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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  678. tests/transforms/test_spatial_pad.py +57 -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 +1,37 @@
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
+ from parameterized import parameterized
18
+
19
+ from monai.transforms import ConvertToMultiChannelBasedOnBratsClassesd
20
+
21
+ TEST_CASE = [
22
+ {"keys": "label"},
23
+ {"label": np.array([[0, 1, 2], [1, 2, 4], [0, 1, 4]])},
24
+ np.array([[[0, 1, 0], [1, 0, 1], [0, 1, 1]], [[0, 1, 1], [1, 1, 1], [0, 1, 1]], [[0, 0, 0], [0, 0, 1], [0, 0, 1]]]),
25
+ ]
26
+
27
+
28
+ class TestConvertToMultiChanneld(unittest.TestCase):
29
+
30
+ @parameterized.expand([TEST_CASE])
31
+ def test_type_shape(self, keys, data, expected_result):
32
+ result = ConvertToMultiChannelBasedOnBratsClassesd(**keys)(data)
33
+ np.testing.assert_equal(result["label"], expected_result)
34
+
35
+
36
+ if __name__ == "__main__":
37
+ unittest.main()
@@ -0,0 +1,86 @@
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.networks import eval_mode
21
+ from monai.transforms import CopyItemsd
22
+ from monai.utils import ensure_tuple
23
+ from tests.test_utils import assert_allclose
24
+
25
+ TEST_CASE_1 = ["img", 1, "img_1"]
26
+
27
+ TEST_CASE_2 = [["img", "seg"], 1, ["img_1", "seg_1"]]
28
+
29
+ TEST_CASE_3 = ["img", 2, ["img_1", "img_2"]]
30
+
31
+ TEST_CASE_4 = [["img", "seg"], 2, ["img_1", "seg_1", "img_2", "seg_2"]]
32
+
33
+
34
+ class TestCopyItemsd(unittest.TestCase):
35
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4])
36
+ def test_numpy_values(self, keys, times, names):
37
+ input_data = {"img": np.array([[0, 1], [1, 2]]), "seg": np.array([[3, 4], [4, 5]])}
38
+ result = CopyItemsd(keys=keys, times=times, names=names)(input_data)
39
+ for name in ensure_tuple(names):
40
+ self.assertTrue(name in result)
41
+ result["img_1"] += 1
42
+ np.testing.assert_allclose(result["img_1"], np.array([[1, 2], [2, 3]]))
43
+ np.testing.assert_allclose(result["img"], np.array([[0, 1], [1, 2]]))
44
+
45
+ def test_default_names(self):
46
+ input_data = {"img": np.array([[0, 1], [1, 2]]), "seg": np.array([[3, 4], [4, 5]])}
47
+ result = CopyItemsd(keys=["img", "seg"], times=2, names=None)(input_data)
48
+ for name in ["img_0", "seg_0", "img_1", "seg_1"]:
49
+ self.assertTrue(name in result)
50
+
51
+ def test_tensor_values(self):
52
+ device = torch.device("cuda:0") if torch.cuda.is_available() else torch.device("cpu:0")
53
+ input_data = {
54
+ "img": torch.tensor([[0, 1], [1, 2]], device=device),
55
+ "seg": torch.tensor([[0, 1], [1, 2]], device=device),
56
+ }
57
+ # test default `times=1`
58
+ result = CopyItemsd(keys="img", names="img_1")(input_data)
59
+ self.assertTrue("img_1" in result)
60
+ result["img_1"] += 1
61
+ assert_allclose(result["img"], torch.tensor([[0, 1], [1, 2]], device=device))
62
+ assert_allclose(result["img_1"], torch.tensor([[1, 2], [2, 3]], device=device))
63
+
64
+ def test_array_values(self):
65
+ input_data = {"img": [[0, 1], [1, 2]], "seg": [[0, 1], [1, 2]]}
66
+ result = CopyItemsd(keys="img", times=1, names="img_1")(input_data)
67
+ self.assertTrue("img_1" in result)
68
+ result["img_1"][0][0] += 1
69
+ np.testing.assert_allclose(result["img"], [[0, 1], [1, 2]])
70
+ np.testing.assert_allclose(result["img_1"], [[1, 1], [1, 2]])
71
+
72
+ def test_graph_tensor_values(self):
73
+ device = torch.device("cuda:0") if torch.cuda.is_available() else torch.device("cpu:0")
74
+ net = torch.nn.PReLU().to(device)
75
+ with eval_mode(net):
76
+ pred = net(torch.tensor([[0.0, 1.0], [1.0, 2.0]], device=device))
77
+ input_data = {"pred": pred, "seg": torch.tensor([[0.0, 1.0], [1.0, 2.0]], device=device)}
78
+ result = CopyItemsd(keys="pred", times=1, names="pred_1")(input_data)
79
+ self.assertTrue("pred_1" in result)
80
+ result["pred_1"] += 1.0
81
+ assert_allclose(result["pred"], torch.tensor([[0.0, 1.0], [1.0, 2.0]], device=device))
82
+ assert_allclose(result["pred_1"], torch.tensor([[1.0, 2.0], [2.0, 3.0]], device=device))
83
+
84
+
85
+ if __name__ == "__main__":
86
+ unittest.main()
@@ -0,0 +1,274 @@
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
+
19
+ from monai.transforms import (
20
+ create_control_grid,
21
+ create_grid,
22
+ create_rotate,
23
+ create_scale,
24
+ create_shear,
25
+ create_translate,
26
+ )
27
+ from tests.test_utils import assert_allclose, is_tf32_env
28
+
29
+
30
+ class TestCreateGrid(unittest.TestCase):
31
+ def test_create_grid(self):
32
+ with self.assertRaisesRegex(TypeError, ""):
33
+ create_grid(None)
34
+ with self.assertRaisesRegex(TypeError, ""):
35
+ create_grid((1, 1), spacing=2.0)
36
+ with self.assertRaisesRegex(TypeError, ""):
37
+ create_grid((1, 1), spacing=2.0)
38
+
39
+ test_assert(create_grid, ((1, 1),), np.array([[[0.0]], [[0.0]], [[1.0]]]))
40
+
41
+ test_assert(create_grid, ((1, 1), None, False), np.array([[[0.0]], [[0.0]]]))
42
+
43
+ test_assert(create_grid, ((1, 1), (1.2, 1.3)), np.array([[[0.0]], [[0.0]], [[1.0]]]))
44
+
45
+ test_assert(create_grid, ((1, 1, 1), (1.2, 1.3, 1.0)), np.array([[[[0.0]]], [[[0.0]]], [[[0.0]]], [[[1.0]]]]))
46
+
47
+ test_assert(create_grid, ((1, 1, 1), (1.2, 1.3, 1.0), False), np.array([[[[0.0]]], [[[0.0]]], [[[0.0]]]]))
48
+
49
+ g = create_grid((1, 1, 1), spacing=(1.2, 1.3, 1.0), dtype=np.int32)
50
+ np.testing.assert_equal(g.dtype, np.int32)
51
+
52
+ g = create_grid((1, 1, 1), spacing=(1.2, 1.3, 1.0), dtype=torch.float64, backend="torch")
53
+ np.testing.assert_equal(g.dtype, torch.float64)
54
+
55
+ test_assert(
56
+ create_grid,
57
+ ((2, 2, 2),),
58
+ np.array(
59
+ [
60
+ [[[-0.5, -0.5], [-0.5, -0.5]], [[0.5, 0.5], [0.5, 0.5]]],
61
+ [[[-0.5, -0.5], [0.5, 0.5]], [[-0.5, -0.5], [0.5, 0.5]]],
62
+ [[[-0.5, 0.5], [-0.5, 0.5]], [[-0.5, 0.5], [-0.5, 0.5]]],
63
+ [[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]],
64
+ ]
65
+ ),
66
+ )
67
+
68
+ test_assert(
69
+ create_grid,
70
+ ((2, 2, 2), (1.2, 1.3, 1.0)),
71
+ np.array(
72
+ [
73
+ [[[-0.6, -0.6], [-0.6, -0.6]], [[0.6, 0.6], [0.6, 0.6]]],
74
+ [[[-0.65, -0.65], [0.65, 0.65]], [[-0.65, -0.65], [0.65, 0.65]]],
75
+ [[[-0.5, 0.5], [-0.5, 0.5]], [[-0.5, 0.5], [-0.5, 0.5]]],
76
+ [[[1.0, 1.0], [1.0, 1.0]], [[1.0, 1.0], [1.0, 1.0]]],
77
+ ]
78
+ ),
79
+ )
80
+
81
+ def test_create_control_grid(self):
82
+ with self.assertRaisesRegex(TypeError, ""):
83
+ create_control_grid(None, None)
84
+ with self.assertRaisesRegex(TypeError, ""):
85
+ create_control_grid((1, 1), 2.0)
86
+
87
+ test_assert(
88
+ create_control_grid,
89
+ ((1.0, 1.0), (1.0, 1.0)),
90
+ np.array(
91
+ [
92
+ [[-1.0, -1.0, -1.0], [0.0, 0.0, 0.0], [1.0, 1.0, 1.0]],
93
+ [[-1.0, 0.0, 1.0], [-1.0, 0.0, 1.0], [-1.0, 0.0, 1.0]],
94
+ [[1.0, 1.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
95
+ ]
96
+ ),
97
+ )
98
+
99
+ test_assert(
100
+ create_control_grid,
101
+ ((1.0, 1.0), (2.0, 2.0)),
102
+ np.array(
103
+ [
104
+ [[-2.0, -2.0, -2.0], [0.0, 0.0, 0.0], [2.0, 2.0, 2.0]],
105
+ [[-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0]],
106
+ [[1.0, 1.0, 1.0], [1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
107
+ ]
108
+ ),
109
+ )
110
+
111
+ test_assert(
112
+ create_control_grid,
113
+ ((2.0, 2.0), (1.0, 1.0)),
114
+ np.array(
115
+ [
116
+ [[-1.5, -1.5, -1.5, -1.5], [-0.5, -0.5, -0.5, -0.5], [0.5, 0.5, 0.5, 0.5], [1.5, 1.5, 1.5, 1.5]],
117
+ [[-1.5, -0.5, 0.5, 1.5], [-1.5, -0.5, 0.5, 1.5], [-1.5, -0.5, 0.5, 1.5], [-1.5, -0.5, 0.5, 1.5]],
118
+ [[1.0, 1.0, 1.0, 1.0], [1.0, 1.0, 1.0, 1.0], [1.0, 1.0, 1.0, 1.0], [1.0, 1.0, 1.0, 1.0]],
119
+ ]
120
+ ),
121
+ )
122
+
123
+ test_assert(
124
+ create_control_grid,
125
+ ((2.0, 2.0), (2.0, 2.0)),
126
+ np.array(
127
+ [
128
+ [[-3.0, -3.0, -3.0, -3.0], [-1.0, -1.0, -1.0, -1.0], [1.0, 1.0, 1.0, 1.0], [3.0, 3.0, 3.0, 3.0]],
129
+ [[-3.0, -1.0, 1.0, 3.0], [-3.0, -1.0, 1.0, 3.0], [-3.0, -1.0, 1.0, 3.0], [-3.0, -1.0, 1.0, 3.0]],
130
+ [[1.0, 1.0, 1.0, 1.0], [1.0, 1.0, 1.0, 1.0], [1.0, 1.0, 1.0, 1.0], [1.0, 1.0, 1.0, 1.0]],
131
+ ]
132
+ ),
133
+ )
134
+
135
+ test_assert(
136
+ create_control_grid,
137
+ ((1.0, 1.0, 1.0), (2.0, 2.0, 2.0), False),
138
+ np.array(
139
+ [
140
+ [
141
+ [[-2.0, -2.0, -2.0], [-2.0, -2.0, -2.0], [-2.0, -2.0, -2.0]],
142
+ [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.0]],
143
+ [[2.0, 2.0, 2.0], [2.0, 2.0, 2.0], [2.0, 2.0, 2.0]],
144
+ ],
145
+ [
146
+ [[-2.0, -2.0, -2.0], [0.0, 0.0, 0.0], [2.0, 2.0, 2.0]],
147
+ [[-2.0, -2.0, -2.0], [0.0, 0.0, 0.0], [2.0, 2.0, 2.0]],
148
+ [[-2.0, -2.0, -2.0], [0.0, 0.0, 0.0], [2.0, 2.0, 2.0]],
149
+ ],
150
+ [
151
+ [[-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0]],
152
+ [[-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0]],
153
+ [[-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0], [-2.0, 0.0, 2.0]],
154
+ ],
155
+ ]
156
+ ),
157
+ )
158
+
159
+
160
+ def test_assert(func, params, expected):
161
+ gpu_test = ("torch_gpu",) if torch.cuda.is_available() else ()
162
+ for b in ("torch", "numpy") + gpu_test:
163
+ if b == "torch_gpu":
164
+ m = func(*params, device="cuda:0", backend="torch")
165
+ else:
166
+ m = func(*params, backend=b)
167
+ assert_allclose(m, expected, type_test=False, rtol=1e-2 if is_tf32_env() else 1e-5, atol=1e-5)
168
+
169
+
170
+ class TestCreateAffine(unittest.TestCase):
171
+ def test_create_rotate(self):
172
+ with self.assertRaisesRegex(TypeError, ""):
173
+ create_rotate(2, None)
174
+
175
+ with self.assertRaisesRegex(ValueError, ""):
176
+ create_rotate(5, 1)
177
+
178
+ test_assert(
179
+ create_rotate,
180
+ (2, 1.1),
181
+ np.array([[0.45359612, -0.89120736, 0.0], [0.89120736, 0.45359612, 0.0], [0.0, 0.0, 1.0]]),
182
+ )
183
+ test_assert(
184
+ create_rotate,
185
+ (3, 1.1),
186
+ np.array(
187
+ [
188
+ [1.0, 0.0, 0.0, 0.0],
189
+ [0.0, 0.45359612, -0.89120736, 0.0],
190
+ [0.0, 0.89120736, 0.45359612, 0.0],
191
+ [0.0, 0.0, 0.0, 1.0],
192
+ ]
193
+ ),
194
+ )
195
+ test_assert(
196
+ create_rotate,
197
+ (3, (1.1, 1)),
198
+ np.array(
199
+ [
200
+ [0.54030231, 0.0, 0.84147098, 0.0],
201
+ [0.74992513, 0.45359612, -0.48152139, 0.0],
202
+ [-0.38168798, 0.89120736, 0.24507903, 0.0],
203
+ [0.0, 0.0, 0.0, 1.0],
204
+ ]
205
+ ),
206
+ )
207
+ test_assert(
208
+ create_rotate,
209
+ (3, (1, 1, 1.1)),
210
+ np.array(
211
+ [
212
+ [0.24507903, -0.48152139, 0.84147098, 0.0],
213
+ [0.80270075, -0.38596121, -0.45464871, 0.0],
214
+ [0.54369824, 0.78687425, 0.29192658, 0.0],
215
+ [0.0, 0.0, 0.0, 1.0],
216
+ ]
217
+ ),
218
+ )
219
+ test_assert(
220
+ create_rotate,
221
+ (3, (0, 0, np.pi / 2)),
222
+ np.array([[0.0, -1.0, 0.0, 0.0], [1.0, 0.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
223
+ )
224
+
225
+ def test_create_shear(self):
226
+ test_assert(create_shear, (2, 1.0), np.array([[1.0, 1.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]))
227
+ test_assert(create_shear, (2, (2.0, 3.0)), np.array([[1.0, 2.0, 0.0], [3.0, 1.0, 0.0], [0.0, 0.0, 1.0]]))
228
+ test_assert(
229
+ create_shear,
230
+ (3, 1.0),
231
+ np.array([[1.0, 1.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
232
+ )
233
+
234
+ def test_create_scale(self):
235
+ test_assert(create_scale, (2, 2), np.array([[2.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]))
236
+ test_assert(create_scale, (2, [2, 2, 2]), np.array([[2.0, 0.0, 0.0], [0.0, 2.0, 0.0], [0.0, 0.0, 1.0]]))
237
+ test_assert(
238
+ create_scale,
239
+ (3, [1.5, 2.4]),
240
+ np.array([[1.5, 0.0, 0.0, 0.0], [0.0, 2.4, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
241
+ )
242
+ test_assert(
243
+ create_scale,
244
+ (3, 1.5),
245
+ np.array([[1.5, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
246
+ )
247
+ test_assert(
248
+ create_scale,
249
+ (3, [1, 2, 3, 4, 5]),
250
+ np.array([[1.0, 0.0, 0.0, 0.0], [0.0, 2.0, 0.0, 0.0], [0.0, 0.0, 3.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
251
+ )
252
+
253
+ def test_create_translate(self):
254
+ test_assert(create_translate, (2, 2), np.array([[1.0, 0.0, 2.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]))
255
+ test_assert(create_translate, (2, [2, 2, 2]), np.array([[1.0, 0.0, 2.0], [0.0, 1.0, 2.0], [0.0, 0.0, 1.0]]))
256
+ test_assert(
257
+ create_translate,
258
+ (3, [1.5, 2.4]),
259
+ np.array([[1.0, 0.0, 0.0, 1.5], [0.0, 1.0, 0.0, 2.4], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
260
+ )
261
+ test_assert(
262
+ create_translate,
263
+ (3, 1.5),
264
+ np.array([[1.0, 0.0, 0.0, 1.5], [0.0, 1.0, 0.0, 0.0], [0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]),
265
+ )
266
+ test_assert(
267
+ create_translate,
268
+ (3, [1, 2, 3, 4, 5]),
269
+ np.array([[1.0, 0.0, 0.0, 1.0], [0.0, 1.0, 0.0, 2.0], [0.0, 0.0, 1.0, 3.0], [0.0, 0.0, 0.0, 1.0]]),
270
+ )
271
+
272
+
273
+ if __name__ == "__main__":
274
+ unittest.main()
@@ -0,0 +1,164 @@
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
+ from parameterized import parameterized
18
+
19
+ from monai.config import USE_COMPILED
20
+ from monai.data.meta_tensor import MetaTensor
21
+ from monai.transforms import CropForeground
22
+ from monai.transforms.lazy.functional import apply_pending
23
+ from tests.test_utils import TEST_NDARRAYS_ALL, assert_allclose
24
+
25
+ TEST_COORDS, TESTS, TEST_LAZY_ERROR = [], [], []
26
+
27
+ for p in TEST_NDARRAYS_ALL:
28
+ TEST_COORDS.append(
29
+ [
30
+ {"select_fn": lambda x: x > 0, "channel_indices": None, "margin": 0},
31
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 1, 2, 1, 0], [0, 0, 0, 0, 0]]]),
32
+ p([[[1, 2, 1], [2, 3, 2], [1, 2, 1]]]),
33
+ True,
34
+ ]
35
+ )
36
+
37
+ TESTS.append(
38
+ [
39
+ {"select_fn": lambda x: x > 1, "channel_indices": None, "margin": 0},
40
+ p([[[0, 0, 0, 0, 0], [0, 1, 1, 1, 0], [0, 1, 3, 1, 0], [0, 1, 1, 1, 0], [0, 0, 0, 0, 0]]]),
41
+ p([[[3]]]),
42
+ False,
43
+ ]
44
+ )
45
+
46
+ TESTS.append(
47
+ [
48
+ {"select_fn": lambda x: x > 0, "channel_indices": 0, "margin": 0},
49
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 1, 2, 1, 0], [0, 0, 0, 0, 0]]]),
50
+ p([[[1, 2, 1], [2, 3, 2], [1, 2, 1]]]),
51
+ True,
52
+ ]
53
+ )
54
+
55
+ TESTS.append(
56
+ [
57
+ {"select_fn": lambda x: x > 0, "channel_indices": None, "margin": 1},
58
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]]),
59
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 0, 0, 0, 0]]]),
60
+ True,
61
+ ]
62
+ )
63
+
64
+ TESTS.append(
65
+ [
66
+ {"select_fn": lambda x: x > 0, "channel_indices": None, "margin": [2, 1], "allow_smaller": True},
67
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]]),
68
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]]),
69
+ True,
70
+ ]
71
+ )
72
+
73
+ TESTS.append(
74
+ [
75
+ {"select_fn": lambda x: x > 0, "channel_indices": None, "margin": [2, 1], "allow_smaller": False},
76
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]]),
77
+ p([[[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]]),
78
+ True,
79
+ ]
80
+ )
81
+
82
+ TESTS.append(
83
+ [
84
+ {"select_fn": lambda x: x > 0, "channel_indices": None, "margin": 0, "k_divisible": 4},
85
+ p([[[0, 0, 0, 0, 0], [0, 1, 2, 1, 0], [0, 2, 3, 2, 0], [0, 1, 2, 1, 0], [0, 0, 0, 0, 0]]]),
86
+ p([[[1, 2, 1, 0], [2, 3, 2, 0], [1, 2, 1, 0], [0, 0, 0, 0]]]),
87
+ True,
88
+ ]
89
+ )
90
+
91
+ TEST_LAZY_ERROR.append(
92
+ [
93
+ {"select_fn": lambda x: x > 0, "channel_indices": None, "margin": 0, "k_divisible": 10},
94
+ p([[[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]]]),
95
+ p(np.zeros((1, 0, 0), dtype=np.int64)),
96
+ True,
97
+ ]
98
+ )
99
+
100
+
101
+ class TestCropForeground(unittest.TestCase):
102
+ @parameterized.expand(TEST_COORDS + TESTS)
103
+ def test_value(self, arguments, image, expected_data, _):
104
+ cropper = CropForeground(**arguments)
105
+ result = cropper(image)
106
+ assert_allclose(result, expected_data, type_test=False)
107
+ self.assertIsInstance(result, MetaTensor)
108
+ self.assertEqual(len(result.applied_operations), 1)
109
+ inv = cropper.inverse(result)
110
+ self.assertIsInstance(inv, MetaTensor)
111
+ self.assertEqual(inv.applied_operations, [])
112
+ self.assertTupleEqual(inv.shape, image.shape)
113
+
114
+ @parameterized.expand(TEST_COORDS)
115
+ def test_return_coords(self, arguments, image, _expected_data, _align_corners):
116
+ arguments["return_coords"] = True
117
+ _, start_coord, end_coord = CropForeground(**arguments)(image)
118
+ arguments["return_coords"] = False
119
+ np.testing.assert_allclose(start_coord, np.asarray([1, 1]))
120
+ np.testing.assert_allclose(end_coord, np.asarray([4, 4]))
121
+
122
+ @parameterized.expand(TEST_COORDS + TESTS)
123
+ def test_pending_ops(self, input_param, image, _expected_data, align_corners):
124
+ crop_fn = CropForeground(**input_param)
125
+ # non-lazy
126
+ expected = crop_fn(image)
127
+ self.assertIsInstance(expected, MetaTensor)
128
+ # lazy
129
+ crop_fn.lazy = True
130
+ pending_result = crop_fn(image)
131
+ self.assertIsInstance(pending_result, MetaTensor)
132
+ assert_allclose(pending_result.peek_pending_affine(), expected.affine)
133
+ assert_allclose(pending_result.peek_pending_shape(), expected.shape[1:])
134
+ # only support nearest
135
+ overrides = {"mode": "nearest", "align_corners": align_corners}
136
+ result = apply_pending(pending_result, overrides=overrides)[0]
137
+ # compare
138
+ assert_allclose(result, expected, rtol=1e-5)
139
+
140
+ @parameterized.expand(TEST_LAZY_ERROR)
141
+ @unittest.skipIf(USE_COMPILED, "skip errors whe use compiled")
142
+ def test_lazy_error(self, input_param, image, _expected_data, align_corners):
143
+ with self.assertRaises(ValueError):
144
+ crop_fn = CropForeground(**input_param)
145
+ # lazy
146
+ crop_fn.lazy = True
147
+ pending_result = crop_fn(image)
148
+ overrides = {"mode": "nearest", "align_corners": align_corners}
149
+ return apply_pending(pending_result, overrides=overrides)[0]
150
+
151
+ @parameterized.expand(TEST_COORDS + TESTS)
152
+ def test_inverse_pending_ops(self, input_param, image, _expected_data, align_corners):
153
+ crop_fn = CropForeground(**input_param)
154
+ crop_fn.lazy = True
155
+ pending_result = crop_fn(image)
156
+ self.assertIsInstance(pending_result, MetaTensor)
157
+ result = apply_pending(pending_result, overrides={"mode": "nearest", "align_corners": align_corners})[0]
158
+ inverted = crop_fn.inverse(result)
159
+ self.assertEqual(image.shape, inverted.shape)
160
+ self.assertTrue((not inverted.applied_operations) and (not inverted.pending_operations))
161
+
162
+
163
+ if __name__ == "__main__":
164
+ unittest.main()