ngio 0.2.8__tar.gz → 0.2.9__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {ngio-0.2.8 → ngio-0.2.9}/PKG-INFO +1 -1
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/_axes.py +4 -7
- {ngio-0.2.8 → ngio-0.2.9}/.copier-answers.yml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.gitattributes +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.github/ISSUE_TEMPLATE.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.github/TEST_FAIL_TEMPLATE.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.github/dependabot.yml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.github/scripts/download_data.sh +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.github/workflows/build_docs.yml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.github/workflows/ci.yml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.gitignore +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/.pre-commit-config.yaml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/LICENSE +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/README.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/_typos.toml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/api/common.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/api/hcs.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/api/images.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/api/ngio.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/api/tables.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/api/utils.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/code_of_conduct.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/contributing.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/getting_started/0_quickstart.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/getting_started/1_ome_zarr_containers.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/getting_started/2_images.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/getting_started/3_tables.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/getting_started/4_masked_images.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/getting_started/5_hcs.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/index.md +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/tutorials/feature_extraction.ipynb +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/tutorials/hcs_processing.ipynb +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/tutorials/image_processing.ipynb +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/docs/tutorials/image_segmentation.ipynb +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/mkdocs.yml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/pyproject.toml +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_array_pipe.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_axes_transforms.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_common_types.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_dimensions.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_masking_roi.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_pyramid.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_roi.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_slicer.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/common/_zoom.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/hcs/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/hcs/plate.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/abstract_image.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/create.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/image.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/label.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/masked_image.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/images/ome_zarr_container.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/_meta_handlers.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/_channels.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/_dataset.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/_ngio_image.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/ngio_specs/_pixel_size.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/v04/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/v04/_custom_models.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/ome_zarr_meta/v04/_v04_spec_utils.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/_validators.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_abstract_backend.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_anndata_utils.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_anndata_v1.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_csv_v1.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_json_v1.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_table_backends.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/backends/_utils.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/tables_container.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/v1/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/v1/_feature_table.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/v1/_generic_table.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/tables/v1/_roi_table.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/utils/__init__.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/utils/_datasets.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/utils/_errors.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/utils/_fractal_fsspec_store.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/utils/_logger.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/src/ngio/utils/_zarr_utils.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/conftest.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/labels/label/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_c1yx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/labels/label/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_cyx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/labels/label/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_czyx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/labels/label/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tcyx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/labels/label/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tczyx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_tyx.zarr/labels/label/0/.zarray +0 -0
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- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_yx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/labels/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/labels/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/labels/label/.zattrs +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/labels/label/.zgroup +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/labels/label/0/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/images/test_image_zyx.zarr/labels/label/1/.zarray +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/meta/base_ome_zarr_image_meta.json +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/meta/base_ome_zarr_image_meta_wrong_axis_order.json +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/meta/base_ome_zarr_label_meta.json +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/meta/base_ome_zarr_well_meta.json +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/data/v04/meta/ome_zarr_well_path_normalization_meta.json +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/common/test_dimensions.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/common/test_pyramid.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/common/test_roi.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/hcs/test_plate.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/hcs/test_well.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/images/test_create.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/images/test_images.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/images/test_masked_images.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/images/test_omezarr_container.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/ome_zarr_meta/test_image_handler.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/ome_zarr_meta/test_unit_ngio_specs.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/ome_zarr_meta/test_unit_v04_utils.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_backends.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_backends_utils.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_feature_table.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_generic_table.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_masking_roi_table_v1.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_roi_table_v1.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_table_group.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/tables/test_validators.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/utils/test_download_datasets.py +0 -0
- {ngio-0.2.8 → ngio-0.2.9}/tests/unit/utils/test_zarr_utils.py +0 -0
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from collections.abc import Collection
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from enum import Enum
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from logging import Logger
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from typing import Literal, TypeVar
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import numpy as np
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from pydantic import BaseModel, ConfigDict, Field
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from ngio.utils import NgioValidationError, NgioValueError
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logger = Logger(__name__)
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from ngio.utils import NgioValidationError, NgioValueError, ngio_logger
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T = TypeVar("T")
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@@ -102,20 +99,20 @@ class Axis(BaseModel):
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def implicit_type_cast(self, cast_type: AxisType) -> "Axis":
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unit = self.unit
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if self.axis_type != cast_type:
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ngio_logger.warning(
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f"Axis {self.on_disk_name} has type {self.axis_type}. "
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f"Casting to {cast_type}."
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if cast_type == AxisType.time and unit is None:
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ngio_logger.warning(
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f"Time axis {self.on_disk_name} has unit {self.unit}. "
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f"Casting to {DefaultSpaceUnit}."
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unit = DefaultTimeUnit
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if cast_type == AxisType.space and unit is None:
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ngio_logger.warning(
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f"Space axis {self.on_disk_name} has unit {unit}. "
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f"Casting to {DefaultSpaceUnit}."
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