import os

import xml.etree.ElementTree as etree

import ij

from loci.formats import ImageReader

from loci.formats import MetadataTools

def get_reader(file, complete_meta):

return reader

# files is a comma separated list of paths to the first ztc

basepath = "/Users/uqdmatt2/Desktop/"

files = [basepath+"Original_File/example stitch_Z0_T0_C0.tiff"]

for fpath in files:

original_metadata = MetadataTools.createOMEXMLMetadata()

reader = get_reader(fpath,original_metadata)

reader.close()

xml_data = original_metadata.dumpXML()

outputdir = os.path.dirname(fpath)

shortname = os.path.basename(fpath)[:-5]

outputpath = os.path.join(outputdir,shortname+".xml")

root = etree.fromstring(xml_data.decode('utf-8','ignore'))

et = etree.ElementTree(root)

et.write(outputpath)