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

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Files changed (776) hide show
  1. monai/__init__.py +1 -1
  2. monai/_version.py +3 -3
  3. monai/apps/auto3dseg/transforms.py +1 -4
  4. monai/data/utils.py +6 -13
  5. monai/inferers/utils.py +1 -2
  6. monai/losses/dice.py +2 -14
  7. monai/losses/ds_loss.py +1 -3
  8. monai/networks/layers/simplelayers.py +2 -14
  9. monai/networks/utils.py +4 -16
  10. monai/transforms/compose.py +28 -11
  11. monai/transforms/croppad/array.py +1 -6
  12. monai/transforms/io/array.py +0 -1
  13. monai/transforms/transform.py +15 -6
  14. monai/transforms/utils.py +1 -2
  15. monai/utils/tf32.py +0 -10
  16. monai/visualize/class_activation_maps.py +5 -8
  17. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
  18. monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
  19. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
  20. tests/apps/__init__.py +10 -0
  21. tests/apps/deepedit/__init__.py +10 -0
  22. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  23. tests/apps/deepgrow/__init__.py +10 -0
  24. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  25. tests/apps/deepgrow/transforms/__init__.py +10 -0
  26. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  27. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  28. tests/apps/detection/__init__.py +10 -0
  29. tests/apps/detection/metrics/__init__.py +10 -0
  30. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  31. tests/apps/detection/networks/__init__.py +10 -0
  32. tests/apps/detection/networks/test_retinanet.py +210 -0
  33. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  34. tests/apps/detection/test_box_transform.py +370 -0
  35. tests/apps/detection/utils/__init__.py +10 -0
  36. tests/apps/detection/utils/test_anchor_box.py +88 -0
  37. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  38. tests/apps/detection/utils/test_box_coder.py +43 -0
  39. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  40. tests/apps/detection/utils/test_detector_utils.py +96 -0
  41. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  42. tests/apps/nuclick/__init__.py +10 -0
  43. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  44. tests/apps/pathology/__init__.py +10 -0
  45. tests/apps/pathology/handlers/__init__.py +10 -0
  46. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  47. tests/apps/pathology/test_lesion_froc.py +333 -0
  48. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  49. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  50. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  51. tests/apps/pathology/transforms/__init__.py +10 -0
  52. tests/apps/pathology/transforms/post/__init__.py +10 -0
  53. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  54. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  55. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  56. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  57. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  58. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  59. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  60. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  61. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  62. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  63. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  64. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  65. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  66. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  67. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  68. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  69. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  70. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  71. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  72. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  73. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  74. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  75. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  76. tests/apps/reconstruction/__init__.py +10 -0
  77. tests/apps/reconstruction/nets/__init__.py +10 -0
  78. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  79. tests/apps/reconstruction/test_complex_utils.py +77 -0
  80. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  81. tests/apps/reconstruction/test_mri_utils.py +37 -0
  82. tests/apps/reconstruction/transforms/__init__.py +10 -0
  83. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  84. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  85. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  86. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  87. tests/apps/test_check_hash.py +53 -0
  88. tests/apps/test_cross_validation.py +74 -0
  89. tests/apps/test_decathlondataset.py +93 -0
  90. tests/apps/test_download_and_extract.py +70 -0
  91. tests/apps/test_download_url_yandex.py +45 -0
  92. tests/apps/test_mednistdataset.py +72 -0
  93. tests/apps/test_mmar_download.py +154 -0
  94. tests/apps/test_tciadataset.py +123 -0
  95. tests/apps/vista3d/__init__.py +10 -0
  96. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  97. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  98. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  99. tests/bundle/__init__.py +10 -0
  100. tests/bundle/test_bundle_ckpt_export.py +107 -0
  101. tests/bundle/test_bundle_download.py +435 -0
  102. tests/bundle/test_bundle_get_data.py +94 -0
  103. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  104. tests/bundle/test_bundle_trt_export.py +147 -0
  105. tests/bundle/test_bundle_utils.py +149 -0
  106. tests/bundle/test_bundle_verify_metadata.py +66 -0
  107. tests/bundle/test_bundle_verify_net.py +76 -0
  108. tests/bundle/test_bundle_workflow.py +272 -0
  109. tests/bundle/test_component_locator.py +38 -0
  110. tests/bundle/test_config_item.py +138 -0
  111. tests/bundle/test_config_parser.py +392 -0
  112. tests/bundle/test_reference_resolver.py +114 -0
  113. tests/config/__init__.py +10 -0
  114. tests/config/test_cv2_dist.py +53 -0
  115. tests/engines/__init__.py +10 -0
  116. tests/engines/test_ensemble_evaluator.py +94 -0
  117. tests/engines/test_prepare_batch_default.py +76 -0
  118. tests/engines/test_prepare_batch_default_dist.py +76 -0
  119. tests/engines/test_prepare_batch_diffusion.py +104 -0
  120. tests/engines/test_prepare_batch_extra_input.py +80 -0
  121. tests/fl/__init__.py +10 -0
  122. tests/fl/monai_algo/__init__.py +10 -0
  123. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  124. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  125. tests/fl/test_fl_monai_algo_stats.py +81 -0
  126. tests/fl/utils/__init__.py +10 -0
  127. tests/fl/utils/test_fl_exchange_object.py +63 -0
  128. tests/handlers/__init__.py +10 -0
  129. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  130. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  131. tests/handlers/test_handler_classification_saver.py +64 -0
  132. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  133. tests/handlers/test_handler_clearml_image.py +65 -0
  134. tests/handlers/test_handler_clearml_stats.py +65 -0
  135. tests/handlers/test_handler_confusion_matrix.py +104 -0
  136. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  137. tests/handlers/test_handler_decollate_batch.py +66 -0
  138. tests/handlers/test_handler_early_stop.py +68 -0
  139. tests/handlers/test_handler_garbage_collector.py +73 -0
  140. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  141. tests/handlers/test_handler_ignite_metric.py +191 -0
  142. tests/handlers/test_handler_lr_scheduler.py +94 -0
  143. tests/handlers/test_handler_mean_dice.py +98 -0
  144. tests/handlers/test_handler_mean_iou.py +76 -0
  145. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  146. tests/handlers/test_handler_metrics_saver.py +89 -0
  147. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  148. tests/handlers/test_handler_mlflow.py +296 -0
  149. tests/handlers/test_handler_nvtx.py +93 -0
  150. tests/handlers/test_handler_panoptic_quality.py +89 -0
  151. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  152. tests/handlers/test_handler_post_processing.py +74 -0
  153. tests/handlers/test_handler_prob_map_producer.py +111 -0
  154. tests/handlers/test_handler_regression_metrics.py +160 -0
  155. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  156. tests/handlers/test_handler_rocauc.py +48 -0
  157. tests/handlers/test_handler_rocauc_dist.py +54 -0
  158. tests/handlers/test_handler_stats.py +281 -0
  159. tests/handlers/test_handler_surface_distance.py +113 -0
  160. tests/handlers/test_handler_tb_image.py +61 -0
  161. tests/handlers/test_handler_tb_stats.py +166 -0
  162. tests/handlers/test_handler_validation.py +59 -0
  163. tests/handlers/test_trt_compile.py +145 -0
  164. tests/handlers/test_write_metrics_reports.py +68 -0
  165. tests/inferers/__init__.py +10 -0
  166. tests/inferers/test_avg_merger.py +179 -0
  167. tests/inferers/test_controlnet_inferers.py +1310 -0
  168. tests/inferers/test_diffusion_inferer.py +236 -0
  169. tests/inferers/test_latent_diffusion_inferer.py +824 -0
  170. tests/inferers/test_patch_inferer.py +309 -0
  171. tests/inferers/test_saliency_inferer.py +55 -0
  172. tests/inferers/test_slice_inferer.py +57 -0
  173. tests/inferers/test_sliding_window_inference.py +377 -0
  174. tests/inferers/test_sliding_window_splitter.py +284 -0
  175. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  176. tests/inferers/test_zarr_avg_merger.py +326 -0
  177. tests/integration/__init__.py +10 -0
  178. tests/integration/test_auto3dseg_ensemble.py +211 -0
  179. tests/integration/test_auto3dseg_hpo.py +189 -0
  180. tests/integration/test_deepedit_interaction.py +122 -0
  181. tests/integration/test_downsample_block.py +50 -0
  182. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  183. tests/integration/test_integration_autorunner.py +201 -0
  184. tests/integration/test_integration_bundle_run.py +240 -0
  185. tests/integration/test_integration_classification_2d.py +282 -0
  186. tests/integration/test_integration_determinism.py +95 -0
  187. tests/integration/test_integration_fast_train.py +231 -0
  188. tests/integration/test_integration_gpu_customization.py +159 -0
  189. tests/integration/test_integration_lazy_samples.py +219 -0
  190. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  191. tests/integration/test_integration_segmentation_3d.py +304 -0
  192. tests/integration/test_integration_sliding_window.py +100 -0
  193. tests/integration/test_integration_stn.py +133 -0
  194. tests/integration/test_integration_unet_2d.py +67 -0
  195. tests/integration/test_integration_workers.py +61 -0
  196. tests/integration/test_integration_workflows.py +365 -0
  197. tests/integration/test_integration_workflows_adversarial.py +173 -0
  198. tests/integration/test_integration_workflows_gan.py +158 -0
  199. tests/integration/test_loader_semaphore.py +48 -0
  200. tests/integration/test_mapping_filed.py +122 -0
  201. tests/integration/test_meta_affine.py +183 -0
  202. tests/integration/test_metatensor_integration.py +114 -0
  203. tests/integration/test_module_list.py +76 -0
  204. tests/integration/test_one_of.py +283 -0
  205. tests/integration/test_pad_collation.py +124 -0
  206. tests/integration/test_reg_loss_integration.py +107 -0
  207. tests/integration/test_retinanet_predict_utils.py +154 -0
  208. tests/integration/test_seg_loss_integration.py +159 -0
  209. tests/integration/test_spatial_combine_transforms.py +185 -0
  210. tests/integration/test_testtimeaugmentation.py +186 -0
  211. tests/integration/test_vis_gradbased.py +69 -0
  212. tests/integration/test_vista3d_utils.py +159 -0
  213. tests/losses/__init__.py +10 -0
  214. tests/losses/deform/__init__.py +10 -0
  215. tests/losses/deform/test_bending_energy.py +88 -0
  216. tests/losses/deform/test_diffusion_loss.py +117 -0
  217. tests/losses/image_dissimilarity/__init__.py +10 -0
  218. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  219. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  220. tests/losses/test_adversarial_loss.py +94 -0
  221. tests/losses/test_barlow_twins_loss.py +109 -0
  222. tests/losses/test_cldice_loss.py +51 -0
  223. tests/losses/test_contrastive_loss.py +86 -0
  224. tests/losses/test_dice_ce_loss.py +123 -0
  225. tests/losses/test_dice_focal_loss.py +124 -0
  226. tests/losses/test_dice_loss.py +227 -0
  227. tests/losses/test_ds_loss.py +189 -0
  228. tests/losses/test_focal_loss.py +379 -0
  229. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  230. tests/losses/test_generalized_dice_loss.py +221 -0
  231. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  232. tests/losses/test_giou_loss.py +62 -0
  233. tests/losses/test_hausdorff_loss.py +264 -0
  234. tests/losses/test_masked_dice_loss.py +152 -0
  235. tests/losses/test_masked_loss.py +87 -0
  236. tests/losses/test_multi_scale.py +86 -0
  237. tests/losses/test_nacl_loss.py +167 -0
  238. tests/losses/test_perceptual_loss.py +122 -0
  239. tests/losses/test_spectral_loss.py +86 -0
  240. tests/losses/test_ssim_loss.py +59 -0
  241. tests/losses/test_sure_loss.py +72 -0
  242. tests/losses/test_tversky_loss.py +198 -0
  243. tests/losses/test_unified_focal_loss.py +66 -0
  244. tests/metrics/__init__.py +10 -0
  245. tests/metrics/test_compute_confusion_matrix.py +294 -0
  246. tests/metrics/test_compute_f_beta.py +80 -0
  247. tests/metrics/test_compute_fid_metric.py +40 -0
  248. tests/metrics/test_compute_froc.py +143 -0
  249. tests/metrics/test_compute_generalized_dice.py +240 -0
  250. tests/metrics/test_compute_meandice.py +306 -0
  251. tests/metrics/test_compute_meaniou.py +223 -0
  252. tests/metrics/test_compute_mmd_metric.py +56 -0
  253. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  254. tests/metrics/test_compute_panoptic_quality.py +113 -0
  255. tests/metrics/test_compute_regression_metrics.py +196 -0
  256. tests/metrics/test_compute_roc_auc.py +155 -0
  257. tests/metrics/test_compute_variance.py +147 -0
  258. tests/metrics/test_cumulative.py +63 -0
  259. tests/metrics/test_cumulative_average.py +74 -0
  260. tests/metrics/test_cumulative_average_dist.py +48 -0
  261. tests/metrics/test_hausdorff_distance.py +209 -0
  262. tests/metrics/test_label_quality_score.py +134 -0
  263. tests/metrics/test_loss_metric.py +57 -0
  264. tests/metrics/test_metrics_reloaded.py +96 -0
  265. tests/metrics/test_ssim_metric.py +78 -0
  266. tests/metrics/test_surface_dice.py +416 -0
  267. tests/metrics/test_surface_distance.py +186 -0
  268. tests/networks/__init__.py +10 -0
  269. tests/networks/blocks/__init__.py +10 -0
  270. tests/networks/blocks/dints_block/__init__.py +10 -0
  271. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  272. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  273. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  274. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  275. tests/networks/blocks/test_adn.py +86 -0
  276. tests/networks/blocks/test_convolutions.py +156 -0
  277. tests/networks/blocks/test_crf_cpu.py +513 -0
  278. tests/networks/blocks/test_crf_cuda.py +528 -0
  279. tests/networks/blocks/test_crossattention.py +185 -0
  280. tests/networks/blocks/test_denseblock.py +105 -0
  281. tests/networks/blocks/test_dynunet_block.py +116 -0
  282. tests/networks/blocks/test_fpn_block.py +88 -0
  283. tests/networks/blocks/test_localnet_block.py +121 -0
  284. tests/networks/blocks/test_mlp.py +78 -0
  285. tests/networks/blocks/test_patchembedding.py +212 -0
  286. tests/networks/blocks/test_regunet_block.py +103 -0
  287. tests/networks/blocks/test_se_block.py +85 -0
  288. tests/networks/blocks/test_se_blocks.py +78 -0
  289. tests/networks/blocks/test_segresnet_block.py +57 -0
  290. tests/networks/blocks/test_selfattention.py +232 -0
  291. tests/networks/blocks/test_simple_aspp.py +87 -0
  292. tests/networks/blocks/test_spatialattention.py +55 -0
  293. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  294. tests/networks/blocks/test_text_encoding.py +49 -0
  295. tests/networks/blocks/test_transformerblock.py +90 -0
  296. tests/networks/blocks/test_unetr_block.py +158 -0
  297. tests/networks/blocks/test_upsample_block.py +134 -0
  298. tests/networks/blocks/warp/__init__.py +10 -0
  299. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  300. tests/networks/blocks/warp/test_warp.py +250 -0
  301. tests/networks/layers/__init__.py +10 -0
  302. tests/networks/layers/filtering/__init__.py +10 -0
  303. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  304. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  305. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  306. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  307. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  308. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  309. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  310. tests/networks/layers/test_affine_transform.py +385 -0
  311. tests/networks/layers/test_apply_filter.py +89 -0
  312. tests/networks/layers/test_channel_pad.py +51 -0
  313. tests/networks/layers/test_conjugate_gradient.py +56 -0
  314. tests/networks/layers/test_drop_path.py +46 -0
  315. tests/networks/layers/test_gaussian.py +317 -0
  316. tests/networks/layers/test_gaussian_filter.py +206 -0
  317. tests/networks/layers/test_get_layers.py +65 -0
  318. tests/networks/layers/test_gmm.py +314 -0
  319. tests/networks/layers/test_grid_pull.py +93 -0
  320. tests/networks/layers/test_hilbert_transform.py +131 -0
  321. tests/networks/layers/test_lltm.py +62 -0
  322. tests/networks/layers/test_median_filter.py +52 -0
  323. tests/networks/layers/test_polyval.py +55 -0
  324. tests/networks/layers/test_preset_filters.py +136 -0
  325. tests/networks/layers/test_savitzky_golay_filter.py +141 -0
  326. tests/networks/layers/test_separable_filter.py +87 -0
  327. tests/networks/layers/test_skip_connection.py +48 -0
  328. tests/networks/layers/test_vector_quantizer.py +89 -0
  329. tests/networks/layers/test_weight_init.py +50 -0
  330. tests/networks/nets/__init__.py +10 -0
  331. tests/networks/nets/dints/__init__.py +10 -0
  332. tests/networks/nets/dints/test_dints_cell.py +110 -0
  333. tests/networks/nets/dints/test_dints_mixop.py +84 -0
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  681. tests/transforms/test_std_shift_intensityd.py +74 -0
  682. tests/transforms/test_threshold_intensity.py +38 -0
  683. tests/transforms/test_threshold_intensityd.py +58 -0
  684. tests/transforms/test_to_contiguous.py +47 -0
  685. tests/transforms/test_to_cupy.py +112 -0
  686. tests/transforms/test_to_cupyd.py +76 -0
  687. tests/transforms/test_to_device.py +42 -0
  688. tests/transforms/test_to_deviced.py +37 -0
  689. tests/transforms/test_to_numpy.py +85 -0
  690. tests/transforms/test_to_numpyd.py +68 -0
  691. tests/transforms/test_to_pil.py +52 -0
  692. tests/transforms/test_to_pild.py +50 -0
  693. tests/transforms/test_to_tensor.py +60 -0
  694. tests/transforms/test_to_tensord.py +71 -0
  695. tests/transforms/test_torchvision.py +66 -0
  696. tests/transforms/test_torchvisiond.py +63 -0
  697. tests/transforms/test_transform.py +62 -0
  698. tests/transforms/test_transpose.py +41 -0
  699. tests/transforms/test_transposed.py +52 -0
  700. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  701. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  702. tests/transforms/test_vote_ensemble.py +84 -0
  703. tests/transforms/test_vote_ensembled.py +107 -0
  704. tests/transforms/test_with_allow_missing_keys.py +76 -0
  705. tests/transforms/test_zoom.py +120 -0
  706. tests/transforms/test_zoomd.py +94 -0
  707. tests/transforms/transform/__init__.py +10 -0
  708. tests/transforms/transform/test_randomizable.py +52 -0
  709. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  710. tests/transforms/utility/__init__.py +10 -0
  711. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  712. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  713. tests/transforms/utility/test_identity.py +29 -0
  714. tests/transforms/utility/test_identityd.py +30 -0
  715. tests/transforms/utility/test_lambda.py +71 -0
  716. tests/transforms/utility/test_lambdad.py +83 -0
  717. tests/transforms/utility/test_rand_lambda.py +87 -0
  718. tests/transforms/utility/test_rand_lambdad.py +77 -0
  719. tests/transforms/utility/test_simulatedelay.py +36 -0
  720. tests/transforms/utility/test_simulatedelayd.py +36 -0
  721. tests/transforms/utility/test_splitdim.py +52 -0
  722. tests/transforms/utility/test_splitdimd.py +96 -0
  723. tests/transforms/utils/__init__.py +10 -0
  724. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  725. tests/transforms/utils/test_get_unique_labels.py +45 -0
  726. tests/transforms/utils/test_print_transform_backends.py +29 -0
  727. tests/transforms/utils/test_soft_clip.py +125 -0
  728. tests/utils/__init__.py +10 -0
  729. tests/utils/enums/__init__.py +10 -0
  730. tests/utils/enums/test_hovernet_loss.py +190 -0
  731. tests/utils/enums/test_ordering.py +289 -0
  732. tests/utils/enums/test_wsireader.py +663 -0
  733. tests/utils/misc/__init__.py +10 -0
  734. tests/utils/misc/test_ensure_tuple.py +53 -0
  735. tests/utils/misc/test_monai_env_vars.py +44 -0
  736. tests/utils/misc/test_monai_utils_misc.py +103 -0
  737. tests/utils/misc/test_str2bool.py +34 -0
  738. tests/utils/misc/test_str2list.py +33 -0
  739. tests/utils/test_alias.py +44 -0
  740. tests/utils/test_component_store.py +73 -0
  741. tests/utils/test_deprecated.py +455 -0
  742. tests/utils/test_enum_bound_interp.py +75 -0
  743. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  744. tests/utils/test_get_package_version.py +34 -0
  745. tests/utils/test_handler_logfile.py +84 -0
  746. tests/utils/test_handler_metric_logger.py +62 -0
  747. tests/utils/test_list_to_dict.py +43 -0
  748. tests/utils/test_look_up_option.py +87 -0
  749. tests/utils/test_optional_import.py +80 -0
  750. tests/utils/test_pad_mode.py +39 -0
  751. tests/utils/test_profiling.py +208 -0
  752. tests/utils/test_rankfilter_dist.py +77 -0
  753. tests/utils/test_require_pkg.py +83 -0
  754. tests/utils/test_sample_slices.py +43 -0
  755. tests/utils/test_set_determinism.py +74 -0
  756. tests/utils/test_squeeze_unsqueeze.py +71 -0
  757. tests/utils/test_state_cacher.py +67 -0
  758. tests/utils/test_torchscript_utils.py +113 -0
  759. tests/utils/test_version.py +91 -0
  760. tests/utils/test_version_after.py +65 -0
  761. tests/utils/type_conversion/__init__.py +10 -0
  762. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  763. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  764. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  765. tests/visualize/__init__.py +10 -0
  766. tests/visualize/test_img2tensorboard.py +46 -0
  767. tests/visualize/test_occlusion_sensitivity.py +128 -0
  768. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  769. tests/visualize/test_vis_cam.py +98 -0
  770. tests/visualize/test_vis_gradcam.py +211 -0
  771. tests/visualize/utils/__init__.py +10 -0
  772. tests/visualize/utils/test_blend_images.py +63 -0
  773. tests/visualize/utils/test_matshow3d.py +133 -0
  774. monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
  775. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
  776. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
@@ -0,0 +1,370 @@
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.apps.detection.transforms.box_ops import convert_mask_to_box
22
+ from monai.apps.detection.transforms.dictionary import (
23
+ AffineBoxToImageCoordinated,
24
+ AffineBoxToWorldCoordinated,
25
+ BoxToMaskd,
26
+ ClipBoxToImaged,
27
+ ConvertBoxModed,
28
+ FlipBoxd,
29
+ MaskToBoxd,
30
+ RandCropBoxByPosNegLabeld,
31
+ RandFlipBoxd,
32
+ RandRotateBox90d,
33
+ RandZoomBoxd,
34
+ RotateBox90d,
35
+ ZoomBoxd,
36
+ )
37
+ from monai.data.meta_tensor import MetaTensor
38
+ from monai.transforms import CastToTyped, Invertd
39
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
40
+
41
+ TESTS_3D = []
42
+ boxes = [[0, 0, 0, 0, 0, 0], [0, 1, 0, 2, 3, 3], [0, 1, 1, 2, 3, 4]]
43
+ labels = [1, 1, 0]
44
+ scores = [[0.2, 0.8], [0.3, 0.7], [0.6, 0.4]]
45
+ image_size = [1, 4, 6, 4]
46
+ image = np.zeros(image_size)
47
+
48
+ for p in TEST_NDARRAYS:
49
+ TESTS_3D.append(
50
+ [
51
+ {"box_keys": "boxes", "dst_mode": "xyzwhd"},
52
+ {"boxes": p(boxes), "image": p(image), "labels": p(labels), "scores": p(scores)},
53
+ p([[0, 0, 0, 0, 0, 0], [0, 1, 0, 2, 2, 3], [0, 1, 1, 2, 2, 3]]),
54
+ p([[0, 0, 0, 0, 0, 0], [0, 3, 0, 1, 9, 4.5], [0, 3, 1.5, 1, 9, 6]]),
55
+ p([[1, -6, -1, 1, -6, -1], [1, -3, -1, 2, 3, 3.5], [1, -3, 0.5, 2, 3, 5]]),
56
+ p([[4, 6, 4, 4, 6, 4], [2, 3, 1, 4, 5, 4], [2, 3, 0, 4, 5, 3]]),
57
+ p([[0, 1, 0, 2, 3, 3], [0, 1, 1, 2, 3, 4]]),
58
+ p([[6, 0, 0, 6, 0, 0], [3, 0, 0, 5, 2, 3], [3, 0, 1, 5, 2, 4]]),
59
+ ]
60
+ )
61
+
62
+ TESTS_2D = []
63
+ boxes = [[0, 1, 2, 2], [0, 0, 1, 1]]
64
+ labels = [1, 0]
65
+ image_size = [1, 2, 2]
66
+ image = np.zeros(image_size)
67
+ for p in TEST_NDARRAYS:
68
+ TESTS_2D.append(
69
+ [{"boxes": p(boxes), "image": p(image), "labels": p(labels)}, p([[[0, 2], [0, 2]], [[1, 0], [0, 0]]])]
70
+ )
71
+
72
+ TESTS_2D_mask = []
73
+ boxes_mask = [[[-1, 0], [0, -1]]]
74
+ for p in TEST_NDARRAYS:
75
+ TESTS_2D_mask.append([p(boxes_mask), (p([[0.0, 0.0, 2.0, 2.0]]), p([0]))])
76
+ boxes_mask = [[[-1, 0], [0, -1]], [[-1, 1], [1, -1]]]
77
+ for p in TEST_NDARRAYS:
78
+ TESTS_2D_mask.append([p(boxes_mask), (p([[0.0, 0.0, 2.0, 2.0], [0.0, 0.0, 2.0, 2.0]]), p([0, 1]))])
79
+
80
+
81
+ class TestBoxTransform(unittest.TestCase):
82
+ @parameterized.expand(TESTS_2D_mask)
83
+ def test_value_2d_mask(self, mask, expected_box_label):
84
+ box_label = convert_mask_to_box(mask)
85
+ assert_allclose(box_label[0], expected_box_label[0], type_test=True, device_test=True, atol=1e-3)
86
+ assert_allclose(box_label[1], expected_box_label[1], type_test=True, device_test=True, atol=1e-3)
87
+
88
+ @parameterized.expand(TESTS_2D)
89
+ def test_value_2d(self, data, expected_mask):
90
+ test_dtype = [torch.float32, torch.float16]
91
+ for dtype in test_dtype:
92
+ data = CastToTyped(keys=["image", "boxes"], dtype=dtype)(data)
93
+ transform_to_mask = BoxToMaskd(
94
+ box_keys="boxes",
95
+ box_mask_keys="box_mask",
96
+ box_ref_image_keys="image",
97
+ label_keys="labels",
98
+ min_fg_label=0,
99
+ ellipse_mask=False,
100
+ )
101
+ transform_to_box = MaskToBoxd(
102
+ box_keys="boxes", box_mask_keys="box_mask", label_keys="labels", min_fg_label=0
103
+ )
104
+ data_mask = transform_to_mask(data)
105
+ assert_allclose(data_mask["box_mask"], expected_mask, type_test=True, device_test=True, atol=1e-3)
106
+ data_back = transform_to_box(data_mask)
107
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
108
+ assert_allclose(data_back["labels"], data["labels"], type_test=False, device_test=False, atol=1e-3)
109
+
110
+ def test_value_3d_mask(self):
111
+ test_dtype = [torch.float32, torch.float16]
112
+ image = np.zeros((1, 32, 33, 34))
113
+ boxes = np.array([[7, 8, 9, 10, 12, 13], [1, 3, 5, 2, 5, 9], [0, 0, 0, 1, 1, 1]])
114
+ data = {"image": image, "boxes": boxes, "labels": np.array((1, 0, 3))}
115
+ for dtype in test_dtype:
116
+ data = CastToTyped(keys=["image", "boxes"], dtype=dtype)(data)
117
+ transform_to_mask = BoxToMaskd(
118
+ box_keys="boxes",
119
+ box_mask_keys="box_mask",
120
+ box_ref_image_keys="image",
121
+ label_keys="labels",
122
+ min_fg_label=0,
123
+ ellipse_mask=False,
124
+ )
125
+ transform_to_box = MaskToBoxd(
126
+ box_keys="boxes", box_mask_keys="box_mask", label_keys="labels", min_fg_label=0
127
+ )
128
+ data_mask = transform_to_mask(data)
129
+ assert_allclose(data_mask["box_mask"].shape, (3, 32, 33, 34), type_test=True, device_test=True, atol=1e-3)
130
+ data_back = transform_to_box(data_mask)
131
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
132
+ assert_allclose(data_back["labels"], data["labels"], type_test=False, device_test=False, atol=1e-3)
133
+
134
+ def test_shape_assertion(self):
135
+ test_dtype = torch.float32
136
+ image = np.zeros((1, 10, 10, 10))
137
+ boxes = np.array([[7, 8, 9, 10, 12, 13]])
138
+ data = {"image": image, "boxes": boxes, "labels": np.array((1,))}
139
+ data = CastToTyped(keys=["image", "boxes"], dtype=test_dtype)(data)
140
+ transform_to_mask = BoxToMaskd(
141
+ box_keys="boxes",
142
+ box_mask_keys="box_mask",
143
+ box_ref_image_keys="image",
144
+ label_keys="labels",
145
+ min_fg_label=0,
146
+ ellipse_mask=False,
147
+ )
148
+ with self.assertRaises(ValueError) as context:
149
+ transform_to_mask(data)
150
+ self.assertTrue("Some boxes are larger than the image." in str(context.exception))
151
+
152
+ @parameterized.expand(TESTS_3D)
153
+ def test_value_3d(
154
+ self,
155
+ keys,
156
+ data,
157
+ expected_convert_result,
158
+ expected_zoom_result,
159
+ expected_zoom_keepsize_result,
160
+ expected_flip_result,
161
+ expected_clip_result,
162
+ expected_rotate_result,
163
+ ):
164
+ test_dtype = [torch.float32]
165
+ for dtype in test_dtype:
166
+ data = CastToTyped(keys=["image", "boxes"], dtype=dtype)(data)
167
+ # test ConvertBoxToStandardModed
168
+ transform_convert_mode = ConvertBoxModed(**keys)
169
+ convert_result = transform_convert_mode(data)
170
+ assert_allclose(
171
+ convert_result["boxes"], expected_convert_result, type_test=True, device_test=True, atol=1e-3
172
+ )
173
+
174
+ invert_transform_convert_mode = Invertd(
175
+ keys=["boxes"], transform=transform_convert_mode, orig_keys=["boxes"]
176
+ )
177
+ data_back = invert_transform_convert_mode(convert_result)
178
+ if "boxes_transforms" in data_back: # if the transform is tracked in dict:
179
+ self.assertEqual(data_back["boxes_transforms"], []) # it should be updated
180
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
181
+
182
+ # test ZoomBoxd
183
+ transform_zoom = ZoomBoxd(
184
+ image_keys="image", box_keys="boxes", box_ref_image_keys="image", zoom=[0.5, 3, 1.5], keep_size=False
185
+ )
186
+ zoom_result = transform_zoom(data)
187
+ self.assertEqual(len(zoom_result["image"].applied_operations), 1)
188
+ assert_allclose(zoom_result["boxes"], expected_zoom_result, type_test=True, device_test=True, atol=1e-3)
189
+ invert_transform_zoom = Invertd(
190
+ keys=["image", "boxes"], transform=transform_zoom, orig_keys=["image", "boxes"]
191
+ )
192
+ data_back = invert_transform_zoom(zoom_result)
193
+ self.assertEqual(data_back["image"].applied_operations, [])
194
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
195
+ assert_allclose(data_back["image"], data["image"], type_test=False, device_test=False, atol=1e-3)
196
+
197
+ transform_zoom = ZoomBoxd(
198
+ image_keys="image", box_keys="boxes", box_ref_image_keys="image", zoom=[0.5, 3, 1.5], keep_size=True
199
+ )
200
+ zoom_result = transform_zoom(data)
201
+ self.assertEqual(len(zoom_result["image"].applied_operations), 1)
202
+ assert_allclose(
203
+ zoom_result["boxes"], expected_zoom_keepsize_result, type_test=True, device_test=True, atol=1e-3
204
+ )
205
+
206
+ # test RandZoomBoxd
207
+ transform_zoom = RandZoomBoxd(
208
+ image_keys="image",
209
+ box_keys="boxes",
210
+ box_ref_image_keys="image",
211
+ prob=1.0,
212
+ min_zoom=(0.3,) * 3,
213
+ max_zoom=(3.0,) * 3,
214
+ keep_size=False,
215
+ )
216
+ zoom_result = transform_zoom(data)
217
+ self.assertEqual(len(zoom_result["image"].applied_operations), 1)
218
+ invert_transform_zoom = Invertd(
219
+ keys=["image", "boxes"], transform=transform_zoom, orig_keys=["image", "boxes"]
220
+ )
221
+ data_back = invert_transform_zoom(zoom_result)
222
+ self.assertEqual(data_back["image"].applied_operations, [])
223
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=0.01)
224
+ assert_allclose(data_back["image"], data["image"], type_test=False, device_test=False, atol=1e-3)
225
+
226
+ # test AffineBoxToImageCoordinated, AffineBoxToWorldCoordinated
227
+ transform_affine = AffineBoxToImageCoordinated(box_keys="boxes", box_ref_image_keys="image")
228
+ if not isinstance(data["image"], MetaTensor): # metadict should be undefined and it's an exception
229
+ with self.assertRaises(Exception) as context:
230
+ transform_affine(deepcopy(data))
231
+ self.assertTrue("Please check whether it is the correct the image meta key." in str(context.exception))
232
+
233
+ data["image"] = MetaTensor(data["image"], meta={"affine": torch.diag(1.0 / torch.Tensor([0.5, 3, 1.5, 1]))})
234
+ affine_result = transform_affine(data)
235
+ if "boxes_transforms" in affine_result:
236
+ self.assertEqual(len(affine_result["boxes_transforms"]), 1)
237
+ assert_allclose(affine_result["boxes"], expected_zoom_result, type_test=True, device_test=True, atol=0.01)
238
+ invert_transform_affine = Invertd(keys=["boxes"], transform=transform_affine, orig_keys=["boxes"])
239
+ data_back = invert_transform_affine(affine_result)
240
+ if "boxes_transforms" in data_back:
241
+ self.assertEqual(data_back["boxes_transforms"], [])
242
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=0.01)
243
+ invert_transform_affine = AffineBoxToWorldCoordinated(box_keys="boxes", box_ref_image_keys="image")
244
+ data_back = invert_transform_affine(affine_result)
245
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=0.01)
246
+
247
+ # test FlipBoxd
248
+ transform_flip = FlipBoxd(
249
+ image_keys="image", box_keys="boxes", box_ref_image_keys="image", spatial_axis=[0, 1, 2]
250
+ )
251
+ flip_result = transform_flip(data)
252
+ if "boxes_transforms" in flip_result:
253
+ self.assertEqual(len(flip_result["boxes_transforms"]), 1)
254
+ assert_allclose(flip_result["boxes"], expected_flip_result, type_test=True, device_test=True, atol=1e-3)
255
+ invert_transform_flip = Invertd(
256
+ keys=["image", "boxes"], transform=transform_flip, orig_keys=["image", "boxes"]
257
+ )
258
+ data_back = invert_transform_flip(flip_result)
259
+ if "boxes_transforms" in data_back:
260
+ self.assertEqual(data_back["boxes_transforms"], [])
261
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
262
+ assert_allclose(data_back["image"], data["image"], type_test=False, device_test=False, atol=1e-3)
263
+
264
+ # test RandFlipBoxd
265
+ for spatial_axis in [(0,), (1,), (2,), (0, 1), (1, 2)]:
266
+ transform_flip = RandFlipBoxd(
267
+ image_keys="image",
268
+ box_keys="boxes",
269
+ box_ref_image_keys="image",
270
+ prob=1.0,
271
+ spatial_axis=spatial_axis,
272
+ )
273
+ flip_result = transform_flip(data)
274
+ if "boxes_transforms" in flip_result:
275
+ self.assertEqual(len(flip_result["boxes_transforms"]), 1)
276
+ invert_transform_flip = Invertd(
277
+ keys=["image", "boxes"], transform=transform_flip, orig_keys=["image", "boxes"]
278
+ )
279
+ data_back = invert_transform_flip(flip_result)
280
+ if "boxes_transforms" in data_back:
281
+ self.assertEqual(data_back["boxes_transforms"], [])
282
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
283
+ assert_allclose(data_back["image"], data["image"], type_test=False, device_test=False, atol=1e-3)
284
+
285
+ # test ClipBoxToImaged
286
+ transform_clip = ClipBoxToImaged(
287
+ box_keys="boxes", box_ref_image_keys="image", label_keys=["labels", "scores"], remove_empty=True
288
+ )
289
+ clip_result = transform_clip(data)
290
+ assert_allclose(clip_result["boxes"], expected_clip_result, type_test=True, device_test=True, atol=1e-3)
291
+ assert_allclose(clip_result["labels"], data["labels"][1:], type_test=True, device_test=True, atol=1e-3)
292
+ assert_allclose(clip_result["scores"], data["scores"][1:], type_test=True, device_test=True, atol=1e-3)
293
+
294
+ transform_clip = ClipBoxToImaged(
295
+ box_keys="boxes", box_ref_image_keys="image", label_keys=[], remove_empty=True
296
+ ) # corner case when label_keys is empty
297
+ clip_result = transform_clip(data)
298
+ assert_allclose(clip_result["boxes"], expected_clip_result, type_test=True, device_test=True, atol=1e-3)
299
+
300
+ # test RandCropBoxByPosNegLabeld
301
+ transform_crop = RandCropBoxByPosNegLabeld(
302
+ image_keys="image", box_keys="boxes", label_keys=["labels", "scores"], spatial_size=2, num_samples=3
303
+ )
304
+ crop_result = transform_crop(data)
305
+ assert len(crop_result) == 3
306
+ for ll in range(3):
307
+ assert_allclose(
308
+ crop_result[ll]["boxes"].shape[0],
309
+ crop_result[ll]["labels"].shape[0],
310
+ type_test=True,
311
+ device_test=True,
312
+ atol=1e-3,
313
+ )
314
+ assert_allclose(
315
+ crop_result[ll]["boxes"].shape[0],
316
+ crop_result[ll]["scores"].shape[0],
317
+ type_test=True,
318
+ device_test=True,
319
+ atol=1e-3,
320
+ )
321
+
322
+ # test RotateBox90d
323
+ transform_rotate = RotateBox90d(
324
+ image_keys="image", box_keys="boxes", box_ref_image_keys="image", k=1, spatial_axes=[0, 1]
325
+ )
326
+ rotate_result = transform_rotate(data)
327
+ self.assertEqual(len(rotate_result["image"].applied_operations), 1)
328
+ assert_allclose(rotate_result["boxes"], expected_rotate_result, type_test=True, device_test=True, atol=1e-3)
329
+ invert_transform_rotate = Invertd(
330
+ keys=["image", "boxes"], transform=transform_rotate, orig_keys=["image", "boxes"]
331
+ )
332
+ data_back = invert_transform_rotate(rotate_result)
333
+ self.assertEqual(data_back["image"].applied_operations, [])
334
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
335
+ assert_allclose(data_back["image"], data["image"], type_test=False, device_test=False, atol=1e-3)
336
+
337
+ transform_rotate = RandRotateBox90d(
338
+ image_keys="image", box_keys="boxes", box_ref_image_keys="image", prob=1.0, max_k=3, spatial_axes=[0, 1]
339
+ )
340
+ rotate_result = transform_rotate(data)
341
+ self.assertEqual(len(rotate_result["image"].applied_operations), 1)
342
+ invert_transform_rotate = Invertd(
343
+ keys=["image", "boxes"], transform=transform_rotate, orig_keys=["image", "boxes"]
344
+ )
345
+ data_back = invert_transform_rotate(rotate_result)
346
+ self.assertEqual(data_back["image"].applied_operations, [])
347
+ assert_allclose(data_back["boxes"], data["boxes"], type_test=False, device_test=False, atol=1e-3)
348
+ assert_allclose(data_back["image"], data["image"], type_test=False, device_test=False, atol=1e-3)
349
+
350
+ def test_crop_shape(self):
351
+ tt = RandCropBoxByPosNegLabeld(
352
+ image_keys=["image"],
353
+ box_keys="box",
354
+ label_keys="label",
355
+ spatial_size=[10, 7, -1],
356
+ whole_box=True,
357
+ num_samples=1,
358
+ pos=1,
359
+ neg=0,
360
+ )
361
+ iii = {
362
+ "image": torch.rand(1, 10, 8, 7),
363
+ "box": torch.tensor(((1.0, 2.0, 3.0, 4.0, 5.0, 6.0),)),
364
+ "label": torch.tensor((1,)).long(),
365
+ }
366
+ self.assertEqual(tt(iii)[0]["image"].shape, (1, 10, 7, 7))
367
+
368
+
369
+ if __name__ == "__main__":
370
+ unittest.main()
@@ -0,0 +1,10 @@
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.
@@ -0,0 +1,88 @@
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 torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.apps.detection.utils.anchor_utils import AnchorGenerator, AnchorGeneratorWithAnchorShape
20
+ from monai.utils import optional_import
21
+ from tests.test_utils import SkipIfBeforePyTorchVersion, assert_allclose, test_script_save
22
+
23
+ _, has_torchvision = optional_import("torchvision")
24
+
25
+ TEST_CASES_2D = [
26
+ [
27
+ {"sizes": ((10, 12, 14, 16), (20, 24, 28, 32)), "aspect_ratios": ((1.0, 0.5, 2.0), (1.0, 0.5, 2.0))},
28
+ (5, 3, 128, 128),
29
+ ((5, 7, 64, 32), (5, 7, 32, 16)),
30
+ ]
31
+ ]
32
+
33
+ TEST_CASES_SHAPE_3D = [
34
+ [
35
+ {"feature_map_scales": (1, 2), "base_anchor_shapes": ((4, 3, 6), (8, 2, 4))},
36
+ (5, 3, 128, 128, 128),
37
+ ((5, 7, 64, 32, 32), (5, 7, 32, 16, 16)),
38
+ ]
39
+ ]
40
+
41
+
42
+ @SkipIfBeforePyTorchVersion((1, 11))
43
+ @unittest.skipUnless(has_torchvision, "Requires torchvision")
44
+ class TestAnchorGenerator(unittest.TestCase):
45
+ @parameterized.expand(TEST_CASES_2D)
46
+ def test_anchor_2d(self, input_param, image_shape, feature_maps_shapes):
47
+ torch_anchor_utils, _ = optional_import("torchvision.models.detection.anchor_utils")
48
+ image_list, _ = optional_import("torchvision.models.detection.image_list")
49
+
50
+ # test it behaves the same with torchvision for 2d
51
+ anchor = AnchorGenerator(**input_param, indexing="xy")
52
+ anchor_ref = torch_anchor_utils.AnchorGenerator(**input_param)
53
+ for a, a_f in zip(anchor.cell_anchors, anchor_ref.cell_anchors):
54
+ assert_allclose(a, a_f, type_test=True, device_test=False, atol=1e-3)
55
+ for a, a_f in zip(anchor.num_anchors_per_location(), anchor_ref.num_anchors_per_location()):
56
+ assert_allclose(a, a_f, type_test=True, device_test=False, atol=1e-3)
57
+
58
+ grid_sizes = [[2, 2], [1, 1]]
59
+ strides = [[torch.tensor(1), torch.tensor(2)], [torch.tensor(2), torch.tensor(4)]]
60
+ for a, a_f in zip(anchor.grid_anchors(grid_sizes, strides), anchor_ref.grid_anchors(grid_sizes, strides)):
61
+ assert_allclose(a, a_f, type_test=True, device_test=False, atol=1e-3)
62
+
63
+ images = torch.rand(image_shape)
64
+ feature_maps = tuple(torch.rand(fs) for fs in feature_maps_shapes)
65
+ result = anchor(images, feature_maps)
66
+ result_ref = anchor_ref(image_list.ImageList(images, ([123, 122],)), feature_maps)
67
+ for a, a_f in zip(result, result_ref):
68
+ assert_allclose(a, a_f, type_test=True, device_test=False, atol=0.1)
69
+
70
+ @parameterized.expand(TEST_CASES_2D)
71
+ def test_script_2d(self, input_param, image_shape, feature_maps_shapes):
72
+ # test whether support torchscript
73
+ anchor = AnchorGenerator(**input_param, indexing="xy")
74
+ images = torch.rand(image_shape)
75
+ feature_maps = tuple(torch.rand(fs) for fs in feature_maps_shapes)
76
+ test_script_save(anchor, images, feature_maps)
77
+
78
+ @parameterized.expand(TEST_CASES_SHAPE_3D)
79
+ def test_script_3d(self, input_param, image_shape, feature_maps_shapes):
80
+ # test whether support torchscript
81
+ anchor = AnchorGeneratorWithAnchorShape(**input_param, indexing="ij")
82
+ images = torch.rand(image_shape)
83
+ feature_maps = tuple(torch.rand(fs) for fs in feature_maps_shapes)
84
+ test_script_save(anchor, images, feature_maps)
85
+
86
+
87
+ if __name__ == "__main__":
88
+ unittest.main()
@@ -0,0 +1,46 @@
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 torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.apps.detection.utils.ATSS_matcher import ATSSMatcher
20
+ from monai.data.box_utils import box_iou
21
+ from tests.test_utils import assert_allclose
22
+
23
+ TEST_CASES = [
24
+ [
25
+ {"num_candidates": 2, "similarity_fn": box_iou, "center_in_gt": False},
26
+ torch.tensor([[0, 1, 2, 3, 2, 5]], dtype=torch.float16),
27
+ torch.tensor([[0, 1, 2, 3, 2, 5], [0, 1, 1, 3, 2, 5], [0, 1, 2, 3, 2, 4]], dtype=torch.float16),
28
+ [3],
29
+ 3,
30
+ torch.tensor([0, -1, -1]),
31
+ ]
32
+ ]
33
+
34
+
35
+ class TestATSS(unittest.TestCase):
36
+ @parameterized.expand(TEST_CASES)
37
+ def test_atss(self, input_param, boxes, anchors, num_anchors_per_level, num_anchors_per_loc, expected_matches):
38
+ matcher = ATSSMatcher(**input_param, debug=True)
39
+ match_quality_matrix, matches = matcher.compute_matches(
40
+ boxes, anchors, num_anchors_per_level, num_anchors_per_loc
41
+ )
42
+ assert_allclose(matches, expected_matches, type_test=True, device_test=True, atol=0)
43
+
44
+
45
+ if __name__ == "__main__":
46
+ 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
+ import torch
17
+
18
+ from monai.apps.detection.utils.box_coder import BoxCoder
19
+ from monai.transforms import CastToType
20
+ from tests.test_utils import assert_allclose
21
+
22
+
23
+ class TestBoxTransform(unittest.TestCase):
24
+ def test_value(self):
25
+ box_coder = BoxCoder(weights=[1, 1, 1, 1, 1, 1])
26
+ test_dtype = [torch.float32, torch.float16]
27
+ for dtype in test_dtype:
28
+ gt_boxes_0 = torch.rand((10, 3)).abs()
29
+ gt_boxes_1 = gt_boxes_0 + torch.rand((10, 3)).abs() + 10
30
+ gt_boxes = torch.cat((gt_boxes_0, gt_boxes_1), dim=1)
31
+ gt_boxes = CastToType(dtype=dtype)(gt_boxes)
32
+
33
+ proposals_0 = (gt_boxes_0 + torch.rand(gt_boxes_0.shape)).abs()
34
+ proposals_1 = proposals_0 + torch.rand(gt_boxes_0.shape).abs() + 10
35
+ proposals = torch.cat((proposals_0, proposals_1), dim=1)
36
+
37
+ rel_gt_boxes = box_coder.encode_single(gt_boxes, proposals)
38
+ gt_back = box_coder.decode_single(rel_gt_boxes, proposals)
39
+ assert_allclose(gt_back, gt_boxes, type_test=True, device_test=True, atol=0.1)
40
+
41
+
42
+ if __name__ == "__main__":
43
+ unittest.main()
@@ -0,0 +1,67 @@
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 torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.apps.detection.utils.box_selector import BoxSelector
20
+ from tests.test_utils import assert_allclose
21
+
22
+ device = "cuda" if torch.cuda.is_available() else "cpu"
23
+ num_anchors = 7
24
+
25
+ TEST_CASE = []
26
+ TEST_CASE.append(
27
+ [ # 2D
28
+ {
29
+ "apply_sigmoid": False,
30
+ "score_thresh": 0.1,
31
+ "topk_candidates_per_level": 2,
32
+ "nms_thresh": 0.1,
33
+ "detections_per_img": 5,
34
+ },
35
+ [torch.tensor([[1, 2, 3, 2, 3, 4], [5, 6, 7, 8, 9, 10]]).to(torch.float16)],
36
+ [torch.tensor([[0.1, 0.6], [0.2, 0.2]])],
37
+ (20, 20, 20),
38
+ torch.tensor([[1, 2, 3, 2, 3, 4], [5, 6, 7, 8, 9, 10]]),
39
+ ]
40
+ )
41
+ TEST_CASE.append(
42
+ [
43
+ {
44
+ "apply_sigmoid": False,
45
+ "score_thresh": 0.1,
46
+ "topk_candidates_per_level": 1,
47
+ "nms_thresh": 0.1,
48
+ "detections_per_img": 5,
49
+ },
50
+ [torch.tensor([[1, 2, 3, 2, 3, 4]]).to(torch.float32), torch.tensor([[5, 6, 7, 8, 9, 10]]).to(torch.float32)],
51
+ [torch.tensor([[0.3, 0.6]]), torch.tensor([[0.2, 0.2]])],
52
+ (20, 20, 8),
53
+ torch.tensor([[1, 2, 3, 2, 3, 4], [5, 6, 7, 8, 9, 8]]),
54
+ ]
55
+ )
56
+
57
+
58
+ class TestBoxSelector(unittest.TestCase):
59
+ @parameterized.expand(TEST_CASE)
60
+ def test_box_selector(self, input_param, boxes, logits, image_shape, expected_results):
61
+ box_selector = BoxSelector(**input_param)
62
+ result = box_selector.select_boxes_per_image(boxes, logits, image_shape)
63
+ assert_allclose(result[0], expected_results, type_test=True, device_test=False, atol=1e-3)
64
+
65
+
66
+ if __name__ == "__main__":
67
+ unittest.main()