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 +1,178 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ import torch
18
+ from parameterized import parameterized
19
+
20
+ from monai.data.meta_obj import set_track_meta
21
+ from monai.data.meta_tensor import MetaTensor
22
+ from monai.data.utils import affine_to_spacing
23
+ from monai.transforms import Spacingd
24
+ from monai.utils import ensure_tuple_rep
25
+ from tests.lazy_transforms_utils import test_resampler_lazy
26
+ from tests.test_utils import TEST_DEVICES, assert_allclose, skip_if_quick
27
+
28
+ TESTS: list[tuple] = []
29
+ for device in TEST_DEVICES:
30
+ TESTS.append(
31
+ (
32
+ "spacing 3d",
33
+ {"image": MetaTensor(torch.ones((2, 10, 15, 20)), affine=torch.eye(4))},
34
+ dict(keys="image", pixdim=(1, 2, 1.4)),
35
+ (2, 10, 8, 15),
36
+ torch.as_tensor(np.diag([1, 2, 1.4, 1.0])),
37
+ *device,
38
+ )
39
+ )
40
+ TESTS.append(
41
+ (
42
+ "spacing 2d",
43
+ {"image": MetaTensor(torch.ones((2, 10, 20)), affine=torch.eye(3))},
44
+ dict(keys="image", pixdim=(1, 2)),
45
+ (2, 10, 10),
46
+ torch.as_tensor(np.diag((1, 2, 1))),
47
+ *device,
48
+ )
49
+ )
50
+ TESTS.append(
51
+ (
52
+ "spacing 2d no metadata",
53
+ {"image": MetaTensor(torch.ones((2, 10, 20)))},
54
+ dict(keys="image", pixdim=(1, 2)),
55
+ (2, 10, 10),
56
+ torch.as_tensor(np.diag((1, 2, 1, 1))),
57
+ *device,
58
+ )
59
+ )
60
+ TESTS.append(
61
+ (
62
+ "interp all",
63
+ {
64
+ "image": MetaTensor(np.arange(20).reshape((2, 1, 10)), affine=torch.eye(4)),
65
+ "seg": MetaTensor(torch.ones((2, 1, 10)), affine=torch.eye(4)),
66
+ },
67
+ dict(keys=("image", "seg"), mode="nearest", pixdim=(1, 0.2)),
68
+ (2, 1, 46),
69
+ torch.as_tensor(np.diag((1, 0.2, 1, 1))),
70
+ *device,
71
+ )
72
+ )
73
+ TESTS.append(
74
+ (
75
+ "interp sep",
76
+ {
77
+ "image": MetaTensor(torch.ones((2, 1, 10)), affine=torch.eye(4)),
78
+ "seg": MetaTensor(torch.ones((2, 1, 10)), affine=torch.eye(4)),
79
+ },
80
+ dict(keys=("image", "seg"), mode=("bilinear", "nearest"), pixdim=(1, 0.2)),
81
+ (2, 1, 46),
82
+ torch.as_tensor(np.diag((1, 0.2, 1, 1))),
83
+ *device,
84
+ )
85
+ )
86
+ TESTS.append(
87
+ (
88
+ "interp sep",
89
+ {
90
+ "image": MetaTensor(torch.ones((2, 1, 10)), affine=torch.eye(4)),
91
+ "seg1": MetaTensor(torch.ones((2, 1, 10)), affine=torch.diag(torch.tensor([2, 2, 2, 1]))),
92
+ "seg2": MetaTensor(torch.ones((2, 1, 10)), affine=torch.eye(4)),
93
+ },
94
+ dict(keys=("image", "seg1", "seg2"), mode=("bilinear", "nearest", "nearest"), pixdim=(1, 1, 1)),
95
+ (2, 1, 10),
96
+ torch.as_tensor(np.diag((1, 1, 1, 1))),
97
+ *device,
98
+ )
99
+ )
100
+
101
+ TESTS_TORCH = []
102
+ for track_meta in (False, True):
103
+ for device in TEST_DEVICES:
104
+ TESTS_TORCH.append([{"keys": "seg", "pixdim": [0.2, 0.3, 1]}, torch.ones(2, 1, 2, 3), track_meta, *device])
105
+
106
+
107
+ class TestSpacingDCase(unittest.TestCase):
108
+ @parameterized.expand(TESTS)
109
+ def test_spacingd(self, _, data, kw_args, expected_shape, expected_affine, device):
110
+ data = {k: v.to(device) for k, v in data.items()}
111
+ tr = Spacingd(**kw_args)
112
+ call_param = {"data": data}
113
+ res = tr(**call_param)
114
+ # test lazy
115
+ if not isinstance(kw_args["keys"], str): # multiple keys
116
+ kw_args["mode"] = ensure_tuple_rep(kw_args["mode"], len(kw_args["keys"]))
117
+ init_param = kw_args.copy()
118
+ for key, mode in zip(kw_args["keys"], kw_args["mode"]):
119
+ init_param["keys"], init_param["mode"] = key, mode
120
+ test_resampler_lazy(tr, res, init_param, call_param, output_key=key)
121
+ else:
122
+ test_resampler_lazy(tr, res, kw_args, call_param, output_key=kw_args["keys"])
123
+ in_img = data["image"]
124
+ out_img = res["image"]
125
+ self.assertEqual(in_img.device, out_img.device)
126
+ # no change in number of keys
127
+ self.assertEqual(tuple(sorted(data)), tuple(sorted(res)))
128
+ np.testing.assert_allclose(out_img.shape, expected_shape)
129
+ assert_allclose(out_img.affine, expected_affine)
130
+
131
+ @parameterized.expand(TESTS_TORCH)
132
+ def test_orntd_torch(self, init_param, img: torch.Tensor, track_meta: bool, device):
133
+ set_track_meta(track_meta)
134
+ tr = Spacingd(**init_param)
135
+ call_param = {"data": {"seg": img.to(device)}}
136
+ res_data = tr(**call_param) # type: ignore
137
+ res = res_data["seg"]
138
+
139
+ if track_meta:
140
+ test_resampler_lazy(tr, res_data, init_param, call_param, output_key="seg")
141
+ self.assertIsInstance(res, MetaTensor)
142
+ assert isinstance(res, MetaTensor) # for mypy type narrowing
143
+ new_spacing = affine_to_spacing(res.affine, 3)
144
+ assert_allclose(new_spacing, init_param["pixdim"], type_test=False)
145
+ self.assertNotEqual(img.shape, res.shape)
146
+ else:
147
+ self.assertIsInstance(res, torch.Tensor)
148
+ self.assertNotIsInstance(res, MetaTensor)
149
+ self.assertNotEqual(img.shape, res.shape)
150
+
151
+ @skip_if_quick
152
+ def test_space_same_shape(self):
153
+ affine_1 = np.array(
154
+ [
155
+ [1.499277e00, 2.699563e-02, 3.805804e-02, -1.948635e02],
156
+ [-2.685805e-02, 1.499757e00, -2.635604e-12, 4.438188e01],
157
+ [-3.805194e-02, -5.999028e-04, 1.499517e00, 4.036536e01],
158
+ [0.000000e00, 0.000000e00, 0.000000e00, 1.000000e00],
159
+ ]
160
+ )
161
+ affine_2 = np.array(
162
+ [
163
+ [1.499275e00, 2.692252e-02, 3.805728e-02, -1.948635e02],
164
+ [-2.693010e-02, 1.499758e00, -4.260525e-05, 4.438188e01],
165
+ [-3.805190e-02, -6.406730e-04, 1.499517e00, 4.036536e01],
166
+ [0.000000e00, 0.000000e00, 0.000000e00, 1.000000e00],
167
+ ]
168
+ )
169
+ img_1 = MetaTensor(np.zeros((1, 238, 145, 315)), affine=affine_1)
170
+ img_2 = MetaTensor(np.zeros((1, 238, 145, 315)), affine=affine_2)
171
+ out = Spacingd(("img_1", "img_2"), pixdim=1)({"img_1": img_1, "img_2": img_2})
172
+ self.assertEqual(out["img_1"].shape, out["img_2"].shape) # ensure_same_shape True
173
+ out = Spacingd(("img_1", "img_2"), pixdim=1, ensure_same_shape=False)({"img_1": img_1, "img_2": img_2})
174
+ self.assertNotEqual(out["img_1"].shape, out["img_2"].shape) # ensure_same_shape False
175
+
176
+
177
+ if __name__ == "__main__":
178
+ unittest.main()
@@ -0,0 +1,82 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ from parameterized import parameterized
17
+
18
+ from monai.transforms import CenterScaleCrop, CenterSpatialCrop, SpatialCrop
19
+ from tests.croppers import CropTest
20
+
21
+ TESTS = [
22
+ [{"roi_center": [1, 1, 1], "roi_size": [2, 2, 2]}, (3, 3, 3, 3), (3, 2, 2, 2)],
23
+ [{"roi_center": [1, 1, 1], "roi_size": [2, 2, 2]}, (3, 1, 1, 1), (3, 1, 1, 1)],
24
+ [{"roi_start": [0, 0, 0], "roi_end": [2, 2, 2]}, (3, 3, 3, 3), (3, 2, 2, 2)],
25
+ [{"roi_start": [0, 0], "roi_end": [2, 2]}, (3, 3, 3, 3), (3, 2, 2, 3)],
26
+ [{"roi_start": [0, 0, 0, 0, 0], "roi_end": [2, 2, 2, 2, 2]}, (3, 3, 3, 3), (3, 2, 2, 2)],
27
+ [{"roi_start": [0, 0, 0, 0, 0], "roi_end": [8, 8, 8, 2, 2]}, (3, 3, 3, 3), (3, 3, 3, 3)],
28
+ [
29
+ {"roi_slices": [slice(s, e) for s, e in zip([None, None, None], [None, None, None])]},
30
+ (3, 11, 12, 15),
31
+ (3, 11, 12, 15),
32
+ ],
33
+ [{"roi_slices": [slice(s, e) for s, e in zip([1, None, 0], [None, None, None])]}, (3, 7, 9, 11), (3, 6, 9, 11)],
34
+ [{"roi_slices": [slice(s, e) for s, e in zip([0, None, None], [-1, None, None])]}, (3, 7, 9, 11), (3, 6, 9, 11)],
35
+ [{"roi_slices": [slice(s, e) for s, e in zip([1, None, None], [None, None, None])]}, (3, 10, 8, 6), (3, 9, 8, 6)],
36
+ [{"roi_slices": [slice(s, e) for s, e in zip([-1, -2, 0], [None, None, 2])]}, (3, 15, 17, 8), (3, 1, 2, 2)],
37
+ [{"roi_slices": [slice(s, e) for s, e in zip([None, None, None], [-2, -1, 2])]}, (3, 13, 8, 6), (3, 11, 7, 2)],
38
+ [{"roi_start": [-1, 0], "roi_end": [5, 5]}, (1, 5, 5), (1, 5, 5)],
39
+ ]
40
+
41
+ TEST_ERRORS = [[{"roi_slices": [slice(s, e, 2) for s, e in zip([-1, -2, 0], [None, None, 2])]}]]
42
+
43
+ TEST_LAZY_ERRORS = [[{"roi_start": [1, 0, 0], "roi_end": [1, 8, 8]}, (3, 3, 3, 3), (3, 0, 3, 3)]]
44
+
45
+ func1 = {CenterSpatialCrop: {"roi_size": [8, 8, 6]}}
46
+ func2 = {SpatialCrop: {"roi_center": [1, 1, 1], "roi_size": [3, 4, 3]}}
47
+ func3 = {CenterScaleCrop: {"roi_scale": [0.6, 0.3, -1]}}
48
+
49
+ TESTS_COMBINE = []
50
+ TESTS_COMBINE.append([[func1, func2, func3], (3, 10, 10, 8)])
51
+ TESTS_COMBINE.append([[func1, func2], (3, 8, 8, 4)])
52
+ TESTS_COMBINE.append([[func1, func3], (3, 8, 8, 4)])
53
+
54
+
55
+ class TestSpatialCrop(CropTest):
56
+ Cropper = SpatialCrop
57
+
58
+ @parameterized.expand(TESTS)
59
+ def test_shape(self, input_param, input_shape, expected_shape):
60
+ self.crop_test(input_param, input_shape, expected_shape)
61
+
62
+ @parameterized.expand(TEST_ERRORS)
63
+ def test_error(self, input_param):
64
+ with self.assertRaises(ValueError):
65
+ SpatialCrop(**input_param)
66
+
67
+ @parameterized.expand(TESTS)
68
+ def test_pending_ops(self, input_param, input_shape, _):
69
+ self.crop_test_pending_ops(input_param, input_shape)
70
+
71
+ @parameterized.expand(TEST_LAZY_ERRORS)
72
+ def test_lazy_error(self, input_param, input_shape, _):
73
+ with self.assertRaises(ValueError):
74
+ return self.crop_test_pending_ops(input_param, input_shape)
75
+
76
+ @parameterized.expand(TESTS_COMBINE)
77
+ def test_combine_ops(self, funcs, input_shape):
78
+ self.crop_test_combine_ops(funcs, input_shape)
79
+
80
+
81
+ if __name__ == "__main__":
82
+ unittest.main()
@@ -0,0 +1,74 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ from parameterized import parameterized
17
+
18
+ from monai.transforms import SpatialCropd
19
+ from tests.croppers import CropTest
20
+
21
+ TESTS = [
22
+ [
23
+ {"keys": ["img"], "roi_center": [1, 1], "roi_size": [2, 2]},
24
+ (1, 3, 3),
25
+ (1, 2, 2),
26
+ (slice(None), slice(None, 2), slice(None, 2)),
27
+ ],
28
+ [
29
+ {"keys": ["img"], "roi_center": [1, 1, 1], "roi_size": [2, 2, 2]},
30
+ (3, 3, 3, 3),
31
+ (3, 2, 2, 2),
32
+ (slice(None), slice(None, 2), slice(None, 2), slice(None, 2)),
33
+ ],
34
+ [
35
+ {"keys": ["img"], "roi_start": [0, 0, 0], "roi_end": [2, 2, 2]},
36
+ (3, 3, 3, 3),
37
+ (3, 2, 2, 2),
38
+ (slice(None), slice(None, 2), slice(None, 2), slice(None, 2)),
39
+ ],
40
+ [
41
+ {"keys": ["img"], "roi_start": [0, 0], "roi_end": [2, 2]},
42
+ (3, 3, 3, 3),
43
+ (3, 2, 2, 3),
44
+ (slice(None), slice(None, 2), slice(None, 2), slice(None)),
45
+ ],
46
+ [
47
+ {"keys": ["img"], "roi_start": [0, 0, 0, 0, 0], "roi_end": [2, 2, 2, 2, 2]},
48
+ (3, 3, 3, 3),
49
+ (3, 2, 2, 2),
50
+ (slice(None), slice(None, 2), slice(None, 2), slice(None, 2)),
51
+ ],
52
+ [
53
+ {"keys": ["img"], "roi_slices": [slice(s, e) for s, e in zip([-1, -2, 0], [None, None, 2])]},
54
+ (3, 3, 3, 3),
55
+ (3, 1, 2, 2),
56
+ (slice(None), slice(-1, None), slice(-2, None), slice(0, 2)),
57
+ ],
58
+ ]
59
+
60
+
61
+ class TestSpatialCropd(CropTest):
62
+ Cropper = SpatialCropd
63
+
64
+ @parameterized.expand(TESTS)
65
+ def test_shape(self, input_param, input_shape, expected_shape, same_area):
66
+ self.crop_test(input_param, input_shape, expected_shape, same_area)
67
+
68
+ @parameterized.expand(TESTS)
69
+ def test_pending_ops(self, input_param, input_shape, _expected_shape, _same_area):
70
+ self.crop_test_pending_ops(input_param, input_shape)
71
+
72
+
73
+ if __name__ == "__main__":
74
+ unittest.main()
@@ -0,0 +1,57 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ from parameterized import parameterized
17
+
18
+ from monai.transforms import BorderPad, DivisiblePad, SpatialPad
19
+ from tests.padders import PadTest
20
+
21
+ TESTS = []
22
+ TESTS.append([{"spatial_size": [3, 4], "method": "end"}, (1, 2, 3), (1, 3, 4)])
23
+ TESTS.append([{"spatial_size": [15, 4, -1], "method": "symmetric"}, (3, 8, 8, 4), (3, 15, 8, 4)])
24
+
25
+ func1 = {SpatialPad: {"spatial_size": [15, 4, -1], "method": "symmetric"}}
26
+ func2 = {BorderPad: {"spatial_border": 2}}
27
+ func3 = {DivisiblePad: {"k": 5, "method": "end"}}
28
+
29
+ TESTS_COMBINE = []
30
+ TESTS_COMBINE.append([[func1, func2, func3], (3, 8, 8, 4), (3, 20, 15, 10)])
31
+ TESTS_COMBINE.append([[func1, func2], (3, 8, 8, 4), (3, 19, 12, 8)])
32
+ TESTS_COMBINE.append([[func2, func2], (3, 8, 8, 4), (3, 16, 16, 12)])
33
+
34
+
35
+ class TestSpatialPad(PadTest):
36
+ Padder = SpatialPad
37
+
38
+ @parameterized.expand(TESTS)
39
+ def test_pad(self, input_param, input_shape, expected_shape):
40
+ self.pad_test(input_param, input_shape, expected_shape)
41
+
42
+ def test_pad_kwargs(self):
43
+ kwargs = {"spatial_size": [15, 8], "method": "end", "mode": "constant"}
44
+ unchanged_slices = [slice(None), slice(None, 8), slice(None, 4)]
45
+ self.pad_test_kwargs(unchanged_slices, **kwargs)
46
+
47
+ @parameterized.expand(TESTS)
48
+ def test_pending_ops(self, input_param, input_shape, _):
49
+ self.pad_test_pending_ops(input_param, input_shape)
50
+
51
+ @parameterized.expand(TESTS_COMBINE)
52
+ def test_combine_ops(self, funcs, input_shape, expected_shape):
53
+ self.pad_test_combine_ops(funcs, input_shape, expected_shape)
54
+
55
+
56
+ if __name__ == "__main__":
57
+ unittest.main()
@@ -0,0 +1,43 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ from parameterized import parameterized
17
+
18
+ from monai.transforms import SpatialPadd
19
+ from tests.padders import PadTest
20
+
21
+ TESTS = [
22
+ [{"keys": ["img"], "spatial_size": [15, 8, 8], "method": "symmetric"}, (3, 8, 8, 5), (3, 15, 8, 8)],
23
+ [{"keys": ["img"], "spatial_size": [15, 8, 8], "method": "end"}, (3, 8, 8, 5), (3, 15, 8, 8)],
24
+ [{"keys": ["img"], "spatial_size": [15, 8, 8], "method": "end"}, (3, 8, 8, 5), (3, 15, 8, 8)],
25
+ [{"keys": ["img"], "spatial_size": [15, 8, -1], "method": "end"}, (3, 8, 5, 4), (3, 15, 8, 4)],
26
+ ]
27
+
28
+
29
+ class TestSpatialPadd(PadTest):
30
+ Padder = SpatialPadd
31
+
32
+ @parameterized.expand(TESTS)
33
+ def test_pad(self, input_param, input_shape, expected_shape):
34
+ modes = ["constant", {"constant"}]
35
+ self.pad_test(input_param, input_shape, expected_shape, modes)
36
+
37
+ @parameterized.expand(TESTS)
38
+ def test_pending_ops(self, input_param, input_shape, _):
39
+ self.pad_test_pending_ops(input_param, input_shape)
40
+
41
+
42
+ if __name__ == "__main__":
43
+ unittest.main()
@@ -0,0 +1,235 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+ from copy import deepcopy
16
+
17
+ import numpy as np
18
+ import torch
19
+ from parameterized import parameterized
20
+
21
+ from monai.data.meta_obj import set_track_meta
22
+ from monai.data.meta_tensor import MetaTensor
23
+ from monai.data.utils import to_affine_nd
24
+ from monai.transforms import SpatialResample
25
+ from monai.utils import optional_import
26
+ from tests.lazy_transforms_utils import test_resampler_lazy
27
+ from tests.test_utils import TEST_DEVICES, TEST_NDARRAYS_ALL, assert_allclose
28
+
29
+ TESTS = []
30
+
31
+ destinations_3d = [
32
+ torch.tensor([[1.0, 0.0, 0.0, 0.0], [0.0, -1.0, 0.0, 1.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
33
+ torch.tensor([[-1.0, 0.0, 0.0, 1.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
34
+ ]
35
+ expected_3d = [
36
+ torch.tensor([[[[4.0, 5.0, 6.0], [1.0, 2.0, 3.0]], [[10.0, 11.0, 12.0], [7.0, 8.0, 9.0]]]]),
37
+ torch.tensor([[[[7.0, 8.0, 9.0], [10.0, 11.0, 12.0]], [[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]]]]),
38
+ ]
39
+
40
+ for dst, expct in zip(destinations_3d, expected_3d):
41
+ for device in TEST_DEVICES:
42
+ for align in (False, True):
43
+ interp = ("nearest", "bilinear")
44
+ for interp_mode in interp:
45
+ for padding_mode in ("zeros", "border", "reflection"):
46
+ TESTS.append(
47
+ [
48
+ torch.arange(12).reshape((1, 2, 2, 3)) + 1.0, # data
49
+ *device,
50
+ {
51
+ "dst_affine": dst,
52
+ "dtype": torch.float64,
53
+ "align_corners": align,
54
+ "mode": interp_mode,
55
+ "padding_mode": padding_mode,
56
+ },
57
+ expct,
58
+ ]
59
+ )
60
+ if optional_import("cupy")[1] and optional_import("scipy.ndimage")[1]:
61
+ TESTS.append(deepcopy(TESTS[-1]))
62
+ TESTS[-1][2].update({"align_corners": True, "mode": 1, "padding_mode": "reflect"}) # type: ignore
63
+
64
+ destinations_2d = [
65
+ torch.tensor([[1.0, 0.0, 0.0], [0.0, -1.0, 1.0], [0.0, 0.0, 1.0]]), # flip the second
66
+ torch.tensor([[-1.0, 0.0, 1.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]), # flip the first
67
+ ]
68
+ expected_2d = [torch.tensor([[[2.0, 1.0], [4.0, 3.0]]]), torch.tensor([[[3.0, 4.0], [1.0, 2.0]]])]
69
+
70
+ for dst, expct in zip(destinations_2d, expected_2d):
71
+ for device in TEST_DEVICES:
72
+ for align in (False, True):
73
+ for interp_mode in ("nearest", "bilinear"):
74
+ TESTS.append(
75
+ [
76
+ torch.arange(4).reshape((1, 2, 2)) + 1.0,
77
+ *device,
78
+ {
79
+ "dst_affine": dst,
80
+ "dtype": torch.float32,
81
+ "align_corners": align,
82
+ "mode": interp_mode,
83
+ "padding_mode": "zeros",
84
+ },
85
+ expct,
86
+ ]
87
+ )
88
+
89
+ TEST_4_5_D = []
90
+ for device in TEST_DEVICES:
91
+ for dtype in (torch.float32, torch.float64):
92
+ # 4D
93
+ TEST_4_5_D.append(
94
+ [
95
+ (1, 2, 2, 3, 1),
96
+ (1, 1, 1, 1, 2),
97
+ *device,
98
+ dtype,
99
+ torch.tensor(
100
+ [
101
+ [[[0.5, 0.0], [0.0, 2.0], [1.5, 1.0]], [[3.5, 3.0], [3.0, 5.0], [4.5, 4.0]]],
102
+ [[[6.5, 6.0], [6.0, 8.0], [7.5, 7.0]], [[9.5, 9.0], [9.0, 11.0], [10.5, 10.0]]],
103
+ ]
104
+ ),
105
+ ]
106
+ )
107
+ # 5D
108
+ TEST_4_5_D.append(
109
+ [
110
+ (1, 2, 2, 3, 1, 1),
111
+ (1, 1, 1, 1, 2, 2),
112
+ *device,
113
+ dtype,
114
+ torch.tensor(
115
+ [
116
+ [
117
+ [[[0.0, 0.0], [0.0, 1.0]], [[0.5, 0.0], [1.5, 1.0]], [[1.0, 2.0], [2.0, 2.0]]],
118
+ [[[3.0, 3.0], [3.0, 4.0]], [[3.5, 3.0], [4.5, 4.0]], [[4.0, 5.0], [5.0, 5.0]]],
119
+ ],
120
+ [
121
+ [[[6.0, 6.0], [6.0, 7.0]], [[6.5, 6.0], [7.5, 7.0]], [[7.0, 8.0], [8.0, 8.0]]],
122
+ [[[9.0, 9.0], [9.0, 10.0]], [[9.5, 9.0], [10.5, 10.0]], [[10.0, 11.0], [11.0, 11.0]]],
123
+ ],
124
+ ]
125
+ ),
126
+ ]
127
+ )
128
+
129
+ TEST_TORCH_INPUT = []
130
+ for track_meta in (True,):
131
+ for t in TEST_4_5_D:
132
+ TEST_TORCH_INPUT.append(t + [track_meta])
133
+
134
+
135
+ class TestSpatialResample(unittest.TestCase):
136
+ @parameterized.expand(TESTS)
137
+ def test_flips(self, img, device, data_param, expected_output):
138
+ for p in TEST_NDARRAYS_ALL:
139
+ img = p(img)
140
+ if isinstance(img, MetaTensor):
141
+ img.affine = torch.eye(4)
142
+ if hasattr(img, "to"):
143
+ img = img.to(device)
144
+ resampler = SpatialResample()
145
+ call_param = data_param.copy()
146
+ call_param["img"] = img
147
+ out = resampler(**call_param)
148
+ assert_allclose(out, expected_output, rtol=1e-2, atol=1e-2)
149
+ assert_allclose(to_affine_nd(len(out.shape) - 1, out.affine), call_param["dst_affine"])
150
+
151
+ test_resampler_lazy(resampler, out, init_param=None, call_param=call_param)
152
+
153
+ @parameterized.expand(TEST_4_5_D)
154
+ def test_4d_5d(self, new_shape, tile, device, dtype, expected_data):
155
+ img = np.arange(12).reshape(new_shape)
156
+ img = np.tile(img, tile)
157
+ img = MetaTensor(img).to(device)
158
+
159
+ dst = torch.tensor([[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, -1.0, 1.5], [0.0, 0.0, 0.0, 1.0]])
160
+ dst = dst.to(dtype)
161
+ init_param = {"dtype": dtype, "align_corners": True}
162
+ call_param = {"img": img, "dst_affine": dst, "align_corners": False}
163
+ resampler = SpatialResample(**init_param)
164
+ out = resampler(**call_param)
165
+ assert_allclose(out, expected_data[None], rtol=1e-2, atol=1e-2)
166
+ assert_allclose(out.affine, dst.to(torch.float32), rtol=1e-2, atol=1e-2)
167
+
168
+ test_resampler_lazy(resampler, out, init_param, call_param)
169
+
170
+ @parameterized.expand(TEST_DEVICES)
171
+ def test_ill_affine(self, device):
172
+ img = MetaTensor(torch.arange(12).reshape(1, 2, 2, 3)).to(device)
173
+ ill_affine = torch.tensor([[1, 0, 0, 0], [0, 0, 0, 0], [0, 0, -1, 1.5], [0, 0, 0, 1]])
174
+ with self.assertRaises(ValueError):
175
+ img.affine = torch.eye(4)
176
+ dst_affine = ill_affine
177
+ SpatialResample()(img=img, dst_affine=dst_affine)
178
+ with self.assertRaises(ValueError):
179
+ img.affine = ill_affine
180
+ dst_affine = torch.eye(4)
181
+ SpatialResample()(img=img, dst_affine=dst_affine)
182
+ if not (optional_import("scipy")[1] and optional_import("cupy")[1]):
183
+ return
184
+ with self.assertRaises(ValueError): # requires scipy
185
+ SpatialResample(mode=1, align_corners=True)(img=img, dst_affine=dst_affine)
186
+ with self.assertRaises(ValueError):
187
+ SpatialResample(mode=1, align_corners=False)(img=img, dst_affine=dst_affine)
188
+
189
+ @parameterized.expand(TEST_TORCH_INPUT)
190
+ def test_input_torch(self, new_shape, tile, device, dtype, expected_data, track_meta):
191
+ set_track_meta(track_meta)
192
+ img = np.arange(12).reshape(new_shape)
193
+ img = torch.as_tensor(np.tile(img, tile)).to(device)
194
+ dst = torch.tensor([[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, -1.0, 1.5], [0.0, 0.0, 0.0, 1.0]])
195
+ dst = dst.to(dtype).to(device)
196
+ init_param = {"dtype": dtype}
197
+ call_param = {"img": img, "dst_affine": dst}
198
+ resampler = SpatialResample(**init_param)
199
+ out = resampler(**call_param)
200
+ assert_allclose(out, expected_data[None], rtol=1e-2, atol=1e-2)
201
+
202
+ test_resampler_lazy(resampler, out, init_param, call_param)
203
+
204
+ if track_meta:
205
+ self.assertIsInstance(out, MetaTensor)
206
+ assert_allclose(out.affine, dst.to(torch.float32), rtol=1e-2, atol=1e-2)
207
+ else:
208
+ self.assertIsInstance(out, torch.Tensor)
209
+ self.assertNotIsInstance(out, MetaTensor)
210
+
211
+ @parameterized.expand(TESTS)
212
+ def test_inverse(self, img, device, data_param, expected_output):
213
+ img = MetaTensor(img, affine=torch.eye(4)).to(device)
214
+ tr = SpatialResample()
215
+ out = tr(img=img, **data_param)
216
+ assert_allclose(out, expected_output, rtol=1e-2, atol=1e-2)
217
+ assert_allclose(to_affine_nd(len(out.shape) - 1, out.affine), data_param["dst_affine"])
218
+
219
+ # inverse
220
+ out = tr.inverse(out)
221
+ assert_allclose(img, out)
222
+ expected_affine = to_affine_nd(len(out.affine) - 1, torch.eye(4))
223
+ assert_allclose(out.affine, expected_affine)
224
+
225
+ def test_unchange(self):
226
+ for i, p in enumerate(TEST_NDARRAYS_ALL):
227
+ set_track_meta(i % 2)
228
+ img = p(np.arange(12).reshape(1, 3, 4))
229
+ result = SpatialResample()(img)
230
+ assert_allclose(result, img, type_test=False)
231
+ set_track_meta(True)
232
+
233
+
234
+ if __name__ == "__main__":
235
+ unittest.main()