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 +1,758 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import logging
15
+ import sys
16
+ import unittest
17
+ from copy import deepcopy
18
+ from io import StringIO
19
+
20
+ import numpy as np
21
+ import torch
22
+ from parameterized import parameterized
23
+
24
+ import monai.transforms as mt
25
+ from monai.data import DataLoader, Dataset
26
+ from monai.transforms.compose import execute_compose
27
+ from monai.transforms.transform import Randomizable
28
+ from monai.utils import set_determinism
29
+
30
+
31
+ def data_from_keys(keys, h, w):
32
+ if keys is None:
33
+ data = torch.arange(h * w).reshape(1, h, w)
34
+ else:
35
+ data = {}
36
+ for i_k, k in enumerate(keys):
37
+ data[k] = torch.arange(h * w).reshape(1, h, w).mul_(i_k * h * w)
38
+ return data
39
+
40
+
41
+ class _RandXform(Randomizable):
42
+
43
+ def randomize(self):
44
+ self.val = self.R.random_sample()
45
+
46
+ def __call__(self, __unused):
47
+ self.randomize()
48
+ return self.val
49
+
50
+
51
+ class TestCompose(unittest.TestCase):
52
+
53
+ def test_empty_compose(self):
54
+ c = mt.Compose()
55
+ i = 1
56
+ self.assertEqual(c(i), 1)
57
+
58
+ def test_non_dict_compose(self):
59
+
60
+ def a(i):
61
+ return i + "a"
62
+
63
+ def b(i):
64
+ return i + "b"
65
+
66
+ c = mt.Compose([a, b, a, b])
67
+ self.assertEqual(c(""), "abab")
68
+
69
+ def test_dict_compose(self):
70
+
71
+ def a(d):
72
+ d = dict(d)
73
+ d["a"] += 1
74
+ return d
75
+
76
+ def b(d):
77
+ d = dict(d)
78
+ d["b"] += 1
79
+ return d
80
+
81
+ transforms = [a, b, a, b, a]
82
+ data = {"a": 0, "b": 0}
83
+ expected = {"a": 3, "b": 2}
84
+
85
+ self.assertDictEqual(mt.Compose(transforms)(data), expected)
86
+ self.assertDictEqual(execute_compose(data, transforms), expected)
87
+
88
+ def test_list_dict_compose(self):
89
+
90
+ def a(d): # transform to handle dict data
91
+ d = dict(d)
92
+ d["a"] += 1
93
+ return d
94
+
95
+ def b(d): # transform to generate a batch list of data
96
+ d = dict(d)
97
+ d["b"] += 1
98
+ d = [d] * 5
99
+ return d
100
+
101
+ def c(d): # transform to handle dict data
102
+ d = dict(d)
103
+ d["c"] += 1
104
+ return d
105
+
106
+ transforms = [a, a, b, c, c]
107
+ data = {"a": 0, "b": 0, "c": 0}
108
+ expected = {"a": 2, "b": 1, "c": 2}
109
+ value = mt.Compose(transforms)(data)
110
+ for item in value:
111
+ self.assertDictEqual(item, expected)
112
+ value = execute_compose(data, transforms)
113
+ for item in value:
114
+ self.assertDictEqual(item, expected)
115
+
116
+ def test_non_dict_compose_with_unpack(self):
117
+
118
+ def a(i, i2):
119
+ return i + "a", i2 + "a2"
120
+
121
+ def b(i, i2):
122
+ return i + "b", i2 + "b2"
123
+
124
+ transforms = [a, b, a, b]
125
+ data = ("", "")
126
+ expected = ("abab", "a2b2a2b2")
127
+ self.assertEqual(mt.Compose(transforms, map_items=False, unpack_items=True)(data), expected)
128
+ self.assertEqual(execute_compose(data, transforms, map_items=False, unpack_items=True), expected)
129
+
130
+ def test_list_non_dict_compose_with_unpack(self):
131
+
132
+ def a(i, i2):
133
+ return i + "a", i2 + "a2"
134
+
135
+ def b(i, i2):
136
+ return i + "b", i2 + "b2"
137
+
138
+ transforms = [a, b, a, b]
139
+ data = [("", ""), ("t", "t")]
140
+ expected = [("abab", "a2b2a2b2"), ("tabab", "ta2b2a2b2")]
141
+ self.assertEqual(mt.Compose(transforms, unpack_items=True)(data), expected)
142
+ self.assertEqual(execute_compose(data, transforms, unpack_items=True), expected)
143
+
144
+ def test_list_non_dict_compose_with_unpack_map_2(self):
145
+
146
+ def a(i, i2):
147
+ return i + "a", i2 + "a2"
148
+
149
+ def b(i, i2):
150
+ return i + "b", i2 + "b2"
151
+
152
+ transforms = [a, b, a, b]
153
+ data = [[("", ""), ("", "")], [("t", "t"), ("t", "t")]]
154
+ expected = [[("abab", "a2b2a2b2"), ("abab", "a2b2a2b2")], [("tabab", "ta2b2a2b2"), ("tabab", "ta2b2a2b2")]]
155
+ self.assertEqual(mt.Compose(transforms, map_items=2, unpack_items=True)(data), expected)
156
+ self.assertEqual(execute_compose(data, transforms, map_items=2, unpack_items=True), expected)
157
+
158
+ def test_list_dict_compose_no_map(self):
159
+
160
+ def a(d): # transform to handle dict data
161
+ d = dict(d)
162
+ d["a"] += 1
163
+ return d
164
+
165
+ def b(d): # transform to generate a batch list of data
166
+ d = dict(d)
167
+ d["b"] += 1
168
+ d = [d] * 5
169
+ return d
170
+
171
+ def c(d): # transform to handle dict data
172
+ d = [dict(di) for di in d]
173
+ for di in d:
174
+ di["c"] += 1
175
+ return d
176
+
177
+ transforms = [a, a, b, c, c]
178
+ data = {"a": 0, "b": 0, "c": 0}
179
+ expected = {"a": 2, "b": 1, "c": 2}
180
+ value = mt.Compose(transforms, map_items=False)(data)
181
+ for item in value:
182
+ self.assertDictEqual(item, expected)
183
+ value = execute_compose(data, transforms, map_items=False)
184
+ for item in value:
185
+ self.assertDictEqual(item, expected)
186
+
187
+ def test_random_compose(self):
188
+
189
+ class _Acc(Randomizable):
190
+ self.rand = 0.0
191
+
192
+ def randomize(self, data=None):
193
+ self.rand = self.R.rand()
194
+
195
+ def __call__(self, data):
196
+ self.randomize()
197
+ return self.rand + data
198
+
199
+ c = mt.Compose([_Acc(), _Acc()])
200
+ self.assertNotAlmostEqual(c(0), c(0))
201
+ c.set_random_state(123)
202
+ self.assertAlmostEqual(c(1), 1.61381597)
203
+ c.set_random_state(223)
204
+ c.randomize()
205
+ self.assertAlmostEqual(c(1), 1.90734751)
206
+
207
+ def test_randomize_warn(self):
208
+
209
+ class _RandomClass(Randomizable):
210
+
211
+ def randomize(self, foo1, foo2):
212
+ pass
213
+
214
+ def __call__(self, data):
215
+ pass
216
+
217
+ c = mt.Compose([_RandomClass(), _RandomClass()])
218
+ with self.assertWarns(Warning):
219
+ c.randomize()
220
+
221
+ def test_err_msg(self):
222
+ transforms = mt.Compose([abs, mt.EnsureChannelFirst(), round])
223
+ with self.assertRaisesRegex(Exception, "EnsureChannelFirst"):
224
+ transforms(42.1)
225
+
226
+ def test_data_loader(self):
227
+ xform_1 = mt.Compose([_RandXform()])
228
+ train_ds = Dataset([1], transform=xform_1)
229
+
230
+ xform_1.set_random_state(123)
231
+ out_1 = train_ds[0]
232
+ self.assertAlmostEqual(out_1, 0.2045649)
233
+
234
+ set_determinism(seed=123)
235
+ train_loader = DataLoader(train_ds, num_workers=0)
236
+ out_1 = next(iter(train_loader))
237
+ self.assertAlmostEqual(out_1.cpu().item(), 0.0409280)
238
+
239
+ if sys.platform != "win32": # skip multi-worker tests on win32
240
+ train_loader = DataLoader(train_ds, num_workers=1)
241
+ out_1 = next(iter(train_loader))
242
+ self.assertAlmostEqual(out_1.cpu().item(), 0.78663897075)
243
+
244
+ train_loader = DataLoader(train_ds, num_workers=2)
245
+ out_1 = next(iter(train_loader))
246
+ self.assertAlmostEqual(out_1.cpu().item(), 0.785907334)
247
+ set_determinism(None)
248
+
249
+ def test_data_loader_2(self):
250
+ set_determinism(seed=123)
251
+ xform_2 = mt.Compose([_RandXform(), _RandXform()])
252
+ train_ds = Dataset([1], transform=xform_2)
253
+
254
+ out_2 = train_ds[0]
255
+ self.assertAlmostEqual(out_2, 0.4092510)
256
+
257
+ train_loader = DataLoader(train_ds, num_workers=0)
258
+ out_2 = next(iter(train_loader))
259
+ self.assertAlmostEqual(out_2.cpu().item(), 0.98921915918)
260
+
261
+ if sys.platform != "win32": # skip multi-worker tests on win32
262
+ train_loader = DataLoader(train_ds, num_workers=1)
263
+ out_2 = next(iter(train_loader))
264
+ self.assertAlmostEqual(out_2.cpu().item(), 0.32985207)
265
+
266
+ train_loader = DataLoader(train_ds, num_workers=2)
267
+ out_1 = next(iter(train_loader))
268
+ self.assertAlmostEqual(out_1.cpu().item(), 0.28602141572)
269
+ set_determinism(None)
270
+
271
+ def test_flatten_and_len(self):
272
+ x = mt.EnsureChannelFirst(channel_dim="no_channel")
273
+ t1 = mt.Compose([x, x, x, x, mt.Compose([mt.Compose([x, x]), x, x])])
274
+
275
+ t2 = t1.flatten()
276
+ for t in t2.transforms:
277
+ self.assertNotIsInstance(t, mt.Compose)
278
+
279
+ # test len
280
+ self.assertEqual(len(t1), 8)
281
+
282
+ def test_backwards_compatible_imports(self):
283
+ from monai.transforms.transform import MapTransform, RandomizableTransform, Transform # noqa: F401
284
+
285
+
286
+ TEST_COMPOSE_EXECUTE_TEST_CASES = [
287
+ [None, tuple()],
288
+ [None, (mt.Rotate(np.pi / 8),)],
289
+ [None, (mt.Flip(0), mt.Flip(1), mt.Rotate90(1), mt.Zoom(0.8), mt.NormalizeIntensity())],
290
+ [("a",), (mt.Rotated(("a",), np.pi / 8),)],
291
+ ]
292
+
293
+
294
+ class TestComposeExecute(unittest.TestCase):
295
+
296
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_TEST_CASES)
297
+ def test_compose_execute_equivalence(self, keys, pipeline):
298
+ data = data_from_keys(keys, 12, 16)
299
+
300
+ expected = mt.Compose(deepcopy(pipeline))(data)
301
+
302
+ for cutoff in range(len(pipeline)):
303
+ c = mt.Compose(deepcopy(pipeline))
304
+ actual = c(c(data, end=cutoff), start=cutoff)
305
+ if isinstance(actual, dict):
306
+ for k in actual.keys():
307
+ self.assertTrue(torch.allclose(expected[k], actual[k]))
308
+ else:
309
+ self.assertTrue(torch.allclose(expected, actual))
310
+
311
+ p = deepcopy(pipeline)
312
+ actual = execute_compose(execute_compose(data, p, start=0, end=cutoff), p, start=cutoff)
313
+ if isinstance(actual, dict):
314
+ for k in actual.keys():
315
+ self.assertTrue(torch.allclose(expected[k], actual[k]))
316
+ else:
317
+ self.assertTrue(torch.allclose(expected, actual))
318
+
319
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_TEST_CASES)
320
+ def test_compose_execute_bad_start_param(self, keys, pipeline):
321
+ data = data_from_keys(keys, 12, 16)
322
+
323
+ c = mt.Compose(deepcopy(pipeline))
324
+ with self.assertRaises(ValueError):
325
+ c(data, start=None)
326
+ with self.assertRaises(ValueError):
327
+ c(data, start=None)
328
+
329
+ with self.assertRaises(ValueError):
330
+ execute_compose(data, deepcopy(pipeline), start=None)
331
+
332
+ c = mt.Compose(deepcopy(pipeline))
333
+ with self.assertRaises(ValueError):
334
+ c(data, start=-1)
335
+ with self.assertRaises(ValueError):
336
+ c(data, start=-1)
337
+
338
+ with self.assertRaises(ValueError):
339
+ execute_compose(data, deepcopy(pipeline), start=-1)
340
+
341
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_TEST_CASES)
342
+ def test_compose_execute_negative_range(self, keys, pipeline):
343
+ data = data_from_keys(keys, 12, 16)
344
+
345
+ with self.assertRaises(ValueError):
346
+ c = mt.Compose(deepcopy(pipeline))
347
+ c(data, start=2, end=1)
348
+
349
+ with self.assertRaises(ValueError):
350
+ execute_compose(data, deepcopy(pipeline), start=2, end=1)
351
+
352
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_TEST_CASES)
353
+ def test_compose_execute_bad_end_param(self, keys, pipeline):
354
+ data = data_from_keys(keys, 12, 16)
355
+
356
+ with self.assertRaises(ValueError):
357
+ c = mt.Compose(deepcopy(pipeline))
358
+ c(data, end=len(pipeline) + 1)
359
+
360
+ with self.assertRaises(ValueError):
361
+ execute_compose(data, deepcopy(pipeline), end=len(pipeline) + 1)
362
+
363
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_TEST_CASES)
364
+ def test_compose_execute_empty_range(self, keys, pipeline):
365
+ data = data_from_keys(keys, 12, 16)
366
+
367
+ c = mt.Compose(deepcopy(pipeline))
368
+ for i in range(len(pipeline)):
369
+ result = c(data, start=i, end=i)
370
+ self.assertIs(data, result)
371
+
372
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_TEST_CASES)
373
+ def test_compose_with_logger(self, keys, pipeline):
374
+ data = data_from_keys(keys, 12, 16)
375
+
376
+ c = mt.Compose(deepcopy(pipeline), log_stats="a_logger_name")
377
+ c(data)
378
+
379
+
380
+ TEST_COMPOSE_EXECUTE_LOGGING_TEST_CASES = [
381
+ [
382
+ None,
383
+ (mt.Flip(0), mt.Spacing((1.2, 1.2)), mt.Flip(1), mt.Rotate90(1), mt.Zoom(0.8), mt.NormalizeIntensity()),
384
+ False,
385
+ (
386
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
387
+ "upcoming 'Flip', transform.lazy: False\n"
388
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
389
+ "upcoming 'Spacing', transform.lazy: False\n"
390
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
391
+ "upcoming 'Flip', transform.lazy: False\n"
392
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
393
+ "upcoming 'Rotate90', transform.lazy: False\n"
394
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
395
+ "upcoming 'Zoom', transform.lazy: False\n"
396
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
397
+ "upcoming 'NormalizeIntensity', transform is not lazy\n"
398
+ ),
399
+ ],
400
+ [
401
+ None,
402
+ (
403
+ mt.Flip(0, lazy=True),
404
+ mt.Spacing((1.2, 1.2), lazy=True),
405
+ mt.Flip(1, lazy=True),
406
+ mt.Rotate90(1),
407
+ mt.Zoom(0.8, lazy=True),
408
+ mt.NormalizeIntensity(),
409
+ ),
410
+ None,
411
+ (
412
+ "INFO - Accumulate pending transforms - lazy: None, pending: 0, "
413
+ "upcoming 'Flip', transform.lazy: True\n"
414
+ "INFO - Accumulate pending transforms - lazy: None, pending: 1, "
415
+ "upcoming 'Spacing', transform.lazy: True\n"
416
+ "INFO - Accumulate pending transforms - lazy: None, pending: 2, "
417
+ "upcoming 'Flip', transform.lazy: True\n"
418
+ "INFO - Apply pending transforms - lazy: None, pending: 3, "
419
+ "upcoming 'Rotate90', transform.lazy: False\n"
420
+ "INFO - Pending transforms applied: applied_operations: 3\n"
421
+ "INFO - Accumulate pending transforms - lazy: None, pending: 0, "
422
+ "upcoming 'Zoom', transform.lazy: True\n"
423
+ "INFO - Apply pending transforms - lazy: None, pending: 1, "
424
+ "upcoming 'NormalizeIntensity', transform is not lazy\n"
425
+ "INFO - Pending transforms applied: applied_operations: 5\n"
426
+ ),
427
+ ],
428
+ [
429
+ None,
430
+ (mt.Flip(0), mt.Spacing((1.2, 1.2)), mt.Flip(1), mt.Rotate90(1), mt.Zoom(0.8), mt.NormalizeIntensity()),
431
+ True,
432
+ (
433
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
434
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
435
+ "INFO - Accumulate pending transforms - lazy: True, pending: 1, "
436
+ "upcoming 'Spacing', transform.lazy: False (overridden)\n"
437
+ "INFO - Accumulate pending transforms - lazy: True, pending: 2, "
438
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
439
+ "INFO - Accumulate pending transforms - lazy: True, pending: 3, "
440
+ "upcoming 'Rotate90', transform.lazy: False (overridden)\n"
441
+ "INFO - Accumulate pending transforms - lazy: True, pending: 4, "
442
+ "upcoming 'Zoom', transform.lazy: False (overridden)\n"
443
+ "INFO - Apply pending transforms - lazy: True, pending: 5, "
444
+ "upcoming 'NormalizeIntensity', transform is not lazy\n"
445
+ "INFO - Pending transforms applied: applied_operations: 5\n"
446
+ ),
447
+ ],
448
+ [
449
+ ("a", "b"),
450
+ (
451
+ mt.Flipd(("a", "b"), 0),
452
+ mt.Spacingd(("a", "b"), 1.2),
453
+ mt.Rotate90d(("a", "b"), 1),
454
+ mt.NormalizeIntensityd(("a",)),
455
+ ),
456
+ True,
457
+ (
458
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 0, "
459
+ "upcoming 'Flipd', transform.lazy: False (overridden)\n"
460
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 0, "
461
+ "upcoming 'Flipd', transform.lazy: False (overridden)\n"
462
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 1, "
463
+ "upcoming 'Spacingd', transform.lazy: False (overridden)\n"
464
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 1, "
465
+ "upcoming 'Spacingd', transform.lazy: False (overridden)\n"
466
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 2, "
467
+ "upcoming 'Rotate90d', transform.lazy: False (overridden)\n"
468
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 2, "
469
+ "upcoming 'Rotate90d', transform.lazy: False (overridden)\n"
470
+ "INFO - Apply pending transforms - lazy: True, key: 'a', pending: 3, "
471
+ "upcoming 'NormalizeIntensityd', transform is not lazy\n"
472
+ "INFO - Pending transforms applied: key: 'a', applied_operations: 3\n"
473
+ "INFO - Pending transforms applied: key: 'b', applied_operations: 3\n"
474
+ ),
475
+ ],
476
+ [
477
+ ("a", "b"),
478
+ (
479
+ mt.Flipd(keys="a", spatial_axis=0),
480
+ mt.Rotate90d(keys="b", k=1, allow_missing_keys=True),
481
+ mt.Zoomd(keys=("a", "b"), zoom=0.8, allow_missing_keys=True),
482
+ mt.Spacingd(keys="a", pixdim=1.2),
483
+ ),
484
+ True,
485
+ (
486
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 0, "
487
+ "upcoming 'Flipd', transform.lazy: False (overridden)\n"
488
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 0, "
489
+ "upcoming 'Rotate90d', transform.lazy: False (overridden)\n"
490
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 1, "
491
+ "upcoming 'Zoomd', transform.lazy: False (overridden)\n"
492
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 1, "
493
+ "upcoming 'Zoomd', transform.lazy: False (overridden)\n"
494
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 2, "
495
+ "upcoming 'Spacingd', transform.lazy: False (overridden)\n"
496
+ "INFO - Pending transforms applied: key: 'a', applied_operations: 3\n"
497
+ "INFO - Pending transforms applied: key: 'b', applied_operations: 2\n"
498
+ ),
499
+ ],
500
+ [
501
+ None,
502
+ (
503
+ mt.Flip(0),
504
+ mt.Spacing((1.2, 1.2)),
505
+ mt.Flip(1),
506
+ mt.ApplyPending(),
507
+ mt.Rotate90(1),
508
+ mt.Zoom(0.8),
509
+ mt.NormalizeIntensity(),
510
+ ),
511
+ False,
512
+ (
513
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
514
+ "upcoming 'Flip', transform.lazy: False\n"
515
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
516
+ "upcoming 'Spacing', transform.lazy: False\n"
517
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
518
+ "upcoming 'Flip', transform.lazy: False\n"
519
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
520
+ "upcoming 'ApplyPending', transform is not lazy\n"
521
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
522
+ "upcoming 'Rotate90', transform.lazy: False\n"
523
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
524
+ "upcoming 'Zoom', transform.lazy: False\n"
525
+ "INFO - Apply pending transforms - lazy: False, pending: 0, "
526
+ "upcoming 'NormalizeIntensity', transform is not lazy\n"
527
+ ),
528
+ ],
529
+ [
530
+ None,
531
+ (
532
+ mt.Flip(0),
533
+ mt.Spacing((1.2, 1.2)),
534
+ mt.Flip(1),
535
+ mt.ApplyPending(),
536
+ mt.Rotate90(1),
537
+ mt.Zoom(0.8),
538
+ mt.NormalizeIntensity(),
539
+ ),
540
+ True,
541
+ (
542
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
543
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
544
+ "INFO - Accumulate pending transforms - lazy: True, pending: 1, "
545
+ "upcoming 'Spacing', transform.lazy: False (overridden)\n"
546
+ "INFO - Accumulate pending transforms - lazy: True, pending: 2, "
547
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
548
+ "INFO - Apply pending transforms - lazy: True, pending: 3, "
549
+ "upcoming 'ApplyPending', transform is not lazy\n"
550
+ "INFO - Pending transforms applied: applied_operations: 3\n"
551
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
552
+ "upcoming 'Rotate90', transform.lazy: False (overridden)\n"
553
+ "INFO - Accumulate pending transforms - lazy: True, pending: 1, "
554
+ "upcoming 'Zoom', transform.lazy: False (overridden)\n"
555
+ "INFO - Apply pending transforms - lazy: True, pending: 2, "
556
+ "upcoming 'NormalizeIntensity', transform is not lazy\n"
557
+ "INFO - Pending transforms applied: applied_operations: 5\n"
558
+ ),
559
+ ],
560
+ [
561
+ ("a", "b"),
562
+ (
563
+ mt.Flipd(keys="a", spatial_axis=0),
564
+ mt.Rotate90d(keys="b", k=1, allow_missing_keys=True),
565
+ mt.ApplyPendingd(keys=("a", "b")),
566
+ mt.Zoomd(keys=("a", "b"), zoom=0.8, allow_missing_keys=True),
567
+ mt.Spacingd(keys="a", pixdim=1.2),
568
+ ),
569
+ True,
570
+ (
571
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 0, "
572
+ "upcoming 'Flipd', transform.lazy: False (overridden)\n"
573
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 0, "
574
+ "upcoming 'Rotate90d', transform.lazy: False (overridden)\n"
575
+ "INFO - Apply pending transforms - lazy: True, key: 'a', pending: 1, "
576
+ "upcoming 'ApplyPendingd', transform is not lazy\n"
577
+ "INFO - Apply pending transforms - lazy: True, key: 'b', pending: 1, "
578
+ "upcoming 'ApplyPendingd', transform is not lazy\n"
579
+ "INFO - Pending transforms applied: key: 'a', applied_operations: 1\n"
580
+ "INFO - Pending transforms applied: key: 'b', applied_operations: 1\n"
581
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 0, "
582
+ "upcoming 'Zoomd', transform.lazy: False (overridden)\n"
583
+ "INFO - Accumulate pending transforms - lazy: True, key: 'b', pending: 0, "
584
+ "upcoming 'Zoomd', transform.lazy: False (overridden)\n"
585
+ "INFO - Accumulate pending transforms - lazy: True, key: 'a', pending: 1, "
586
+ "upcoming 'Spacingd', transform.lazy: False (overridden)\n"
587
+ "INFO - Pending transforms applied: key: 'a', applied_operations: 3\n"
588
+ "INFO - Pending transforms applied: key: 'b', applied_operations: 2\n"
589
+ ),
590
+ ],
591
+ ]
592
+
593
+ TEST_COMPOSE_LAZY_ON_CALL_LOGGING_TEST_CASES = [
594
+ [
595
+ mt.Compose,
596
+ (mt.Flip(0), mt.Spacing((1.2, 1.2))),
597
+ True,
598
+ (
599
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
600
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
601
+ "INFO - Accumulate pending transforms - lazy: True, pending: 1, "
602
+ "upcoming 'Spacing', transform.lazy: False (overridden)\n"
603
+ "INFO - Pending transforms applied: applied_operations: 2\n"
604
+ ),
605
+ ],
606
+ [
607
+ mt.SomeOf,
608
+ (mt.Flip(0),),
609
+ True,
610
+ (
611
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
612
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
613
+ "INFO - Pending transforms applied: applied_operations: 1\n"
614
+ ),
615
+ ],
616
+ [
617
+ mt.RandomOrder,
618
+ (mt.Flip(0),),
619
+ True,
620
+ (
621
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
622
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
623
+ "INFO - Pending transforms applied: applied_operations: 1\n"
624
+ ),
625
+ ],
626
+ [
627
+ mt.OneOf,
628
+ (mt.Flip(0),),
629
+ True,
630
+ (
631
+ "INFO - Accumulate pending transforms - lazy: True, pending: 0, "
632
+ "upcoming 'Flip', transform.lazy: False (overridden)\n"
633
+ "INFO - Pending transforms applied: applied_operations: 1\n"
634
+ ),
635
+ ],
636
+ [
637
+ mt.OneOf,
638
+ (mt.Flip(0),),
639
+ False,
640
+ ("INFO - Apply pending transforms - lazy: False, pending: 0, " "upcoming 'Flip', transform.lazy: False\n"),
641
+ ],
642
+ ]
643
+
644
+
645
+ class TestComposeExecuteWithLogging(unittest.TestCase):
646
+ LOGGER_NAME = "a_logger_name"
647
+
648
+ def init_logger(self, name=LOGGER_NAME):
649
+ stream = StringIO()
650
+ handler = logging.StreamHandler(stream)
651
+ formatter = logging.Formatter("%(levelname)s - %(message)s")
652
+ handler.setFormatter(formatter)
653
+ logger = logging.getLogger(name)
654
+ logger.setLevel(logging.INFO)
655
+ while len(logger.handlers) > 0:
656
+ logger.removeHandler(logger.handlers[-1])
657
+ logger.addHandler(handler)
658
+ return handler, stream
659
+
660
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_LOGGING_TEST_CASES)
661
+ def test_compose_with_logging(self, keys, pipeline, lazy, expected):
662
+ handler, stream = self.init_logger(name=self.LOGGER_NAME)
663
+
664
+ data = data_from_keys(keys, 12, 16)
665
+ c = mt.Compose(deepcopy(pipeline), lazy=lazy, log_stats=self.LOGGER_NAME)
666
+ c(data)
667
+
668
+ handler.flush()
669
+ actual = stream.getvalue()
670
+ self.assertEqual(actual, expected)
671
+
672
+ @parameterized.expand(TEST_COMPOSE_LAZY_ON_CALL_LOGGING_TEST_CASES)
673
+ def test_compose_lazy_on_call_with_logging(self, compose_type, pipeline, lazy_on_call, expected):
674
+ handler, stream = self.init_logger(name=self.LOGGER_NAME)
675
+
676
+ data = data_from_keys(None, 12, 16)
677
+ c = compose_type(deepcopy(pipeline), log_stats=self.LOGGER_NAME)
678
+ c(data, lazy=lazy_on_call)
679
+
680
+ handler.flush()
681
+ actual = stream.getvalue()
682
+ self.assertEqual(actual, expected)
683
+
684
+
685
+ class TestOps:
686
+
687
+ @staticmethod
688
+ def concat(value):
689
+
690
+ def _inner(data):
691
+ return data + value
692
+
693
+ return _inner
694
+
695
+ @staticmethod
696
+ def concatd(value):
697
+
698
+ def _inner(data):
699
+ return {k: v + value for k, v in data.items()}
700
+
701
+ return _inner
702
+
703
+ @staticmethod
704
+ def concata(value):
705
+
706
+ def _inner(data1, data2):
707
+ return data1 + value, data2 + value
708
+
709
+ return _inner
710
+
711
+
712
+ TEST_COMPOSE_EXECUTE_FLAG_TEST_CASES = [
713
+ [{}, ("",), (TestOps.concat("a"), TestOps.concat("b"))],
714
+ [{"unpack_items": True}, ("x", "y"), (TestOps.concat("a"), TestOps.concat("b"))],
715
+ [{"map_items": False}, {"x": "1", "y": "2"}, (TestOps.concatd("a"), TestOps.concatd("b"))],
716
+ [{"unpack_items": True, "map_items": False}, ("x", "y"), (TestOps.concata("a"), TestOps.concata("b"))],
717
+ ]
718
+
719
+
720
+ class TestComposeExecuteWithFlags(unittest.TestCase):
721
+
722
+ @parameterized.expand(TEST_COMPOSE_EXECUTE_FLAG_TEST_CASES)
723
+ def test_compose_execute_equivalence_with_flags(self, flags, data, pipeline):
724
+ expected = mt.Compose(pipeline, **flags)(data)
725
+
726
+ for cutoff in range(len(pipeline)):
727
+ c = mt.Compose(deepcopy(pipeline), **flags)
728
+ actual = c(c(data, end=cutoff), start=cutoff)
729
+ if isinstance(actual, dict):
730
+ for k in actual.keys():
731
+ self.assertEqual(expected[k], actual[k])
732
+ else:
733
+ self.assertEqual(expected, actual)
734
+
735
+ p = deepcopy(pipeline)
736
+ actual = execute_compose(execute_compose(data, p, start=0, end=cutoff, **flags), p, start=cutoff, **flags)
737
+ if isinstance(actual, dict):
738
+ for k in actual.keys():
739
+ self.assertEqual(expected[k], actual[k])
740
+ else:
741
+ self.assertEqual(expected, actual)
742
+
743
+
744
+ class TestComposeCallableInput(unittest.TestCase):
745
+
746
+ def test_value_error_when_not_sequence(self):
747
+ data = torch.tensor(np.random.randn(1, 5, 5))
748
+
749
+ xform = mt.Compose([mt.Flip(0), mt.Flip(0)])
750
+ res = xform(data)
751
+ np.testing.assert_allclose(data, res, atol=1e-3)
752
+
753
+ with self.assertRaises(ValueError):
754
+ mt.Compose(mt.Flip(0), mt.Flip(0))(data)
755
+
756
+
757
+ if __name__ == "__main__":
758
+ unittest.main()