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 +1,119 @@
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.data.box_utils import convert_box_to_standard_mode
20
+ from monai.transforms.spatial.array import ConvertBoxToPoints, ConvertPointsToBoxes
21
+ from tests.test_utils import assert_allclose
22
+
23
+ TEST_CASE_POINTS_2D = [
24
+ [
25
+ torch.tensor([[10, 20, 30, 40], [50, 60, 70, 80]]),
26
+ "xyxy",
27
+ torch.tensor([[[10, 20], [30, 20], [30, 40], [10, 40]], [[50, 60], [70, 60], [70, 80], [50, 80]]]),
28
+ ],
29
+ [torch.tensor([[10, 20, 20, 20]]), "ccwh", torch.tensor([[[0, 10], [20, 10], [20, 30], [0, 30]]])],
30
+ ]
31
+ TEST_CASE_POINTS_3D = [
32
+ [
33
+ torch.tensor([[10, 20, 30, 40, 50, 60], [70, 80, 90, 100, 110, 120]]),
34
+ "xyzxyz",
35
+ torch.tensor(
36
+ [
37
+ [
38
+ [10, 20, 30],
39
+ [40, 20, 30],
40
+ [40, 50, 30],
41
+ [10, 50, 30],
42
+ [10, 20, 60],
43
+ [40, 20, 60],
44
+ [40, 50, 60],
45
+ [10, 50, 60],
46
+ ],
47
+ [
48
+ [70, 80, 90],
49
+ [100, 80, 90],
50
+ [100, 110, 90],
51
+ [70, 110, 90],
52
+ [70, 80, 120],
53
+ [100, 80, 120],
54
+ [100, 110, 120],
55
+ [70, 110, 120],
56
+ ],
57
+ ]
58
+ ),
59
+ ],
60
+ [
61
+ torch.tensor([[10, 20, 30, 10, 10, 10]]),
62
+ "cccwhd",
63
+ torch.tensor(
64
+ [
65
+ [
66
+ [5, 15, 25],
67
+ [15, 15, 25],
68
+ [15, 25, 25],
69
+ [5, 25, 25],
70
+ [5, 15, 35],
71
+ [15, 15, 35],
72
+ [15, 25, 35],
73
+ [5, 25, 35],
74
+ ]
75
+ ]
76
+ ),
77
+ ],
78
+ [
79
+ torch.tensor([[10, 20, 30, 40, 50, 60]]),
80
+ "xxyyzz",
81
+ torch.tensor(
82
+ [
83
+ [
84
+ [10, 30, 50],
85
+ [20, 30, 50],
86
+ [20, 40, 50],
87
+ [10, 40, 50],
88
+ [10, 30, 60],
89
+ [20, 30, 60],
90
+ [20, 40, 60],
91
+ [10, 40, 60],
92
+ ]
93
+ ]
94
+ ),
95
+ ],
96
+ ]
97
+
98
+ TEST_CASES = TEST_CASE_POINTS_2D + TEST_CASE_POINTS_3D
99
+
100
+
101
+ class TestConvertBoxToPoints(unittest.TestCase):
102
+ @parameterized.expand(TEST_CASES)
103
+ def test_convert_box_to_points(self, boxes, mode, expected_points):
104
+ transform = ConvertBoxToPoints(mode=mode)
105
+ converted_points = transform(boxes)
106
+ assert_allclose(converted_points, expected_points, type_test=False)
107
+
108
+
109
+ class TestConvertPointsToBoxes(unittest.TestCase):
110
+ @parameterized.expand(TEST_CASES)
111
+ def test_convert_box_to_points(self, boxes, mode, points):
112
+ transform = ConvertPointsToBoxes()
113
+ converted_boxes = transform(points)
114
+ expected_boxes = convert_box_to_standard_mode(boxes, mode)
115
+ assert_allclose(converted_boxes, expected_boxes, type_test=False)
116
+
117
+
118
+ if __name__ == "__main__":
119
+ unittest.main()
@@ -0,0 +1,134 @@
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.data import MetaTensor, set_track_meta
21
+ from monai.transforms.spatial.array import GridPatch
22
+ from tests.test_utils import TEST_NDARRAYS, SkipIfBeforePyTorchVersion, assert_allclose
23
+
24
+ A = np.arange(16).repeat(3).reshape(4, 4, 3).transpose(2, 0, 1)
25
+ A11 = A[:, :2, :2]
26
+ A12 = A[:, :2, 2:]
27
+ A21 = A[:, 2:, :2]
28
+ A22 = A[:, 2:, 2:]
29
+
30
+ TEST_CASE_0 = [{"patch_size": (2, 2)}, A, [A11, A12, A21, A22]]
31
+ TEST_CASE_1 = [{"patch_size": (2, 2), "num_patches": 3}, A, [A11, A12, A21]]
32
+ TEST_CASE_2 = [{"patch_size": (2, 2), "num_patches": 5}, A, [A11, A12, A21, A22, np.zeros((3, 2, 2))]]
33
+ TEST_CASE_3 = [{"patch_size": (2, 2), "offset": (0, 0)}, A, [A11, A12, A21, A22]]
34
+ TEST_CASE_4 = [{"patch_size": (2, 2), "offset": (0, 0)}, A, [A11, A12, A21, A22]]
35
+ TEST_CASE_5 = [{"patch_size": (2, 2), "offset": (2, 2)}, A, [A22]]
36
+ TEST_CASE_6 = [{"patch_size": (2, 2), "offset": (0, 2)}, A, [A12, A22]]
37
+ TEST_CASE_7 = [{"patch_size": (2, 2), "offset": (2, 0)}, A, [A21, A22]]
38
+ TEST_CASE_8 = [{"patch_size": (2, 2), "num_patches": 3, "sort_fn": "max"}, A, [A22, A21, A12]]
39
+ TEST_CASE_9 = [{"patch_size": (2, 2), "num_patches": 4, "sort_fn": "min"}, A, [A11, A12, A21, A22]]
40
+ TEST_CASE_10 = [{"patch_size": (2, 2), "overlap": 0.5, "num_patches": 3}, A, [A11, A[:, :2, 1:3], A12]]
41
+ TEST_CASE_11 = [
42
+ {"patch_size": (3, 3), "num_patches": 2, "constant_values": 255, "pad_mode": "constant"},
43
+ A,
44
+ [A[:, :3, :3], np.pad(A[:, :3, 3:], ((0, 0), (0, 0), (0, 2)), mode="constant", constant_values=255)],
45
+ ]
46
+ TEST_CASE_12 = [
47
+ {"patch_size": (3, 3), "offset": (-2, -2), "num_patches": 2, "pad_mode": "constant"},
48
+ A,
49
+ [np.zeros((3, 3, 3)), np.pad(A[:, :1, 1:4], ((0, 0), (2, 0), (0, 0)), mode="constant")],
50
+ ]
51
+ # Only threshold filtering
52
+ TEST_CASE_13 = [{"patch_size": (2, 2), "threshold": 50.0}, A, [A11]]
53
+ TEST_CASE_14 = [{"patch_size": (2, 2), "threshold": 150.0}, A, [A11, A12, A21]]
54
+ # threshold filtering with num_patches more than available patches (no effect)
55
+ TEST_CASE_15 = [{"patch_size": (2, 2), "num_patches": 3, "threshold": 50.0}, A, [A11]]
56
+ # threshold filtering with num_patches less than available patches (count filtering)
57
+ TEST_CASE_16 = [{"patch_size": (2, 2), "num_patches": 2, "threshold": 150.0}, A, [A11, A12]]
58
+
59
+ TEST_CASE_META_0 = [
60
+ {"patch_size": (2, 2)},
61
+ A,
62
+ [A11, A12, A21, A22],
63
+ [{"location": [0, 0]}, {"location": [0, 2]}, {"location": [2, 0]}, {"location": [2, 2]}],
64
+ ]
65
+
66
+ TEST_CASE_META_1 = [
67
+ {"patch_size": (2, 2)},
68
+ MetaTensor(x=A, meta={"path": "path/to/file"}),
69
+ [A11, A12, A21, A22],
70
+ [
71
+ {"location": [0, 0], "path": "path/to/file"},
72
+ {"location": [0, 2], "path": "path/to/file"},
73
+ {"location": [2, 0], "path": "path/to/file"},
74
+ {"location": [2, 2], "path": "path/to/file"},
75
+ ],
76
+ ]
77
+
78
+ TEST_CASES = []
79
+ for p in TEST_NDARRAYS:
80
+ TEST_CASES.append([p, *TEST_CASE_0])
81
+ TEST_CASES.append([p, *TEST_CASE_1])
82
+ TEST_CASES.append([p, *TEST_CASE_2])
83
+ TEST_CASES.append([p, *TEST_CASE_3])
84
+ TEST_CASES.append([p, *TEST_CASE_4])
85
+ TEST_CASES.append([p, *TEST_CASE_5])
86
+ TEST_CASES.append([p, *TEST_CASE_6])
87
+ TEST_CASES.append([p, *TEST_CASE_7])
88
+ TEST_CASES.append([p, *TEST_CASE_8])
89
+ TEST_CASES.append([p, *TEST_CASE_9])
90
+ TEST_CASES.append([p, *TEST_CASE_10])
91
+ TEST_CASES.append([p, *TEST_CASE_11])
92
+ TEST_CASES.append([p, *TEST_CASE_12])
93
+ TEST_CASES.append([p, *TEST_CASE_13])
94
+ TEST_CASES.append([p, *TEST_CASE_14])
95
+ TEST_CASES.append([p, *TEST_CASE_15])
96
+ TEST_CASES.append([p, *TEST_CASE_16])
97
+
98
+
99
+ class TestGridPatch(unittest.TestCase):
100
+ @parameterized.expand(TEST_CASES)
101
+ @SkipIfBeforePyTorchVersion((1, 11, 1))
102
+ def test_grid_patch(self, in_type, input_parameters, image, expected):
103
+ input_image = in_type(image)
104
+ splitter = GridPatch(**input_parameters)
105
+ output = splitter(input_image)
106
+ self.assertEqual(len(output), len(expected))
107
+ for output_patch, expected_patch in zip(output, expected):
108
+ assert_allclose(
109
+ output_patch,
110
+ in_type(expected_patch),
111
+ type_test=False,
112
+ device_test=bool(isinstance(in_type(expected_patch), torch.Tensor)),
113
+ )
114
+
115
+ @parameterized.expand([TEST_CASE_META_0, TEST_CASE_META_1])
116
+ @SkipIfBeforePyTorchVersion((1, 9, 1))
117
+ def test_grid_patch_meta(self, input_parameters, image, expected, expected_meta):
118
+ set_track_meta(True)
119
+ splitter = GridPatch(**input_parameters)
120
+ output = splitter(image)
121
+ self.assertEqual(len(output), len(expected))
122
+ if "path" in expected_meta[0]:
123
+ self.assertTrue(output.meta["path"] == expected_meta[0]["path"])
124
+ for output_patch, expected_patch, expected_patch_meta in zip(output, expected, expected_meta):
125
+ assert_allclose(output_patch, expected_patch, type_test=False)
126
+ self.assertIsInstance(output_patch, MetaTensor)
127
+ self.assertEqual(output_patch.meta["location"], expected_patch_meta["location"])
128
+ self.assertTrue(output_patch.meta["spatial_shape"], list(output_patch.shape[1:]))
129
+ if "path" in expected_meta[0]:
130
+ self.assertEqual(output_patch.meta["path"], expected_patch_meta["path"])
131
+
132
+
133
+ if __name__ == "__main__":
134
+ 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 numpy as np
17
+ import torch
18
+ from parameterized import parameterized
19
+
20
+ from monai.transforms.spatial.dictionary import GridPatchd
21
+ from tests.test_utils import TEST_NDARRAYS, SkipIfBeforePyTorchVersion, assert_allclose
22
+
23
+ A = np.arange(16).repeat(3).reshape(4, 4, 3).transpose(2, 0, 1)
24
+ A11 = A[:, :2, :2]
25
+ A12 = A[:, :2, 2:]
26
+ A21 = A[:, 2:, :2]
27
+ A22 = A[:, 2:, 2:]
28
+
29
+ TEST_CASE_0 = [{"patch_size": (2, 2)}, {"image": A}, [A11, A12, A21, A22]]
30
+ TEST_CASE_1 = [{"patch_size": (2, 2), "num_patches": 3}, {"image": A}, [A11, A12, A21]]
31
+ TEST_CASE_2 = [{"patch_size": (2, 2), "num_patches": 5}, {"image": A}, [A11, A12, A21, A22, np.zeros((3, 2, 2))]]
32
+ TEST_CASE_3 = [{"patch_size": (2, 2), "offset": (0, 0)}, {"image": A}, [A11, A12, A21, A22]]
33
+ TEST_CASE_4 = [{"patch_size": (2, 2), "offset": (0, 0)}, {"image": A}, [A11, A12, A21, A22]]
34
+ TEST_CASE_5 = [{"patch_size": (2, 2), "offset": (2, 2)}, {"image": A}, [A22]]
35
+ TEST_CASE_6 = [{"patch_size": (2, 2), "offset": (0, 2)}, {"image": A}, [A12, A22]]
36
+ TEST_CASE_7 = [{"patch_size": (2, 2), "offset": (2, 0)}, {"image": A}, [A21, A22]]
37
+ TEST_CASE_8 = [{"patch_size": (2, 2), "num_patches": 3, "sort_fn": "max"}, {"image": A}, [A22, A21, A12]]
38
+ TEST_CASE_9 = [{"patch_size": (2, 2), "num_patches": 4, "sort_fn": "min"}, {"image": A}, [A11, A12, A21, A22]]
39
+ TEST_CASE_10 = [{"patch_size": (2, 2), "overlap": 0.5, "num_patches": 3}, {"image": A}, [A11, A[:, :2, 1:3], A12]]
40
+ TEST_CASE_11 = [
41
+ {"patch_size": (3, 3), "num_patches": 2, "constant_values": 255, "pad_mode": "constant"},
42
+ {"image": A},
43
+ [A[:, :3, :3], np.pad(A[:, :3, 3:], ((0, 0), (0, 0), (0, 2)), mode="constant", constant_values=255)],
44
+ ]
45
+ TEST_CASE_12 = [
46
+ {"patch_size": (3, 3), "offset": (-2, -2), "num_patches": 2, "pad_mode": "constant"},
47
+ {"image": A},
48
+ [np.zeros((3, 3, 3)), np.pad(A[:, :1, 1:4], ((0, 0), (2, 0), (0, 0)), mode="constant")],
49
+ ]
50
+ # Only threshold filtering
51
+ TEST_CASE_13 = [{"patch_size": (2, 2), "threshold": 50.0}, {"image": A}, [A11]]
52
+ TEST_CASE_14 = [{"patch_size": (2, 2), "threshold": 150.0}, {"image": A}, [A11, A12, A21]]
53
+ # threshold filtering with num_patches more than available patches (no effect)
54
+ TEST_CASE_15 = [{"patch_size": (2, 2), "threshold": 50.0, "num_patches": 3}, {"image": A}, [A11]]
55
+ # threshold filtering with num_patches less than available patches (count filtering)
56
+ TEST_CASE_16 = [{"patch_size": (2, 2), "threshold": 150.0, "num_patches": 2}, {"image": A}, [A11, A12]]
57
+
58
+ TEST_SINGLE = []
59
+ for p in TEST_NDARRAYS:
60
+ TEST_SINGLE.append([p, *TEST_CASE_0])
61
+ TEST_SINGLE.append([p, *TEST_CASE_1])
62
+ TEST_SINGLE.append([p, *TEST_CASE_2])
63
+ TEST_SINGLE.append([p, *TEST_CASE_3])
64
+ TEST_SINGLE.append([p, *TEST_CASE_4])
65
+ TEST_SINGLE.append([p, *TEST_CASE_5])
66
+ TEST_SINGLE.append([p, *TEST_CASE_6])
67
+ TEST_SINGLE.append([p, *TEST_CASE_7])
68
+ TEST_SINGLE.append([p, *TEST_CASE_8])
69
+ TEST_SINGLE.append([p, *TEST_CASE_9])
70
+ TEST_SINGLE.append([p, *TEST_CASE_10])
71
+ TEST_SINGLE.append([p, *TEST_CASE_11])
72
+ TEST_SINGLE.append([p, *TEST_CASE_12])
73
+ TEST_SINGLE.append([p, *TEST_CASE_13])
74
+ TEST_SINGLE.append([p, *TEST_CASE_14])
75
+ TEST_SINGLE.append([p, *TEST_CASE_15])
76
+ TEST_SINGLE.append([p, *TEST_CASE_16])
77
+
78
+
79
+ class TestGridPatchd(unittest.TestCase):
80
+ @parameterized.expand(TEST_SINGLE)
81
+ @SkipIfBeforePyTorchVersion((1, 11, 1))
82
+ def test_grid_patchd(self, in_type, input_parameters, image_dict, expected):
83
+ image_key = "image"
84
+ input_dict = {}
85
+ for k, v in image_dict.items():
86
+ input_dict[k] = v
87
+ if k == image_key:
88
+ input_dict[k] = in_type(v)
89
+ splitter = GridPatchd(keys=image_key, **input_parameters)
90
+ output = splitter(input_dict)
91
+ self.assertEqual(len(output[image_key]), len(expected))
92
+ for output_patch, expected_patch in zip(output[image_key], expected):
93
+ assert_allclose(
94
+ output_patch,
95
+ in_type(expected_patch),
96
+ type_test=False,
97
+ device_test=bool(isinstance(in_type(expected_patch), torch.Tensor)),
98
+ )
99
+
100
+
101
+ if __name__ == "__main__":
102
+ unittest.main()
@@ -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
+
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.data import MetaTensor, set_track_meta
21
+ from monai.transforms.spatial.array import RandGridPatch
22
+ from monai.utils import set_determinism
23
+ from tests.test_utils import TEST_NDARRAYS, SkipIfBeforePyTorchVersion, assert_allclose
24
+
25
+ A = np.arange(16).repeat(3).reshape(4, 4, 3).transpose(2, 0, 1)
26
+ A11 = A[:, :2, :2]
27
+ A12 = A[:, :2, 2:]
28
+ A21 = A[:, 2:, :2]
29
+ A22 = A[:, 2:, 2:]
30
+
31
+ TEST_CASE_0 = [{"patch_size": (2, 2), "min_offset": 0, "max_offset": 0}, A, [A11, A12, A21, A22]]
32
+ TEST_CASE_1 = [{"patch_size": (2, 2), "min_offset": 0, "num_patches": 3}, A, [A11, A12, A21]]
33
+ TEST_CASE_2 = [
34
+ {"patch_size": (2, 2), "min_offset": 0, "max_offset": 0, "num_patches": 5},
35
+ A,
36
+ [A11, A12, A21, A22, np.zeros((3, 2, 2))],
37
+ ]
38
+ TEST_CASE_3 = [{"patch_size": (2, 2), "min_offset": 0, "max_offset": 0}, A, [A11, A12, A21, A22]]
39
+ TEST_CASE_4 = [{"patch_size": (2, 2)}, A, [A11, A12, A21, A22]]
40
+ TEST_CASE_5 = [{"patch_size": (2, 2), "min_offset": 2, "max_offset": 2}, A, [A22]]
41
+ TEST_CASE_6 = [{"patch_size": (2, 2), "min_offset": (0, 2), "max_offset": (0, 2)}, A, [A12, A22]]
42
+ TEST_CASE_7 = [{"patch_size": (2, 2), "min_offset": 1, "max_offset": 2}, A, [A22]]
43
+ TEST_CASE_8 = [
44
+ {"patch_size": (2, 2), "min_offset": 0, "max_offset": 1, "num_patches": 1, "sort_fn": "max"},
45
+ A,
46
+ [A[:, 1:3, 1:3]],
47
+ ]
48
+ TEST_CASE_9 = [
49
+ {
50
+ "patch_size": (3, 3),
51
+ "min_offset": -3,
52
+ "max_offset": -1,
53
+ "sort_fn": "min",
54
+ "num_patches": 1,
55
+ "pad_mode": "constant",
56
+ "constant_values": 255,
57
+ },
58
+ A,
59
+ [np.pad(A[:, :2, 1:], ((0, 0), (1, 0), (0, 0)), mode="constant", constant_values=255)],
60
+ ]
61
+ TEST_CASE_10 = [{"patch_size": (2, 2), "min_offset": 0, "max_offset": 0, "threshold": 50.0}, A, [A11]]
62
+ TEST_CASE_11 = [{"patch_size": (2, 2), "sort_fn": "random", "num_patches": 2}, A, [A11, A12]]
63
+ TEST_CASE_12 = [{"patch_size": (2, 2), "sort_fn": "random", "num_patches": 4}, A, [A11, A12, A21, A22]]
64
+ TEST_CASE_13 = [
65
+ {"patch_size": (2, 2), "min_offset": 0, "max_offset": 1, "num_patches": 1, "sort_fn": "random"},
66
+ A,
67
+ [A[:, 1:3, 1:3]],
68
+ ]
69
+
70
+ TEST_CASE_META_0 = [
71
+ {"patch_size": (2, 2)},
72
+ A,
73
+ [A11, A12, A21, A22],
74
+ [{"location": [0, 0]}, {"location": [0, 2]}, {"location": [2, 0]}, {"location": [2, 2]}],
75
+ ]
76
+
77
+ TEST_CASE_META_1 = [
78
+ {"patch_size": (2, 2)},
79
+ MetaTensor(x=A, meta={"path": "path/to/file"}),
80
+ [A11, A12, A21, A22],
81
+ [
82
+ {"location": [0, 0], "path": "path/to/file"},
83
+ {"location": [0, 2], "path": "path/to/file"},
84
+ {"location": [2, 0], "path": "path/to/file"},
85
+ {"location": [2, 2], "path": "path/to/file"},
86
+ ],
87
+ ]
88
+
89
+ TEST_SINGLE = []
90
+ for p in TEST_NDARRAYS:
91
+ TEST_SINGLE.append([p, *TEST_CASE_0])
92
+ TEST_SINGLE.append([p, *TEST_CASE_1])
93
+ TEST_SINGLE.append([p, *TEST_CASE_2])
94
+ TEST_SINGLE.append([p, *TEST_CASE_3])
95
+ TEST_SINGLE.append([p, *TEST_CASE_4])
96
+ TEST_SINGLE.append([p, *TEST_CASE_5])
97
+ TEST_SINGLE.append([p, *TEST_CASE_6])
98
+ TEST_SINGLE.append([p, *TEST_CASE_7])
99
+ TEST_SINGLE.append([p, *TEST_CASE_8])
100
+ TEST_SINGLE.append([p, *TEST_CASE_9])
101
+ TEST_SINGLE.append([p, *TEST_CASE_10])
102
+ TEST_SINGLE.append([p, *TEST_CASE_11])
103
+ TEST_SINGLE.append([p, *TEST_CASE_12])
104
+ TEST_SINGLE.append([p, *TEST_CASE_13])
105
+
106
+
107
+ class TestRandGridPatch(unittest.TestCase):
108
+ def setUp(self):
109
+ set_determinism(seed=1234)
110
+
111
+ def tearDown(self):
112
+ set_determinism(None)
113
+
114
+ @parameterized.expand(TEST_SINGLE)
115
+ @SkipIfBeforePyTorchVersion((1, 11, 1))
116
+ def test_rand_grid_patch(self, in_type, input_parameters, image, expected):
117
+ input_image = in_type(image)
118
+ splitter = RandGridPatch(**input_parameters)
119
+ splitter.set_random_state(1234)
120
+ output = splitter(input_image)
121
+ self.assertEqual(len(output), len(expected))
122
+ for output_patch, expected_patch in zip(output, expected):
123
+ assert_allclose(
124
+ output_patch,
125
+ in_type(expected_patch),
126
+ type_test=False,
127
+ device_test=bool(isinstance(in_type(expected_patch), torch.Tensor)),
128
+ )
129
+
130
+ @parameterized.expand([TEST_CASE_META_0, TEST_CASE_META_1])
131
+ @SkipIfBeforePyTorchVersion((1, 9, 1))
132
+ def test_rand_grid_patch_meta(self, input_parameters, image, expected, expected_meta):
133
+ set_track_meta(True)
134
+ splitter = RandGridPatch(**input_parameters)
135
+ splitter.set_random_state(1234)
136
+ output = splitter(image)
137
+ self.assertEqual(len(output), len(expected))
138
+ if "path" in expected_meta[0]:
139
+ self.assertTrue(output.meta["path"] == expected_meta[0]["path"])
140
+ for output_patch, expected_patch, expected_patch_meta in zip(output, expected, expected_meta):
141
+ assert_allclose(output_patch, expected_patch, type_test=False)
142
+ self.assertTrue(isinstance(output_patch, MetaTensor))
143
+ self.assertTrue(output_patch.meta["location"] == expected_patch_meta["location"])
144
+ self.assertTrue(output_patch.meta["spatial_shape"], list(output_patch.shape[1:]))
145
+ if "path" in expected_meta[0]:
146
+ self.assertTrue(output_patch.meta["path"] == expected_patch_meta["path"])
147
+
148
+
149
+ if __name__ == "__main__":
150
+ 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.transforms.spatial.dictionary import RandGridPatchd
21
+ from monai.utils import set_determinism
22
+ from tests.test_utils import TEST_NDARRAYS, SkipIfBeforePyTorchVersion, assert_allclose
23
+
24
+ A = np.arange(16).repeat(3).reshape(4, 4, 3).transpose(2, 0, 1)
25
+ A11 = A[:, :2, :2]
26
+ A12 = A[:, :2, 2:]
27
+ A21 = A[:, 2:, :2]
28
+ A22 = A[:, 2:, 2:]
29
+
30
+ TEST_CASE_0 = [{"patch_size": (2, 2), "min_offset": 0, "max_offset": 0}, {"image": A}, [A11, A12, A21, A22]]
31
+ TEST_CASE_1 = [{"patch_size": (2, 2), "min_offset": 0, "num_patches": 3}, {"image": A}, [A11, A12, A21]]
32
+ TEST_CASE_2 = [
33
+ {"patch_size": (2, 2), "min_offset": 0, "max_offset": 0, "num_patches": 5},
34
+ {"image": A},
35
+ [A11, A12, A21, A22, np.zeros((3, 2, 2))],
36
+ ]
37
+ TEST_CASE_3 = [{"patch_size": (2, 2), "min_offset": 0, "max_offset": 0}, {"image": A}, [A11, A12, A21, A22]]
38
+ TEST_CASE_4 = [{"patch_size": (2, 2)}, {"image": A}, [A11, A12, A21, A22]]
39
+ TEST_CASE_5 = [{"patch_size": (2, 2), "min_offset": 2, "max_offset": 2}, {"image": A}, [A22]]
40
+ TEST_CASE_6 = [{"patch_size": (2, 2), "min_offset": (0, 2), "max_offset": (0, 2)}, {"image": A}, [A12, A22]]
41
+ TEST_CASE_7 = [{"patch_size": (2, 2), "min_offset": 1, "max_offset": 2}, {"image": A}, [A22]]
42
+ TEST_CASE_8 = [
43
+ {"patch_size": (2, 2), "min_offset": 0, "max_offset": 1, "num_patches": 1, "sort_fn": "max"},
44
+ {"image": A},
45
+ [A[:, 1:3, 1:3]],
46
+ ]
47
+ TEST_CASE_9 = [
48
+ {
49
+ "patch_size": (3, 3),
50
+ "min_offset": -3,
51
+ "max_offset": -1,
52
+ "sort_fn": "min",
53
+ "num_patches": 1,
54
+ "pad_mode": "constant",
55
+ "constant_values": 255,
56
+ },
57
+ {"image": A},
58
+ [np.pad(A[:, :2, 1:], ((0, 0), (1, 0), (0, 0)), mode="constant", constant_values=255)],
59
+ ]
60
+ TEST_CASE_10 = [{"patch_size": (2, 2), "min_offset": 0, "max_offset": 0, "threshold": 50.0}, {"image": A}, [A11]]
61
+ TEST_CASE_11 = [{"patch_size": (2, 2), "sort_fn": "random", "num_patches": 2}, {"image": A}, [A11, A12]]
62
+ TEST_CASE_12 = [{"patch_size": (2, 2), "sort_fn": "random", "num_patches": 4}, {"image": A}, [A11, A12, A21, A22]]
63
+ TEST_CASE_13 = [
64
+ {"patch_size": (2, 2), "min_offset": 0, "max_offset": 1, "num_patches": 1, "sort_fn": "random"},
65
+ {"image": A},
66
+ [A[:, 1:3, 1:3]],
67
+ ]
68
+
69
+ TEST_SINGLE = []
70
+ for p in TEST_NDARRAYS:
71
+ TEST_SINGLE.append([p, *TEST_CASE_0])
72
+ TEST_SINGLE.append([p, *TEST_CASE_1])
73
+ TEST_SINGLE.append([p, *TEST_CASE_2])
74
+ TEST_SINGLE.append([p, *TEST_CASE_3])
75
+ TEST_SINGLE.append([p, *TEST_CASE_4])
76
+ TEST_SINGLE.append([p, *TEST_CASE_5])
77
+ TEST_SINGLE.append([p, *TEST_CASE_6])
78
+ TEST_SINGLE.append([p, *TEST_CASE_7])
79
+ TEST_SINGLE.append([p, *TEST_CASE_8])
80
+ TEST_SINGLE.append([p, *TEST_CASE_9])
81
+ TEST_SINGLE.append([p, *TEST_CASE_10])
82
+ TEST_SINGLE.append([p, *TEST_CASE_11])
83
+ TEST_SINGLE.append([p, *TEST_CASE_12])
84
+ TEST_SINGLE.append([p, *TEST_CASE_13])
85
+
86
+
87
+ class TestRandGridPatchd(unittest.TestCase):
88
+ def setUp(self):
89
+ set_determinism(seed=1234)
90
+
91
+ def tearDown(self):
92
+ set_determinism(None)
93
+
94
+ @parameterized.expand(TEST_SINGLE)
95
+ @SkipIfBeforePyTorchVersion((1, 11, 1))
96
+ def test_rand_grid_patchd(self, in_type, input_parameters, image_dict, expected):
97
+ image_key = "image"
98
+ input_dict = {}
99
+ for k, v in image_dict.items():
100
+ input_dict[k] = v
101
+ if k == image_key:
102
+ input_dict[k] = in_type(v)
103
+ splitter = RandGridPatchd(keys=image_key, **input_parameters)
104
+ splitter.set_random_state(1234)
105
+ output = splitter(input_dict)
106
+ self.assertEqual(len(output[image_key]), len(expected))
107
+ for output_patch, expected_patch in zip(output[image_key], expected):
108
+ assert_allclose(
109
+ output_patch,
110
+ in_type(expected_patch),
111
+ type_test=False,
112
+ device_test=bool(isinstance(in_type(expected_patch), torch.Tensor)),
113
+ )
114
+
115
+
116
+ if __name__ == "__main__":
117
+ unittest.main()