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 +1,233 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import os
15
+ import tempfile
16
+ import unittest
17
+
18
+ import torch
19
+ import torch.optim as optim
20
+ from ignite.engine import Engine
21
+ from parameterized import parameterized
22
+
23
+ from monai.handlers import CheckpointLoader, CheckpointSaver
24
+
25
+ TEST_CASE_1 = [
26
+ True,
27
+ None,
28
+ False,
29
+ None,
30
+ 1,
31
+ None,
32
+ False,
33
+ False,
34
+ False,
35
+ True,
36
+ 0,
37
+ None,
38
+ ["test_checkpoint_final_iteration=40.pt"],
39
+ ]
40
+
41
+ TEST_CASE_2 = [
42
+ False,
43
+ None,
44
+ True,
45
+ "val_loss",
46
+ 2,
47
+ None,
48
+ False,
49
+ True,
50
+ False,
51
+ False,
52
+ 0,
53
+ None,
54
+ ["test_checkpoint_key_metric=32.pt", "test_checkpoint_key_metric=40.pt"],
55
+ ]
56
+
57
+ TEST_CASE_3 = [
58
+ False,
59
+ None,
60
+ False,
61
+ None,
62
+ 1,
63
+ None,
64
+ False,
65
+ True,
66
+ False,
67
+ True,
68
+ 2,
69
+ 2,
70
+ ["test_checkpoint_epoch=2.pt", "test_checkpoint_epoch=4.pt"],
71
+ ]
72
+
73
+ TEST_CASE_4 = [
74
+ False,
75
+ None,
76
+ False,
77
+ None,
78
+ 1,
79
+ None,
80
+ False,
81
+ False,
82
+ False,
83
+ False,
84
+ 10,
85
+ 2,
86
+ ["test_checkpoint_iteration=30.pt", "test_checkpoint_iteration=40.pt"],
87
+ ]
88
+
89
+ TEST_CASE_5 = [
90
+ True,
91
+ None,
92
+ False,
93
+ None,
94
+ 1,
95
+ None,
96
+ False,
97
+ False,
98
+ False,
99
+ True,
100
+ 0,
101
+ None,
102
+ ["test_checkpoint_final_iteration=40.pt"],
103
+ True,
104
+ ]
105
+
106
+ TEST_CASE_6 = [True, "final_model.pt", False, None, 1, None, False, False, False, True, 0, None, ["final_model.pt"]]
107
+
108
+ TEST_CASE_7 = [False, None, True, "val_loss", 1, "model.pt", False, False, False, True, 0, None, ["model.pt"]]
109
+
110
+ TEST_CASE_8 = [False, None, True, "val_loss", 1, "model.pt", False, True, False, True, 0, None, ["model.pt"]]
111
+
112
+
113
+ class TestHandlerCheckpointSaver(unittest.TestCase):
114
+
115
+ @parameterized.expand(
116
+ [TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4, TEST_CASE_5, TEST_CASE_6, TEST_CASE_7, TEST_CASE_8]
117
+ )
118
+ def test_file(
119
+ self,
120
+ save_final,
121
+ final_filename,
122
+ save_key_metric,
123
+ key_metric_name,
124
+ key_metric_n_saved,
125
+ key_metric_filename,
126
+ key_metric_save_state,
127
+ key_metric_greater_or_equal,
128
+ key_metric_negative_sign,
129
+ epoch_level,
130
+ save_interval,
131
+ n_saved,
132
+ filenames,
133
+ multi_devices=False,
134
+ ):
135
+ data = [0] * 8
136
+
137
+ # set up engine
138
+ def _train_func(engine, batch):
139
+ engine.state.metrics["val_loss"] = engine.state.iteration
140
+
141
+ engine = Engine(_train_func)
142
+
143
+ # set up testing handler
144
+ net = torch.nn.PReLU()
145
+ if multi_devices:
146
+ net = torch.nn.DataParallel(net)
147
+ optimizer = optim.SGD(net.parameters(), lr=0.02)
148
+ with tempfile.TemporaryDirectory() as tempdir:
149
+ handler = CheckpointSaver(
150
+ tempdir,
151
+ {"net": net, "opt": optimizer},
152
+ "CheckpointSaver",
153
+ "test",
154
+ save_final,
155
+ final_filename,
156
+ save_key_metric,
157
+ key_metric_name,
158
+ key_metric_n_saved,
159
+ key_metric_filename,
160
+ key_metric_save_state,
161
+ key_metric_greater_or_equal,
162
+ key_metric_negative_sign,
163
+ epoch_level,
164
+ save_interval,
165
+ n_saved,
166
+ )
167
+ handler.attach(engine)
168
+ engine.run(data, max_epochs=2)
169
+ engine.run(data, max_epochs=5)
170
+ for filename in filenames:
171
+ self.assertTrue(os.path.exists(os.path.join(tempdir, filename)))
172
+
173
+ def test_exception(self):
174
+ net = torch.nn.PReLU()
175
+
176
+ # set up engine
177
+ def _train_func(engine, batch):
178
+ raise RuntimeError("test exception.")
179
+
180
+ engine = Engine(_train_func)
181
+
182
+ # set up testing handler
183
+ with tempfile.TemporaryDirectory() as tempdir:
184
+ stats_handler = CheckpointSaver(tempdir, {"net": net}, save_final=True)
185
+ stats_handler.attach(engine)
186
+
187
+ with self.assertRaises(RuntimeError):
188
+ engine.run(range(3), max_epochs=2)
189
+ self.assertTrue(os.path.exists(os.path.join(tempdir, "net_final_iteration=1.pt")))
190
+
191
+ def test_load_state_dict(self):
192
+ net = torch.nn.PReLU()
193
+
194
+ # set up engine
195
+ def _train_func(engine, batch):
196
+ engine.state.metrics["val_loss"] = engine.state.iteration
197
+
198
+ engine = Engine(_train_func)
199
+
200
+ # set up testing handler
201
+ with tempfile.TemporaryDirectory() as tempdir:
202
+ engine = Engine(_train_func)
203
+ CheckpointSaver(
204
+ save_dir=tempdir,
205
+ save_dict={"net": net},
206
+ save_key_metric=True,
207
+ key_metric_name="val_loss",
208
+ key_metric_n_saved=2,
209
+ key_metric_save_state=True,
210
+ key_metric_negative_sign=True,
211
+ ).attach(engine)
212
+ engine.run(range(3), max_epochs=3)
213
+
214
+ saver = CheckpointSaver(
215
+ save_dir=tempdir,
216
+ save_dict={"net": net},
217
+ save_key_metric=True,
218
+ key_metric_name="val_loss",
219
+ key_metric_n_saved=2,
220
+ key_metric_negative_sign=True,
221
+ )
222
+ engine = Engine(_train_func)
223
+ CheckpointLoader(os.path.join(tempdir, "net_key_metric=-6.pt"), {"checkpointer": saver}).attach(engine)
224
+ engine.run(range(1), max_epochs=1)
225
+
226
+ resumed = saver._key_metric_checkpoint._saved
227
+ for i in range(2):
228
+ self.assertEqual(resumed[1 - i].priority, -3 * (i + 1))
229
+ self.assertEqual(resumed[1 - i].filename, f"net_key_metric=-{3 * (i + 1)}.pt")
230
+
231
+
232
+ if __name__ == "__main__":
233
+ unittest.main()
@@ -0,0 +1,64 @@
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 csv
15
+ import os
16
+ import tempfile
17
+ import unittest
18
+
19
+ import numpy as np
20
+ import torch
21
+ from ignite.engine import Engine
22
+
23
+ from monai.data import decollate_batch
24
+ from monai.data.csv_saver import CSVSaver
25
+ from monai.handlers import ClassificationSaver
26
+
27
+
28
+ class TestHandlerClassificationSaver(unittest.TestCase):
29
+
30
+ def test_saved_content(self):
31
+ with tempfile.TemporaryDirectory() as tempdir:
32
+ # set up engine
33
+ def _train_func(engine, batch):
34
+ engine.state.batch = decollate_batch(batch)
35
+ return [torch.zeros(1) for _ in range(8)]
36
+
37
+ engine = Engine(_train_func)
38
+
39
+ # set up testing handler
40
+ saver = CSVSaver(output_dir=tempdir, filename="predictions2.csv", delimiter="\t")
41
+ ClassificationSaver(output_dir=tempdir, filename="predictions1.csv", delimiter="\t").attach(engine)
42
+ ClassificationSaver(saver=saver).attach(engine)
43
+
44
+ data = [{"filename_or_obj": ["testfile" + str(i) for i in range(8)]}]
45
+ engine.run(data, max_epochs=1)
46
+
47
+ def _test_file(filename):
48
+ filepath = os.path.join(tempdir, filename)
49
+ self.assertTrue(os.path.exists(filepath))
50
+ with open(filepath) as f:
51
+ reader = csv.reader(f, delimiter="\t")
52
+ i = 0
53
+ for row in reader:
54
+ self.assertEqual(row[0], "testfile" + str(i))
55
+ self.assertEqual(np.array(row[1:]).astype(np.float32), 0.0)
56
+ i += 1
57
+ self.assertEqual(i, 8)
58
+
59
+ _test_file("predictions1.csv")
60
+ _test_file("predictions2.csv")
61
+
62
+
63
+ if __name__ == "__main__":
64
+ unittest.main()
@@ -0,0 +1,77 @@
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 csv
15
+ import os
16
+ import tempfile
17
+ import unittest
18
+
19
+ import numpy as np
20
+ import torch
21
+ import torch.distributed as dist
22
+ from ignite.engine import Engine
23
+
24
+ from monai.data import decollate_batch
25
+ from monai.handlers import ClassificationSaver
26
+ from tests.test_utils import DistCall, DistTestCase
27
+
28
+
29
+ class DistributedHandlerClassificationSaver(DistTestCase):
30
+ @DistCall(nnodes=1, nproc_per_node=2)
31
+ def test_saved_content(self):
32
+ with tempfile.TemporaryDirectory() as tempdir:
33
+ rank = dist.get_rank()
34
+
35
+ # set up engine
36
+ def _train_func(engine, batch):
37
+ engine.state.batch = decollate_batch(batch)
38
+ return [torch.zeros(1) for _ in range(8 + rank * 2)]
39
+
40
+ engine = Engine(_train_func)
41
+
42
+ # set up testing handler
43
+ saver = ClassificationSaver(output_dir=tempdir, filename="predictions.csv", save_rank=1)
44
+ saver.attach(engine)
45
+
46
+ # rank 0 has 8 images, rank 1 has 10 images
47
+ data = [
48
+ {
49
+ "filename_or_obj": ["testfile" + str(i) for i in range(8 * rank, (8 + rank) * (rank + 1))],
50
+ "data_shape": torch.ones((8 + rank * 2, 1, 1)),
51
+ }
52
+ ]
53
+ # rank 1 has more iterations
54
+ if rank == 1:
55
+ data.append(
56
+ {
57
+ "filename_or_obj": ["testfile" + str(i) for i in range(18, 28)],
58
+ "data_shape": torch.ones((10, 1, 1)),
59
+ }
60
+ )
61
+
62
+ engine.run(data, max_epochs=1)
63
+ filepath = os.path.join(tempdir, "predictions.csv")
64
+ if rank == 1:
65
+ self.assertTrue(os.path.exists(filepath))
66
+ with open(filepath) as f:
67
+ reader = csv.reader(f)
68
+ i = 0
69
+ for row in reader:
70
+ self.assertEqual(row[0], "testfile" + str(i))
71
+ self.assertEqual(np.array(row[1:]).astype(np.float32), 0.0)
72
+ i += 1
73
+ self.assertEqual(i, 28)
74
+
75
+
76
+ if __name__ == "__main__":
77
+ unittest.main()
@@ -0,0 +1,65 @@
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 tempfile
15
+ import unittest
16
+ from os import environ
17
+
18
+ from monai.handlers import ClearMLImageHandler
19
+ from monai.utils import optional_import
20
+
21
+ Task, has_clearml = optional_import("clearml", name="Task")
22
+ get_active_config_file, has_get_active_config_file = optional_import(
23
+ "clearml.backend_config.defs", name="get_active_config_file"
24
+ )
25
+ _, has_tb = optional_import("torch.utils.tensorboard", name="SummaryWriter")
26
+
27
+
28
+ @unittest.skipUnless(has_clearml, "Requires 'clearml' installation")
29
+ @unittest.skipUnless(has_tb, "Requires SummaryWriter installation")
30
+ @unittest.skipIf(not has_get_active_config_file, "ClearML 'get_active_config_file' not found")
31
+ class TestHandlerClearMLImageHandler(unittest.TestCase):
32
+
33
+ def test_task_init(self):
34
+ handle, path = tempfile.mkstemp()
35
+ with open(handle, "w") as new_config:
36
+ if get_active_config_file():
37
+ with open(get_active_config_file()) as old_config:
38
+ new_config.write(old_config.read())
39
+ new_config.write(
40
+ "\nsdk.development.vcs_repo_detect_async: false\nsdk.development.report_use_subprocess: false\n"
41
+ )
42
+ environ["CLEARML_CONFIG_FILE"] = path
43
+ try:
44
+ Task.force_store_standalone_script(True)
45
+ Task.set_offline(offline_mode=True)
46
+ ClearMLImageHandler(
47
+ project_name="MONAI",
48
+ task_name="monai_experiment",
49
+ output_uri=True,
50
+ tags=None,
51
+ reuse_last_task_id=True,
52
+ continue_last_task=False,
53
+ auto_connect_frameworks=True,
54
+ auto_connect_arg_parser=False,
55
+ )
56
+ except Exception as exc:
57
+ self.fail(exc)
58
+ self.assertEqual(Task.current_task().name, "monai_experiment")
59
+ self.assertEqual(Task.current_task()._project_name[1], "MONAI")
60
+ # Close ClearML Task
61
+ Task.current_task().close()
62
+
63
+
64
+ if __name__ == "__main__":
65
+ unittest.main()
@@ -0,0 +1,65 @@
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 tempfile
15
+ import unittest
16
+ from os import environ
17
+
18
+ from monai.handlers import ClearMLStatsHandler
19
+ from monai.utils import optional_import
20
+
21
+ Task, has_clearml = optional_import("clearml", name="Task")
22
+ get_active_config_file, has_get_active_config_file = optional_import(
23
+ "clearml.backend_config.defs", name="get_active_config_file"
24
+ )
25
+ _, has_tb = optional_import("torch.utils.tensorboard", name="SummaryWriter")
26
+
27
+
28
+ @unittest.skipUnless(has_clearml, "Requires 'clearml' installation")
29
+ @unittest.skipUnless(has_tb, "Requires SummaryWriter installation")
30
+ @unittest.skipIf(not has_get_active_config_file, "ClearML 'get_active_config_file' not found")
31
+ class TestHandlerClearMLStatsHandler(unittest.TestCase):
32
+
33
+ def test_task_init(self):
34
+ handle, path = tempfile.mkstemp()
35
+ with open(handle, "w") as new_config:
36
+ if get_active_config_file():
37
+ with open(get_active_config_file()) as old_config:
38
+ new_config.write(old_config.read())
39
+ new_config.write(
40
+ "\nsdk.development.vcs_repo_detect_async: false\nsdk.development.report_use_subprocess: false\n"
41
+ )
42
+ environ["CLEARML_CONFIG_FILE"] = path
43
+ try:
44
+ Task.force_store_standalone_script(True)
45
+ Task.set_offline(offline_mode=True)
46
+ ClearMLStatsHandler(
47
+ project_name="MONAI",
48
+ task_name="monai_experiment",
49
+ output_uri=True,
50
+ tags=None,
51
+ reuse_last_task_id=True,
52
+ continue_last_task=False,
53
+ auto_connect_frameworks=True,
54
+ auto_connect_arg_parser=False,
55
+ )
56
+ except Exception as exc:
57
+ self.fail(exc)
58
+ self.assertEqual(Task.current_task().name, "monai_experiment")
59
+ self.assertEqual(Task.current_task()._project_name[1], "MONAI")
60
+ # Close ClearML Task
61
+ Task.current_task().close()
62
+
63
+
64
+ if __name__ == "__main__":
65
+ unittest.main()
@@ -0,0 +1,104 @@
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 typing import Any
16
+
17
+ import torch
18
+ from ignite.engine import Engine
19
+ from parameterized import parameterized
20
+
21
+ from monai.handlers import ConfusionMatrix
22
+ from tests.test_utils import assert_allclose
23
+
24
+ TEST_CASE_1 = [{"include_background": True, "save_details": False, "metric_name": "f1"}, 0.75]
25
+ TEST_CASE_2 = [{"include_background": False, "save_details": False, "metric_name": "ppv"}, 1.0]
26
+ TEST_CASE_3 = [{"save_details": False, "metric_name": "f1", "reduction": "mean_batch"}, torch.tensor([0.6667, 0.8000])]
27
+ TEST_CASE_SEG_1 = [{"include_background": True, "metric_name": "tpr"}, 0.7]
28
+
29
+ data_1: dict[Any, Any] = {
30
+ "y_pred": torch.tensor(
31
+ [
32
+ [[[0.0, 1.0], [0.0, 0.0]], [[0.0, 0.0], [1.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]]],
33
+ [[[0.0, 0.0], [0.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]], [[0.0, 1.0], [1.0, 0.0]]],
34
+ ]
35
+ ),
36
+ "y": torch.tensor(
37
+ [
38
+ [[[0.0, 1.0], [0.0, 0.0]], [[0.0, 0.0], [1.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]]],
39
+ [[[0.0, 0.0], [0.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]], [[0.0, 1.0], [1.0, 0.0]]],
40
+ ]
41
+ ),
42
+ }
43
+
44
+ data_2: dict[Any, Any] = {
45
+ "y_pred": torch.tensor([[[[0.0, 1.0], [1.0, 0.0]], [[1.0, 0.0], [1.0, 1.0]], [[0.0, 1.0], [0.0, 0.0]]]]),
46
+ "y": torch.tensor([[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]]),
47
+ }
48
+
49
+
50
+ class TestHandlerConfusionMatrix(unittest.TestCase):
51
+ # TODO test multi node averaged confusion matrix
52
+
53
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3])
54
+ def test_compute(self, input_params, expected_avg):
55
+ metric = ConfusionMatrix(**input_params)
56
+ # test input a list of channel-first tensor
57
+ y_pred = [torch.Tensor([[0], [1]]), torch.Tensor([[1], [0]])]
58
+ y = [torch.Tensor([[0], [1]]), torch.Tensor([[0], [1]])]
59
+ metric.update([y_pred, y])
60
+
61
+ y_pred = torch.Tensor([[[0], [1]], [[1], [0]]])
62
+ y = torch.Tensor([[[0], [1]], [[1], [0]]])
63
+ metric.update([y_pred, y])
64
+
65
+ avg_metric = metric.compute()
66
+ assert_allclose(avg_metric, expected_avg, atol=1e-4, rtol=1e-4, type_test=False)
67
+
68
+ @parameterized.expand([TEST_CASE_SEG_1])
69
+ def test_compute_seg(self, input_params, expected_avg):
70
+ metric = ConfusionMatrix(**input_params)
71
+
72
+ def _val_func(engine, batch):
73
+ pass
74
+
75
+ engine = Engine(_val_func)
76
+ metric.attach(engine, "confusion_matrix")
77
+
78
+ y_pred = data_1["y_pred"]
79
+ y = data_1["y"]
80
+ metric.update([y_pred, y])
81
+
82
+ y_pred = data_2["y_pred"]
83
+ y = data_2["y"]
84
+ metric.update([y_pred, y])
85
+
86
+ avg_metric = metric.compute()
87
+ self.assertAlmostEqual(avg_metric, expected_avg, places=4)
88
+
89
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
90
+ def test_shape_mismatch(self, input_params, _expected):
91
+ metric = ConfusionMatrix(**input_params)
92
+ with self.assertRaises((AssertionError, ValueError)):
93
+ y_pred = torch.Tensor([[0, 1], [1, 0]])
94
+ y = torch.ones((2, 3))
95
+ metric.update([y_pred, y])
96
+
97
+ with self.assertRaises((AssertionError, ValueError)):
98
+ y_pred = torch.Tensor([[0, 1], [1, 0]])
99
+ y = torch.ones((3, 2))
100
+ metric.update([y_pred, y])
101
+
102
+
103
+ if __name__ == "__main__":
104
+ unittest.main()
@@ -0,0 +1,70 @@
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
+ import torch.distributed as dist
19
+ from ignite.engine import Engine
20
+
21
+ from monai.handlers import ConfusionMatrix
22
+ from tests.test_utils import DistCall, DistTestCase
23
+
24
+
25
+ class DistributedConfusionMatrix(DistTestCase):
26
+ @DistCall(nnodes=1, nproc_per_node=2)
27
+ def test_compute(self):
28
+ self._compute()
29
+
30
+ def _compute(self):
31
+ device = f"cuda:{dist.get_rank()}" if torch.cuda.is_available() else "cpu"
32
+ metric = ConfusionMatrix(include_background=True, metric_name="tpr")
33
+
34
+ def _val_func(engine, batch):
35
+ pass
36
+
37
+ engine = Engine(_val_func)
38
+ metric.attach(engine, "confusion_matrix")
39
+ if dist.get_rank() == 0:
40
+ y_pred = torch.tensor(
41
+ [
42
+ [[[0.0, 1.0], [0.0, 0.0]], [[0.0, 0.0], [1.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]]],
43
+ [[[0.0, 0.0], [0.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]], [[0.0, 1.0], [1.0, 0.0]]],
44
+ ],
45
+ device=device,
46
+ )
47
+ y = torch.tensor(
48
+ [
49
+ [[[0.0, 1.0], [0.0, 0.0]], [[0.0, 0.0], [1.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]]],
50
+ [[[0.0, 0.0], [0.0, 1.0]], [[1.0, 0.0], [0.0, 0.0]], [[0.0, 1.0], [1.0, 0.0]]],
51
+ ],
52
+ device=device,
53
+ )
54
+ metric.update([y_pred, y])
55
+
56
+ if dist.get_rank() == 1:
57
+ y_pred = torch.tensor(
58
+ [[[[0.0, 1.0], [1.0, 0.0]], [[1.0, 0.0], [1.0, 1.0]], [[0.0, 1.0], [0.0, 0.0]]]], device=device
59
+ )
60
+ y = torch.tensor(
61
+ [[[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]]], device=device
62
+ )
63
+ metric.update([y_pred, y])
64
+
65
+ avg_metric = metric.compute()
66
+ np.testing.assert_allclose(avg_metric, 0.7, rtol=1e-04, atol=1e-04)
67
+
68
+
69
+ if __name__ == "__main__":
70
+ unittest.main()