merge.py

#!/usr/bin/env python
import os
import sys
import glob
import json
import argparse
p = argparse.ArgumentParser()
p.add_argument("dir", nargs="+")
a = p.parse_args()
rv = dict()

for dir in a.dir:
    if os.path.exists(f"{dir}/.zattrs"):
        with open(f"{dir}/.zattrs") as o:
            rv.update(json.load(o))
    else:
        multiscale = {"datasets":[],"version":"0.1"}
        for path in sorted(glob.glob(f"{dir}/[0-9]*")):
            path = path.split("/")[-1]
            multiscale["datasets"].append({"path": path})
        rv["multiscales"] = [multiscale]

    with open(f"{dir}/omero.json", "r") as o:
        omero = json.load(o)

    rv["omero"] = {}
    if "version" not in omero:
        omero["version" ] = "0.1"
    for x in ("version", "channels", "rdefs"):
        rv["omero"][x] = omero[x]

    rv["omero"]["id"] = omero["id"]
    rv["omero"]["name"] = omero["meta"]["imageName"]
    for ch in rv["omero"]["channels"]:
        for x in ("reverseIntensity", "emissionWave"):
            ch.pop(x, None)
    rv["omero"]["rdefs"].pop("invertAxis", None)
    rv["omero"]["rdefs"].pop("projection", None)

    with open(f"{dir}/.zattrs", "w") as o:
        o.write(json.dumps(rv, indent=4, sort_keys=True))