VibFrame to AnnData

Python package for staged conversion of TWave VibFrame data into reusable AnnData datasets.

The workflow is intentionally split in two phases:

1. Ingest raw VibFrame data once into an AnnData base (obs, obsm, uns).
2. Add, recalculate or remove features from the raw signals already stored in AnnData, without reopening the original VibFrame.

For datasets that fit comfortably in memory:

from vibframe_anndata import add_features, import_raw, remove_features, write_h5ad

adata = import_raw("dataset.vibframe.zip")
write_h5ad(adata, "dataset_raw.h5ad")

adata = add_features(
    adata,
    {
        "version": 1,
        "features": [
            {"name": "rms", "source": "waveform"},
            {"name": "kurtosis", "source": "waveform"},
        ],
    },
)

adata = remove_features(adata, ["kurtosis"])
write_h5ad(adata, "dataset_features.h5ad")

For datasets larger than RAM, use the blockwise H5AD APIs:

from vibframe_anndata import import_raw_to_h5ad, add_features_to_h5ad

base = import_raw_to_h5ad(
    "dataset.vibframe.zip",
    "dataset_raw.h5ad",
    config={
        "version": 1,
        "raw_import": {"on_missing_signal": "nan"},
        "output": {"dtype": "float32"},
    },
    block_size_mib=8,
)

add_features_to_h5ad(
    base,
    {
        "version": 1,
        "output": {"dtype": "float32"},
        "feature_policy": {"on_error": "nan"},
        "features": [{"name": "rms", "source": "waveform"}],
    },
    output="dataset_features.h5ad",
    block_rows=256,
)

The large-file path is transactional: raw samples are read in observation blocks and the destination is replaced only after all feature blocks succeed.

Install from PyPI after the first release:

python -m pip install vibframe-anndata

Install for development:

python -m pip install -e ".[dev]"

The repository intentionally does not version the project data/ directory. The mandatory CI fixture is generated deterministically from versioned synthetic source.

License

The software package is released under the BSD 3-Clause License, allowing academic and research users to inspect, modify and redistribute the code while retaining the copyright and license notices.

The BSD license applies to the software source code distributed by this project. External or reference datasets, VibFrame captures and other third-party material are not relicensed by this repository unless explicitly stated. Release archives exclude VibFrame reference binaries and the local data/ tree.

Documentation

• Documentation index
• Architecture
• AnnData data contract
• Configuration
• Metric support
• Testing and CI
• Known limitations
• Requirements compliance
• 0.1.0 release procedure
• Roadmap / 0.2.0 debt
• Changelog