defaults.py

# File with defaults for ease of use
from typing import Union
from pathlib import PosixPath, Path
import json


def exparams_from_meta(meta: Union[dict, PosixPath, str], extras=["ph"]):
    """
    Obtain parameters from metadata of hdf5 file
    """
    meta = meta if isinstance(meta, dict) else load_attributes(meta)
    base = {
        "tree": {"general": {"None": ["area", "volume", "eccentricity"]}},
        "multichannel_ops": {},
    }

    av_channels = {
        "Citrine",
        "GFP",
        "GFPFast",
        "mCherry",
        "pHluorin405",
        "Flavin",
        "Cy5",
        "mKO2",
    }

    default_reductions = {"np_max"}
    default_metrics = {
        "mean",
        "median",
        "imBackground",
        "max2p5pc",
        "max2p5pc_med",
        "max2p5px",
        "max2p5px_med",
    }
    default_rm = {r: default_metrics for r in default_reductions}

    av_flch = av_channels.intersection(meta["channels/channel"]).difference(
        {"Brightfield, DIC"}
    )

    for ch in av_flch:
        base["tree"][ch] = default_rm

    base["sub_bg"] = av_flch

    # Additional extraction
    if "ph" in extras and {"pHluorin405", "GFPFast"}.issubset(av_flch):

        sets = {
            b + a: (x, y)
            for a, x in zip(
                ["", "_bgsub"],
                (
                    ["GFPFast", "pHluorin405"],
                    ["GFPFast_bgsub", "pHluorin405_bgsub"],
                ),
            )
            for b, y in zip(["em_ratio", "gsum"], ["div0", "np_add"])
        }
        for i, v in sets.items():
            base["multichannel_ops"][i] = [
                *v,
                default_rm,
            ]

    return base


def load_attributes(file: str, group="/"):
    with h5py.File(file, "r") as f:
        meta = dict(f[group].attrs.items())
    return meta