compress_to_h5

compress_to_h5(
    cadzow_npy,
    out_h5,
    recording,
    scale=0,
    sglx_meta=None,
    h=None,
    chunk=_COMPRESS_CHUNK,
    overlap=_COMPRESS_OVERLAP,
    epsilon=150.0,
    alpha=28.0,
    fs=250.0,
    t0_sync=None,
    fs_sync=None,
    channels=None,
    n_jobs=4,
)

Compress a Cadzow-denoised .npy into a single HDF5 archive of LFPCompressed chunks.

Each written chunk of chunk samples is extended by overlap samples on each side before SVD + wavelet-packet compression. Only the central chunk columns of Vh_hat are stored, eliminating wavelet-reconstruction boundary artefacts. Decompressed chunks are concatenated without overlap during reading.

HDF5 layout

///meta attrs: nc, ns_total, fs, compress_chunk, compress_overlap, epsilon, alpha, sglx_meta (JSON), geometry_x, geometry_y ///chunks// datasets: U_scaled (nc, r), vh_indices (n_kept,) int32, vh_values (n_kept,) float32 attrs: ns_original, ns_extended, left_overlap, vh_shape, epsilon, alpha, cr_svd, cr_wp, cr_total, rmse

where = f’{scale:02d}‘, e.g. ’00’, ‘01’, … Multiple recordings and/or scales can coexist in a single file; merging two files is a plain group copy.

Files are written with the module-level _H5_LIBVER constant (currently ("earliest", "v110")), which pins the HDF5 format to features available since HDF5 1.10 (2017) and makes the output readable by any modern HDF5 installation without version negotiation.

Parameters

Name	Type	Description	Default
cadzow_npy	path - like	Path to the (ns, nc) float32 Cadzow checkpoint (time-first).	required
out_h5	path - like	Output HDF5 file (created or overwritten).	required
recording	str	Unique key for this recording (e.g. a probe-insertion UUID). Top-level HDF5 group name; allows multiple recordings to coexist in one file.	required
scale	int	Resolution level (zero-padded to two digits in the path). 0 = base resolution. Default 0.	0
sglx_meta	dict or None	Original spikeglx metadata (sr.meta). Stored verbatim as JSON.	None
h	dict or None	Probe header. Defaults to NP1 geometry for nc channels.	None
chunk	int	Written chunk size (samples). Default 2048 = 2^11.	_COMPRESS_CHUNK
overlap	int	Guard-band samples each side. Default 128.	_COMPRESS_OVERLAP
epsilon	float	SVD threshold multiplier. Default 150.	150.0
alpha	float	WP threshold multiplier. Default 28.	28.0
fs	float	Sampling rate [Hz] written into metadata. Default 250.	250.0
channels	dict or None	Optional per-channel brain location annotations. Accepted keys (all optional): x (ML, metres), y (AP, metres), z (DV, metres), atlas_id (int32 array), acronym (list of str). Matches the dict returned by LFPackReader.channels_full. Written only to the 00 scale; ignored when scale != 0.	None