_grid_pull.py +93 -0
  331. tests/networks/layers/test_hilbert_transform.py +131 -0
  332. tests/networks/layers/test_lltm.py +62 -0
  333. tests/networks/layers/test_median_filter.py +52 -0
  334. tests/networks/layers/test_polyval.py +55 -0
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  681. tests/transforms/test_sobel_gradientd.py +212 -0
  682. tests/transforms/test_spacing.py +381 -0
  683. tests/transforms/test_spacingd.py +178 -0
  684. tests/transforms/test_spatial_crop.py +82 -0
  685. tests/transforms/test_spatial_cropd.py +74 -0
  686. tests/transforms/test_spatial_pad.py +57 -0
  687. tests/transforms/test_spatial_padd.py +43 -0
  688. tests/transforms/test_spatial_resample.py +235 -0
  689. tests/transforms/test_squeezedim.py +62 -0
  690. tests/transforms/test_squeezedimd.py +98 -0
  691. tests/transforms/test_std_shift_intensity.py +76 -0
  692. tests/transforms/test_std_shift_intensityd.py +74 -0
  693. tests/transforms/test_threshold_intensity.py +38 -0
  694. tests/transforms/test_threshold_intensityd.py +58 -0
  695. tests/transforms/test_to_contiguous.py +47 -0
  696. tests/transforms/test_to_cupy.py +112 -0
  697. tests/transforms/test_to_cupyd.py +76 -0
  698. tests/transforms/test_to_device.py +42 -0
  699. tests/transforms/test_to_deviced.py +37 -0
  700. tests/transforms/test_to_numpy.py +85 -0
  701. tests/transforms/test_to_numpyd.py +68 -0
  702. tests/transforms/test_to_pil.py +52 -0
  703. tests/transforms/test_to_pild.py +50 -0
  704. tests/transforms/test_to_tensor.py +60 -0
  705. tests/transforms/test_to_tensord.py +71 -0
  706. tests/transforms/test_torchvision.py +66 -0
  707. tests/transforms/test_torchvisiond.py +63 -0
  708. tests/transforms/test_transform.py +62 -0
  709. tests/transforms/test_transpose.py +41 -0
  710. tests/transforms/test_transposed.py +52 -0
  711. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  712. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  713. tests/transforms/test_vote_ensemble.py +84 -0
  714. tests/transforms/test_vote_ensembled.py +107 -0
  715. tests/transforms/test_with_allow_missing_keys.py +76 -0
  716. tests/transforms/test_zoom.py +120 -0
  717. tests/transforms/test_zoomd.py +94 -0
  718. tests/transforms/transform/__init__.py +10 -0
  719. tests/transforms/transform/test_randomizable.py +52 -0
  720. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  721. tests/transforms/utility/__init__.py +10 -0
  722. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  723. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  724. tests/transforms/utility/test_identity.py +29 -0
  725. tests/transforms/utility/test_identityd.py +30 -0
  726. tests/transforms/utility/test_lambda.py +71 -0
  727. tests/transforms/utility/test_lambdad.py +83 -0
  728. tests/transforms/utility/test_rand_lambda.py +87 -0
  729. tests/transforms/utility/test_rand_lambdad.py +77 -0
  730. tests/transforms/utility/test_simulatedelay.py +36 -0
  731. tests/transforms/utility/test_simulatedelayd.py +36 -0
  732. tests/transforms/utility/test_splitdim.py +52 -0
  733. tests/transforms/utility/test_splitdimd.py +96 -0
  734. tests/transforms/utils/__init__.py +10 -0
  735. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  736. tests/transforms/utils/test_get_unique_labels.py +45 -0
  737. tests/transforms/utils/test_print_transform_backends.py +29 -0
  738. tests/transforms/utils/test_soft_clip.py +125 -0
  739. tests/utils/__init__.py +10 -0
  740. tests/utils/enums/__init__.py +10 -0
  741. tests/utils/enums/test_hovernet_loss.py +190 -0
  742. tests/utils/enums/test_ordering.py +289 -0
  743. tests/utils/enums/test_wsireader.py +663 -0
  744. tests/utils/misc/__init__.py +10 -0
  745. tests/utils/misc/test_ensure_tuple.py +53 -0
  746. tests/utils/misc/test_monai_env_vars.py +44 -0
  747. tests/utils/misc/test_monai_utils_misc.py +103 -0
  748. tests/utils/misc/test_str2bool.py +34 -0
  749. tests/utils/misc/test_str2list.py +33 -0
  750. tests/utils/test_alias.py +44 -0
  751. tests/utils/test_component_store.py +73 -0
  752. tests/utils/test_deprecated.py +455 -0
  753. tests/utils/test_enum_bound_interp.py +75 -0
  754. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  755. tests/utils/test_get_package_version.py +34 -0
  756. tests/utils/test_handler_logfile.py +84 -0
  757. tests/utils/test_handler_metric_logger.py +62 -0
  758. tests/utils/test_list_to_dict.py +43 -0
  759. tests/utils/test_look_up_option.py +87 -0
  760. tests/utils/test_optional_import.py +80 -0
  761. tests/utils/test_pad_mode.py +39 -0
  762. tests/utils/test_profiling.py +208 -0
  763. tests/utils/test_rankfilter_dist.py +77 -0
  764. tests/utils/test_require_pkg.py +83 -0
  765. tests/utils/test_sample_slices.py +43 -0
  766. tests/utils/test_set_determinism.py +74 -0
  767. tests/utils/test_squeeze_unsqueeze.py +71 -0
  768. tests/utils/test_state_cacher.py +67 -0
  769. tests/utils/test_torchscript_utils.py +113 -0
  770. tests/utils/test_version.py +91 -0
  771. tests/utils/test_version_after.py +65 -0
  772. tests/utils/type_conversion/__init__.py +10 -0
  773. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  774. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  775. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  776. tests/visualize/__init__.py +10 -0
  777. tests/visualize/test_img2tensorboard.py +46 -0
  778. tests/visualize/test_occlusion_sensitivity.py +128 -0
  779. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  780. tests/visualize/test_vis_cam.py +98 -0
  781. tests/visualize/test_vis_gradcam.py +211 -0
  782. tests/visualize/utils/__init__.py +10 -0
  783. tests/visualize/utils/test_blend_images.py +63 -0
  784. tests/visualize/utils/test_matshow3d.py +133 -0
  785. monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
  786. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/LICENSE +0 -0
  787. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/WHEEL +0 -0
@@ -0,0 +1,221 @@
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 logging
15
+ import os
16
+ import sys
17
+ import tempfile
18
+ import unittest
19
+ from io import StringIO
20
+ from unittest.mock import patch
21
+
22
+ import numpy as np
23
+ import torch
24
+ from parameterized import parameterized
25
+
26
+ from monai.data.meta_tensor import MetaTensor
27
+ from monai.transforms import DataStats
28
+
29
+ TEST_CASE_1 = [
30
+ {
31
+ "prefix": "test data",
32
+ "data_type": False,
33
+ "data_shape": False,
34
+ "value_range": False,
35
+ "data_value": False,
36
+ "additional_info": None,
37
+ "name": "DataStats",
38
+ },
39
+ np.array([[0, 1], [1, 2]]),
40
+ "test data statistics:",
41
+ ]
42
+
43
+ TEST_CASE_2 = [
44
+ {
45
+ "prefix": "test data",
46
+ "data_type": True,
47
+ "data_shape": False,
48
+ "value_range": False,
49
+ "data_value": False,
50
+ "additional_info": None,
51
+ "name": "DataStats",
52
+ },
53
+ np.array([[0, 1], [1, 2]]),
54
+ "test data statistics:\nType: <class 'numpy.ndarray'>",
55
+ ]
56
+
57
+ TEST_CASE_3 = [
58
+ {
59
+ "prefix": "test data",
60
+ "data_type": True,
61
+ "data_shape": True,
62
+ "value_range": False,
63
+ "data_value": False,
64
+ "additional_info": None,
65
+ "name": "DataStats",
66
+ },
67
+ np.array([[0, 1], [1, 2]]),
68
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)",
69
+ ]
70
+
71
+ TEST_CASE_4 = [
72
+ {
73
+ "prefix": "test data",
74
+ "data_type": True,
75
+ "data_shape": True,
76
+ "value_range": True,
77
+ "data_value": False,
78
+ "additional_info": None,
79
+ "name": "DataStats",
80
+ },
81
+ np.array([[0, 1], [1, 2]]),
82
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\nValue range: (0, 2)",
83
+ ]
84
+
85
+ TEST_CASE_5 = [
86
+ {
87
+ "prefix": "test data",
88
+ "data_type": True,
89
+ "data_shape": True,
90
+ "value_range": True,
91
+ "data_value": True,
92
+ "additional_info": None,
93
+ "name": "DataStats",
94
+ },
95
+ np.array([[0, 1], [1, 2]]),
96
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\nValue range: (0, 2)\nValue: [[0 1]\n [1 2]]",
97
+ ]
98
+
99
+ TEST_CASE_6 = [
100
+ {
101
+ "prefix": "test data",
102
+ "data_type": True,
103
+ "data_shape": True,
104
+ "value_range": True,
105
+ "data_value": True,
106
+ "additional_info": np.mean,
107
+ "name": "DataStats",
108
+ },
109
+ np.array([[0, 1], [1, 2]]),
110
+ (
111
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\n"
112
+ "Value range: (0, 2)\nValue: [[0 1]\n [1 2]]\nAdditional info: 1.0"
113
+ ),
114
+ ]
115
+
116
+ TEST_CASE_7 = [
117
+ {
118
+ "prefix": "test data",
119
+ "data_type": True,
120
+ "data_shape": True,
121
+ "value_range": True,
122
+ "data_value": True,
123
+ "additional_info": lambda x: torch.mean(x.float()),
124
+ "name": "DataStats",
125
+ },
126
+ torch.tensor([[0, 1], [1, 2]]).to("cuda" if torch.cuda.is_available() else "cpu"),
127
+ (
128
+ "test data statistics:\nType: <class 'torch.Tensor'>\nShape: torch.Size([2, 2])\nValue range: (0, 2)\n"
129
+ "Value: tensor([[0, 1],\n [1, 2]])\nAdditional info: 1.0"
130
+ ),
131
+ ]
132
+
133
+ TEST_CASE_8 = [
134
+ {
135
+ "prefix": "test data",
136
+ "data_type": True,
137
+ "data_shape": True,
138
+ "value_range": True,
139
+ "data_value": True,
140
+ "additional_info": np.mean,
141
+ "name": "DataStats",
142
+ },
143
+ np.array([[0, 1], [1, 2]]),
144
+ "test data statistics:\nType: <class 'numpy.ndarray'> int64\nShape: (2, 2)\nValue range: (0, 2)\n"
145
+ "Value: [[0 1]\n [1 2]]\nAdditional info: 1.0\n",
146
+ ]
147
+
148
+ TEST_CASE_9 = [
149
+ np.array([[0, 1], [1, 2]]),
150
+ "test data statistics:\nType: <class 'numpy.ndarray'> int64\nShape: (2, 2)\nValue range: (0, 2)\n"
151
+ "Value: [[0 1]\n [1 2]]\n"
152
+ "Meta info: '(input is not a MetaTensor)'\n"
153
+ "Additional info: 1.0\n",
154
+ ]
155
+
156
+ TEST_CASE_10 = [
157
+ MetaTensor(
158
+ torch.tensor([[0, 1], [1, 2]]),
159
+ affine=torch.as_tensor([[2, 0, 0, 0], [0, 2, 0, 0], [0, 0, 2, 0], [0, 0, 0, 1]], dtype=torch.float64),
160
+ meta={"some": "info"},
161
+ ),
162
+ "test data statistics:\nType: <class 'monai.data.meta_tensor.MetaTensor'> torch.int64\n"
163
+ "Shape: torch.Size([2, 2])\nValue range: (0, 2)\n"
164
+ "Value: tensor([[0, 1],\n [1, 2]])\n"
165
+ "Meta info: {'some': 'info', affine: tensor([[2., 0., 0., 0.],\n"
166
+ " [0., 2., 0., 0.],\n"
167
+ " [0., 0., 2., 0.],\n"
168
+ " [0., 0., 0., 1.]], dtype=torch.float64), space: RAS}\n"
169
+ "Additional info: 1.0\n",
170
+ ]
171
+
172
+
173
+ class TestDataStats(unittest.TestCase):
174
+
175
+ @parameterized.expand(
176
+ [TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4, TEST_CASE_5, TEST_CASE_6, TEST_CASE_7, TEST_CASE_8]
177
+ )
178
+ def test_value(self, input_param, input_data, expected_print):
179
+ transform = DataStats(**input_param)
180
+ _ = transform(input_data)
181
+
182
+ @parameterized.expand([TEST_CASE_9, TEST_CASE_10])
183
+ def test_file(self, input_data, expected_print):
184
+ with tempfile.TemporaryDirectory() as tempdir:
185
+ filename = os.path.join(tempdir, "test_data_stats.log")
186
+ handler = logging.FileHandler(filename, mode="w")
187
+ handler.setLevel(logging.INFO)
188
+ name = "DataStats"
189
+ logger = logging.getLogger(name)
190
+ logger.addHandler(handler)
191
+ input_param = {
192
+ "prefix": "test data",
193
+ "data_type": True,
194
+ "data_shape": True,
195
+ "value_range": True,
196
+ "data_value": True,
197
+ "meta_info": True,
198
+ "additional_info": np.mean,
199
+ "name": name,
200
+ }
201
+ transform = DataStats(**input_param)
202
+ _ = transform(input_data)
203
+ for h in logger.handlers[:]:
204
+ h.close()
205
+ logger.removeHandler(h)
206
+ with open(filename) as f:
207
+ content = f.read()
208
+ if sys.platform != "win32":
209
+ self.assertEqual(content, expected_print)
210
+
211
+ def test_multiple_data_stats(self):
212
+ with patch("sys.stdout", new=StringIO()) as out:
213
+ input_data = np.array([[0, 1], [1, 2]])
214
+ transform = DataStats()
215
+ _ = DataStats()
216
+ _ = transform(input_data)
217
+ print(out.getvalue().strip())
218
+
219
+
220
+ if __name__ == "__main__":
221
+ unittest.main()
@@ -0,0 +1,249 @@
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 logging
15
+ import os
16
+ import sys
17
+ import tempfile
18
+ import unittest
19
+
20
+ import numpy as np
21
+ import torch
22
+ from parameterized import parameterized
23
+
24
+ from monai.data.meta_tensor import MetaTensor
25
+ from monai.transforms import DataStatsd
26
+
27
+ TEST_CASE_1 = [
28
+ {
29
+ "keys": "img",
30
+ "prefix": "test data",
31
+ "data_type": False,
32
+ "data_shape": False,
33
+ "value_range": False,
34
+ "data_value": False,
35
+ "additional_info": None,
36
+ "name": "DataStats",
37
+ },
38
+ {"img": np.array([[0, 1], [1, 2]])},
39
+ "test data statistics:",
40
+ ]
41
+
42
+ TEST_CASE_2 = [
43
+ {
44
+ "keys": "img",
45
+ "prefix": "test data",
46
+ "data_type": True,
47
+ "data_shape": False,
48
+ "value_range": False,
49
+ "data_value": False,
50
+ "additional_info": None,
51
+ "name": "DataStats",
52
+ },
53
+ {"img": np.array([[0, 1], [1, 2]])},
54
+ "test data statistics:\nType: <class 'numpy.ndarray'>",
55
+ ]
56
+
57
+ TEST_CASE_3 = [
58
+ {
59
+ "keys": "img",
60
+ "prefix": "test data",
61
+ "data_type": True,
62
+ "data_shape": True,
63
+ "value_range": False,
64
+ "data_value": False,
65
+ "additional_info": None,
66
+ "name": "DataStats",
67
+ },
68
+ {"img": np.array([[0, 1], [1, 2]])},
69
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)",
70
+ ]
71
+
72
+ TEST_CASE_4 = [
73
+ {
74
+ "keys": "img",
75
+ "prefix": "test data",
76
+ "data_type": True,
77
+ "data_shape": True,
78
+ "value_range": True,
79
+ "data_value": False,
80
+ "additional_info": None,
81
+ "name": "DataStats",
82
+ },
83
+ {"img": np.array([[0, 1], [1, 2]])},
84
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\nValue range: (0, 2)",
85
+ ]
86
+
87
+ TEST_CASE_5 = [
88
+ {
89
+ "keys": "img",
90
+ "prefix": "test data",
91
+ "data_type": True,
92
+ "data_shape": True,
93
+ "value_range": True,
94
+ "data_value": True,
95
+ "additional_info": None,
96
+ "name": "DataStats",
97
+ },
98
+ {"img": np.array([[0, 1], [1, 2]])},
99
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\nValue range: (0, 2)\nValue: [[0 1]\n [1 2]]",
100
+ ]
101
+
102
+ TEST_CASE_6 = [
103
+ {
104
+ "keys": "img",
105
+ "prefix": "test data",
106
+ "data_type": True,
107
+ "data_shape": True,
108
+ "value_range": True,
109
+ "data_value": True,
110
+ "additional_info": np.mean,
111
+ "name": "DataStats",
112
+ },
113
+ {"img": np.array([[0, 1], [1, 2]])},
114
+ (
115
+ "test data statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\n"
116
+ "Value range: (0, 2)\nValue: [[0 1]\n [1 2]]\nAdditional info: 1.0"
117
+ ),
118
+ ]
119
+
120
+ TEST_CASE_7 = [
121
+ {
122
+ "keys": "img",
123
+ "prefix": "test data",
124
+ "data_type": True,
125
+ "data_shape": True,
126
+ "value_range": True,
127
+ "data_value": True,
128
+ "additional_info": lambda x: torch.mean(x.float()),
129
+ "name": "DataStats",
130
+ },
131
+ {"img": torch.tensor([[0, 1], [1, 2]]).to("cuda" if torch.cuda.is_available() else "cpu")},
132
+ (
133
+ "test data statistics:\nType: <class 'torch.Tensor'>\nShape: torch.Size([2, 2])\nValue range: (0, 2)\n"
134
+ "Value: tensor([[0, 1],\n [1, 2]])\nAdditional info: 1.0"
135
+ ),
136
+ ]
137
+
138
+ TEST_CASE_8 = [
139
+ {
140
+ "keys": ("img", "affine"),
141
+ "prefix": ("image", "affine"),
142
+ "data_type": True,
143
+ "data_shape": True,
144
+ "value_range": (True, False),
145
+ "data_value": (False, True),
146
+ "additional_info": (np.mean, None),
147
+ "name": "DataStats",
148
+ },
149
+ {"img": np.array([[0, 1], [1, 2]]), "affine": np.eye(2, 2)},
150
+ "affine statistics:\nType: <class 'numpy.ndarray'>\nShape: (2, 2)\nValue: [[1. 0.]\n [0. 1.]]",
151
+ ]
152
+
153
+ TEST_CASE_9 = [
154
+ {
155
+ "keys": "img",
156
+ "prefix": "test data",
157
+ "data_shape": True,
158
+ "value_range": True,
159
+ "data_value": True,
160
+ "meta_info": False,
161
+ "additional_info": np.mean,
162
+ "name": "DataStats",
163
+ },
164
+ {"img": np.array([[0, 1], [1, 2]])},
165
+ "test data statistics:\nType: <class 'numpy.ndarray'> int64\nShape: (2, 2)\nValue range: (0, 2)\n"
166
+ "Value: [[0 1]\n [1 2]]\nAdditional info: 1.0\n",
167
+ ]
168
+
169
+ TEST_CASE_10 = [
170
+ {"img": np.array([[0, 1], [1, 2]])},
171
+ "test data statistics:\nType: <class 'numpy.ndarray'> int64\nShape: (2, 2)\nValue range: (0, 2)\n"
172
+ "Value: [[0 1]\n [1 2]]\n"
173
+ "Meta info: '(input is not a MetaTensor)'\n"
174
+ "Additional info: 1.0\n",
175
+ ]
176
+
177
+ TEST_CASE_11 = [
178
+ {
179
+ "img": (
180
+ MetaTensor(
181
+ torch.tensor([[0, 1], [1, 2]]),
182
+ affine=torch.as_tensor([[2, 0, 0, 0], [0, 2, 0, 0], [0, 0, 2, 0], [0, 0, 0, 1]], dtype=torch.float64),
183
+ meta={"some": "info"},
184
+ )
185
+ )
186
+ },
187
+ "test data statistics:\nType: <class 'monai.data.meta_tensor.MetaTensor'> torch.int64\n"
188
+ "Shape: torch.Size([2, 2])\nValue range: (0, 2)\n"
189
+ "Value: tensor([[0, 1],\n [1, 2]])\n"
190
+ "Meta info: {'some': 'info', affine: tensor([[2., 0., 0., 0.],\n"
191
+ " [0., 2., 0., 0.],\n"
192
+ " [0., 0., 2., 0.],\n"
193
+ " [0., 0., 0., 1.]], dtype=torch.float64), space: RAS}\n"
194
+ "Additional info: 1.0\n",
195
+ ]
196
+
197
+
198
+ class TestDataStatsd(unittest.TestCase):
199
+
200
+ @parameterized.expand(
201
+ [
202
+ TEST_CASE_1,
203
+ TEST_CASE_2,
204
+ TEST_CASE_3,
205
+ TEST_CASE_4,
206
+ TEST_CASE_5,
207
+ TEST_CASE_6,
208
+ TEST_CASE_7,
209
+ TEST_CASE_8,
210
+ TEST_CASE_9,
211
+ ]
212
+ )
213
+ def test_value(self, input_param, input_data, expected_print):
214
+ transform = DataStatsd(**input_param)
215
+ _ = transform(input_data)
216
+
217
+ @parameterized.expand([TEST_CASE_10, TEST_CASE_11])
218
+ def test_file(self, input_data, expected_print):
219
+ with tempfile.TemporaryDirectory() as tempdir:
220
+ filename = os.path.join(tempdir, "test_stats.log")
221
+ handler = logging.FileHandler(filename, mode="w")
222
+ handler.setLevel(logging.INFO)
223
+ name = "DataStats"
224
+ logger = logging.getLogger(name)
225
+ logger.addHandler(handler)
226
+ input_param = {
227
+ "keys": "img",
228
+ "prefix": "test data",
229
+ "data_shape": True,
230
+ "value_range": True,
231
+ "data_value": True,
232
+ "meta_info": True,
233
+ "additional_info": np.mean,
234
+ "name": name,
235
+ }
236
+ transform = DataStatsd(**input_param)
237
+ _ = transform(input_data)
238
+ for h in logger.handlers[:]:
239
+ h.close()
240
+ logger.removeHandler(h)
241
+ del handler
242
+ with open(filename) as f:
243
+ content = f.read()
244
+ if sys.platform != "win32":
245
+ self.assertEqual(content, expected_print)
246
+
247
+
248
+ if __name__ == "__main__":
249
+ unittest.main()
@@ -0,0 +1,58 @@
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 sys
15
+ import time
16
+ import unittest
17
+
18
+ from parameterized import parameterized
19
+
20
+ from monai.transforms import DeleteItemsd
21
+ from monai.utils.enums import PostFix
22
+
23
+ TEST_CASE_1 = [{"keys": [str(i) for i in range(30)]}, 20]
24
+
25
+ TEST_CASE_2 = [{"keys": ["image/" + str(i) for i in range(30)], "sep": "/"}, 20]
26
+
27
+ TEST_CASE_3 = [{"keys": "meta_dict%0008\\|[0-9]", "sep": "%", "use_re": True}]
28
+
29
+
30
+ class TestDeleteItemsd(unittest.TestCase):
31
+
32
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
33
+ def test_memory(self, input_param, expected_key_size):
34
+ input_data = {"image": {}} if "sep" in input_param else {}
35
+ for i in range(50):
36
+ if "sep" in input_param:
37
+ input_data["image"][str(i)] = [time.time()] * 100000
38
+ else:
39
+ input_data[str(i)] = [time.time()] * 100000
40
+ result = DeleteItemsd(**input_param)(input_data)
41
+ if "sep" in input_param:
42
+ self.assertEqual(len(result["image"].keys()), expected_key_size)
43
+ else:
44
+ self.assertEqual(len(result.keys()), expected_key_size)
45
+ self.assertGreaterEqual(
46
+ sys.getsizeof(input_data) * float(expected_key_size) / len(input_data), sys.getsizeof(result)
47
+ )
48
+
49
+ @parameterized.expand([TEST_CASE_3])
50
+ def test_re(self, input_param):
51
+ input_data = {"image": [1, 2, 3], PostFix.meta(): {"0008|0005": 1, "0008|1050": 2, "0008test": 3}}
52
+ result = DeleteItemsd(**input_param)(input_data)
53
+ self.assertEqual(result[PostFix.meta()]["0008test"], 3)
54
+ self.assertEqual(len(result[PostFix.meta()]), 1)
55
+
56
+
57
+ if __name__ == "__main__":
58
+ unittest.main()
@@ -0,0 +1,159 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ import torch
18
+ from parameterized import parameterized
19
+
20
+ from monai.transforms import DetectEnvelope
21
+ from monai.utils import OptionalImportError
22
+ from tests.test_utils import TEST_NDARRAYS, SkipIfModule, SkipIfNoModule, assert_allclose
23
+
24
+ n_samples = 500
25
+ hann_windowed_sine = np.sin(2 * np.pi * 10 * np.linspace(0, 1, n_samples)) * np.hanning(n_samples)
26
+
27
+ # SINGLE-CHANNEL VALUE TESTS
28
+ # using np.expand_dims() to add length 1 channel dimension at dimension 0
29
+
30
+ TEST_CASE_1D_SINE = [
31
+ {}, # args (empty, so use default)
32
+ np.expand_dims(hann_windowed_sine, 0), # Input data: Hann windowed sine wave
33
+ np.expand_dims(np.hanning(n_samples), 0), # Expected output: the Hann window
34
+ 1e-4, # absolute tolerance
35
+ ]
36
+
37
+ TEST_CASE_2D_SINE = [
38
+ {}, # args (empty, so use default (i.e. process along first spatial dimension, axis=1)
39
+ # Create 10 identical windowed sine waves as a 2D numpy array
40
+ np.expand_dims(np.stack([hann_windowed_sine] * 10, axis=1), 0),
41
+ # Expected output: Set of 10 identical Hann windows
42
+ np.expand_dims(np.stack([np.hanning(n_samples)] * 10, axis=1), 0),
43
+ 1e-4, # absolute tolerance
44
+ ]
45
+
46
+ TEST_CASE_3D_SINE = [
47
+ {}, # args (empty, so use default (i.e. process along first spatial dimension, axis=1)
48
+ # Create 100 identical windowed sine waves as a (n_samples x 10 x 10) 3D numpy array
49
+ np.expand_dims(np.stack([np.stack([hann_windowed_sine] * 10, axis=1)] * 10, axis=2), 0),
50
+ # Expected output: Set of 100 identical Hann windows in (n_samples x 10 x 10) 3D numpy array
51
+ np.expand_dims(np.stack([np.stack([np.hanning(n_samples)] * 10, axis=1)] * 10, axis=2), 0),
52
+ 1e-4, # absolute tolerance
53
+ ]
54
+
55
+ TEST_CASE_2D_SINE_AXIS_1 = [
56
+ {"axis": 2}, # set axis argument to 1
57
+ # Create 10 identical windowed sine waves as a 2D numpy array
58
+ np.expand_dims(np.stack([hann_windowed_sine] * 10, axis=1), 0),
59
+ # Expected output: absolute value of each sample of the waveform, repeated (i.e. flat envelopes)
60
+ np.expand_dims(np.abs(np.repeat(hann_windowed_sine, 10).reshape((n_samples, 10))), 0),
61
+ 1e-4, # absolute tolerance
62
+ ]
63
+
64
+ TEST_CASE_1D_SINE_PADDING_N = [
65
+ {"n": 512}, # args (empty, so use default)
66
+ np.expand_dims(hann_windowed_sine, 0), # Input data: Hann windowed sine wave
67
+ np.expand_dims(np.concatenate([np.hanning(500), np.zeros(12)]), 0), # Expected output: the Hann window
68
+ 1e-3, # absolute tolerance
69
+ ]
70
+
71
+ # MULTI-CHANNEL VALUE TEST
72
+
73
+ TEST_CASE_2_CHAN_3D_SINE = [
74
+ {}, # args (empty, so use default (i.e. process along first spatial dimension, axis=1)
75
+ # Create 100 identical windowed sine waves as a (n_samples x 10 x 10) 3D numpy array, twice (2 channels)
76
+ torch.as_tensor(np.stack([np.stack([np.stack([hann_windowed_sine] * 10, axis=1)] * 10, axis=2)] * 2, axis=0)),
77
+ # Expected output: Set of 100 identical Hann windows in (n_samples x 10 x 10) 3D numpy array, twice (2 channels)
78
+ torch.as_tensor(np.stack([np.stack([np.stack([np.hanning(n_samples)] * 10, axis=1)] * 10, axis=2)] * 2, axis=0)),
79
+ 1e-4, # absolute tolerance
80
+ ]
81
+
82
+ # EXCEPTION TESTS
83
+
84
+ TEST_CASE_INVALID_AXIS_1 = [
85
+ {"axis": 3}, # set axis argument to 3 when only 3 dimensions (1 channel + 2 spatial)
86
+ np.expand_dims(np.stack([hann_windowed_sine] * 10, axis=1), 0), # Create 2D dataset
87
+ "__call__", # method expected to raise exception
88
+ ]
89
+
90
+ TEST_CASE_INVALID_AXIS_2 = [
91
+ {"axis": -1}, # set axis argument negative
92
+ np.expand_dims(np.stack([hann_windowed_sine] * 10, axis=1), 0), # Create 2D dataset
93
+ "__init__", # method expected to raise exception
94
+ ]
95
+
96
+ TEST_CASE_INVALID_N = [
97
+ {"n": 0}, # set FFT length to zero
98
+ np.expand_dims(np.stack([hann_windowed_sine] * 10, axis=1), 0), # Create 2D dataset
99
+ "__call__", # method expected to raise exception
100
+ ]
101
+
102
+ TEST_CASE_INVALID_DTYPE = [
103
+ {},
104
+ np.expand_dims(np.array(hann_windowed_sine, dtype=complex), 0), # complex numbers are invalid
105
+ "__call__", # method expected to raise exception
106
+ ]
107
+
108
+ TEST_CASE_INVALID_IMG_LEN = [
109
+ {},
110
+ np.expand_dims(np.array([]), 0), # empty array is invalid
111
+ "__call__", # method expected to raise exception
112
+ ]
113
+
114
+ TEST_CASE_INVALID_OBJ = [{}, "a string", "__call__"] # method expected to raise exception
115
+
116
+
117
+ @SkipIfNoModule("torch.fft")
118
+ class TestDetectEnvelope(unittest.TestCase):
119
+ @parameterized.expand(
120
+ [
121
+ TEST_CASE_1D_SINE,
122
+ TEST_CASE_2D_SINE,
123
+ TEST_CASE_3D_SINE,
124
+ TEST_CASE_2D_SINE_AXIS_1,
125
+ TEST_CASE_1D_SINE_PADDING_N,
126
+ TEST_CASE_2_CHAN_3D_SINE,
127
+ ]
128
+ )
129
+ def test_value(self, arguments, image, expected_data, atol):
130
+ for p in TEST_NDARRAYS:
131
+ result = DetectEnvelope(**arguments)(p(image))
132
+ assert_allclose(result, p(expected_data), atol=atol, type_test="tensor")
133
+
134
+ @parameterized.expand(
135
+ [
136
+ TEST_CASE_INVALID_AXIS_1,
137
+ TEST_CASE_INVALID_AXIS_2,
138
+ TEST_CASE_INVALID_N,
139
+ TEST_CASE_INVALID_DTYPE,
140
+ TEST_CASE_INVALID_IMG_LEN,
141
+ ]
142
+ )
143
+ def test_value_error(self, arguments, image, method):
144
+ if method == "__init__":
145
+ self.assertRaises(ValueError, DetectEnvelope, **arguments)
146
+ elif method == "__call__":
147
+ self.assertRaises(ValueError, DetectEnvelope(**arguments), image)
148
+ else:
149
+ self.fail("Expected raising method invalid. Should be __init__ or __call__.")
150
+
151
+
152
+ @SkipIfModule("torch.fft")
153
+ class TestHilbertTransformNoFFTMod(unittest.TestCase):
154
+ def test_no_fft_module_error(self):
155
+ self.assertRaises(OptionalImportError, DetectEnvelope(), np.random.rand(1, 10))
156
+
157
+
158
+ if __name__ == "__main__":
159
+ unittest.main()