EMPIAR-11537.py

#!/usr/bin/env python
# Generate companion files for the TIFF files of the
# first sample dataset of EMPIAR-11537 available from
# https://ftp.ebi.ac.uk/empiar/world_availability/11537/data/4G_Run%201/

import re
import sys
import uuid
import xml.etree.ElementTree as ET

OME_ATTRIBUTES = {
    'UUID': "urn:uuid:%s" % uuid.uuid4(),
    'xmlns': 'http://www.openmicroscopy.org/Schemas/OME/2016-06',
    'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
    'xsi:schemaLocation': 'http://www.openmicroscopy.org/Schemas/OME/2016-06 \
http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd',
}

root = ET.Element("OME", attrib=OME_ATTRIBUTES)

image = ET.SubElement(root, "Image", attrib = {
    'ID': 'Image:0', 'Name': '4G_Run 1'})
pixels = ET.SubElement(image, "Pixels", attrib = {
    'ID': 'Pixels:0:0',
    'DimensionOrder': "XYZCT",
    'Type': 'uint16',
    'SizeX': '14976',
    'SizeY': '14976',
    'SizeZ': '3419',
    'SizeT': '1',
    'SizeC': '1',
    'PhysicalSizeX': '50',
    'PhysicalSizeXUnit': 'Å',
    'PhysicalSizeY': '50',
    'PhysicalSizeYUnit': 'Å'})

# Requires a file_list.txt file with all the TIFF files 
with open('file_list.txt', 'r') as f:
    tiffs = [line.rstrip() for line in f]

for i in range(len(tiffs)):
    tiffdata = ET.SubElement(pixels, "TiffData", attrib={
        "FirstC": "0",
        "FirstT": "0",
        "FirstZ": str(i),
        "IFD": "0",
        "PlaneCount": "1"})
    ET.SubElement(tiffdata, "UUID", {
        "FileName": tiffs[i]}).text =  "urn:uuid:%s" % uuid.uuid4()

kwargs = {
  "encoding": "UTF-8",
  "xml_declaration": True
}
ET.ElementTree(root).write("EMPIAR-11537.companion.ome", **kwargs)