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

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Files changed (779) hide show
  1. monai/__init__.py +1 -1
  2. monai/_version.py +3 -3
  3. monai/apps/auto3dseg/transforms.py +1 -4
  4. monai/data/meta_tensor.py +5 -0
  5. monai/data/utils.py +6 -13
  6. monai/inferers/utils.py +1 -2
  7. monai/losses/dice.py +2 -14
  8. monai/losses/ds_loss.py +1 -3
  9. monai/networks/layers/simplelayers.py +2 -14
  10. monai/networks/utils.py +4 -16
  11. monai/transforms/compose.py +28 -11
  12. monai/transforms/croppad/array.py +1 -6
  13. monai/transforms/io/array.py +0 -1
  14. monai/transforms/transform.py +15 -6
  15. monai/transforms/utils.py +1 -2
  16. monai/utils/jupyter_utils.py +1 -1
  17. monai/utils/tf32.py +0 -10
  18. monai/visualize/class_activation_maps.py +5 -8
  19. monai/visualize/img2tensorboard.py +2 -2
  20. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
  21. monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
  22. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
  23. tests/apps/__init__.py +10 -0
  24. tests/apps/deepedit/__init__.py +10 -0
  25. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  26. tests/apps/deepgrow/__init__.py +10 -0
  27. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  28. tests/apps/deepgrow/transforms/__init__.py +10 -0
  29. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  30. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  31. tests/apps/detection/__init__.py +10 -0
  32. tests/apps/detection/metrics/__init__.py +10 -0
  33. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  34. tests/apps/detection/networks/__init__.py +10 -0
  35. tests/apps/detection/networks/test_retinanet.py +210 -0
  36. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  37. tests/apps/detection/test_box_transform.py +370 -0
  38. tests/apps/detection/utils/__init__.py +10 -0
  39. tests/apps/detection/utils/test_anchor_box.py +88 -0
  40. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  41. tests/apps/detection/utils/test_box_coder.py +43 -0
  42. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  43. tests/apps/detection/utils/test_detector_utils.py +96 -0
  44. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  45. tests/apps/nuclick/__init__.py +10 -0
  46. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  47. tests/apps/pathology/__init__.py +10 -0
  48. tests/apps/pathology/handlers/__init__.py +10 -0
  49. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  50. tests/apps/pathology/test_lesion_froc.py +333 -0
  51. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  52. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  53. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  54. tests/apps/pathology/transforms/__init__.py +10 -0
  55. tests/apps/pathology/transforms/post/__init__.py +10 -0
  56. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  57. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  58. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  59. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  60. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  61. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  62. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  63. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  64. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  65. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  66. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  67. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  68. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  69. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  70. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  71. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  72. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  73. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  74. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  75. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  76. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  77. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  78. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  79. tests/apps/reconstruction/__init__.py +10 -0
  80. tests/apps/reconstruction/nets/__init__.py +10 -0
  81. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  82. tests/apps/reconstruction/test_complex_utils.py +77 -0
  83. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  84. tests/apps/reconstruction/test_mri_utils.py +37 -0
  85. tests/apps/reconstruction/transforms/__init__.py +10 -0
  86. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  87. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  88. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  89. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  90. tests/apps/test_check_hash.py +53 -0
  91. tests/apps/test_cross_validation.py +74 -0
  92. tests/apps/test_decathlondataset.py +93 -0
  93. tests/apps/test_download_and_extract.py +70 -0
  94. tests/apps/test_download_url_yandex.py +45 -0
  95. tests/apps/test_mednistdataset.py +72 -0
  96. tests/apps/test_mmar_download.py +154 -0
  97. tests/apps/test_tciadataset.py +123 -0
  98. tests/apps/vista3d/__init__.py +10 -0
  99. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  100. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  101. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  102. tests/bundle/__init__.py +10 -0
  103. tests/bundle/test_bundle_ckpt_export.py +107 -0
  104. tests/bundle/test_bundle_download.py +435 -0
  105. tests/bundle/test_bundle_get_data.py +94 -0
  106. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  107. tests/bundle/test_bundle_trt_export.py +147 -0
  108. tests/bundle/test_bundle_utils.py +149 -0
  109. tests/bundle/test_bundle_verify_metadata.py +66 -0
  110. tests/bundle/test_bundle_verify_net.py +76 -0
  111. tests/bundle/test_bundle_workflow.py +272 -0
  112. tests/bundle/test_component_locator.py +38 -0
  113. tests/bundle/test_config_item.py +138 -0
  114. tests/bundle/test_config_parser.py +392 -0
  115. tests/bundle/test_reference_resolver.py +114 -0
  116. tests/config/__init__.py +10 -0
  117. tests/config/test_cv2_dist.py +53 -0
  118. tests/engines/__init__.py +10 -0
  119. tests/engines/test_ensemble_evaluator.py +94 -0
  120. tests/engines/test_prepare_batch_default.py +76 -0
  121. tests/engines/test_prepare_batch_default_dist.py +76 -0
  122. tests/engines/test_prepare_batch_diffusion.py +104 -0
  123. tests/engines/test_prepare_batch_extra_input.py +80 -0
  124. tests/fl/__init__.py +10 -0
  125. tests/fl/monai_algo/__init__.py +10 -0
  126. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  127. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  128. tests/fl/test_fl_monai_algo_stats.py +81 -0
  129. tests/fl/utils/__init__.py +10 -0
  130. tests/fl/utils/test_fl_exchange_object.py +63 -0
  131. tests/handlers/__init__.py +10 -0
  132. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  133. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  134. tests/handlers/test_handler_classification_saver.py +64 -0
  135. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  136. tests/handlers/test_handler_clearml_image.py +65 -0
  137. tests/handlers/test_handler_clearml_stats.py +65 -0
  138. tests/handlers/test_handler_confusion_matrix.py +104 -0
  139. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  140. tests/handlers/test_handler_decollate_batch.py +66 -0
  141. tests/handlers/test_handler_early_stop.py +68 -0
  142. tests/handlers/test_handler_garbage_collector.py +73 -0
  143. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  144. tests/handlers/test_handler_ignite_metric.py +191 -0
  145. tests/handlers/test_handler_lr_scheduler.py +94 -0
  146. tests/handlers/test_handler_mean_dice.py +98 -0
  147. tests/handlers/test_handler_mean_iou.py +76 -0
  148. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  149. tests/handlers/test_handler_metrics_saver.py +89 -0
  150. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  151. tests/handlers/test_handler_mlflow.py +296 -0
  152. tests/handlers/test_handler_nvtx.py +93 -0
  153. tests/handlers/test_handler_panoptic_quality.py +89 -0
  154. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  155. tests/handlers/test_handler_post_processing.py +74 -0
  156. tests/handlers/test_handler_prob_map_producer.py +111 -0
  157. tests/handlers/test_handler_regression_metrics.py +160 -0
  158. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  159. tests/handlers/test_handler_rocauc.py +48 -0
  160. tests/handlers/test_handler_rocauc_dist.py +54 -0
  161. tests/handlers/test_handler_stats.py +281 -0
  162. tests/handlers/test_handler_surface_distance.py +113 -0
  163. tests/handlers/test_handler_tb_image.py +61 -0
  164. tests/handlers/test_handler_tb_stats.py +166 -0
  165. tests/handlers/test_handler_validation.py +59 -0
  166. tests/handlers/test_trt_compile.py +145 -0
  167. tests/handlers/test_write_metrics_reports.py +68 -0
  168. tests/inferers/__init__.py +10 -0
  169. tests/inferers/test_avg_merger.py +179 -0
  170. tests/inferers/test_controlnet_inferers.py +1310 -0
  171. tests/inferers/test_diffusion_inferer.py +236 -0
  172. tests/inferers/test_latent_diffusion_inferer.py +824 -0
  173. tests/inferers/test_patch_inferer.py +309 -0
  174. tests/inferers/test_saliency_inferer.py +55 -0
  175. tests/inferers/test_slice_inferer.py +57 -0
  176. tests/inferers/test_sliding_window_inference.py +377 -0
  177. tests/inferers/test_sliding_window_splitter.py +284 -0
  178. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  179. tests/inferers/test_zarr_avg_merger.py +326 -0
  180. tests/integration/__init__.py +10 -0
  181. tests/integration/test_auto3dseg_ensemble.py +211 -0
  182. tests/integration/test_auto3dseg_hpo.py +189 -0
  183. tests/integration/test_deepedit_interaction.py +122 -0
  184. tests/integration/test_downsample_block.py +50 -0
  185. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  186. tests/integration/test_integration_autorunner.py +201 -0
  187. tests/integration/test_integration_bundle_run.py +240 -0
  188. tests/integration/test_integration_classification_2d.py +282 -0
  189. tests/integration/test_integration_determinism.py +95 -0
  190. tests/integration/test_integration_fast_train.py +231 -0
  191. tests/integration/test_integration_gpu_customization.py +159 -0
  192. tests/integration/test_integration_lazy_samples.py +219 -0
  193. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  194. tests/integration/test_integration_segmentation_3d.py +304 -0
  195. tests/integration/test_integration_sliding_window.py +100 -0
  196. tests/integration/test_integration_stn.py +133 -0
  197. tests/integration/test_integration_unet_2d.py +67 -0
  198. tests/integration/test_integration_workers.py +61 -0
  199. tests/integration/test_integration_workflows.py +365 -0
  200. tests/integration/test_integration_workflows_adversarial.py +173 -0
  201. tests/integration/test_integration_workflows_gan.py +158 -0
  202. tests/integration/test_loader_semaphore.py +48 -0
  203. tests/integration/test_mapping_filed.py +122 -0
  204. tests/integration/test_meta_affine.py +183 -0
  205. tests/integration/test_metatensor_integration.py +114 -0
  206. tests/integration/test_module_list.py +76 -0
  207. tests/integration/test_one_of.py +283 -0
  208. tests/integration/test_pad_collation.py +124 -0
  209. tests/integration/test_reg_loss_integration.py +107 -0
  210. tests/integration/test_retinanet_predict_utils.py +154 -0
  211. tests/integration/test_seg_loss_integration.py +159 -0
  212. tests/integration/test_spatial_combine_transforms.py +185 -0
  213. tests/integration/test_testtimeaugmentation.py +186 -0
  214. tests/integration/test_vis_gradbased.py +69 -0
  215. tests/integration/test_vista3d_utils.py +159 -0
  216. tests/losses/__init__.py +10 -0
  217. tests/losses/deform/__init__.py +10 -0
  218. tests/losses/deform/test_bending_energy.py +88 -0
  219. tests/losses/deform/test_diffusion_loss.py +117 -0
  220. tests/losses/image_dissimilarity/__init__.py +10 -0
  221. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  222. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  223. tests/losses/test_adversarial_loss.py +94 -0
  224. tests/losses/test_barlow_twins_loss.py +109 -0
  225. tests/losses/test_cldice_loss.py +51 -0
  226. tests/losses/test_contrastive_loss.py +86 -0
  227. tests/losses/test_dice_ce_loss.py +123 -0
  228. tests/losses/test_dice_focal_loss.py +124 -0
  229. tests/losses/test_dice_loss.py +227 -0
  230. tests/losses/test_ds_loss.py +189 -0
  231. tests/losses/test_focal_loss.py +379 -0
  232. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  233. tests/losses/test_generalized_dice_loss.py +221 -0
  234. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  235. tests/losses/test_giou_loss.py +62 -0
  236. tests/losses/test_hausdorff_loss.py +264 -0
  237. tests/losses/test_masked_dice_loss.py +152 -0
  238. tests/losses/test_masked_loss.py +87 -0
  239. tests/losses/test_multi_scale.py +86 -0
  240. tests/losses/test_nacl_loss.py +167 -0
  241. tests/losses/test_perceptual_loss.py +122 -0
  242. tests/losses/test_spectral_loss.py +86 -0
  243. tests/losses/test_ssim_loss.py +59 -0
  244. tests/losses/test_sure_loss.py +72 -0
  245. tests/losses/test_tversky_loss.py +198 -0
  246. tests/losses/test_unified_focal_loss.py +66 -0
  247. tests/metrics/__init__.py +10 -0
  248. tests/metrics/test_compute_confusion_matrix.py +294 -0
  249. tests/metrics/test_compute_f_beta.py +80 -0
  250. tests/metrics/test_compute_fid_metric.py +40 -0
  251. tests/metrics/test_compute_froc.py +143 -0
  252. tests/metrics/test_compute_generalized_dice.py +240 -0
  253. tests/metrics/test_compute_meandice.py +306 -0
  254. tests/metrics/test_compute_meaniou.py +223 -0
  255. tests/metrics/test_compute_mmd_metric.py +56 -0
  256. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  257. tests/metrics/test_compute_panoptic_quality.py +113 -0
  258. tests/metrics/test_compute_regression_metrics.py +196 -0
  259. tests/metrics/test_compute_roc_auc.py +155 -0
  260. tests/metrics/test_compute_variance.py +147 -0
  261. tests/metrics/test_cumulative.py +63 -0
  262. tests/metrics/test_cumulative_average.py +74 -0
  263. tests/metrics/test_cumulative_average_dist.py +48 -0
  264. tests/metrics/test_hausdorff_distance.py +209 -0
  265. tests/metrics/test_label_quality_score.py +134 -0
  266. tests/metrics/test_loss_metric.py +57 -0
  267. tests/metrics/test_metrics_reloaded.py +96 -0
  268. tests/metrics/test_ssim_metric.py +78 -0
  269. tests/metrics/test_surface_dice.py +416 -0
  270. tests/metrics/test_surface_distance.py +186 -0
  271. tests/networks/__init__.py +10 -0
  272. tests/networks/blocks/__init__.py +10 -0
  273. tests/networks/blocks/dints_block/__init__.py +10 -0
  274. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  275. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  276. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  277. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  278. tests/networks/blocks/test_adn.py +86 -0
  279. tests/networks/blocks/test_convolutions.py +156 -0
  280. tests/networks/blocks/test_crf_cpu.py +513 -0
  281. tests/networks/blocks/test_crf_cuda.py +528 -0
  282. tests/networks/blocks/test_crossattention.py +185 -0
  283. tests/networks/blocks/test_denseblock.py +105 -0
  284. tests/networks/blocks/test_dynunet_block.py +116 -0
  285. tests/networks/blocks/test_fpn_block.py +88 -0
  286. tests/networks/blocks/test_localnet_block.py +121 -0
  287. tests/networks/blocks/test_mlp.py +78 -0
  288. tests/networks/blocks/test_patchembedding.py +212 -0
  289. tests/networks/blocks/test_regunet_block.py +103 -0
  290. tests/networks/blocks/test_se_block.py +85 -0
  291. tests/networks/blocks/test_se_blocks.py +78 -0
  292. tests/networks/blocks/test_segresnet_block.py +57 -0
  293. tests/networks/blocks/test_selfattention.py +232 -0
  294. tests/networks/blocks/test_simple_aspp.py +87 -0
  295. tests/networks/blocks/test_spatialattention.py +55 -0
  296. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  297. tests/networks/blocks/test_text_encoding.py +49 -0
  298. tests/networks/blocks/test_transformerblock.py +90 -0
  299. tests/networks/blocks/test_unetr_block.py +158 -0
  300. tests/networks/blocks/test_upsample_block.py +134 -0
  301. tests/networks/blocks/warp/__init__.py +10 -0
  302. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  303. tests/networks/blocks/warp/test_warp.py +250 -0
  304. tests/networks/layers/__init__.py +10 -0
  305. tests/networks/layers/filtering/__init__.py +10 -0
  306. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  307. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  308. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  309. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  310. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  311. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  312. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  313. tests/networks/layers/test_affine_transform.py +385 -0
  314. tests/networks/layers/test_apply_filter.py +89 -0
  315. tests/networks/layers/test_channel_pad.py +51 -0
  316. tests/networks/layers/test_conjugate_gradient.py +56 -0
  317. tests/networks/layers/test_drop_path.py +46 -0
  318. tests/networks/layers/test_gaussian.py +317 -0
  319. tests/networks/layers/test_gaussian_filter.py +206 -0
  320. tests/networks/layers/test_get_layers.py +65 -0
  321. tests/networks/layers/test_gmm.py +314 -0
  322. tests/networks/layers/test_grid_pull.py +93 -0
  323. tests/networks/layers/test_hilbert_transform.py +131 -0
  324. tests/networks/layers/test_lltm.py +62 -0
  325. tests/networks/layers/test_median_filter.py +52 -0
  326. tests/networks/layers/test_polyval.py +55 -0
  327. tests/networks/layers/test_preset_filters.py +136 -0
  328. tests/networks/layers/test_savitzky_golay_filter.py +141 -0
  329. tests/networks/layers/test_separable_filter.py +87 -0
  330. tests/networks/layers/test_skip_connection.py +48 -0
  331. tests/networks/layers/test_vector_quantizer.py +89 -0
  332. tests/networks/layers/test_weight_init.py +50 -0
  333. tests/networks/nets/__init__.py +10 -0
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  680. tests/transforms/test_spatial_resample.py +235 -0
  681. tests/transforms/test_squeezedim.py +62 -0
  682. tests/transforms/test_squeezedimd.py +98 -0
  683. tests/transforms/test_std_shift_intensity.py +76 -0
  684. tests/transforms/test_std_shift_intensityd.py +74 -0
  685. tests/transforms/test_threshold_intensity.py +38 -0
  686. tests/transforms/test_threshold_intensityd.py +58 -0
  687. tests/transforms/test_to_contiguous.py +47 -0
  688. tests/transforms/test_to_cupy.py +112 -0
  689. tests/transforms/test_to_cupyd.py +76 -0
  690. tests/transforms/test_to_device.py +42 -0
  691. tests/transforms/test_to_deviced.py +37 -0
  692. tests/transforms/test_to_numpy.py +85 -0
  693. tests/transforms/test_to_numpyd.py +68 -0
  694. tests/transforms/test_to_pil.py +52 -0
  695. tests/transforms/test_to_pild.py +50 -0
  696. tests/transforms/test_to_tensor.py +60 -0
  697. tests/transforms/test_to_tensord.py +71 -0
  698. tests/transforms/test_torchvision.py +66 -0
  699. tests/transforms/test_torchvisiond.py +63 -0
  700. tests/transforms/test_transform.py +62 -0
  701. tests/transforms/test_transpose.py +41 -0
  702. tests/transforms/test_transposed.py +52 -0
  703. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  704. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  705. tests/transforms/test_vote_ensemble.py +84 -0
  706. tests/transforms/test_vote_ensembled.py +107 -0
  707. tests/transforms/test_with_allow_missing_keys.py +76 -0
  708. tests/transforms/test_zoom.py +120 -0
  709. tests/transforms/test_zoomd.py +94 -0
  710. tests/transforms/transform/__init__.py +10 -0
  711. tests/transforms/transform/test_randomizable.py +52 -0
  712. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  713. tests/transforms/utility/__init__.py +10 -0
  714. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  715. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  716. tests/transforms/utility/test_identity.py +29 -0
  717. tests/transforms/utility/test_identityd.py +30 -0
  718. tests/transforms/utility/test_lambda.py +71 -0
  719. tests/transforms/utility/test_lambdad.py +83 -0
  720. tests/transforms/utility/test_rand_lambda.py +87 -0
  721. tests/transforms/utility/test_rand_lambdad.py +77 -0
  722. tests/transforms/utility/test_simulatedelay.py +36 -0
  723. tests/transforms/utility/test_simulatedelayd.py +36 -0
  724. tests/transforms/utility/test_splitdim.py +52 -0
  725. tests/transforms/utility/test_splitdimd.py +96 -0
  726. tests/transforms/utils/__init__.py +10 -0
  727. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  728. tests/transforms/utils/test_get_unique_labels.py +45 -0
  729. tests/transforms/utils/test_print_transform_backends.py +29 -0
  730. tests/transforms/utils/test_soft_clip.py +125 -0
  731. tests/utils/__init__.py +10 -0
  732. tests/utils/enums/__init__.py +10 -0
  733. tests/utils/enums/test_hovernet_loss.py +190 -0
  734. tests/utils/enums/test_ordering.py +289 -0
  735. tests/utils/enums/test_wsireader.py +663 -0
  736. tests/utils/misc/__init__.py +10 -0
  737. tests/utils/misc/test_ensure_tuple.py +53 -0
  738. tests/utils/misc/test_monai_env_vars.py +44 -0
  739. tests/utils/misc/test_monai_utils_misc.py +103 -0
  740. tests/utils/misc/test_str2bool.py +34 -0
  741. tests/utils/misc/test_str2list.py +33 -0
  742. tests/utils/test_alias.py +44 -0
  743. tests/utils/test_component_store.py +73 -0
  744. tests/utils/test_deprecated.py +455 -0
  745. tests/utils/test_enum_bound_interp.py +75 -0
  746. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  747. tests/utils/test_get_package_version.py +34 -0
  748. tests/utils/test_handler_logfile.py +84 -0
  749. tests/utils/test_handler_metric_logger.py +62 -0
  750. tests/utils/test_list_to_dict.py +43 -0
  751. tests/utils/test_look_up_option.py +87 -0
  752. tests/utils/test_optional_import.py +80 -0
  753. tests/utils/test_pad_mode.py +39 -0
  754. tests/utils/test_profiling.py +208 -0
  755. tests/utils/test_rankfilter_dist.py +77 -0
  756. tests/utils/test_require_pkg.py +83 -0
  757. tests/utils/test_sample_slices.py +43 -0
  758. tests/utils/test_set_determinism.py +74 -0
  759. tests/utils/test_squeeze_unsqueeze.py +71 -0
  760. tests/utils/test_state_cacher.py +67 -0
  761. tests/utils/test_torchscript_utils.py +113 -0
  762. tests/utils/test_version.py +91 -0
  763. tests/utils/test_version_after.py +65 -0
  764. tests/utils/type_conversion/__init__.py +10 -0
  765. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  766. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  767. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  768. tests/visualize/__init__.py +10 -0
  769. tests/visualize/test_img2tensorboard.py +46 -0
  770. tests/visualize/test_occlusion_sensitivity.py +128 -0
  771. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  772. tests/visualize/test_vis_cam.py +98 -0
  773. tests/visualize/test_vis_gradcam.py +211 -0
  774. tests/visualize/utils/__init__.py +10 -0
  775. tests/visualize/utils/test_blend_images.py +63 -0
  776. tests/visualize/utils/test_matshow3d.py +133 -0
  777. monai_weekly-1.5.dev2505.dist-info/RECORD +0 -427
  778. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
  779. {monai_weekly-1.5.dev2505.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
@@ -0,0 +1,159 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+ from unittest.case import skipUnless
16
+
17
+ import numpy as np
18
+ import torch
19
+ from parameterized import parameterized
20
+
21
+ from monai.transforms.utils import convert_points_to_disc, keep_merge_components_with_points, sample_points_from_label
22
+ from monai.utils import min_version
23
+ from monai.utils.module import optional_import
24
+ from tests.test_utils import skip_if_no_cuda, skip_if_quick
25
+
26
+ cp, has_cp = optional_import("cupy")
27
+ cucim_skimage, has_cucim = optional_import("cucim.skimage")
28
+ measure, has_measure = optional_import("skimage.measure", "0.14.2", min_version)
29
+
30
+ device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
31
+
32
+
33
+ TESTS_SAMPLE_POINTS_FROM_LABEL = []
34
+ for use_center in [True, False]:
35
+ labels = torch.zeros(1, 1, 32, 32, 32)
36
+ labels[0, 0, 5:10, 5:10, 5:10] = 1
37
+ labels[0, 0, 10:15, 10:15, 10:15] = 3
38
+ labels[0, 0, 20:25, 20:25, 20:25] = 5
39
+ TESTS_SAMPLE_POINTS_FROM_LABEL.append(
40
+ [{"labels": labels, "label_set": (1, 3, 5), "use_center": use_center}, (3, 1, 3), (3, 1)]
41
+ )
42
+
43
+ TEST_CONVERT_POINTS_TO_DISC = []
44
+ for radius in [1, 2]:
45
+ for disc in [True, False]:
46
+ image_size = (32, 32, 32)
47
+ point = torch.randn(3, 1, 3)
48
+ point_label = torch.randint(0, 4, (3, 1))
49
+ expected_shape = (point.shape[0], 2, *image_size)
50
+ TEST_CONVERT_POINTS_TO_DISC.append(
51
+ [
52
+ {"image_size": image_size, "point": point, "point_label": point_label, "radius": radius, "disc": disc},
53
+ expected_shape,
54
+ ]
55
+ )
56
+ image_size = (16, 32, 64)
57
+ point = torch.tensor([[[8, 16, 42], [2, 8, 21]]])
58
+ point_label = torch.tensor([[1, 0]])
59
+ expected_shape = (point.shape[0], 2, *image_size)
60
+ TEST_CONVERT_POINTS_TO_DISC.append(
61
+ [
62
+ {"image_size": image_size, "point": point, "point_label": point_label, "radius": radius, "disc": disc},
63
+ expected_shape,
64
+ ]
65
+ )
66
+
67
+ TEST_CONVERT_POINTS_TO_DISC_VALUE = []
68
+ image_size = (16, 32, 64)
69
+ point = torch.tensor([[[8, 16, 42], [2, 8, 21]]])
70
+ point_label = torch.tensor([[1, 0]])
71
+ expected_shape = (point.shape[0], 2, *image_size)
72
+ for radius in [5, 10]:
73
+ for disc in [True, False]:
74
+ TEST_CONVERT_POINTS_TO_DISC_VALUE.append(
75
+ [
76
+ {"image_size": image_size, "point": point, "point_label": point_label, "radius": radius, "disc": disc},
77
+ [point, point_label],
78
+ ]
79
+ )
80
+
81
+
82
+ TEST_LCC_MASK_POINT_TORCH = []
83
+ for bs in [1, 2]:
84
+ for num_points in [1, 3]:
85
+ shape = (bs, 1, 128, 32, 32)
86
+ TEST_LCC_MASK_POINT_TORCH.append(
87
+ [
88
+ {
89
+ "img_pos": torch.randint(0, 2, shape, dtype=torch.bool),
90
+ "img_neg": torch.randint(0, 2, shape, dtype=torch.bool),
91
+ "point_coords": torch.randint(0, 10, (bs, num_points, 3)),
92
+ "point_labels": torch.randint(0, 4, (bs, num_points)),
93
+ },
94
+ shape,
95
+ ]
96
+ )
97
+
98
+ TEST_LCC_MASK_POINT_NP = []
99
+ for bs in [1, 2]:
100
+ for num_points in [1, 3]:
101
+ shape = (bs, 1, 32, 32, 64)
102
+ TEST_LCC_MASK_POINT_NP.append(
103
+ [
104
+ {
105
+ "img_pos": np.random.randint(0, 2, shape, dtype=bool),
106
+ "img_neg": np.random.randint(0, 2, shape, dtype=bool),
107
+ "point_coords": np.random.randint(0, 5, (bs, num_points, 3)),
108
+ "point_labels": np.random.randint(0, 4, (bs, num_points)),
109
+ },
110
+ shape,
111
+ ]
112
+ )
113
+
114
+
115
+ @skipUnless(has_measure or cucim_skimage, "skimage or cucim.skimage required")
116
+ class TestSamplePointsFromLabel(unittest.TestCase):
117
+ @parameterized.expand(TESTS_SAMPLE_POINTS_FROM_LABEL)
118
+ def test_shape(self, input_data, expected_point_shape, expected_point_label_shape):
119
+ point, point_label = sample_points_from_label(**input_data)
120
+ self.assertEqual(point.shape, expected_point_shape)
121
+ self.assertEqual(point_label.shape, expected_point_label_shape)
122
+
123
+
124
+ class TestConvertPointsToDisc(unittest.TestCase):
125
+ @parameterized.expand(TEST_CONVERT_POINTS_TO_DISC)
126
+ def test_shape(self, input_data, expected_shape):
127
+ result = convert_points_to_disc(**input_data)
128
+ self.assertEqual(result.shape, expected_shape)
129
+
130
+ @parameterized.expand(TEST_CONVERT_POINTS_TO_DISC_VALUE)
131
+ def test_value(self, input_data, points):
132
+ result = convert_points_to_disc(**input_data)
133
+ point, point_label = points
134
+ for i in range(point.shape[0]):
135
+ for j in range(point.shape[1]):
136
+ self.assertEqual(result[i, point_label[i, j], point[i, j][0], point[i, j][1], point[i, j][2]], True)
137
+
138
+
139
+ @skipUnless(has_measure or cucim_skimage, "skimage or cucim.skimage required")
140
+ class TestKeepMergeComponentsWithPoints(unittest.TestCase):
141
+ @skip_if_quick
142
+ @skip_if_no_cuda
143
+ @skipUnless(has_cp and cucim_skimage, "cupy and cucim.skimage required")
144
+ @parameterized.expand(TEST_LCC_MASK_POINT_TORCH)
145
+ def test_cp_shape(self, input_data, shape):
146
+ for key in input_data:
147
+ input_data[key] = input_data[key].to(device)
148
+ mask = keep_merge_components_with_points(**input_data)
149
+ self.assertEqual(mask.shape, shape)
150
+
151
+ @skipUnless(has_measure, "skimage required")
152
+ @parameterized.expand(TEST_LCC_MASK_POINT_NP)
153
+ def test_np_shape(self, input_data, shape):
154
+ mask = keep_merge_components_with_points(**input_data)
155
+ self.assertEqual(mask.shape, shape)
156
+
157
+
158
+ if __name__ == "__main__":
159
+ unittest.main()
@@ -0,0 +1,10 @@
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.
@@ -0,0 +1,10 @@
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.
@@ -0,0 +1,88 @@
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 parameterized import parameterized
19
+
20
+ from monai.losses.deform import BendingEnergyLoss
21
+
22
+ device = "cuda" if torch.cuda.is_available() else "cpu"
23
+
24
+ TEST_CASES = [
25
+ [{}, {"pred": torch.ones((1, 3, 5, 5, 5), device=device)}, 0.0],
26
+ [{}, {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5)}, 0.0],
27
+ [
28
+ {"normalize": False},
29
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5) ** 2},
30
+ 4.0,
31
+ ],
32
+ [
33
+ {"normalize": False},
34
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, :].expand(1, 2, 5, 5) ** 2},
35
+ 4.0,
36
+ ],
37
+ [{"normalize": False}, {"pred": torch.arange(0, 5, device=device)[None, None, :].expand(1, 1, 5) ** 2}, 4.0],
38
+ [
39
+ {"normalize": True},
40
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5) ** 2},
41
+ 100.0,
42
+ ],
43
+ [
44
+ {"normalize": True},
45
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, :].expand(1, 2, 5, 5) ** 2},
46
+ 100.0,
47
+ ],
48
+ [{"normalize": True}, {"pred": torch.arange(0, 5, device=device)[None, None, :].expand(1, 1, 5) ** 2}, 100.0],
49
+ ]
50
+
51
+
52
+ class TestBendingEnergy(unittest.TestCase):
53
+
54
+ @parameterized.expand(TEST_CASES)
55
+ def test_shape(self, input_param, input_data, expected_val):
56
+ result = BendingEnergyLoss(**input_param).forward(**input_data)
57
+ np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5)
58
+
59
+ def test_ill_shape(self):
60
+ loss = BendingEnergyLoss()
61
+ # not in 3-d, 4-d, 5-d
62
+ with self.assertRaisesRegex(ValueError, "Expecting 3-d, 4-d or 5-d"):
63
+ loss.forward(torch.ones((1, 3), device=device))
64
+ with self.assertRaisesRegex(ValueError, "Expecting 3-d, 4-d or 5-d"):
65
+ loss.forward(torch.ones((1, 4, 5, 5, 5, 5), device=device))
66
+ with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
67
+ loss.forward(torch.ones((1, 3, 4, 5, 5), device=device))
68
+ with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
69
+ loss.forward(torch.ones((1, 3, 5, 4, 5)))
70
+ with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
71
+ loss.forward(torch.ones((1, 3, 5, 5, 4)))
72
+
73
+ # number of vector components unequal to number of spatial dims
74
+ with self.assertRaisesRegex(ValueError, "Number of vector components"):
75
+ loss.forward(torch.ones((1, 2, 5, 5, 5)))
76
+ with self.assertRaisesRegex(ValueError, "Number of vector components"):
77
+ loss.forward(torch.ones((1, 2, 5, 5, 5)))
78
+
79
+ def test_ill_opts(self):
80
+ pred = torch.rand(1, 3, 5, 5, 5).to(device=device)
81
+ with self.assertRaisesRegex(ValueError, ""):
82
+ BendingEnergyLoss(reduction="unknown")(pred)
83
+ with self.assertRaisesRegex(ValueError, ""):
84
+ BendingEnergyLoss(reduction=None)(pred)
85
+
86
+
87
+ if __name__ == "__main__":
88
+ unittest.main()
@@ -0,0 +1,117 @@
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 parameterized import parameterized
19
+
20
+ from monai.losses.deform import DiffusionLoss
21
+
22
+ device = "cuda" if torch.cuda.is_available() else "cpu"
23
+
24
+ TEST_CASES = [
25
+ # all first partials are zero, so the diffusion loss is also zero
26
+ [{}, {"pred": torch.ones((1, 3, 5, 5, 5), device=device)}, 0.0],
27
+ # all first partials are one, so the diffusion loss is also one
28
+ [{}, {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5)}, 1.0],
29
+ # before expansion, the first partials are 2, 4, 6, so the diffusion loss is (2^2 + 4^2 + 6^2) / 3 = 18.67
30
+ [
31
+ {"normalize": False},
32
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5) ** 2},
33
+ 56.0 / 3.0,
34
+ ],
35
+ # same as the previous case
36
+ [
37
+ {"normalize": False},
38
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, :].expand(1, 2, 5, 5) ** 2},
39
+ 56.0 / 3.0,
40
+ ],
41
+ # same as the previous case
42
+ [{"normalize": False}, {"pred": torch.arange(0, 5, device=device)[None, None, :].expand(1, 1, 5) ** 2}, 56.0 / 3.0],
43
+ # we have shown in the demo notebook that
44
+ # diffusion loss is scale-invariant when the all axes have the same resolution
45
+ [
46
+ {"normalize": True},
47
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, None, :].expand(1, 3, 5, 5, 5) ** 2},
48
+ 56.0 / 3.0,
49
+ ],
50
+ [
51
+ {"normalize": True},
52
+ {"pred": torch.arange(0, 5, device=device)[None, None, None, :].expand(1, 2, 5, 5) ** 2},
53
+ 56.0 / 3.0,
54
+ ],
55
+ [{"normalize": True}, {"pred": torch.arange(0, 5, device=device)[None, None, :].expand(1, 1, 5) ** 2}, 56.0 / 3.0],
56
+ # for the following case, consider the following 2D matrix:
57
+ # tensor([[[[0, 1, 2],
58
+ # [1, 2, 3],
59
+ # [2, 3, 4],
60
+ # [3, 4, 5],
61
+ # [4, 5, 6]],
62
+ # [[0, 1, 2],
63
+ # [1, 2, 3],
64
+ # [2, 3, 4],
65
+ # [3, 4, 5],
66
+ # [4, 5, 6]]]])
67
+ # the first partials wrt x are all ones, and so are the first partials wrt y
68
+ # the diffusion loss, when normalization is not applied, is 1^2 + 1^2 = 2
69
+ [{"normalize": False}, {"pred": torch.stack([torch.arange(i, i + 3) for i in range(5)]).expand(1, 2, 5, 3)}, 2.0],
70
+ # consider the same matrix, this time with normalization applied, using the same notation as in the demo notebook,
71
+ # the coefficients to be divided out are (1, 5/3) for partials wrt x and (3/5, 1) for partials wrt y
72
+ # the diffusion loss is then (1/1)^2 + (1/(5/3))^2 + (1/(3/5))^2 + (1/1)^2 = (1 + 9/25 + 25/9 + 1) / 2 = 2.5689
73
+ [
74
+ {"normalize": True},
75
+ {"pred": torch.stack([torch.arange(i, i + 3) for i in range(5)]).expand(1, 2, 5, 3)},
76
+ (1.0 + 9.0 / 25.0 + 25.0 / 9.0 + 1.0) / 2.0,
77
+ ],
78
+ ]
79
+
80
+
81
+ class TestDiffusionLoss(unittest.TestCase):
82
+
83
+ @parameterized.expand(TEST_CASES)
84
+ def test_shape(self, input_param, input_data, expected_val):
85
+ result = DiffusionLoss(**input_param).forward(**input_data)
86
+ np.testing.assert_allclose(result.detach().cpu().numpy(), expected_val, rtol=1e-5)
87
+
88
+ def test_ill_shape(self):
89
+ loss = DiffusionLoss()
90
+ # not in 3-d, 4-d, 5-d
91
+ with self.assertRaisesRegex(ValueError, "Expecting 3-d, 4-d or 5-d"):
92
+ loss.forward(torch.ones((1, 3), device=device))
93
+ with self.assertRaisesRegex(ValueError, "Expecting 3-d, 4-d or 5-d"):
94
+ loss.forward(torch.ones((1, 4, 5, 5, 5, 5), device=device))
95
+ with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
96
+ loss.forward(torch.ones((1, 3, 2, 5, 5), device=device))
97
+ with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
98
+ loss.forward(torch.ones((1, 3, 5, 2, 5)))
99
+ with self.assertRaisesRegex(ValueError, "All spatial dimensions"):
100
+ loss.forward(torch.ones((1, 3, 5, 5, 2)))
101
+
102
+ # number of vector components unequal to number of spatial dims
103
+ with self.assertRaisesRegex(ValueError, "Number of vector components"):
104
+ loss.forward(torch.ones((1, 2, 5, 5, 5)))
105
+ with self.assertRaisesRegex(ValueError, "Number of vector components"):
106
+ loss.forward(torch.ones((1, 2, 5, 5, 5)))
107
+
108
+ def test_ill_opts(self):
109
+ pred = torch.rand(1, 3, 5, 5, 5).to(device=device)
110
+ with self.assertRaisesRegex(ValueError, ""):
111
+ DiffusionLoss(reduction="unknown")(pred)
112
+ with self.assertRaisesRegex(ValueError, ""):
113
+ DiffusionLoss(reduction=None)(pred)
114
+
115
+
116
+ if __name__ == "__main__":
117
+ unittest.main()
@@ -0,0 +1,10 @@
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.
@@ -0,0 +1,150 @@
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
+ from __future__ import annotations
12
+
13
+ import os
14
+ import unittest
15
+ from pathlib import Path
16
+
17
+ import numpy as np
18
+ import torch
19
+ from parameterized import parameterized
20
+
21
+ from monai import transforms
22
+ from monai.losses.image_dissimilarity import GlobalMutualInformationLoss
23
+ from tests.test_utils import SkipIfBeforePyTorchVersion, download_url_or_skip_test, skip_if_quick, testing_data_config
24
+
25
+ device = "cuda:0" if torch.cuda.is_available() else "cpu"
26
+
27
+ TESTS_PATH = Path(__file__).parents[2]
28
+ FILE_PATH = os.path.join(TESTS_PATH, "testing_data", "temp_" + "mri.nii")
29
+
30
+ EXPECTED_VALUE = {
31
+ "xyz_translation": [
32
+ -1.5860257,
33
+ -0.62433463,
34
+ -0.38217825,
35
+ -0.2905613,
36
+ -0.23233329,
37
+ -0.1961407,
38
+ -0.16905619,
39
+ -0.15100679,
40
+ -0.13666219,
41
+ -0.12635908,
42
+ ],
43
+ "xyz_rotation": [
44
+ -1.5860257,
45
+ -0.30265224,
46
+ -0.18666176,
47
+ -0.15887907,
48
+ -0.1625064,
49
+ -0.16603896,
50
+ -0.19222091,
51
+ -0.18158069,
52
+ -0.167644,
53
+ -0.16698098,
54
+ ],
55
+ }
56
+
57
+
58
+ @skip_if_quick
59
+ class TestGlobalMutualInformationLoss(unittest.TestCase):
60
+ def setUp(self):
61
+ config = testing_data_config("images", "Prostate_T2W_AX_1")
62
+ download_url_or_skip_test(
63
+ url=config["url"],
64
+ filepath=FILE_PATH,
65
+ hash_val=config.get("hash_val"),
66
+ hash_type=config.get("hash_type", "sha256"),
67
+ )
68
+
69
+ @SkipIfBeforePyTorchVersion((1, 9))
70
+ def test_bspline(self):
71
+ loss_fn = GlobalMutualInformationLoss(kernel_type="b-spline", num_bins=32, sigma_ratio=0.015)
72
+
73
+ transform_params_dict = {
74
+ "xyz_translation": [(i, i, i) for i in range(10)],
75
+ "xyz_rotation": [(np.pi / 100 * i, np.pi / 100 * i, np.pi / 100 * i) for i in range(10)],
76
+ }
77
+
78
+ def transformation(translate_params=(0.0, 0.0, 0.0), rotate_params=(0.0, 0.0, 0.0)):
79
+ """
80
+ Read and transform Prostate_T2W_AX_1.nii
81
+ Args:
82
+ translate_params: a tuple of 3 floats, translation is in pixel/voxel relative to the center of the input
83
+ image. Defaults to no translation.
84
+ rotate_params: a rotation angle in radians, a tuple of 3 floats for 3D.
85
+ Defaults to no rotation.
86
+ Returns:
87
+ numpy array of shape HWD
88
+ """
89
+ transform_list = [
90
+ transforms.LoadImaged(keys="img", image_only=True),
91
+ transforms.Affined(
92
+ keys="img",
93
+ translate_params=translate_params,
94
+ rotate_params=rotate_params,
95
+ device=None,
96
+ padding_mode="border",
97
+ ),
98
+ transforms.NormalizeIntensityd(keys=["img"]),
99
+ ]
100
+ transformation = transforms.Compose(transform_list)
101
+ return transformation({"img": FILE_PATH})["img"]
102
+
103
+ a1 = transformation()
104
+ a1 = a1.clone().unsqueeze(0).unsqueeze(0).to(device)
105
+
106
+ for mode in transform_params_dict:
107
+ transform_params_list = transform_params_dict[mode]
108
+ expected_value_list = EXPECTED_VALUE[mode]
109
+ for transform_params, expected_value in zip(transform_params_list, expected_value_list):
110
+ a2 = transformation(
111
+ translate_params=transform_params if "translation" in mode else (0.0, 0.0, 0.0),
112
+ rotate_params=transform_params if "rotation" in mode else (0.0, 0.0, 0.0),
113
+ )
114
+ a2 = a2.clone().unsqueeze(0).unsqueeze(0).to(device)
115
+ result = loss_fn(a2, a1).detach().cpu().numpy()
116
+ np.testing.assert_allclose(result, expected_value, rtol=0.08, atol=0.05)
117
+
118
+
119
+ class TestGlobalMutualInformationLossIll(unittest.TestCase):
120
+ @parameterized.expand(
121
+ [
122
+ (torch.ones((1, 2), dtype=torch.float), torch.ones((1, 3), dtype=torch.float)), # mismatched_simple_dims
123
+ (
124
+ torch.ones((1, 3, 3), dtype=torch.float),
125
+ torch.ones((1, 3), dtype=torch.float),
126
+ ), # mismatched_advanced_dims
127
+ ]
128
+ )
129
+ def test_ill_shape(self, input1, input2):
130
+ loss = GlobalMutualInformationLoss()
131
+ with self.assertRaises(ValueError):
132
+ loss.forward(input1, input2)
133
+
134
+ @parameterized.expand(
135
+ [
136
+ (0, "mean", ValueError, ""), # num_bins_zero
137
+ (-1, "mean", ValueError, ""), # num_bins_negative
138
+ (64, "unknown", ValueError, ""), # reduction_unknown
139
+ (64, None, ValueError, ""), # reduction_none
140
+ ]
141
+ )
142
+ def test_ill_opts(self, num_bins, reduction, expected_exception, expected_message):
143
+ pred = torch.ones((1, 3, 3, 3, 3), dtype=torch.float, device=device)
144
+ target = torch.ones((1, 3, 3, 3, 3), dtype=torch.float, device=device)
145
+ with self.assertRaisesRegex(expected_exception, expected_message):
146
+ GlobalMutualInformationLoss(num_bins=num_bins, reduction=reduction)(pred, target)
147
+
148
+
149
+ if __name__ == "__main__":
150
+ unittest.main()