feat(libcommon): Add NIfTI neuroimaging file support#3273
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Add support for NIfTI (.nii, .nii.gz) neuroimaging files in the Dataset Viewer. This enables viewing of brain imaging datasets such as BIDS-formatted neuroimaging studies. Changes: - Bump datasets dependency from 4.1.1 to ^4.4.1 (includes Nifti type) - Add nibabel ^5.0.0 dependency for NIfTI file handling - Add NiftiSource TypedDict and create_nifti_file() in asset.py - Add nifti() handler and dispatch in features.py - Handle both encoded (bytes/dict) and decoded (nibabel) Nifti cells - Update url_preparator.py for Nifti URL signing - Update rows.py to prevent truncation of Nifti columns - Update rows_utils.py for multithreaded Nifti uploads - Add test fixtures with minimal 2x2x2 NIfTI test file Closes #1 (Nifti Support for Neuroimaging Datasets)
- Use hasattr(value, 'to_bytes') instead of isinstance check to support Nifti1Image, Nifti2Image, and other nibabel types - Preserve original file extension (.nii vs .nii.gz) - Remove unused nibabel import
Regenerate all service and job lockfiles to pull in datasets 4.4.1 which includes the Nifti feature type. This fixes the CI failures where services couldn't import Nifti from datasets. Updated lockfiles: - libs/libapi/poetry.lock - services/admin/poetry.lock - services/api/poetry.lock - services/rows/poetry.lock - services/search/poetry.lock - services/sse-api/poetry.lock - services/webhook/poetry.lock - services/worker/poetry.lock - jobs/cache_maintenance/poetry.lock - jobs/mongodb_migration/poetry.lock
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Summary
This PR adds support for NIfTI (.nii, .nii.gz) neuroimaging files in the Dataset Viewer, enabling viewing of brain imaging datasets such as BIDS-formatted neuroimaging studies.
Changes:
datasetsdependency from 4.1.1 to ^4.4.1 (includes native Nifti type)nibabel ^5.0.0dependency for NIfTI file handlingFiles Modified
libs/libcommon/pyproject.tomllibs/libcommon/src/libcommon/viewer_utils/features.pylibs/libcommon/src/libcommon/viewer_utils/asset.pylibs/libcommon/src/libcommon/url_preparator.pylibs/libcommon/src/libcommon/viewer_utils/rows.pylibs/libapi/src/libapi/rows_utils.pylibs/libcommon/tests/Test Plan
test_get_cell_value_value[nifti-True/False],test_to_features_list[nifti])Affected Dataset
This fixes the Dataset Viewer for: https://huggingface.co/datasets/hugging-science/arc-aphasia-bids
Closes #3272