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 +1,52 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ from parameterized import parameterized
18
+
19
+ from monai.transforms import RandShiftIntensity
20
+ from tests.test_utils import TEST_NDARRAYS, NumpyImageTestCase2D, assert_allclose
21
+
22
+
23
+ class TestRandShiftIntensity(NumpyImageTestCase2D):
24
+ @parameterized.expand([[p] for p in TEST_NDARRAYS])
25
+ def test_value(self, p):
26
+ shifter = RandShiftIntensity(offsets=1.0, prob=1.0)
27
+ shifter.set_random_state(seed=0)
28
+ im = p(self.imt)
29
+ result = shifter(im, factor=1.0)
30
+ np.random.seed(0)
31
+ # simulate the randomize() of transform
32
+ np.random.random()
33
+ expected = self.imt + np.random.uniform(low=-1.0, high=1.0)
34
+ assert_allclose(result, expected, type_test="tensor")
35
+
36
+ @parameterized.expand([[p] for p in TEST_NDARRAYS])
37
+ def test_channel_wise(self, p):
38
+ scaler = RandShiftIntensity(offsets=3.0, channel_wise=True, prob=1.0)
39
+ scaler.set_random_state(seed=0)
40
+ im = p(self.imt)
41
+ result = scaler(im)
42
+ np.random.seed(0)
43
+ # simulate the randomize() of transform
44
+ np.random.random()
45
+ channel_num = self.imt.shape[0]
46
+ factor = [np.random.uniform(low=-3.0, high=3.0) for _ in range(channel_num)]
47
+ expected = p(np.stack([np.asarray((self.imt[i]) + factor[i]) for i in range(channel_num)]).astype(np.float32))
48
+ assert_allclose(result, expected, atol=0, rtol=1e-5, type_test=False)
49
+
50
+
51
+ if __name__ == "__main__":
52
+ unittest.main()
@@ -0,0 +1,67 @@
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
+
18
+ from monai.transforms import IntensityStatsd, RandShiftIntensityd
19
+ from monai.utils.enums import PostFix
20
+ from tests.test_utils import TEST_NDARRAYS, NumpyImageTestCase2D, assert_allclose
21
+
22
+
23
+ class TestRandShiftIntensityd(NumpyImageTestCase2D):
24
+ def test_value(self):
25
+ key = "img"
26
+ for p in TEST_NDARRAYS:
27
+ shifter = RandShiftIntensityd(keys=[key], offsets=1.0, prob=1.0)
28
+ shifter.set_random_state(seed=0)
29
+ result = shifter({key: p(self.imt)})
30
+ np.random.seed(0)
31
+ # simulate the randomize() of transform
32
+ np.random.random()
33
+ expected = self.imt + np.random.uniform(low=-1.0, high=1.0)
34
+ assert_allclose(result[key], p(expected), type_test="tensor")
35
+
36
+ def test_factor(self):
37
+ key = "img"
38
+ stats = IntensityStatsd(keys=key, ops="max", key_prefix="orig")
39
+ shifter = RandShiftIntensityd(keys=[key], offsets=1.0, factor_key=["orig_max"], prob=1.0)
40
+ data = {key: self.imt, PostFix.meta(key): {"affine": None}}
41
+ shifter.set_random_state(seed=0)
42
+ result = shifter(stats(data))
43
+ np.random.seed(0)
44
+ # simulate the randomize() of transform
45
+ np.random.random()
46
+ expected = self.imt + np.random.uniform(low=-1.0, high=1.0) * np.nanmax(self.imt)
47
+ np.testing.assert_allclose(result[key], expected)
48
+
49
+ def test_channel_wise(self):
50
+ key = "img"
51
+ for p in TEST_NDARRAYS:
52
+ scaler = RandShiftIntensityd(keys=[key], offsets=3.0, prob=1.0, channel_wise=True)
53
+ scaler.set_random_state(seed=0)
54
+ result = scaler({key: p(self.imt)})
55
+ np.random.seed(0)
56
+ # simulate the randomize function of transform
57
+ np.random.random()
58
+ channel_num = self.imt.shape[0]
59
+ factor = [np.random.uniform(low=-3.0, high=3.0) for _ in range(channel_num)]
60
+ expected = p(
61
+ np.stack([np.asarray((self.imt[i]) + factor[i]) for i in range(channel_num)]).astype(np.float32)
62
+ )
63
+ assert_allclose(result[key], p(expected), type_test="tensor")
64
+
65
+
66
+ if __name__ == "__main__":
67
+ unittest.main()
@@ -0,0 +1,83 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ from parameterized import parameterized
18
+
19
+ from monai.transforms import RandSimulateLowResolution
20
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
21
+
22
+ TESTS = []
23
+ for p in TEST_NDARRAYS:
24
+ TESTS.append(
25
+ [
26
+ dict(prob=1.0, zoom_range=(0.8, 0.81)),
27
+ p(
28
+ np.array(
29
+ [
30
+ [
31
+ [[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11], [12, 13, 14, 15]],
32
+ [[16, 17, 18, 19], [20, 21, 22, 23], [24, 25, 26, 27], [28, 29, 30, 31]],
33
+ [[32, 33, 34, 35], [36, 37, 38, 39], [40, 41, 42, 43], [44, 45, 46, 47]],
34
+ [[48, 49, 50, 51], [52, 53, 54, 55], [56, 57, 58, 59], [60, 61, 62, 63]],
35
+ ]
36
+ ]
37
+ )
38
+ ),
39
+ np.array(
40
+ [
41
+ [
42
+ [
43
+ [0.0000, 0.6250, 1.3750, 2.0000],
44
+ [2.5000, 3.1250, 3.8750, 4.5000],
45
+ [5.5000, 6.1250, 6.8750, 7.5000],
46
+ [8.0000, 8.6250, 9.3750, 10.0000],
47
+ ],
48
+ [
49
+ [10.0000, 10.6250, 11.3750, 12.0000],
50
+ [12.5000, 13.1250, 13.8750, 14.5000],
51
+ [15.5000, 16.1250, 16.8750, 17.5000],
52
+ [18.0000, 18.6250, 19.3750, 20.0000],
53
+ ],
54
+ [
55
+ [22.0000, 22.6250, 23.3750, 24.0000],
56
+ [24.5000, 25.1250, 25.8750, 26.5000],
57
+ [27.5000, 28.1250, 28.8750, 29.5000],
58
+ [30.0000, 30.6250, 31.3750, 32.0000],
59
+ ],
60
+ [
61
+ [32.0000, 32.6250, 33.3750, 34.0000],
62
+ [34.5000, 35.1250, 35.8750, 36.5000],
63
+ [37.5000, 38.1250, 38.8750, 39.5000],
64
+ [40.0000, 40.6250, 41.3750, 42.0000],
65
+ ],
66
+ ]
67
+ ]
68
+ ),
69
+ ]
70
+ )
71
+
72
+
73
+ class TestRandGaussianSmooth(unittest.TestCase):
74
+ @parameterized.expand(TESTS)
75
+ def test_value(self, arguments, image, expected_data):
76
+ randsimlowres = RandSimulateLowResolution(**arguments)
77
+ randsimlowres.set_random_state(seed=0)
78
+ result = randsimlowres(image)
79
+ assert_allclose(result, expected_data, rtol=1e-4, type_test="tensor")
80
+
81
+
82
+ if __name__ == "__main__":
83
+ unittest.main()
@@ -0,0 +1,73 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ from parameterized import parameterized
18
+
19
+ from monai.transforms import RandSimulateLowResolutiond
20
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
21
+
22
+ TESTS = []
23
+ for p in TEST_NDARRAYS:
24
+ TESTS.append(
25
+ [
26
+ dict(keys=["img", "seg"], prob=1.0, zoom_range=(0.8, 0.81)),
27
+ {"img": p(np.arange(64).reshape(1, 4, 4, 4)), "seg": p(np.arange(64).reshape(1, 4, 4, 4))},
28
+ np.array(
29
+ [
30
+ [
31
+ [
32
+ [0.0000, 0.6250, 1.3750, 2.0000],
33
+ [2.5000, 3.1250, 3.8750, 4.5000],
34
+ [5.5000, 6.1250, 6.8750, 7.5000],
35
+ [8.0000, 8.6250, 9.3750, 10.0000],
36
+ ],
37
+ [
38
+ [10.0000, 10.6250, 11.3750, 12.0000],
39
+ [12.5000, 13.1250, 13.8750, 14.5000],
40
+ [15.5000, 16.1250, 16.8750, 17.5000],
41
+ [18.0000, 18.6250, 19.3750, 20.0000],
42
+ ],
43
+ [
44
+ [22.0000, 22.6250, 23.3750, 24.0000],
45
+ [24.5000, 25.1250, 25.8750, 26.5000],
46
+ [27.5000, 28.1250, 28.8750, 29.5000],
47
+ [30.0000, 30.6250, 31.3750, 32.0000],
48
+ ],
49
+ [
50
+ [32.0000, 32.6250, 33.3750, 34.0000],
51
+ [34.5000, 35.1250, 35.8750, 36.5000],
52
+ [37.5000, 38.1250, 38.8750, 39.5000],
53
+ [40.0000, 40.6250, 41.3750, 42.0000],
54
+ ],
55
+ ]
56
+ ]
57
+ ),
58
+ ]
59
+ )
60
+
61
+
62
+ class TestRandGaussianSmoothd(unittest.TestCase):
63
+ @parameterized.expand(TESTS)
64
+ def test_value(self, arguments, image, expected_data):
65
+ converter = RandSimulateLowResolutiond(**arguments)
66
+ converter.set_random_state(seed=0)
67
+ result = converter(image)
68
+ assert_allclose(result["img"], expected_data, rtol=1e-4, type_test=False)
69
+ assert_allclose(result["seg"], expected_data, rtol=1e-4, type_test=False)
70
+
71
+
72
+ if __name__ == "__main__":
73
+ unittest.main()
@@ -0,0 +1,107 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ from parameterized import parameterized
18
+
19
+ from monai.data.meta_tensor import MetaTensor
20
+ from monai.transforms import RandScaleCrop, RandSpatialCrop
21
+ from monai.transforms.lazy.functional import apply_pending
22
+ from tests.croppers import CropTest
23
+ from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
24
+
25
+ TEST_SHAPES = [
26
+ [{"roi_size": [3, 3, -1], "random_center": True}, (3, 3, 3, 4), (3, 3, 3, 4)],
27
+ [{"roi_size": [3, 3, 3], "random_center": True}, (3, 3, 3, 3), (3, 3, 3, 3)],
28
+ [{"roi_size": [3, 3, 3], "random_center": False}, (3, 3, 3, 3), (3, 3, 3, 3)],
29
+ [{"roi_size": [3, 3, 2], "random_center": False, "random_size": False}, (3, 3, 3, 3), (3, 3, 3, 2)],
30
+ ]
31
+
32
+ TEST_VALUES = [
33
+ [
34
+ {"roi_size": [3, 3], "random_center": False},
35
+ np.array([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 1, 2, 1, 0], [0, 0, 0, 0, 0]]]),
36
+ ]
37
+ ]
38
+
39
+ TEST_RANDOM_SHAPES = [
40
+ [
41
+ {"roi_size": [3, 3, 3], "max_roi_size": [5, -1, 4], "random_center": True, "random_size": True},
42
+ (1, 4, 5, 6),
43
+ (1, 4, 4, 3),
44
+ ],
45
+ [{"roi_size": 3, "max_roi_size": 4, "random_center": True, "random_size": True}, (1, 4, 5, 6), (1, 3, 4, 3)],
46
+ ]
47
+
48
+ func1 = {RandSpatialCrop: {"roi_size": [8, 7, -1], "random_center": True, "random_size": False}}
49
+ func2 = {RandScaleCrop: {"roi_scale": [0.5, 0.6, -1.0], "random_center": True, "random_size": True}}
50
+ func3 = {RandScaleCrop: {"roi_scale": [1.0, 0.5, -1.0], "random_center": False, "random_size": False}}
51
+
52
+ TESTS_COMBINE = []
53
+ TESTS_COMBINE.append([[func1, func2, func3], (3, 10, 10, 8)])
54
+ TESTS_COMBINE.append([[func1, func2], (3, 8, 8, 4)])
55
+ TESTS_COMBINE.append([[func2, func2], (3, 8, 8, 4)])
56
+
57
+
58
+ class TestRandSpatialCrop(CropTest):
59
+ Cropper = RandSpatialCrop
60
+
61
+ @parameterized.expand(TEST_SHAPES)
62
+ def test_shape(self, input_param, input_shape, expected_shape):
63
+ self.crop_test(input_param, input_shape, expected_shape)
64
+
65
+ @parameterized.expand(TEST_VALUES)
66
+ def test_value(self, input_param, input_data):
67
+ for im_type in TEST_NDARRAYS_ALL:
68
+ with self.subTest(im_type=im_type):
69
+ cropper = RandSpatialCrop(**input_param)
70
+ result = cropper(im_type(input_data))
71
+ roi = [(2 - i // 2, 2 + i - i // 2) for i in cropper._size]
72
+ assert_allclose(result, input_data[:, roi[0][0] : roi[0][1], roi[1][0] : roi[1][1]], type_test="tensor")
73
+
74
+ @parameterized.expand(TEST_RANDOM_SHAPES)
75
+ def test_random_shape(self, input_param, input_shape, expected_shape):
76
+ for im_type in TEST_NDARRAYS_ALL:
77
+ with self.subTest(im_type=im_type):
78
+ cropper = RandSpatialCrop(**input_param)
79
+ cropper.set_random_state(seed=123)
80
+ input_data = im_type(np.random.randint(0, 2, input_shape))
81
+ expected = cropper(input_data)
82
+ self.assertTupleEqual(expected.shape, expected_shape)
83
+
84
+ # lazy
85
+ # reset random seed to ensure the same results
86
+ cropper.set_random_state(seed=123)
87
+ cropper.lazy = True
88
+ pending_result = cropper(input_data)
89
+ self.assertIsInstance(pending_result, MetaTensor)
90
+ assert_allclose(pending_result.peek_pending_affine(), expected.affine)
91
+ assert_allclose(pending_result.peek_pending_shape(), expected.shape[1:])
92
+ # only support nearest
93
+ result = apply_pending(pending_result, overrides={"mode": "nearest", "align_corners": False})[0]
94
+ # compare
95
+ assert_allclose(result, expected, rtol=1e-5)
96
+
97
+ @parameterized.expand(TEST_SHAPES)
98
+ def test_pending_ops(self, input_param, input_shape, _):
99
+ self.crop_test_pending_ops(input_param, input_shape)
100
+
101
+ @parameterized.expand(TESTS_COMBINE)
102
+ def test_combine_ops(self, funcs, input_shape):
103
+ self.crop_test_combine_ops(funcs, input_shape)
104
+
105
+
106
+ if __name__ == "__main__":
107
+ unittest.main()
@@ -0,0 +1,128 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ from parameterized import parameterized
18
+
19
+ from monai.data.meta_tensor import MetaTensor
20
+ from monai.transforms import RandSpatialCropSamples
21
+ from monai.transforms.lazy.functional import apply_pending
22
+ from tests.croppers import CropTest
23
+ from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
24
+
25
+ TEST_CASE_1 = [
26
+ {"roi_size": [3, 3, 3], "num_samples": 4, "random_center": True, "random_size": False},
27
+ (3, 4, 4, 4),
28
+ [(3, 3, 3, 3), (3, 3, 3, 3), (3, 3, 3, 3), (3, 3, 3, 3)],
29
+ np.array(
30
+ [
31
+ [
32
+ [[21, 22, 23], [25, 26, 27], [29, 30, 31]],
33
+ [[37, 38, 39], [41, 42, 43], [45, 46, 47]],
34
+ [[53, 54, 55], [57, 58, 59], [61, 62, 63]],
35
+ ],
36
+ [
37
+ [[85, 86, 87], [89, 90, 91], [93, 94, 95]],
38
+ [[101, 102, 103], [105, 106, 107], [109, 110, 111]],
39
+ [[117, 118, 119], [121, 122, 123], [125, 126, 127]],
40
+ ],
41
+ [
42
+ [[149, 150, 151], [153, 154, 155], [157, 158, 159]],
43
+ [[165, 166, 167], [169, 170, 171], [173, 174, 175]],
44
+ [[181, 182, 183], [185, 186, 187], [189, 190, 191]],
45
+ ],
46
+ ]
47
+ ),
48
+ ]
49
+
50
+ TEST_CASE_2 = [
51
+ {"roi_size": [3, 3, 3], "num_samples": 8, "random_center": False, "random_size": True},
52
+ (3, 4, 4, 4),
53
+ [(3, 4, 4, 3), (3, 4, 3, 3), (3, 3, 4, 4), (3, 4, 4, 4), (3, 3, 3, 4), (3, 3, 3, 3), (3, 3, 3, 3), (3, 3, 3, 3)],
54
+ np.array(
55
+ [
56
+ [
57
+ [[21, 22, 23], [25, 26, 27], [29, 30, 31]],
58
+ [[37, 38, 39], [41, 42, 43], [45, 46, 47]],
59
+ [[53, 54, 55], [57, 58, 59], [61, 62, 63]],
60
+ ],
61
+ [
62
+ [[85, 86, 87], [89, 90, 91], [93, 94, 95]],
63
+ [[101, 102, 103], [105, 106, 107], [109, 110, 111]],
64
+ [[117, 118, 119], [121, 122, 123], [125, 126, 127]],
65
+ ],
66
+ [
67
+ [[149, 150, 151], [153, 154, 155], [157, 158, 159]],
68
+ [[165, 166, 167], [169, 170, 171], [173, 174, 175]],
69
+ [[181, 182, 183], [185, 186, 187], [189, 190, 191]],
70
+ ],
71
+ ]
72
+ ),
73
+ ]
74
+
75
+ TEST_INVERSE_LIST = [
76
+ [(1, 2, 2), {"roi_size": (1, 1), "num_samples": 4, "random_size": False}],
77
+ [(1, 3, 2), {"roi_size": (1, 1), "num_samples": 100, "random_size": False}],
78
+ [(3, 10, 11, 12), {"roi_size": (3, 5, 4), "num_samples": 7, "random_size": False}],
79
+ [(3, 10, 11, 12), {"roi_size": (10, 11, 12), "num_samples": 3, "random_size": False}],
80
+ [(3, 10, 11, 12), {"roi_size": (3, 4, 5), "num_samples": 100, "random_size": False}],
81
+ ]
82
+
83
+
84
+ class TestRandSpatialCropSamples(CropTest):
85
+ Cropper = RandSpatialCropSamples
86
+
87
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
88
+ def test_shape(self, input_param, input_shape, expected_shape, expected_last_item):
89
+ input_data = np.arange(192).reshape(*input_shape)
90
+
91
+ for p in TEST_NDARRAYS_ALL:
92
+ xform = RandSpatialCropSamples(**input_param)
93
+ xform.set_random_state(1234)
94
+ result = xform(p(input_data))
95
+
96
+ np.testing.assert_equal(len(result), input_param["num_samples"])
97
+ for i, (item, expected) in enumerate(zip(result, expected_shape)):
98
+ self.assertTupleEqual(item.shape, expected)
99
+ self.assertEqual(item.meta["patch_index"], i)
100
+ assert_allclose(result[-1], expected_last_item, type_test="tensor")
101
+
102
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
103
+ def test_pending_ops(self, input_param, input_shape, _expected_shape, _expected_last_item):
104
+ input_data = np.arange(192).reshape(*input_shape)
105
+
106
+ for p in TEST_NDARRAYS_ALL:
107
+ xform = RandSpatialCropSamples(**input_param)
108
+ image = p(input_data)
109
+ # non-lazy
110
+ xform.set_random_state(1234)
111
+ expected = xform(image)
112
+ self.assertIsInstance(expected[0], MetaTensor)
113
+ # lazy
114
+ xform.set_random_state(1234)
115
+ xform.lazy = True
116
+ pending_result = xform(image)
117
+ for i, _pending_result in enumerate(pending_result):
118
+ self.assertIsInstance(_pending_result, MetaTensor)
119
+ assert_allclose(_pending_result.peek_pending_affine(), expected[i].affine)
120
+ assert_allclose(_pending_result.peek_pending_shape(), expected[i].shape[1:])
121
+ # only support nearest
122
+ result = apply_pending(_pending_result, overrides={"mode": "nearest", "align_corners": False})[0]
123
+ # compare
124
+ assert_allclose(result, expected[i], rtol=1e-5)
125
+
126
+
127
+ if __name__ == "__main__":
128
+ unittest.main()
@@ -0,0 +1,147 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ from parameterized import parameterized
18
+
19
+ from monai.data.meta_tensor import MetaTensor
20
+ from monai.transforms import Compose, DivisiblePadd, RandSpatialCropSamplesd
21
+ from monai.transforms.lazy.functional import apply_pending
22
+ from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
23
+
24
+ TEST_CASE_1 = [
25
+ {"keys": ["img", "seg"], "num_samples": 4, "roi_size": [2, 2, 2], "random_center": True, "random_size": True},
26
+ {"img": np.arange(81).reshape(3, 3, 3, 3), "seg": np.arange(81, 0, -1).reshape(3, 3, 3, 3)},
27
+ [(3, 2, 2, 2), (3, 2, 3, 3), (3, 2, 3, 2), (3, 2, 3, 2)],
28
+ {
29
+ "img": np.array(
30
+ [
31
+ [[[1, 2], [4, 5], [7, 8]], [[10, 11], [13, 14], [16, 17]]],
32
+ [[[28, 29], [31, 32], [34, 35]], [[37, 38], [40, 41], [43, 44]]],
33
+ [[[55, 56], [58, 59], [61, 62]], [[64, 65], [67, 68], [70, 71]]],
34
+ ]
35
+ ),
36
+ "seg": np.array(
37
+ [
38
+ [[[80, 79], [77, 76], [74, 73]], [[71, 70], [68, 67], [65, 64]]],
39
+ [[[53, 52], [50, 49], [47, 46]], [[44, 43], [41, 40], [38, 37]]],
40
+ [[[26, 25], [23, 22], [20, 19]], [[17, 16], [14, 13], [11, 10]]],
41
+ ]
42
+ ),
43
+ },
44
+ ]
45
+
46
+ TEST_CASE_2 = []
47
+ for p in TEST_NDARRAYS_ALL:
48
+ TEST_CASE_2.append(
49
+ [
50
+ {
51
+ "keys": ["img", "seg"],
52
+ "num_samples": 8,
53
+ "roi_size": [2, 2, 3],
54
+ "random_center": False,
55
+ "random_size": True,
56
+ },
57
+ {"img": p(np.arange(81).reshape(3, 3, 3, 3)), "seg": p(np.arange(81, 0, -1).reshape(3, 3, 3, 3))},
58
+ [
59
+ (3, 2, 2, 3),
60
+ (3, 2, 2, 3),
61
+ (3, 3, 3, 3),
62
+ (3, 2, 3, 3),
63
+ (3, 3, 3, 3),
64
+ (3, 2, 3, 3),
65
+ (3, 2, 3, 3),
66
+ (3, 3, 2, 3),
67
+ ],
68
+ {
69
+ "img": p(
70
+ np.array(
71
+ [
72
+ [[[0, 1, 2], [3, 4, 5]], [[9, 10, 11], [12, 13, 14]], [[18, 19, 20], [21, 22, 23]]],
73
+ [[[27, 28, 29], [30, 31, 32]], [[36, 37, 38], [39, 40, 41]], [[45, 46, 47], [48, 49, 50]]],
74
+ [[[54, 55, 56], [57, 58, 59]], [[63, 64, 65], [66, 67, 68]], [[72, 73, 74], [75, 76, 77]]],
75
+ ]
76
+ )
77
+ ),
78
+ "seg": p(
79
+ np.array(
80
+ [
81
+ [[[81, 80, 79], [78, 77, 76]], [[72, 71, 70], [69, 68, 67]], [[63, 62, 61], [60, 59, 58]]],
82
+ [[[54, 53, 52], [51, 50, 49]], [[45, 44, 43], [42, 41, 40]], [[36, 35, 34], [33, 32, 31]]],
83
+ [[[27, 26, 25], [24, 23, 22]], [[18, 17, 16], [15, 14, 13]], [[9, 8, 7], [6, 5, 4]]],
84
+ ]
85
+ )
86
+ ),
87
+ },
88
+ ]
89
+ )
90
+
91
+
92
+ class TestRandSpatialCropSamplesd(unittest.TestCase):
93
+ @parameterized.expand([TEST_CASE_1, *TEST_CASE_2])
94
+ def test_shape(self, input_param, input_data, expected_shape, expected_last):
95
+ xform = RandSpatialCropSamplesd(**input_param)
96
+ xform.set_random_state(1234)
97
+ result = xform(input_data)
98
+ _len = len(tuple(input_data.keys()))
99
+ self.assertTupleEqual(tuple(result[0].keys())[:_len], tuple(input_data.keys()))
100
+ for item, expected in zip(result, expected_shape):
101
+ self.assertTupleEqual(item["img"].shape, expected)
102
+ self.assertTupleEqual(item["seg"].shape, expected)
103
+ for i, item in enumerate(result):
104
+ self.assertEqual(item["img"].meta["patch_index"], i)
105
+ self.assertEqual(item["seg"].meta["patch_index"], i)
106
+ assert_allclose(item["img"], expected_last["img"], type_test=False)
107
+ assert_allclose(item["seg"], expected_last["seg"], type_test=False)
108
+
109
+ def test_deep_copy(self):
110
+ data = {"img": np.ones((1, 10, 11, 12))}
111
+ num_samples = 3
112
+ sampler = RandSpatialCropSamplesd(
113
+ keys=["img"], roi_size=(3, 3, 3), num_samples=num_samples, random_center=True, random_size=False
114
+ )
115
+ transform = Compose([DivisiblePadd(keys="img", k=5), sampler])
116
+ samples = transform(data)
117
+ self.assertEqual(len(samples), num_samples)
118
+ for sample in samples:
119
+ self.assertEqual(len(sample["img"].applied_operations), len(transform))
120
+
121
+ @parameterized.expand([TEST_CASE_1, *TEST_CASE_2])
122
+ def test_pending_ops(self, input_param, input_data, _expected_shape, _expected_last):
123
+ xform = RandSpatialCropSamplesd(**input_param)
124
+ # non-lazy
125
+ xform.set_random_state(1234)
126
+ expected = xform(input_data)
127
+ self.assertIsInstance(expected[0]["img"], MetaTensor)
128
+
129
+ # lazy
130
+ xform.set_random_state(1234)
131
+ xform.lazy = True
132
+ pending_result = xform(input_data)
133
+ for i, _pending_result in enumerate(pending_result):
134
+ self.assertIsInstance(_pending_result["img"], MetaTensor)
135
+ assert_allclose(_pending_result["img"].peek_pending_affine(), expected[i]["img"].affine)
136
+ assert_allclose(_pending_result["img"].peek_pending_shape(), expected[i]["img"].shape[1:])
137
+ # only support nearest
138
+ overrides = {"mode": "nearest", "align_corners": False}
139
+ result_img = apply_pending(_pending_result["img"], overrides=overrides)[0]
140
+ result_seg = apply_pending(_pending_result["seg"], overrides=overrides)[0]
141
+ # compare
142
+ assert_allclose(result_img, expected[i]["img"], rtol=1e-5)
143
+ assert_allclose(result_seg, expected[i]["seg"], rtol=1e-5)
144
+
145
+
146
+ if __name__ == "__main__":
147
+ unittest.main()