How to use the phylib.io.alf.EphysAlfCreator function in phylib

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github int-brain-lab / ibllib / ibllib / ephys / spikes.py View on Github external
def ks2_to_alf(ks_path, out_path, ampfactor=1, label=None, force=True):
    """
    Convert Kilosort 2 output to ALF dataset for single probe data
    :param ks_path:
    :param out_path:
    :return:

    TODO change/remove `ampfactor` after seeing how amplitudes are calculated by ks2
    """
    m = ephysqc.phy_model_from_ks2_path(ks_path)
    ephysqc.unit_metrics_ks2(ks_path, m, save=True)
    ac = alf.EphysAlfCreator(m)
    ac.convert(out_path, label=label, force=force, ampfactor=ampfactor)
github cortex-lab / phy / phy / apps / __init__.py View on Github external
"""Convert an ephys dataset into ALF. If several directories are specified, it is assumed
    that each directory contains the data for one probe of the same recording."""
    from phylib.io.alf import EphysAlfCreator
    from phylib.io.merge import Merger
    from phylib.io.model import load_model

    out_dir = Path(out_dir)

    if len(subdirs) >= 2:
        # Merge in the `merged` subdirectory inside the output directory.
        m = Merger(subdirs, out_dir / '_tmp_merged')
        model = m.merge()
    else:
        model = load_model(Path(subdirs[0]) / 'params.py')

    c = EphysAlfCreator(model)
    c.convert(out_dir)