monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2507__py3-none-any.whl

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Files changed (776) 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/inferers/utils.py +1 -2
  6. monai/losses/dice.py +2 -14
  7. monai/losses/ds_loss.py +1 -3
  8. monai/networks/layers/simplelayers.py +2 -14
  9. monai/networks/utils.py +4 -16
  10. monai/transforms/compose.py +28 -11
  11. monai/transforms/croppad/array.py +1 -6
  12. monai/transforms/io/array.py +0 -1
  13. monai/transforms/transform.py +15 -6
  14. monai/transforms/utils.py +1 -2
  15. monai/utils/tf32.py +0 -10
  16. monai/visualize/class_activation_maps.py +5 -8
  17. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
  18. monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
  19. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
  20. tests/apps/__init__.py +10 -0
  21. tests/apps/deepedit/__init__.py +10 -0
  22. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  23. tests/apps/deepgrow/__init__.py +10 -0
  24. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  25. tests/apps/deepgrow/transforms/__init__.py +10 -0
  26. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  27. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  28. tests/apps/detection/__init__.py +10 -0
  29. tests/apps/detection/metrics/__init__.py +10 -0
  30. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  31. tests/apps/detection/networks/__init__.py +10 -0
  32. tests/apps/detection/networks/test_retinanet.py +210 -0
  33. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  34. tests/apps/detection/test_box_transform.py +370 -0
  35. tests/apps/detection/utils/__init__.py +10 -0
  36. tests/apps/detection/utils/test_anchor_box.py +88 -0
  37. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  38. tests/apps/detection/utils/test_box_coder.py +43 -0
  39. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  40. tests/apps/detection/utils/test_detector_utils.py +96 -0
  41. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  42. tests/apps/nuclick/__init__.py +10 -0
  43. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  44. tests/apps/pathology/__init__.py +10 -0
  45. tests/apps/pathology/handlers/__init__.py +10 -0
  46. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  47. tests/apps/pathology/test_lesion_froc.py +333 -0
  48. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  49. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  50. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  51. tests/apps/pathology/transforms/__init__.py +10 -0
  52. tests/apps/pathology/transforms/post/__init__.py +10 -0
  53. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  54. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  55. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  56. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  57. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  58. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  59. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  60. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  61. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  62. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  63. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  64. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  65. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  66. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  67. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  68. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  69. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  70. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  71. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  72. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  73. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  74. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  75. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  76. tests/apps/reconstruction/__init__.py +10 -0
  77. tests/apps/reconstruction/nets/__init__.py +10 -0
  78. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  79. tests/apps/reconstruction/test_complex_utils.py +77 -0
  80. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  81. tests/apps/reconstruction/test_mri_utils.py +37 -0
  82. tests/apps/reconstruction/transforms/__init__.py +10 -0
  83. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  84. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  85. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  86. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  87. tests/apps/test_check_hash.py +53 -0
  88. tests/apps/test_cross_validation.py +74 -0
  89. tests/apps/test_decathlondataset.py +93 -0
  90. tests/apps/test_download_and_extract.py +70 -0
  91. tests/apps/test_download_url_yandex.py +45 -0
  92. tests/apps/test_mednistdataset.py +72 -0
  93. tests/apps/test_mmar_download.py +154 -0
  94. tests/apps/test_tciadataset.py +123 -0
  95. tests/apps/vista3d/__init__.py +10 -0
  96. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  97. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  98. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  99. tests/bundle/__init__.py +10 -0
  100. tests/bundle/test_bundle_ckpt_export.py +107 -0
  101. tests/bundle/test_bundle_download.py +435 -0
  102. tests/bundle/test_bundle_get_data.py +94 -0
  103. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  104. tests/bundle/test_bundle_trt_export.py +147 -0
  105. tests/bundle/test_bundle_utils.py +149 -0
  106. tests/bundle/test_bundle_verify_metadata.py +66 -0
  107. tests/bundle/test_bundle_verify_net.py +76 -0
  108. tests/bundle/test_bundle_workflow.py +272 -0
  109. tests/bundle/test_component_locator.py +38 -0
  110. tests/bundle/test_config_item.py +138 -0
  111. tests/bundle/test_config_parser.py +392 -0
  112. tests/bundle/test_reference_resolver.py +114 -0
  113. tests/config/__init__.py +10 -0
  114. tests/config/test_cv2_dist.py +53 -0
  115. tests/engines/__init__.py +10 -0
  116. tests/engines/test_ensemble_evaluator.py +94 -0
  117. tests/engines/test_prepare_batch_default.py +76 -0
  118. tests/engines/test_prepare_batch_default_dist.py +76 -0
  119. tests/engines/test_prepare_batch_diffusion.py +104 -0
  120. tests/engines/test_prepare_batch_extra_input.py +80 -0
  121. tests/fl/__init__.py +10 -0
  122. tests/fl/monai_algo/__init__.py +10 -0
  123. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  124. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  125. tests/fl/test_fl_monai_algo_stats.py +81 -0
  126. tests/fl/utils/__init__.py +10 -0
  127. tests/fl/utils/test_fl_exchange_object.py +63 -0
  128. tests/handlers/__init__.py +10 -0
  129. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  130. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  131. tests/handlers/test_handler_classification_saver.py +64 -0
  132. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  133. tests/handlers/test_handler_clearml_image.py +65 -0
  134. tests/handlers/test_handler_clearml_stats.py +65 -0
  135. tests/handlers/test_handler_confusion_matrix.py +104 -0
  136. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  137. tests/handlers/test_handler_decollate_batch.py +66 -0
  138. tests/handlers/test_handler_early_stop.py +68 -0
  139. tests/handlers/test_handler_garbage_collector.py +73 -0
  140. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  141. tests/handlers/test_handler_ignite_metric.py +191 -0
  142. tests/handlers/test_handler_lr_scheduler.py +94 -0
  143. tests/handlers/test_handler_mean_dice.py +98 -0
  144. tests/handlers/test_handler_mean_iou.py +76 -0
  145. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  146. tests/handlers/test_handler_metrics_saver.py +89 -0
  147. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  148. tests/handlers/test_handler_mlflow.py +296 -0
  149. tests/handlers/test_handler_nvtx.py +93 -0
  150. tests/handlers/test_handler_panoptic_quality.py +89 -0
  151. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  152. tests/handlers/test_handler_post_processing.py +74 -0
  153. tests/handlers/test_handler_prob_map_producer.py +111 -0
  154. tests/handlers/test_handler_regression_metrics.py +160 -0
  155. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  156. tests/handlers/test_handler_rocauc.py +48 -0
  157. tests/handlers/test_handler_rocauc_dist.py +54 -0
  158. tests/handlers/test_handler_stats.py +281 -0
  159. tests/handlers/test_handler_surface_distance.py +113 -0
  160. tests/handlers/test_handler_tb_image.py +61 -0
  161. tests/handlers/test_handler_tb_stats.py +166 -0
  162. tests/handlers/test_handler_validation.py +59 -0
  163. tests/handlers/test_trt_compile.py +145 -0
  164. tests/handlers/test_write_metrics_reports.py +68 -0
  165. tests/inferers/__init__.py +10 -0
  166. tests/inferers/test_avg_merger.py +179 -0
  167. tests/inferers/test_controlnet_inferers.py +1310 -0
  168. tests/inferers/test_diffusion_inferer.py +236 -0
  169. tests/inferers/test_latent_diffusion_inferer.py +824 -0
  170. tests/inferers/test_patch_inferer.py +309 -0
  171. tests/inferers/test_saliency_inferer.py +55 -0
  172. tests/inferers/test_slice_inferer.py +57 -0
  173. tests/inferers/test_sliding_window_inference.py +377 -0
  174. tests/inferers/test_sliding_window_splitter.py +284 -0
  175. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  176. tests/inferers/test_zarr_avg_merger.py +326 -0
  177. tests/integration/__init__.py +10 -0
  178. tests/integration/test_auto3dseg_ensemble.py +211 -0
  179. tests/integration/test_auto3dseg_hpo.py +189 -0
  180. tests/integration/test_deepedit_interaction.py +122 -0
  181. tests/integration/test_downsample_block.py +50 -0
  182. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  183. tests/integration/test_integration_autorunner.py +201 -0
  184. tests/integration/test_integration_bundle_run.py +240 -0
  185. tests/integration/test_integration_classification_2d.py +282 -0
  186. tests/integration/test_integration_determinism.py +95 -0
  187. tests/integration/test_integration_fast_train.py +231 -0
  188. tests/integration/test_integration_gpu_customization.py +159 -0
  189. tests/integration/test_integration_lazy_samples.py +219 -0
  190. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  191. tests/integration/test_integration_segmentation_3d.py +304 -0
  192. tests/integration/test_integration_sliding_window.py +100 -0
  193. tests/integration/test_integration_stn.py +133 -0
  194. tests/integration/test_integration_unet_2d.py +67 -0
  195. tests/integration/test_integration_workers.py +61 -0
  196. tests/integration/test_integration_workflows.py +365 -0
  197. tests/integration/test_integration_workflows_adversarial.py +173 -0
  198. tests/integration/test_integration_workflows_gan.py +158 -0
  199. tests/integration/test_loader_semaphore.py +48 -0
  200. tests/integration/test_mapping_filed.py +122 -0
  201. tests/integration/test_meta_affine.py +183 -0
  202. tests/integration/test_metatensor_integration.py +114 -0
  203. tests/integration/test_module_list.py +76 -0
  204. tests/integration/test_one_of.py +283 -0
  205. tests/integration/test_pad_collation.py +124 -0
  206. tests/integration/test_reg_loss_integration.py +107 -0
  207. tests/integration/test_retinanet_predict_utils.py +154 -0
  208. tests/integration/test_seg_loss_integration.py +159 -0
  209. tests/integration/test_spatial_combine_transforms.py +185 -0
  210. tests/integration/test_testtimeaugmentation.py +186 -0
  211. tests/integration/test_vis_gradbased.py +69 -0
  212. tests/integration/test_vista3d_utils.py +159 -0
  213. tests/losses/__init__.py +10 -0
  214. tests/losses/deform/__init__.py +10 -0
  215. tests/losses/deform/test_bending_energy.py +88 -0
  216. tests/losses/deform/test_diffusion_loss.py +117 -0
  217. tests/losses/image_dissimilarity/__init__.py +10 -0
  218. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  219. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  220. tests/losses/test_adversarial_loss.py +94 -0
  221. tests/losses/test_barlow_twins_loss.py +109 -0
  222. tests/losses/test_cldice_loss.py +51 -0
  223. tests/losses/test_contrastive_loss.py +86 -0
  224. tests/losses/test_dice_ce_loss.py +123 -0
  225. tests/losses/test_dice_focal_loss.py +124 -0
  226. tests/losses/test_dice_loss.py +227 -0
  227. tests/losses/test_ds_loss.py +189 -0
  228. tests/losses/test_focal_loss.py +379 -0
  229. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  230. tests/losses/test_generalized_dice_loss.py +221 -0
  231. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  232. tests/losses/test_giou_loss.py +62 -0
  233. tests/losses/test_hausdorff_loss.py +264 -0
  234. tests/losses/test_masked_dice_loss.py +152 -0
  235. tests/losses/test_masked_loss.py +87 -0
  236. tests/losses/test_multi_scale.py +86 -0
  237. tests/losses/test_nacl_loss.py +167 -0
  238. tests/losses/test_perceptual_loss.py +122 -0
  239. tests/losses/test_spectral_loss.py +86 -0
  240. tests/losses/test_ssim_loss.py +59 -0
  241. tests/losses/test_sure_loss.py +72 -0
  242. tests/losses/test_tversky_loss.py +198 -0
  243. tests/losses/test_unified_focal_loss.py +66 -0
  244. tests/metrics/__init__.py +10 -0
  245. tests/metrics/test_compute_confusion_matrix.py +294 -0
  246. tests/metrics/test_compute_f_beta.py +80 -0
  247. tests/metrics/test_compute_fid_metric.py +40 -0
  248. tests/metrics/test_compute_froc.py +143 -0
  249. tests/metrics/test_compute_generalized_dice.py +240 -0
  250. tests/metrics/test_compute_meandice.py +306 -0
  251. tests/metrics/test_compute_meaniou.py +223 -0
  252. tests/metrics/test_compute_mmd_metric.py +56 -0
  253. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  254. tests/metrics/test_compute_panoptic_quality.py +113 -0
  255. tests/metrics/test_compute_regression_metrics.py +196 -0
  256. tests/metrics/test_compute_roc_auc.py +155 -0
  257. tests/metrics/test_compute_variance.py +147 -0
  258. tests/metrics/test_cumulative.py +63 -0
  259. tests/metrics/test_cumulative_average.py +74 -0
  260. tests/metrics/test_cumulative_average_dist.py +48 -0
  261. tests/metrics/test_hausdorff_distance.py +209 -0
  262. tests/metrics/test_label_quality_score.py +134 -0
  263. tests/metrics/test_loss_metric.py +57 -0
  264. tests/metrics/test_metrics_reloaded.py +96 -0
  265. tests/metrics/test_ssim_metric.py +78 -0
  266. tests/metrics/test_surface_dice.py +416 -0
  267. tests/metrics/test_surface_distance.py +186 -0
  268. tests/networks/__init__.py +10 -0
  269. tests/networks/blocks/__init__.py +10 -0
  270. tests/networks/blocks/dints_block/__init__.py +10 -0
  271. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  272. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  273. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  274. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  275. tests/networks/blocks/test_adn.py +86 -0
  276. tests/networks/blocks/test_convolutions.py +156 -0
  277. tests/networks/blocks/test_crf_cpu.py +513 -0
  278. tests/networks/blocks/test_crf_cuda.py +528 -0
  279. tests/networks/blocks/test_crossattention.py +185 -0
  280. tests/networks/blocks/test_denseblock.py +105 -0
  281. tests/networks/blocks/test_dynunet_block.py +116 -0
  282. tests/networks/blocks/test_fpn_block.py +88 -0
  283. tests/networks/blocks/test_localnet_block.py +121 -0
  284. tests/networks/blocks/test_mlp.py +78 -0
  285. tests/networks/blocks/test_patchembedding.py +212 -0
  286. tests/networks/blocks/test_regunet_block.py +103 -0
  287. tests/networks/blocks/test_se_block.py +85 -0
  288. tests/networks/blocks/test_se_blocks.py +78 -0
  289. tests/networks/blocks/test_segresnet_block.py +57 -0
  290. tests/networks/blocks/test_selfattention.py +232 -0
  291. tests/networks/blocks/test_simple_aspp.py +87 -0
  292. tests/networks/blocks/test_spatialattention.py +55 -0
  293. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  294. tests/networks/blocks/test_text_encoding.py +49 -0
  295. tests/networks/blocks/test_transformerblock.py +90 -0
  296. tests/networks/blocks/test_unetr_block.py +158 -0
  297. tests/networks/blocks/test_upsample_block.py +134 -0
  298. tests/networks/blocks/warp/__init__.py +10 -0
  299. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  300. tests/networks/blocks/warp/test_warp.py +250 -0
  301. tests/networks/layers/__init__.py +10 -0
  302. tests/networks/layers/filtering/__init__.py +10 -0
  303. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  304. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  305. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  306. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  307. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  308. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  309. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  310. tests/networks/layers/test_affine_transform.py +385 -0
  311. tests/networks/layers/test_apply_filter.py +89 -0
  312. tests/networks/layers/test_channel_pad.py +51 -0
  313. tests/networks/layers/test_conjugate_gradient.py +56 -0
  314. tests/networks/layers/test_drop_path.py +46 -0
  315. tests/networks/layers/test_gaussian.py +317 -0
  316. tests/networks/layers/test_gaussian_filter.py +206 -0
  317. tests/networks/layers/test_get_layers.py +65 -0
  318. tests/networks/layers/test_gmm.py +314 -0
  319. tests/networks/layers/test_grid_pull.py +93 -0
  320. tests/networks/layers/test_hilbert_transform.py +131 -0
  321. tests/networks/layers/test_lltm.py +62 -0
  322. tests/networks/layers/test_median_filter.py +52 -0
  323. tests/networks/layers/test_polyval.py +55 -0
  324. tests/networks/layers/test_preset_filters.py +136 -0
  325. tests/networks/layers/test_savitzky_golay_filter.py +141 -0
  326. tests/networks/layers/test_separable_filter.py +87 -0
  327. tests/networks/layers/test_skip_connection.py +48 -0
  328. tests/networks/layers/test_vector_quantizer.py +89 -0
  329. tests/networks/layers/test_weight_init.py +50 -0
  330. tests/networks/nets/__init__.py +10 -0
  331. tests/networks/nets/dints/__init__.py +10 -0
  332. tests/networks/nets/dints/test_dints_cell.py +110 -0
  333. tests/networks/nets/dints/test_dints_mixop.py +84 -0
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  681. tests/transforms/test_std_shift_intensityd.py +74 -0
  682. tests/transforms/test_threshold_intensity.py +38 -0
  683. tests/transforms/test_threshold_intensityd.py +58 -0
  684. tests/transforms/test_to_contiguous.py +47 -0
  685. tests/transforms/test_to_cupy.py +112 -0
  686. tests/transforms/test_to_cupyd.py +76 -0
  687. tests/transforms/test_to_device.py +42 -0
  688. tests/transforms/test_to_deviced.py +37 -0
  689. tests/transforms/test_to_numpy.py +85 -0
  690. tests/transforms/test_to_numpyd.py +68 -0
  691. tests/transforms/test_to_pil.py +52 -0
  692. tests/transforms/test_to_pild.py +50 -0
  693. tests/transforms/test_to_tensor.py +60 -0
  694. tests/transforms/test_to_tensord.py +71 -0
  695. tests/transforms/test_torchvision.py +66 -0
  696. tests/transforms/test_torchvisiond.py +63 -0
  697. tests/transforms/test_transform.py +62 -0
  698. tests/transforms/test_transpose.py +41 -0
  699. tests/transforms/test_transposed.py +52 -0
  700. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  701. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  702. tests/transforms/test_vote_ensemble.py +84 -0
  703. tests/transforms/test_vote_ensembled.py +107 -0
  704. tests/transforms/test_with_allow_missing_keys.py +76 -0
  705. tests/transforms/test_zoom.py +120 -0
  706. tests/transforms/test_zoomd.py +94 -0
  707. tests/transforms/transform/__init__.py +10 -0
  708. tests/transforms/transform/test_randomizable.py +52 -0
  709. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  710. tests/transforms/utility/__init__.py +10 -0
  711. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  712. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  713. tests/transforms/utility/test_identity.py +29 -0
  714. tests/transforms/utility/test_identityd.py +30 -0
  715. tests/transforms/utility/test_lambda.py +71 -0
  716. tests/transforms/utility/test_lambdad.py +83 -0
  717. tests/transforms/utility/test_rand_lambda.py +87 -0
  718. tests/transforms/utility/test_rand_lambdad.py +77 -0
  719. tests/transforms/utility/test_simulatedelay.py +36 -0
  720. tests/transforms/utility/test_simulatedelayd.py +36 -0
  721. tests/transforms/utility/test_splitdim.py +52 -0
  722. tests/transforms/utility/test_splitdimd.py +96 -0
  723. tests/transforms/utils/__init__.py +10 -0
  724. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  725. tests/transforms/utils/test_get_unique_labels.py +45 -0
  726. tests/transforms/utils/test_print_transform_backends.py +29 -0
  727. tests/transforms/utils/test_soft_clip.py +125 -0
  728. tests/utils/__init__.py +10 -0
  729. tests/utils/enums/__init__.py +10 -0
  730. tests/utils/enums/test_hovernet_loss.py +190 -0
  731. tests/utils/enums/test_ordering.py +289 -0
  732. tests/utils/enums/test_wsireader.py +663 -0
  733. tests/utils/misc/__init__.py +10 -0
  734. tests/utils/misc/test_ensure_tuple.py +53 -0
  735. tests/utils/misc/test_monai_env_vars.py +44 -0
  736. tests/utils/misc/test_monai_utils_misc.py +103 -0
  737. tests/utils/misc/test_str2bool.py +34 -0
  738. tests/utils/misc/test_str2list.py +33 -0
  739. tests/utils/test_alias.py +44 -0
  740. tests/utils/test_component_store.py +73 -0
  741. tests/utils/test_deprecated.py +455 -0
  742. tests/utils/test_enum_bound_interp.py +75 -0
  743. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  744. tests/utils/test_get_package_version.py +34 -0
  745. tests/utils/test_handler_logfile.py +84 -0
  746. tests/utils/test_handler_metric_logger.py +62 -0
  747. tests/utils/test_list_to_dict.py +43 -0
  748. tests/utils/test_look_up_option.py +87 -0
  749. tests/utils/test_optional_import.py +80 -0
  750. tests/utils/test_pad_mode.py +39 -0
  751. tests/utils/test_profiling.py +208 -0
  752. tests/utils/test_rankfilter_dist.py +77 -0
  753. tests/utils/test_require_pkg.py +83 -0
  754. tests/utils/test_sample_slices.py +43 -0
  755. tests/utils/test_set_determinism.py +74 -0
  756. tests/utils/test_squeeze_unsqueeze.py +71 -0
  757. tests/utils/test_state_cacher.py +67 -0
  758. tests/utils/test_torchscript_utils.py +113 -0
  759. tests/utils/test_version.py +91 -0
  760. tests/utils/test_version_after.py +65 -0
  761. tests/utils/type_conversion/__init__.py +10 -0
  762. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  763. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  764. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  765. tests/visualize/__init__.py +10 -0
  766. tests/visualize/test_img2tensorboard.py +46 -0
  767. tests/visualize/test_occlusion_sensitivity.py +128 -0
  768. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  769. tests/visualize/test_vis_cam.py +98 -0
  770. tests/visualize/test_vis_gradcam.py +211 -0
  771. tests/visualize/utils/__init__.py +10 -0
  772. tests/visualize/utils/test_blend_images.py +63 -0
  773. tests/visualize/utils/test_matshow3d.py +133 -0
  774. monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
  775. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
  776. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
@@ -0,0 +1,90 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import sys
15
+ import unittest
16
+
17
+ import numpy as np
18
+ import torch.multiprocessing as mp
19
+ from parameterized import parameterized
20
+
21
+ from monai.data import DataLoader, Dataset
22
+ from monai.transforms import IntensityStatsd
23
+ from monai.utils.enums import PostFix
24
+
25
+ TEST_CASE_1 = [
26
+ {"keys": "img", "ops": ["max", "mean"], "key_prefix": "orig", "meta_keys": "test_meta"},
27
+ {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]]), "test_meta": {"affine": None}},
28
+ "test_meta",
29
+ {"orig_max": 3.0, "orig_mean": 1.5},
30
+ ]
31
+
32
+ TEST_CASE_2 = [
33
+ {"keys": "img", "ops": "std", "key_prefix": "orig"},
34
+ {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])},
35
+ PostFix.meta("img"),
36
+ {"orig_std": 1.118034},
37
+ ]
38
+
39
+ TEST_CASE_3 = [
40
+ {"keys": "img", "ops": [np.mean, "max", np.min], "key_prefix": "orig"},
41
+ {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])},
42
+ PostFix.meta("img"),
43
+ {"orig_custom_0": 1.5, "orig_max": 3.0, "orig_custom_1": 0.0},
44
+ ]
45
+
46
+ TEST_CASE_4 = [
47
+ {"keys": "img", "ops": ["max", "mean"], "key_prefix": "orig", "channel_wise": True, "meta_key_postfix": "meta"},
48
+ {"img": np.array([[[0.0, 1.0], [2.0, 3.0]], [[4.0, 5.0], [6.0, 7.0]]]), "img_meta": {"affine": None}},
49
+ "img_meta",
50
+ {"orig_max": [3.0, 7.0], "orig_mean": [1.5, 5.5]},
51
+ ]
52
+
53
+
54
+ class TestIntensityStatsd(unittest.TestCase):
55
+
56
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4])
57
+ def test_value(self, input_param, data, meta_key, expected):
58
+ meta = IntensityStatsd(**input_param)(data)[meta_key]
59
+ for k, v in expected.items():
60
+ self.assertTrue(k in meta)
61
+ np.testing.assert_allclose(v, meta[k], atol=1e-3)
62
+
63
+ def test_dataloader(self):
64
+ dataset = Dataset(
65
+ data=[{"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])}, {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]])}],
66
+ transform=IntensityStatsd(keys="img", ops=["max", "mean"], key_prefix="orig"),
67
+ )
68
+ # set num workers = 0 for mac / win
69
+ num_workers = 2 if sys.platform == "linux" else 0
70
+ dataloader = DataLoader(dataset=dataset, num_workers=num_workers, batch_size=2)
71
+ orig_method = mp.get_start_method()
72
+ mp.set_start_method("spawn", force=True)
73
+
74
+ for d in dataloader:
75
+ meta = d[PostFix.meta("img")]
76
+ np.testing.assert_allclose(meta["orig_max"], [3.0, 3.0], atol=1e-3)
77
+ np.testing.assert_allclose(meta["orig_mean"], [1.5, 1.5], atol=1e-3)
78
+ # restore the mp method
79
+ mp.set_start_method(orig_method, force=True)
80
+
81
+ def test_mask(self):
82
+ data = {"img": np.array([[[0.0, 1.0], [2.0, 3.0]]]), "img_mask": np.array([[[1, 0], [1, 0]]], dtype=bool)}
83
+ stats = IntensityStatsd(keys="img", ops=["max", "mean"], mask_keys="img_mask", key_prefix="orig")
84
+ meta = stats(data)[PostFix.meta("img")]
85
+ np.testing.assert_allclose(meta["orig_max"], 2.0, atol=1e-3)
86
+ np.testing.assert_allclose(meta["orig_mean"], 1.0, atol=1e-3)
87
+
88
+
89
+ if __name__ == "__main__":
90
+ unittest.main()
@@ -0,0 +1,521 @@
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 random
15
+ import sys
16
+ import unittest
17
+ from copy import deepcopy
18
+ from functools import partial
19
+ from typing import TYPE_CHECKING
20
+ from unittest.case import skipUnless
21
+
22
+ import numpy as np
23
+ import torch
24
+ from parameterized import parameterized
25
+
26
+ from monai.data import CacheDataset, DataLoader, MetaTensor, create_test_image_2d, create_test_image_3d, decollate_batch
27
+ from monai.networks.nets import UNet
28
+ from monai.transforms import (
29
+ Affined,
30
+ BorderPadd,
31
+ CenterScaleCropd,
32
+ CenterSpatialCropd,
33
+ Compose,
34
+ CropForegroundd,
35
+ DivisiblePadd,
36
+ EnsureChannelFirstd,
37
+ Flipd,
38
+ FromMetaTensord,
39
+ InvertibleTransform,
40
+ Lambdad,
41
+ LoadImaged,
42
+ Orientationd,
43
+ RandAffined,
44
+ RandAxisFlipd,
45
+ RandCropByLabelClassesd,
46
+ RandCropByPosNegLabeld,
47
+ RandFlipd,
48
+ RandLambdad,
49
+ Randomizable,
50
+ RandRotate90d,
51
+ RandRotated,
52
+ RandSpatialCropd,
53
+ RandSpatialCropSamplesd,
54
+ RandWeightedCropd,
55
+ RandZoomd,
56
+ Resized,
57
+ ResizeWithPadOrCrop,
58
+ ResizeWithPadOrCropd,
59
+ Rotate90d,
60
+ Rotated,
61
+ Spacingd,
62
+ SpatialCropd,
63
+ SpatialPadd,
64
+ ToMetaTensord,
65
+ Transposed,
66
+ Zoomd,
67
+ allow_missing_keys_mode,
68
+ convert_applied_interp_mode,
69
+ reset_ops_id,
70
+ )
71
+ from monai.utils import first, get_seed, optional_import, set_determinism
72
+ from tests.test_utils import make_nifti_image, make_rand_affine
73
+
74
+ if TYPE_CHECKING:
75
+ has_nib = True
76
+ else:
77
+ _, has_nib = optional_import("nibabel")
78
+
79
+ KEYS = ["image", "label"]
80
+
81
+ TESTS: list[tuple] = []
82
+
83
+ # For pad, start with odd/even images and add odd/even amounts
84
+ for name in ("1D even", "1D odd"):
85
+ for val in (3, 4):
86
+ for t in (
87
+ partial(SpatialPadd, spatial_size=val, method="symmetric"),
88
+ partial(SpatialPadd, spatial_size=val, method="end"),
89
+ partial(BorderPadd, spatial_border=[val, val + 1]),
90
+ partial(DivisiblePadd, k=val),
91
+ partial(ResizeWithPadOrCropd, spatial_size=20 + val),
92
+ partial(CenterSpatialCropd, roi_size=10 + val),
93
+ partial(CenterScaleCropd, roi_scale=0.8),
94
+ partial(CropForegroundd, source_key="label"),
95
+ partial(SpatialCropd, roi_center=10, roi_size=10 + val),
96
+ partial(SpatialCropd, roi_center=11, roi_size=10 + val),
97
+ partial(SpatialCropd, roi_start=val, roi_end=17),
98
+ partial(SpatialCropd, roi_start=val, roi_end=16),
99
+ partial(RandSpatialCropd, roi_size=12 + val),
100
+ partial(ResizeWithPadOrCropd, spatial_size=21 - val),
101
+ ):
102
+ TESTS.append((t.func.__name__ + name, name, 0, True, t(KEYS))) # type: ignore
103
+
104
+ # non-sensical tests: crop bigger or pad smaller or -ve values
105
+ for t in (
106
+ partial(DivisiblePadd, k=-3),
107
+ partial(CenterSpatialCropd, roi_size=-3),
108
+ partial(RandSpatialCropd, roi_size=-3),
109
+ partial(SpatialPadd, spatial_size=15),
110
+ partial(BorderPadd, spatial_border=[15, 16]),
111
+ partial(CenterSpatialCropd, roi_size=30),
112
+ partial(SpatialCropd, roi_center=10, roi_size=100),
113
+ partial(SpatialCropd, roi_start=3, roi_end=100),
114
+ ):
115
+ TESTS.append((t.func.__name__ + "bad 1D even", "1D even", 0, True, t(KEYS))) # type: ignore
116
+
117
+ TESTS.append(
118
+ (
119
+ "SpatialPadd (x2) 2d",
120
+ "2D",
121
+ 0,
122
+ True,
123
+ SpatialPadd(KEYS, spatial_size=[111, 113], method="end"),
124
+ SpatialPadd(KEYS, spatial_size=[118, 117]),
125
+ )
126
+ )
127
+
128
+ TESTS.append(("SpatialPadd 3d", "3D", 0, True, SpatialPadd(KEYS, spatial_size=[112, 113, 116])))
129
+
130
+ TESTS.append(("SpatialCropd 2d", "2D", 0, True, SpatialCropd(KEYS, [49, 51], [90, 89])))
131
+
132
+ TESTS.append(
133
+ (
134
+ "SpatialCropd 3d",
135
+ "3D",
136
+ 0,
137
+ True,
138
+ SpatialCropd(KEYS, roi_slices=[slice(s, e) for s, e in zip([None, None, -99], [None, -2, None])]),
139
+ )
140
+ )
141
+
142
+ TESTS.append(("SpatialCropd 2d", "2D", 0, True, SpatialCropd(KEYS, [49, 51], [390, 89])))
143
+
144
+ TESTS.append(("SpatialCropd 3d", "3D", 0, True, SpatialCropd(KEYS, [49, 51, 44], [90, 89, 93])))
145
+
146
+ TESTS.append(("RandSpatialCropd 2d", "2D", 0, True, RandSpatialCropd(KEYS, [96, 93], None, True, False)))
147
+
148
+ TESTS.append(("RandSpatialCropd 3d", "3D", 0, True, RandSpatialCropd(KEYS, [96, 93, 92], None, False, False)))
149
+
150
+ TESTS.append(("BorderPadd 2d", "2D", 0, True, BorderPadd(KEYS, [3, 7, 2, 5])))
151
+
152
+ TESTS.append(("BorderPadd 2d", "2D", 0, True, BorderPadd(KEYS, [3, 7])))
153
+
154
+ TESTS.append(("BorderPadd 3d", "3D", 0, True, BorderPadd(KEYS, [4])))
155
+
156
+ TESTS.append(("DivisiblePadd 2d", "2D", 0, True, DivisiblePadd(KEYS, k=4)))
157
+
158
+ TESTS.append(("DivisiblePadd 3d", "3D", 0, True, DivisiblePadd(KEYS, k=[4, 8, 11])))
159
+
160
+ TESTS.append(("CenterSpatialCropd 2d", "2D", 0, True, CenterSpatialCropd(KEYS, roi_size=95)))
161
+
162
+ TESTS.append(("CenterSpatialCropd 3d", "3D", 0, True, CenterSpatialCropd(KEYS, roi_size=[95, 97, 98])))
163
+
164
+ TESTS.append(("CropForegroundd 2d", "2D", 0, True, CropForegroundd(KEYS, source_key="label", margin=2)))
165
+
166
+ TESTS.append(("CropForegroundd 3d", "3D", 0, True, CropForegroundd(KEYS, source_key="label", k_divisible=[5, 101, 2])))
167
+
168
+ TESTS.append(("ResizeWithPadOrCropd 3d", "3D", 0, True, ResizeWithPadOrCropd(KEYS, [201, 150, 105])))
169
+
170
+ TESTS.append(("Flipd 3d", "3D", 0, True, Flipd(KEYS, [1, 2])))
171
+ TESTS.append(("Flipd 3d", "3D", 0, True, Flipd(KEYS, [1, 2])))
172
+
173
+ TESTS.append(("RandFlipd 3d", "3D", 0, True, RandFlipd(KEYS, 1, [1, 2])))
174
+
175
+ TESTS.append(("RandAxisFlipd 3d", "3D", 0, True, RandAxisFlipd(KEYS, 1)))
176
+ TESTS.append(("RandAxisFlipd 3d", "3D", 0, True, RandAxisFlipd(KEYS, 1)))
177
+
178
+ for acc in [True, False]:
179
+ TESTS.append(("Orientationd 3d", "3D", 0, True, Orientationd(KEYS, "RAS", as_closest_canonical=acc)))
180
+
181
+ TESTS.append(("Rotate90d 2d", "2D", 0, True, Rotate90d(KEYS)))
182
+
183
+ TESTS.append(("Rotate90d 3d", "3D", 0, True, Rotate90d(KEYS, k=2, spatial_axes=(1, 2))))
184
+
185
+ TESTS.append(("RandRotate90d 3d", "3D", 0, True, RandRotate90d(KEYS, prob=1, spatial_axes=(1, 2))))
186
+
187
+ TESTS.append(("Spacingd 3d", "3D", 3e-2, True, Spacingd(KEYS, [0.5, 0.7, 0.9], diagonal=False)))
188
+
189
+ TESTS.append(("Resized 2d", "2D", 2e-1, True, Resized(KEYS, [50, 47])))
190
+
191
+ TESTS.append(("Resized 3d", "3D", 5e-2, True, Resized(KEYS, [201, 150, 78])))
192
+
193
+ TESTS.append(("Resized longest 2d", "2D", 2e-1, True, Resized(KEYS, 47, "longest", "area")))
194
+
195
+ TESTS.append(("Resized longest 3d", "3D", 5e-2, True, Resized(KEYS, 201, "longest", "trilinear", True)))
196
+
197
+ TESTS.append(
198
+ ("Lambdad 2d", "2D", 5e-2, False, Lambdad(KEYS, func=lambda x: x + 5, inv_func=lambda x: x - 5, overwrite=True))
199
+ )
200
+
201
+ TESTS.append(
202
+ (
203
+ "RandLambdad 3d",
204
+ "3D",
205
+ 5e-2,
206
+ False,
207
+ RandLambdad(KEYS, func=lambda x: x * 10, inv_func=lambda x: x / 10, overwrite=True, prob=0.5),
208
+ )
209
+ )
210
+
211
+ TESTS.append(("Zoomd 1d", "1D odd", 0, True, Zoomd(KEYS, zoom=2, keep_size=False)))
212
+
213
+ TESTS.append(("Zoomd 2d", "2D", 2e-1, True, Zoomd(KEYS, zoom=0.9)))
214
+
215
+ TESTS.append(("Zoomd 3d", "3D", 3e-2, True, Zoomd(KEYS, zoom=[2.5, 1, 3], keep_size=False)))
216
+
217
+ TESTS.append(("RandZoom 3d", "3D", 9e-2, True, RandZoomd(KEYS, 1, [0.5, 0.6, 0.9], [1.1, 1, 1.05], keep_size=True)))
218
+
219
+ TESTS.append(("RandRotated, prob 0", "2D", 0, True, RandRotated(KEYS, prob=0, dtype=np.float64)))
220
+
221
+ TESTS.append(
222
+ (
223
+ "Rotated 2d",
224
+ "2D",
225
+ 8e-2,
226
+ True,
227
+ Rotated(KEYS, random.uniform(np.pi / 6, np.pi), keep_size=True, align_corners=False, dtype=np.float64),
228
+ )
229
+ )
230
+
231
+ TESTS.append(
232
+ (
233
+ "Rotated 3d",
234
+ "3D",
235
+ 1e-1,
236
+ True,
237
+ Rotated(KEYS, [random.uniform(np.pi / 6, np.pi) for _ in range(3)], True, dtype=np.float64),
238
+ )
239
+ )
240
+
241
+ TESTS.append(
242
+ (
243
+ "RandRotated 3d",
244
+ "3D",
245
+ 1e-1,
246
+ True,
247
+ RandRotated(KEYS, *[random.uniform(np.pi / 6, np.pi) for _ in range(3)], 1, dtype=np.float64), # type: ignore
248
+ )
249
+ )
250
+
251
+ TESTS.append(("Transposed 2d", "2D", 0, False, Transposed(KEYS, [0, 2, 1]))) # channel=0
252
+
253
+ TESTS.append(("Transposed 3d", "3D", 0, False, Transposed(KEYS, [0, 3, 1, 2]))) # channel=0
254
+
255
+ TESTS.append(
256
+ (
257
+ "Affine 3d",
258
+ "3D",
259
+ 1e-1,
260
+ True,
261
+ Affined(
262
+ KEYS,
263
+ spatial_size=[155, 179, 192],
264
+ rotate_params=[np.pi / 6, -np.pi / 5, np.pi / 7],
265
+ shear_params=[0.5, 0.5],
266
+ translate_params=[10, 5, -4],
267
+ scale_params=[0.8, 1.3],
268
+ ),
269
+ )
270
+ )
271
+
272
+ TESTS.append(
273
+ (
274
+ "RandAffine 3d",
275
+ "3D",
276
+ 1e-1,
277
+ True,
278
+ RandAffined(
279
+ KEYS,
280
+ [155, 179, 192],
281
+ prob=1,
282
+ padding_mode="zeros",
283
+ rotate_range=[np.pi / 6, -np.pi / 5, np.pi / 7],
284
+ shear_range=[(0.5, 0.5)],
285
+ translate_range=[10, 5, -4],
286
+ scale_range=[(0.8, 1.2), (0.9, 1.3)],
287
+ ),
288
+ )
289
+ )
290
+
291
+ TESTS.append(("RandAffine 3d", "3D", 0, True, RandAffined(KEYS, spatial_size=None, prob=0)))
292
+
293
+ TESTS.append(
294
+ (
295
+ "RandCropByLabelClassesd 2d",
296
+ "2D",
297
+ 1e-7,
298
+ True,
299
+ RandCropByLabelClassesd(KEYS, "label", (99, 96), ratios=[1, 2, 3, 4, 5], num_classes=5, num_samples=10),
300
+ )
301
+ )
302
+
303
+ TESTS.append(
304
+ ("RandCropByPosNegLabeld 2d", "2D", 1e-7, True, RandCropByPosNegLabeld(KEYS, "label", (99, 96), num_samples=10))
305
+ )
306
+
307
+ TESTS.append(("RandSpatialCropSamplesd 2d", "2D", 1e-7, True, RandSpatialCropSamplesd(KEYS, (90, 91), num_samples=10)))
308
+
309
+ TESTS.append(("RandWeightedCropd 2d", "2D", 1e-7, True, RandWeightedCropd(KEYS, "label", (90, 91), num_samples=10)))
310
+
311
+ TESTS_COMPOSE_X2 = [(t[0] + " Compose", t[1], t[2], t[3], Compose(Compose(t[4:]))) for t in TESTS]
312
+
313
+ TESTS = TESTS + TESTS_COMPOSE_X2
314
+
315
+ NUM_SAMPLES = 5
316
+ N_SAMPLES_TESTS = [
317
+ [RandCropByLabelClassesd(KEYS, "label", (110, 99), [1, 2, 3, 4, 5], num_classes=5, num_samples=NUM_SAMPLES)],
318
+ [RandCropByPosNegLabeld(KEYS, "label", (110, 99), num_samples=NUM_SAMPLES)],
319
+ [RandSpatialCropSamplesd(KEYS, (90, 91), num_samples=NUM_SAMPLES, random_size=False)],
320
+ [RandWeightedCropd(KEYS, "label", (90, 91), num_samples=NUM_SAMPLES)],
321
+ ]
322
+
323
+
324
+ def no_collation(x):
325
+ return x
326
+
327
+
328
+ class TestInverse(unittest.TestCase):
329
+ """Test inverse methods.
330
+
331
+ If tests are failing, the following function might be useful for displaying
332
+ `x`, `fx`, `f⁻¹fx` and `x - f⁻¹fx`.
333
+
334
+ .. code-block:: python
335
+
336
+ def plot_im(orig, fwd_bck, fwd):
337
+ import matplotlib.pyplot as plt
338
+ diff_orig_fwd_bck = orig - fwd_bck
339
+ ims_to_show = [orig, fwd, fwd_bck, diff_orig_fwd_bck]
340
+ titles = ["x", "fx", "f⁻¹fx", "x - f⁻¹fx"]
341
+ fig, axes = plt.subplots(1, 4, gridspec_kw={"width_ratios": [i.shape[1] for i in ims_to_show]})
342
+ vmin = min(np.array(i).min() for i in [orig, fwd_bck, fwd])
343
+ vmax = max(np.array(i).max() for i in [orig, fwd_bck, fwd])
344
+ for im, title, ax in zip(ims_to_show, titles, axes):
345
+ _vmin, _vmax = (vmin, vmax) if id(im) != id(diff_orig_fwd_bck) else (None, None)
346
+ im = np.squeeze(np.array(im))
347
+ while im.ndim > 2:
348
+ im = im[..., im.shape[-1] // 2]
349
+ im_show = ax.imshow(np.squeeze(im), vmin=_vmin, vmax=_vmax)
350
+ ax.set_title(title, fontsize=25)
351
+ ax.axis("off")
352
+ fig.colorbar(im_show, ax=ax)
353
+ plt.show()
354
+
355
+ This can then be added to the exception:
356
+
357
+ .. code-block:: python
358
+
359
+ except AssertionError:
360
+ print(
361
+ f"Failed: {name}. Mean diff = {mean_diff} (expected <= {acceptable_diff}), unmodified diff: {unmodded_diff}"
362
+ )
363
+ if orig[0].ndim > 1:
364
+ plot_im(orig, fwd_bck, unmodified)
365
+ """
366
+
367
+ def setUp(self):
368
+ if not has_nib:
369
+ self.skipTest("nibabel required for test_inverse")
370
+
371
+ set_determinism(seed=0)
372
+
373
+ self.all_data = {}
374
+
375
+ affine = make_rand_affine()
376
+ affine[0] *= 2
377
+
378
+ for size in [10, 11]:
379
+ # pad 5 onto both ends so that cropping can be lossless
380
+ im_1d = np.pad(np.arange(size), 5)[None]
381
+ name = "1D even" if size % 2 == 0 else "1D odd"
382
+ self.all_data[name] = {
383
+ "image": torch.as_tensor(np.array(im_1d, copy=True)),
384
+ "label": torch.as_tensor(np.array(im_1d, copy=True)),
385
+ "other": torch.as_tensor(np.array(im_1d, copy=True)),
386
+ }
387
+
388
+ im_2d_fname, seg_2d_fname = (make_nifti_image(i) for i in create_test_image_2d(101, 100))
389
+ im_3d_fname, seg_3d_fname = (make_nifti_image(i, affine) for i in create_test_image_3d(100, 101, 107))
390
+
391
+ load_ims = Compose(
392
+ [LoadImaged(KEYS), EnsureChannelFirstd(KEYS, channel_dim="no_channel"), FromMetaTensord(KEYS)]
393
+ )
394
+ self.all_data["2D"] = load_ims({"image": im_2d_fname, "label": seg_2d_fname})
395
+ self.all_data["3D"] = load_ims({"image": im_3d_fname, "label": seg_3d_fname})
396
+
397
+ def tearDown(self):
398
+ set_determinism(seed=None)
399
+
400
+ def check_inverse(self, name, keys, orig_d, fwd_bck_d, unmodified_d, acceptable_diff):
401
+ for key in keys:
402
+ orig = orig_d[key]
403
+ fwd_bck = fwd_bck_d[key]
404
+ if isinstance(fwd_bck, torch.Tensor):
405
+ fwd_bck = fwd_bck.cpu().numpy()
406
+ unmodified = unmodified_d[key]
407
+ if isinstance(orig, np.ndarray):
408
+ mean_diff = np.mean(np.abs(orig - fwd_bck))
409
+ resized = ResizeWithPadOrCrop(orig.shape[1:])(unmodified)
410
+ if isinstance(resized, torch.Tensor):
411
+ resized = resized.detach().cpu().numpy()
412
+ unmodded_diff = np.mean(np.abs(orig - resized))
413
+ try:
414
+ self.assertLessEqual(mean_diff, acceptable_diff)
415
+ except AssertionError:
416
+ print(
417
+ f"Failed: {name}. Mean diff = {mean_diff} (expected <= {acceptable_diff}), unmodified diff: {unmodded_diff}"
418
+ )
419
+ if orig[0].ndim == 1:
420
+ print("orig", orig[0])
421
+ print("fwd_bck", fwd_bck[0])
422
+ print("unmod", unmodified[0])
423
+ raise
424
+
425
+ @parameterized.expand(TESTS)
426
+ def test_inverse(self, _, data_name, acceptable_diff, is_meta, *transforms):
427
+ name = _
428
+
429
+ data = self.all_data[data_name]
430
+ if is_meta:
431
+ data = ToMetaTensord(KEYS)(data)
432
+
433
+ forwards = [data.copy()]
434
+
435
+ # Apply forwards
436
+ for t in transforms:
437
+ if isinstance(t, Randomizable):
438
+ t.set_random_state(seed=get_seed())
439
+ forwards.append(t(forwards[-1]))
440
+
441
+ # Apply inverses
442
+ fwd_bck = forwards[-1].copy()
443
+ for i, t in enumerate(reversed(transforms)):
444
+ if isinstance(t, InvertibleTransform):
445
+ if isinstance(fwd_bck, list):
446
+ for j, _fwd_bck in enumerate(fwd_bck):
447
+ fwd_bck = t.inverse(_fwd_bck)
448
+ self.check_inverse(
449
+ name, data.keys(), forwards[-i - 2], fwd_bck, forwards[-1][j], acceptable_diff
450
+ )
451
+ else:
452
+ fwd_bck = t.inverse(fwd_bck)
453
+ self.check_inverse(name, data.keys(), forwards[-i - 2], fwd_bck, forwards[-1], acceptable_diff)
454
+
455
+ # skip this test if multiprocessing uses 'spawn', as the check is only basic anyway
456
+ @skipUnless(torch.multiprocessing.get_start_method() == "spawn", "requires spawn")
457
+ def test_fail(self):
458
+ t1 = SpatialPadd("image", [10, 5])
459
+ data = t1(self.all_data["2D"])
460
+
461
+ # Check that error is thrown when inverse are used out of order.
462
+ t2 = ResizeWithPadOrCropd("image", [10, 5])
463
+ with self.assertRaises(RuntimeError):
464
+ t2.inverse(data)
465
+
466
+ @parameterized.expand(N_SAMPLES_TESTS)
467
+ def test_inverse_inferred_seg(self, extra_transform):
468
+ test_data = []
469
+ for _ in range(20):
470
+ image, label = create_test_image_2d(100, 101)
471
+ test_data.append({"image": image, "label": label.astype(np.float32)})
472
+
473
+ batch_size = 10
474
+ # num workers = 0 for mac
475
+ num_workers = 2 if sys.platform == "linux" else 0
476
+ transforms = Compose(
477
+ [EnsureChannelFirstd(KEYS, channel_dim="no_channel"), SpatialPadd(KEYS, (150, 153)), extra_transform]
478
+ )
479
+
480
+ dataset = CacheDataset(test_data, transform=transforms, progress=False)
481
+ loader = DataLoader(dataset, batch_size=batch_size, shuffle=False, num_workers=num_workers)
482
+
483
+ device = "cuda" if torch.cuda.is_available() else "cpu"
484
+ model = UNet(spatial_dims=2, in_channels=1, out_channels=1, channels=(2, 4), strides=(1,)).to(device)
485
+
486
+ data = first(loader)
487
+ self.assertEqual(data["image"].shape[0], batch_size * NUM_SAMPLES)
488
+
489
+ labels = data["label"].to(device)
490
+ self.assertIsInstance(labels, MetaTensor)
491
+ segs = model(labels).detach().cpu()
492
+ segs_decollated = decollate_batch(segs)
493
+ self.assertIsInstance(segs_decollated[0], MetaTensor)
494
+ # inverse of individual segmentation
495
+ seg_metatensor = first(segs_decollated)
496
+ # test to convert interpolation mode for 1 data of model output batch
497
+ convert_applied_interp_mode(seg_metatensor.applied_operations, mode="nearest", align_corners=None)
498
+
499
+ # manually invert the last crop samples
500
+ xform = seg_metatensor.applied_operations.pop(-1)
501
+ shape_before_extra_xform = xform["orig_size"]
502
+ resizer = ResizeWithPadOrCrop(spatial_size=shape_before_extra_xform)
503
+ with resizer.trace_transform(False):
504
+ seg_metatensor = resizer(seg_metatensor)
505
+ no_ops_id_tensor = reset_ops_id(deepcopy(seg_metatensor))
506
+
507
+ with allow_missing_keys_mode(transforms):
508
+ inv_seg = transforms.inverse({"label": seg_metatensor})["label"]
509
+ inv_seg_1 = transforms.inverse({"label": no_ops_id_tensor})["label"]
510
+ self.assertEqual(inv_seg.shape[1:], test_data[0]["label"].shape)
511
+ self.assertEqual(inv_seg_1.shape[1:], test_data[0]["label"].shape)
512
+
513
+ # # Inverse of batch
514
+ # batch_inverter = BatchInverseTransform(transforms, loader, collate_fn=no_collation, detach=True)
515
+ # with allow_missing_keys_mode(transforms):
516
+ # inv_batch = batch_inverter(first(loader))
517
+ # self.assertEqual(inv_batch[0]["label"].shape[1:], test_data[0]["label"].shape)
518
+
519
+
520
+ if __name__ == "__main__":
521
+ unittest.main()