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 +1,711 @@
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 os
15
+ import unittest
16
+ from pathlib import Path
17
+
18
+ import numpy as np
19
+ import torch
20
+ from parameterized import parameterized
21
+ from PIL import Image
22
+
23
+ from monai.transforms import UltrasoundConfidenceMapTransform
24
+ from monai.utils import optional_import
25
+ from tests.test_utils import assert_allclose
26
+
27
+ _, has_scipy = optional_import("scipy")
28
+
29
+ TESTS_PATH = Path(__file__).parents[1]
30
+
31
+ TEST_INPUT = np.array(
32
+ [
33
+ [1, 2, 3, 23, 13, 22, 5, 1, 2, 3],
34
+ [1, 2, 3, 12, 4, 6, 9, 1, 2, 3],
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+ [1, 2, 3, 8, 7, 10, 11, 1, 2, 3],
36
+ [1, 2, 3, 14, 15, 16, 17, 1, 2, 3],
37
+ [1, 2, 3, 18, 19, 20, 21, 1, 2, 3],
38
+ [1, 2, 3, 24, 25, 26, 27, 1, 2, 3],
39
+ [1, 2, 3, 28, 29, 30, 31, 1, 2, 3],
40
+ [1, 2, 3, 32, 33, 34, 35, 1, 2, 3],
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+ [1, 2, 3, 36, 37, 38, 39, 1, 2, 3],
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+ [1, 2, 3, 40, 41, 42, 43, 1, 2, 3],
43
+ ],
44
+ dtype=np.float32,
45
+ )
46
+
47
+ TEST_MASK = np.array(
48
+ [
49
+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
50
+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [1, 1, 1, 0, 0, 0, 1, 1, 1, 0],
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+ [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
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+ ],
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+ dtype=np.float32,
61
+ )
62
+
63
+ SINK_ALL_OUTPUT = np.array(
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+ [
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+ [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
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+ [
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+ ],
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+ dtype=np.float32,
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+ )
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+
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+ SINK_MID_OUTPUT = np.array(
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+ )
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+
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+ SINK_MIN_OUTPUT = np.array(
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+ 0.9481472656653798,
380
+ ],
381
+ [
382
+ 0.9999816006081851,
383
+ 0.9999127861527936,
384
+ 0.9995832399159849,
385
+ 0.6133274396648696,
386
+ 0.6086364734302403,
387
+ 0.6034602717119345,
388
+ 0.5978473214165134,
389
+ 0.0,
390
+ 0.8382338778894218,
391
+ 0.9477082231321966,
392
+ ],
393
+ ],
394
+ dtype=np.float32,
395
+ )
396
+
397
+ SINK_MASK_OUTPUT = np.array(
398
+ [
399
+ [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0],
400
+ [0.0, 0.0, 0.0, 0.9047934405899283, 0.9936046284605553, 0.9448690902377527, 0.0, 0.0, 0.0, 0.8363773255131761],
401
+ [0.0, 0.0, 0.0, 0.90375200446097, 0.9434594475474036, 0.4716831449516178, 0.0, 0.0, 0.0, 0.7364197333910302],
402
+ [
403
+ 0.0,
404
+ 0.0,
405
+ 0.0,
406
+ 0.09080438801405301,
407
+ 0.06774182873204163,
408
+ 0.038207095016625024,
409
+ 0.0,
410
+ 0.0,
411
+ 0.0,
412
+ 0.6745641479264269,
413
+ ],
414
+ [
415
+ 0.0,
416
+ 0.0,
417
+ 0.0,
418
+ 0.01731082802870267,
419
+ 0.013540929458217351,
420
+ 0.007321202161532623,
421
+ 0.0,
422
+ 0.0,
423
+ 0.0,
424
+ 0.6341231654271253,
425
+ ],
426
+ [
427
+ 0.0,
428
+ 0.0,
429
+ 0.0,
430
+ 0.0006444251665178544,
431
+ 0.0005397129128756325,
432
+ 0.0003048384803626333,
433
+ 0.0,
434
+ 0.0,
435
+ 0.0,
436
+ 0.6070178708536365,
437
+ ],
438
+ [
439
+ 0.0,
440
+ 0.0,
441
+ 0.0,
442
+ 5.406078586212675e-05,
443
+ 4.416783924970537e-05,
444
+ 2.4597362039020103e-05,
445
+ 0.0,
446
+ 0.0,
447
+ 0.0,
448
+ 0.5889413683184284,
449
+ ],
450
+ [
451
+ 0.0,
452
+ 0.0,
453
+ 0.0,
454
+ 4.39259327223233e-06,
455
+ 3.6050656774754658e-06,
456
+ 2.0127120155893425e-06,
457
+ 0.0,
458
+ 0.0,
459
+ 0.0,
460
+ 0.5774279920364456,
461
+ ],
462
+ [
463
+ 0.0,
464
+ 0.0,
465
+ 0.0,
466
+ 4.0740501726718113e-07,
467
+ 3.374875487404489e-07,
468
+ 1.9113630985667455e-07,
469
+ 0.0,
470
+ 0.0,
471
+ 0.0,
472
+ 0.5709897726747111,
473
+ ],
474
+ [
475
+ 3.2266922388030425e-17,
476
+ 1.801110982679718e-14,
477
+ 9.325899448306927e-12,
478
+ 3.913608442133728e-07,
479
+ 3.9581822403393465e-07,
480
+ 4.02383505118481e-07,
481
+ 4.14820241328287e-07,
482
+ 4.281640797396309e-06,
483
+ 0.0023900192231620593,
484
+ 0.5686882523793125,
485
+ ],
486
+ ],
487
+ dtype=np.float32,
488
+ )
489
+
490
+
491
+ @unittest.skipUnless(has_scipy, "Requires scipy")
492
+ class TestUltrasoundConfidenceMapTransform(unittest.TestCase):
493
+ def setUp(self):
494
+ self.input_img_np = np.expand_dims(TEST_INPUT, axis=0) # mock image (numpy array)
495
+ self.input_mask_np = np.expand_dims(TEST_MASK, axis=0) # mock mask (numpy array)
496
+
497
+ self.input_img_torch = torch.from_numpy(TEST_INPUT).unsqueeze(0) # mock image (torch tensor)
498
+ self.input_mask_torch = torch.from_numpy(TEST_MASK).unsqueeze(0) # mock mask (torch tensor)
499
+
500
+ self.real_input_img_paths = [
501
+ os.path.join(TESTS_PATH, "testing_data", "ultrasound_confidence_map", "neck_input.png"),
502
+ os.path.join(TESTS_PATH, "testing_data", "ultrasound_confidence_map", "femur_input.png"),
503
+ ]
504
+
505
+ self.real_result_npy_paths = [
506
+ os.path.join(TESTS_PATH, "testing_data", "ultrasound_confidence_map", "neck_result.npy"),
507
+ os.path.join(TESTS_PATH, "testing_data", "ultrasound_confidence_map", "femur_result.npy"),
508
+ ]
509
+
510
+ self.real_input_paramaters = [
511
+ {"alpha": 2.0, "beta": 90, "gamma": 0.03},
512
+ {"alpha": 2.0, "beta": 90, "gamma": 0.06},
513
+ ]
514
+
515
+ def test_parameters(self):
516
+ # Unknown mode
517
+ with self.assertRaises(ValueError):
518
+ UltrasoundConfidenceMapTransform(mode="unknown")
519
+
520
+ # Unknown sink_mode
521
+ with self.assertRaises(ValueError):
522
+ UltrasoundConfidenceMapTransform(sink_mode="unknown")
523
+
524
+ @parameterized.expand(
525
+ [("all", SINK_ALL_OUTPUT), ("mid", SINK_MID_OUTPUT), ("min", SINK_MIN_OUTPUT), ("mask", SINK_MASK_OUTPUT, True)]
526
+ )
527
+ def test_ultrasound_confidence_map_transform(self, sink_mode, expected_output, use_mask=False):
528
+ # RGB image
529
+ input_img_rgb = np.expand_dims(np.repeat(self.input_img_np, 3, axis=0), axis=0)
530
+ input_img_rgb_torch = torch.from_numpy(input_img_rgb)
531
+
532
+ transform = UltrasoundConfidenceMapTransform(sink_mode=sink_mode)
533
+
534
+ if use_mask:
535
+ result_torch = transform(input_img_rgb_torch, self.input_mask_torch)
536
+ result_np = transform(input_img_rgb, self.input_mask_np)
537
+ else:
538
+ result_torch = transform(input_img_rgb_torch)
539
+ result_np = transform(input_img_rgb)
540
+
541
+ self.assertIsInstance(result_torch, torch.Tensor)
542
+ assert_allclose(result_torch, torch.tensor(expected_output), rtol=1e-4, atol=1e-4)
543
+ self.assertIsInstance(result_np, np.ndarray)
544
+ assert_allclose(result_np, expected_output, rtol=1e-4, atol=1e-4)
545
+
546
+ @parameterized.expand(
547
+ [
548
+ ("all", SINK_ALL_OUTPUT),
549
+ ("mid", SINK_MID_OUTPUT),
550
+ ("min", SINK_MIN_OUTPUT),
551
+ ("mask", SINK_MASK_OUTPUT, True), # Adding a flag for mask cases
552
+ ]
553
+ )
554
+ def test_multi_channel_2d(self, sink_mode, expected_output, use_mask=False):
555
+ input_img_rgb = np.expand_dims(np.repeat(self.input_img_np, 17, axis=0), axis=0)
556
+ input_img_rgb_torch = torch.from_numpy(input_img_rgb)
557
+
558
+ transform = UltrasoundConfidenceMapTransform(sink_mode=sink_mode)
559
+
560
+ if use_mask:
561
+ result_torch = transform(input_img_rgb_torch, self.input_mask_torch)
562
+ result_np = transform(input_img_rgb, self.input_mask_np)
563
+ else:
564
+ result_torch = transform(input_img_rgb_torch)
565
+ result_np = transform(input_img_rgb)
566
+
567
+ self.assertIsInstance(result_torch, torch.Tensor)
568
+ assert_allclose(result_torch, torch.tensor(expected_output), rtol=1e-4, atol=1e-4)
569
+ self.assertIsInstance(result_np, np.ndarray)
570
+ assert_allclose(result_np, expected_output, rtol=1e-4, atol=1e-4)
571
+
572
+ @parameterized.expand([("all",), ("mid",), ("min",), ("mask",)])
573
+ def test_non_one_first_dim(self, sink_mode):
574
+ transform = UltrasoundConfidenceMapTransform(sink_mode=sink_mode)
575
+ input_img_rgb = np.repeat(self.input_img_np, 3, axis=0)
576
+ input_img_rgb_torch = torch.from_numpy(input_img_rgb)
577
+
578
+ if sink_mode == "mask":
579
+ with self.assertRaises(ValueError):
580
+ transform(input_img_rgb_torch, self.input_mask_torch)
581
+ with self.assertRaises(ValueError):
582
+ transform(input_img_rgb, self.input_mask_np)
583
+ else:
584
+ with self.assertRaises(ValueError):
585
+ transform(input_img_rgb_torch)
586
+ with self.assertRaises(ValueError):
587
+ transform(input_img_rgb)
588
+
589
+ @parameterized.expand([("all",), ("mid",), ("min",), ("mask",)])
590
+ def test_no_first_dim(self, sink_mode):
591
+ input_img_rgb = self.input_img_np[0]
592
+ input_img_rgb_torch = torch.from_numpy(input_img_rgb)
593
+
594
+ transform = UltrasoundConfidenceMapTransform(sink_mode=sink_mode)
595
+
596
+ with self.assertRaises(ValueError):
597
+ transform(input_img_rgb_torch)
598
+ with self.assertRaises(ValueError):
599
+ transform(input_img_rgb)
600
+
601
+ if sink_mode == "mask":
602
+ with self.assertRaises(ValueError):
603
+ transform(input_img_rgb_torch, self.input_mask_torch)
604
+ with self.assertRaises(ValueError):
605
+ transform(input_img_rgb, self.input_mask_np)
606
+
607
+ @parameterized.expand([("all",), ("mid",), ("min",)])
608
+ def test_sink_mode(self, mode):
609
+ transform = UltrasoundConfidenceMapTransform(sink_mode=mode)
610
+
611
+ # This should not raise an exception for torch tensor
612
+ result_torch = transform(self.input_img_torch)
613
+ self.assertIsInstance(result_torch, torch.Tensor)
614
+
615
+ # This should not raise an exception for numpy array
616
+ result_np = transform(self.input_img_np)
617
+ self.assertIsInstance(result_np, np.ndarray)
618
+
619
+ def test_sink_mask(self):
620
+ transform = UltrasoundConfidenceMapTransform(sink_mode="mask")
621
+
622
+ # This should not raise an exception for torch tensor with mask
623
+ result_torch = transform(self.input_img_torch, self.input_mask_torch)
624
+ self.assertIsInstance(result_torch, torch.Tensor)
625
+
626
+ # This should not raise an exception for numpy array with mask
627
+ result_np = transform(self.input_img_np, self.input_mask_np)
628
+ self.assertIsInstance(result_np, np.ndarray)
629
+
630
+ # This should raise an exception for torch tensor without mask
631
+ with self.assertRaises(ValueError):
632
+ transform(self.input_img_torch)
633
+
634
+ # This should raise an exception for numpy array without mask
635
+ with self.assertRaises(ValueError):
636
+ transform(self.input_img_np)
637
+
638
+ def test_func(self):
639
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="all")
640
+ output = transform(self.input_img_np)
641
+ assert_allclose(output, SINK_ALL_OUTPUT, rtol=1e-4, atol=1e-4)
642
+
643
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="mid")
644
+ output = transform(self.input_img_np)
645
+ assert_allclose(output, SINK_MID_OUTPUT, rtol=1e-4, atol=1e-4)
646
+
647
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="min")
648
+ output = transform(self.input_img_np)
649
+ assert_allclose(output, SINK_MIN_OUTPUT, rtol=1e-4, atol=1e-4)
650
+
651
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="mask")
652
+ output = transform(self.input_img_np, self.input_mask_np)
653
+ assert_allclose(output, SINK_MASK_OUTPUT, rtol=1e-4, atol=1e-4)
654
+
655
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="all")
656
+ output = transform(self.input_img_torch)
657
+ assert_allclose(output, torch.tensor(SINK_ALL_OUTPUT), rtol=1e-4, atol=1e-4)
658
+
659
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="mid")
660
+ output = transform(self.input_img_torch)
661
+ assert_allclose(output, torch.tensor(SINK_MID_OUTPUT), rtol=1e-4, atol=1e-4)
662
+
663
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="min")
664
+ output = transform(self.input_img_torch)
665
+ assert_allclose(output, torch.tensor(SINK_MIN_OUTPUT), rtol=1e-4, atol=1e-4)
666
+
667
+ transform = UltrasoundConfidenceMapTransform(alpha=2.0, beta=90.0, gamma=0.05, mode="B", sink_mode="mask")
668
+ output = transform(self.input_img_torch, self.input_mask_torch)
669
+ assert_allclose(output, torch.tensor(SINK_MASK_OUTPUT), rtol=1e-4, atol=1e-4)
670
+
671
+ def test_against_official_code(self):
672
+ # This test is to compare the output of the transform with the official code
673
+ # The official code is available at:
674
+ # https://campar.in.tum.de/Main/AthanasiosKaramalisCode
675
+
676
+ for input_img_path, result_npy_path, params in zip(
677
+ self.real_input_img_paths, self.real_result_npy_paths, self.real_input_paramaters
678
+ ):
679
+ input_img = np.array(Image.open(input_img_path))
680
+ input_img = np.expand_dims(input_img, axis=0)
681
+
682
+ result_img = np.load(result_npy_path)
683
+
684
+ transform = UltrasoundConfidenceMapTransform(sink_mode="all", **params)
685
+ output = transform(input_img)
686
+
687
+ assert_allclose(output, result_img, rtol=1e-4, atol=1e-4)
688
+
689
+ def test_against_official_code_using_cg(self):
690
+ # This test is to compare the output of the transform with the official code
691
+ # The official code is available at:
692
+ # https://campar.in.tum.de/Main/AthanasiosKaramalisCode
693
+
694
+ for input_img_path, result_npy_path, params in zip(
695
+ self.real_input_img_paths, self.real_result_npy_paths, self.real_input_paramaters
696
+ ):
697
+ input_img = np.array(Image.open(input_img_path))
698
+ input_img = np.expand_dims(input_img, axis=0)
699
+
700
+ result_img = np.load(result_npy_path)
701
+
702
+ transform = UltrasoundConfidenceMapTransform(
703
+ sink_mode="all", use_cg=True, cg_tol=1.0e-6, cg_maxiter=300, **params
704
+ )
705
+ output = transform(input_img)
706
+
707
+ assert_allclose(output, result_img, rtol=1e-2, atol=1e-2)
708
+
709
+
710
+ if __name__ == "__main__":
711
+ unittest.main()