feat(bids): Add BIDS dataset loader for neuroimaging data #1
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parquet scan options and docs
* more parquet stream arg docs * minor * minor
less api calls when resolving data_files
set dev version
This commit will be squashed.
* fix polars cast_column issue * remove debug statements * cast large_strings to string for image handling
allow streaming hdf5 files
retry open hf file
* keep hffs cache in workers when streaming * bonus: reorder hffs args to improve caching
* Update document_dataset.mdx * Update document_dataset.mdx OCR
* Add custom suffix support to from_generator * Renamed a new arg to fingerprint * Changed name to config_id in builder * Change version * Added a test * Version update * Update version * Update tests/test_arrow_dataset.py * Rename config_id to fingerprint in generator.py * Apply suggestions from code review * Update src/datasets/io/generator.py * Apply suggestions from code review --------- Co-authored-by: Quentin Lhoest <[email protected]>
* Add nifti support * update docs * update nifti after testing locally and from remote hub * update setup.py to add nibabel and update docs * add nifti_dataset * fix nifti dataset documentation * add nibabel to test dependency * Add section for creating a medical imaging dataset --------- Co-authored-by: Quentin Lhoest <[email protected]>
* WIP: shuffle working, interleave_ds not yet * remove debug statements * add test * update test * use recursive overwriting of generator seeds * update test description * remove debugging strings * return instances of baseexiterable instead of modifying inplace * add test to make sure multiple iterations over data are deterministic
* fix ci compressionfs * again * style
* update signature for _batch_setitems * arguments passthrough
…ggingface#7833) Adressing issue 7832
…huggingface#7831) * Fix argument passing in stratified shuffle split NumPy 2.0 changed the behavior of the `copy=False` parameter to be stricter. When `train_test_split` converted Arrow arrays to NumPy format for stratification, it triggered this error for non-contiguous arrays. Using `np.asarray()` allows copying when necessary, which is the recommended migration path per NumPy 2.0 documentation. * make style --------- Co-authored-by: Quentin Lhoest <[email protected]>
* add 3.14 * update ci * go home tf * torchcodec * numba * fix ci * no lz4 in python 3.14 * fix tests * again * again * again
* WIP: add audio, tests failing * WIP: add mono argument, tests failing * change from mono to num_channels in documentation, audio tests passing * update docs and move test for audio * update audio * update docstring for audio * Apply suggestions from code review --------- Co-authored-by: Quentin Lhoest <[email protected]>
fsspec 2025.10.0
release: 4.4.0
better streaming retries
…gingface#7848) remove mode parameter in docstring of pdf and video feature
* WIP: allow uploading of nifti * remove debug statements and fix test * remove debug statements * remove debug statements
Change arxiv to hg papers
* fix some broken links * some more --------- Co-authored-by: Quentin Lhoest <[email protected]>
* WIP: nifti vis working, now improve * seems to work fine, tests not there yet * remove uncommented lines
* try latest papaya * try niivue * update repr_html for nifti to work better with niivue * remove papaya files * remove papaya from setup.py * use ipyniivue * update nifti feature to use ipyniivue * add 3d crosshair for orientation * remove docstring
- Remove deprecated `trust_remote_code=True` from tests (not needed for packaged modules) - Fix ruff linting errors (import sorting, trailing newlines) - Apply ruff formatter for consistent code style - Convert set() generators to set comprehensions (C401)
- Update setup.py to include nibabel in BIDS extra - Update docs to clarify nibabel is included - Add nibabel availability check in _info() - Move os import to module level - Update test skipif to check both pybids and nibabel
Author
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Apologies for the accidental close - was cleaning up branches on my fork and it auto-closed linked PRs. Note: If you sync with the latest upstream main, the code footprint should be smaller since your NiiVue visualization work (huggingface#7878) is now merged. Happy to rebase if helpful! |
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Summary
Hey Tobias! 👋
Following up on your neuroimaging initiative in Discord - I implemented a BIDS dataset loader that builds on your Nifti feature work.
This enables
load_dataset('bids', data_dir='/path/to/bids')for neuroimaging researchers.Changes
src/datasets/packaged_modules/bids/- BIDS loader using PyBIDS + your Nifti featureUsage
Testing
make qualitypassesAlso opened upstream PR: huggingface#7886
Let me know if you'd like any changes! 🧠