monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2508__py3-none-any.whl

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Files changed (787) hide show
  1. monai/__init__.py +1 -1
  2. monai/_version.py +3 -3
  3. monai/apps/auto3dseg/transforms.py +1 -4
  4. monai/data/utils.py +6 -13
  5. monai/handlers/__init__.py +1 -0
  6. monai/handlers/average_precision.py +53 -0
  7. monai/inferers/inferer.py +10 -7
  8. monai/inferers/utils.py +1 -2
  9. monai/losses/dice.py +2 -14
  10. monai/losses/ds_loss.py +1 -3
  11. monai/metrics/__init__.py +1 -0
  12. monai/metrics/average_precision.py +187 -0
  13. monai/networks/layers/simplelayers.py +2 -14
  14. monai/networks/utils.py +4 -16
  15. monai/transforms/compose.py +28 -11
  16. monai/transforms/croppad/array.py +1 -6
  17. monai/transforms/io/array.py +0 -1
  18. monai/transforms/transform.py +15 -6
  19. monai/transforms/utility/array.py +2 -12
  20. monai/transforms/utils.py +1 -2
  21. monai/transforms/utils_pytorch_numpy_unification.py +2 -4
  22. monai/utils/enums.py +3 -2
  23. monai/utils/module.py +6 -6
  24. monai/utils/tf32.py +0 -10
  25. monai/visualize/class_activation_maps.py +5 -8
  26. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/METADATA +21 -17
  27. monai_weekly-1.5.dev2508.dist-info/RECORD +1185 -0
  28. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/top_level.txt +1 -0
  29. tests/apps/__init__.py +10 -0
  30. tests/apps/deepedit/__init__.py +10 -0
  31. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  32. tests/apps/deepgrow/__init__.py +10 -0
  33. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  34. tests/apps/deepgrow/transforms/__init__.py +10 -0
  35. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  36. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  37. tests/apps/detection/__init__.py +10 -0
  38. tests/apps/detection/metrics/__init__.py +10 -0
  39. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  40. tests/apps/detection/networks/__init__.py +10 -0
  41. tests/apps/detection/networks/test_retinanet.py +210 -0
  42. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  43. tests/apps/detection/test_box_transform.py +370 -0
  44. tests/apps/detection/utils/__init__.py +10 -0
  45. tests/apps/detection/utils/test_anchor_box.py +88 -0
  46. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  47. tests/apps/detection/utils/test_box_coder.py +43 -0
  48. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  49. tests/apps/detection/utils/test_detector_utils.py +96 -0
  50. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  51. tests/apps/nuclick/__init__.py +10 -0
  52. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  53. tests/apps/pathology/__init__.py +10 -0
  54. tests/apps/pathology/handlers/__init__.py +10 -0
  55. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  56. tests/apps/pathology/test_lesion_froc.py +333 -0
  57. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  58. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  59. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  60. tests/apps/pathology/transforms/__init__.py +10 -0
  61. tests/apps/pathology/transforms/post/__init__.py +10 -0
  62. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  63. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  64. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  65. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  66. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  67. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  68. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  69. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  70. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  71. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  72. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  73. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  74. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  75. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  76. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  77. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  78. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  79. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  80. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  81. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  82. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  83. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  84. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  85. tests/apps/reconstruction/__init__.py +10 -0
  86. tests/apps/reconstruction/nets/__init__.py +10 -0
  87. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  88. tests/apps/reconstruction/test_complex_utils.py +77 -0
  89. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  90. tests/apps/reconstruction/test_mri_utils.py +37 -0
  91. tests/apps/reconstruction/transforms/__init__.py +10 -0
  92. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  93. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  94. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  95. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  96. tests/apps/test_check_hash.py +53 -0
  97. tests/apps/test_cross_validation.py +74 -0
  98. tests/apps/test_decathlondataset.py +93 -0
  99. tests/apps/test_download_and_extract.py +70 -0
  100. tests/apps/test_download_url_yandex.py +45 -0
  101. tests/apps/test_mednistdataset.py +72 -0
  102. tests/apps/test_mmar_download.py +154 -0
  103. tests/apps/test_tciadataset.py +123 -0
  104. tests/apps/vista3d/__init__.py +10 -0
  105. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  106. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  107. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  108. tests/bundle/__init__.py +10 -0
  109. tests/bundle/test_bundle_ckpt_export.py +107 -0
  110. tests/bundle/test_bundle_download.py +435 -0
  111. tests/bundle/test_bundle_get_data.py +94 -0
  112. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  113. tests/bundle/test_bundle_trt_export.py +147 -0
  114. tests/bundle/test_bundle_utils.py +149 -0
  115. tests/bundle/test_bundle_verify_metadata.py +66 -0
  116. tests/bundle/test_bundle_verify_net.py +76 -0
  117. tests/bundle/test_bundle_workflow.py +272 -0
  118. tests/bundle/test_component_locator.py +38 -0
  119. tests/bundle/test_config_item.py +138 -0
  120. tests/bundle/test_config_parser.py +392 -0
  121. tests/bundle/test_reference_resolver.py +114 -0
  122. tests/config/__init__.py +10 -0
  123. tests/config/test_cv2_dist.py +53 -0
  124. tests/engines/__init__.py +10 -0
  125. tests/engines/test_ensemble_evaluator.py +94 -0
  126. tests/engines/test_prepare_batch_default.py +76 -0
  127. tests/engines/test_prepare_batch_default_dist.py +76 -0
  128. tests/engines/test_prepare_batch_diffusion.py +104 -0
  129. tests/engines/test_prepare_batch_extra_input.py +80 -0
  130. tests/fl/__init__.py +10 -0
  131. tests/fl/monai_algo/__init__.py +10 -0
  132. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  133. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  134. tests/fl/test_fl_monai_algo_stats.py +81 -0
  135. tests/fl/utils/__init__.py +10 -0
  136. tests/fl/utils/test_fl_exchange_object.py +63 -0
  137. tests/handlers/__init__.py +10 -0
  138. tests/handlers/test_handler_average_precision.py +79 -0
  139. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  140. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  141. tests/handlers/test_handler_classification_saver.py +64 -0
  142. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  143. tests/handlers/test_handler_clearml_image.py +65 -0
  144. tests/handlers/test_handler_clearml_stats.py +65 -0
  145. tests/handlers/test_handler_confusion_matrix.py +104 -0
  146. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  147. tests/handlers/test_handler_decollate_batch.py +66 -0
  148. tests/handlers/test_handler_early_stop.py +68 -0
  149. tests/handlers/test_handler_garbage_collector.py +73 -0
  150. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  151. tests/handlers/test_handler_ignite_metric.py +191 -0
  152. tests/handlers/test_handler_lr_scheduler.py +94 -0
  153. tests/handlers/test_handler_mean_dice.py +98 -0
  154. tests/handlers/test_handler_mean_iou.py +76 -0
  155. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  156. tests/handlers/test_handler_metrics_saver.py +89 -0
  157. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  158. tests/handlers/test_handler_mlflow.py +296 -0
  159. tests/handlers/test_handler_nvtx.py +93 -0
  160. tests/handlers/test_handler_panoptic_quality.py +89 -0
  161. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  162. tests/handlers/test_handler_post_processing.py +74 -0
  163. tests/handlers/test_handler_prob_map_producer.py +111 -0
  164. tests/handlers/test_handler_regression_metrics.py +160 -0
  165. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  166. tests/handlers/test_handler_rocauc.py +48 -0
  167. tests/handlers/test_handler_rocauc_dist.py +54 -0
  168. tests/handlers/test_handler_stats.py +281 -0
  169. tests/handlers/test_handler_surface_distance.py +113 -0
  170. tests/handlers/test_handler_tb_image.py +61 -0
  171. tests/handlers/test_handler_tb_stats.py +166 -0
  172. tests/handlers/test_handler_validation.py +59 -0
  173. tests/handlers/test_trt_compile.py +145 -0
  174. tests/handlers/test_write_metrics_reports.py +68 -0
  175. tests/inferers/__init__.py +10 -0
  176. tests/inferers/test_avg_merger.py +179 -0
  177. tests/inferers/test_controlnet_inferers.py +1388 -0
  178. tests/inferers/test_diffusion_inferer.py +236 -0
  179. tests/inferers/test_latent_diffusion_inferer.py +884 -0
  180. tests/inferers/test_patch_inferer.py +309 -0
  181. tests/inferers/test_saliency_inferer.py +55 -0
  182. tests/inferers/test_slice_inferer.py +57 -0
  183. tests/inferers/test_sliding_window_inference.py +377 -0
  184. tests/inferers/test_sliding_window_splitter.py +284 -0
  185. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  186. tests/inferers/test_zarr_avg_merger.py +326 -0
  187. tests/integration/__init__.py +10 -0
  188. tests/integration/test_auto3dseg_ensemble.py +211 -0
  189. tests/integration/test_auto3dseg_hpo.py +189 -0
  190. tests/integration/test_deepedit_interaction.py +122 -0
  191. tests/integration/test_downsample_block.py +50 -0
  192. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  193. tests/integration/test_integration_autorunner.py +201 -0
  194. tests/integration/test_integration_bundle_run.py +240 -0
  195. tests/integration/test_integration_classification_2d.py +282 -0
  196. tests/integration/test_integration_determinism.py +95 -0
  197. tests/integration/test_integration_fast_train.py +231 -0
  198. tests/integration/test_integration_gpu_customization.py +159 -0
  199. tests/integration/test_integration_lazy_samples.py +219 -0
  200. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  201. tests/integration/test_integration_segmentation_3d.py +304 -0
  202. tests/integration/test_integration_sliding_window.py +100 -0
  203. tests/integration/test_integration_stn.py +133 -0
  204. tests/integration/test_integration_unet_2d.py +67 -0
  205. tests/integration/test_integration_workers.py +61 -0
  206. tests/integration/test_integration_workflows.py +365 -0
  207. tests/integration/test_integration_workflows_adversarial.py +173 -0
  208. tests/integration/test_integration_workflows_gan.py +158 -0
  209. tests/integration/test_loader_semaphore.py +48 -0
  210. tests/integration/test_mapping_filed.py +122 -0
  211. tests/integration/test_meta_affine.py +183 -0
  212. tests/integration/test_metatensor_integration.py +114 -0
  213. tests/integration/test_module_list.py +76 -0
  214. tests/integration/test_one_of.py +283 -0
  215. tests/integration/test_pad_collation.py +124 -0
  216. tests/integration/test_reg_loss_integration.py +107 -0
  217. tests/integration/test_retinanet_predict_utils.py +154 -0
  218. tests/integration/test_seg_loss_integration.py +159 -0
  219. tests/integration/test_spatial_combine_transforms.py +185 -0
  220. tests/integration/test_testtimeaugmentation.py +186 -0
  221. tests/integration/test_vis_gradbased.py +69 -0
  222. tests/integration/test_vista3d_utils.py +159 -0
  223. tests/losses/__init__.py +10 -0
  224. tests/losses/deform/__init__.py +10 -0
  225. tests/losses/deform/test_bending_energy.py +88 -0
  226. tests/losses/deform/test_diffusion_loss.py +117 -0
  227. tests/losses/image_dissimilarity/__init__.py +10 -0
  228. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  229. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  230. tests/losses/test_adversarial_loss.py +94 -0
  231. tests/losses/test_barlow_twins_loss.py +109 -0
  232. tests/losses/test_cldice_loss.py +51 -0
  233. tests/losses/test_contrastive_loss.py +86 -0
  234. tests/losses/test_dice_ce_loss.py +123 -0
  235. tests/losses/test_dice_focal_loss.py +124 -0
  236. tests/losses/test_dice_loss.py +227 -0
  237. tests/losses/test_ds_loss.py +189 -0
  238. tests/losses/test_focal_loss.py +379 -0
  239. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  240. tests/losses/test_generalized_dice_loss.py +221 -0
  241. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  242. tests/losses/test_giou_loss.py +62 -0
  243. tests/losses/test_hausdorff_loss.py +264 -0
  244. tests/losses/test_masked_dice_loss.py +152 -0
  245. tests/losses/test_masked_loss.py +87 -0
  246. tests/losses/test_multi_scale.py +86 -0
  247. tests/losses/test_nacl_loss.py +167 -0
  248. tests/losses/test_perceptual_loss.py +122 -0
  249. tests/losses/test_spectral_loss.py +86 -0
  250. tests/losses/test_ssim_loss.py +59 -0
  251. tests/losses/test_sure_loss.py +72 -0
  252. tests/losses/test_tversky_loss.py +198 -0
  253. tests/losses/test_unified_focal_loss.py +66 -0
  254. tests/metrics/__init__.py +10 -0
  255. tests/metrics/test_compute_average_precision.py +162 -0
  256. tests/metrics/test_compute_confusion_matrix.py +294 -0
  257. tests/metrics/test_compute_f_beta.py +80 -0
  258. tests/metrics/test_compute_fid_metric.py +40 -0
  259. tests/metrics/test_compute_froc.py +143 -0
  260. tests/metrics/test_compute_generalized_dice.py +240 -0
  261. tests/metrics/test_compute_meandice.py +306 -0
  262. tests/metrics/test_compute_meaniou.py +223 -0
  263. tests/metrics/test_compute_mmd_metric.py +56 -0
  264. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  265. tests/metrics/test_compute_panoptic_quality.py +113 -0
  266. tests/metrics/test_compute_regression_metrics.py +196 -0
  267. tests/metrics/test_compute_roc_auc.py +155 -0
  268. tests/metrics/test_compute_variance.py +147 -0
  269. tests/metrics/test_cumulative.py +63 -0
  270. tests/metrics/test_cumulative_average.py +74 -0
  271. tests/metrics/test_cumulative_average_dist.py +48 -0
  272. tests/metrics/test_hausdorff_distance.py +209 -0
  273. tests/metrics/test_label_quality_score.py +134 -0
  274. tests/metrics/test_loss_metric.py +57 -0
  275. tests/metrics/test_metrics_reloaded.py +96 -0
  276. tests/metrics/test_ssim_metric.py +78 -0
  277. tests/metrics/test_surface_dice.py +416 -0
  278. tests/metrics/test_surface_distance.py +186 -0
  279. tests/networks/__init__.py +10 -0
  280. tests/networks/blocks/__init__.py +10 -0
  281. tests/networks/blocks/dints_block/__init__.py +10 -0
  282. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  283. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  284. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  285. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  286. tests/networks/blocks/test_adn.py +86 -0
  287. tests/networks/blocks/test_convolutions.py +156 -0
  288. tests/networks/blocks/test_crf_cpu.py +513 -0
  289. tests/networks/blocks/test_crf_cuda.py +528 -0
  290. tests/networks/blocks/test_crossattention.py +185 -0
  291. tests/networks/blocks/test_denseblock.py +105 -0
  292. tests/networks/blocks/test_dynunet_block.py +116 -0
  293. tests/networks/blocks/test_fpn_block.py +88 -0
  294. tests/networks/blocks/test_localnet_block.py +121 -0
  295. tests/networks/blocks/test_mlp.py +78 -0
  296. tests/networks/blocks/test_patchembedding.py +212 -0
  297. tests/networks/blocks/test_regunet_block.py +103 -0
  298. tests/networks/blocks/test_se_block.py +85 -0
  299. tests/networks/blocks/test_se_blocks.py +78 -0
  300. tests/networks/blocks/test_segresnet_block.py +57 -0
  301. tests/networks/blocks/test_selfattention.py +232 -0
  302. tests/networks/blocks/test_simple_aspp.py +87 -0
  303. tests/networks/blocks/test_spatialattention.py +55 -0
  304. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  305. tests/networks/blocks/test_text_encoding.py +49 -0
  306. tests/networks/blocks/test_transformerblock.py +90 -0
  307. tests/networks/blocks/test_unetr_block.py +158 -0
  308. tests/networks/blocks/test_upsample_block.py +134 -0
  309. tests/networks/blocks/warp/__init__.py +10 -0
  310. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  311. tests/networks/blocks/warp/test_warp.py +250 -0
  312. tests/networks/layers/__init__.py +10 -0
  313. tests/networks/layers/filtering/__init__.py +10 -0
  314. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  315. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  316. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  317. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  318. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  319. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  320. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  321. tests/networks/layers/test_affine_transform.py +385 -0
  322. tests/networks/layers/test_apply_filter.py +89 -0
  323. tests/networks/layers/test_channel_pad.py +51 -0
  324. tests/networks/layers/test_conjugate_gradient.py +56 -0
  325. tests/networks/layers/test_drop_path.py +46 -0
  326. tests/networks/layers/test_gaussian.py +317 -0
  327. tests/networks/layers/test_gaussian_filter.py +206 -0
  328. tests/networks/layers/test_get_layers.py +65 -0
  329. tests/networks/layers/test_gmm.py +314 -0
  330. tests/networks/layers/test_grid_pull.py +93 -0
  331. tests/networks/layers/test_hilbert_transform.py +131 -0
  332. tests/networks/layers/test_lltm.py +62 -0
  333. tests/networks/layers/test_median_filter.py +52 -0
  334. tests/networks/layers/test_polyval.py +55 -0
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  681. tests/transforms/test_sobel_gradientd.py +212 -0
  682. tests/transforms/test_spacing.py +381 -0
  683. tests/transforms/test_spacingd.py +178 -0
  684. tests/transforms/test_spatial_crop.py +82 -0
  685. tests/transforms/test_spatial_cropd.py +74 -0
  686. tests/transforms/test_spatial_pad.py +57 -0
  687. tests/transforms/test_spatial_padd.py +43 -0
  688. tests/transforms/test_spatial_resample.py +235 -0
  689. tests/transforms/test_squeezedim.py +62 -0
  690. tests/transforms/test_squeezedimd.py +98 -0
  691. tests/transforms/test_std_shift_intensity.py +76 -0
  692. tests/transforms/test_std_shift_intensityd.py +74 -0
  693. tests/transforms/test_threshold_intensity.py +38 -0
  694. tests/transforms/test_threshold_intensityd.py +58 -0
  695. tests/transforms/test_to_contiguous.py +47 -0
  696. tests/transforms/test_to_cupy.py +112 -0
  697. tests/transforms/test_to_cupyd.py +76 -0
  698. tests/transforms/test_to_device.py +42 -0
  699. tests/transforms/test_to_deviced.py +37 -0
  700. tests/transforms/test_to_numpy.py +85 -0
  701. tests/transforms/test_to_numpyd.py +68 -0
  702. tests/transforms/test_to_pil.py +52 -0
  703. tests/transforms/test_to_pild.py +50 -0
  704. tests/transforms/test_to_tensor.py +60 -0
  705. tests/transforms/test_to_tensord.py +71 -0
  706. tests/transforms/test_torchvision.py +66 -0
  707. tests/transforms/test_torchvisiond.py +63 -0
  708. tests/transforms/test_transform.py +62 -0
  709. tests/transforms/test_transpose.py +41 -0
  710. tests/transforms/test_transposed.py +52 -0
  711. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  712. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  713. tests/transforms/test_vote_ensemble.py +84 -0
  714. tests/transforms/test_vote_ensembled.py +107 -0
  715. tests/transforms/test_with_allow_missing_keys.py +76 -0
  716. tests/transforms/test_zoom.py +120 -0
  717. tests/transforms/test_zoomd.py +94 -0
  718. tests/transforms/transform/__init__.py +10 -0
  719. tests/transforms/transform/test_randomizable.py +52 -0
  720. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  721. tests/transforms/utility/__init__.py +10 -0
  722. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  723. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  724. tests/transforms/utility/test_identity.py +29 -0
  725. tests/transforms/utility/test_identityd.py +30 -0
  726. tests/transforms/utility/test_lambda.py +71 -0
  727. tests/transforms/utility/test_lambdad.py +83 -0
  728. tests/transforms/utility/test_rand_lambda.py +87 -0
  729. tests/transforms/utility/test_rand_lambdad.py +77 -0
  730. tests/transforms/utility/test_simulatedelay.py +36 -0
  731. tests/transforms/utility/test_simulatedelayd.py +36 -0
  732. tests/transforms/utility/test_splitdim.py +52 -0
  733. tests/transforms/utility/test_splitdimd.py +96 -0
  734. tests/transforms/utils/__init__.py +10 -0
  735. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  736. tests/transforms/utils/test_get_unique_labels.py +45 -0
  737. tests/transforms/utils/test_print_transform_backends.py +29 -0
  738. tests/transforms/utils/test_soft_clip.py +125 -0
  739. tests/utils/__init__.py +10 -0
  740. tests/utils/enums/__init__.py +10 -0
  741. tests/utils/enums/test_hovernet_loss.py +190 -0
  742. tests/utils/enums/test_ordering.py +289 -0
  743. tests/utils/enums/test_wsireader.py +663 -0
  744. tests/utils/misc/__init__.py +10 -0
  745. tests/utils/misc/test_ensure_tuple.py +53 -0
  746. tests/utils/misc/test_monai_env_vars.py +44 -0
  747. tests/utils/misc/test_monai_utils_misc.py +103 -0
  748. tests/utils/misc/test_str2bool.py +34 -0
  749. tests/utils/misc/test_str2list.py +33 -0
  750. tests/utils/test_alias.py +44 -0
  751. tests/utils/test_component_store.py +73 -0
  752. tests/utils/test_deprecated.py +455 -0
  753. tests/utils/test_enum_bound_interp.py +75 -0
  754. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  755. tests/utils/test_get_package_version.py +34 -0
  756. tests/utils/test_handler_logfile.py +84 -0
  757. tests/utils/test_handler_metric_logger.py +62 -0
  758. tests/utils/test_list_to_dict.py +43 -0
  759. tests/utils/test_look_up_option.py +87 -0
  760. tests/utils/test_optional_import.py +80 -0
  761. tests/utils/test_pad_mode.py +39 -0
  762. tests/utils/test_profiling.py +208 -0
  763. tests/utils/test_rankfilter_dist.py +77 -0
  764. tests/utils/test_require_pkg.py +83 -0
  765. tests/utils/test_sample_slices.py +43 -0
  766. tests/utils/test_set_determinism.py +74 -0
  767. tests/utils/test_squeeze_unsqueeze.py +71 -0
  768. tests/utils/test_state_cacher.py +67 -0
  769. tests/utils/test_torchscript_utils.py +113 -0
  770. tests/utils/test_version.py +91 -0
  771. tests/utils/test_version_after.py +65 -0
  772. tests/utils/type_conversion/__init__.py +10 -0
  773. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  774. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  775. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  776. tests/visualize/__init__.py +10 -0
  777. tests/visualize/test_img2tensorboard.py +46 -0
  778. tests/visualize/test_occlusion_sensitivity.py +128 -0
  779. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  780. tests/visualize/test_vis_cam.py +98 -0
  781. tests/visualize/test_vis_gradcam.py +211 -0
  782. tests/visualize/utils/__init__.py +10 -0
  783. tests/visualize/utils/test_blend_images.py +63 -0
  784. tests/visualize/utils/test_matshow3d.py +133 -0
  785. monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
  786. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/LICENSE +0 -0
  787. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2508.dist-info}/WHEEL +0 -0
@@ -0,0 +1,282 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import os
15
+ import unittest
16
+ import warnings
17
+
18
+ import numpy as np
19
+ import torch
20
+ from torch.utils.data import DataLoader
21
+
22
+ import monai
23
+ from monai.apps import download_and_extract
24
+ from monai.data import decollate_batch
25
+ from monai.metrics import ROCAUCMetric
26
+ from monai.networks import eval_mode
27
+ from monai.networks.nets import DenseNet121
28
+ from monai.transforms import (
29
+ Activations,
30
+ AsDiscrete,
31
+ Compose,
32
+ EnsureChannelFirst,
33
+ LoadImage,
34
+ RandFlip,
35
+ RandRotate,
36
+ RandZoom,
37
+ ScaleIntensity,
38
+ Transpose,
39
+ )
40
+ from monai.utils import set_determinism
41
+ from tests.test_utils import DistTestCase, TimedCall, skip_if_downloading_fails, skip_if_quick, testing_data_config
42
+ from tests.testing_data.integration_answers import test_integration_value
43
+
44
+ TASK = "integration_classification_2d"
45
+
46
+
47
+ class MedNISTDataset(torch.utils.data.Dataset):
48
+ def __init__(self, image_files, labels, transforms):
49
+ self.image_files = image_files
50
+ self.labels = labels
51
+ self.transforms = transforms
52
+
53
+ def __len__(self):
54
+ return len(self.image_files)
55
+
56
+ def __getitem__(self, index):
57
+ return self.transforms(self.image_files[index]), self.labels[index]
58
+
59
+
60
+ def run_training_test(root_dir, train_x, train_y, val_x, val_y, device="cuda:0", num_workers=10):
61
+ monai.config.print_config()
62
+ # define transforms for image and classification
63
+ train_transforms = Compose(
64
+ [
65
+ LoadImage(image_only=True, simple_keys=True),
66
+ EnsureChannelFirst(channel_dim="no_channel"),
67
+ Transpose(indices=[0, 2, 1]),
68
+ ScaleIntensity(),
69
+ RandRotate(range_x=np.pi / 12, prob=0.5, keep_size=True, dtype=np.float64),
70
+ RandFlip(spatial_axis=0, prob=0.5),
71
+ RandZoom(min_zoom=0.9, max_zoom=1.1, prob=0.5),
72
+ ]
73
+ )
74
+ train_transforms.set_random_state(1234)
75
+ val_transforms = Compose(
76
+ [
77
+ LoadImage(image_only=True, simple_keys=True),
78
+ EnsureChannelFirst(channel_dim="no_channel"),
79
+ Transpose(indices=[0, 2, 1]),
80
+ ScaleIntensity(),
81
+ ]
82
+ )
83
+ y_pred_trans = Compose([Activations(softmax=True)])
84
+ y_trans = AsDiscrete(to_onehot=len(np.unique(train_y)))
85
+ auc_metric = ROCAUCMetric()
86
+
87
+ # create train, val data loaders
88
+ train_ds = MedNISTDataset(train_x, train_y, train_transforms)
89
+ train_loader = DataLoader(train_ds, batch_size=300, shuffle=True, num_workers=num_workers)
90
+
91
+ val_ds = MedNISTDataset(val_x, val_y, val_transforms)
92
+ val_loader = DataLoader(val_ds, batch_size=300, num_workers=num_workers)
93
+
94
+ model = DenseNet121(spatial_dims=2, in_channels=1, out_channels=len(np.unique(train_y))).to(device)
95
+ loss_function = torch.nn.CrossEntropyLoss()
96
+ optimizer = torch.optim.Adam(model.parameters(), 1e-5)
97
+ epoch_num = 1
98
+ val_interval = 1
99
+
100
+ # start training validation
101
+ best_metric = -1
102
+ best_metric_epoch = -1
103
+ epoch_loss_values = []
104
+ metric_values = []
105
+ model_filename = os.path.join(root_dir, "best_metric_model.pth")
106
+ for epoch in range(epoch_num):
107
+ print("-" * 10)
108
+ print(f"Epoch {epoch + 1}/{epoch_num}")
109
+ model.train()
110
+ epoch_loss = 0
111
+ step = 0
112
+ for batch_data in train_loader:
113
+ step += 1
114
+ inputs, labels = batch_data[0].to(device), batch_data[1].to(device)
115
+ optimizer.zero_grad()
116
+ outputs = model(inputs)
117
+ loss = loss_function(outputs, labels)
118
+ loss.backward()
119
+ optimizer.step()
120
+ epoch_loss += loss.item()
121
+ epoch_loss /= step
122
+ epoch_loss_values.append(epoch_loss)
123
+ print(f"epoch {epoch + 1} average loss:{epoch_loss:0.4f}")
124
+
125
+ if (epoch + 1) % val_interval == 0:
126
+ with eval_mode(model):
127
+ y_pred = torch.tensor([], dtype=torch.float32, device=device)
128
+ y = torch.tensor([], dtype=torch.long, device=device)
129
+ for val_data in val_loader:
130
+ val_images, val_labels = (val_data[0].to(device), val_data[1].to(device))
131
+ y_pred = torch.cat([y_pred, model(val_images)], dim=0)
132
+ y = torch.cat([y, val_labels], dim=0)
133
+
134
+ # compute accuracy
135
+ acc_value = torch.eq(y_pred.argmax(dim=1), y)
136
+ acc_metric = acc_value.sum().item() / len(acc_value)
137
+ # decollate prediction and label and execute post processing
138
+ y_pred = [y_pred_trans(i) for i in decollate_batch(y_pred)]
139
+ y = [y_trans(i) for i in decollate_batch(y, detach=False)]
140
+ # compute AUC
141
+ auc_metric(y_pred, y)
142
+ auc_value = auc_metric.aggregate()
143
+ auc_metric.reset()
144
+ metric_values.append(auc_value)
145
+ if auc_value > best_metric:
146
+ best_metric = auc_value
147
+ best_metric_epoch = epoch + 1
148
+ torch.save(model.state_dict(), model_filename)
149
+ print("saved new best metric model")
150
+ print(
151
+ f"current epoch {epoch + 1} current AUC: {auc_value:0.4f} "
152
+ f"current accuracy: {acc_metric:0.4f} best AUC: {best_metric:0.4f} at epoch {best_metric_epoch}"
153
+ )
154
+ print(f"train completed, best_metric: {best_metric:0.4f} at epoch: {best_metric_epoch}")
155
+ return epoch_loss_values, best_metric, best_metric_epoch
156
+
157
+
158
+ def run_inference_test(root_dir, test_x, test_y, device="cuda:0", num_workers=10):
159
+ # define transforms for image and classification
160
+ val_transforms = Compose(
161
+ [LoadImage(image_only=True), EnsureChannelFirst(channel_dim="no_channel"), ScaleIntensity()]
162
+ )
163
+ val_ds = MedNISTDataset(test_x, test_y, val_transforms)
164
+ val_loader = DataLoader(val_ds, batch_size=300, num_workers=num_workers)
165
+
166
+ model = DenseNet121(spatial_dims=2, in_channels=1, out_channels=len(np.unique(test_y))).to(device)
167
+
168
+ model_filename = os.path.join(root_dir, "best_metric_model.pth")
169
+ model.load_state_dict(torch.load(model_filename))
170
+ y_true = []
171
+ y_pred = []
172
+ with eval_mode(model):
173
+ for test_data in val_loader:
174
+ test_images, test_labels = test_data[0].to(device), test_data[1].to(device)
175
+ pred = model(test_images).argmax(dim=1)
176
+ for i in range(len(pred)):
177
+ y_true.append(test_labels[i].item())
178
+ y_pred.append(pred[i].item())
179
+ tps = [np.sum((np.asarray(y_true) == idx) & (np.asarray(y_pred) == idx)) for idx in np.unique(test_y)]
180
+ return tps
181
+
182
+
183
+ @skip_if_quick
184
+ class IntegrationClassification2D(DistTestCase):
185
+ def setUp(self):
186
+ set_determinism(seed=0)
187
+ self.data_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "../testing_data")
188
+ data_dir = os.path.join(self.data_dir, "MedNIST")
189
+ dataset_file = os.path.join(self.data_dir, "MedNIST.tar.gz")
190
+
191
+ if not os.path.exists(data_dir):
192
+ with skip_if_downloading_fails():
193
+ data_spec = testing_data_config("images", "mednist")
194
+ download_and_extract(
195
+ data_spec["url"],
196
+ dataset_file,
197
+ self.data_dir,
198
+ hash_val=data_spec["hash_val"],
199
+ hash_type=data_spec["hash_type"],
200
+ )
201
+
202
+ assert os.path.exists(data_dir)
203
+
204
+ class_names = sorted(x for x in os.listdir(data_dir) if os.path.isdir(os.path.join(data_dir, x)))
205
+ image_files = [
206
+ [os.path.join(data_dir, class_name, x) for x in sorted(os.listdir(os.path.join(data_dir, class_name)))]
207
+ for class_name in class_names
208
+ ]
209
+ image_file_list, image_classes = [], []
210
+ for i, _ in enumerate(class_names):
211
+ image_file_list.extend(image_files[i])
212
+ image_classes.extend([i] * len(image_files[i]))
213
+
214
+ # split train, val, test
215
+ valid_frac, test_frac = 0.1, 0.1
216
+ self.train_x, self.train_y = [], []
217
+ self.val_x, self.val_y = [], []
218
+ self.test_x, self.test_y = [], []
219
+ for i in range(len(image_classes)):
220
+ rann = np.random.random()
221
+ if rann < valid_frac:
222
+ self.val_x.append(image_file_list[i])
223
+ self.val_y.append(image_classes[i])
224
+ elif rann < test_frac + valid_frac:
225
+ self.test_x.append(image_file_list[i])
226
+ self.test_y.append(image_classes[i])
227
+ else:
228
+ self.train_x.append(image_file_list[i])
229
+ self.train_y.append(image_classes[i])
230
+
231
+ self.device = "cuda:0" if torch.cuda.is_available() else "cpu:0"
232
+
233
+ def tearDown(self):
234
+ set_determinism(seed=None)
235
+ try:
236
+ os.remove(os.path.join(self.data_dir, "best_metric_model.pth"))
237
+ except FileNotFoundError:
238
+ warnings.warn("not found best_metric_model.pth, training skipped?")
239
+ pass
240
+
241
+ def train_and_infer(self, idx=0):
242
+ results = []
243
+ if not os.path.exists(os.path.join(self.data_dir, "MedNIST")):
244
+ # skip test if no MedNIST dataset
245
+ return results
246
+
247
+ set_determinism(seed=0)
248
+ losses, best_metric, best_metric_epoch = run_training_test(
249
+ self.data_dir, self.train_x, self.train_y, self.val_x, self.val_y, device=self.device
250
+ )
251
+ infer_metric = run_inference_test(self.data_dir, self.test_x, self.test_y, device=self.device)
252
+
253
+ print(f"integration_classification_2d {losses}")
254
+ print("best metric", best_metric)
255
+ print("infer metric", infer_metric)
256
+ # check training properties
257
+ self.assertTrue(test_integration_value(TASK, key="losses", data=losses, rtol=1e-2))
258
+ self.assertTrue(test_integration_value(TASK, key="best_metric", data=best_metric, rtol=1e-4))
259
+ np.testing.assert_allclose(best_metric_epoch, 4)
260
+ model_file = os.path.join(self.data_dir, "best_metric_model.pth")
261
+ self.assertTrue(os.path.exists(model_file))
262
+ # check inference properties
263
+ self.assertTrue(test_integration_value(TASK, key="infer_prop", data=np.asarray(infer_metric), rtol=1))
264
+ results.extend(losses)
265
+ results.append(best_metric)
266
+ results.extend(infer_metric)
267
+ return results
268
+
269
+ def test_training(self):
270
+ repeated = []
271
+ for i in range(1):
272
+ results = self.train_and_infer(i)
273
+ repeated.append(results)
274
+ np.testing.assert_allclose(repeated[0], repeated[1])
275
+
276
+ @TimedCall(seconds=2000, skip_timing=not torch.cuda.is_available(), force_quit=False, daemon=False)
277
+ def test_timing(self):
278
+ self.train_and_infer()
279
+
280
+
281
+ if __name__ == "__main__":
282
+ unittest.main()
@@ -0,0 +1,95 @@
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 torch.utils.data import DataLoader, Dataset
19
+
20
+ from monai.data import create_test_image_2d
21
+ from monai.losses import DiceLoss
22
+ from monai.networks.nets import UNet
23
+ from monai.transforms import Compose, EnsureChannelFirst, RandRotate90, RandSpatialCrop, ScaleIntensity
24
+ from monai.utils import set_determinism
25
+ from tests.test_utils import DistTestCase, TimedCall
26
+
27
+
28
+ def run_test(batch_size=64, train_steps=200, device="cuda:0"):
29
+ class _TestBatch(Dataset):
30
+ def __init__(self, transforms):
31
+ self.transforms = transforms
32
+
33
+ def __getitem__(self, _unused_id):
34
+ im, seg = create_test_image_2d(128, 128, noise_max=1, num_objs=4, num_seg_classes=1)
35
+ seed = np.random.randint(2147483647)
36
+ self.transforms.set_random_state(seed=seed)
37
+ im = self.transforms(im)
38
+ self.transforms.set_random_state(seed=seed)
39
+ seg = self.transforms(seg)
40
+ return im, seg
41
+
42
+ def __len__(self):
43
+ return train_steps
44
+
45
+ net = UNet(
46
+ spatial_dims=2, in_channels=1, out_channels=1, channels=(4, 8, 16, 32), strides=(2, 2, 2), num_res_units=2
47
+ ).to(device)
48
+
49
+ loss = DiceLoss(sigmoid=True)
50
+ opt = torch.optim.Adam(net.parameters(), 1e-2)
51
+ train_transforms = Compose(
52
+ [
53
+ EnsureChannelFirst(channel_dim="no_channel"),
54
+ ScaleIntensity(),
55
+ RandSpatialCrop((96, 96), random_size=False),
56
+ RandRotate90(),
57
+ ]
58
+ )
59
+
60
+ src = DataLoader(_TestBatch(train_transforms), batch_size=batch_size, shuffle=True)
61
+
62
+ net.train()
63
+ epoch_loss = 0
64
+ step = 0
65
+ for img, seg in src:
66
+ step += 1
67
+ opt.zero_grad()
68
+ output = net(img.to(device))
69
+ step_loss = loss(output, seg.to(device))
70
+ step_loss.backward()
71
+ opt.step()
72
+ epoch_loss += step_loss.item()
73
+ epoch_loss /= step
74
+
75
+ return epoch_loss, step
76
+
77
+
78
+ class TestDeterminism(DistTestCase):
79
+ def setUp(self):
80
+ self.device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu:0")
81
+
82
+ def tearDown(self):
83
+ set_determinism(seed=None)
84
+
85
+ @TimedCall(seconds=150, skip_timing=not torch.cuda.is_available())
86
+ def test_training(self):
87
+ set_determinism(seed=0)
88
+ loss, step = run_test(device=self.device)
89
+ print(f"Deterministic loss {loss} at training step {step}")
90
+ np.testing.assert_allclose(step, 4)
91
+ np.testing.assert_allclose(loss, 0.536134, rtol=1e-4)
92
+
93
+
94
+ if __name__ == "__main__":
95
+ unittest.main()
@@ -0,0 +1,231 @@
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 math
15
+ import os
16
+ import shutil
17
+ import tempfile
18
+ import time
19
+ import unittest
20
+ from glob import glob
21
+
22
+ import nibabel as nib
23
+ import numpy as np
24
+ import torch
25
+
26
+ import monai
27
+ from monai.data import CacheDataset, ThreadDataLoader, create_test_image_3d, decollate_batch
28
+ from monai.inferers import sliding_window_inference
29
+ from monai.losses import DiceCELoss
30
+ from monai.metrics import DiceMetric
31
+ from monai.networks.layers import Norm
32
+ from monai.networks.nets import UNet
33
+ from monai.optimizers import Novograd
34
+ from monai.transforms import (
35
+ AsDiscrete,
36
+ Compose,
37
+ CropForegroundd,
38
+ EnsureChannelFirstd,
39
+ FgBgToIndicesd,
40
+ LoadImaged,
41
+ RandAffined,
42
+ RandAxisFlipd,
43
+ RandCropByPosNegLabeld,
44
+ RandFlipd,
45
+ RandGaussianNoised,
46
+ RandRotate90d,
47
+ RandRotated,
48
+ RandStdShiftIntensityd,
49
+ RandZoomd,
50
+ ScaleIntensityd,
51
+ Spacingd,
52
+ ToDeviced,
53
+ )
54
+ from monai.utils import set_determinism
55
+ from tests.test_utils import DistTestCase, TimedCall, skip_if_no_cuda, skip_if_quick
56
+
57
+
58
+ @skip_if_no_cuda
59
+ @skip_if_quick
60
+ class IntegrationFastTrain(DistTestCase):
61
+ def setUp(self):
62
+ set_determinism(seed=0)
63
+ monai.config.print_config()
64
+
65
+ self.data_dir = tempfile.mkdtemp()
66
+ for i in range(41):
67
+ im, seg = create_test_image_3d(128, 128, 128, num_seg_classes=1, channel_dim=-1)
68
+ n = nib.Nifti1Image(im, np.eye(4))
69
+ nib.save(n, os.path.join(self.data_dir, f"img{i:d}.nii.gz"))
70
+ n = nib.Nifti1Image(seg, np.eye(4))
71
+ nib.save(n, os.path.join(self.data_dir, f"seg{i:d}.nii.gz"))
72
+
73
+ def tearDown(self):
74
+ set_determinism(seed=None)
75
+ shutil.rmtree(self.data_dir)
76
+
77
+ # test the fast training speed is as expected
78
+ @TimedCall(seconds=100, daemon=False, force_quit=False)
79
+ def test_train_timing(self):
80
+ images = sorted(glob(os.path.join(self.data_dir, "img*.nii.gz")))
81
+ segs = sorted(glob(os.path.join(self.data_dir, "seg*.nii.gz")))
82
+ train_files = [{"image": img, "label": seg} for img, seg in zip(images[:32], segs[:32])]
83
+ val_files = [{"image": img, "label": seg} for img, seg in zip(images[-9:], segs[-9:])]
84
+
85
+ device = torch.device("cuda:0")
86
+ # define transforms for train and validation
87
+ train_transforms = Compose(
88
+ [
89
+ LoadImaged(keys=["image", "label"]),
90
+ EnsureChannelFirstd(keys=["image", "label"]),
91
+ Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "nearest")),
92
+ ScaleIntensityd(keys="image"),
93
+ CropForegroundd(keys=["image", "label"], source_key="image"),
94
+ # pre-compute foreground and background indexes
95
+ # and cache them to accelerate training
96
+ FgBgToIndicesd(keys="label", fg_postfix="_fg", bg_postfix="_bg"),
97
+ # move the data to GPU and cache to avoid CPU -> GPU sync in every epoch
98
+ ToDeviced(keys=["image", "label"], device=device),
99
+ # randomly crop out patch samples from big
100
+ # image based on pos / neg ratio
101
+ # the image centers of negative samples
102
+ # must be in valid image area
103
+ RandCropByPosNegLabeld(
104
+ keys=["image", "label"],
105
+ label_key="label",
106
+ spatial_size=(64, 64, 64),
107
+ pos=1,
108
+ neg=1,
109
+ num_samples=4,
110
+ fg_indices_key="label_fg",
111
+ bg_indices_key="label_bg",
112
+ ),
113
+ RandFlipd(keys=["image", "label"], prob=0.5, spatial_axis=[1, 2]),
114
+ RandAxisFlipd(keys=["image", "label"], prob=0.5),
115
+ RandRotate90d(keys=["image", "label"], prob=0.5, spatial_axes=(1, 2)),
116
+ RandZoomd(keys=["image", "label"], prob=0.5, min_zoom=0.8, max_zoom=1.2, keep_size=True),
117
+ RandRotated(
118
+ keys=["image", "label"],
119
+ prob=0.5,
120
+ range_x=np.pi / 4,
121
+ mode=("bilinear", "nearest"),
122
+ align_corners=True,
123
+ dtype=np.float64,
124
+ ),
125
+ RandAffined(keys=["image", "label"], prob=0.5, rotate_range=np.pi / 2, mode=("bilinear", "nearest")),
126
+ RandGaussianNoised(keys="image", prob=0.5),
127
+ RandStdShiftIntensityd(keys="image", prob=0.5, factors=0.05, nonzero=True),
128
+ ]
129
+ )
130
+
131
+ val_transforms = Compose(
132
+ [
133
+ LoadImaged(keys=["image", "label"]),
134
+ EnsureChannelFirstd(keys=["image", "label"]),
135
+ Spacingd(keys=["image", "label"], pixdim=(1.0, 1.0, 1.0), mode=("bilinear", "nearest")),
136
+ ScaleIntensityd(keys="image"),
137
+ CropForegroundd(keys=["image", "label"], source_key="image"),
138
+ # move the data to GPU and cache to avoid CPU -> GPU sync in every epoch
139
+ ToDeviced(keys=["image", "label"], device=device),
140
+ ]
141
+ )
142
+
143
+ max_epochs = 5
144
+ learning_rate = 2e-4
145
+ val_interval = 1 # do validation for every epoch
146
+
147
+ # set CacheDataset, ThreadDataLoader and DiceCE loss for MONAI fast training
148
+ train_ds = CacheDataset(data=train_files, transform=train_transforms, cache_rate=1.0, num_workers=8)
149
+ val_ds = CacheDataset(data=val_files, transform=val_transforms, cache_rate=1.0, runtime_cache=True)
150
+ # disable multi-workers because `ThreadDataLoader` works with multi-threads
151
+ train_loader = ThreadDataLoader(train_ds, num_workers=0, batch_size=4, shuffle=True)
152
+ val_loader = ThreadDataLoader(val_ds, num_workers=0, batch_size=1)
153
+
154
+ loss_function = DiceCELoss(to_onehot_y=True, softmax=True, squared_pred=True, batch=True)
155
+ model = UNet(
156
+ spatial_dims=3,
157
+ in_channels=1,
158
+ out_channels=2,
159
+ channels=(16, 32, 64, 128, 256),
160
+ strides=(2, 2, 2, 2),
161
+ num_res_units=2,
162
+ norm=Norm.BATCH,
163
+ ).to(device)
164
+
165
+ # Novograd paper suggests to use a bigger LR than Adam,
166
+ # because Adam does normalization by element-wise second moments
167
+ optimizer = Novograd(model.parameters(), learning_rate * 10)
168
+ scaler = torch.cuda.amp.GradScaler()
169
+
170
+ post_pred = AsDiscrete(argmax=True, to_onehot=2)
171
+ post_label = AsDiscrete(to_onehot=2)
172
+
173
+ dice_metric = DiceMetric(include_background=True, reduction="mean", get_not_nans=False)
174
+
175
+ best_metric = -1
176
+ total_start = time.time()
177
+ for epoch in range(max_epochs):
178
+ epoch_start = time.time()
179
+ print("-" * 10)
180
+ print(f"epoch {epoch + 1}/{max_epochs}")
181
+ model.train()
182
+ epoch_loss = 0
183
+ step = 0
184
+ for batch_data in train_loader:
185
+ step_start = time.time()
186
+ step += 1
187
+ optimizer.zero_grad()
188
+ # set AMP for training
189
+ with torch.cuda.amp.autocast():
190
+ outputs = model(batch_data["image"])
191
+ loss = loss_function(outputs, batch_data["label"])
192
+ scaler.scale(loss).backward()
193
+ scaler.step(optimizer)
194
+ scaler.update()
195
+ epoch_loss += loss.item()
196
+ epoch_len = math.ceil(len(train_ds) / train_loader.batch_size)
197
+ print(
198
+ f"{step}/{epoch_len}, train_loss: {loss.item():.4f}" f" step time: {(time.time() - step_start):.4f}"
199
+ )
200
+ epoch_loss /= step
201
+ print(f"epoch {epoch + 1} average loss: {epoch_loss:.4f}")
202
+
203
+ if (epoch + 1) % val_interval == 0:
204
+ model.eval()
205
+ with torch.no_grad():
206
+ for val_data in val_loader:
207
+ roi_size = (96, 96, 96)
208
+ sw_batch_size = 4
209
+ # set AMP for validation
210
+ with torch.cuda.amp.autocast():
211
+ val_outputs = sliding_window_inference(val_data["image"], roi_size, sw_batch_size, model)
212
+
213
+ val_outputs = [post_pred(i) for i in decollate_batch(val_outputs)]
214
+ val_labels = [post_label(i) for i in decollate_batch(val_data["label"])]
215
+ dice_metric(y_pred=val_outputs, y=val_labels)
216
+
217
+ metric = dice_metric.aggregate().item()
218
+ dice_metric.reset()
219
+ if metric > best_metric:
220
+ best_metric = metric
221
+ print(f"epoch: {epoch + 1} current mean dice: {metric:.4f}, best mean dice: {best_metric:.4f}")
222
+ print(f"time consuming of epoch {epoch + 1} is: {(time.time() - epoch_start):.4f}")
223
+
224
+ total_time = time.time() - total_start
225
+ print(f"train completed, best_metric: {best_metric:.4f} total time: {total_time:.4f}")
226
+ # test expected metrics
227
+ self.assertGreater(best_metric, 0.95)
228
+
229
+
230
+ if __name__ == "__main__":
231
+ unittest.main()