Data preprocessing error

[niuhulu-rui]

这是我的配置文件：

dataset paths

wsi_paths: /data2/longdan/datasets/naomo/kfb12023-11-21_07_00_45.svs output_path: ./example/output/preprocessing

basic setups

patch_size: 1024 patch_overlap: 6.25 target_mag: 40 processes: 8 overwrite: True

macenko stain normalization

normalize_stains: True

finding patches

min_intersection_ratio: 0.05 运行命令行： python3 ./preprocessing/patch_extraction/main_extraction.py --config ./example/preprocessing_example.yaml 运行结果： Traceback (most recent call last): File "/data2/longdan/project/CellViT-main/./preprocessing/patch_extraction/main_extraction.py", line 29, in configuration, logger = configuration_parser.get_config() File "/data2/longdan/project/CellViT-main/preprocessing/patch_extraction/src/cli.py", line 590, in get_config yaml_config = PreProcessingYamlConfig(**yaml_config) File "/data2/longdan/anaconda3/envs/cellvit_env/lib/python3.9/site-packages/pydantic/main.py", line 212, in init validated_self = self.__pydantic_validator__.validate_python(data, self_instance=self) pydantic_core._pydantic_core.ValidationError: 28 validation errors for PreProcessingYamlConfig wsi_extension Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing wsi_filelist Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing target_mpp Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing downsample Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing level Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing context_scales Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing check_resolution Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing annotation_paths Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing annotation_extension Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing incomplete_annotations Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing label_map_file Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing save_only_annotated_patches Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing exclude_classes Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing store_masks Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing generate_thumbnails Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing overlapping_labels Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing normalization_vector_json Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing adjust_brightness Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing tissue_annotation Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing tissue_annotation_intersection_ratio Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing masked_otsu Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing otsu_annotation Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing filter_patches Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing apply_prefilter Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing log_path Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing log_level Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing hardware_selection Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing wsi_properties Field required [type=missing, input_value={'wsi_paths': '/data2/lon...tersection_ratio': 0.05}, input_type=dict] For further information visit https://errors.pydantic.dev/2.9/v/missing

[FabianHoerst]

Hi,

I think the pydantic version is not the one specified in the requirements.