monai-weekly 1.5.dev2505__py3-none-any.whl → 1.5.dev2507__py3-none-any.whl

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Files changed (779) 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/meta_tensor.py +5 -0
  5. monai/data/utils.py +6 -13
  6. monai/inferers/utils.py +1 -2
  7. monai/losses/dice.py +2 -14
  8. monai/losses/ds_loss.py +1 -3
  9. monai/networks/layers/simplelayers.py +2 -14
  10. monai/networks/utils.py +4 -16
  11. monai/transforms/compose.py +28 -11
  12. monai/transforms/croppad/array.py +1 -6
  13. monai/transforms/io/array.py +0 -1
  14. monai/transforms/transform.py +15 -6
  15. monai/transforms/utils.py +1 -2
  16. monai/utils/jupyter_utils.py +1 -1
  17. monai/utils/tf32.py +0 -10
  18. monai/visualize/class_activation_maps.py +5 -8
  19. monai/visualize/img2tensorboard.py +2 -2
  20. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
  21. monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
  22. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
  23. tests/apps/__init__.py +10 -0
  24. tests/apps/deepedit/__init__.py +10 -0
  25. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  26. tests/apps/deepgrow/__init__.py +10 -0
  27. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  28. tests/apps/deepgrow/transforms/__init__.py +10 -0
  29. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  30. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  31. tests/apps/detection/__init__.py +10 -0
  32. tests/apps/detection/metrics/__init__.py +10 -0
  33. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  34. tests/apps/detection/networks/__init__.py +10 -0
  35. tests/apps/detection/networks/test_retinanet.py +210 -0
  36. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  37. tests/apps/detection/test_box_transform.py +370 -0
  38. tests/apps/detection/utils/__init__.py +10 -0
  39. tests/apps/detection/utils/test_anchor_box.py +88 -0
  40. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  41. tests/apps/detection/utils/test_box_coder.py +43 -0
  42. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  43. tests/apps/detection/utils/test_detector_utils.py +96 -0
  44. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  45. tests/apps/nuclick/__init__.py +10 -0
  46. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  47. tests/apps/pathology/__init__.py +10 -0
  48. tests/apps/pathology/handlers/__init__.py +10 -0
  49. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  50. tests/apps/pathology/test_lesion_froc.py +333 -0
  51. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  52. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  53. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  54. tests/apps/pathology/transforms/__init__.py +10 -0
  55. tests/apps/pathology/transforms/post/__init__.py +10 -0
  56. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  57. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  58. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  59. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  60. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  61. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  62. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  63. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  64. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  65. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  66. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  67. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  68. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  69. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  70. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  71. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  72. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  73. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  74. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  75. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  76. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  77. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  78. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  79. tests/apps/reconstruction/__init__.py +10 -0
  80. tests/apps/reconstruction/nets/__init__.py +10 -0
  81. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  82. tests/apps/reconstruction/test_complex_utils.py +77 -0
  83. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  84. tests/apps/reconstruction/test_mri_utils.py +37 -0
  85. tests/apps/reconstruction/transforms/__init__.py +10 -0
  86. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  87. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  88. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  89. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  90. tests/apps/test_check_hash.py +53 -0
  91. tests/apps/test_cross_validation.py +74 -0
  92. tests/apps/test_decathlondataset.py +93 -0
  93. tests/apps/test_download_and_extract.py +70 -0
  94. tests/apps/test_download_url_yandex.py +45 -0
  95. tests/apps/test_mednistdataset.py +72 -0
  96. tests/apps/test_mmar_download.py +154 -0
  97. tests/apps/test_tciadataset.py +123 -0
  98. tests/apps/vista3d/__init__.py +10 -0
  99. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  100. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  101. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  102. tests/bundle/__init__.py +10 -0
  103. tests/bundle/test_bundle_ckpt_export.py +107 -0
  104. tests/bundle/test_bundle_download.py +435 -0
  105. tests/bundle/test_bundle_get_data.py +94 -0
  106. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  107. tests/bundle/test_bundle_trt_export.py +147 -0
  108. tests/bundle/test_bundle_utils.py +149 -0
  109. tests/bundle/test_bundle_verify_metadata.py +66 -0
  110. tests/bundle/test_bundle_verify_net.py +76 -0
  111. tests/bundle/test_bundle_workflow.py +272 -0
  112. tests/bundle/test_component_locator.py +38 -0
  113. tests/bundle/test_config_item.py +138 -0
  114. tests/bundle/test_config_parser.py +392 -0
  115. tests/bundle/test_reference_resolver.py +114 -0
  116. tests/config/__init__.py +10 -0
  117. tests/config/test_cv2_dist.py +53 -0
  118. tests/engines/__init__.py +10 -0
  119. tests/engines/test_ensemble_evaluator.py +94 -0
  120. tests/engines/test_prepare_batch_default.py +76 -0
  121. tests/engines/test_prepare_batch_default_dist.py +76 -0
  122. tests/engines/test_prepare_batch_diffusion.py +104 -0
  123. tests/engines/test_prepare_batch_extra_input.py +80 -0
  124. tests/fl/__init__.py +10 -0
  125. tests/fl/monai_algo/__init__.py +10 -0
  126. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  127. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  128. tests/fl/test_fl_monai_algo_stats.py +81 -0
  129. tests/fl/utils/__init__.py +10 -0
  130. tests/fl/utils/test_fl_exchange_object.py +63 -0
  131. tests/handlers/__init__.py +10 -0
  132. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  133. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  134. tests/handlers/test_handler_classification_saver.py +64 -0
  135. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  136. tests/handlers/test_handler_clearml_image.py +65 -0
  137. tests/handlers/test_handler_clearml_stats.py +65 -0
  138. tests/handlers/test_handler_confusion_matrix.py +104 -0
  139. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  140. tests/handlers/test_handler_decollate_batch.py +66 -0
  141. tests/handlers/test_handler_early_stop.py +68 -0
  142. tests/handlers/test_handler_garbage_collector.py +73 -0
  143. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  144. tests/handlers/test_handler_ignite_metric.py +191 -0
  145. tests/handlers/test_handler_lr_scheduler.py +94 -0
  146. tests/handlers/test_handler_mean_dice.py +98 -0
  147. tests/handlers/test_handler_mean_iou.py +76 -0
  148. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  149. tests/handlers/test_handler_metrics_saver.py +89 -0
  150. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  151. tests/handlers/test_handler_mlflow.py +296 -0
  152. tests/handlers/test_handler_nvtx.py +93 -0
  153. tests/handlers/test_handler_panoptic_quality.py +89 -0
  154. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  155. tests/handlers/test_handler_post_processing.py +74 -0
  156. tests/handlers/test_handler_prob_map_producer.py +111 -0
  157. tests/handlers/test_handler_regression_metrics.py +160 -0
  158. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  159. tests/handlers/test_handler_rocauc.py +48 -0
  160. tests/handlers/test_handler_rocauc_dist.py +54 -0
  161. tests/handlers/test_handler_stats.py +281 -0
  162. tests/handlers/test_handler_surface_distance.py +113 -0
  163. tests/handlers/test_handler_tb_image.py +61 -0
  164. tests/handlers/test_handler_tb_stats.py +166 -0
  165. tests/handlers/test_handler_validation.py +59 -0
  166. tests/handlers/test_trt_compile.py +145 -0
  167. tests/handlers/test_write_metrics_reports.py +68 -0
  168. tests/inferers/__init__.py +10 -0
  169. tests/inferers/test_avg_merger.py +179 -0
  170. tests/inferers/test_controlnet_inferers.py +1310 -0
  171. tests/inferers/test_diffusion_inferer.py +236 -0
  172. tests/inferers/test_latent_diffusion_inferer.py +824 -0
  173. tests/inferers/test_patch_inferer.py +309 -0
  174. tests/inferers/test_saliency_inferer.py +55 -0
  175. tests/inferers/test_slice_inferer.py +57 -0
  176. tests/inferers/test_sliding_window_inference.py +377 -0
  177. tests/inferers/test_sliding_window_splitter.py +284 -0
  178. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  179. tests/inferers/test_zarr_avg_merger.py +326 -0
  180. tests/integration/__init__.py +10 -0
  181. tests/integration/test_auto3dseg_ensemble.py +211 -0
  182. tests/integration/test_auto3dseg_hpo.py +189 -0
  183. tests/integration/test_deepedit_interaction.py +122 -0
  184. tests/integration/test_downsample_block.py +50 -0
  185. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  186. tests/integration/test_integration_autorunner.py +201 -0
  187. tests/integration/test_integration_bundle_run.py +240 -0
  188. tests/integration/test_integration_classification_2d.py +282 -0
  189. tests/integration/test_integration_determinism.py +95 -0
  190. tests/integration/test_integration_fast_train.py +231 -0
  191. tests/integration/test_integration_gpu_customization.py +159 -0
  192. tests/integration/test_integration_lazy_samples.py +219 -0
  193. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  194. tests/integration/test_integration_segmentation_3d.py +304 -0
  195. tests/integration/test_integration_sliding_window.py +100 -0
  196. tests/integration/test_integration_stn.py +133 -0
  197. tests/integration/test_integration_unet_2d.py +67 -0
  198. tests/integration/test_integration_workers.py +61 -0
  199. tests/integration/test_integration_workflows.py +365 -0
  200. tests/integration/test_integration_workflows_adversarial.py +173 -0
  201. tests/integration/test_integration_workflows_gan.py +158 -0
  202. tests/integration/test_loader_semaphore.py +48 -0
  203. tests/integration/test_mapping_filed.py +122 -0
  204. tests/integration/test_meta_affine.py +183 -0
  205. tests/integration/test_metatensor_integration.py +114 -0
  206. tests/integration/test_module_list.py +76 -0
  207. tests/integration/test_one_of.py +283 -0
  208. tests/integration/test_pad_collation.py +124 -0
  209. tests/integration/test_reg_loss_integration.py +107 -0
  210. tests/integration/test_retinanet_predict_utils.py +154 -0
  211. tests/integration/test_seg_loss_integration.py +159 -0
  212. tests/integration/test_spatial_combine_transforms.py +185 -0
  213. tests/integration/test_testtimeaugmentation.py +186 -0
  214. tests/integration/test_vis_gradbased.py +69 -0
  215. tests/integration/test_vista3d_utils.py +159 -0
  216. tests/losses/__init__.py +10 -0
  217. tests/losses/deform/__init__.py +10 -0
  218. tests/losses/deform/test_bending_energy.py +88 -0
  219. tests/losses/deform/test_diffusion_loss.py +117 -0
  220. tests/losses/image_dissimilarity/__init__.py +10 -0
  221. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  222. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  223. tests/losses/test_adversarial_loss.py +94 -0
  224. tests/losses/test_barlow_twins_loss.py +109 -0
  225. tests/losses/test_cldice_loss.py +51 -0
  226. tests/losses/test_contrastive_loss.py +86 -0
  227. tests/losses/test_dice_ce_loss.py +123 -0
  228. tests/losses/test_dice_focal_loss.py +124 -0
  229. tests/losses/test_dice_loss.py +227 -0
  230. tests/losses/test_ds_loss.py +189 -0
  231. tests/losses/test_focal_loss.py +379 -0
  232. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  233. tests/losses/test_generalized_dice_loss.py +221 -0
  234. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  235. tests/losses/test_giou_loss.py +62 -0
  236. tests/losses/test_hausdorff_loss.py +264 -0
  237. tests/losses/test_masked_dice_loss.py +152 -0
  238. tests/losses/test_masked_loss.py +87 -0
  239. tests/losses/test_multi_scale.py +86 -0
  240. tests/losses/test_nacl_loss.py +167 -0
  241. tests/losses/test_perceptual_loss.py +122 -0
  242. tests/losses/test_spectral_loss.py +86 -0
  243. tests/losses/test_ssim_loss.py +59 -0
  244. tests/losses/test_sure_loss.py +72 -0
  245. tests/losses/test_tversky_loss.py +198 -0
  246. tests/losses/test_unified_focal_loss.py +66 -0
  247. tests/metrics/__init__.py +10 -0
  248. tests/metrics/test_compute_confusion_matrix.py +294 -0
  249. tests/metrics/test_compute_f_beta.py +80 -0
  250. tests/metrics/test_compute_fid_metric.py +40 -0
  251. tests/metrics/test_compute_froc.py +143 -0
  252. tests/metrics/test_compute_generalized_dice.py +240 -0
  253. tests/metrics/test_compute_meandice.py +306 -0
  254. tests/metrics/test_compute_meaniou.py +223 -0
  255. tests/metrics/test_compute_mmd_metric.py +56 -0
  256. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  257. tests/metrics/test_compute_panoptic_quality.py +113 -0
  258. tests/metrics/test_compute_regression_metrics.py +196 -0
  259. tests/metrics/test_compute_roc_auc.py +155 -0
  260. tests/metrics/test_compute_variance.py +147 -0
  261. tests/metrics/test_cumulative.py +63 -0
  262. tests/metrics/test_cumulative_average.py +74 -0
  263. tests/metrics/test_cumulative_average_dist.py +48 -0
  264. tests/metrics/test_hausdorff_distance.py +209 -0
  265. tests/metrics/test_label_quality_score.py +134 -0
  266. tests/metrics/test_loss_metric.py +57 -0
  267. tests/metrics/test_metrics_reloaded.py +96 -0
  268. tests/metrics/test_ssim_metric.py +78 -0
  269. tests/metrics/test_surface_dice.py +416 -0
  270. tests/metrics/test_surface_distance.py +186 -0
  271. tests/networks/__init__.py +10 -0
  272. tests/networks/blocks/__init__.py +10 -0
  273. tests/networks/blocks/dints_block/__init__.py +10 -0
  274. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  275. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  276. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  277. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  278. tests/networks/blocks/test_adn.py +86 -0
  279. tests/networks/blocks/test_convolutions.py +156 -0
  280. tests/networks/blocks/test_crf_cpu.py +513 -0
  281. tests/networks/blocks/test_crf_cuda.py +528 -0
  282. tests/networks/blocks/test_crossattention.py +185 -0
  283. tests/networks/blocks/test_denseblock.py +105 -0
  284. tests/networks/blocks/test_dynunet_block.py +116 -0
  285. tests/networks/blocks/test_fpn_block.py +88 -0
  286. tests/networks/blocks/test_localnet_block.py +121 -0
  287. tests/networks/blocks/test_mlp.py +78 -0
  288. tests/networks/blocks/test_patchembedding.py +212 -0
  289. tests/networks/blocks/test_regunet_block.py +103 -0
  290. tests/networks/blocks/test_se_block.py +85 -0
  291. tests/networks/blocks/test_se_blocks.py +78 -0
  292. tests/networks/blocks/test_segresnet_block.py +57 -0
  293. tests/networks/blocks/test_selfattention.py +232 -0
  294. tests/networks/blocks/test_simple_aspp.py +87 -0
  295. tests/networks/blocks/test_spatialattention.py +55 -0
  296. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  297. tests/networks/blocks/test_text_encoding.py +49 -0
  298. tests/networks/blocks/test_transformerblock.py +90 -0
  299. tests/networks/blocks/test_unetr_block.py +158 -0
  300. tests/networks/blocks/test_upsample_block.py +134 -0
  301. tests/networks/blocks/warp/__init__.py +10 -0
  302. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  303. tests/networks/blocks/warp/test_warp.py +250 -0
  304. tests/networks/layers/__init__.py +10 -0
  305. tests/networks/layers/filtering/__init__.py +10 -0
  306. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  307. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  308. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  309. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  310. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  311. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  312. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  313. tests/networks/layers/test_affine_transform.py +385 -0
  314. tests/networks/layers/test_apply_filter.py +89 -0
  315. tests/networks/layers/test_channel_pad.py +51 -0
  316. tests/networks/layers/test_conjugate_gradient.py +56 -0
  317. tests/networks/layers/test_drop_path.py +46 -0
  318. tests/networks/layers/test_gaussian.py +317 -0
  319. tests/networks/layers/test_gaussian_filter.py +206 -0
  320. tests/networks/layers/test_get_layers.py +65 -0
  321. tests/networks/layers/test_gmm.py +314 -0
  322. tests/networks/layers/test_grid_pull.py +93 -0
  323. tests/networks/layers/test_hilbert_transform.py +131 -0
  324. tests/networks/layers/test_lltm.py +62 -0
  325. tests/networks/layers/test_median_filter.py +52 -0
  326. tests/networks/layers/test_polyval.py +55 -0
  327. tests/networks/layers/test_preset_filters.py +136 -0
  328. tests/networks/layers/test_savitzky_golay_filter.py +141 -0
  329. tests/networks/layers/test_separable_filter.py +87 -0
  330. tests/networks/layers/test_skip_connection.py +48 -0
  331. tests/networks/layers/test_vector_quantizer.py +89 -0
  332. tests/networks/layers/test_weight_init.py +50 -0
  333. tests/networks/nets/__init__.py +10 -0
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  680. tests/transforms/test_spatial_resample.py +235 -0
  681. tests/transforms/test_squeezedim.py +62 -0
  682. tests/transforms/test_squeezedimd.py +98 -0
  683. tests/transforms/test_std_shift_intensity.py +76 -0
  684. tests/transforms/test_std_shift_intensityd.py +74 -0
  685. tests/transforms/test_threshold_intensity.py +38 -0
  686. tests/transforms/test_threshold_intensityd.py +58 -0
  687. tests/transforms/test_to_contiguous.py +47 -0
  688. tests/transforms/test_to_cupy.py +112 -0
  689. tests/transforms/test_to_cupyd.py +76 -0
  690. tests/transforms/test_to_device.py +42 -0
  691. tests/transforms/test_to_deviced.py +37 -0
  692. tests/transforms/test_to_numpy.py +85 -0
  693. tests/transforms/test_to_numpyd.py +68 -0
  694. tests/transforms/test_to_pil.py +52 -0
  695. tests/transforms/test_to_pild.py +50 -0
  696. tests/transforms/test_to_tensor.py +60 -0
  697. tests/transforms/test_to_tensord.py +71 -0
  698. tests/transforms/test_torchvision.py +66 -0
  699. tests/transforms/test_torchvisiond.py +63 -0
  700. tests/transforms/test_transform.py +62 -0
  701. tests/transforms/test_transpose.py +41 -0
  702. tests/transforms/test_transposed.py +52 -0
  703. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  704. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  705. tests/transforms/test_vote_ensemble.py +84 -0
  706. tests/transforms/test_vote_ensembled.py +107 -0
  707. tests/transforms/test_with_allow_missing_keys.py +76 -0
  708. tests/transforms/test_zoom.py +120 -0
  709. tests/transforms/test_zoomd.py +94 -0
  710. tests/transforms/transform/__init__.py +10 -0
  711. tests/transforms/transform/test_randomizable.py +52 -0
  712. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  713. tests/transforms/utility/__init__.py +10 -0
  714. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  715. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  716. tests/transforms/utility/test_identity.py +29 -0
  717. tests/transforms/utility/test_identityd.py +30 -0
  718. tests/transforms/utility/test_lambda.py +71 -0
  719. tests/transforms/utility/test_lambdad.py +83 -0
  720. tests/transforms/utility/test_rand_lambda.py +87 -0
  721. tests/transforms/utility/test_rand_lambdad.py +77 -0
  722. tests/transforms/utility/test_simulatedelay.py +36 -0
  723. tests/transforms/utility/test_simulatedelayd.py +36 -0
  724. tests/transforms/utility/test_splitdim.py +52 -0
  725. tests/transforms/utility/test_splitdimd.py +96 -0
  726. tests/transforms/utils/__init__.py +10 -0
  727. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  728. tests/transforms/utils/test_get_unique_labels.py +45 -0
  729. tests/transforms/utils/test_print_transform_backends.py +29 -0
  730. tests/transforms/utils/test_soft_clip.py +125 -0
  731. tests/utils/__init__.py +10 -0
  732. tests/utils/enums/__init__.py +10 -0
  733. tests/utils/enums/test_hovernet_loss.py +190 -0
  734. tests/utils/enums/test_ordering.py +289 -0
  735. tests/utils/enums/test_wsireader.py +663 -0
  736. tests/utils/misc/__init__.py +10 -0
  737. tests/utils/misc/test_ensure_tuple.py +53 -0
  738. tests/utils/misc/test_monai_env_vars.py +44 -0
  739. tests/utils/misc/test_monai_utils_misc.py +103 -0
  740. tests/utils/misc/test_str2bool.py +34 -0
  741. tests/utils/misc/test_str2list.py +33 -0
  742. tests/utils/test_alias.py +44 -0
  743. tests/utils/test_component_store.py +73 -0
  744. tests/utils/test_deprecated.py +455 -0
  745. tests/utils/test_enum_bound_interp.py +75 -0
  746. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  747. tests/utils/test_get_package_version.py +34 -0
  748. tests/utils/test_handler_logfile.py +84 -0
  749. tests/utils/test_handler_metric_logger.py +62 -0
  750. tests/utils/test_list_to_dict.py +43 -0
  751. tests/utils/test_look_up_option.py +87 -0
  752. tests/utils/test_optional_import.py +80 -0
  753. tests/utils/test_pad_mode.py +39 -0
  754. tests/utils/test_profiling.py +208 -0
  755. tests/utils/test_rankfilter_dist.py +77 -0
  756. tests/utils/test_require_pkg.py +83 -0
  757. tests/utils/test_sample_slices.py +43 -0
  758. tests/utils/test_set_determinism.py +74 -0
  759. tests/utils/test_squeeze_unsqueeze.py +71 -0
  760. tests/utils/test_state_cacher.py +67 -0
  761. tests/utils/test_torchscript_utils.py +113 -0
  762. tests/utils/test_version.py +91 -0
  763. tests/utils/test_version_after.py +65 -0
  764. tests/utils/type_conversion/__init__.py +10 -0
  765. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  766. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  767. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  768. tests/visualize/__init__.py +10 -0
  769. tests/visualize/test_img2tensorboard.py +46 -0
  770. tests/visualize/test_occlusion_sensitivity.py +128 -0
  771. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  772. tests/visualize/test_vis_cam.py +98 -0
  773. tests/visualize/test_vis_gradcam.py +211 -0
  774. tests/visualize/utils/__init__.py +10 -0
  775. tests/visualize/utils/test_blend_images.py +63 -0
  776. tests/visualize/utils/test_matshow3d.py +133 -0
  777. monai_weekly-1.5.dev2505.dist-info/RECORD +0 -427
  778. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
  779. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
@@ -0,0 +1,289 @@
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.transforms import (
21
+ Compose,
22
+ CuCIM,
23
+ Flip,
24
+ Flipd,
25
+ OneOf,
26
+ RandAdjustContrast,
27
+ RandCuCIM,
28
+ RandFlip,
29
+ RandomizableTrait,
30
+ Rotate90,
31
+ ToCupy,
32
+ ToNumpy,
33
+ TorchVision,
34
+ ToTensor,
35
+ ToTensord,
36
+ )
37
+ from monai.utils import Range, optional_import
38
+ from tests.test_utils import HAS_CUPY
39
+
40
+ _, has_nvtx = optional_import("torch._C._nvtx", descriptor="NVTX is not installed. Are you sure you have a CUDA build?")
41
+ _, has_tvt = optional_import("torchvision.transforms")
42
+ _, has_cut = optional_import("cucim.core.operations.expose.transform")
43
+
44
+ TEST_CASE_ARRAY_0 = [np.random.randn(3, 3)]
45
+ TEST_CASE_ARRAY_1 = [np.random.randn(3, 10, 10)]
46
+
47
+ TEST_CASE_DICT_0 = [{"image": np.random.randn(3, 3)}]
48
+ TEST_CASE_DICT_1 = [{"image": np.random.randn(3, 10, 10)}]
49
+
50
+ TEST_CASE_TORCH_0 = [torch.randn(3, 3)]
51
+ TEST_CASE_TORCH_1 = [torch.randn(3, 10, 10)]
52
+
53
+ TEST_CASE_WRAPPER = [np.random.randn(3, 10, 10)]
54
+
55
+ TEST_CASE_RECURSIVE_0 = [
56
+ torch.randn(3, 3),
57
+ Compose([ToNumpy(), Flip(), RandAdjustContrast(prob=0.0), RandFlip(prob=1.0), ToTensor()]),
58
+ ]
59
+ TEST_CASE_RECURSIVE_1 = [
60
+ torch.randn(3, 3),
61
+ Compose([ToNumpy(), Flip(), Compose([RandAdjustContrast(prob=0.0), RandFlip(prob=1.0)]), ToTensor()]),
62
+ ]
63
+ TEST_CASE_RECURSIVE_2 = [
64
+ torch.randn(3, 3),
65
+ Compose([ToNumpy(), Flip(), OneOf([RandAdjustContrast(prob=0.0), RandFlip(prob=1.0)], weights=[0, 1]), ToTensor()]),
66
+ ]
67
+ TEST_CASE_RECURSIVE_LIST = [
68
+ torch.randn(3, 3),
69
+ [ToNumpy(), Flip(), RandAdjustContrast(prob=0.0), RandFlip(prob=1.0), ToTensor()],
70
+ ]
71
+
72
+
73
+ @unittest.skipUnless(has_nvtx, "Required torch._C._nvtx for NVTX Range!")
74
+ class TestNVTXRangeDecorator(unittest.TestCase):
75
+ @parameterized.expand([TEST_CASE_ARRAY_0, TEST_CASE_ARRAY_1])
76
+ def test_tranform_array(self, input):
77
+ transforms = Compose([Range("random flip")(Flip()), Range()(ToTensor())])
78
+ # Apply transforms
79
+ output = transforms(input)
80
+
81
+ # Decorate with NVTX Range
82
+ transforms1 = Range()(transforms)
83
+ transforms2 = Range("Transforms2")(transforms)
84
+ transforms3 = Range(name="Transforms3", methods="__call__")(transforms)
85
+
86
+ # Apply transforms with Range
87
+ output1 = transforms1(input)
88
+ output2 = transforms2(input)
89
+ output3 = transforms3(input)
90
+
91
+ # Check the outputs
92
+ self.assertIsInstance(output, torch.Tensor)
93
+ self.assertIsInstance(output1, torch.Tensor)
94
+ self.assertIsInstance(output2, torch.Tensor)
95
+ self.assertIsInstance(output3, torch.Tensor)
96
+ np.testing.assert_equal(output.numpy(), output1.numpy())
97
+ np.testing.assert_equal(output.numpy(), output2.numpy())
98
+ np.testing.assert_equal(output.numpy(), output3.numpy())
99
+
100
+ @parameterized.expand([TEST_CASE_DICT_0, TEST_CASE_DICT_1])
101
+ def test_tranform_dict(self, input):
102
+ transforms = Compose([Range("random flip dict")(Flipd(keys="image")), Range()(ToTensord("image"))])
103
+ # Apply transforms
104
+ output = transforms(input)["image"]
105
+
106
+ # Decorate with NVTX Range
107
+ transforms1 = Range()(transforms)
108
+ transforms2 = Range("Transforms2")(transforms)
109
+ transforms3 = Range(name="Transforms3", methods="__call__")(transforms)
110
+
111
+ # Apply transforms with Range
112
+ output1 = transforms1(input)["image"]
113
+ output2 = transforms2(input)["image"]
114
+ output3 = transforms3(input)["image"]
115
+
116
+ # Check the outputs
117
+ self.assertIsInstance(output, torch.Tensor)
118
+ self.assertIsInstance(output1, torch.Tensor)
119
+ self.assertIsInstance(output2, torch.Tensor)
120
+ self.assertIsInstance(output3, torch.Tensor)
121
+ np.testing.assert_equal(output.numpy(), output1.numpy())
122
+ np.testing.assert_equal(output.numpy(), output2.numpy())
123
+ np.testing.assert_equal(output.numpy(), output3.numpy())
124
+
125
+ @parameterized.expand([TEST_CASE_WRAPPER])
126
+ @unittest.skipUnless(HAS_CUPY, "Requires CuPy.")
127
+ @unittest.skipUnless(has_cut, "Requires cuCIM transforms.")
128
+ @unittest.skipUnless(has_tvt, "Requires torchvision transforms.")
129
+ def test_wrapper_tranforms(self, input):
130
+ transform_list = [
131
+ ToTensor(),
132
+ TorchVision(name="RandomHorizontalFlip", p=1.0),
133
+ ToCupy(),
134
+ CuCIM(name="image_flip", spatial_axis=-1),
135
+ RandCuCIM(name="rand_image_rotate_90", prob=1.0, max_k=1, spatial_axis=(-2, -1)),
136
+ ]
137
+
138
+ transforms = Compose(transform_list)
139
+ transforms_range = Compose([Range()(t) for t in transform_list])
140
+
141
+ # Apply transforms
142
+ output = transforms(input)
143
+
144
+ # Apply transforms with Range
145
+ output_r = transforms_range(input)
146
+
147
+ # Check the outputs
148
+ np.testing.assert_equal(output.get(), output_r.get())
149
+
150
+ @parameterized.expand([TEST_CASE_RECURSIVE_0, TEST_CASE_RECURSIVE_1, TEST_CASE_RECURSIVE_2])
151
+ def test_recursive_tranforms(self, input, transforms):
152
+ transforms_range = Range(name="Recursive Compose", recursive=True)(transforms)
153
+
154
+ # Apply transforms
155
+ output = transforms(input)
156
+
157
+ # Apply transforms with Range
158
+ output_r = transforms_range(input)
159
+
160
+ # Check the outputs
161
+ self.assertEqual(transforms.map_items, transforms_range.map_items)
162
+ self.assertEqual(transforms.unpack_items, transforms_range.unpack_items)
163
+ np.testing.assert_equal(output.numpy(), output_r.numpy())
164
+
165
+ @parameterized.expand([TEST_CASE_RECURSIVE_LIST])
166
+ def test_recursive_list_tranforms(self, input, transform_list):
167
+ transforms_list_range = Range(recursive=True)(transform_list)
168
+
169
+ # Apply transforms
170
+ output = Compose(transform_list)(input)
171
+
172
+ # Apply transforms with Range
173
+ output_r = Compose(transforms_list_range)(input)
174
+
175
+ # Check the outputs
176
+ np.testing.assert_equal(output.numpy(), output_r.numpy())
177
+
178
+ @parameterized.expand([TEST_CASE_ARRAY_1])
179
+ def test_tranform_randomized(self, input):
180
+ # Compose deterministic and randomized transforms
181
+ transforms = Compose(
182
+ [
183
+ Range("flip")(Flip()),
184
+ Rotate90(),
185
+ Range()(RandAdjustContrast(prob=0.0)),
186
+ Range("random flip")(RandFlip(prob=1.0)),
187
+ ToTensor(),
188
+ ]
189
+ )
190
+ # Apply transforms
191
+ output = transforms(input)
192
+
193
+ # Decorate with NVTX Range
194
+ transforms1 = Range()(transforms)
195
+ transforms2 = Range("Transforms2")(transforms)
196
+ transforms3 = Range(name="Transforms3", methods="__call__")(transforms)
197
+
198
+ # Apply transforms with Range
199
+ output1 = transforms1(input)
200
+ output2 = transforms2(input)
201
+ output3 = transforms3(input)
202
+
203
+ # Check if the outputs are equal
204
+ self.assertIsInstance(output, torch.Tensor)
205
+ self.assertIsInstance(output1, torch.Tensor)
206
+ self.assertIsInstance(output2, torch.Tensor)
207
+ self.assertIsInstance(output3, torch.Tensor)
208
+ np.testing.assert_equal(output.numpy(), output1.numpy())
209
+ np.testing.assert_equal(output.numpy(), output2.numpy())
210
+ np.testing.assert_equal(output.numpy(), output3.numpy())
211
+
212
+ # Check if the first randomized is RandAdjustContrast
213
+ for tran in transforms.transforms:
214
+ if isinstance(tran, RandomizableTrait):
215
+ self.assertIsInstance(tran, RandAdjustContrast)
216
+ break
217
+
218
+ @parameterized.expand([TEST_CASE_TORCH_0, TEST_CASE_TORCH_1])
219
+ def test_network(self, input):
220
+ # Create a network
221
+ model = torch.nn.Sequential(torch.nn.ReLU(), torch.nn.Sigmoid())
222
+
223
+ # Forward
224
+ output = model(input)
225
+
226
+ # Decorate with NVTX Range
227
+ model1 = Range()(model)
228
+ model2 = Range("Model2")(model)
229
+ model3 = Range(name="Model3", methods="forward")(model)
230
+
231
+ # Forward with Range
232
+ output1 = model1(input)
233
+ output2 = model2(input)
234
+ output3 = model3(input)
235
+
236
+ # Check the outputs
237
+ self.assertIsInstance(output, torch.Tensor)
238
+ self.assertIsInstance(output1, torch.Tensor)
239
+ self.assertIsInstance(output2, torch.Tensor)
240
+ self.assertIsInstance(output3, torch.Tensor)
241
+ np.testing.assert_equal(output.numpy(), output1.numpy())
242
+ np.testing.assert_equal(output.numpy(), output2.numpy())
243
+ np.testing.assert_equal(output.numpy(), output3.numpy())
244
+
245
+ @parameterized.expand([TEST_CASE_TORCH_0, TEST_CASE_TORCH_1])
246
+ def test_loss(self, input):
247
+ # Create a network and loss
248
+ model = torch.nn.Sigmoid()
249
+ loss = torch.nn.BCELoss()
250
+ pred = model(input)
251
+ target = torch.empty_like(input).random_(2)
252
+
253
+ # Loss evaluation
254
+ output = loss(pred, target)
255
+
256
+ # Decorate with NVTX Range
257
+ loss1 = Range()(loss)
258
+ loss2 = Range("Loss2")(loss)
259
+ loss3 = Range(name="Loss3", methods="forward")(loss)
260
+
261
+ # Loss evaluation with Range
262
+ output1 = loss1(pred, target)
263
+ output2 = loss2(pred, target)
264
+ output3 = loss3(pred, target)
265
+
266
+ # Check the outputs
267
+ self.assertIsInstance(output, torch.Tensor)
268
+ self.assertIsInstance(output1, torch.Tensor)
269
+ self.assertIsInstance(output2, torch.Tensor)
270
+ self.assertIsInstance(output3, torch.Tensor)
271
+ np.testing.assert_equal(output.numpy(), output1.numpy())
272
+ np.testing.assert_equal(output.numpy(), output2.numpy())
273
+ np.testing.assert_equal(output.numpy(), output3.numpy())
274
+
275
+ def test_context_manager(self):
276
+ model = torch.nn.Sigmoid()
277
+ loss = torch.nn.BCELoss()
278
+
279
+ with Range():
280
+ input = torch.randn(3, requires_grad=True)
281
+ target = torch.empty(3).random_(2)
282
+
283
+ with Range("Model"):
284
+ output = loss(model(input), target)
285
+ output.backward()
286
+
287
+
288
+ if __name__ == "__main__":
289
+ unittest.main()
@@ -0,0 +1,143 @@
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.transforms import Compose, Flip, RandFlip, RandFlipD, RandomizableTrait, ToTensor, ToTensorD
21
+ from monai.transforms.nvtx import (
22
+ Mark,
23
+ MarkD,
24
+ RandMark,
25
+ RandMarkD,
26
+ RandRangePop,
27
+ RandRangePopD,
28
+ RandRangePush,
29
+ RandRangePushD,
30
+ RangePop,
31
+ RangePopD,
32
+ RangePush,
33
+ RangePushD,
34
+ )
35
+ from monai.utils import optional_import
36
+
37
+ _, has_nvtx = optional_import("torch._C._nvtx", descriptor="NVTX is not installed. Are you sure you have a CUDA build?")
38
+
39
+ TEST_CASE_ARRAY_0 = [np.random.randn(3, 3)]
40
+ TEST_CASE_ARRAY_1 = [np.random.randn(3, 10, 10)]
41
+ TEST_CASE_DICT_0 = [{"image": np.random.randn(3, 3)}]
42
+ TEST_CASE_DICT_1 = [{"image": np.random.randn(3, 10, 10)}]
43
+
44
+
45
+ class TestNVTXTransforms(unittest.TestCase):
46
+
47
+ @parameterized.expand([TEST_CASE_ARRAY_0, TEST_CASE_ARRAY_1, TEST_CASE_DICT_0, TEST_CASE_DICT_1])
48
+ @unittest.skipUnless(has_nvtx, "CUDA is required for NVTX!")
49
+ def test_nvtx_transfroms_alone(self, input):
50
+ transforms = Compose(
51
+ [
52
+ Mark("Mark: Transforms Start!"),
53
+ RangePush("Range: RandFlipD"),
54
+ RangePop(),
55
+ RandRangePush("Range: ToTensorD"),
56
+ RandRangePop(),
57
+ RandMark("Mark: Transforms End!"),
58
+ ]
59
+ )
60
+ output = transforms(input)
61
+ self.assertEqual(id(input), id(output))
62
+
63
+ # Check if chain of randomizable/non-randomizable transforms is not broken
64
+ for tran in transforms.transforms:
65
+ if isinstance(tran, RandomizableTrait):
66
+ self.assertIsInstance(tran, RangePush)
67
+ break
68
+
69
+ @parameterized.expand([TEST_CASE_ARRAY_0, TEST_CASE_ARRAY_1])
70
+ @unittest.skipUnless(has_nvtx, "CUDA is required for NVTX!")
71
+ def test_nvtx_transfroms_array(self, input):
72
+ # with prob == 0.0
73
+ transforms = Compose(
74
+ [
75
+ RandMark("Mark: Transforms Start!"),
76
+ RandRangePush("Range: RandFlip"),
77
+ RandFlip(prob=0.0),
78
+ RandRangePop(),
79
+ RangePush("Range: ToTensor"),
80
+ ToTensor(),
81
+ RangePop(),
82
+ Mark("Mark: Transforms End!"),
83
+ ]
84
+ )
85
+ output = transforms(input)
86
+ self.assertIsInstance(output, torch.Tensor)
87
+ np.testing.assert_array_equal(input, output)
88
+ # with prob == 1.0
89
+ transforms = Compose(
90
+ [
91
+ RandMark("Mark: Transforms Start!"),
92
+ RandRangePush("Range: RandFlip"),
93
+ RandFlip(prob=1.0),
94
+ RandRangePop(),
95
+ RangePush("Range: ToTensor"),
96
+ ToTensor(),
97
+ RangePop(),
98
+ Mark("Mark: Transforms End!"),
99
+ ]
100
+ )
101
+ output = transforms(input)
102
+ self.assertIsInstance(output, torch.Tensor)
103
+ np.testing.assert_array_equal(input, Flip()(output.numpy()))
104
+
105
+ @parameterized.expand([TEST_CASE_DICT_0, TEST_CASE_DICT_1])
106
+ @unittest.skipUnless(has_nvtx, "CUDA is required for NVTX!")
107
+ def test_nvtx_transfroms_dict(self, input):
108
+ # with prob == 0.0
109
+ transforms = Compose(
110
+ [
111
+ RandMarkD("Mark: Transforms (p=0) Start!"),
112
+ RandRangePushD("Range: RandFlipD"),
113
+ RandFlipD(keys="image", prob=0.0),
114
+ RandRangePopD(),
115
+ RangePushD("Range: ToTensorD"),
116
+ ToTensorD(keys=("image")),
117
+ RangePopD(),
118
+ MarkD("Mark: Transforms (p=0) End!"),
119
+ ]
120
+ )
121
+ output = transforms(input)
122
+ self.assertIsInstance(output["image"], torch.Tensor)
123
+ np.testing.assert_array_equal(input["image"], output["image"])
124
+ # with prob == 1.0
125
+ transforms = Compose(
126
+ [
127
+ RandMarkD("Mark: Transforms (p=1) Start!"),
128
+ RandRangePushD("Range: RandFlipD"),
129
+ RandFlipD(keys="image", prob=1.0),
130
+ RandRangePopD(),
131
+ RangePushD("Range: ToTensorD"),
132
+ ToTensorD(keys=("image")),
133
+ RangePopD(),
134
+ MarkD("Mark: Transforms (p=1) End!"),
135
+ ]
136
+ )
137
+ output = transforms(input)
138
+ self.assertIsInstance(output["image"], torch.Tensor)
139
+ np.testing.assert_array_equal(input["image"], Flip()(output["image"].numpy()))
140
+
141
+
142
+ if __name__ == "__main__":
143
+ unittest.main()
@@ -0,0 +1,247 @@
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 nibabel as nib
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.transforms import Orientation, create_rotate, create_translate
24
+ from tests.lazy_transforms_utils import test_resampler_lazy
25
+ from tests.test_utils import TEST_DEVICES, assert_allclose
26
+
27
+ TESTS = []
28
+ for device in TEST_DEVICES:
29
+ TESTS.append(
30
+ [
31
+ {"axcodes": "RAS"},
32
+ torch.arange(12).reshape((2, 1, 2, 3)),
33
+ torch.eye(4),
34
+ torch.arange(12).reshape((2, 1, 2, 3)),
35
+ "RAS",
36
+ *device,
37
+ ]
38
+ )
39
+ TESTS.append(
40
+ [
41
+ {"axcodes": "ALS"},
42
+ torch.arange(12).reshape((2, 1, 2, 3)),
43
+ torch.as_tensor(np.diag([-1, -1, 1, 1])),
44
+ torch.tensor([[[[3, 4, 5]], [[0, 1, 2]]], [[[9, 10, 11]], [[6, 7, 8]]]]),
45
+ "ALS",
46
+ *device,
47
+ ]
48
+ )
49
+ TESTS.append(
50
+ [
51
+ {"axcodes": "RAS"},
52
+ torch.arange(12).reshape((2, 1, 2, 3)),
53
+ torch.as_tensor(np.diag([-1, -1, 1, 1])),
54
+ torch.tensor([[[[3, 4, 5], [0, 1, 2]]], [[[9, 10, 11], [6, 7, 8]]]]),
55
+ "RAS",
56
+ *device,
57
+ ]
58
+ )
59
+ TESTS.append(
60
+ [
61
+ {"axcodes": "AL"},
62
+ torch.arange(6).reshape((2, 1, 3)),
63
+ torch.eye(3),
64
+ torch.tensor([[[0], [1], [2]], [[3], [4], [5]]]),
65
+ "AL",
66
+ *device,
67
+ ]
68
+ )
69
+ TESTS.append(
70
+ [
71
+ {"axcodes": "L"},
72
+ torch.arange(6).reshape((2, 3)),
73
+ torch.eye(2),
74
+ torch.tensor([[2, 1, 0], [5, 4, 3]]),
75
+ "L",
76
+ *device,
77
+ ]
78
+ )
79
+ TESTS.append(
80
+ [
81
+ {"axcodes": "L"},
82
+ torch.arange(6).reshape((2, 3)),
83
+ torch.eye(2),
84
+ torch.tensor([[2, 1, 0], [5, 4, 3]]),
85
+ "L",
86
+ *device,
87
+ ]
88
+ )
89
+ TESTS.append(
90
+ [
91
+ {"axcodes": "L"},
92
+ torch.arange(6).reshape((2, 3)),
93
+ torch.as_tensor(np.diag([-1, 1])),
94
+ torch.arange(6).reshape((2, 3)),
95
+ "L",
96
+ *device,
97
+ ]
98
+ )
99
+ TESTS.append(
100
+ [
101
+ {"axcodes": "LPS"},
102
+ torch.arange(12).reshape((2, 1, 2, 3)),
103
+ torch.as_tensor(
104
+ create_translate(3, (10, 20, 30))
105
+ @ create_rotate(3, (np.pi / 2, np.pi / 2, np.pi / 4))
106
+ @ np.diag([-1, 1, 1, 1])
107
+ ),
108
+ torch.tensor([[[[2, 5]], [[1, 4]], [[0, 3]]], [[[8, 11]], [[7, 10]], [[6, 9]]]]),
109
+ "LPS",
110
+ *device,
111
+ ]
112
+ )
113
+ TESTS.append(
114
+ [
115
+ {"as_closest_canonical": True},
116
+ torch.arange(12).reshape((2, 1, 2, 3)),
117
+ torch.as_tensor(
118
+ create_translate(3, (10, 20, 30))
119
+ @ create_rotate(3, (np.pi / 2, np.pi / 2, np.pi / 4))
120
+ @ np.diag([-1, 1, 1, 1])
121
+ ),
122
+ torch.tensor([[[[0, 3]], [[1, 4]], [[2, 5]]], [[[6, 9]], [[7, 10]], [[8, 11]]]]),
123
+ "RAS",
124
+ *device,
125
+ ]
126
+ )
127
+ TESTS.append(
128
+ [
129
+ {"as_closest_canonical": True},
130
+ torch.arange(6).reshape((1, 2, 3)),
131
+ torch.as_tensor(create_translate(2, (10, 20)) @ create_rotate(2, (np.pi / 3)) @ np.diag([-1, -0.2, 1])),
132
+ torch.tensor([[[3, 0], [4, 1], [5, 2]]]),
133
+ "RA",
134
+ *device,
135
+ ]
136
+ )
137
+ TESTS.append(
138
+ [
139
+ {"axcodes": "LP"},
140
+ torch.arange(6).reshape((1, 2, 3)),
141
+ torch.as_tensor(create_translate(2, (10, 20)) @ create_rotate(2, (np.pi / 3)) @ np.diag([-1, -0.2, 1])),
142
+ torch.tensor([[[2, 5], [1, 4], [0, 3]]]),
143
+ "LP",
144
+ *device,
145
+ ]
146
+ )
147
+ TESTS.append(
148
+ [
149
+ {"axcodes": "LPID", "labels": tuple(zip("LPIC", "RASD"))},
150
+ torch.zeros((1, 2, 3, 4, 5)),
151
+ torch.as_tensor(np.diag([-1, -0.2, -1, 1, 1])),
152
+ torch.zeros((1, 2, 3, 4, 5)),
153
+ "LPID",
154
+ *device,
155
+ ]
156
+ )
157
+ TESTS.append(
158
+ [
159
+ {"as_closest_canonical": True, "labels": tuple(zip("LPIC", "RASD"))},
160
+ torch.zeros((1, 2, 3, 4, 5)),
161
+ torch.as_tensor(np.diag([-1, -0.2, -1, 1, 1])),
162
+ torch.zeros((1, 2, 3, 4, 5)),
163
+ "RASD",
164
+ *device,
165
+ ]
166
+ )
167
+
168
+ TESTS_TORCH = []
169
+ for track_meta in (False, True):
170
+ for device in TEST_DEVICES:
171
+ TESTS_TORCH.append([{"axcodes": "LPS"}, torch.zeros((1, 3, 4, 5)), track_meta, *device])
172
+
173
+ ILL_CASES = [
174
+ # too short axcodes
175
+ [{"axcodes": "RA"}, torch.arange(12).reshape((2, 1, 2, 3)), torch.eye(4)]
176
+ ]
177
+
178
+
179
+ class TestOrientationCase(unittest.TestCase):
180
+ @parameterized.expand(TESTS)
181
+ def test_ornt_meta(
182
+ self,
183
+ init_param,
184
+ img: torch.Tensor,
185
+ affine: torch.Tensor,
186
+ expected_data: torch.Tensor,
187
+ expected_code: str,
188
+ device,
189
+ ):
190
+ img = MetaTensor(img, affine=affine).to(device)
191
+ ornt = Orientation(**init_param)
192
+ call_param = {"data_array": img}
193
+ res = ornt(**call_param) # type: ignore[arg-type]
194
+ if img.ndim in (3, 4):
195
+ test_resampler_lazy(ornt, res, init_param, call_param)
196
+
197
+ assert_allclose(res, expected_data.to(device))
198
+ new_code = nib.orientations.aff2axcodes(res.affine.cpu(), labels=ornt.labels) # type: ignore
199
+ self.assertEqual("".join(new_code), expected_code)
200
+
201
+ @parameterized.expand(TESTS_TORCH)
202
+ def test_ornt_torch(self, init_param, img: torch.Tensor, track_meta: bool, device):
203
+ set_track_meta(track_meta)
204
+ ornt = Orientation(**init_param)
205
+
206
+ img = img.to(device)
207
+ expected_data = img.clone()
208
+ expected_code = ornt.axcodes
209
+
210
+ res = ornt(img)
211
+ assert_allclose(res, expected_data)
212
+ if track_meta:
213
+ self.assertIsInstance(res, MetaTensor)
214
+ assert isinstance(res, MetaTensor) # for mypy type narrowing
215
+ new_code = nib.orientations.aff2axcodes(res.affine.cpu(), labels=ornt.labels)
216
+ self.assertEqual("".join(new_code), expected_code)
217
+ else:
218
+ self.assertIsInstance(res, torch.Tensor)
219
+ self.assertNotIsInstance(res, MetaTensor)
220
+
221
+ @parameterized.expand(ILL_CASES)
222
+ def test_bad_params(self, init_param, img: torch.Tensor, affine: torch.Tensor):
223
+ img = MetaTensor(img, affine=affine)
224
+ with self.assertRaises(ValueError):
225
+ Orientation(**init_param)(img)
226
+
227
+ @parameterized.expand(TEST_DEVICES)
228
+ def test_inverse(self, device):
229
+ img_t = torch.rand((1, 10, 9, 8), dtype=torch.float32, device=device)
230
+ affine = torch.tensor(
231
+ [[0, 0, -1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]], dtype=torch.float32, device="cpu"
232
+ )
233
+ meta = {"fname": "somewhere"}
234
+ img = MetaTensor(img_t, affine=affine, meta=meta)
235
+ tr = Orientation("LPS")
236
+ # check that image and affine have changed
237
+ img = tr(img)
238
+ self.assertNotEqual(img.shape, img_t.shape)
239
+ self.assertGreater((affine - img.affine).max(), 0.5)
240
+ # check that with inverse, image affine are back to how they were
241
+ img = tr.inverse(img)
242
+ self.assertEqual(img.shape, img_t.shape)
243
+ self.assertLess((affine - img.affine).max(), 1e-2)
244
+
245
+
246
+ if __name__ == "__main__":
247
+ unittest.main()