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 +1,95 @@
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 torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.networks import eval_mode
20
+ from monai.networks.layers import Act
21
+ from monai.networks.nets import AutoEncoder
22
+ from tests.test_utils import test_script_save
23
+
24
+ device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
25
+
26
+ TEST_CASE_0 = [ # single channel 2D, batch 4, no residual
27
+ {
28
+ "spatial_dims": 2,
29
+ "in_channels": 1,
30
+ "out_channels": 1,
31
+ "channels": (4, 8, 16),
32
+ "strides": (2, 2, 2),
33
+ "num_res_units": 0,
34
+ },
35
+ (1, 1, 128, 128),
36
+ (1, 1, 128, 128),
37
+ ]
38
+
39
+ TEST_CASE_1 = [ # single channel 2D, batch 4
40
+ {"spatial_dims": 2, "in_channels": 1, "out_channels": 1, "channels": (4, 8, 16), "strides": (2, 2, 2)},
41
+ (1, 1, 128, 128),
42
+ (1, 1, 128, 128),
43
+ ]
44
+
45
+ TEST_CASE_2 = [ # 3-channel 2D, batch 4, LeakyReLU activation
46
+ {
47
+ "spatial_dims": 2,
48
+ "in_channels": 3,
49
+ "out_channels": 3,
50
+ "channels": (4, 8, 16),
51
+ "strides": (2, 2, 2),
52
+ "act": (Act.LEAKYRELU, {"negative_slope": 0.2}),
53
+ },
54
+ (1, 3, 128, 128),
55
+ (1, 3, 128, 128),
56
+ ]
57
+
58
+ TEST_CASE_3 = [ # 4-channel 3D, batch 4
59
+ {"spatial_dims": 3, "in_channels": 4, "out_channels": 3, "channels": (4, 8, 16), "strides": (2, 2, 2)},
60
+ (1, 4, 128, 128, 128),
61
+ (1, 3, 128, 128, 128),
62
+ ]
63
+
64
+ CASES = [TEST_CASE_0, TEST_CASE_1, TEST_CASE_2, TEST_CASE_3]
65
+
66
+
67
+ TEST_CASE_FAIL = { # 2-channel 2D, should fail because of stride/channel mismatch.
68
+ "spatial_dims": 2,
69
+ "in_channels": 2,
70
+ "out_channels": 2,
71
+ "channels": (4, 8, 16),
72
+ "strides": (2, 2),
73
+ }
74
+
75
+
76
+ class TestAutoEncoder(unittest.TestCase):
77
+ @parameterized.expand(CASES)
78
+ def test_shape(self, input_param, input_shape, expected_shape):
79
+ net = AutoEncoder(**input_param).to(device)
80
+ with eval_mode(net):
81
+ result = net.forward(torch.randn(input_shape).to(device))
82
+ self.assertEqual(result.shape, expected_shape)
83
+
84
+ def test_script(self):
85
+ net = AutoEncoder(spatial_dims=2, in_channels=1, out_channels=1, channels=(4, 8), strides=(2, 2))
86
+ test_data = torch.randn(2, 1, 32, 32)
87
+ test_script_save(net, test_data)
88
+
89
+ def test_channel_stride_difference(self):
90
+ with self.assertRaises(ValueError):
91
+ AutoEncoder(**TEST_CASE_FAIL)
92
+
93
+
94
+ if __name__ == "__main__":
95
+ unittest.main()
@@ -0,0 +1,337 @@
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
+ from unittest import skipUnless
18
+
19
+ import torch
20
+ from parameterized import parameterized
21
+
22
+ from monai.apps import download_url
23
+ from monai.networks import eval_mode
24
+ from monai.networks.nets import AutoencoderKL
25
+ from monai.utils import optional_import
26
+ from tests.test_utils import SkipIfBeforePyTorchVersion, skip_if_downloading_fails, testing_data_config
27
+
28
+ tqdm, has_tqdm = optional_import("tqdm", name="tqdm")
29
+ _, has_einops = optional_import("einops")
30
+
31
+ device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
32
+
33
+
34
+ CASES_NO_ATTENTION = [
35
+ [
36
+ {
37
+ "spatial_dims": 2,
38
+ "in_channels": 1,
39
+ "out_channels": 1,
40
+ "channels": (4, 4, 4),
41
+ "latent_channels": 4,
42
+ "attention_levels": (False, False, False),
43
+ "num_res_blocks": 1,
44
+ "norm_num_groups": 4,
45
+ "with_encoder_nonlocal_attn": False,
46
+ "with_decoder_nonlocal_attn": False,
47
+ },
48
+ (1, 1, 16, 16),
49
+ (1, 1, 16, 16),
50
+ (1, 4, 4, 4),
51
+ ],
52
+ [
53
+ {
54
+ "spatial_dims": 3,
55
+ "in_channels": 1,
56
+ "out_channels": 1,
57
+ "channels": (4, 4, 4),
58
+ "latent_channels": 4,
59
+ "attention_levels": (False, False, False),
60
+ "num_res_blocks": 1,
61
+ "norm_num_groups": 4,
62
+ "with_encoder_nonlocal_attn": False,
63
+ "with_decoder_nonlocal_attn": False,
64
+ },
65
+ (1, 1, 16, 16, 16),
66
+ (1, 1, 16, 16, 16),
67
+ (1, 4, 4, 4, 4),
68
+ ],
69
+ ]
70
+
71
+ CASES_ATTENTION = [
72
+ [
73
+ {
74
+ "spatial_dims": 2,
75
+ "in_channels": 1,
76
+ "out_channels": 1,
77
+ "channels": (4, 4, 4),
78
+ "latent_channels": 4,
79
+ "attention_levels": (False, False, False),
80
+ "num_res_blocks": 1,
81
+ "norm_num_groups": 4,
82
+ },
83
+ (1, 1, 16, 16),
84
+ (1, 1, 16, 16),
85
+ (1, 4, 4, 4),
86
+ ],
87
+ [
88
+ {
89
+ "spatial_dims": 2,
90
+ "in_channels": 1,
91
+ "out_channels": 1,
92
+ "channels": (4, 4, 4),
93
+ "latent_channels": 4,
94
+ "attention_levels": (False, False, False),
95
+ "num_res_blocks": (1, 1, 2),
96
+ "norm_num_groups": 4,
97
+ },
98
+ (1, 1, 16, 16),
99
+ (1, 1, 16, 16),
100
+ (1, 4, 4, 4),
101
+ ],
102
+ [
103
+ {
104
+ "spatial_dims": 2,
105
+ "in_channels": 1,
106
+ "out_channels": 1,
107
+ "channels": (4, 4, 4),
108
+ "latent_channels": 4,
109
+ "attention_levels": (False, False, False),
110
+ "num_res_blocks": 1,
111
+ "norm_num_groups": 4,
112
+ },
113
+ (1, 1, 16, 16),
114
+ (1, 1, 16, 16),
115
+ (1, 4, 4, 4),
116
+ ],
117
+ [
118
+ {
119
+ "spatial_dims": 2,
120
+ "in_channels": 1,
121
+ "out_channels": 1,
122
+ "channels": (4, 4, 4),
123
+ "latent_channels": 4,
124
+ "attention_levels": (False, False, False),
125
+ "num_res_blocks": 1,
126
+ "norm_num_groups": 4,
127
+ "with_encoder_nonlocal_attn": False,
128
+ },
129
+ (1, 1, 16, 16),
130
+ (1, 1, 16, 16),
131
+ (1, 4, 4, 4),
132
+ ],
133
+ [
134
+ {
135
+ "spatial_dims": 2,
136
+ "in_channels": 1,
137
+ "out_channels": 1,
138
+ "channels": (4, 4, 4),
139
+ "latent_channels": 4,
140
+ "attention_levels": (False, False, True),
141
+ "num_res_blocks": 1,
142
+ "norm_num_groups": 4,
143
+ },
144
+ (1, 1, 16, 16),
145
+ (1, 1, 16, 16),
146
+ (1, 4, 4, 4),
147
+ ],
148
+ [
149
+ {
150
+ "spatial_dims": 3,
151
+ "in_channels": 1,
152
+ "out_channels": 1,
153
+ "channels": (4, 4, 4),
154
+ "latent_channels": 4,
155
+ "attention_levels": (False, False, True),
156
+ "num_res_blocks": 1,
157
+ "norm_num_groups": 4,
158
+ },
159
+ (1, 1, 16, 16, 16),
160
+ (1, 1, 16, 16, 16),
161
+ (1, 4, 4, 4, 4),
162
+ ],
163
+ ]
164
+
165
+ if has_einops:
166
+ CASES = CASES_NO_ATTENTION + CASES_ATTENTION
167
+ else:
168
+ CASES = CASES_NO_ATTENTION
169
+
170
+
171
+ class TestAutoEncoderKL(unittest.TestCase):
172
+ @parameterized.expand(CASES)
173
+ def test_shape(self, input_param, input_shape, expected_shape, expected_latent_shape):
174
+ net = AutoencoderKL(**input_param).to(device)
175
+ with eval_mode(net):
176
+ result = net.forward(torch.randn(input_shape).to(device))
177
+ self.assertEqual(result[0].shape, expected_shape)
178
+ self.assertEqual(result[1].shape, expected_latent_shape)
179
+ self.assertEqual(result[2].shape, expected_latent_shape)
180
+
181
+ @parameterized.expand(CASES)
182
+ @SkipIfBeforePyTorchVersion((1, 11))
183
+ def test_shape_with_convtranspose_and_checkpointing(
184
+ self, input_param, input_shape, expected_shape, expected_latent_shape
185
+ ):
186
+ input_param = input_param.copy()
187
+ input_param.update({"use_checkpoint": True, "use_convtranspose": True})
188
+ net = AutoencoderKL(**input_param).to(device)
189
+ with eval_mode(net):
190
+ result = net.forward(torch.randn(input_shape).to(device))
191
+ self.assertEqual(result[0].shape, expected_shape)
192
+ self.assertEqual(result[1].shape, expected_latent_shape)
193
+ self.assertEqual(result[2].shape, expected_latent_shape)
194
+
195
+ def test_model_channels_not_multiple_of_norm_num_group(self):
196
+ with self.assertRaises(ValueError):
197
+ AutoencoderKL(
198
+ spatial_dims=2,
199
+ in_channels=1,
200
+ out_channels=1,
201
+ channels=(24, 24, 24),
202
+ attention_levels=(False, False, False),
203
+ latent_channels=8,
204
+ num_res_blocks=1,
205
+ norm_num_groups=16,
206
+ )
207
+
208
+ def test_model_num_channels_not_same_size_of_attention_levels(self):
209
+ with self.assertRaises(ValueError):
210
+ AutoencoderKL(
211
+ spatial_dims=2,
212
+ in_channels=1,
213
+ out_channels=1,
214
+ channels=(24, 24, 24),
215
+ attention_levels=(False, False),
216
+ latent_channels=8,
217
+ num_res_blocks=1,
218
+ norm_num_groups=16,
219
+ )
220
+
221
+ def test_model_num_channels_not_same_size_of_num_res_blocks(self):
222
+ with self.assertRaises(ValueError):
223
+ AutoencoderKL(
224
+ spatial_dims=2,
225
+ in_channels=1,
226
+ out_channels=1,
227
+ channels=(24, 24, 24),
228
+ attention_levels=(False, False, False),
229
+ latent_channels=8,
230
+ num_res_blocks=(8, 8),
231
+ norm_num_groups=16,
232
+ )
233
+
234
+ def test_shape_reconstruction(self):
235
+ input_param, input_shape, expected_shape, _ = CASES[0]
236
+ net = AutoencoderKL(**input_param).to(device)
237
+ with eval_mode(net):
238
+ result = net.reconstruct(torch.randn(input_shape).to(device))
239
+ self.assertEqual(result.shape, expected_shape)
240
+
241
+ @SkipIfBeforePyTorchVersion((1, 11))
242
+ def test_shape_reconstruction_with_convtranspose_and_checkpointing(self):
243
+ input_param, input_shape, expected_shape, _ = CASES[0]
244
+ input_param = input_param.copy()
245
+ input_param.update({"use_checkpoint": True, "use_convtranspose": True})
246
+ net = AutoencoderKL(**input_param).to(device)
247
+ with eval_mode(net):
248
+ result = net.reconstruct(torch.randn(input_shape).to(device))
249
+ self.assertEqual(result.shape, expected_shape)
250
+
251
+ def test_shape_encode(self):
252
+ input_param, input_shape, _, expected_latent_shape = CASES[0]
253
+ net = AutoencoderKL(**input_param).to(device)
254
+ with eval_mode(net):
255
+ result = net.encode(torch.randn(input_shape).to(device))
256
+ self.assertEqual(result[0].shape, expected_latent_shape)
257
+ self.assertEqual(result[1].shape, expected_latent_shape)
258
+
259
+ @SkipIfBeforePyTorchVersion((1, 11))
260
+ def test_shape_encode_with_convtranspose_and_checkpointing(self):
261
+ input_param, input_shape, _, expected_latent_shape = CASES[0]
262
+ input_param = input_param.copy()
263
+ input_param.update({"use_checkpoint": True, "use_convtranspose": True})
264
+ net = AutoencoderKL(**input_param).to(device)
265
+ with eval_mode(net):
266
+ result = net.encode(torch.randn(input_shape).to(device))
267
+ self.assertEqual(result[0].shape, expected_latent_shape)
268
+ self.assertEqual(result[1].shape, expected_latent_shape)
269
+
270
+ def test_shape_sampling(self):
271
+ input_param, _, _, expected_latent_shape = CASES[0]
272
+ net = AutoencoderKL(**input_param).to(device)
273
+ with eval_mode(net):
274
+ result = net.sampling(
275
+ torch.randn(expected_latent_shape).to(device), torch.randn(expected_latent_shape).to(device)
276
+ )
277
+ self.assertEqual(result.shape, expected_latent_shape)
278
+
279
+ @SkipIfBeforePyTorchVersion((1, 11))
280
+ def test_shape_sampling_convtranspose_and_checkpointing(self):
281
+ input_param, _, _, expected_latent_shape = CASES[0]
282
+ input_param = input_param.copy()
283
+ input_param.update({"use_checkpoint": True, "use_convtranspose": True})
284
+ net = AutoencoderKL(**input_param).to(device)
285
+ with eval_mode(net):
286
+ result = net.sampling(
287
+ torch.randn(expected_latent_shape).to(device), torch.randn(expected_latent_shape).to(device)
288
+ )
289
+ self.assertEqual(result.shape, expected_latent_shape)
290
+
291
+ def test_shape_decode(self):
292
+ input_param, expected_input_shape, _, latent_shape = CASES[0]
293
+ net = AutoencoderKL(**input_param).to(device)
294
+ with eval_mode(net):
295
+ result = net.decode(torch.randn(latent_shape).to(device))
296
+ self.assertEqual(result.shape, expected_input_shape)
297
+
298
+ @SkipIfBeforePyTorchVersion((1, 11))
299
+ def test_shape_decode_convtranspose_and_checkpointing(self):
300
+ input_param, expected_input_shape, _, latent_shape = CASES[0]
301
+ input_param = input_param.copy()
302
+ input_param.update({"use_checkpoint": True, "use_convtranspose": True})
303
+ net = AutoencoderKL(**input_param).to(device)
304
+ with eval_mode(net):
305
+ result = net.decode(torch.randn(latent_shape).to(device))
306
+ self.assertEqual(result.shape, expected_input_shape)
307
+
308
+ @skipUnless(has_einops, "Requires einops")
309
+ def test_compatibility_with_monai_generative(self):
310
+ # test loading weights from a model saved in MONAI Generative, version 0.2.3
311
+ with skip_if_downloading_fails():
312
+ net = AutoencoderKL(
313
+ spatial_dims=2,
314
+ in_channels=1,
315
+ out_channels=1,
316
+ channels=(4, 4, 4),
317
+ latent_channels=4,
318
+ attention_levels=(False, False, True),
319
+ num_res_blocks=1,
320
+ norm_num_groups=4,
321
+ ).to(device)
322
+
323
+ tmpdir = tempfile.mkdtemp()
324
+ key = "autoencoderkl_monai_generative_weights"
325
+ url = testing_data_config("models", key, "url")
326
+ hash_type = testing_data_config("models", key, "hash_type")
327
+ hash_val = testing_data_config("models", key, "hash_val")
328
+ filename = "autoencoderkl_monai_generative_weights.pt"
329
+
330
+ weight_path = os.path.join(tmpdir, filename)
331
+ download_url(url=url, filepath=weight_path, hash_val=hash_val, hash_type=hash_type)
332
+
333
+ net.load_old_state_dict(torch.load(weight_path), verbose=False)
334
+
335
+
336
+ if __name__ == "__main__":
337
+ unittest.main()
@@ -0,0 +1,102 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.networks import eval_mode
20
+ from monai.networks.nets import BasicUNet
21
+ from tests.test_utils import test_script_save
22
+
23
+ CASES_1D = []
24
+ for mode in ["pixelshuffle", "nontrainable", "deconv", None]:
25
+ kwargs = {"spatial_dims": 1, "in_channels": 5, "out_channels": 8}
26
+ if mode is not None:
27
+ kwargs["upsample"] = mode # type: ignore
28
+ CASES_1D.append([kwargs, (10, 5, 33), (10, 8, 33)])
29
+
30
+ CASES_2D = []
31
+ for mode in ["pixelshuffle", "nontrainable", "deconv"]:
32
+ for d1 in range(33, 64, 14):
33
+ for d2 in range(63, 33, -21):
34
+ in_channels, out_channels = 2, 3
35
+ CASES_2D.append(
36
+ [
37
+ {
38
+ "spatial_dims": 2,
39
+ "in_channels": in_channels,
40
+ "out_channels": out_channels,
41
+ "features": (12, 12, 13, 14, 15, 16),
42
+ "upsample": mode,
43
+ },
44
+ (2, in_channels, d1, d2),
45
+ (2, out_channels, d1, d2),
46
+ ]
47
+ )
48
+ CASES_3D = [
49
+ [ # single channel 3D, batch 2
50
+ {
51
+ "spatial_dims": 3,
52
+ "in_channels": 1,
53
+ "out_channels": 2,
54
+ "features": (16, 20, 21, 22, 23, 11),
55
+ "upsample": "pixelshuffle",
56
+ },
57
+ (2, 1, 33, 34, 35),
58
+ (2, 2, 33, 34, 35),
59
+ ],
60
+ [ # 2-channel 3D, batch 3
61
+ {
62
+ "spatial_dims": 3,
63
+ "in_channels": 2,
64
+ "out_channels": 7,
65
+ "features": (14, 15, 16, 17, 18, 11),
66
+ "upsample": "deconv",
67
+ },
68
+ (3, 2, 33, 37, 34),
69
+ (3, 7, 33, 37, 34),
70
+ ],
71
+ [ # 4-channel 3D, batch 5
72
+ {
73
+ "spatial_dims": 3,
74
+ "in_channels": 4,
75
+ "out_channels": 2,
76
+ "features": (14, 15, 16, 17, 18, 10),
77
+ "upsample": "nontrainable",
78
+ },
79
+ (5, 4, 34, 35, 37),
80
+ (5, 2, 34, 35, 37),
81
+ ],
82
+ ]
83
+
84
+
85
+ class TestBasicUNET(unittest.TestCase):
86
+ @parameterized.expand(CASES_1D + CASES_2D + CASES_3D)
87
+ def test_shape(self, input_param, input_shape, expected_shape):
88
+ device = "cuda" if torch.cuda.is_available() else "cpu"
89
+ print(input_param)
90
+ net = BasicUNet(**input_param).to(device)
91
+ with eval_mode(net):
92
+ result = net(torch.randn(input_shape).to(device))
93
+ self.assertEqual(result.shape, expected_shape)
94
+
95
+ def test_script(self):
96
+ net = BasicUNet(spatial_dims=2, in_channels=1, out_channels=3)
97
+ test_data = torch.randn(16, 1, 32, 32)
98
+ test_script_save(net, test_data)
99
+
100
+
101
+ if __name__ == "__main__":
102
+ unittest.main()
@@ -0,0 +1,109 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.networks import eval_mode
20
+ from monai.networks.nets import BasicUNetPlusPlus
21
+ from tests.test_utils import test_script_save
22
+
23
+ CASES_1D = []
24
+ for mode in ["pixelshuffle", "nontrainable", "deconv", None]:
25
+ kwargs = {"spatial_dims": 1, "in_channels": 5, "out_channels": 8}
26
+ if mode is not None:
27
+ kwargs["upsample"] = mode # type: ignore
28
+ CASES_1D.append([kwargs, (10, 5, 33), (10, 8, 33)])
29
+
30
+ CASES_2D = []
31
+ for mode in ["pixelshuffle", "nontrainable", "deconv"]:
32
+ for d1 in range(33, 64, 14):
33
+ for d2 in range(63, 33, -21):
34
+ in_channels, out_channels = 2, 3
35
+ CASES_2D.append(
36
+ [
37
+ {
38
+ "spatial_dims": 2,
39
+ "in_channels": in_channels,
40
+ "out_channels": out_channels,
41
+ "features": (12, 12, 13, 14, 15, 16),
42
+ "upsample": mode,
43
+ },
44
+ (2, in_channels, d1, d2),
45
+ (2, out_channels, d1, d2),
46
+ ]
47
+ )
48
+ CASES_3D = [
49
+ [ # single channel 3D, batch 2
50
+ {
51
+ "spatial_dims": 3,
52
+ "in_channels": 1,
53
+ "out_channels": 2,
54
+ "features": (16, 20, 21, 22, 23, 11),
55
+ "upsample": "pixelshuffle",
56
+ },
57
+ (2, 1, 33, 34, 35),
58
+ (2, 2, 33, 34, 35),
59
+ ],
60
+ [ # 2-channel 3D, batch 3
61
+ {
62
+ "spatial_dims": 3,
63
+ "in_channels": 2,
64
+ "out_channels": 7,
65
+ "features": (14, 15, 16, 17, 18, 11),
66
+ "upsample": "deconv",
67
+ },
68
+ (3, 2, 33, 37, 34),
69
+ (3, 7, 33, 37, 34),
70
+ ],
71
+ [ # 4-channel 3D, batch 5
72
+ {
73
+ "spatial_dims": 3,
74
+ "in_channels": 4,
75
+ "out_channels": 2,
76
+ "features": (14, 15, 16, 17, 18, 10),
77
+ "upsample": "nontrainable",
78
+ },
79
+ (5, 4, 34, 35, 37),
80
+ (5, 2, 34, 35, 37),
81
+ ],
82
+ ]
83
+
84
+
85
+ class TestBasicUNETPlusPlus(unittest.TestCase):
86
+ @parameterized.expand(CASES_1D + CASES_2D + CASES_3D)
87
+ def test_shape(self, input_param, input_shape, expected_shape):
88
+ device = "cuda" if torch.cuda.is_available() else "cpu"
89
+ print(input_param)
90
+ net = BasicUNetPlusPlus(**input_param).to(device)
91
+ with eval_mode(net):
92
+ result = net(torch.randn(input_shape).to(device))
93
+ self.assertEqual(result[0].shape, expected_shape)
94
+
95
+ def test_deep_supervision_shape(self):
96
+ net = BasicUNetPlusPlus(spatial_dims=2, deep_supervision=True, in_channels=3, out_channels=3)
97
+ test_data = torch.randn(16, 3, 32, 32)
98
+ with eval_mode(net):
99
+ result = net(test_data)
100
+ self.assertEqual(result[0].shape, test_data.shape)
101
+
102
+ def test_script(self):
103
+ net = BasicUNetPlusPlus(spatial_dims=2, deep_supervision=True, in_channels=1, out_channels=3)
104
+ test_data = torch.randn(16, 1, 32, 32)
105
+ test_script_save(net, test_data)
106
+
107
+
108
+ if __name__ == "__main__":
109
+ unittest.main()
@@ -0,0 +1,55 @@
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
+
20
+ from monai.networks.nets import UNet
21
+ from tests.test_utils import command_line_tests, skip_if_windows
22
+
23
+
24
+ @skip_if_windows
25
+ class TestBundleInit(unittest.TestCase):
26
+ def test_bundle(self):
27
+ with tempfile.TemporaryDirectory() as tempdir:
28
+ net = UNet(2, 1, 1, [4, 8], [2])
29
+ torch.save(net.state_dict(), tempdir + "/test.pt")
30
+
31
+ bundle_root = tempdir + "/test_bundle"
32
+
33
+ cmd = [
34
+ "coverage",
35
+ "run",
36
+ "-m",
37
+ "monai.bundle",
38
+ "init_bundle",
39
+ bundle_root,
40
+ tempdir + "/test.pt",
41
+ "--dataset_license",
42
+ "True",
43
+ ]
44
+ command_line_tests(cmd)
45
+
46
+ self.assertTrue(os.path.exists(bundle_root + "/configs/metadata.json"))
47
+ self.assertTrue(os.path.exists(bundle_root + "/configs/inference.json"))
48
+ self.assertTrue(os.path.exists(bundle_root + "/models/model.pt"))
49
+ self.assertTrue(os.path.exists(bundle_root + "/LICENSE"))
50
+ self.assertTrue(os.path.exists(bundle_root + "/docs/README.md"))
51
+ self.assertTrue(os.path.exists(bundle_root + "/docs/data_license.txt"))
52
+
53
+
54
+ if __name__ == "__main__":
55
+ unittest.main()