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 +1,283 @@
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
+ import monai.transforms.intensity.array as ia
22
+ import monai.transforms.spatial.array as sa
23
+ import monai.transforms.spatial.dictionary as sd
24
+ from monai.data import MetaTensor
25
+ from monai.transforms import (
26
+ InvertibleTransform,
27
+ OneOf,
28
+ RandScaleIntensity,
29
+ RandScaleIntensityd,
30
+ RandShiftIntensity,
31
+ RandShiftIntensityd,
32
+ Resize,
33
+ Resized,
34
+ Transform,
35
+ )
36
+ from monai.transforms.compose import Compose
37
+ from monai.transforms.transform import MapTransform
38
+ from monai.utils.enums import TraceKeys
39
+
40
+
41
+ class X(Transform):
42
+
43
+ def __call__(self, x):
44
+ return x
45
+
46
+
47
+ class Y(Transform):
48
+
49
+ def __call__(self, x):
50
+ return x
51
+
52
+
53
+ class A(Transform):
54
+
55
+ def __call__(self, x):
56
+ return x + 1
57
+
58
+
59
+ class B(Transform):
60
+
61
+ def __call__(self, x):
62
+ return x + 2
63
+
64
+
65
+ class C(Transform):
66
+
67
+ def __call__(self, x):
68
+ return x + 3
69
+
70
+
71
+ class MapBase(MapTransform):
72
+
73
+ def __init__(self, keys):
74
+ super().__init__(keys)
75
+ self.fwd_fn, self.inv_fn = None, None
76
+
77
+ def __call__(self, data):
78
+ d = deepcopy(dict(data))
79
+ for key in self.key_iterator(d):
80
+ d[key] = self.fwd_fn(d[key])
81
+ return d
82
+
83
+
84
+ class NonInv(MapBase):
85
+
86
+ def __init__(self, keys):
87
+ super().__init__(keys)
88
+ self.fwd_fn = lambda x: x * 2
89
+
90
+
91
+ class Inv(MapBase, InvertibleTransform):
92
+
93
+ def __call__(self, data):
94
+ d = deepcopy(dict(data))
95
+ for key in self.key_iterator(d):
96
+ d[key] = self.fwd_fn(d[key])
97
+ self.push_transform(d, key)
98
+ return d
99
+
100
+ def inverse(self, data):
101
+ d = deepcopy(dict(data))
102
+ for key in self.key_iterator(d):
103
+ d[key] = self.inv_fn(d[key])
104
+ self.pop_transform(d, key)
105
+ return d
106
+
107
+
108
+ class InvA(Inv):
109
+
110
+ def __init__(self, keys):
111
+ super().__init__(keys)
112
+ self.fwd_fn = lambda x: x + 1
113
+ self.inv_fn = lambda x: x - 1
114
+
115
+
116
+ class InvB(Inv):
117
+
118
+ def __init__(self, keys):
119
+ super().__init__(keys)
120
+ self.fwd_fn = lambda x: x + 100
121
+ self.inv_fn = lambda x: x - 100
122
+
123
+
124
+ TESTS = [((X(), Y(), X()), (1, 2, 1), (0.25, 0.5, 0.25))]
125
+
126
+ KEYS = ["x", "y"]
127
+ TEST_INVERSES = [
128
+ (OneOf((InvA(KEYS), InvB(KEYS))), True, True),
129
+ (OneOf((OneOf((InvA(KEYS), InvB(KEYS))), OneOf((InvB(KEYS), InvA(KEYS))))), True, False),
130
+ (OneOf((Compose((InvA(KEYS), InvB(KEYS))), Compose((InvB(KEYS), InvA(KEYS))))), True, False),
131
+ (OneOf((NonInv(KEYS), NonInv(KEYS))), False, False),
132
+ ]
133
+
134
+
135
+ class TestOneOf(unittest.TestCase):
136
+
137
+ @parameterized.expand(TESTS)
138
+ def test_normalize_weights(self, transforms, input_weights, expected_weights):
139
+ tr = OneOf(transforms, input_weights)
140
+ self.assertTupleEqual(tr.weights, expected_weights)
141
+
142
+ def test_no_weights_arg(self):
143
+ p = OneOf((X(), Y(), X(), Y()))
144
+ expected_weights = (0.25,) * 4
145
+ self.assertTupleEqual(p.weights, expected_weights)
146
+
147
+ def test_len_and_flatten(self):
148
+ p1 = OneOf((X(), Y()), (1, 3)) # 0.25, 0.75
149
+ p2 = OneOf((Y(), Y()), (2, 2)) # 0.5. 0.5
150
+ p = OneOf((p1, p2, X()), (1, 2, 1)) # 0.25, 0.5, 0.25
151
+ expected_order = (X, Y, Y, Y, X)
152
+ expected_weights = (0.25 * 0.25, 0.25 * 0.75, 0.5 * 0.5, 0.5 * 0.5, 0.25)
153
+ self.assertEqual(len(p), len(expected_order))
154
+ self.assertTupleEqual(p.flatten().weights, expected_weights)
155
+
156
+ def test_compose_flatten_does_not_affect_one_of(self):
157
+ p = Compose([A(), B(), OneOf([C(), Inv(KEYS), Compose([X(), Y()])])])
158
+ f = p.flatten()
159
+
160
+ # in this case the flattened transform should be the same.
161
+
162
+ def _match(a, b):
163
+ self.assertEqual(type(a), type(b))
164
+ for a_, b_ in zip(a.transforms, b.transforms):
165
+ self.assertEqual(type(a_), type(b_))
166
+ if isinstance(a_, (Compose, OneOf)):
167
+ _match(a_, b_)
168
+
169
+ _match(p, f)
170
+
171
+ @parameterized.expand(TEST_INVERSES)
172
+ def test_inverse(self, transform, invertible, use_metatensor):
173
+ data = {k: MetaTensor((i + 1) * 10.0) for i, k in enumerate(KEYS)}
174
+ fwd_data = transform(data)
175
+
176
+ if invertible:
177
+ for k in KEYS:
178
+ t = fwd_data[k].applied_operations[-1]
179
+ # make sure the OneOf index was stored
180
+ self.assertEqual(t[TraceKeys.CLASS_NAME], OneOf.__name__)
181
+ # make sure index exists and is in bounds
182
+ self.assertTrue(0 <= t[TraceKeys.EXTRA_INFO]["index"] < len(transform))
183
+
184
+ # call the inverse
185
+ fwd_inv_data = transform.inverse(fwd_data)
186
+
187
+ if invertible:
188
+ for k in KEYS:
189
+ # check data is same as original (and different from forward)
190
+ self.assertEqual(fwd_inv_data[k], data[k])
191
+ self.assertNotEqual(fwd_inv_data[k], fwd_data[k])
192
+ else:
193
+ # if not invertible, should not change the data
194
+ self.assertDictEqual(fwd_data, fwd_inv_data)
195
+
196
+ def test_inverse_compose(self):
197
+ transform = Compose(
198
+ [
199
+ Resized(keys="img", spatial_size=[100, 100, 100]),
200
+ OneOf(
201
+ [
202
+ RandScaleIntensityd(keys="img", factors=0.5, prob=1.0),
203
+ RandShiftIntensityd(keys="img", offsets=0.5, prob=1.0),
204
+ ]
205
+ ),
206
+ OneOf(
207
+ [
208
+ RandScaleIntensityd(keys="img", factors=0.5, prob=1.0),
209
+ RandShiftIntensityd(keys="img", offsets=0.5, prob=1.0),
210
+ ]
211
+ ),
212
+ ]
213
+ )
214
+ transform.set_random_state(seed=0)
215
+ result = transform({"img": np.ones((1, 101, 102, 103))})
216
+ result = transform.inverse(result)
217
+ # invert to the original spatial shape
218
+ self.assertTupleEqual(result["img"].shape, (1, 101, 102, 103))
219
+
220
+ def test_inverse_metatensor(self):
221
+ transform = Compose(
222
+ [
223
+ Resize(spatial_size=[100, 100, 100]),
224
+ OneOf([RandScaleIntensity(factors=0.5, prob=1.0), RandShiftIntensity(offsets=0.5, prob=1.0)]),
225
+ OneOf([RandScaleIntensity(factors=0.5, prob=1.0), RandShiftIntensity(offsets=0.5, prob=1.0)]),
226
+ ]
227
+ )
228
+ transform.set_random_state(seed=0)
229
+ result = transform(np.ones((1, 101, 102, 103)))
230
+ self.assertTupleEqual(result.shape, (1, 100, 100, 100))
231
+ result = transform.inverse(result)
232
+ self.assertTupleEqual(result.shape, (1, 101, 102, 103))
233
+
234
+ def test_one_of(self):
235
+ p = OneOf((A(), B(), C()), (1, 2, 1))
236
+ counts = [0] * 3
237
+ for _i in range(10000):
238
+ out = p(1.0)
239
+ counts[int(out - 2)] += 1
240
+ self.assertAlmostEqual(counts[0] / 10000, 0.25, delta=1.0)
241
+ self.assertAlmostEqual(counts[1] / 10000, 0.50, delta=1.0)
242
+ self.assertAlmostEqual(counts[2] / 10000, 0.25, delta=1.0)
243
+
244
+
245
+ TEST_ONEOF_EXTENDED_TEST_CASES = [
246
+ [None, tuple()],
247
+ [None, (sa.Rotate(np.pi / 8),)],
248
+ [None, (sa.Flip(0), sa.Flip(1), sa.Rotate90(1), sa.Zoom(0.8), ia.NormalizeIntensity())],
249
+ [("a",), (sd.Rotated(("a",), np.pi / 8),)],
250
+ ]
251
+
252
+
253
+ class TestOneOfAPITests(unittest.TestCase):
254
+
255
+ @staticmethod
256
+ def data_from_keys(keys):
257
+ if keys is None:
258
+ data = torch.unsqueeze(torch.tensor(np.arange(12 * 16).reshape(12, 16)), dim=0)
259
+ else:
260
+ data = {}
261
+ for i_k, k in enumerate(keys):
262
+ data[k] = torch.unsqueeze(torch.tensor(np.arange(12 * 16)).reshape(12, 16) + i_k * 192, dim=0)
263
+ return data
264
+
265
+ @parameterized.expand(TEST_ONEOF_EXTENDED_TEST_CASES)
266
+ def test_execute_change_start_end(self, keys, pipeline):
267
+ data = self.data_from_keys(keys)
268
+
269
+ c = OneOf(deepcopy(pipeline))
270
+ with self.assertRaises(ValueError):
271
+ c(data, start=1)
272
+ with self.assertRaises(ValueError):
273
+ c(data, start=1)
274
+
275
+ c = OneOf(deepcopy(pipeline))
276
+ with self.assertRaises(ValueError):
277
+ c(data, end=1)
278
+ with self.assertRaises(ValueError):
279
+ c(data, end=1)
280
+
281
+
282
+ if __name__ == "__main__":
283
+ unittest.main()
@@ -0,0 +1,124 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import random
15
+ import unittest
16
+ from functools import wraps
17
+
18
+ import numpy as np
19
+ import torch
20
+ from parameterized import parameterized
21
+
22
+ from monai.data import CacheDataset, DataLoader
23
+ from monai.data.utils import decollate_batch, pad_list_data_collate
24
+ from monai.transforms import (
25
+ BatchInverseTransform,
26
+ Compose,
27
+ PadListDataCollate,
28
+ RandRotate,
29
+ RandRotate90,
30
+ RandRotate90d,
31
+ RandRotated,
32
+ RandSpatialCrop,
33
+ RandSpatialCropd,
34
+ RandZoom,
35
+ RandZoomd,
36
+ ToTensor,
37
+ )
38
+ from monai.utils import set_determinism
39
+
40
+
41
+ @wraps(pad_list_data_collate)
42
+ def _testing_collate(x):
43
+ return pad_list_data_collate(batch=x, method="end", mode="constant")
44
+
45
+
46
+ TESTS: list[tuple] = []
47
+
48
+ for pad_collate in [_testing_collate, PadListDataCollate(method="end", mode="constant")]:
49
+ TESTS.append((dict, pad_collate, RandSpatialCropd("image", roi_size=[8, 7], random_size=True)))
50
+ TESTS.append((dict, pad_collate, RandRotated("image", prob=1, range_x=np.pi, keep_size=False, dtype=np.float64)))
51
+ TESTS.append((dict, pad_collate, RandZoomd("image", prob=1, min_zoom=1.1, max_zoom=2.0, keep_size=False)))
52
+ TESTS.append(
53
+ (dict, pad_collate, Compose([RandRotate90d("image", prob=1, max_k=3), RandRotate90d("image", prob=1, max_k=4)]))
54
+ )
55
+
56
+ TESTS.append((list, pad_collate, RandSpatialCrop(roi_size=[8, 7], random_size=True)))
57
+ TESTS.append((list, pad_collate, RandRotate(prob=1, range_x=np.pi, keep_size=False, dtype=np.float64)))
58
+ TESTS.append((list, pad_collate, RandZoom(prob=1, min_zoom=1.1, max_zoom=2.0, keep_size=False)))
59
+ TESTS.append((list, pad_collate, Compose([RandRotate90(prob=1, max_k=2), ToTensor()])))
60
+
61
+
62
+ class _Dataset(torch.utils.data.Dataset):
63
+
64
+ def __init__(self, images, labels, transforms):
65
+ self.images = images
66
+ self.labels = labels
67
+ self.transform = transforms
68
+
69
+ def __len__(self):
70
+ return len(self.images)
71
+
72
+ def __getitem__(self, index):
73
+ return self.transform(self.images[index]), self.labels[index]
74
+
75
+
76
+ class TestPadCollation(unittest.TestCase):
77
+
78
+ def setUp(self) -> None:
79
+ set_determinism(seed=0)
80
+ # image is non square to throw rotation errors
81
+ im = np.arange(0, 10 * 9).reshape(1, 10, 9)
82
+ num_elements = 20
83
+ self.dict_data = [{"image": im} for _ in range(num_elements)]
84
+ self.list_data = [im for _ in range(num_elements)]
85
+ self.list_labels = [random.randint(0, 1) for _ in range(num_elements)]
86
+
87
+ def tearDown(self) -> None:
88
+ set_determinism(None)
89
+
90
+ @parameterized.expand(TESTS)
91
+ def test_pad_collation(self, t_type, collate_method, transform):
92
+ if t_type is dict:
93
+ dataset = CacheDataset(self.dict_data, transform, progress=False)
94
+ else:
95
+ dataset = _Dataset(self.list_data, self.list_labels, transform)
96
+
97
+ # Default collation should raise an error
98
+ loader_fail = DataLoader(dataset, batch_size=10)
99
+ with self.assertRaises(RuntimeError):
100
+ for _ in loader_fail:
101
+ pass
102
+
103
+ # Padded collation shouldn't
104
+ loader = DataLoader(dataset, batch_size=10, collate_fn=collate_method)
105
+ # check collation in forward direction
106
+ for data in loader:
107
+ if t_type is dict:
108
+ shapes = []
109
+ decollated_data = decollate_batch(data)
110
+ for d in decollated_data:
111
+ output = PadListDataCollate.inverse(d)
112
+ shapes.append(output["image"].shape)
113
+ self.assertTrue(len(output["image"].applied_operations), len(dataset.transform.transforms))
114
+ self.assertTrue(len(set(shapes)) > 1) # inverted shapes must be different because of random xforms
115
+
116
+ if t_type is dict:
117
+ batch_inverse = BatchInverseTransform(dataset.transform, loader)
118
+ for data in loader:
119
+ output = batch_inverse(data)
120
+ self.assertEqual(output[0]["image"].shape, (1, 10, 9))
121
+
122
+
123
+ if __name__ == "__main__":
124
+ unittest.main()
@@ -0,0 +1,107 @@
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
+ import torch.nn as nn
18
+ import torch.optim as optim
19
+ from parameterized import parameterized
20
+
21
+ from monai.losses import BendingEnergyLoss, GlobalMutualInformationLoss, LocalNormalizedCrossCorrelationLoss
22
+ from tests.test_utils import SkipIfBeforePyTorchVersion
23
+
24
+ TEST_CASES = [
25
+ [BendingEnergyLoss, {}, ["pred"], 3],
26
+ [LocalNormalizedCrossCorrelationLoss, {"kernel_size": 7, "kernel_type": "rectangular"}, ["pred", "target"]],
27
+ [LocalNormalizedCrossCorrelationLoss, {"kernel_size": 5, "kernel_type": "triangular"}, ["pred", "target"]],
28
+ [LocalNormalizedCrossCorrelationLoss, {"kernel_size": 3, "kernel_type": "gaussian"}, ["pred", "target"]],
29
+ [GlobalMutualInformationLoss, {"num_bins": 10}, ["pred", "target"]],
30
+ [GlobalMutualInformationLoss, {"kernel_type": "b-spline", "num_bins": 10}, ["pred", "target"]],
31
+ ]
32
+
33
+
34
+ class TestRegLossIntegration(unittest.TestCase):
35
+ def setUp(self):
36
+ torch.backends.cudnn.deterministic = True
37
+ torch.backends.cudnn.benchmark = False
38
+ torch.manual_seed(0)
39
+ self.device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu:0")
40
+
41
+ def tearDown(self):
42
+ torch.backends.cudnn.deterministic = False
43
+ torch.backends.cudnn.benchmark = True
44
+
45
+ @parameterized.expand(TEST_CASES)
46
+ @SkipIfBeforePyTorchVersion((1, 9))
47
+ def test_convergence(self, loss_type, loss_args, forward_args, pred_channels=1):
48
+ """
49
+ The goal of this test is to assess if the gradient of the loss function
50
+ is correct by testing if we can train a one layer neural network
51
+ to segment one image.
52
+ We verify that the loss is decreasing in almost all SGD steps.
53
+ """
54
+ learning_rate = 0.001
55
+ max_iter = 100
56
+
57
+ # define a simple 3d example
58
+ target = torch.rand((1, 1, 5, 5, 5), device=self.device)
59
+ image = 12 * target + 27
60
+ image = image.to(device=self.device)
61
+
62
+ # define a one layer model
63
+ class OnelayerNet(nn.Module):
64
+ def __init__(self):
65
+ super().__init__()
66
+ self.layer = nn.Sequential(
67
+ nn.Conv3d(in_channels=1, out_channels=1, kernel_size=3, padding=1),
68
+ nn.ReLU(),
69
+ nn.Conv3d(in_channels=1, out_channels=pred_channels, kernel_size=3, padding=1),
70
+ )
71
+
72
+ def forward(self, x):
73
+ return self.layer(x)
74
+
75
+ # initialise the network
76
+ net = OnelayerNet().to(self.device)
77
+
78
+ # initialize the loss
79
+ loss = loss_type(**loss_args).to(self.device)
80
+
81
+ # initialize a SGD optimizer
82
+ optimizer = optim.Adam(net.parameters(), lr=learning_rate)
83
+
84
+ # declare first for pylint
85
+ init_loss = None
86
+
87
+ # train the network
88
+ for it in range(max_iter):
89
+ # set the gradient to zero
90
+ optimizer.zero_grad()
91
+
92
+ # forward pass
93
+ output = net(image)
94
+ loss_input = {"pred": output, "target": target}
95
+
96
+ loss_val = loss(**{k: loss_input[k] for k in forward_args})
97
+ if it == 0:
98
+ init_loss = loss_val
99
+
100
+ # backward pass
101
+ loss_val.backward()
102
+ optimizer.step()
103
+ self.assertGreater(init_loss, loss_val, "loss did not decrease")
104
+
105
+
106
+ if __name__ == "__main__":
107
+ unittest.main()
@@ -0,0 +1,154 @@
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.predict_utils import ensure_dict_value_to_list_, predict_with_inferer
20
+ from monai.inferers import SlidingWindowInferer
21
+
22
+ TEST_CASE_1 = [ # 3D, batch 3, 2 input channel
23
+ {
24
+ "pretrained": False,
25
+ "spatial_dims": 3,
26
+ "n_input_channels": 2,
27
+ "num_classes": 3,
28
+ "conv1_t_size": 7,
29
+ "conv1_t_stride": (2, 2, 2),
30
+ },
31
+ (3, 2, 32, 64, 48),
32
+ ]
33
+
34
+ TEST_CASE_2 = [ # 2D, batch 2, 1 input channel
35
+ {
36
+ "pretrained": False,
37
+ "spatial_dims": 2,
38
+ "n_input_channels": 1,
39
+ "num_classes": 3,
40
+ "conv1_t_size": [7, 7],
41
+ "conv1_t_stride": [2, 2],
42
+ },
43
+ (2, 1, 32, 64),
44
+ ]
45
+
46
+ TEST_CASE_2_A = [ # 2D, batch 2, 1 input channel, shortcut type A
47
+ {
48
+ "pretrained": False,
49
+ "spatial_dims": 2,
50
+ "n_input_channels": 1,
51
+ "num_classes": 3,
52
+ "shortcut_type": "A",
53
+ "conv1_t_size": (7, 7),
54
+ "conv1_t_stride": 2,
55
+ },
56
+ (2, 1, 32, 64),
57
+ ]
58
+
59
+ TEST_CASE_3 = [ # 1D, batch 1, 2 input channels
60
+ {
61
+ "pretrained": False,
62
+ "spatial_dims": 1,
63
+ "n_input_channels": 2,
64
+ "num_classes": 3,
65
+ "conv1_t_size": [3],
66
+ "conv1_t_stride": 1,
67
+ },
68
+ (1, 2, 32),
69
+ ]
70
+
71
+ TEST_CASE_3_A = [ # 1D, batch 1, 2 input channels
72
+ {"pretrained": False, "spatial_dims": 1, "n_input_channels": 2, "num_classes": 3, "shortcut_type": "A"},
73
+ (1, 2, 32),
74
+ ]
75
+
76
+ TEST_CASE_4 = [ # 2D, batch 2, 1 input channel
77
+ {"pretrained": False, "spatial_dims": 2, "n_input_channels": 1, "num_classes": 3, "feed_forward": False},
78
+ (2, 1, 32, 64),
79
+ ]
80
+
81
+ TEST_CASES = []
82
+ TEST_CASES = [TEST_CASE_1, TEST_CASE_2, TEST_CASE_2_A]
83
+
84
+ TEST_CASES_TS = [TEST_CASE_1]
85
+
86
+
87
+ class NaiveNetwork(torch.nn.Module):
88
+
89
+ def __init__(self, spatial_dims, num_classes, **kwargs):
90
+ super().__init__()
91
+ self.spatial_dims = spatial_dims
92
+ self.num_classes = num_classes
93
+ self.num_anchors = 1
94
+ self.cls_key = "cls"
95
+ self.box_reg_key = "box_reg"
96
+ self.size_divisible = 1
97
+
98
+ def forward(self, images):
99
+ out_cls_shape = (images.shape[0], self.num_classes * self.num_anchors) + images.shape[-self.spatial_dims :]
100
+ out_box_reg_shape = (images.shape[0], 2 * self.spatial_dims * self.num_anchors) + images.shape[
101
+ -self.spatial_dims :
102
+ ]
103
+ return {self.cls_key: torch.randn(out_cls_shape), self.box_reg_key: [torch.randn(out_box_reg_shape)]}
104
+
105
+
106
+ class NaiveNetwork2(torch.nn.Module):
107
+
108
+ def __init__(self, spatial_dims, num_classes, **kwargs):
109
+ super().__init__()
110
+ self.spatial_dims = spatial_dims
111
+ self.num_classes = num_classes
112
+ self.num_anchors = 1
113
+ self.cls_key = "cls"
114
+ self.box_reg_key = "box_reg"
115
+ self.size_divisible = 1
116
+
117
+ def forward(self, images):
118
+ out_cls_shape = (images.shape[0], self.num_classes * self.num_anchors) + images.shape[-self.spatial_dims :]
119
+ out_box_reg_shape = (images.shape[0], 2 * self.spatial_dims * self.num_anchors) + images.shape[
120
+ -self.spatial_dims :
121
+ ]
122
+ return {self.cls_key: [torch.randn(out_cls_shape)] * 2, self.box_reg_key: [torch.randn(out_box_reg_shape)] * 2}
123
+
124
+
125
+ class TestPredictor(unittest.TestCase):
126
+
127
+ @parameterized.expand(TEST_CASES)
128
+ def test_naive_predictor(self, input_param, input_shape):
129
+ net = NaiveNetwork(**input_param)
130
+ net2 = NaiveNetwork2(**input_param)
131
+ inferer = SlidingWindowInferer(roi_size=16, overlap=0.25, cache_roi_weight_map=True)
132
+ network_output_keys = ["cls", "box_reg"]
133
+
134
+ input_data = torch.randn(input_shape)
135
+
136
+ result = predict_with_inferer(input_data, net, network_output_keys, inferer=inferer)
137
+ self.assertTrue(len(result["cls"]) == 1)
138
+
139
+ result = net(input_data)
140
+ self.assertTrue(len(result["cls"]) == input_data.shape[0])
141
+ ensure_dict_value_to_list_(result)
142
+ self.assertTrue(len(result["cls"]) == 1)
143
+
144
+ result = predict_with_inferer(input_data, net2, network_output_keys, inferer=inferer)
145
+ self.assertTrue(len(result["cls"]) == 2)
146
+
147
+ result = net2(input_data)
148
+ self.assertTrue(len(result["cls"]) == 2)
149
+ ensure_dict_value_to_list_(result)
150
+ self.assertTrue(len(result["cls"]) == 2)
151
+
152
+
153
+ if __name__ == "__main__":
154
+ unittest.main()