smftools.analysis.compute.metrics_store

metrics_store.py — Per-run Zarr store for computed per-read analysis metrics.

Keeps raw signal caches pristine by storing derived metrics separately. Row ordering matches the companion <run>.zarr barcode-sorted obs.

Structure:

<run>_metrics.zarr/
    obs/
        ls_nrl_bp_<mask>        float (n_obs,)  — NaN where not computed
        ls_snr_<mask>           float (n_obs,)
        ls_peak_power_<mask>    float (n_obs,)
        ls_fwhm_bp_<mask>       float (n_obs,)
    obsm/
        ls_power_<mask>         float (n_obs, n_freqs)
        ls_freqs_<mask>         float (n_freqs,)  — shared frequency grid

Usage:

from smftools.analysis.compute import metrics_store

# Writing (analyses driver):
store = metrics_store.open_or_create(path, n_obs)
metrics_store.write_obs_array(store, "ls_nrl_bp_full_locus", arr)
metrics_store.write_obsm_array(store, "ls_power_full_locus", power_mat)
metrics_store.write_obsm_array(store, "ls_freqs_full_locus", freqs)
metrics_store.consolidate(path)

# Reading:
store = metrics_store.open_metrics_store(path)
nrl = store["obs"]["ls_nrl_bp_full_locus"][:]
power = store["obsm"]["ls_power_full_locus"][:]

Functions

consolidate(path)	Consolidate Zarr metadata so arrays are visible in read mode.
open_metrics_store(path)	Open an existing metrics store read-only.
open_or_create(path, n_obs)	Open an existing metrics store in append mode, or create a new one.
write_obs_array(store, col, values)	Write or overwrite a full-length (n_obs,) obs metric array.
write_obsm_array(store, key, values)	Write or overwrite an obsm array (2D for per-read power, 1D for shared freqs).

smftools.analysis.compute.metrics_store.open_or_create(path, n_obs)

Open an existing metrics store in append mode, or create a new one.

Return type:

object

Parameters

path : Path to the <run>_metrics.zarr directory. n_obs : Total number of obs rows (must match the companion signal Zarr).

Returns

zarr.Group

smftools.analysis.compute.metrics_store.write_obs_array(store, col, values)

Write or overwrite a full-length (n_obs,) obs metric array.

Return type:

None

smftools.analysis.compute.metrics_store.write_obsm_array(store, key, values)

Write or overwrite an obsm array (2D for per-read power, 1D for shared freqs).

Return type:

None

smftools.analysis.compute.metrics_store.consolidate(path)

Consolidate Zarr metadata so arrays are visible in read mode.

Return type:

None

smftools.analysis.compute.metrics_store.open_metrics_store(path)

Open an existing metrics store read-only.