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

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Files changed (779) hide show
  1. monai/__init__.py +1 -1
  2. monai/_version.py +3 -3
  3. monai/apps/auto3dseg/transforms.py +1 -4
  4. monai/data/meta_tensor.py +5 -0
  5. monai/data/utils.py +6 -13
  6. monai/inferers/utils.py +1 -2
  7. monai/losses/dice.py +2 -14
  8. monai/losses/ds_loss.py +1 -3
  9. monai/networks/layers/simplelayers.py +2 -14
  10. monai/networks/utils.py +4 -16
  11. monai/transforms/compose.py +28 -11
  12. monai/transforms/croppad/array.py +1 -6
  13. monai/transforms/io/array.py +0 -1
  14. monai/transforms/transform.py +15 -6
  15. monai/transforms/utils.py +1 -2
  16. monai/utils/jupyter_utils.py +1 -1
  17. monai/utils/tf32.py +0 -10
  18. monai/visualize/class_activation_maps.py +5 -8
  19. monai/visualize/img2tensorboard.py +2 -2
  20. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
  21. monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
  22. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
  23. tests/apps/__init__.py +10 -0
  24. tests/apps/deepedit/__init__.py +10 -0
  25. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  26. tests/apps/deepgrow/__init__.py +10 -0
  27. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  28. tests/apps/deepgrow/transforms/__init__.py +10 -0
  29. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  30. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  31. tests/apps/detection/__init__.py +10 -0
  32. tests/apps/detection/metrics/__init__.py +10 -0
  33. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  34. tests/apps/detection/networks/__init__.py +10 -0
  35. tests/apps/detection/networks/test_retinanet.py +210 -0
  36. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  37. tests/apps/detection/test_box_transform.py +370 -0
  38. tests/apps/detection/utils/__init__.py +10 -0
  39. tests/apps/detection/utils/test_anchor_box.py +88 -0
  40. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  41. tests/apps/detection/utils/test_box_coder.py +43 -0
  42. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  43. tests/apps/detection/utils/test_detector_utils.py +96 -0
  44. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  45. tests/apps/nuclick/__init__.py +10 -0
  46. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  47. tests/apps/pathology/__init__.py +10 -0
  48. tests/apps/pathology/handlers/__init__.py +10 -0
  49. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  50. tests/apps/pathology/test_lesion_froc.py +333 -0
  51. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  52. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  53. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  54. tests/apps/pathology/transforms/__init__.py +10 -0
  55. tests/apps/pathology/transforms/post/__init__.py +10 -0
  56. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  57. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  58. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  59. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  60. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  61. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  62. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  63. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  64. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  65. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  66. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  67. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  68. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  69. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  70. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  71. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  72. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  73. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  74. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  75. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  76. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  77. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  78. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  79. tests/apps/reconstruction/__init__.py +10 -0
  80. tests/apps/reconstruction/nets/__init__.py +10 -0
  81. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  82. tests/apps/reconstruction/test_complex_utils.py +77 -0
  83. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  84. tests/apps/reconstruction/test_mri_utils.py +37 -0
  85. tests/apps/reconstruction/transforms/__init__.py +10 -0
  86. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  87. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  88. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  89. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  90. tests/apps/test_check_hash.py +53 -0
  91. tests/apps/test_cross_validation.py +74 -0
  92. tests/apps/test_decathlondataset.py +93 -0
  93. tests/apps/test_download_and_extract.py +70 -0
  94. tests/apps/test_download_url_yandex.py +45 -0
  95. tests/apps/test_mednistdataset.py +72 -0
  96. tests/apps/test_mmar_download.py +154 -0
  97. tests/apps/test_tciadataset.py +123 -0
  98. tests/apps/vista3d/__init__.py +10 -0
  99. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  100. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  101. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  102. tests/bundle/__init__.py +10 -0
  103. tests/bundle/test_bundle_ckpt_export.py +107 -0
  104. tests/bundle/test_bundle_download.py +435 -0
  105. tests/bundle/test_bundle_get_data.py +94 -0
  106. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  107. tests/bundle/test_bundle_trt_export.py +147 -0
  108. tests/bundle/test_bundle_utils.py +149 -0
  109. tests/bundle/test_bundle_verify_metadata.py +66 -0
  110. tests/bundle/test_bundle_verify_net.py +76 -0
  111. tests/bundle/test_bundle_workflow.py +272 -0
  112. tests/bundle/test_component_locator.py +38 -0
  113. tests/bundle/test_config_item.py +138 -0
  114. tests/bundle/test_config_parser.py +392 -0
  115. tests/bundle/test_reference_resolver.py +114 -0
  116. tests/config/__init__.py +10 -0
  117. tests/config/test_cv2_dist.py +53 -0
  118. tests/engines/__init__.py +10 -0
  119. tests/engines/test_ensemble_evaluator.py +94 -0
  120. tests/engines/test_prepare_batch_default.py +76 -0
  121. tests/engines/test_prepare_batch_default_dist.py +76 -0
  122. tests/engines/test_prepare_batch_diffusion.py +104 -0
  123. tests/engines/test_prepare_batch_extra_input.py +80 -0
  124. tests/fl/__init__.py +10 -0
  125. tests/fl/monai_algo/__init__.py +10 -0
  126. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  127. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  128. tests/fl/test_fl_monai_algo_stats.py +81 -0
  129. tests/fl/utils/__init__.py +10 -0
  130. tests/fl/utils/test_fl_exchange_object.py +63 -0
  131. tests/handlers/__init__.py +10 -0
  132. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  133. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  134. tests/handlers/test_handler_classification_saver.py +64 -0
  135. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  136. tests/handlers/test_handler_clearml_image.py +65 -0
  137. tests/handlers/test_handler_clearml_stats.py +65 -0
  138. tests/handlers/test_handler_confusion_matrix.py +104 -0
  139. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  140. tests/handlers/test_handler_decollate_batch.py +66 -0
  141. tests/handlers/test_handler_early_stop.py +68 -0
  142. tests/handlers/test_handler_garbage_collector.py +73 -0
  143. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  144. tests/handlers/test_handler_ignite_metric.py +191 -0
  145. tests/handlers/test_handler_lr_scheduler.py +94 -0
  146. tests/handlers/test_handler_mean_dice.py +98 -0
  147. tests/handlers/test_handler_mean_iou.py +76 -0
  148. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  149. tests/handlers/test_handler_metrics_saver.py +89 -0
  150. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  151. tests/handlers/test_handler_mlflow.py +296 -0
  152. tests/handlers/test_handler_nvtx.py +93 -0
  153. tests/handlers/test_handler_panoptic_quality.py +89 -0
  154. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  155. tests/handlers/test_handler_post_processing.py +74 -0
  156. tests/handlers/test_handler_prob_map_producer.py +111 -0
  157. tests/handlers/test_handler_regression_metrics.py +160 -0
  158. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  159. tests/handlers/test_handler_rocauc.py +48 -0
  160. tests/handlers/test_handler_rocauc_dist.py +54 -0
  161. tests/handlers/test_handler_stats.py +281 -0
  162. tests/handlers/test_handler_surface_distance.py +113 -0
  163. tests/handlers/test_handler_tb_image.py +61 -0
  164. tests/handlers/test_handler_tb_stats.py +166 -0
  165. tests/handlers/test_handler_validation.py +59 -0
  166. tests/handlers/test_trt_compile.py +145 -0
  167. tests/handlers/test_write_metrics_reports.py +68 -0
  168. tests/inferers/__init__.py +10 -0
  169. tests/inferers/test_avg_merger.py +179 -0
  170. tests/inferers/test_controlnet_inferers.py +1310 -0
  171. tests/inferers/test_diffusion_inferer.py +236 -0
  172. tests/inferers/test_latent_diffusion_inferer.py +824 -0
  173. tests/inferers/test_patch_inferer.py +309 -0
  174. tests/inferers/test_saliency_inferer.py +55 -0
  175. tests/inferers/test_slice_inferer.py +57 -0
  176. tests/inferers/test_sliding_window_inference.py +377 -0
  177. tests/inferers/test_sliding_window_splitter.py +284 -0
  178. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  179. tests/inferers/test_zarr_avg_merger.py +326 -0
  180. tests/integration/__init__.py +10 -0
  181. tests/integration/test_auto3dseg_ensemble.py +211 -0
  182. tests/integration/test_auto3dseg_hpo.py +189 -0
  183. tests/integration/test_deepedit_interaction.py +122 -0
  184. tests/integration/test_downsample_block.py +50 -0
  185. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  186. tests/integration/test_integration_autorunner.py +201 -0
  187. tests/integration/test_integration_bundle_run.py +240 -0
  188. tests/integration/test_integration_classification_2d.py +282 -0
  189. tests/integration/test_integration_determinism.py +95 -0
  190. tests/integration/test_integration_fast_train.py +231 -0
  191. tests/integration/test_integration_gpu_customization.py +159 -0
  192. tests/integration/test_integration_lazy_samples.py +219 -0
  193. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  194. tests/integration/test_integration_segmentation_3d.py +304 -0
  195. tests/integration/test_integration_sliding_window.py +100 -0
  196. tests/integration/test_integration_stn.py +133 -0
  197. tests/integration/test_integration_unet_2d.py +67 -0
  198. tests/integration/test_integration_workers.py +61 -0
  199. tests/integration/test_integration_workflows.py +365 -0
  200. tests/integration/test_integration_workflows_adversarial.py +173 -0
  201. tests/integration/test_integration_workflows_gan.py +158 -0
  202. tests/integration/test_loader_semaphore.py +48 -0
  203. tests/integration/test_mapping_filed.py +122 -0
  204. tests/integration/test_meta_affine.py +183 -0
  205. tests/integration/test_metatensor_integration.py +114 -0
  206. tests/integration/test_module_list.py +76 -0
  207. tests/integration/test_one_of.py +283 -0
  208. tests/integration/test_pad_collation.py +124 -0
  209. tests/integration/test_reg_loss_integration.py +107 -0
  210. tests/integration/test_retinanet_predict_utils.py +154 -0
  211. tests/integration/test_seg_loss_integration.py +159 -0
  212. tests/integration/test_spatial_combine_transforms.py +185 -0
  213. tests/integration/test_testtimeaugmentation.py +186 -0
  214. tests/integration/test_vis_gradbased.py +69 -0
  215. tests/integration/test_vista3d_utils.py +159 -0
  216. tests/losses/__init__.py +10 -0
  217. tests/losses/deform/__init__.py +10 -0
  218. tests/losses/deform/test_bending_energy.py +88 -0
  219. tests/losses/deform/test_diffusion_loss.py +117 -0
  220. tests/losses/image_dissimilarity/__init__.py +10 -0
  221. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  222. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  223. tests/losses/test_adversarial_loss.py +94 -0
  224. tests/losses/test_barlow_twins_loss.py +109 -0
  225. tests/losses/test_cldice_loss.py +51 -0
  226. tests/losses/test_contrastive_loss.py +86 -0
  227. tests/losses/test_dice_ce_loss.py +123 -0
  228. tests/losses/test_dice_focal_loss.py +124 -0
  229. tests/losses/test_dice_loss.py +227 -0
  230. tests/losses/test_ds_loss.py +189 -0
  231. tests/losses/test_focal_loss.py +379 -0
  232. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  233. tests/losses/test_generalized_dice_loss.py +221 -0
  234. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  235. tests/losses/test_giou_loss.py +62 -0
  236. tests/losses/test_hausdorff_loss.py +264 -0
  237. tests/losses/test_masked_dice_loss.py +152 -0
  238. tests/losses/test_masked_loss.py +87 -0
  239. tests/losses/test_multi_scale.py +86 -0
  240. tests/losses/test_nacl_loss.py +167 -0
  241. tests/losses/test_perceptual_loss.py +122 -0
  242. tests/losses/test_spectral_loss.py +86 -0
  243. tests/losses/test_ssim_loss.py +59 -0
  244. tests/losses/test_sure_loss.py +72 -0
  245. tests/losses/test_tversky_loss.py +198 -0
  246. tests/losses/test_unified_focal_loss.py +66 -0
  247. tests/metrics/__init__.py +10 -0
  248. tests/metrics/test_compute_confusion_matrix.py +294 -0
  249. tests/metrics/test_compute_f_beta.py +80 -0
  250. tests/metrics/test_compute_fid_metric.py +40 -0
  251. tests/metrics/test_compute_froc.py +143 -0
  252. tests/metrics/test_compute_generalized_dice.py +240 -0
  253. tests/metrics/test_compute_meandice.py +306 -0
  254. tests/metrics/test_compute_meaniou.py +223 -0
  255. tests/metrics/test_compute_mmd_metric.py +56 -0
  256. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  257. tests/metrics/test_compute_panoptic_quality.py +113 -0
  258. tests/metrics/test_compute_regression_metrics.py +196 -0
  259. tests/metrics/test_compute_roc_auc.py +155 -0
  260. tests/metrics/test_compute_variance.py +147 -0
  261. tests/metrics/test_cumulative.py +63 -0
  262. tests/metrics/test_cumulative_average.py +74 -0
  263. tests/metrics/test_cumulative_average_dist.py +48 -0
  264. tests/metrics/test_hausdorff_distance.py +209 -0
  265. tests/metrics/test_label_quality_score.py +134 -0
  266. tests/metrics/test_loss_metric.py +57 -0
  267. tests/metrics/test_metrics_reloaded.py +96 -0
  268. tests/metrics/test_ssim_metric.py +78 -0
  269. tests/metrics/test_surface_dice.py +416 -0
  270. tests/metrics/test_surface_distance.py +186 -0
  271. tests/networks/__init__.py +10 -0
  272. tests/networks/blocks/__init__.py +10 -0
  273. tests/networks/blocks/dints_block/__init__.py +10 -0
  274. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  275. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  276. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  277. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  278. tests/networks/blocks/test_adn.py +86 -0
  279. tests/networks/blocks/test_convolutions.py +156 -0
  280. tests/networks/blocks/test_crf_cpu.py +513 -0
  281. tests/networks/blocks/test_crf_cuda.py +528 -0
  282. tests/networks/blocks/test_crossattention.py +185 -0
  283. tests/networks/blocks/test_denseblock.py +105 -0
  284. tests/networks/blocks/test_dynunet_block.py +116 -0
  285. tests/networks/blocks/test_fpn_block.py +88 -0
  286. tests/networks/blocks/test_localnet_block.py +121 -0
  287. tests/networks/blocks/test_mlp.py +78 -0
  288. tests/networks/blocks/test_patchembedding.py +212 -0
  289. tests/networks/blocks/test_regunet_block.py +103 -0
  290. tests/networks/blocks/test_se_block.py +85 -0
  291. tests/networks/blocks/test_se_blocks.py +78 -0
  292. tests/networks/blocks/test_segresnet_block.py +57 -0
  293. tests/networks/blocks/test_selfattention.py +232 -0
  294. tests/networks/blocks/test_simple_aspp.py +87 -0
  295. tests/networks/blocks/test_spatialattention.py +55 -0
  296. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  297. tests/networks/blocks/test_text_encoding.py +49 -0
  298. tests/networks/blocks/test_transformerblock.py +90 -0
  299. tests/networks/blocks/test_unetr_block.py +158 -0
  300. tests/networks/blocks/test_upsample_block.py +134 -0
  301. tests/networks/blocks/warp/__init__.py +10 -0
  302. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  303. tests/networks/blocks/warp/test_warp.py +250 -0
  304. tests/networks/layers/__init__.py +10 -0
  305. tests/networks/layers/filtering/__init__.py +10 -0
  306. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  307. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  308. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  309. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  310. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  311. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  312. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  313. tests/networks/layers/test_affine_transform.py +385 -0
  314. tests/networks/layers/test_apply_filter.py +89 -0
  315. tests/networks/layers/test_channel_pad.py +51 -0
  316. tests/networks/layers/test_conjugate_gradient.py +56 -0
  317. tests/networks/layers/test_drop_path.py +46 -0
  318. tests/networks/layers/test_gaussian.py +317 -0
  319. tests/networks/layers/test_gaussian_filter.py +206 -0
  320. tests/networks/layers/test_get_layers.py +65 -0
  321. tests/networks/layers/test_gmm.py +314 -0
  322. tests/networks/layers/test_grid_pull.py +93 -0
  323. tests/networks/layers/test_hilbert_transform.py +131 -0
  324. tests/networks/layers/test_lltm.py +62 -0
  325. tests/networks/layers/test_median_filter.py +52 -0
  326. tests/networks/layers/test_polyval.py +55 -0
  327. tests/networks/layers/test_preset_filters.py +136 -0
  328. tests/networks/layers/test_savitzky_golay_filter.py +141 -0
  329. tests/networks/layers/test_separable_filter.py +87 -0
  330. tests/networks/layers/test_skip_connection.py +48 -0
  331. tests/networks/layers/test_vector_quantizer.py +89 -0
  332. tests/networks/layers/test_weight_init.py +50 -0
  333. tests/networks/nets/__init__.py +10 -0
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  680. tests/transforms/test_spatial_resample.py +235 -0
  681. tests/transforms/test_squeezedim.py +62 -0
  682. tests/transforms/test_squeezedimd.py +98 -0
  683. tests/transforms/test_std_shift_intensity.py +76 -0
  684. tests/transforms/test_std_shift_intensityd.py +74 -0
  685. tests/transforms/test_threshold_intensity.py +38 -0
  686. tests/transforms/test_threshold_intensityd.py +58 -0
  687. tests/transforms/test_to_contiguous.py +47 -0
  688. tests/transforms/test_to_cupy.py +112 -0
  689. tests/transforms/test_to_cupyd.py +76 -0
  690. tests/transforms/test_to_device.py +42 -0
  691. tests/transforms/test_to_deviced.py +37 -0
  692. tests/transforms/test_to_numpy.py +85 -0
  693. tests/transforms/test_to_numpyd.py +68 -0
  694. tests/transforms/test_to_pil.py +52 -0
  695. tests/transforms/test_to_pild.py +50 -0
  696. tests/transforms/test_to_tensor.py +60 -0
  697. tests/transforms/test_to_tensord.py +71 -0
  698. tests/transforms/test_torchvision.py +66 -0
  699. tests/transforms/test_torchvisiond.py +63 -0
  700. tests/transforms/test_transform.py +62 -0
  701. tests/transforms/test_transpose.py +41 -0
  702. tests/transforms/test_transposed.py +52 -0
  703. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  704. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  705. tests/transforms/test_vote_ensemble.py +84 -0
  706. tests/transforms/test_vote_ensembled.py +107 -0
  707. tests/transforms/test_with_allow_missing_keys.py +76 -0
  708. tests/transforms/test_zoom.py +120 -0
  709. tests/transforms/test_zoomd.py +94 -0
  710. tests/transforms/transform/__init__.py +10 -0
  711. tests/transforms/transform/test_randomizable.py +52 -0
  712. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  713. tests/transforms/utility/__init__.py +10 -0
  714. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  715. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  716. tests/transforms/utility/test_identity.py +29 -0
  717. tests/transforms/utility/test_identityd.py +30 -0
  718. tests/transforms/utility/test_lambda.py +71 -0
  719. tests/transforms/utility/test_lambdad.py +83 -0
  720. tests/transforms/utility/test_rand_lambda.py +87 -0
  721. tests/transforms/utility/test_rand_lambdad.py +77 -0
  722. tests/transforms/utility/test_simulatedelay.py +36 -0
  723. tests/transforms/utility/test_simulatedelayd.py +36 -0
  724. tests/transforms/utility/test_splitdim.py +52 -0
  725. tests/transforms/utility/test_splitdimd.py +96 -0
  726. tests/transforms/utils/__init__.py +10 -0
  727. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  728. tests/transforms/utils/test_get_unique_labels.py +45 -0
  729. tests/transforms/utils/test_print_transform_backends.py +29 -0
  730. tests/transforms/utils/test_soft_clip.py +125 -0
  731. tests/utils/__init__.py +10 -0
  732. tests/utils/enums/__init__.py +10 -0
  733. tests/utils/enums/test_hovernet_loss.py +190 -0
  734. tests/utils/enums/test_ordering.py +289 -0
  735. tests/utils/enums/test_wsireader.py +663 -0
  736. tests/utils/misc/__init__.py +10 -0
  737. tests/utils/misc/test_ensure_tuple.py +53 -0
  738. tests/utils/misc/test_monai_env_vars.py +44 -0
  739. tests/utils/misc/test_monai_utils_misc.py +103 -0
  740. tests/utils/misc/test_str2bool.py +34 -0
  741. tests/utils/misc/test_str2list.py +33 -0
  742. tests/utils/test_alias.py +44 -0
  743. tests/utils/test_component_store.py +73 -0
  744. tests/utils/test_deprecated.py +455 -0
  745. tests/utils/test_enum_bound_interp.py +75 -0
  746. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  747. tests/utils/test_get_package_version.py +34 -0
  748. tests/utils/test_handler_logfile.py +84 -0
  749. tests/utils/test_handler_metric_logger.py +62 -0
  750. tests/utils/test_list_to_dict.py +43 -0
  751. tests/utils/test_look_up_option.py +87 -0
  752. tests/utils/test_optional_import.py +80 -0
  753. tests/utils/test_pad_mode.py +39 -0
  754. tests/utils/test_profiling.py +208 -0
  755. tests/utils/test_rankfilter_dist.py +77 -0
  756. tests/utils/test_require_pkg.py +83 -0
  757. tests/utils/test_sample_slices.py +43 -0
  758. tests/utils/test_set_determinism.py +74 -0
  759. tests/utils/test_squeeze_unsqueeze.py +71 -0
  760. tests/utils/test_state_cacher.py +67 -0
  761. tests/utils/test_torchscript_utils.py +113 -0
  762. tests/utils/test_version.py +91 -0
  763. tests/utils/test_version_after.py +65 -0
  764. tests/utils/type_conversion/__init__.py +10 -0
  765. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  766. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  767. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  768. tests/visualize/__init__.py +10 -0
  769. tests/visualize/test_img2tensorboard.py +46 -0
  770. tests/visualize/test_occlusion_sensitivity.py +128 -0
  771. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  772. tests/visualize/test_vis_cam.py +98 -0
  773. tests/visualize/test_vis_gradcam.py +211 -0
  774. tests/visualize/utils/__init__.py +10 -0
  775. tests/visualize/utils/test_blend_images.py +63 -0
  776. tests/visualize/utils/test_matshow3d.py +133 -0
  777. monai_weekly-1.5.dev2505.dist-info/RECORD +0 -427
  778. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
  779. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
@@ -0,0 +1,66 @@
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.engines import SupervisedEvaluator
19
+ from monai.handlers import DecollateBatch, PostProcessing
20
+ from monai.transforms import Activationsd, AsDiscreted, Compose, CopyItemsd
21
+ from tests.test_utils import assert_allclose
22
+
23
+
24
+ class TestHandlerDecollateBatch(unittest.TestCase):
25
+ def test_compute(self):
26
+ data = [
27
+ {"image": torch.tensor([[[[2.0], [3.0]]]]), "filename": ["test1"]},
28
+ {"image": torch.tensor([[[[6.0], [8.0]]]]), "filename": ["test2"]},
29
+ ]
30
+
31
+ handlers = [
32
+ DecollateBatch(event="MODEL_COMPLETED"),
33
+ PostProcessing(
34
+ transform=Compose(
35
+ [
36
+ Activationsd(keys="pred", sigmoid=True),
37
+ CopyItemsd(keys="filename", times=1, names="filename_bak"),
38
+ AsDiscreted(keys="pred", threshold=0.5, to_onehot=2),
39
+ ]
40
+ )
41
+ ),
42
+ ]
43
+ # set up engine, PostProcessing handler works together with postprocessing transforms of engine
44
+ engine = SupervisedEvaluator(
45
+ device=torch.device("cpu:0"),
46
+ val_data_loader=data,
47
+ epoch_length=2,
48
+ network=torch.nn.PReLU(),
49
+ # set decollate=False and execute some postprocessing first, then decollate in handlers
50
+ postprocessing=lambda x: dict(pred=x["pred"] + 1.0),
51
+ decollate=False,
52
+ val_handlers=handlers,
53
+ )
54
+ engine.run()
55
+
56
+ expected = torch.tensor([[[[1.0], [1.0]], [[0.0], [0.0]]]])
57
+
58
+ for o, e in zip(engine.state.output, expected):
59
+ assert_allclose(o["pred"], e)
60
+ filename = o.get("filename_bak")
61
+ if filename is not None:
62
+ self.assertEqual(filename, "test2")
63
+
64
+
65
+ if __name__ == "__main__":
66
+ unittest.main()
@@ -0,0 +1,68 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ from ignite.engine import Engine, Events
17
+
18
+ from monai.handlers import EarlyStopHandler
19
+
20
+
21
+ class TestHandlerEarlyStop(unittest.TestCase):
22
+
23
+ def test_early_stop_train_loss(self):
24
+
25
+ def _train_func(engine, batch):
26
+ return {"loss": 1.5}
27
+
28
+ trainer = Engine(_train_func)
29
+ EarlyStopHandler(
30
+ patience=5, score_function=lambda x: x.state.output["loss"], trainer=trainer, epoch_level=False
31
+ ).attach(trainer)
32
+
33
+ trainer.run(range(4), max_epochs=2)
34
+ self.assertEqual(trainer.state.iteration, 6)
35
+ self.assertEqual(trainer.state.epoch, 2)
36
+
37
+ def test_early_stop_val_metric(self):
38
+
39
+ def _train_func(engine, batch):
40
+ pass
41
+
42
+ trainer = Engine(_train_func)
43
+ validator = Engine(_train_func)
44
+ validator.state.metrics["val_acc"] = 0.90
45
+
46
+ @trainer.on(Events.EPOCH_COMPLETED)
47
+ def run_validation(engine):
48
+ validator.state.metrics["val_acc"] += 0.01
49
+ validator.run(range(3))
50
+
51
+ handler = EarlyStopHandler(
52
+ patience=3,
53
+ score_function=lambda x: x.state.metrics["val_acc"],
54
+ trainer=None,
55
+ min_delta=0.1,
56
+ cumulative_delta=True,
57
+ epoch_level=True,
58
+ )
59
+ handler.attach(validator)
60
+ handler.set_trainer(trainer=trainer)
61
+
62
+ trainer.run(range(3), max_epochs=5)
63
+ self.assertEqual(trainer.state.iteration, 12)
64
+ self.assertEqual(trainer.state.epoch, 4)
65
+
66
+
67
+ if __name__ == "__main__":
68
+ unittest.main()
@@ -0,0 +1,73 @@
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 gc
15
+ import unittest
16
+ from unittest import skipUnless
17
+
18
+ import torch
19
+ from ignite.engine import Engine
20
+ from parameterized import parameterized
21
+
22
+ from monai.data import Dataset
23
+ from monai.handlers import GarbageCollector
24
+ from monai.utils import IgniteInfo, min_version, optional_import
25
+
26
+ Events, has_ignite = optional_import("ignite.engine", IgniteInfo.OPT_IMPORT_VERSION, min_version, "Events")
27
+
28
+ TEST_CASE_0 = [[0, 1, 2], "epoch"]
29
+
30
+ TEST_CASE_1 = [[0, 1, 2], "iteration"]
31
+
32
+ TEST_CASE_2 = [[0, 1, 2], Events.EPOCH_COMPLETED]
33
+
34
+
35
+ class TestHandlerGarbageCollector(unittest.TestCase):
36
+
37
+ @skipUnless(has_ignite, "Requires ignite")
38
+ @parameterized.expand([TEST_CASE_0, TEST_CASE_1, TEST_CASE_2])
39
+ def test_content(self, data, trigger_event):
40
+ # set up engine
41
+ gb_count_dict = {}
42
+
43
+ def _train_func(engine, batch):
44
+ # store garbage collection counts
45
+ if trigger_event == Events.EPOCH_COMPLETED or trigger_event.lower() == "epoch":
46
+ if engine.state.iteration % engine.state.epoch_length == 1:
47
+ gb_count_dict[engine.state.epoch] = gc.get_count()
48
+ elif trigger_event.lower() == "iteration":
49
+ gb_count_dict[engine.state.iteration] = gc.get_count()
50
+
51
+ engine = Engine(_train_func)
52
+
53
+ # set up testing handler
54
+ dataset = Dataset(data, transform=None)
55
+ data_loader = torch.utils.data.DataLoader(dataset, batch_size=1)
56
+ GarbageCollector(trigger_event=trigger_event, log_level=30).attach(engine)
57
+
58
+ engine.run(data_loader, max_epochs=5)
59
+
60
+ first_count = 0
61
+ for iter, gb_count in gb_count_dict.items():
62
+ # At least one zero-generation object is collected
63
+ # self.assertGreaterEqual(gb_count[0], 0)
64
+ if iter > 1:
65
+ # Since we are collecting all objects from all generations manually at each call,
66
+ # starting from the second call, there shouldn't be any 1st and 2nd
67
+ # generation objects available to collect.
68
+ self.assertEqual(gb_count[1], first_count)
69
+ self.assertEqual(gb_count[2], first_count)
70
+
71
+
72
+ if __name__ == "__main__":
73
+ unittest.main()
@@ -0,0 +1,111 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import numpy as np
17
+ import torch
18
+ from ignite.engine import Engine
19
+
20
+ from monai.handlers import HausdorffDistance
21
+ from tests.test_utils import assert_allclose
22
+
23
+
24
+ def create_spherical_seg_3d(
25
+ radius: float = 20.0, centre: tuple[int, int, int] = (49, 49, 49), im_shape: tuple[int, int, int] = (99, 99, 99)
26
+ ) -> np.ndarray:
27
+ """
28
+ Return a 3D image with a sphere inside. Voxel values will be
29
+ 1 inside the sphere, and 0 elsewhere.
30
+
31
+ Args:
32
+ radius: radius of sphere (in terms of number of voxels, can be partial)
33
+ centre: location of sphere centre.
34
+ im_shape: shape of image to create
35
+
36
+ See also:
37
+ :py:meth:`~create_test_image_3d`
38
+ """
39
+ # Create image
40
+ image = np.zeros(im_shape, dtype=np.int32)
41
+ spy, spx, spz = np.ogrid[
42
+ -centre[0] : im_shape[0] - centre[0], -centre[1] : im_shape[1] - centre[1], -centre[2] : im_shape[2] - centre[2]
43
+ ]
44
+ circle = (spx * spx + spy * spy + spz * spz) <= radius * radius
45
+
46
+ image[circle] = 1
47
+ image[~circle] = 0
48
+ return image
49
+
50
+
51
+ sampler_sphere = torch.Tensor(create_spherical_seg_3d(radius=20, centre=(20, 20, 20))).unsqueeze(0).unsqueeze(0)
52
+ # test input a list of channel-first tensor
53
+ sampler_sphere_gt = [torch.Tensor(create_spherical_seg_3d(radius=20, centre=(10, 20, 20))).unsqueeze(0)]
54
+ sampler_sphere_zeros = torch.zeros_like(sampler_sphere)
55
+
56
+ TEST_SAMPLE_1 = [sampler_sphere, sampler_sphere_gt]
57
+ TEST_SAMPLE_2 = [sampler_sphere_gt, sampler_sphere_gt]
58
+ TEST_SAMPLE_3 = [sampler_sphere_zeros, sampler_sphere_gt]
59
+ TEST_SAMPLE_4 = [sampler_sphere_zeros, sampler_sphere_zeros]
60
+
61
+
62
+ class TestHandlerHausdorffDistance(unittest.TestCase):
63
+ # TODO test multi node Hausdorff Distance
64
+
65
+ def test_compute(self):
66
+ hd_metric = HausdorffDistance(include_background=True)
67
+
68
+ def _val_func(engine, batch):
69
+ pass
70
+
71
+ engine = Engine(_val_func)
72
+ hd_metric.attach(engine, "hausdorff_distance")
73
+
74
+ y_pred, y = TEST_SAMPLE_1
75
+ hd_metric.update([y_pred, y])
76
+ self.assertEqual(hd_metric.compute(), 10)
77
+ y_pred, y = TEST_SAMPLE_2
78
+ hd_metric.update([y_pred, y])
79
+ self.assertEqual(hd_metric.compute(), 5)
80
+ y_pred, y = TEST_SAMPLE_3
81
+ hd_metric.update([y_pred, y])
82
+ self.assertEqual(hd_metric.compute(), float("inf"))
83
+ y_pred, y = TEST_SAMPLE_4
84
+ hd_metric.update([y_pred, y])
85
+ self.assertEqual(hd_metric.compute(), float("inf"))
86
+
87
+ def test_shape_mismatch(self):
88
+ hd_metric = HausdorffDistance(include_background=True)
89
+ with self.assertRaises((AssertionError, ValueError)):
90
+ y_pred = TEST_SAMPLE_1[0]
91
+ y = torch.ones((1, 1, 10, 10, 10))
92
+ hd_metric.update([y_pred, y])
93
+
94
+ def test_reduction(self):
95
+ hd_metric = HausdorffDistance(include_background=True, reduction="mean_channel")
96
+
97
+ def _val_func(engine, batch):
98
+ pass
99
+
100
+ engine = Engine(_val_func)
101
+ hd_metric.attach(engine, "hausdorff_distance")
102
+
103
+ y_pred, y = TEST_SAMPLE_1
104
+ hd_metric.update([y_pred, y])
105
+ y_pred, y = TEST_SAMPLE_2
106
+ hd_metric.update([y_pred, y])
107
+ assert_allclose(hd_metric.compute().float(), torch.tensor([10.0, 0.0]))
108
+
109
+
110
+ if __name__ == "__main__":
111
+ unittest.main()
@@ -0,0 +1,191 @@
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.handlers import IgniteMetricHandler, from_engine
20
+ from monai.losses import DiceLoss
21
+ from monai.metrics import LossMetric
22
+ from tests.test_utils import SkipIfNoModule, assert_allclose, optional_import
23
+
24
+ try:
25
+ _, has_ignite = optional_import("ignite")
26
+ from ignite.engine import Engine, Events
27
+ except ImportError:
28
+ has_ignite = False
29
+
30
+ TEST_CASE_1 = [
31
+ {"reduction": "none", "include_background": True},
32
+ {},
33
+ {"output_transform": from_engine(["pred", "label"])},
34
+ 0.25,
35
+ ]
36
+ TEST_CASE_2 = [
37
+ {"reduction": "mean", "include_background": False},
38
+ {},
39
+ {"output_transform": from_engine(["pred", "label"])},
40
+ 0.5,
41
+ ]
42
+ TEST_CASE_3 = [
43
+ {"reduction": "none"},
44
+ {"reduction": "mean_channel"},
45
+ {"output_transform": from_engine(["pred", "label"])},
46
+ torch.Tensor([0.5, 0]),
47
+ ]
48
+
49
+ TEST_CASES = [
50
+ [
51
+ {"include_background": True, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
52
+ {
53
+ "input": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
54
+ "target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
55
+ },
56
+ 0,
57
+ ],
58
+ [
59
+ {"include_background": False, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
60
+ {
61
+ "input": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
62
+ "target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
63
+ },
64
+ 0,
65
+ ],
66
+ [
67
+ {"include_background": True, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
68
+ {
69
+ "input": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
70
+ "target": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[0.0, 0.0], [0.0, 0.0]]]]),
71
+ },
72
+ 1,
73
+ ],
74
+ [
75
+ {"include_background": False, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
76
+ {
77
+ "input": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[0.0, 0.0], [0.0, 0.0]]]]),
78
+ "target": torch.tensor([[[[0.0, 0.0], [0.0, 0.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
79
+ },
80
+ 1,
81
+ ],
82
+ [
83
+ {"include_background": True, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
84
+ {
85
+ "input": torch.tensor([[[[0.0, 1.0], [0.0, 1.0]], [[0.0, 1.0], [0.0, 1.0]]]]),
86
+ "target": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
87
+ },
88
+ 0.333333,
89
+ ],
90
+ [
91
+ {"include_background": False, "smooth_nr": 1e-6, "smooth_dr": 1e-6},
92
+ {
93
+ "input": torch.tensor([[[[0.0, 1.0], [0.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
94
+ "target": torch.tensor([[[[1.0, 0.0], [1.0, 0.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
95
+ },
96
+ 0,
97
+ ],
98
+ ]
99
+
100
+
101
+ class TestHandlerIgniteMetricHandler(unittest.TestCase):
102
+ @SkipIfNoModule("ignite")
103
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
104
+ def test_metric_fn(self, loss_params, metric_params, handler_params, expected_avg):
105
+ loss_fn = DiceLoss(**loss_params)
106
+ metric_fn = LossMetric(loss_fn=loss_fn, **metric_params)
107
+ ignite_metric = IgniteMetricHandler(metric_fn=metric_fn, **handler_params)
108
+
109
+ def _val_func(engine, batch):
110
+ pass
111
+
112
+ engine = Engine(_val_func)
113
+ ignite_metric.attach(engine=engine, name="ignite_dice_loss")
114
+ y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
115
+ y = torch.tensor([[[[0.0, 1.0]], [[0.0, 1.0]]]])
116
+ engine.state.output = {"pred": y_pred, "label": y}
117
+ engine.fire_event(Events.ITERATION_COMPLETED)
118
+
119
+ y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
120
+ y = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
121
+ engine.state.output = {"pred": y_pred, "label": y}
122
+ engine.fire_event(Events.ITERATION_COMPLETED)
123
+
124
+ engine.fire_event(Events.EPOCH_COMPLETED)
125
+ assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_avg, atol=1e-4, rtol=1e-4, type_test=False)
126
+
127
+ @SkipIfNoModule("ignite")
128
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
129
+ def test_loss_fn(self, loss_params, metric_params, handler_params, expected_avg):
130
+ loss_fn = DiceLoss(**loss_params)
131
+ ignite_metric = IgniteMetricHandler(loss_fn=loss_fn, **handler_params, **metric_params)
132
+
133
+ def _val_func(engine, batch):
134
+ pass
135
+
136
+ engine = Engine(_val_func)
137
+ ignite_metric.attach(engine=engine, name="ignite_dice_loss")
138
+ y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
139
+ y = torch.tensor([[[[0.0, 1.0]], [[0.0, 1.0]]]])
140
+ engine.state.output = {"pred": y_pred, "label": y}
141
+ engine.fire_event(Events.ITERATION_COMPLETED)
142
+
143
+ y_pred = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
144
+ y = torch.tensor([[[[0.0, 1.0]], [[1.0, 0.0]]]])
145
+ engine.state.output = {"pred": y_pred, "label": y}
146
+ engine.fire_event(Events.ITERATION_COMPLETED)
147
+
148
+ engine.fire_event(Events.EPOCH_COMPLETED)
149
+ assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_avg, atol=1e-4, rtol=1e-4, type_test=False)
150
+
151
+ @SkipIfNoModule("ignite")
152
+ @parameterized.expand(TEST_CASES)
153
+ def test_dice_loss(self, input_param, input_data, expected_val):
154
+ loss_fn = DiceLoss(**input_param)
155
+ ignite_metric = IgniteMetricHandler(loss_fn=loss_fn, output_transform=from_engine(["pred", "label"]))
156
+
157
+ def _val_func(engine, batch):
158
+ pass
159
+
160
+ engine = Engine(_val_func)
161
+ ignite_metric.attach(engine=engine, name="ignite_dice_loss")
162
+ y_pred = input_data["input"]
163
+ y = input_data["target"]
164
+ engine.state.output = {"pred": y_pred, "label": y}
165
+ engine.fire_event(Events.ITERATION_COMPLETED)
166
+
167
+ engine.fire_event(Events.EPOCH_COMPLETED)
168
+ assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_val, atol=1e-4, rtol=1e-4, type_test=False)
169
+
170
+ @SkipIfNoModule("ignite")
171
+ @parameterized.expand(TEST_CASES[0:2])
172
+ def test_old_ignite_metric(self, input_param, input_data, expected_val):
173
+ loss_fn = DiceLoss(**input_param)
174
+ ignite_metric = IgniteMetricHandler(loss_fn=loss_fn, output_transform=from_engine(["pred", "label"]))
175
+
176
+ def _val_func(engine, batch):
177
+ pass
178
+
179
+ engine = Engine(_val_func)
180
+ ignite_metric.attach(engine=engine, name="ignite_dice_loss")
181
+ y_pred = input_data["input"]
182
+ y = input_data["target"]
183
+ engine.state.output = {"pred": y_pred, "label": y}
184
+ engine.fire_event(Events.ITERATION_COMPLETED)
185
+
186
+ engine.fire_event(Events.EPOCH_COMPLETED)
187
+ assert_allclose(engine.state.metrics["ignite_dice_loss"], expected_val, atol=1e-4, rtol=1e-4, type_test=False)
188
+
189
+
190
+ if __name__ == "__main__":
191
+ unittest.main()
@@ -0,0 +1,94 @@
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 logging
15
+ import os
16
+ import re
17
+ import tempfile
18
+ import unittest
19
+
20
+ import numpy as np
21
+ import torch
22
+ from ignite.engine import Engine, Events
23
+
24
+ from monai.handlers import LrScheduleHandler
25
+
26
+
27
+ class TestHandlerLrSchedule(unittest.TestCase):
28
+
29
+ def test_content(self):
30
+ data = [0] * 8
31
+ test_lr = 0.1
32
+ gamma = 0.1
33
+
34
+ # set up engine
35
+ def _train_func(engine, batch):
36
+ pass
37
+
38
+ val_engine = Engine(_train_func)
39
+ train_engine = Engine(_train_func)
40
+
41
+ @train_engine.on(Events.EPOCH_COMPLETED)
42
+ def run_validation(engine):
43
+ val_engine.run(data)
44
+ val_engine.state.metrics["val_loss"] = 1
45
+
46
+ # set up testing handler
47
+ net = torch.nn.PReLU()
48
+
49
+ def _reduce_lr_on_plateau():
50
+ optimizer = torch.optim.SGD(net.parameters(), test_lr)
51
+ lr_scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(optimizer, patience=1)
52
+ handler = LrScheduleHandler(lr_scheduler, step_transform=lambda x: val_engine.state.metrics["val_loss"])
53
+ handler.attach(train_engine)
54
+ return handler
55
+
56
+ with tempfile.TemporaryDirectory() as tempdir:
57
+ key_to_handler = "test_log_lr"
58
+ key_to_print = "Current learning rate"
59
+ filename = os.path.join(tempdir, "test_lr.log")
60
+ # test with additional logging handler
61
+ file_saver = logging.FileHandler(filename, mode="w")
62
+ file_saver.setLevel(logging.INFO)
63
+ logger = logging.getLogger(key_to_handler)
64
+ logger.setLevel(logging.INFO)
65
+ logger.addHandler(file_saver)
66
+
67
+ def _reduce_on_step():
68
+ optimizer = torch.optim.SGD(net.parameters(), test_lr)
69
+ lr_scheduler = torch.optim.lr_scheduler.StepLR(optimizer, step_size=2, gamma=gamma)
70
+ handler = LrScheduleHandler(lr_scheduler, name=key_to_handler)
71
+ handler.attach(train_engine)
72
+ return handler
73
+
74
+ schedulers = _reduce_lr_on_plateau(), _reduce_on_step()
75
+
76
+ train_engine.run(data, max_epochs=5)
77
+ file_saver.close()
78
+ logger.removeHandler(file_saver)
79
+
80
+ with open(filename) as f:
81
+ output_str = f.read()
82
+ has_key_word = re.compile(f".*{key_to_print}.*")
83
+ content_count = 0
84
+ for line in output_str.split("\n"):
85
+ if has_key_word.match(line):
86
+ content_count += 1
87
+ self.assertTrue(content_count > 0)
88
+
89
+ for scheduler in schedulers:
90
+ np.testing.assert_allclose(scheduler.lr_scheduler._last_lr[0], 0.001)
91
+
92
+
93
+ if __name__ == "__main__":
94
+ unittest.main()