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 +1,435 @@
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 json
15
+ import os
16
+ import tempfile
17
+ import unittest
18
+ from unittest.case import skipUnless
19
+ from unittest.mock import patch
20
+
21
+ import numpy as np
22
+ import torch
23
+ from parameterized import parameterized
24
+
25
+ import monai.networks.nets as nets
26
+ from monai.apps import check_hash
27
+ from monai.bundle import ConfigParser, create_workflow, load
28
+ from monai.bundle.scripts import _examine_monai_version, _list_latest_versions, download
29
+ from monai.utils import optional_import
30
+ from tests.test_utils import (
31
+ SkipIfBeforePyTorchVersion,
32
+ assert_allclose,
33
+ command_line_tests,
34
+ skip_if_downloading_fails,
35
+ skip_if_no_cuda,
36
+ skip_if_quick,
37
+ )
38
+
39
+ _, has_huggingface_hub = optional_import("huggingface_hub")
40
+
41
+ TEST_CASE_1 = ["test_bundle", None]
42
+
43
+ TEST_CASE_2 = ["test_bundle", "0.1.1"]
44
+
45
+ TEST_CASE_3 = [
46
+ ["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
47
+ "test_bundle",
48
+ "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/test_bundle.zip",
49
+ "a131d39a0af717af32d19e565b434928",
50
+ ]
51
+
52
+ TEST_CASE_4 = [
53
+ ["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
54
+ "test_bundle",
55
+ "monai-test/test_bundle",
56
+ ]
57
+
58
+ TEST_CASE_5 = [
59
+ ["models/model.pt", "models/model.ts", "configs/train.json"],
60
+ "brats_mri_segmentation",
61
+ "https://api.ngc.nvidia.com/v2/models/nvidia/monaihosting/brats_mri_segmentation/versions/0.4.0/files/brats_mri_segmentation_v0.4.0.zip",
62
+ ]
63
+
64
+ TEST_CASE_6 = [["models/model.pt", "configs/train.json"], "renalStructures_CECT_segmentation", "0.1.0"]
65
+
66
+ TEST_CASE_7 = [
67
+ ["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"],
68
+ "test_bundle",
69
+ "Project-MONAI/MONAI-extra-test-data/0.8.1",
70
+ "cuda" if torch.cuda.is_available() else "cpu",
71
+ "model.pt",
72
+ ]
73
+
74
+ TEST_CASE_8 = [
75
+ "spleen_ct_segmentation",
76
+ "cuda" if torch.cuda.is_available() else "cpu",
77
+ {"spatial_dims": 3, "out_channels": 5},
78
+ ]
79
+
80
+ TEST_CASE_9 = [
81
+ ["test_output.pt", "test_input.pt"],
82
+ "test_bundle",
83
+ "0.1.1",
84
+ "Project-MONAI/MONAI-extra-test-data/0.8.1",
85
+ "cuda" if torch.cuda.is_available() else "cpu",
86
+ "model.ts",
87
+ ]
88
+
89
+ TEST_CASE_10 = [
90
+ ["network.json", "test_output.pt", "test_input.pt", "large_files.yaml"],
91
+ "test_bundle",
92
+ "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/test_bundle_v0.1.3.zip",
93
+ {"model.pt": "27952767e2e154e3b0ee65defc5aed38", "model.ts": "97746870fe591f69ac09827175b00675"},
94
+ ]
95
+
96
+
97
+ class TestDownload(unittest.TestCase):
98
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
99
+ @skip_if_quick
100
+ def test_github_download_bundle(self, bundle_name, version):
101
+ bundle_files = ["model.pt", "model.ts", "network.json", "test_output.pt", "test_input.pt"]
102
+ repo = "Project-MONAI/MONAI-extra-test-data/0.8.1"
103
+ hash_val = "a131d39a0af717af32d19e565b434928"
104
+ with skip_if_downloading_fails():
105
+ # download a whole bundle from github releases
106
+ with tempfile.TemporaryDirectory() as tempdir:
107
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--name", bundle_name, "--source", "github"]
108
+ cmd += ["--bundle_dir", tempdir, "--repo", repo]
109
+ if version is not None:
110
+ cmd += ["--version", version]
111
+ command_line_tests(cmd)
112
+ for file in bundle_files:
113
+ file_path = os.path.join(tempdir, "test_bundle", file)
114
+ self.assertTrue(os.path.exists(file_path))
115
+ if file == "network.json":
116
+ self.assertTrue(check_hash(filepath=file_path, val=hash_val))
117
+
118
+ @parameterized.expand([TEST_CASE_3])
119
+ @skip_if_quick
120
+ def test_url_download_bundle(self, bundle_files, bundle_name, url, hash_val):
121
+ with skip_if_downloading_fails():
122
+ # download a single file from url, also use `args_file`
123
+ with tempfile.TemporaryDirectory() as tempdir:
124
+ def_args = {"name": bundle_name, "bundle_dir": tempdir, "url": ""}
125
+ def_args_file = os.path.join(tempdir, "def_args.json")
126
+ parser = ConfigParser()
127
+ parser.export_config_file(config=def_args, filepath=def_args_file)
128
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
129
+ cmd += ["--url", url, "--source", "github"]
130
+ command_line_tests(cmd)
131
+ for file in bundle_files:
132
+ file_path = os.path.join(tempdir, bundle_name, file)
133
+ self.assertTrue(os.path.exists(file_path))
134
+ if file == "network.json":
135
+ self.assertTrue(check_hash(filepath=file_path, val=hash_val))
136
+
137
+ @parameterized.expand([TEST_CASE_4])
138
+ @skip_if_quick
139
+ @skipUnless(has_huggingface_hub, "Requires `huggingface_hub`.")
140
+ def test_hf_hub_download_bundle(self, bundle_files, bundle_name, repo):
141
+ with skip_if_downloading_fails():
142
+ with tempfile.TemporaryDirectory() as tempdir:
143
+ cmd = [
144
+ "coverage",
145
+ "run",
146
+ "-m",
147
+ "monai.bundle",
148
+ "download",
149
+ "--name",
150
+ bundle_name,
151
+ "--source",
152
+ "huggingface_hub",
153
+ ]
154
+ cmd += ["--bundle_dir", tempdir, "--repo", repo, "--progress", "False"]
155
+ command_line_tests(cmd)
156
+ for file in bundle_files:
157
+ file_path = os.path.join(tempdir, bundle_name, file)
158
+ self.assertTrue(os.path.exists(file_path))
159
+
160
+ @parameterized.expand([TEST_CASE_5])
161
+ @skip_if_quick
162
+ def test_monaihosting_url_download_bundle(self, bundle_files, bundle_name, url):
163
+ with skip_if_downloading_fails():
164
+ # download a single file from url, also use `args_file`
165
+ with tempfile.TemporaryDirectory() as tempdir:
166
+ def_args = {"name": bundle_name, "bundle_dir": tempdir, "url": ""}
167
+ def_args_file = os.path.join(tempdir, "def_args.json")
168
+ parser = ConfigParser()
169
+ parser.export_config_file(config=def_args, filepath=def_args_file)
170
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
171
+ cmd += ["--url", url, "--progress", "False"]
172
+ command_line_tests(cmd)
173
+ for file in bundle_files:
174
+ file_path = os.path.join(tempdir, bundle_name, file)
175
+ self.assertTrue(os.path.exists(file_path))
176
+
177
+ @parameterized.expand([TEST_CASE_5])
178
+ @skip_if_quick
179
+ def test_ngc_private_source_download_bundle(self, bundle_files, bundle_name, _url):
180
+ with skip_if_downloading_fails():
181
+ # download a single file from url, also use `args_file`
182
+ with tempfile.TemporaryDirectory() as tempdir:
183
+ def_args = {"name": bundle_name, "bundle_dir": tempdir}
184
+ def_args_file = os.path.join(tempdir, "def_args.json")
185
+ parser = ConfigParser()
186
+ parser.export_config_file(config=def_args, filepath=def_args_file)
187
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
188
+ cmd += ["--progress", "False", "--source", "ngc_private"]
189
+ command_line_tests(cmd)
190
+ for file in bundle_files:
191
+ file_path = os.path.join(tempdir, bundle_name, file)
192
+ self.assertTrue(os.path.exists(file_path))
193
+
194
+ @parameterized.expand([TEST_CASE_6])
195
+ @skip_if_quick
196
+ def test_monaihosting_source_download_bundle(self, bundle_files, bundle_name, version):
197
+ with skip_if_downloading_fails():
198
+ # download a single file from url, also use `args_file`
199
+ with tempfile.TemporaryDirectory() as tempdir:
200
+ def_args = {"name": bundle_name, "bundle_dir": tempdir, "version": version}
201
+ def_args_file = os.path.join(tempdir, "def_args.json")
202
+ parser = ConfigParser()
203
+ parser.export_config_file(config=def_args, filepath=def_args_file)
204
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
205
+ cmd += ["--progress", "False", "--source", "monaihosting"]
206
+ command_line_tests(cmd)
207
+ for file in bundle_files:
208
+ file_path = os.path.join(tempdir, bundle_name, file)
209
+ self.assertTrue(os.path.exists(file_path))
210
+
211
+ @patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2"})
212
+ def test_examine_monai_version(self, mock_get_versions):
213
+ self.assertTrue(_examine_monai_version("1.1")[0]) # Should return True, compatible
214
+ self.assertTrue(_examine_monai_version("1.2rc1")[0]) # Should return True, compatible
215
+ self.assertFalse(_examine_monai_version("1.3")[0]) # Should return False, not compatible
216
+
217
+ @patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2rc1"})
218
+ def test_examine_monai_version_rc(self, mock_get_versions):
219
+ self.assertTrue(_examine_monai_version("1.2")[0]) # Should return True, compatible
220
+ self.assertFalse(_examine_monai_version("1.3")[0]) # Should return False, not compatible
221
+
222
+ def test_list_latest_versions(self):
223
+ """Test listing of the latest versions."""
224
+ data = {
225
+ "modelVersions": [
226
+ {"createdDate": "2021-01-01", "versionId": "1.0"},
227
+ {"createdDate": "2021-01-02", "versionId": "1.1"},
228
+ {"createdDate": "2021-01-03", "versionId": "1.2"},
229
+ ]
230
+ }
231
+ self.assertEqual(_list_latest_versions(data), ["1.2", "1.1", "1.0"])
232
+ self.assertEqual(_list_latest_versions(data, max_versions=2), ["1.2", "1.1"])
233
+ data = {
234
+ "modelVersions": [
235
+ {"createdDate": "2021-01-01", "versionId": "1.0"},
236
+ {"createdDate": "2021-01-02", "versionId": "1.1"},
237
+ ]
238
+ }
239
+ self.assertEqual(_list_latest_versions(data), ["1.1", "1.0"])
240
+
241
+ @skip_if_quick
242
+ @patch("monai.bundle.scripts.get_versions", return_value={"version": "1.2"})
243
+ def test_download_monaihosting(self, mock_get_versions):
244
+ """Test checking MONAI version from a metadata file."""
245
+ with patch("monai.bundle.scripts.logger") as mock_logger:
246
+ with tempfile.TemporaryDirectory() as tempdir:
247
+ download(name="spleen_ct_segmentation", bundle_dir=tempdir, source="monaihosting")
248
+ # Should have a warning message because the latest version is using monai > 1.2
249
+ mock_logger.warning.assert_called_once()
250
+
251
+ @skip_if_quick
252
+ @patch("monai.bundle.scripts.get_versions", return_value={"version": "1.3"})
253
+ def test_download_ngc(self, mock_get_versions):
254
+ """Test checking MONAI version from a metadata file."""
255
+ with patch("monai.bundle.scripts.logger") as mock_logger:
256
+ with tempfile.TemporaryDirectory() as tempdir:
257
+ download(name="spleen_ct_segmentation", bundle_dir=tempdir, source="ngc")
258
+ mock_logger.warning.assert_not_called()
259
+
260
+
261
+ @skip_if_no_cuda
262
+ class TestLoad(unittest.TestCase):
263
+ @parameterized.expand([TEST_CASE_7])
264
+ @skip_if_quick
265
+ def test_load_weights(self, bundle_files, bundle_name, repo, device, model_file):
266
+ with skip_if_downloading_fails():
267
+ # download bundle, and load weights from the downloaded path
268
+ with tempfile.TemporaryDirectory() as tempdir:
269
+ # load weights
270
+ weights = load(
271
+ name=bundle_name,
272
+ model_file=model_file,
273
+ bundle_dir=tempdir,
274
+ repo=repo,
275
+ source="github",
276
+ progress=False,
277
+ device=device,
278
+ return_state_dict=True,
279
+ )
280
+ # prepare network
281
+ with open(os.path.join(tempdir, bundle_name, bundle_files[2])) as f:
282
+ net_args = json.load(f)["network_def"]
283
+ model_name = net_args["_target_"]
284
+ del net_args["_target_"]
285
+ model = getattr(nets, model_name)(**net_args)
286
+ model.to(device)
287
+ model.load_state_dict(weights)
288
+ model.eval()
289
+
290
+ # prepare data and test
291
+ input_tensor = torch.load(os.path.join(tempdir, bundle_name, bundle_files[4]), map_location=device)
292
+ output = model.forward(input_tensor)
293
+ expected_output = torch.load(os.path.join(tempdir, bundle_name, bundle_files[3]), map_location=device)
294
+ assert_allclose(output, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
295
+
296
+ # load instantiated model directly and test, since the bundle has been downloaded,
297
+ # there is no need to input `repo`
298
+ _model_2 = getattr(nets, model_name)(**net_args)
299
+ model_2 = load(
300
+ name=bundle_name,
301
+ model=_model_2,
302
+ model_file=model_file,
303
+ bundle_dir=tempdir,
304
+ progress=False,
305
+ device=device,
306
+ source="github",
307
+ return_state_dict=False,
308
+ )
309
+ model_2.eval()
310
+ output_2 = model_2.forward(input_tensor)
311
+ assert_allclose(output_2, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
312
+
313
+ # test compatibility with return_state_dict=True.
314
+ model_3 = load(
315
+ name=bundle_name,
316
+ model_file=model_file,
317
+ bundle_dir=tempdir,
318
+ progress=False,
319
+ device=device,
320
+ net_name=model_name,
321
+ source="github",
322
+ return_state_dict=False,
323
+ **net_args,
324
+ )
325
+ model_3.eval()
326
+ output_3 = model_3.forward(input_tensor)
327
+ assert_allclose(output_3, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
328
+
329
+ @parameterized.expand([TEST_CASE_8])
330
+ @skip_if_quick
331
+ def test_load_weights_with_net_override(self, bundle_name, device, net_override):
332
+ with skip_if_downloading_fails():
333
+ # download bundle, and load weights from the downloaded path
334
+ with tempfile.TemporaryDirectory() as tempdir:
335
+ # load weights
336
+ model = load(
337
+ name=bundle_name,
338
+ bundle_dir=tempdir,
339
+ source="monaihosting",
340
+ progress=False,
341
+ device=device,
342
+ return_state_dict=False,
343
+ )
344
+
345
+ # prepare data and test
346
+ input_tensor = torch.rand(1, 1, 96, 96, 96).to(device)
347
+ output = model(input_tensor)
348
+ model_path = f"{tempdir}/spleen_ct_segmentation/models/model.pt"
349
+ workflow = create_workflow(
350
+ config_file=f"{tempdir}/spleen_ct_segmentation/configs/train.json", workflow_type="train"
351
+ )
352
+ expected_model = workflow.network_def.to(device)
353
+ expected_model.load_state_dict(torch.load(model_path))
354
+ expected_output = expected_model(input_tensor)
355
+ assert_allclose(output, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
356
+
357
+ # using net_override to override kwargs in network directly
358
+ model_2 = load(
359
+ name=bundle_name,
360
+ bundle_dir=tempdir,
361
+ source="monaihosting",
362
+ progress=False,
363
+ device=device,
364
+ return_state_dict=False,
365
+ net_override=net_override,
366
+ )
367
+
368
+ # prepare data and test
369
+ input_tensor = torch.rand(1, 1, 96, 96, 96).to(device)
370
+ output = model_2(input_tensor)
371
+ expected_shape = (1, 5, 96, 96, 96)
372
+ np.testing.assert_equal(output.shape, expected_shape)
373
+
374
+ @parameterized.expand([TEST_CASE_9])
375
+ @skip_if_quick
376
+ @SkipIfBeforePyTorchVersion((1, 7, 1))
377
+ def test_load_ts_module(self, bundle_files, bundle_name, version, repo, device, model_file):
378
+ with skip_if_downloading_fails():
379
+ # load ts module
380
+ with tempfile.TemporaryDirectory() as tempdir:
381
+ # load ts module
382
+ model_ts, metadata, extra_file_dict = load(
383
+ name=bundle_name,
384
+ version=version,
385
+ model_file=model_file,
386
+ load_ts_module=True,
387
+ bundle_dir=tempdir,
388
+ repo=repo,
389
+ progress=False,
390
+ device=device,
391
+ source="github",
392
+ config_files=("network.json",),
393
+ )
394
+
395
+ # prepare and test ts
396
+ input_tensor = torch.load(os.path.join(tempdir, bundle_name, bundle_files[1]), map_location=device)
397
+ output = model_ts.forward(input_tensor)
398
+ expected_output = torch.load(os.path.join(tempdir, bundle_name, bundle_files[0]), map_location=device)
399
+ assert_allclose(output, expected_output, atol=1e-4, rtol=1e-4, type_test=False)
400
+ # test metadata
401
+ self.assertTrue(metadata["pytorch_version"] == "1.7.1")
402
+ # test extra_file_dict
403
+ self.assertTrue("network.json" in extra_file_dict.keys())
404
+
405
+
406
+ class TestDownloadLargefiles(unittest.TestCase):
407
+ @parameterized.expand([TEST_CASE_10])
408
+ @skip_if_quick
409
+ def test_url_download_large_files(self, bundle_files, bundle_name, url, hash_val):
410
+ with skip_if_downloading_fails():
411
+ # download a single file from url, also use `args_file`
412
+ with tempfile.TemporaryDirectory() as tempdir:
413
+ def_args = {"name": bundle_name, "bundle_dir": tempdir, "url": ""}
414
+ def_args_file = os.path.join(tempdir, "def_args.json")
415
+ parser = ConfigParser()
416
+ parser.export_config_file(config=def_args, filepath=def_args_file)
417
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download", "--args_file", def_args_file]
418
+ cmd += ["--url", url, "--source", "github"]
419
+ command_line_tests(cmd)
420
+ for file in bundle_files:
421
+ file_path = os.path.join(tempdir, bundle_name, file)
422
+ print(file_path)
423
+ self.assertTrue(os.path.exists(file_path))
424
+
425
+ # download large files
426
+ bundle_path = os.path.join(tempdir, bundle_name)
427
+ cmd = ["coverage", "run", "-m", "monai.bundle", "download_large_files", "--bundle_path", bundle_path]
428
+ command_line_tests(cmd)
429
+ for file in ["model.pt", "model.ts"]:
430
+ file_path = os.path.join(tempdir, bundle_name, f"models/{file}")
431
+ self.assertTrue(check_hash(filepath=file_path, val=hash_val[file]))
432
+
433
+
434
+ if __name__ == "__main__":
435
+ unittest.main()
@@ -0,0 +1,94 @@
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
+ from parameterized import parameterized
17
+
18
+ from monai.bundle import get_all_bundles_list, get_bundle_info, get_bundle_versions
19
+ from monai.utils import optional_import
20
+ from tests.test_utils import SkipIfNoModule, skip_if_downloading_fails, skip_if_quick, skip_if_windows
21
+
22
+ requests, _ = optional_import("requests")
23
+
24
+ TEST_CASE_1 = [{"bundle_name": "brats_mri_segmentation", "tag": "hosting_storage_v1"}]
25
+
26
+ TEST_CASE_2 = [
27
+ {"bundle_name": "spleen_ct_segmentation", "version": "0.1.0", "auth_token": None, "tag": "hosting_storage_v1"}
28
+ ]
29
+
30
+ TEST_CASE_3 = [{"tag": "hosting_storage_v1"}]
31
+
32
+ TEST_CASE_4 = [{"tag": "dev"}]
33
+
34
+ TEST_CASE_5 = [{"bundle_name": "brats_mri_segmentation", "tag": "dev"}]
35
+
36
+ TEST_CASE_6 = [{"bundle_name": "spleen_ct_segmentation", "version": "0.1.0", "auth_token": None, "tag": "dev"}]
37
+
38
+ TEST_CASE_FAKE_TOKEN_1 = [{"bundle_name": "spleen_ct_segmentation", "version": "0.1.0", "auth_token": "ghp_errortoken"}]
39
+
40
+ TEST_CASE_FAKE_TOKEN_2 = [
41
+ {"bundle_name": "spleen_ct_segmentation", "version": "0.1.0", "auth_token": "ghp_errortoken", "tag": "dev"}
42
+ ]
43
+
44
+
45
+ @skip_if_windows
46
+ @SkipIfNoModule("requests")
47
+ class TestGetBundleData(unittest.TestCase):
48
+ @parameterized.expand([TEST_CASE_3, TEST_CASE_4])
49
+ @skip_if_quick
50
+ def test_get_all_bundles_list(self, params):
51
+ with skip_if_downloading_fails():
52
+ output = get_all_bundles_list(**params)
53
+ self.assertIsInstance(output, list)
54
+ self.assertIsInstance(output[0], tuple)
55
+ self.assertTrue(len(output[0]) == 2)
56
+
57
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_5])
58
+ @skip_if_quick
59
+ def test_get_bundle_versions(self, params):
60
+ with skip_if_downloading_fails():
61
+ output = get_bundle_versions(**params)
62
+ self.assertIsInstance(output, dict)
63
+ self.assertIn("latest_version", output)
64
+ self.assertIn("all_versions", output)
65
+ self.assertIn("0.1.0", output["all_versions"])
66
+
67
+ @parameterized.expand([TEST_CASE_1, TEST_CASE_2])
68
+ @skip_if_quick
69
+ def test_get_bundle_info(self, params):
70
+ with skip_if_downloading_fails():
71
+ output = get_bundle_info(**params)
72
+ self.assertIsInstance(output, dict)
73
+ for key in ["id", "name", "size", "download_count", "browser_download_url"]:
74
+ self.assertTrue(key in output)
75
+
76
+ @parameterized.expand([TEST_CASE_5, TEST_CASE_6])
77
+ @skip_if_quick
78
+ def test_get_bundle_info_monaihosting(self, params):
79
+ with skip_if_downloading_fails():
80
+ output = get_bundle_info(**params)
81
+ self.assertIsInstance(output, dict)
82
+ for key in ["name", "browser_download_url"]:
83
+ self.assertTrue(key in output)
84
+
85
+ @parameterized.expand([TEST_CASE_FAKE_TOKEN_1, TEST_CASE_FAKE_TOKEN_2])
86
+ @skip_if_quick
87
+ def test_fake_token(self, params):
88
+ with skip_if_downloading_fails():
89
+ with self.assertRaises(requests.exceptions.HTTPError):
90
+ get_bundle_info(**params)
91
+
92
+
93
+ if __name__ == "__main__":
94
+ unittest.main()
@@ -0,0 +1,41 @@
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 tempfile
15
+ import unittest
16
+ from unittest.case import skipUnless
17
+ from unittest.mock import patch
18
+
19
+ from parameterized import parameterized
20
+
21
+ from monai.bundle import push_to_hf_hub
22
+ from monai.utils import optional_import
23
+ from tests.test_utils import skip_if_quick
24
+
25
+ huggingface_hub, has_huggingface_hub = optional_import("huggingface_hub")
26
+
27
+ TEST_CASE_1 = ["monai-test/test_bundle_push", "test_bundle"]
28
+
29
+
30
+ class TestPushToHuggingFaceHub(unittest.TestCase):
31
+ @parameterized.expand([TEST_CASE_1])
32
+ @skip_if_quick
33
+ @skipUnless(has_huggingface_hub, "Requires `huggingface_hub` package.")
34
+ @patch.object(huggingface_hub.HfApi, "create_repo")
35
+ @patch.object(huggingface_hub.HfApi, "upload_folder")
36
+ @patch.object(huggingface_hub.HfApi, "create_tag")
37
+ def test_push_to_huggingface_hub(self, repo, bundle_name, test_createrepo, test_uploadfolder, test_createtag):
38
+ test_uploadfolder.return_value = "https://hf.co/repo/test"
39
+ with tempfile.TemporaryDirectory() as tempdir:
40
+ repo_url = push_to_hf_hub(repo, bundle_name, tempdir)
41
+ self.assertEqual("https://hf.co/repo/test", repo_url)