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 +1,377 @@
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 itertools
15
+ import unittest
16
+
17
+ import numpy as np
18
+ import torch
19
+ from parameterized import parameterized
20
+
21
+ from monai.data.utils import list_data_collate
22
+ from monai.inferers import SlidingWindowInferer, SlidingWindowInfererAdapt, sliding_window_inference
23
+ from monai.utils import optional_import
24
+ from tests.test_utils import TEST_TORCH_AND_META_TENSORS, skip_if_no_cuda, test_is_quick
25
+
26
+ _, has_tqdm = optional_import("tqdm")
27
+
28
+ TEST_CASES = [
29
+ [(2, 3, 16), (4,), 3, 0.25, "constant", torch.device("cpu:0")], # 1D small roi
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+ [(2, 3, 16, 15, 7, 9), 4, 3, 0.25, "constant", torch.device("cpu:0")], # 4D small roi
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+ [(1, 3, 16, 15, 7), (4, -1, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
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+ [(2, 3, 16, 15, 7), (4, -1, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
33
+ [(3, 3, 16, 15, 7), (4, -1, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
34
+ [(2, 3, 16, 15, 7), (4, -1, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
35
+ [(1, 3, 16, 15, 7), (4, 10, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
36
+ [(1, 3, 16, 15, 7), (20, 22, 23), 10, 0.25, "constant", torch.device("cpu:0")], # 3D large roi
37
+ [(2, 3, 15, 7), (2, 6), 1000, 0.25, "constant", torch.device("cpu:0")], # 2D small roi, large batch
38
+ [(1, 3, 16, 7), (80, 50), 7, 0.25, "constant", torch.device("cpu:0")], # 2D large roi
39
+ [(1, 3, 16, 15, 7), (20, 22, 23), 10, 0.5, "constant", torch.device("cpu:0")], # 3D large overlap
40
+ [(1, 3, 16, 7), (80, 50), 7, 0.5, "gaussian", torch.device("cpu:0")], # 2D large overlap, gaussian
41
+ [(1, 3, 16, 15, 7), (4, 10, 7), 3, 0.25, "gaussian", torch.device("cpu:0")], # 3D small roi, gaussian
42
+ [(3, 3, 16, 15, 7), (4, 10, 7), 3, 0.25, "gaussian", torch.device("cpu:0")], # 3D small roi, gaussian
43
+ [(1, 3, 16, 15, 7), (4, 10, 7), 3, 0.25, "gaussian", torch.device("cuda:0")], # test inference on gpu if availabe
44
+ [(1, 3, 16, 15, 7), (4, 1, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
45
+ [(5, 3, 16, 15, 7), (4, 1, 7), 3, 0.25, "constant", torch.device("cpu:0")], # 3D small roi
46
+ ]
47
+
48
+ _devices = [["cpu", "cuda:0"]] if torch.cuda.is_available() else [["cpu"]]
49
+ _windows = [
50
+ [(2, 3, 10, 11), (7, 10), 0.8, 5],
51
+ [(2, 3, 10, 11), (15, 12), 0, 2],
52
+ [(2, 3, 10, 11), (10, 11), 0, 3],
53
+ [(2, 3, 511, 237), (96, 80), 0.4, 5],
54
+ [(2, 3, 512, 245), (96, 80), 0, 5],
55
+ [(2, 3, 512, 245), (512, 80), 0.125, 5],
56
+ [(2, 3, 10, 11, 12), (7, 8, 10), 0.2, 2],
57
+ ]
58
+ if not test_is_quick():
59
+ _windows += [
60
+ [(2, 1, 125, 512, 200), (96, 97, 98), (0.4, 0.32, 0), 20],
61
+ [(2, 1, 10, 512, 200), (96, 97, 98), (0.4, 0.12, 0), 21],
62
+ [(2, 3, 100, 100, 200), (50, 50, 100), 0, 8],
63
+ ]
64
+
65
+ BUFFER_CASES: list = []
66
+ for x in _windows:
67
+ for s in (1, 3, 4):
68
+ for d in (-1, 0, 1):
69
+ BUFFER_CASES.extend([x, s, d, dev] for dev in itertools.product(*_devices * 3))
70
+
71
+
72
+ class TestSlidingWindowInference(unittest.TestCase):
73
+ @parameterized.expand(BUFFER_CASES)
74
+ def test_buffers(self, size_params, buffer_steps, buffer_dim, device_params):
75
+ def mult_two(patch, *args, **kwargs):
76
+ return 2.0 * patch
77
+
78
+ img_size, roi_size, overlap, sw_batch_size = size_params
79
+ img_device, device, sw_device = device_params
80
+ dtype = [torch.float, torch.double][roi_size[0] % 2] # test different input dtype
81
+ mode = ["constant", "gaussian"][img_size[1] % 2]
82
+ image = torch.randint(0, 255, size=img_size, dtype=dtype, device=img_device)
83
+ sw = sliding_window_inference(
84
+ image,
85
+ roi_size,
86
+ sw_batch_size,
87
+ mult_two,
88
+ overlap,
89
+ mode=mode,
90
+ sw_device=sw_device,
91
+ device=device,
92
+ buffer_steps=buffer_steps,
93
+ buffer_dim=buffer_dim,
94
+ )
95
+ max_diff = torch.max(torch.abs(image.to(sw) - 0.5 * sw)).item()
96
+ self.assertGreater(0.001, max_diff)
97
+
98
+ @parameterized.expand(TEST_CASES)
99
+ def test_sliding_window_default(self, image_shape, roi_shape, sw_batch_size, overlap, mode, device):
100
+ n_total = np.prod(image_shape)
101
+ if mode == "constant":
102
+ inputs = torch.arange(n_total, dtype=torch.float).reshape(*image_shape)
103
+ else:
104
+ inputs = torch.ones(*image_shape, dtype=torch.float)
105
+ if device.type == "cuda" and not torch.cuda.is_available():
106
+ device = torch.device("cpu:0")
107
+
108
+ def compute(data):
109
+ return data + 1
110
+
111
+ if mode == "constant":
112
+ expected_val = np.arange(n_total, dtype=np.float32).reshape(*image_shape) + 1.0
113
+ else:
114
+ expected_val = np.ones(image_shape, dtype=np.float32) + 1.0
115
+ result = sliding_window_inference(inputs.to(device), roi_shape, sw_batch_size, compute, overlap, mode=mode)
116
+ np.testing.assert_string_equal(device.type, result.device.type)
117
+ np.testing.assert_allclose(result.cpu().numpy(), expected_val)
118
+
119
+ result = SlidingWindowInferer(roi_shape, sw_batch_size, overlap, mode)(inputs.to(device), compute)
120
+ np.testing.assert_string_equal(device.type, result.device.type)
121
+ np.testing.assert_allclose(result.cpu().numpy(), expected_val)
122
+
123
+ @parameterized.expand([[x] for x in TEST_TORCH_AND_META_TENSORS])
124
+ def test_default_device(self, data_type):
125
+ device = "cuda" if torch.cuda.is_available() else "cpu:0"
126
+ inputs = data_type(torch.ones((3, 16, 15, 7))).to(device=device)
127
+ inputs = list_data_collate([inputs]) # make a proper batch
128
+ roi_shape = (4, 10, 7)
129
+ sw_batch_size = 10
130
+
131
+ def compute(data):
132
+ return data + 1
133
+
134
+ inputs.requires_grad = True
135
+ result = sliding_window_inference(inputs, roi_shape, sw_batch_size, compute)
136
+ self.assertTrue(result.requires_grad)
137
+ np.testing.assert_string_equal(inputs.device.type, result.device.type)
138
+ expected_val = np.ones((1, 3, 16, 15, 7), dtype=np.float32) + 1
139
+ np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val)
140
+
141
+ @parameterized.expand(list(itertools.product(TEST_TORCH_AND_META_TENSORS, ("cpu", "cuda"), ("cpu", "cuda", None))))
142
+ @skip_if_no_cuda
143
+ def test_sw_device(self, data_type, device, sw_device):
144
+ inputs = data_type(torch.ones((3, 16, 15, 7))).to(device=device)
145
+ inputs = list_data_collate([inputs]) # make a proper batch
146
+ roi_shape = (4, 10, 7)
147
+ sw_batch_size = 10
148
+
149
+ def compute(data):
150
+ self.assertEqual(data.device.type, sw_device or device)
151
+ return data + torch.tensor(1, device=sw_device or device)
152
+
153
+ result = sliding_window_inference(inputs, roi_shape, sw_batch_size, compute, sw_device=sw_device, device="cpu")
154
+ np.testing.assert_string_equal("cpu", result.device.type)
155
+ expected_val = np.ones((1, 3, 16, 15, 7), dtype=np.float32) + 1
156
+ np.testing.assert_allclose(result.cpu().numpy(), expected_val)
157
+
158
+ def test_sigma(self):
159
+ device = "cuda" if torch.cuda.is_available() else "cpu:0"
160
+ inputs = torch.ones((1, 1, 7, 7)).to(device=device)
161
+ roi_shape = (3, 3)
162
+ sw_batch_size = 10
163
+
164
+ class _Pred:
165
+ add = 1
166
+
167
+ def compute(self, data):
168
+ self.add += 1
169
+ return data + self.add
170
+
171
+ result = sliding_window_inference(
172
+ inputs,
173
+ roi_shape,
174
+ sw_batch_size,
175
+ _Pred().compute,
176
+ overlap=0.5,
177
+ padding_mode="constant",
178
+ cval=-1,
179
+ mode="constant",
180
+ sigma_scale=1.0,
181
+ )
182
+
183
+ expected = np.array(
184
+ [
185
+ [
186
+ [
187
+ [3.0000, 3.0000, 3.0000, 3.0000, 3.0000, 3.0000, 3.0000],
188
+ [3.0000, 3.0000, 3.0000, 3.0000, 3.0000, 3.0000, 3.0000],
189
+ [3.3333, 3.3333, 3.3333, 3.3333, 3.3333, 3.3333, 3.3333],
190
+ [3.6667, 3.6667, 3.6667, 3.6667, 3.6667, 3.6667, 3.6667],
191
+ [4.3333, 4.3333, 4.3333, 4.3333, 4.3333, 4.3333, 4.3333],
192
+ [4.5000, 4.5000, 4.5000, 4.5000, 4.5000, 4.5000, 4.5000],
193
+ [5.0000, 5.0000, 5.0000, 5.0000, 5.0000, 5.0000, 5.0000],
194
+ ]
195
+ ]
196
+ ]
197
+ )
198
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
199
+ result = sliding_window_inference(
200
+ inputs,
201
+ roi_shape,
202
+ sw_batch_size,
203
+ _Pred().compute,
204
+ overlap=0.5,
205
+ padding_mode="constant",
206
+ cval=-1,
207
+ mode="gaussian",
208
+ sigma_scale=1.0,
209
+ progress=has_tqdm,
210
+ )
211
+ expected = np.array(
212
+ [
213
+ [
214
+ [
215
+ [3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0],
216
+ [3.0, 3.0, 3.0, 3.0, 3.0, 3.0, 3.0],
217
+ [3.3271625, 3.3271623, 3.3271623, 3.3271623, 3.3271623, 3.3271623, 3.3271625],
218
+ [3.6728377, 3.6728377, 3.6728377, 3.6728377, 3.6728377, 3.6728377, 3.6728377],
219
+ [4.3271623, 4.3271623, 4.3271627, 4.3271627, 4.3271627, 4.3271623, 4.3271623],
220
+ [4.513757, 4.513757, 4.513757, 4.513757, 4.513757, 4.513757, 4.513757],
221
+ [4.9999995, 5.0, 5.0, 5.0, 5.0, 5.0, 4.9999995],
222
+ ]
223
+ ]
224
+ ]
225
+ )
226
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
227
+
228
+ result = SlidingWindowInferer(roi_shape, sw_batch_size, overlap=0.5, mode="gaussian", sigma_scale=1.0)(
229
+ inputs, _Pred().compute
230
+ )
231
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
232
+
233
+ result = SlidingWindowInferer(roi_shape, sw_batch_size, overlap=0.5, mode="gaussian", sigma_scale=[1.0, 1.0])(
234
+ inputs, _Pred().compute
235
+ )
236
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
237
+
238
+ result = SlidingWindowInferer(
239
+ roi_shape, sw_batch_size, overlap=0.5, mode="gaussian", sigma_scale=[1.0, 1.0], cache_roi_weight_map=True
240
+ )(inputs, _Pred().compute)
241
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
242
+
243
+ def test_cval(self):
244
+ device = "cuda" if torch.cuda.is_available() else "cpu:0"
245
+ inputs = torch.ones((1, 1, 3, 3)).to(device=device)
246
+ roi_shape = (5, 5)
247
+ sw_batch_size = 10
248
+
249
+ def compute(data):
250
+ return data + data.sum()
251
+
252
+ result = sliding_window_inference(
253
+ inputs,
254
+ roi_shape,
255
+ sw_batch_size,
256
+ compute,
257
+ overlap=0.5,
258
+ padding_mode="constant",
259
+ cval=-1,
260
+ mode="constant",
261
+ sigma_scale=1.0,
262
+ )
263
+ expected = np.ones((1, 1, 3, 3)) * -6.0
264
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
265
+
266
+ result = SlidingWindowInferer(roi_shape, sw_batch_size, overlap=0.5, mode="constant", cval=-1)(inputs, compute)
267
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
268
+
269
+ def test_args_kwargs(self):
270
+ device = "cuda" if torch.cuda.is_available() else "cpu:0"
271
+ inputs = torch.ones((1, 1, 3, 3)).to(device=device)
272
+ t1 = torch.ones(1).to(device=device)
273
+ t2 = torch.ones(1).to(device=device)
274
+ roi_shape = (5, 5)
275
+ sw_batch_size = 10
276
+
277
+ def compute(data, test1, test2):
278
+ return data + test1 + test2
279
+
280
+ result = sliding_window_inference(
281
+ inputs,
282
+ roi_shape,
283
+ sw_batch_size,
284
+ compute,
285
+ 0.5,
286
+ "constant",
287
+ 1.0,
288
+ "constant",
289
+ 0.0,
290
+ device,
291
+ device,
292
+ has_tqdm,
293
+ None,
294
+ None,
295
+ None,
296
+ 0,
297
+ False,
298
+ t1,
299
+ test2=t2,
300
+ )
301
+ expected = np.ones((1, 1, 3, 3)) + 2.0
302
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
303
+
304
+ result = SlidingWindowInferer(
305
+ roi_shape, sw_batch_size, overlap=0.5, mode="constant", cval=-1, progress=has_tqdm
306
+ )(inputs, compute, t1, test2=t2)
307
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
308
+
309
+ result = SlidingWindowInfererAdapt(
310
+ roi_shape, sw_batch_size, overlap=0.5, mode="constant", cval=-1, progress=has_tqdm
311
+ )(inputs, compute, t1, test2=t2)
312
+ np.testing.assert_allclose(result.cpu().numpy(), expected, rtol=1e-4)
313
+
314
+ def test_multioutput(self):
315
+ device = "cuda" if torch.cuda.is_available() else "cpu:0"
316
+ inputs = torch.ones((1, 6, 20, 20)).to(device=device)
317
+ roi_shape = (8, 8)
318
+ sw_batch_size = 10
319
+
320
+ def compute(data):
321
+ return data + 1, data[:, ::3, ::2, ::2] + 2, data[:, ::2, ::4, ::4] + 3
322
+
323
+ def compute_dict(data):
324
+ return {1: data + 1, 2: data[:, ::3, ::2, ::2] + 2, 3: data[:, ::2, ::4, ::4] + 3}
325
+
326
+ result = sliding_window_inference(
327
+ inputs,
328
+ roi_shape,
329
+ sw_batch_size,
330
+ compute,
331
+ 0.5,
332
+ "constant",
333
+ 1.0,
334
+ "constant",
335
+ 0.0,
336
+ device,
337
+ device,
338
+ has_tqdm,
339
+ None,
340
+ )
341
+ result_dict = sliding_window_inference(
342
+ inputs,
343
+ roi_shape,
344
+ sw_batch_size,
345
+ compute_dict,
346
+ 0.5,
347
+ "constant",
348
+ 1.0,
349
+ "constant",
350
+ 0.0,
351
+ device,
352
+ device,
353
+ has_tqdm,
354
+ None,
355
+ )
356
+ expected = (np.ones((1, 6, 20, 20)) + 1, np.ones((1, 2, 10, 10)) + 2, np.ones((1, 3, 5, 5)) + 3)
357
+ expected_dict = {1: np.ones((1, 6, 20, 20)) + 1, 2: np.ones((1, 2, 10, 10)) + 2, 3: np.ones((1, 3, 5, 5)) + 3}
358
+ for rr, ee in zip(result, expected):
359
+ np.testing.assert_allclose(rr.cpu().numpy(), ee, rtol=1e-4)
360
+ for rr, _ in zip(result_dict, expected_dict):
361
+ np.testing.assert_allclose(result_dict[rr].cpu().numpy(), expected_dict[rr], rtol=1e-4)
362
+
363
+ result = SlidingWindowInferer(
364
+ roi_shape, sw_batch_size, overlap=0.5, mode="constant", cval=-1, progress=has_tqdm
365
+ )(inputs, compute)
366
+ for rr, ee in zip(result, expected):
367
+ np.testing.assert_allclose(rr.cpu().numpy(), ee, rtol=1e-4)
368
+
369
+ result_dict = SlidingWindowInferer(
370
+ roi_shape, sw_batch_size, overlap=0.5, mode="constant", cval=-1, progress=has_tqdm
371
+ )(inputs, compute_dict)
372
+ for rr, _ in zip(result_dict, expected_dict):
373
+ np.testing.assert_allclose(result_dict[rr].cpu().numpy(), expected_dict[rr], rtol=1e-4)
374
+
375
+
376
+ if __name__ == "__main__":
377
+ unittest.main()
@@ -0,0 +1,284 @@
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 torch
17
+ from parameterized import parameterized
18
+ from torch.nn.functional import pad
19
+
20
+ from monai.inferers import SlidingWindowSplitter
21
+ from tests.test_utils import assert_allclose
22
+
23
+ # ----------------------------------------------------------------------------
24
+ # Tensor test cases
25
+ # ----------------------------------------------------------------------------
26
+ # random int tensor (0, 255)
27
+ TENSOR_4x4 = torch.randint(low=0, high=255, size=(2, 3, 4, 4), dtype=torch.float32)
28
+
29
+ # random int tensor (0, 255) with artifacts at [..., :2, 2:]
30
+ TENSOR_4x4_artifact = TENSOR_4x4.clone()
31
+ TENSOR_4x4_artifact[..., :2, 2:] = 512.0
32
+
33
+ # no-overlapping 2x2
34
+ TEST_CASE_TENSOR_0 = [
35
+ TENSOR_4x4,
36
+ {"patch_size": (2, 2), "overlap": 0.0},
37
+ [
38
+ (TENSOR_4x4[..., :2, :2], (0, 0)),
39
+ (TENSOR_4x4[..., :2, 2:], (0, 2)),
40
+ (TENSOR_4x4[..., 2:, :2], (2, 0)),
41
+ (TENSOR_4x4[..., 2:, 2:], (2, 2)),
42
+ ],
43
+ ]
44
+
45
+ # no-overlapping 3x3 with pad
46
+ TEST_CASE_TENSOR_1 = [
47
+ TENSOR_4x4,
48
+ {"patch_size": (3, 3), "overlap": 0.0, "pad_mode": "constant"},
49
+ [
50
+ (TENSOR_4x4[..., :3, :3], (0, 0)),
51
+ (pad(TENSOR_4x4[..., :3, 3:], (0, 2)), (0, 3)),
52
+ (pad(TENSOR_4x4[..., 3:, :3], (0, 0, 0, 2)), (3, 0)),
53
+ (pad(TENSOR_4x4[..., 3:, 3:], (0, 2, 0, 2)), (3, 3)),
54
+ ],
55
+ ]
56
+
57
+ # overlapping 2x2 with fraction
58
+ TEST_CASE_TENSOR_2 = [
59
+ TENSOR_4x4,
60
+ {"patch_size": (2, 2), "overlap": (0.5, 0.5)},
61
+ [
62
+ (TENSOR_4x4[..., 0:2, 0:2], (0, 0)),
63
+ (TENSOR_4x4[..., 0:2, 1:3], (0, 1)),
64
+ (TENSOR_4x4[..., 0:2, 2:4], (0, 2)),
65
+ (TENSOR_4x4[..., 1:3, 0:2], (1, 0)),
66
+ (TENSOR_4x4[..., 1:3, 1:3], (1, 1)),
67
+ (TENSOR_4x4[..., 1:3, 2:4], (1, 2)),
68
+ (TENSOR_4x4[..., 2:4, 0:2], (2, 0)),
69
+ (TENSOR_4x4[..., 2:4, 1:3], (2, 1)),
70
+ (TENSOR_4x4[..., 2:4, 2:4], (2, 2)),
71
+ ],
72
+ ]
73
+
74
+ # overlapping 3x3 with fraction (non-divisible)
75
+ TEST_CASE_TENSOR_3 = [
76
+ TENSOR_4x4,
77
+ {"patch_size": (3, 3), "overlap": 2.0 / 3.0},
78
+ [
79
+ (TENSOR_4x4[..., :3, :3], (0, 0)),
80
+ (TENSOR_4x4[..., :3, 1:], (0, 1)),
81
+ (TENSOR_4x4[..., 1:, :3], (1, 0)),
82
+ (TENSOR_4x4[..., 1:, 1:], (1, 1)),
83
+ ],
84
+ ]
85
+
86
+ # overlapping 2x2 with number of pixels
87
+ TEST_CASE_TENSOR_4 = [
88
+ TENSOR_4x4,
89
+ {"patch_size": (2, 2), "overlap": (1, 1)},
90
+ [
91
+ (TENSOR_4x4[..., 0:2, 0:2], (0, 0)),
92
+ (TENSOR_4x4[..., 0:2, 1:3], (0, 1)),
93
+ (TENSOR_4x4[..., 0:2, 2:4], (0, 2)),
94
+ (TENSOR_4x4[..., 1:3, 0:2], (1, 0)),
95
+ (TENSOR_4x4[..., 1:3, 1:3], (1, 1)),
96
+ (TENSOR_4x4[..., 1:3, 2:4], (1, 2)),
97
+ (TENSOR_4x4[..., 2:4, 0:2], (2, 0)),
98
+ (TENSOR_4x4[..., 2:4, 1:3], (2, 1)),
99
+ (TENSOR_4x4[..., 2:4, 2:4], (2, 2)),
100
+ ],
101
+ ]
102
+
103
+ # overlapping 3x3 with number of pixels (non-divisible)
104
+ TEST_CASE_TENSOR_5 = [
105
+ TENSOR_4x4,
106
+ {"patch_size": (3, 3), "overlap": 2},
107
+ [
108
+ (TENSOR_4x4[..., :3, :3], (0, 0)),
109
+ (TENSOR_4x4[..., :3, 1:], (0, 1)),
110
+ (TENSOR_4x4[..., 1:, :3], (1, 0)),
111
+ (TENSOR_4x4[..., 1:, 1:], (1, 1)),
112
+ ],
113
+ ]
114
+ # non-overlapping 2x2 with positive offset
115
+ TEST_CASE_TENSOR_6 = [
116
+ TENSOR_4x4,
117
+ {"patch_size": (2, 2), "offset": 1},
118
+ [
119
+ (TENSOR_4x4[..., 1:3, 1:3], (1, 1)),
120
+ (pad(TENSOR_4x4[..., 1:3, 3:], (0, 1)), (1, 3)),
121
+ (pad(TENSOR_4x4[..., 3:, 1:3], (0, 0, 0, 1)), (3, 1)),
122
+ (pad(TENSOR_4x4[..., 3:, 3:], (0, 1, 0, 1)), (3, 3)),
123
+ ],
124
+ ]
125
+
126
+ # non-overlapping 2x2 with negative offset
127
+ TEST_CASE_TENSOR_7 = [
128
+ TENSOR_4x4,
129
+ {"patch_size": (2, 2), "offset": -1},
130
+ [
131
+ (pad(TENSOR_4x4[..., :1, :1], (1, 0, 1, 0)), (-1, -1)),
132
+ (pad(TENSOR_4x4[..., :1, 1:3], (0, 0, 1, 0)), (-1, 1)),
133
+ (pad(TENSOR_4x4[..., :1, 3:], (0, 1, 1, 0)), (-1, 3)),
134
+ (pad(TENSOR_4x4[..., 1:3, :1], (1, 0)), (1, -1)),
135
+ (TENSOR_4x4[..., 1:3, 1:3], (1, 1)),
136
+ (pad(TENSOR_4x4[..., 1:3, 3:], (0, 1)), (1, 3)),
137
+ (pad(TENSOR_4x4[..., 3:, :1], (1, 0, 0, 1)), (3, -1)),
138
+ (pad(TENSOR_4x4[..., 3:, 1:3], (0, 0, 0, 1)), (3, 1)),
139
+ (pad(TENSOR_4x4[..., 3:, 3:], (0, 1, 0, 1)), (3, 3)),
140
+ ],
141
+ ]
142
+
143
+ # non-overlapping 2x2 with positive offset and no padding
144
+ TEST_CASE_TENSOR_8 = [
145
+ TENSOR_4x4,
146
+ {"patch_size": (2, 2), "offset": 1, "pad_mode": None},
147
+ [(TENSOR_4x4[..., 1:3, 1:3], (1, 1))],
148
+ ]
149
+
150
+
151
+ # ----------------------------------------------------------------------------
152
+ # Filtering function test cases
153
+ # ----------------------------------------------------------------------------
154
+ def gen_filter(filter_type, value=None):
155
+ """ "Generate patch filtering function for testing"""
156
+ if filter_type.lower() == "high":
157
+
158
+ def my_filter(patch, location):
159
+ if torch.any(patch > value):
160
+ return True
161
+ return False
162
+
163
+ elif filter_type.lower() == "low":
164
+
165
+ def my_filter(patch, location):
166
+ if torch.any(patch < value):
167
+ return True
168
+ return False
169
+
170
+ elif filter_type.lower() == "location":
171
+
172
+ def my_filter(patch, location):
173
+ if location in value:
174
+ return True
175
+ return False
176
+
177
+ return my_filter
178
+
179
+
180
+ TEST_CASE_FILTER_FN_0 = [
181
+ TENSOR_4x4_artifact,
182
+ {"patch_size": (2, 2), "filter_fn": gen_filter("low", 256)},
183
+ [
184
+ (TENSOR_4x4_artifact[..., :2, :2], (0, 0)),
185
+ (TENSOR_4x4_artifact[..., 2:, :2], (2, 0)),
186
+ (TENSOR_4x4_artifact[..., 2:, 2:], (2, 2)),
187
+ ],
188
+ ]
189
+
190
+ TEST_CASE_FILTER_FN_1 = [
191
+ TENSOR_4x4_artifact,
192
+ {"patch_size": (2, 2), "filter_fn": gen_filter("high", 256)},
193
+ [(TENSOR_4x4_artifact[..., :2, 2:], (0, 2))],
194
+ ]
195
+
196
+ TEST_CASE_FILTER_FN_2 = [
197
+ TENSOR_4x4_artifact,
198
+ {"patch_size": (2, 2), "filter_fn": gen_filter("location", [(2, 2), (2, 0)])},
199
+ [(TENSOR_4x4_artifact[..., 2:, :2], (2, 0)), (TENSOR_4x4_artifact[..., 2:, 2:], (2, 2))],
200
+ ]
201
+
202
+
203
+ # ----------------------------------------------------------------------------
204
+ # Error test cases
205
+ # ----------------------------------------------------------------------------
206
+ def extra_parameter_filter(patch, location, extra):
207
+ return
208
+
209
+
210
+ def missing_parameter_filter(patch):
211
+ return
212
+
213
+
214
+ # invalid overlap: float 1.0
215
+ TEST_CASE_ERROR_0 = [TENSOR_4x4, {"patch_size": (2, 2), "overlap": 1.0}, ValueError]
216
+ # invalid overlap: negative float
217
+ TEST_CASE_ERROR_1 = [TENSOR_4x4, {"patch_size": (2, 2), "overlap": -0.1}, ValueError]
218
+ # invalid overlap: negative integer
219
+ TEST_CASE_ERROR_2 = [TENSOR_4x4, {"patch_size": (2, 2), "overlap": -1}, ValueError]
220
+ # invalid overlap: integer larger than patch size
221
+ TEST_CASE_ERROR_3 = [TENSOR_4x4, {"patch_size": (2, 2), "overlap": 3}, ValueError]
222
+
223
+ # invalid offset: positive and larger than image size
224
+ TEST_CASE_ERROR_4 = [TENSOR_4x4, {"patch_size": (2, 2), "offset": 4}, ValueError]
225
+ # invalid offset: negative and larger than patch size (in magnitude)
226
+ TEST_CASE_ERROR_5 = [TENSOR_4x4, {"patch_size": (2, 2), "offset": -3, "pad_mode": "constant"}, ValueError]
227
+ # invalid offset: negative and no padding
228
+ TEST_CASE_ERROR_6 = [TENSOR_4x4, {"patch_size": (2, 2), "offset": -1, "pad_mode": None}, ValueError]
229
+
230
+ # invalid filter function: with more than two positional parameters
231
+ TEST_CASE_ERROR_7 = [TENSOR_4x4, {"patch_size": (2, 2), "filter_fn": extra_parameter_filter}, ValueError]
232
+ # invalid filter function: with less than two positional parameters
233
+ TEST_CASE_ERROR_8 = [TENSOR_4x4, {"patch_size": (2, 2), "filter_fn": missing_parameter_filter}, ValueError]
234
+ # invalid filter function: non-callable
235
+ TEST_CASE_ERROR_9 = [TENSOR_4x4, {"patch_size": (2, 2), "filter_fn": 1}, ValueError]
236
+
237
+
238
+ class SlidingWindowSplitterTests(unittest.TestCase):
239
+ @parameterized.expand(
240
+ [
241
+ TEST_CASE_TENSOR_0,
242
+ TEST_CASE_TENSOR_1,
243
+ TEST_CASE_TENSOR_2,
244
+ TEST_CASE_TENSOR_3,
245
+ TEST_CASE_TENSOR_4,
246
+ TEST_CASE_TENSOR_5,
247
+ TEST_CASE_TENSOR_6,
248
+ TEST_CASE_TENSOR_7,
249
+ TEST_CASE_TENSOR_8,
250
+ TEST_CASE_FILTER_FN_0,
251
+ TEST_CASE_FILTER_FN_1,
252
+ TEST_CASE_FILTER_FN_2,
253
+ ]
254
+ )
255
+ def test_split_patches_tensor(self, image, arguments, expected):
256
+ patches = SlidingWindowSplitter(**arguments)(image)
257
+ patches = list(patches)
258
+ self.assertEqual(len(patches), len(expected))
259
+ for p, e in zip(patches, expected):
260
+ assert_allclose(p[0], e[0])
261
+ self.assertTupleEqual(p[1], e[1])
262
+
263
+ @parameterized.expand(
264
+ [
265
+ TEST_CASE_ERROR_0,
266
+ TEST_CASE_ERROR_1,
267
+ TEST_CASE_ERROR_2,
268
+ TEST_CASE_ERROR_3,
269
+ TEST_CASE_ERROR_4,
270
+ TEST_CASE_ERROR_5,
271
+ TEST_CASE_ERROR_6,
272
+ TEST_CASE_ERROR_7,
273
+ TEST_CASE_ERROR_8,
274
+ TEST_CASE_ERROR_9,
275
+ ]
276
+ )
277
+ def test_split_patches_errors(self, image, arguments, expected_error):
278
+ with self.assertRaises(expected_error):
279
+ patches = SlidingWindowSplitter(**arguments)(image)
280
+ patches = list(patches)
281
+
282
+
283
+ if __name__ == "__main__":
284
+ unittest.main()