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 +1,62 @@
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.data import MetaTensor
20
+ from monai.transforms import SqueezeDim
21
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
22
+
23
+ TESTS, TESTS_FAIL = [], []
24
+ for p in TEST_NDARRAYS:
25
+ TESTS.append([{"dim": None}, p(np.random.rand(1, 2, 1, 3)), (2, 3)])
26
+ TESTS.append([{"dim": 2}, p(np.random.rand(1, 2, 1, 8, 16)), (1, 2, 8, 16)])
27
+ TESTS.append([{"dim": -1}, p(np.random.rand(1, 1, 16, 8, 1)), (1, 1, 16, 8)])
28
+ TESTS.append([{}, p(np.random.rand(1, 2, 1, 3)), (2, 1, 3)])
29
+
30
+ TESTS_FAIL.append([ValueError, {"dim": -2}, p(np.random.rand(1, 1, 16, 8, 1))])
31
+ TESTS_FAIL.append([TypeError, {"dim": 0.5}, p(np.random.rand(1, 1, 16, 8, 1))])
32
+
33
+
34
+ class TestSqueezeDim(unittest.TestCase):
35
+ @parameterized.expand(TESTS)
36
+ def test_shape(self, input_param, test_data, expected_shape):
37
+ result = SqueezeDim(**input_param)(test_data)
38
+ self.assertTupleEqual(result.shape, expected_shape)
39
+ if "dim" in input_param and input_param["dim"] == 2 and isinstance(result, MetaTensor):
40
+ assert_allclose(result.affine.shape, [3, 3])
41
+
42
+ @parameterized.expand(TESTS_FAIL)
43
+ def test_invalid_inputs(self, exception, input_param, test_data):
44
+ with self.assertRaises(exception):
45
+ SqueezeDim(**input_param)(test_data)
46
+
47
+ def test_affine_ill_inputs(self):
48
+ img = MetaTensor(
49
+ np.random.rand(1, 2, 1, 3),
50
+ affine=[
51
+ [-0.7422, 0.0, 0.0, 186.3210],
52
+ [0.0, 0.0, -3.0, 70.6580],
53
+ [0.0, -0.7422, 0.0, 189.4130],
54
+ [0.0, 0.0, 0.0, 1.0],
55
+ ],
56
+ )
57
+ with self.assertWarns(UserWarning):
58
+ SqueezeDim(dim=2)(img)
59
+
60
+
61
+ if __name__ == "__main__":
62
+ unittest.main()
@@ -0,0 +1,98 @@
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.data import MetaTensor
20
+ from monai.transforms import SqueezeDimd
21
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
22
+
23
+ TESTS, TESTS_FAIL = [], []
24
+ for p in TEST_NDARRAYS:
25
+ TESTS.append(
26
+ [
27
+ {"keys": ["img", "seg"], "dim": None},
28
+ {"img": p(np.random.rand(1, 2, 1, 3)), "seg": p(np.random.randint(0, 2, size=[1, 2, 1, 3]))},
29
+ (2, 3),
30
+ ]
31
+ )
32
+
33
+ TESTS.append(
34
+ [
35
+ {"keys": ["img", "seg"], "dim": 2},
36
+ {"img": p(np.random.rand(1, 2, 1, 8, 16)), "seg": p(np.random.randint(0, 2, size=[1, 2, 1, 8, 16]))},
37
+ (1, 2, 8, 16),
38
+ ]
39
+ )
40
+
41
+ TESTS.append(
42
+ [
43
+ {"keys": ["img", "seg"], "dim": -1},
44
+ {"img": p(np.random.rand(1, 1, 16, 8, 1)), "seg": p(np.random.randint(0, 2, size=[1, 1, 16, 8, 1]))},
45
+ (1, 1, 16, 8),
46
+ ]
47
+ )
48
+
49
+ TESTS.append(
50
+ [
51
+ {"keys": ["img", "seg"]},
52
+ {"img": p(np.random.rand(1, 2, 1, 3)), "seg": p(np.random.randint(0, 2, size=[1, 2, 1, 3]))},
53
+ (2, 1, 3),
54
+ ]
55
+ )
56
+
57
+ TESTS.append(
58
+ [
59
+ {"keys": ["img", "seg"], "dim": 0},
60
+ {"img": p(np.random.rand(1, 2, 1, 3)), "seg": p(np.random.randint(0, 2, size=[1, 2, 1, 3]))},
61
+ (2, 1, 3),
62
+ ]
63
+ )
64
+
65
+ TESTS_FAIL.append(
66
+ [
67
+ ValueError,
68
+ {"keys": ["img", "seg"], "dim": -2},
69
+ {"img": p(np.random.rand(1, 1, 16, 8, 1)), "seg": p(np.random.randint(0, 2, size=[1, 1, 16, 8, 1]))},
70
+ ]
71
+ )
72
+
73
+ TESTS_FAIL.append(
74
+ [
75
+ TypeError,
76
+ {"keys": ["img", "seg"], "dim": 0.5},
77
+ {"img": p(np.random.rand(1, 1, 16, 8, 1)), "seg": p(np.random.randint(0, 2, size=[1, 1, 16, 8, 1]))},
78
+ ]
79
+ )
80
+
81
+
82
+ class TestSqueezeDim(unittest.TestCase):
83
+ @parameterized.expand(TESTS)
84
+ def test_shape(self, input_param, test_data, expected_shape):
85
+ result = SqueezeDimd(**input_param)(test_data)
86
+ self.assertTupleEqual(result["img"].shape, expected_shape)
87
+ self.assertTupleEqual(result["seg"].shape, expected_shape)
88
+ if "dim" in input_param and isinstance(result["img"], MetaTensor) and input_param["dim"] == 2:
89
+ assert_allclose(result["img"].affine.shape, [3, 3])
90
+
91
+ @parameterized.expand(TESTS_FAIL)
92
+ def test_invalid_inputs(self, exception, input_param, test_data):
93
+ with self.assertRaises(exception):
94
+ SqueezeDimd(**input_param)(test_data)
95
+
96
+
97
+ if __name__ == "__main__":
98
+ unittest.main()
@@ -0,0 +1,76 @@
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
+
18
+ from monai.transforms import ShiftIntensity, StdShiftIntensity
19
+ from monai.utils import dtype_numpy_to_torch
20
+ from tests.test_utils import TEST_NDARRAYS, NumpyImageTestCase2D, assert_allclose
21
+
22
+
23
+ class TestStdShiftIntensity(NumpyImageTestCase2D):
24
+ def test_value(self):
25
+ for p in TEST_NDARRAYS:
26
+ imt = p(self.imt)
27
+ factor = np.random.rand()
28
+ offset = np.std(self.imt) * factor
29
+ shifter = ShiftIntensity(offset=offset)
30
+ expected = shifter(imt)
31
+ std_shifter = StdShiftIntensity(factor=factor)
32
+ result = std_shifter(imt)
33
+ assert_allclose(result, expected, atol=0, rtol=1e-5, type_test=False)
34
+
35
+ def test_zerostd(self):
36
+ for p in TEST_NDARRAYS:
37
+ image = p(np.ones([2, 3, 3], dtype=np.float32))
38
+ for nonzero in [True, False]:
39
+ for channel_wise in [True, False]:
40
+ factor = np.random.rand()
41
+ std_shifter = StdShiftIntensity(factor=factor, nonzero=nonzero, channel_wise=channel_wise)
42
+ result = std_shifter(image)
43
+ assert_allclose(result, image, atol=0, rtol=1e-5, type_test=False)
44
+
45
+ def test_nonzero(self):
46
+ for p in TEST_NDARRAYS:
47
+ image = p(np.asarray([[4.0, 0.0, 2.0], [0, 2, 4]])) # std = 1
48
+ factor = np.random.rand()
49
+ std_shifter = StdShiftIntensity(factor=factor, nonzero=True)
50
+ result = std_shifter(image)
51
+ expected = p(np.asarray([[4 + factor, 0, 2 + factor], [0, 2 + factor, 4 + factor]], dtype=np.float32))
52
+ assert_allclose(result, expected, atol=0, rtol=1e-5, type_test=False)
53
+
54
+ def test_channel_wise(self):
55
+ for p in TEST_NDARRAYS:
56
+ image = p(np.stack((np.asarray([1.0, 2.0]), np.asarray([1.0, 1.0])))) # std: 0.5, 0
57
+ factor = np.random.rand()
58
+ std_shifter = StdShiftIntensity(factor=factor, channel_wise=True)
59
+ result = std_shifter(image)
60
+ expected = p(
61
+ np.stack((np.asarray([1 + 0.5 * factor, 2 + 0.5 * factor]), np.asarray([1, 1]))).astype(np.float32)
62
+ )
63
+ assert_allclose(result, expected, atol=0, rtol=1e-5, type_test=False)
64
+
65
+ def test_dtype(self):
66
+ trans_dtype = np.float32
67
+ for dtype in [int, np.float32, np.float64]:
68
+ image = np.random.rand(2, 2, 2).astype(dtype)
69
+ factor = np.random.rand()
70
+ std_shifter = StdShiftIntensity(factor=factor, dtype=trans_dtype)
71
+ result = std_shifter(image)
72
+ np.testing.assert_equal(result.dtype, dtype_numpy_to_torch(trans_dtype))
73
+
74
+
75
+ if __name__ == "__main__":
76
+ unittest.main()
@@ -0,0 +1,74 @@
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
+
18
+ from monai.transforms import ShiftIntensityd, StdShiftIntensityd
19
+ from monai.utils import dtype_numpy_to_torch
20
+ from tests.test_utils import NumpyImageTestCase2D
21
+
22
+
23
+ class TestStdShiftIntensityd(NumpyImageTestCase2D):
24
+ def test_value(self):
25
+ key = "img"
26
+ factor = np.random.rand()
27
+ offset = np.std(self.imt) * factor
28
+ shifter = ShiftIntensityd(keys=[key], offset=offset)
29
+ expected = shifter({key: self.imt})
30
+ std_shifter = StdShiftIntensityd(keys=[key], factor=factor)
31
+ result = std_shifter({key: self.imt})
32
+ np.testing.assert_allclose(result[key], expected[key], rtol=1e-5)
33
+
34
+ def test_zerostd(self):
35
+ key = "img"
36
+ image = np.ones([2, 3, 3])
37
+ for nonzero in [True, False]:
38
+ for channel_wise in [True, False]:
39
+ factor = np.random.rand()
40
+ std_shifter = StdShiftIntensityd(keys=[key], factor=factor, nonzero=nonzero, channel_wise=channel_wise)
41
+ result = std_shifter({key: image})
42
+ np.testing.assert_allclose(result[key], image, rtol=1e-5)
43
+
44
+ def test_nonzero(self):
45
+ key = "img"
46
+ image = np.asarray([[4.0, 0.0, 2.0], [0, 2, 4]]) # std = 1
47
+ factor = np.random.rand()
48
+ std_shifter = StdShiftIntensityd(keys=[key], factor=factor, nonzero=True)
49
+ result = std_shifter({key: image})
50
+ expected = np.asarray([[4 + factor, 0, 2 + factor], [0, 2 + factor, 4 + factor]])
51
+ np.testing.assert_allclose(result[key], expected, rtol=1e-5)
52
+
53
+ def test_channel_wise(self):
54
+ key = "img"
55
+ image = np.stack((np.asarray([1.0, 2.0]), np.asarray([1.0, 1.0]))) # std: 0.5, 0
56
+ factor = np.random.rand()
57
+ std_shifter = StdShiftIntensityd(keys=[key], factor=factor, channel_wise=True)
58
+ result = std_shifter({key: image})
59
+ expected = np.stack((np.asarray([1 + 0.5 * factor, 2 + 0.5 * factor]), np.asarray([1, 1])))
60
+ np.testing.assert_allclose(result[key], expected, rtol=1e-5)
61
+
62
+ def test_dtype(self):
63
+ key = "img"
64
+ trans_dtype = np.float32
65
+ for dtype in [int, np.float32, np.float64]:
66
+ image = np.random.rand(2, 2, 2).astype(dtype)
67
+ factor = np.random.rand()
68
+ std_shifter = StdShiftIntensityd(keys=[key], factor=factor, dtype=trans_dtype)
69
+ result = std_shifter({key: image})
70
+ np.testing.assert_equal(result[key].dtype, dtype_numpy_to_torch(trans_dtype))
71
+
72
+
73
+ if __name__ == "__main__":
74
+ unittest.main()
@@ -0,0 +1,38 @@
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 ThresholdIntensity
20
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
21
+
22
+ TESTS = []
23
+ for p in TEST_NDARRAYS:
24
+ TESTS.append([p, {"threshold": 5, "above": True, "cval": 0}, (0, 0, 0, 0, 0, 0, 6, 7, 8, 9)])
25
+ TESTS.append([p, {"threshold": 5, "above": False, "cval": 0}, (0, 1, 2, 3, 4, 0, 0, 0, 0, 0)])
26
+ TESTS.append([p, {"threshold": 5, "above": True, "cval": 5}, (5, 5, 5, 5, 5, 5, 6, 7, 8, 9)])
27
+
28
+
29
+ class TestThresholdIntensity(unittest.TestCase):
30
+ @parameterized.expand(TESTS)
31
+ def test_value(self, in_type, input_param, expected_value):
32
+ test_data = in_type(np.arange(10))
33
+ result = ThresholdIntensity(**input_param)(test_data)
34
+ assert_allclose(result, in_type(expected_value), type_test="tensor")
35
+
36
+
37
+ if __name__ == "__main__":
38
+ unittest.main()
@@ -0,0 +1,58 @@
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 ThresholdIntensityd
20
+ from tests.test_utils import TEST_NDARRAYS, assert_allclose
21
+
22
+ TESTS = []
23
+ for p in TEST_NDARRAYS:
24
+ TESTS.append(
25
+ [
26
+ p,
27
+ {"keys": ["image", "label", "extra"], "threshold": 5, "above": True, "cval": 0},
28
+ (0, 0, 0, 0, 0, 0, 6, 7, 8, 9),
29
+ ]
30
+ )
31
+ TESTS.append(
32
+ [
33
+ p,
34
+ {"keys": ["image", "label", "extra"], "threshold": 5, "above": False, "cval": 0},
35
+ (0, 1, 2, 3, 4, 0, 0, 0, 0, 0),
36
+ ]
37
+ )
38
+ TESTS.append(
39
+ [
40
+ p,
41
+ {"keys": ["image", "label", "extra"], "threshold": 5, "above": True, "cval": 5},
42
+ (5, 5, 5, 5, 5, 5, 6, 7, 8, 9),
43
+ ]
44
+ )
45
+
46
+
47
+ class TestThresholdIntensityd(unittest.TestCase):
48
+ @parameterized.expand(TESTS)
49
+ def test_value(self, in_type, input_param, expected_value):
50
+ test_data = {"image": in_type(np.arange(10)), "label": in_type(np.arange(10)), "extra": in_type(np.arange(10))}
51
+ result = ThresholdIntensityd(**input_param)(test_data)
52
+ assert_allclose(result["image"], in_type(expected_value), type_test="tensor")
53
+ assert_allclose(result["label"], in_type(expected_value), type_test="tensor")
54
+ assert_allclose(result["extra"], in_type(expected_value), type_test="tensor")
55
+
56
+
57
+ if __name__ == "__main__":
58
+ unittest.main()
@@ -0,0 +1,47 @@
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 convert_to_contiguous
20
+ from tests.test_utils import assert_allclose
21
+
22
+
23
+ class TestToContiguous(unittest.TestCase):
24
+ def test_contiguous_dict(self):
25
+ tochange = np.moveaxis(np.zeros((2, 3, 4)), 0, -1)
26
+ test_dict = {"test_key": [[1]], 0: np.array(0), 1: np.array([0]), "nested": {"nested": [tochange]}}
27
+ output = convert_to_contiguous(test_dict)
28
+ self.assertEqual(output["test_key"], [[1]])
29
+ assert_allclose(output[0], np.array(0))
30
+ assert_allclose(output[1], np.array([0]))
31
+ self.assertTrue(output["nested"]["nested"][0].flags.c_contiguous)
32
+
33
+ def test_contiguous_seq(self):
34
+ tochange = torch.zeros(2, 3, 4).transpose(0, 1)
35
+ test_seq = [[[1]], np.array(0), np.array([0]), torch.tensor(1.0), [[tochange]], "test_string", (1, 2, 3)]
36
+ output = convert_to_contiguous(test_seq)
37
+ self.assertEqual(output[0], [[1]])
38
+ assert_allclose(output[1], np.array(0))
39
+ assert_allclose(output[2], np.array([0]))
40
+ assert_allclose(output[3], torch.tensor(1.0))
41
+ self.assertTrue(output[4][0][0].is_contiguous())
42
+ self.assertEqual(output[5], "test_string")
43
+ self.assertEqual(output[6], (1, 2, 3))
44
+
45
+
46
+ if __name__ == "__main__":
47
+ unittest.main()
@@ -0,0 +1,112 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+ from unittest import skipUnless
16
+
17
+ import numpy as np
18
+ import torch
19
+
20
+ from monai.transforms import ToCupy
21
+ from monai.utils import optional_import
22
+ from tests.test_utils import HAS_CUPY, skip_if_no_cuda
23
+
24
+ cp, _ = optional_import("cupy")
25
+
26
+
27
+ @skipUnless(HAS_CUPY, "CuPy is required.")
28
+ class TestToCupy(unittest.TestCase):
29
+ def test_cupy_input(self):
30
+ test_data = cp.array([[1, 2], [3, 4]], dtype=cp.float32)
31
+ test_data = cp.rot90(test_data)
32
+ self.assertFalse(test_data.flags["C_CONTIGUOUS"])
33
+ result = ToCupy()(test_data)
34
+ self.assertTrue(result.dtype == cp.float32)
35
+ self.assertTrue(isinstance(result, cp.ndarray))
36
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
37
+ cp.testing.assert_allclose(result, test_data)
38
+
39
+ def test_cupy_input_dtype(self):
40
+ test_data = cp.array([[1, 2], [3, 4]], dtype=cp.float32)
41
+ test_data = cp.rot90(test_data)
42
+ self.assertFalse(test_data.flags["C_CONTIGUOUS"])
43
+ result = ToCupy(cp.uint8)(test_data)
44
+ self.assertTrue(result.dtype == cp.uint8)
45
+ self.assertTrue(isinstance(result, cp.ndarray))
46
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
47
+ cp.testing.assert_allclose(result, test_data)
48
+
49
+ def test_numpy_input(self):
50
+ test_data = np.array([[1, 2], [3, 4]], dtype=np.float32)
51
+ test_data = np.rot90(test_data)
52
+ self.assertFalse(test_data.flags["C_CONTIGUOUS"])
53
+ result = ToCupy()(test_data)
54
+ self.assertTrue(result.dtype == cp.float32)
55
+ self.assertTrue(isinstance(result, cp.ndarray))
56
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
57
+ cp.testing.assert_allclose(result, test_data)
58
+
59
+ def test_numpy_input_dtype(self):
60
+ test_data = np.array([[1, 2], [3, 4]], dtype=np.float32)
61
+ test_data = np.rot90(test_data)
62
+ self.assertFalse(test_data.flags["C_CONTIGUOUS"])
63
+ result = ToCupy(np.uint8)(test_data)
64
+ self.assertEqual(result.dtype, cp.uint8)
65
+ self.assertIsInstance(result, cp.ndarray)
66
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
67
+ cp.testing.assert_allclose(result, test_data)
68
+
69
+ def test_tensor_input(self):
70
+ test_data = torch.tensor([[1, 2], [3, 4]], dtype=torch.float32)
71
+ test_data = test_data.rot90()
72
+ self.assertFalse(test_data.is_contiguous())
73
+ result = ToCupy()(test_data)
74
+ self.assertEqual(result.dtype, cp.float32)
75
+ self.assertIsInstance(result, cp.ndarray)
76
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
77
+ cp.testing.assert_allclose(result, test_data)
78
+
79
+ @skip_if_no_cuda
80
+ def test_tensor_cuda_input(self):
81
+ test_data = torch.tensor([[1, 2], [3, 4]], dtype=torch.float32).cuda()
82
+ test_data = test_data.rot90()
83
+ self.assertFalse(test_data.is_contiguous())
84
+ result = ToCupy()(test_data)
85
+ self.assertEqual(result.dtype, cp.float32)
86
+ self.assertIsInstance(result, cp.ndarray)
87
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
88
+ cp.testing.assert_allclose(result, test_data)
89
+
90
+ @skip_if_no_cuda
91
+ def test_tensor_cuda_input_dtype(self):
92
+ test_data = torch.tensor([[1, 2], [3, 4]], dtype=torch.uint8).cuda()
93
+ test_data = test_data.rot90()
94
+ self.assertFalse(test_data.is_contiguous())
95
+
96
+ result = ToCupy(dtype="float32")(test_data)
97
+ self.assertEqual(result.dtype, cp.float32)
98
+ self.assertIsInstance(result, cp.ndarray)
99
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
100
+ cp.testing.assert_allclose(result, test_data)
101
+
102
+ def test_list_tuple(self):
103
+ test_data = [[1, 2], [3, 4]]
104
+ result = ToCupy(wrap_sequence=True)(test_data)
105
+ cp.testing.assert_allclose(result, cp.asarray(test_data))
106
+ test_data = ((1, 2), (3, 4))
107
+ result = ToCupy(wrap_sequence=True)(test_data)
108
+ cp.testing.assert_allclose(result, cp.asarray(test_data))
109
+
110
+
111
+ if __name__ == "__main__":
112
+ unittest.main()
@@ -0,0 +1,76 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+ from unittest import skipUnless
16
+
17
+ import numpy as np
18
+ import torch
19
+
20
+ from monai.transforms import ToCupyd
21
+ from monai.utils import optional_import
22
+ from tests.test_utils import HAS_CUPY, skip_if_no_cuda
23
+
24
+ cp, _ = optional_import("cupy")
25
+
26
+
27
+ @skipUnless(HAS_CUPY, "CuPy is required.")
28
+ class TestToCupyd(unittest.TestCase):
29
+ def test_cupy_input(self):
30
+ test_data = cp.array([[1, 2], [3, 4]])
31
+ test_data = cp.rot90(test_data)
32
+ self.assertFalse(test_data.flags["C_CONTIGUOUS"])
33
+ result = ToCupyd(keys="img")({"img": test_data})["img"]
34
+ self.assertTrue(isinstance(result, cp.ndarray))
35
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
36
+ cp.testing.assert_allclose(result, test_data)
37
+
38
+ def test_numpy_input(self):
39
+ test_data = np.array([[1, 2], [3, 4]])
40
+ test_data = np.rot90(test_data)
41
+ self.assertFalse(test_data.flags["C_CONTIGUOUS"])
42
+ result = ToCupyd(keys="img")({"img": test_data})["img"]
43
+ self.assertTrue(isinstance(result, cp.ndarray))
44
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
45
+ cp.testing.assert_allclose(result, test_data)
46
+
47
+ def test_tensor_input(self):
48
+ test_data = torch.tensor([[1, 2], [3, 4]])
49
+ test_data = test_data.rot90()
50
+ self.assertFalse(test_data.is_contiguous())
51
+ result = ToCupyd(keys="img")({"img": test_data})["img"]
52
+ self.assertTrue(isinstance(result, cp.ndarray))
53
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
54
+ cp.testing.assert_allclose(result, test_data.numpy())
55
+
56
+ @skip_if_no_cuda
57
+ def test_tensor_cuda_input(self):
58
+ test_data = torch.tensor([[1, 2], [3, 4]]).cuda()
59
+ test_data = test_data.rot90()
60
+ self.assertFalse(test_data.is_contiguous())
61
+ result = ToCupyd(keys="img")({"img": test_data})["img"]
62
+ self.assertTrue(isinstance(result, cp.ndarray))
63
+ self.assertTrue(result.flags["C_CONTIGUOUS"])
64
+ cp.testing.assert_allclose(result, test_data.cpu().numpy())
65
+
66
+ def test_list_tuple(self):
67
+ test_data = [[1, 2], [3, 4]]
68
+ result = ToCupyd(keys="img", wrap_sequence=True)({"img": test_data})["img"]
69
+ cp.testing.assert_allclose(result, cp.asarray(test_data))
70
+ test_data = ((1, 2), (3, 4))
71
+ result = ToCupyd(keys="img", wrap_sequence=True)({"img": test_data})["img"]
72
+ cp.testing.assert_allclose(result, cp.asarray(test_data))
73
+
74
+
75
+ if __name__ == "__main__":
76
+ unittest.main()