monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2507__py3-none-any.whl

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Files changed (776) hide show
  1. monai/__init__.py +1 -1
  2. monai/_version.py +3 -3
  3. monai/apps/auto3dseg/transforms.py +1 -4
  4. monai/data/utils.py +6 -13
  5. monai/inferers/utils.py +1 -2
  6. monai/losses/dice.py +2 -14
  7. monai/losses/ds_loss.py +1 -3
  8. monai/networks/layers/simplelayers.py +2 -14
  9. monai/networks/utils.py +4 -16
  10. monai/transforms/compose.py +28 -11
  11. monai/transforms/croppad/array.py +1 -6
  12. monai/transforms/io/array.py +0 -1
  13. monai/transforms/transform.py +15 -6
  14. monai/transforms/utils.py +1 -2
  15. monai/utils/tf32.py +0 -10
  16. monai/visualize/class_activation_maps.py +5 -8
  17. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/METADATA +2 -2
  18. monai_weekly-1.5.dev2507.dist-info/RECORD +1181 -0
  19. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/top_level.txt +1 -0
  20. tests/apps/__init__.py +10 -0
  21. tests/apps/deepedit/__init__.py +10 -0
  22. tests/apps/deepedit/test_deepedit_transforms.py +314 -0
  23. tests/apps/deepgrow/__init__.py +10 -0
  24. tests/apps/deepgrow/test_deepgrow_dataset.py +109 -0
  25. tests/apps/deepgrow/transforms/__init__.py +10 -0
  26. tests/apps/deepgrow/transforms/test_deepgrow_interaction.py +97 -0
  27. tests/apps/deepgrow/transforms/test_deepgrow_transforms.py +556 -0
  28. tests/apps/detection/__init__.py +10 -0
  29. tests/apps/detection/metrics/__init__.py +10 -0
  30. tests/apps/detection/metrics/test_detection_coco_metrics.py +69 -0
  31. tests/apps/detection/networks/__init__.py +10 -0
  32. tests/apps/detection/networks/test_retinanet.py +210 -0
  33. tests/apps/detection/networks/test_retinanet_detector.py +203 -0
  34. tests/apps/detection/test_box_transform.py +370 -0
  35. tests/apps/detection/utils/__init__.py +10 -0
  36. tests/apps/detection/utils/test_anchor_box.py +88 -0
  37. tests/apps/detection/utils/test_atss_box_matcher.py +46 -0
  38. tests/apps/detection/utils/test_box_coder.py +43 -0
  39. tests/apps/detection/utils/test_detector_boxselector.py +67 -0
  40. tests/apps/detection/utils/test_detector_utils.py +96 -0
  41. tests/apps/detection/utils/test_hardnegsampler.py +54 -0
  42. tests/apps/nuclick/__init__.py +10 -0
  43. tests/apps/nuclick/test_nuclick_transforms.py +259 -0
  44. tests/apps/pathology/__init__.py +10 -0
  45. tests/apps/pathology/handlers/__init__.py +10 -0
  46. tests/apps/pathology/handlers/test_from_engine_hovernet.py +38 -0
  47. tests/apps/pathology/test_lesion_froc.py +333 -0
  48. tests/apps/pathology/test_pathology_prob_nms.py +55 -0
  49. tests/apps/pathology/test_prepare_batch_hovernet.py +70 -0
  50. tests/apps/pathology/test_sliding_window_hovernet_inference.py +303 -0
  51. tests/apps/pathology/transforms/__init__.py +10 -0
  52. tests/apps/pathology/transforms/post/__init__.py +10 -0
  53. tests/apps/pathology/transforms/post/test_generate_distance_map.py +51 -0
  54. tests/apps/pathology/transforms/post/test_generate_distance_mapd.py +70 -0
  55. tests/apps/pathology/transforms/post/test_generate_instance_border.py +49 -0
  56. tests/apps/pathology/transforms/post/test_generate_instance_borderd.py +59 -0
  57. tests/apps/pathology/transforms/post/test_generate_instance_centroid.py +53 -0
  58. tests/apps/pathology/transforms/post/test_generate_instance_centroidd.py +56 -0
  59. tests/apps/pathology/transforms/post/test_generate_instance_contour.py +58 -0
  60. tests/apps/pathology/transforms/post/test_generate_instance_contourd.py +61 -0
  61. tests/apps/pathology/transforms/post/test_generate_instance_type.py +51 -0
  62. tests/apps/pathology/transforms/post/test_generate_instance_typed.py +53 -0
  63. tests/apps/pathology/transforms/post/test_generate_succinct_contour.py +55 -0
  64. tests/apps/pathology/transforms/post/test_generate_succinct_contourd.py +57 -0
  65. tests/apps/pathology/transforms/post/test_generate_watershed_markers.py +53 -0
  66. tests/apps/pathology/transforms/post/test_generate_watershed_markersd.py +83 -0
  67. tests/apps/pathology/transforms/post/test_generate_watershed_mask.py +77 -0
  68. tests/apps/pathology/transforms/post/test_generate_watershed_maskd.py +77 -0
  69. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processing.py +61 -0
  70. tests/apps/pathology/transforms/post/test_hovernet_instance_map_post_processingd.py +66 -0
  71. tests/apps/pathology/transforms/post/test_hovernet_nuclear_type_post_processing.py +66 -0
  72. tests/apps/pathology/transforms/post/test_watershed.py +60 -0
  73. tests/apps/pathology/transforms/post/test_watershedd.py +70 -0
  74. tests/apps/pathology/transforms/test_pathology_he_stain.py +230 -0
  75. tests/apps/pathology/transforms/test_pathology_he_stain_dict.py +225 -0
  76. tests/apps/reconstruction/__init__.py +10 -0
  77. tests/apps/reconstruction/nets/__init__.py +10 -0
  78. tests/apps/reconstruction/nets/test_recon_net_utils.py +82 -0
  79. tests/apps/reconstruction/test_complex_utils.py +77 -0
  80. tests/apps/reconstruction/test_fastmri_reader.py +82 -0
  81. tests/apps/reconstruction/test_mri_utils.py +37 -0
  82. tests/apps/reconstruction/transforms/__init__.py +10 -0
  83. tests/apps/reconstruction/transforms/test_kspace_mask.py +50 -0
  84. tests/apps/reconstruction/transforms/test_reference_based_normalize_intensity.py +77 -0
  85. tests/apps/reconstruction/transforms/test_reference_based_spatial_cropd.py +57 -0
  86. tests/apps/test_auto3dseg_bundlegen.py +156 -0
  87. tests/apps/test_check_hash.py +53 -0
  88. tests/apps/test_cross_validation.py +74 -0
  89. tests/apps/test_decathlondataset.py +93 -0
  90. tests/apps/test_download_and_extract.py +70 -0
  91. tests/apps/test_download_url_yandex.py +45 -0
  92. tests/apps/test_mednistdataset.py +72 -0
  93. tests/apps/test_mmar_download.py +154 -0
  94. tests/apps/test_tciadataset.py +123 -0
  95. tests/apps/vista3d/__init__.py +10 -0
  96. tests/apps/vista3d/test_point_based_window_inferer.py +77 -0
  97. tests/apps/vista3d/test_vista3d_sampler.py +100 -0
  98. tests/apps/vista3d/test_vista3d_transforms.py +94 -0
  99. tests/bundle/__init__.py +10 -0
  100. tests/bundle/test_bundle_ckpt_export.py +107 -0
  101. tests/bundle/test_bundle_download.py +435 -0
  102. tests/bundle/test_bundle_get_data.py +94 -0
  103. tests/bundle/test_bundle_push_to_hf_hub.py +41 -0
  104. tests/bundle/test_bundle_trt_export.py +147 -0
  105. tests/bundle/test_bundle_utils.py +149 -0
  106. tests/bundle/test_bundle_verify_metadata.py +66 -0
  107. tests/bundle/test_bundle_verify_net.py +76 -0
  108. tests/bundle/test_bundle_workflow.py +272 -0
  109. tests/bundle/test_component_locator.py +38 -0
  110. tests/bundle/test_config_item.py +138 -0
  111. tests/bundle/test_config_parser.py +392 -0
  112. tests/bundle/test_reference_resolver.py +114 -0
  113. tests/config/__init__.py +10 -0
  114. tests/config/test_cv2_dist.py +53 -0
  115. tests/engines/__init__.py +10 -0
  116. tests/engines/test_ensemble_evaluator.py +94 -0
  117. tests/engines/test_prepare_batch_default.py +76 -0
  118. tests/engines/test_prepare_batch_default_dist.py +76 -0
  119. tests/engines/test_prepare_batch_diffusion.py +104 -0
  120. tests/engines/test_prepare_batch_extra_input.py +80 -0
  121. tests/fl/__init__.py +10 -0
  122. tests/fl/monai_algo/__init__.py +10 -0
  123. tests/fl/monai_algo/test_fl_monai_algo.py +251 -0
  124. tests/fl/monai_algo/test_fl_monai_algo_dist.py +117 -0
  125. tests/fl/test_fl_monai_algo_stats.py +81 -0
  126. tests/fl/utils/__init__.py +10 -0
  127. tests/fl/utils/test_fl_exchange_object.py +63 -0
  128. tests/handlers/__init__.py +10 -0
  129. tests/handlers/test_handler_checkpoint_loader.py +182 -0
  130. tests/handlers/test_handler_checkpoint_saver.py +233 -0
  131. tests/handlers/test_handler_classification_saver.py +64 -0
  132. tests/handlers/test_handler_classification_saver_dist.py +77 -0
  133. tests/handlers/test_handler_clearml_image.py +65 -0
  134. tests/handlers/test_handler_clearml_stats.py +65 -0
  135. tests/handlers/test_handler_confusion_matrix.py +104 -0
  136. tests/handlers/test_handler_confusion_matrix_dist.py +70 -0
  137. tests/handlers/test_handler_decollate_batch.py +66 -0
  138. tests/handlers/test_handler_early_stop.py +68 -0
  139. tests/handlers/test_handler_garbage_collector.py +73 -0
  140. tests/handlers/test_handler_hausdorff_distance.py +111 -0
  141. tests/handlers/test_handler_ignite_metric.py +191 -0
  142. tests/handlers/test_handler_lr_scheduler.py +94 -0
  143. tests/handlers/test_handler_mean_dice.py +98 -0
  144. tests/handlers/test_handler_mean_iou.py +76 -0
  145. tests/handlers/test_handler_metrics_reloaded.py +149 -0
  146. tests/handlers/test_handler_metrics_saver.py +89 -0
  147. tests/handlers/test_handler_metrics_saver_dist.py +120 -0
  148. tests/handlers/test_handler_mlflow.py +296 -0
  149. tests/handlers/test_handler_nvtx.py +93 -0
  150. tests/handlers/test_handler_panoptic_quality.py +89 -0
  151. tests/handlers/test_handler_parameter_scheduler.py +136 -0
  152. tests/handlers/test_handler_post_processing.py +74 -0
  153. tests/handlers/test_handler_prob_map_producer.py +111 -0
  154. tests/handlers/test_handler_regression_metrics.py +160 -0
  155. tests/handlers/test_handler_regression_metrics_dist.py +245 -0
  156. tests/handlers/test_handler_rocauc.py +48 -0
  157. tests/handlers/test_handler_rocauc_dist.py +54 -0
  158. tests/handlers/test_handler_stats.py +281 -0
  159. tests/handlers/test_handler_surface_distance.py +113 -0
  160. tests/handlers/test_handler_tb_image.py +61 -0
  161. tests/handlers/test_handler_tb_stats.py +166 -0
  162. tests/handlers/test_handler_validation.py +59 -0
  163. tests/handlers/test_trt_compile.py +145 -0
  164. tests/handlers/test_write_metrics_reports.py +68 -0
  165. tests/inferers/__init__.py +10 -0
  166. tests/inferers/test_avg_merger.py +179 -0
  167. tests/inferers/test_controlnet_inferers.py +1310 -0
  168. tests/inferers/test_diffusion_inferer.py +236 -0
  169. tests/inferers/test_latent_diffusion_inferer.py +824 -0
  170. tests/inferers/test_patch_inferer.py +309 -0
  171. tests/inferers/test_saliency_inferer.py +55 -0
  172. tests/inferers/test_slice_inferer.py +57 -0
  173. tests/inferers/test_sliding_window_inference.py +377 -0
  174. tests/inferers/test_sliding_window_splitter.py +284 -0
  175. tests/inferers/test_wsi_sliding_window_splitter.py +249 -0
  176. tests/inferers/test_zarr_avg_merger.py +326 -0
  177. tests/integration/__init__.py +10 -0
  178. tests/integration/test_auto3dseg_ensemble.py +211 -0
  179. tests/integration/test_auto3dseg_hpo.py +189 -0
  180. tests/integration/test_deepedit_interaction.py +122 -0
  181. tests/integration/test_downsample_block.py +50 -0
  182. tests/integration/test_hovernet_nuclear_type_post_processingd.py +71 -0
  183. tests/integration/test_integration_autorunner.py +201 -0
  184. tests/integration/test_integration_bundle_run.py +240 -0
  185. tests/integration/test_integration_classification_2d.py +282 -0
  186. tests/integration/test_integration_determinism.py +95 -0
  187. tests/integration/test_integration_fast_train.py +231 -0
  188. tests/integration/test_integration_gpu_customization.py +159 -0
  189. tests/integration/test_integration_lazy_samples.py +219 -0
  190. tests/integration/test_integration_nnunetv2_runner.py +96 -0
  191. tests/integration/test_integration_segmentation_3d.py +304 -0
  192. tests/integration/test_integration_sliding_window.py +100 -0
  193. tests/integration/test_integration_stn.py +133 -0
  194. tests/integration/test_integration_unet_2d.py +67 -0
  195. tests/integration/test_integration_workers.py +61 -0
  196. tests/integration/test_integration_workflows.py +365 -0
  197. tests/integration/test_integration_workflows_adversarial.py +173 -0
  198. tests/integration/test_integration_workflows_gan.py +158 -0
  199. tests/integration/test_loader_semaphore.py +48 -0
  200. tests/integration/test_mapping_filed.py +122 -0
  201. tests/integration/test_meta_affine.py +183 -0
  202. tests/integration/test_metatensor_integration.py +114 -0
  203. tests/integration/test_module_list.py +76 -0
  204. tests/integration/test_one_of.py +283 -0
  205. tests/integration/test_pad_collation.py +124 -0
  206. tests/integration/test_reg_loss_integration.py +107 -0
  207. tests/integration/test_retinanet_predict_utils.py +154 -0
  208. tests/integration/test_seg_loss_integration.py +159 -0
  209. tests/integration/test_spatial_combine_transforms.py +185 -0
  210. tests/integration/test_testtimeaugmentation.py +186 -0
  211. tests/integration/test_vis_gradbased.py +69 -0
  212. tests/integration/test_vista3d_utils.py +159 -0
  213. tests/losses/__init__.py +10 -0
  214. tests/losses/deform/__init__.py +10 -0
  215. tests/losses/deform/test_bending_energy.py +88 -0
  216. tests/losses/deform/test_diffusion_loss.py +117 -0
  217. tests/losses/image_dissimilarity/__init__.py +10 -0
  218. tests/losses/image_dissimilarity/test_global_mutual_information_loss.py +150 -0
  219. tests/losses/image_dissimilarity/test_local_normalized_cross_correlation_loss.py +162 -0
  220. tests/losses/test_adversarial_loss.py +94 -0
  221. tests/losses/test_barlow_twins_loss.py +109 -0
  222. tests/losses/test_cldice_loss.py +51 -0
  223. tests/losses/test_contrastive_loss.py +86 -0
  224. tests/losses/test_dice_ce_loss.py +123 -0
  225. tests/losses/test_dice_focal_loss.py +124 -0
  226. tests/losses/test_dice_loss.py +227 -0
  227. tests/losses/test_ds_loss.py +189 -0
  228. tests/losses/test_focal_loss.py +379 -0
  229. tests/losses/test_generalized_dice_focal_loss.py +85 -0
  230. tests/losses/test_generalized_dice_loss.py +221 -0
  231. tests/losses/test_generalized_wasserstein_dice_loss.py +234 -0
  232. tests/losses/test_giou_loss.py +62 -0
  233. tests/losses/test_hausdorff_loss.py +264 -0
  234. tests/losses/test_masked_dice_loss.py +152 -0
  235. tests/losses/test_masked_loss.py +87 -0
  236. tests/losses/test_multi_scale.py +86 -0
  237. tests/losses/test_nacl_loss.py +167 -0
  238. tests/losses/test_perceptual_loss.py +122 -0
  239. tests/losses/test_spectral_loss.py +86 -0
  240. tests/losses/test_ssim_loss.py +59 -0
  241. tests/losses/test_sure_loss.py +72 -0
  242. tests/losses/test_tversky_loss.py +198 -0
  243. tests/losses/test_unified_focal_loss.py +66 -0
  244. tests/metrics/__init__.py +10 -0
  245. tests/metrics/test_compute_confusion_matrix.py +294 -0
  246. tests/metrics/test_compute_f_beta.py +80 -0
  247. tests/metrics/test_compute_fid_metric.py +40 -0
  248. tests/metrics/test_compute_froc.py +143 -0
  249. tests/metrics/test_compute_generalized_dice.py +240 -0
  250. tests/metrics/test_compute_meandice.py +306 -0
  251. tests/metrics/test_compute_meaniou.py +223 -0
  252. tests/metrics/test_compute_mmd_metric.py +56 -0
  253. tests/metrics/test_compute_multiscalessim_metric.py +83 -0
  254. tests/metrics/test_compute_panoptic_quality.py +113 -0
  255. tests/metrics/test_compute_regression_metrics.py +196 -0
  256. tests/metrics/test_compute_roc_auc.py +155 -0
  257. tests/metrics/test_compute_variance.py +147 -0
  258. tests/metrics/test_cumulative.py +63 -0
  259. tests/metrics/test_cumulative_average.py +74 -0
  260. tests/metrics/test_cumulative_average_dist.py +48 -0
  261. tests/metrics/test_hausdorff_distance.py +209 -0
  262. tests/metrics/test_label_quality_score.py +134 -0
  263. tests/metrics/test_loss_metric.py +57 -0
  264. tests/metrics/test_metrics_reloaded.py +96 -0
  265. tests/metrics/test_ssim_metric.py +78 -0
  266. tests/metrics/test_surface_dice.py +416 -0
  267. tests/metrics/test_surface_distance.py +186 -0
  268. tests/networks/__init__.py +10 -0
  269. tests/networks/blocks/__init__.py +10 -0
  270. tests/networks/blocks/dints_block/__init__.py +10 -0
  271. tests/networks/blocks/dints_block/test_acn_block.py +41 -0
  272. tests/networks/blocks/dints_block/test_factorized_increase.py +37 -0
  273. tests/networks/blocks/dints_block/test_factorized_reduce.py +37 -0
  274. tests/networks/blocks/dints_block/test_p3d_block.py +78 -0
  275. tests/networks/blocks/test_adn.py +86 -0
  276. tests/networks/blocks/test_convolutions.py +156 -0
  277. tests/networks/blocks/test_crf_cpu.py +513 -0
  278. tests/networks/blocks/test_crf_cuda.py +528 -0
  279. tests/networks/blocks/test_crossattention.py +185 -0
  280. tests/networks/blocks/test_denseblock.py +105 -0
  281. tests/networks/blocks/test_dynunet_block.py +116 -0
  282. tests/networks/blocks/test_fpn_block.py +88 -0
  283. tests/networks/blocks/test_localnet_block.py +121 -0
  284. tests/networks/blocks/test_mlp.py +78 -0
  285. tests/networks/blocks/test_patchembedding.py +212 -0
  286. tests/networks/blocks/test_regunet_block.py +103 -0
  287. tests/networks/blocks/test_se_block.py +85 -0
  288. tests/networks/blocks/test_se_blocks.py +78 -0
  289. tests/networks/blocks/test_segresnet_block.py +57 -0
  290. tests/networks/blocks/test_selfattention.py +232 -0
  291. tests/networks/blocks/test_simple_aspp.py +87 -0
  292. tests/networks/blocks/test_spatialattention.py +55 -0
  293. tests/networks/blocks/test_subpixel_upsample.py +87 -0
  294. tests/networks/blocks/test_text_encoding.py +49 -0
  295. tests/networks/blocks/test_transformerblock.py +90 -0
  296. tests/networks/blocks/test_unetr_block.py +158 -0
  297. tests/networks/blocks/test_upsample_block.py +134 -0
  298. tests/networks/blocks/warp/__init__.py +10 -0
  299. tests/networks/blocks/warp/test_dvf2ddf.py +72 -0
  300. tests/networks/blocks/warp/test_warp.py +250 -0
  301. tests/networks/layers/__init__.py +10 -0
  302. tests/networks/layers/filtering/__init__.py +10 -0
  303. tests/networks/layers/filtering/test_bilateral_approx_cpu.py +399 -0
  304. tests/networks/layers/filtering/test_bilateral_approx_cuda.py +404 -0
  305. tests/networks/layers/filtering/test_bilateral_precise.py +437 -0
  306. tests/networks/layers/filtering/test_phl_cpu.py +259 -0
  307. tests/networks/layers/filtering/test_phl_cuda.py +167 -0
  308. tests/networks/layers/filtering/test_trainable_bilateral.py +474 -0
  309. tests/networks/layers/filtering/test_trainable_joint_bilateral.py +609 -0
  310. tests/networks/layers/test_affine_transform.py +385 -0
  311. tests/networks/layers/test_apply_filter.py +89 -0
  312. tests/networks/layers/test_channel_pad.py +51 -0
  313. tests/networks/layers/test_conjugate_gradient.py +56 -0
  314. tests/networks/layers/test_drop_path.py +46 -0
  315. tests/networks/layers/test_gaussian.py +317 -0
  316. tests/networks/layers/test_gaussian_filter.py +206 -0
  317. tests/networks/layers/test_get_layers.py +65 -0
  318. tests/networks/layers/test_gmm.py +314 -0
  319. tests/networks/layers/test_grid_pull.py +93 -0
  320. tests/networks/layers/test_hilbert_transform.py +131 -0
  321. tests/networks/layers/test_lltm.py +62 -0
  322. tests/networks/layers/test_median_filter.py +52 -0
  323. tests/networks/layers/test_polyval.py +55 -0
  324. tests/networks/layers/test_preset_filters.py +136 -0
  325. tests/networks/layers/test_savitzky_golay_filter.py +141 -0
  326. tests/networks/layers/test_separable_filter.py +87 -0
  327. tests/networks/layers/test_skip_connection.py +48 -0
  328. tests/networks/layers/test_vector_quantizer.py +89 -0
  329. tests/networks/layers/test_weight_init.py +50 -0
  330. tests/networks/nets/__init__.py +10 -0
  331. tests/networks/nets/dints/__init__.py +10 -0
  332. tests/networks/nets/dints/test_dints_cell.py +110 -0
  333. tests/networks/nets/dints/test_dints_mixop.py +84 -0
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  681. tests/transforms/test_std_shift_intensityd.py +74 -0
  682. tests/transforms/test_threshold_intensity.py +38 -0
  683. tests/transforms/test_threshold_intensityd.py +58 -0
  684. tests/transforms/test_to_contiguous.py +47 -0
  685. tests/transforms/test_to_cupy.py +112 -0
  686. tests/transforms/test_to_cupyd.py +76 -0
  687. tests/transforms/test_to_device.py +42 -0
  688. tests/transforms/test_to_deviced.py +37 -0
  689. tests/transforms/test_to_numpy.py +85 -0
  690. tests/transforms/test_to_numpyd.py +68 -0
  691. tests/transforms/test_to_pil.py +52 -0
  692. tests/transforms/test_to_pild.py +50 -0
  693. tests/transforms/test_to_tensor.py +60 -0
  694. tests/transforms/test_to_tensord.py +71 -0
  695. tests/transforms/test_torchvision.py +66 -0
  696. tests/transforms/test_torchvisiond.py +63 -0
  697. tests/transforms/test_transform.py +62 -0
  698. tests/transforms/test_transpose.py +41 -0
  699. tests/transforms/test_transposed.py +52 -0
  700. tests/transforms/test_ultrasound_confidence_map_transform.py +711 -0
  701. tests/transforms/test_utils_pytorch_numpy_unification.py +90 -0
  702. tests/transforms/test_vote_ensemble.py +84 -0
  703. tests/transforms/test_vote_ensembled.py +107 -0
  704. tests/transforms/test_with_allow_missing_keys.py +76 -0
  705. tests/transforms/test_zoom.py +120 -0
  706. tests/transforms/test_zoomd.py +94 -0
  707. tests/transforms/transform/__init__.py +10 -0
  708. tests/transforms/transform/test_randomizable.py +52 -0
  709. tests/transforms/transform/test_randomizable_transform_type.py +37 -0
  710. tests/transforms/utility/__init__.py +10 -0
  711. tests/transforms/utility/test_apply_transform_to_points.py +81 -0
  712. tests/transforms/utility/test_apply_transform_to_pointsd.py +185 -0
  713. tests/transforms/utility/test_identity.py +29 -0
  714. tests/transforms/utility/test_identityd.py +30 -0
  715. tests/transforms/utility/test_lambda.py +71 -0
  716. tests/transforms/utility/test_lambdad.py +83 -0
  717. tests/transforms/utility/test_rand_lambda.py +87 -0
  718. tests/transforms/utility/test_rand_lambdad.py +77 -0
  719. tests/transforms/utility/test_simulatedelay.py +36 -0
  720. tests/transforms/utility/test_simulatedelayd.py +36 -0
  721. tests/transforms/utility/test_splitdim.py +52 -0
  722. tests/transforms/utility/test_splitdimd.py +96 -0
  723. tests/transforms/utils/__init__.py +10 -0
  724. tests/transforms/utils/test_correct_crop_centers.py +36 -0
  725. tests/transforms/utils/test_get_unique_labels.py +45 -0
  726. tests/transforms/utils/test_print_transform_backends.py +29 -0
  727. tests/transforms/utils/test_soft_clip.py +125 -0
  728. tests/utils/__init__.py +10 -0
  729. tests/utils/enums/__init__.py +10 -0
  730. tests/utils/enums/test_hovernet_loss.py +190 -0
  731. tests/utils/enums/test_ordering.py +289 -0
  732. tests/utils/enums/test_wsireader.py +663 -0
  733. tests/utils/misc/__init__.py +10 -0
  734. tests/utils/misc/test_ensure_tuple.py +53 -0
  735. tests/utils/misc/test_monai_env_vars.py +44 -0
  736. tests/utils/misc/test_monai_utils_misc.py +103 -0
  737. tests/utils/misc/test_str2bool.py +34 -0
  738. tests/utils/misc/test_str2list.py +33 -0
  739. tests/utils/test_alias.py +44 -0
  740. tests/utils/test_component_store.py +73 -0
  741. tests/utils/test_deprecated.py +455 -0
  742. tests/utils/test_enum_bound_interp.py +75 -0
  743. tests/utils/test_evenly_divisible_all_gather_dist.py +50 -0
  744. tests/utils/test_get_package_version.py +34 -0
  745. tests/utils/test_handler_logfile.py +84 -0
  746. tests/utils/test_handler_metric_logger.py +62 -0
  747. tests/utils/test_list_to_dict.py +43 -0
  748. tests/utils/test_look_up_option.py +87 -0
  749. tests/utils/test_optional_import.py +80 -0
  750. tests/utils/test_pad_mode.py +39 -0
  751. tests/utils/test_profiling.py +208 -0
  752. tests/utils/test_rankfilter_dist.py +77 -0
  753. tests/utils/test_require_pkg.py +83 -0
  754. tests/utils/test_sample_slices.py +43 -0
  755. tests/utils/test_set_determinism.py +74 -0
  756. tests/utils/test_squeeze_unsqueeze.py +71 -0
  757. tests/utils/test_state_cacher.py +67 -0
  758. tests/utils/test_torchscript_utils.py +113 -0
  759. tests/utils/test_version.py +91 -0
  760. tests/utils/test_version_after.py +65 -0
  761. tests/utils/type_conversion/__init__.py +10 -0
  762. tests/utils/type_conversion/test_convert_data_type.py +152 -0
  763. tests/utils/type_conversion/test_get_equivalent_dtype.py +65 -0
  764. tests/utils/type_conversion/test_safe_dtype_range.py +99 -0
  765. tests/visualize/__init__.py +10 -0
  766. tests/visualize/test_img2tensorboard.py +46 -0
  767. tests/visualize/test_occlusion_sensitivity.py +128 -0
  768. tests/visualize/test_plot_2d_or_3d_image.py +74 -0
  769. tests/visualize/test_vis_cam.py +98 -0
  770. tests/visualize/test_vis_gradcam.py +211 -0
  771. tests/visualize/utils/__init__.py +10 -0
  772. tests/visualize/utils/test_blend_images.py +63 -0
  773. tests/visualize/utils/test_matshow3d.py +133 -0
  774. monai_weekly-1.5.dev2506.dist-info/RECORD +0 -427
  775. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/LICENSE +0 -0
  776. {monai_weekly-1.5.dev2506.dist-info → monai_weekly-1.5.dev2507.dist-info}/WHEEL +0 -0
@@ -0,0 +1,212 @@
1
+ # Copyright (c) MONAI Consortium
2
+ # Licensed under the Apache License, Version 2.0 (the "License");
3
+ # you may not use this file except in compliance with the License.
4
+ # You may obtain a copy of the License at
5
+ # http://www.apache.org/licenses/LICENSE-2.0
6
+ # Unless required by applicable law or agreed to in writing, software
7
+ # distributed under the License is distributed on an "AS IS" BASIS,
8
+ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
9
+ # See the License for the specific language governing permissions and
10
+ # limitations under the License.
11
+
12
+ from __future__ import annotations
13
+
14
+ import unittest
15
+
16
+ import torch
17
+ from parameterized import parameterized
18
+
19
+ from monai.transforms import SobelGradientsd
20
+ from tests.test_utils import assert_allclose
21
+
22
+ IMAGE = torch.zeros(1, 16, 16, dtype=torch.float32)
23
+ IMAGE[0, 8, :] = 1
24
+
25
+ # Output with reflect padding
26
+ OUTPUT_3x3 = torch.zeros(2, 16, 16, dtype=torch.float32)
27
+ OUTPUT_3x3[0, 7, :] = 0.5
28
+ OUTPUT_3x3[0, 9, :] = -0.5
29
+
30
+ # Output with zero padding
31
+ OUTPUT_3x3_ZERO_PAD = OUTPUT_3x3.clone()
32
+ OUTPUT_3x3_ZERO_PAD[1, 7, 0] = OUTPUT_3x3_ZERO_PAD[1, 9, 0] = 0.125
33
+ OUTPUT_3x3_ZERO_PAD[1, 8, 0] = 0.25
34
+ OUTPUT_3x3_ZERO_PAD[1, 7, -1] = OUTPUT_3x3_ZERO_PAD[1, 9, -1] = -0.125
35
+ OUTPUT_3x3_ZERO_PAD[1, 8, -1] = -0.25
36
+ OUTPUT_3x3_ZERO_PAD[0, 7, 0] = OUTPUT_3x3_ZERO_PAD[0, 7, -1] = 3.0 / 8.0
37
+ OUTPUT_3x3_ZERO_PAD[0, 9, 0] = OUTPUT_3x3_ZERO_PAD[0, 9, -1] = -3.0 / 8.0
38
+
39
+ TEST_CASE_0 = [{"image": IMAGE}, {"keys": "image", "kernel_size": 3, "dtype": torch.float32}, {"image": OUTPUT_3x3}]
40
+ TEST_CASE_1 = [{"image": IMAGE}, {"keys": "image", "kernel_size": 3, "dtype": torch.float64}, {"image": OUTPUT_3x3}]
41
+ TEST_CASE_2 = [
42
+ {"image": IMAGE},
43
+ {"keys": "image", "kernel_size": 3, "dtype": torch.float32, "new_key_prefix": "sobel_"},
44
+ {"sobel_image": OUTPUT_3x3},
45
+ ]
46
+ TEST_CASE_3 = [
47
+ {"image": IMAGE},
48
+ {"keys": "image", "kernel_size": 3, "spatial_axes": 0, "dtype": torch.float32},
49
+ {"image": OUTPUT_3x3[0][None, ...]},
50
+ ]
51
+ TEST_CASE_4 = [
52
+ {"image": IMAGE},
53
+ {"keys": "image", "kernel_size": 3, "spatial_axes": 1, "dtype": torch.float32},
54
+ {"image": OUTPUT_3x3[1][None, ...]},
55
+ ]
56
+ TEST_CASE_5 = [
57
+ {"image": IMAGE},
58
+ {"keys": "image", "kernel_size": 3, "spatial_axes": [1], "dtype": torch.float32},
59
+ {"image": OUTPUT_3x3[1][None, ...]},
60
+ ]
61
+ TEST_CASE_6 = [
62
+ {"image": IMAGE},
63
+ {"keys": "image", "kernel_size": 3, "spatial_axes": [0, 1], "normalize_kernels": True, "dtype": torch.float32},
64
+ {"image": OUTPUT_3x3},
65
+ ]
66
+ TEST_CASE_7 = [
67
+ {"image": IMAGE},
68
+ {"keys": "image", "kernel_size": 3, "spatial_axes": (0, 1), "padding_mode": "reflect", "dtype": torch.float32},
69
+ {"image": OUTPUT_3x3},
70
+ ]
71
+ TEST_CASE_8 = [
72
+ {"image": IMAGE},
73
+ {"keys": "image", "kernel_size": 3, "spatial_axes": (0, 1), "padding_mode": "zeros", "dtype": torch.float32},
74
+ {"image": OUTPUT_3x3_ZERO_PAD},
75
+ ]
76
+ TEST_CASE_9 = [ # Non-normalized kernels
77
+ {"image": IMAGE},
78
+ {"keys": "image", "kernel_size": 3, "spatial_axes": (0, 1), "normalize_kernels": False, "dtype": torch.float32},
79
+ {"image": OUTPUT_3x3 * 8.0},
80
+ ]
81
+ TEST_CASE_10 = [ # Normalized gradients and normalized kernels
82
+ {"image": IMAGE},
83
+ {
84
+ "keys": "image",
85
+ "kernel_size": 3,
86
+ "spatial_axes": (0, 1),
87
+ "normalize_kernels": True,
88
+ "normalize_gradients": True,
89
+ "dtype": torch.float32,
90
+ },
91
+ {"image": torch.cat([OUTPUT_3x3[0:1] + 0.5, OUTPUT_3x3[1:2]])},
92
+ ]
93
+ TEST_CASE_11 = [ # Normalized gradients but non-normalized kernels
94
+ {"image": IMAGE},
95
+ {
96
+ "keys": "image",
97
+ "kernel_size": 3,
98
+ "spatial_axes": (0, 1),
99
+ "normalize_kernels": False,
100
+ "normalize_gradients": True,
101
+ "dtype": torch.float32,
102
+ },
103
+ {"image": torch.cat([OUTPUT_3x3[0:1] + 0.5, OUTPUT_3x3[1:2]])},
104
+ ]
105
+
106
+ TEST_CASE_KERNEL_0 = [
107
+ {"keys": "image", "kernel_size": 3, "dtype": torch.float64},
108
+ (torch.tensor([-0.5, 0.0, 0.5], dtype=torch.float64), torch.tensor([0.25, 0.5, 0.25], dtype=torch.float64)),
109
+ ]
110
+ TEST_CASE_KERNEL_1 = [
111
+ {"keys": "image", "kernel_size": 5, "dtype": torch.float64},
112
+ (
113
+ torch.tensor([-0.1250, -0.2500, 0.0000, 0.2500, 0.1250], dtype=torch.float64),
114
+ torch.tensor([0.0625, 0.2500, 0.3750, 0.2500, 0.0625], dtype=torch.float64),
115
+ ),
116
+ ]
117
+ TEST_CASE_KERNEL_2 = [
118
+ {"keys": "image", "kernel_size": 7, "dtype": torch.float64},
119
+ (
120
+ torch.tensor([-0.03125, -0.125, -0.15625, 0.0, 0.15625, 0.125, 0.03125], dtype=torch.float64),
121
+ torch.tensor([0.015625, 0.09375, 0.234375, 0.3125, 0.234375, 0.09375, 0.015625], dtype=torch.float64),
122
+ ),
123
+ ]
124
+ TEST_CASE_KERNEL_NON_NORMALIZED_0 = [
125
+ {"keys": "image", "kernel_size": 3, "normalize_kernels": False, "dtype": torch.float64},
126
+ (torch.tensor([-1.0, 0.0, 1.0], dtype=torch.float64), torch.tensor([1.0, 2.0, 1.0], dtype=torch.float64)),
127
+ ]
128
+ TEST_CASE_KERNEL_NON_NORMALIZED_1 = [
129
+ {"keys": "image", "kernel_size": 5, "normalize_kernels": False, "dtype": torch.float64},
130
+ (
131
+ torch.tensor([-1.0, -2.0, 0.0, 2.0, 1.0], dtype=torch.float64),
132
+ torch.tensor([1.0, 4.0, 6.0, 4.0, 1.0], dtype=torch.float64),
133
+ ),
134
+ ]
135
+ TEST_CASE_KERNEL_NON_NORMALIZED_2 = [
136
+ {"keys": "image", "kernel_size": 7, "normalize_kernels": False, "dtype": torch.float64},
137
+ (
138
+ torch.tensor([-1.0, -4.0, -5.0, 0.0, 5.0, 4.0, 1.0], dtype=torch.float64),
139
+ torch.tensor([1.0, 6.0, 15.0, 20.0, 15.0, 6.0, 1.0], dtype=torch.float64),
140
+ ),
141
+ ]
142
+ TEST_CASE_ERROR_0 = [{"image": IMAGE}, {"keys": "image", "kernel_size": 1}] # kernel size less than 3
143
+ TEST_CASE_ERROR_1 = [{"image": IMAGE}, {"keys": "image", "kernel_size": 4}] # even kernel size
144
+ TEST_CASE_ERROR_2 = [{"image": IMAGE}, {"keys": "image", "spatial_axes": "horizontal"}] # wrong type direction
145
+ TEST_CASE_ERROR_3 = [{"image": IMAGE}, {"keys": "image", "spatial_axes": 3}] # wrong direction
146
+ TEST_CASE_ERROR_4 = [{"image": IMAGE}, {"keys": "image", "spatial_axes": [3]}] # wrong direction in a list
147
+ TEST_CASE_ERROR_5 = [
148
+ {"image": IMAGE},
149
+ {"keys": "image", "spatial_axes": [0, 4]},
150
+ ] # correct and wrong direction in a list
151
+
152
+
153
+ class SobelGradientTests(unittest.TestCase):
154
+ backend = None
155
+
156
+ @parameterized.expand(
157
+ [
158
+ TEST_CASE_0,
159
+ TEST_CASE_1,
160
+ TEST_CASE_2,
161
+ TEST_CASE_3,
162
+ TEST_CASE_4,
163
+ TEST_CASE_5,
164
+ TEST_CASE_6,
165
+ TEST_CASE_7,
166
+ TEST_CASE_8,
167
+ TEST_CASE_9,
168
+ TEST_CASE_10,
169
+ TEST_CASE_11,
170
+ ]
171
+ )
172
+ def test_sobel_gradients(self, image_dict, arguments, expected_grad):
173
+ sobel = SobelGradientsd(**arguments)
174
+ grad = sobel(image_dict)
175
+ key = "image" if "new_key_prefix" not in arguments else arguments["new_key_prefix"] + arguments["keys"]
176
+ assert_allclose(grad[key], expected_grad[key])
177
+
178
+ @parameterized.expand(
179
+ [
180
+ TEST_CASE_KERNEL_0,
181
+ TEST_CASE_KERNEL_1,
182
+ TEST_CASE_KERNEL_2,
183
+ TEST_CASE_KERNEL_NON_NORMALIZED_0,
184
+ TEST_CASE_KERNEL_NON_NORMALIZED_1,
185
+ TEST_CASE_KERNEL_NON_NORMALIZED_2,
186
+ ]
187
+ )
188
+ def test_sobel_kernels(self, arguments, expected_kernels):
189
+ sobel = SobelGradientsd(**arguments)
190
+ self.assertEqual(sobel.kernel_diff.dtype, expected_kernels[0].dtype)
191
+ self.assertEqual(sobel.kernel_smooth.dtype, expected_kernels[0].dtype)
192
+ assert_allclose(sobel.kernel_diff, expected_kernels[0])
193
+ assert_allclose(sobel.kernel_smooth, expected_kernels[1])
194
+
195
+ @parameterized.expand(
196
+ [
197
+ TEST_CASE_ERROR_0,
198
+ TEST_CASE_ERROR_1,
199
+ TEST_CASE_ERROR_2,
200
+ TEST_CASE_ERROR_3,
201
+ TEST_CASE_ERROR_4,
202
+ TEST_CASE_ERROR_5,
203
+ ]
204
+ )
205
+ def test_sobel_gradients_error(self, image_dict, arguments):
206
+ with self.assertRaises(ValueError):
207
+ sobel = SobelGradientsd(**arguments)
208
+ sobel(image_dict)
209
+
210
+
211
+ if __name__ == "__main__":
212
+ unittest.main()
@@ -0,0 +1,381 @@
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.config import USE_COMPILED
21
+ from monai.data.meta_obj import set_track_meta
22
+ from monai.data.meta_tensor import MetaTensor
23
+ from monai.data.utils import affine_to_spacing
24
+ from monai.transforms import Spacing
25
+ from monai.utils import fall_back_tuple
26
+ from tests.lazy_transforms_utils import test_resampler_lazy
27
+ from tests.test_utils import TEST_DEVICES, TEST_NDARRAYS_ALL, assert_allclose, skip_if_quick
28
+
29
+ TESTS: list[list] = []
30
+ for device in TEST_DEVICES:
31
+ TESTS.append(
32
+ [
33
+ {"pixdim": (1.0, 1.5), "padding_mode": "zeros", "dtype": float},
34
+ torch.arange(4).reshape((1, 2, 2)) + 1.0, # data
35
+ torch.eye(4),
36
+ {},
37
+ torch.tensor([[[1.0, 1.0], [3.0, 2.0]]]),
38
+ *device,
39
+ ]
40
+ )
41
+ TESTS.append(
42
+ [
43
+ {"pixdim": 1.0, "padding_mode": "zeros", "dtype": float},
44
+ torch.ones((1, 2, 1, 2)), # data
45
+ torch.eye(4),
46
+ {},
47
+ torch.tensor([[[[1.0, 1.0]], [[1.0, 1.0]]]]),
48
+ *device,
49
+ ]
50
+ )
51
+ TESTS.append(
52
+ [
53
+ {"pixdim": 2.0, "padding_mode": "zeros", "dtype": float},
54
+ torch.arange(4).reshape((1, 2, 2)) + 1.0, # data
55
+ torch.eye(4),
56
+ {},
57
+ torch.tensor([[[1.0, 0.0], [0.0, 0.0]]]),
58
+ *device,
59
+ ]
60
+ )
61
+ TESTS.append(
62
+ [
63
+ {"pixdim": (1.0, 1.0, 1.0), "padding_mode": "zeros", "dtype": float},
64
+ torch.ones((1, 2, 1, 2)), # data
65
+ torch.eye(4),
66
+ {},
67
+ torch.tensor([[[[1.0, 1.0]], [[1.0, 1.0]]]]),
68
+ *device,
69
+ ]
70
+ )
71
+ TESTS.append(
72
+ [
73
+ {"pixdim": (1.0, 0.2, 1.5), "diagonal": False, "padding_mode": "zeros", "align_corners": True},
74
+ torch.ones((1, 2, 1, 2)), # data
75
+ torch.tensor([[2, 1, 0, 4], [-1, -3, 0, 5], [0, 0, 2.0, 5], [0, 0, 0, 1]]),
76
+ {},
77
+ (
78
+ torch.tensor([[[[0.75, 0.75]], [[0.75, 0.75]], [[0.75, 0.75]]]])
79
+ if USE_COMPILED
80
+ else torch.tensor([[[[0.95527864, 0.95527864]], [[1.0, 1.0]], [[1.0, 1.0]]]])
81
+ ),
82
+ *device,
83
+ ]
84
+ )
85
+ TESTS.append(
86
+ [
87
+ {"pixdim": (3.0, 1.0), "padding_mode": "zeros"},
88
+ torch.arange(24).reshape((2, 3, 4)), # data
89
+ torch.as_tensor(np.diag([-3.0, 0.2, 1.5, 1])),
90
+ {},
91
+ torch.tensor([[[0, 0], [4, 0], [8, 0]], [[12, 0], [16, 0], [20, 0]]]),
92
+ *device,
93
+ ]
94
+ )
95
+ TESTS.append(
96
+ [
97
+ {"pixdim": (3.0, 1.0), "padding_mode": "zeros"},
98
+ torch.arange(24).reshape((2, 3, 4)), # data
99
+ torch.eye(4),
100
+ {},
101
+ torch.tensor([[[0, 1, 2, 3], [0, 0, 0, 0]], [[12, 13, 14, 15], [0, 0, 0, 0]]]),
102
+ *device,
103
+ ]
104
+ )
105
+ TESTS.append(
106
+ [
107
+ {"pixdim": (1.0, 1.0), "align_corners": True},
108
+ torch.arange(24).reshape((2, 3, 4)), # data
109
+ torch.eye(4),
110
+ {},
111
+ torch.tensor(
112
+ [[[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11]], [[12, 13, 14, 15], [16, 17, 18, 19], [20, 21, 22, 23]]]
113
+ ),
114
+ *device,
115
+ ]
116
+ )
117
+ TESTS.append(
118
+ [
119
+ {"pixdim": (4.0, 5.0, 6.0)},
120
+ torch.arange(24).reshape((1, 2, 3, 4)), # data
121
+ torch.tensor([[-4, 0, 0, 4], [0, 5, 0, -5], [0, 0, 6, -6], [0, 0, 0, 1]]),
122
+ {},
123
+ torch.arange(24).reshape((1, 2, 3, 4)), # data
124
+ *device,
125
+ ]
126
+ )
127
+ TESTS.append(
128
+ [
129
+ {"pixdim": (4.0, 5.0, 6.0), "diagonal": True},
130
+ torch.arange(24).reshape((1, 2, 3, 4)), # data
131
+ torch.tensor([[-4, 0, 0, 4], [0, 5, 0, 0], [0, 0, 6, 0], [0, 0, 0, 1]]),
132
+ {},
133
+ torch.tensor(
134
+ [[[[12, 13, 14, 15], [16, 17, 18, 19], [20, 21, 22, 23]], [[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11]]]]
135
+ ),
136
+ *device,
137
+ ]
138
+ )
139
+ TESTS.append(
140
+ [
141
+ {"pixdim": (4.0, 5.0, 6.0), "padding_mode": "border", "diagonal": True},
142
+ torch.arange(24).reshape((1, 2, 3, 4)), # data
143
+ torch.tensor([[-4, 0, 0, -4], [0, 5, 0, 0], [0, 0, 6, 0], [0, 0, 0, 1]]),
144
+ {},
145
+ torch.tensor(
146
+ [[[[12, 13, 14, 15], [16, 17, 18, 19], [20, 21, 22, 23]], [[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11]]]]
147
+ ),
148
+ *device,
149
+ ]
150
+ )
151
+ TESTS.append(
152
+ [
153
+ {"pixdim": (4.0, 5.0, 6.0), "padding_mode": "border", "diagonal": True},
154
+ torch.arange(24).reshape((1, 2, 3, 4)), # data
155
+ torch.tensor([[-4, 0, 0, -4], [0, 5, 0, 0], [0, 0, 6, 0], [0, 0, 0, 1]]),
156
+ {"mode": "nearest"},
157
+ torch.tensor(
158
+ [[[[12, 13, 14, 15], [16, 17, 18, 19], [20, 21, 22, 23]], [[0, 1, 2, 3], [4, 5, 6, 7], [8, 9, 10, 11]]]]
159
+ ),
160
+ *device,
161
+ ]
162
+ )
163
+ TESTS.append(
164
+ [
165
+ {"pixdim": (1.9, 4.0), "padding_mode": "zeros", "diagonal": True},
166
+ torch.arange(24).reshape((1, 4, 6)), # data
167
+ torch.tensor([[-4, 0, 0, -4], [0, 5, 0, 0], [0, 0, 6, 0], [0, 0, 0, 1]]),
168
+ {"mode": "nearest"},
169
+ torch.tensor(
170
+ [
171
+ [
172
+ [18.0, 19.0, 20.0, 20.0, 21.0, 22.0, 23.0],
173
+ [18.0, 19.0, 20.0, 20.0, 21.0, 22.0, 23.0],
174
+ [12.0, 13.0, 14.0, 14.0, 15.0, 16.0, 17.0],
175
+ [12.0, 13.0, 14.0, 14.0, 15.0, 16.0, 17.0],
176
+ [6.0, 7.0, 8.0, 8.0, 9.0, 10.0, 11.0],
177
+ [6.0, 7.0, 8.0, 8.0, 9.0, 10.0, 11.0],
178
+ [0.0, 1.0, 2.0, 2.0, 3.0, 4.0, 5.0],
179
+ ]
180
+ ]
181
+ ),
182
+ *device,
183
+ ]
184
+ )
185
+ TESTS.append(
186
+ [
187
+ {"pixdim": (5.0, 3.0), "padding_mode": "border", "diagonal": True, "dtype": torch.float32},
188
+ torch.arange(24).reshape((1, 4, 6)), # data
189
+ torch.tensor([[-4, 0, 0, 0], [0, 5, 0, 0], [0, 0, 6, 0], [0, 0, 0, 1]]),
190
+ {"mode": "bilinear"},
191
+ torch.tensor(
192
+ [
193
+ [
194
+ [18.0, 18.6, 19.2, 19.8, 20.400002, 21.0, 21.6, 22.2, 22.8],
195
+ [10.5, 11.1, 11.700001, 12.299999, 12.900001, 13.5, 14.1, 14.700001, 15.3],
196
+ [3.0, 3.6000001, 4.2000003, 4.8, 5.4000006, 6.0, 6.6000004, 7.200001, 7.8],
197
+ ]
198
+ ]
199
+ ),
200
+ *device,
201
+ ]
202
+ )
203
+ TESTS.append(
204
+ [
205
+ {"pixdim": (5.0, 3.0), "padding_mode": "zeros", "diagonal": True, "dtype": torch.float32},
206
+ torch.arange(24).reshape((1, 4, 6)), # data
207
+ torch.tensor([[-4, 0, 0, 0], [0, 5, 0, 0], [0, 0, 6, 0], [0, 0, 0, 1]]),
208
+ {"mode": "bilinear"},
209
+ torch.tensor(
210
+ [
211
+ [
212
+ [18.0000, 18.6000, 19.2000, 19.8000, 20.4000, 21.0000, 21.6000, 22.2000, 22.8000],
213
+ [10.5000, 11.1000, 11.7000, 12.3000, 12.9000, 13.5000, 14.1000, 14.7000, 15.3000],
214
+ [3.0000, 3.6000, 4.2000, 4.8000, 5.4000, 6.0000, 6.6000, 7.2000, 7.8000],
215
+ ]
216
+ ]
217
+ ),
218
+ *device,
219
+ ]
220
+ )
221
+ TESTS.append(
222
+ [
223
+ {"pixdim": [-1, -1, 0.5], "padding_mode": "zeros", "dtype": float},
224
+ torch.ones((1, 2, 1, 2)), # data
225
+ torch.eye(4),
226
+ {},
227
+ torch.tensor([[[[1.0, 1.0, 1.0]], [[1.0, 1.0, 1.0]]]]),
228
+ *device,
229
+ ]
230
+ )
231
+ TESTS.append( # 5D input
232
+ [
233
+ {"pixdim": [-1, -1, 0.5], "padding_mode": "zeros", "dtype": float, "align_corners": True},
234
+ torch.ones((1, 2, 2, 2, 1)), # data
235
+ torch.eye(4),
236
+ {},
237
+ torch.ones((1, 2, 2, 3, 1)),
238
+ *device,
239
+ ]
240
+ )
241
+ TESTS.append( # 5D input
242
+ [
243
+ {"pixdim": 0.5, "padding_mode": "constant", "mode": "nearest", "scale_extent": True},
244
+ torch.ones((1, 368, 336, 368)), # data
245
+ torch.tensor(
246
+ [
247
+ [0.41, 0.005, 0.008, -79.7],
248
+ [-0.0049, 0.592, 0.0664, -57.4],
249
+ [-0.0073, -0.0972, 0.404, -32.1],
250
+ [0.0, 0.0, 0.0, 1.0],
251
+ ]
252
+ ),
253
+ {},
254
+ torch.ones((1, 302, 403, 301)),
255
+ *device,
256
+ ]
257
+ )
258
+
259
+ TESTS_TORCH = []
260
+ for track_meta in (False, True):
261
+ for p in TEST_NDARRAYS_ALL:
262
+ TESTS_TORCH.append([[1.2, 1.3, 0.9], p(torch.zeros((1, 3, 4, 5))), track_meta])
263
+
264
+ TEST_INVERSE = []
265
+ for d in TEST_DEVICES:
266
+ for recompute in (False, True):
267
+ for align in (False, True):
268
+ for scale_extent in (False, True):
269
+ TEST_INVERSE.append([*d, recompute, align, scale_extent])
270
+
271
+
272
+ @skip_if_quick
273
+ class TestSpacingCase(unittest.TestCase):
274
+ @parameterized.expand(TESTS)
275
+ def test_spacing(
276
+ self,
277
+ init_param: dict,
278
+ img: torch.Tensor,
279
+ affine: torch.Tensor,
280
+ data_param: dict,
281
+ expected_output: torch.Tensor,
282
+ device: torch.device,
283
+ ):
284
+ img = MetaTensor(img, affine=affine).to(device)
285
+ tr = Spacing(**init_param)
286
+ call_param = data_param.copy()
287
+ call_param["data_array"] = img
288
+ res: MetaTensor = tr(**call_param) # type: ignore
289
+ self.assertEqual(img.device, res.device)
290
+
291
+ test_resampler_lazy(tr, res, init_param=init_param, call_param=call_param)
292
+
293
+ assert_allclose(res, expected_output, atol=1e-1, rtol=1e-1)
294
+ sr = min(len(res.shape) - 1, 3)
295
+ if isinstance(init_param["pixdim"], float):
296
+ init_param["pixdim"] = [init_param["pixdim"]] * sr
297
+ init_pixdim = init_param["pixdim"][:sr]
298
+ norm = affine_to_spacing(res.affine, sr).cpu().numpy()
299
+ assert_allclose(fall_back_tuple(init_pixdim, norm), norm, type_test=False) # type: ignore
300
+
301
+ @parameterized.expand(TESTS_TORCH)
302
+ def test_spacing_torch(self, pixdim, img, track_meta: bool):
303
+ set_track_meta(track_meta)
304
+ init_param = {"pixdim": pixdim}
305
+ tr = Spacing(**init_param)
306
+ call_param = {"data_array": img}
307
+ res = tr(**call_param)
308
+
309
+ if track_meta:
310
+ self.assertIsInstance(res, MetaTensor)
311
+ new_spacing = affine_to_spacing(res.affine, 3) # type: ignore
312
+ assert_allclose(new_spacing, pixdim, type_test=False)
313
+ self.assertNotEqual(img.shape, res.shape)
314
+ test_resampler_lazy(tr, res, init_param=init_param, call_param=call_param)
315
+ else:
316
+ self.assertIsInstance(res, torch.Tensor)
317
+ self.assertNotIsInstance(res, MetaTensor)
318
+ self.assertNotEqual(img.shape, res.shape)
319
+ set_track_meta(True)
320
+
321
+ @parameterized.expand(TEST_INVERSE)
322
+ def test_inverse(self, device, recompute, align, scale_extent):
323
+ img_t = torch.rand((1, 10, 9, 8), dtype=torch.float32, device=device)
324
+ affine = torch.tensor(
325
+ [[0, 0, -1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]], dtype=torch.float32, device="cpu"
326
+ )
327
+ meta = {"fname": "somewhere"}
328
+ img = MetaTensor(img_t, affine=affine, meta=meta)
329
+ tr = Spacing(pixdim=[1.1, 1.2, 0.9], recompute_affine=recompute, align_corners=align, scale_extent=scale_extent)
330
+ # check that image and affine have changed
331
+ img = tr(img)
332
+ self.assertNotEqual(img.shape, img_t.shape)
333
+ l2_norm_affine = ((affine - img.affine) ** 2).sum() ** 0.5
334
+ self.assertGreater(l2_norm_affine, 5e-2)
335
+ # check that with inverse, image affine are back to how they were
336
+ img = tr.inverse(img)
337
+ self.assertEqual(img.applied_operations, [])
338
+ self.assertEqual(img.shape, img_t.shape)
339
+ l2_norm_affine = ((affine - img.affine) ** 2).sum() ** 0.5
340
+ self.assertLess(l2_norm_affine, 5e-2)
341
+
342
+ @parameterized.expand(TEST_INVERSE)
343
+ def test_inverse_mn_mx(self, device, recompute, align, scale_extent):
344
+ img_t = torch.rand((1, 10, 9, 8), dtype=torch.float32, device=device)
345
+ affine = torch.tensor(
346
+ [[0, 0, -1, 0], [1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 0, 1]], dtype=torch.float32, device="cpu"
347
+ )
348
+ img = MetaTensor(img_t, affine=affine, meta={"fname": "somewhere"})
349
+ choices = [(None, None), [1.2, None], [None, 0.7], [0.7, 0.9]]
350
+ idx = np.random.choice(range(len(choices)), size=1)[0]
351
+ tr = Spacing(
352
+ pixdim=[1.1, 1.2, 0.9],
353
+ recompute_affine=recompute,
354
+ align_corners=align,
355
+ scale_extent=scale_extent,
356
+ min_pixdim=[0.9, None, choices[idx][0]],
357
+ max_pixdim=[1.1, 1.1, choices[idx][1]],
358
+ )
359
+ img_out = tr(img)
360
+ if isinstance(img_out, MetaTensor):
361
+ assert_allclose(
362
+ img_out.pixdim, [1.0, 1.125, 0.888889] if recompute else [1.0, 1.2, 0.9], type_test=False, rtol=1e-4
363
+ )
364
+ img_out = tr.inverse(img_out)
365
+ self.assertEqual(img_out.applied_operations, [])
366
+ self.assertEqual(img_out.shape, img_t.shape)
367
+ self.assertLess(((affine - img_out.affine) ** 2).sum() ** 0.5, 5e-2)
368
+
369
+ def test_property_no_change(self):
370
+ affine = torch.tensor(
371
+ [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]], dtype=torch.float32, device="cpu"
372
+ )
373
+ affine[:3] *= 1 - 1e-4 # make sure it's not exactly target but close to the target
374
+ img = MetaTensor(torch.rand((1, 10, 9, 8), dtype=torch.float32), affine=affine, meta={"fname": "somewhere"})
375
+ tr = Spacing(pixdim=[1.0, 1.0, 1.0])
376
+ tr(img)
377
+ assert_allclose(tr.pixdim, [1.0, 1.0, 1.0], type_test=False)
378
+
379
+
380
+ if __name__ == "__main__":
381
+ unittest.main()