Investigation for https://forum.image.sc/t/how-to-calculate-xy-position-of-an-image-for-a-reference-image-scn-file-and-ome-xml/33030/5

test.py

#!/usr/bin/env python

"""
   <Image ID="Image:0" Name="image_0000247585 (R0)">
      <AcquisitionDate>2020-01-15T06:29:11.537</AcquisitionDate>
      <Description>Collection ImageCollection__0000042467</Description>
      <InstrumentRef ID="Instrument:0"/>
      <ObjectiveSettings ID="Objective:0:0"/>
      <Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" PhysicalSizeX="16.438446163366336" PhysicalSizeXUnit="µm" PhysicalSizeY="16.438446015424162" PhysicalSizeYUnit="µm" SignificantBits="8" SizeC="3" SizeT="1" SizeX="1616" SizeY="4668" SizeZ="1" Type="uint8">
         <Channel ID="Channel:0:0" IlluminationType="Transmitted" SamplesPerPixel="3">
            <LightPath/>
         </Channel>
         <MetadataOnly/>
         <Plane PositionX="0" PositionXUnit="reference frame" PositionY="0" PositionYUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
      </Pixels>
   </Image>
"""


import xml.etree.ElementTree as ET


NS = "{http://www.openmicroscopy.org/Schemas/OME/2016-06}"
tree = ET.parse("test.ome.xml")
root = tree.getroot()
images = {}
for img in root.findall(NS + "Image"):
    name = img.attrib["Name"]
    base, res = name.split(" ")
    if base not in images:
        images[base] = img
    else:
        previous = images[base].attrib["Name"].split(" ")[1]
        if res < previous:
            images[base] = img
for base, img in images.items():
        name = img.attrib["Name"]
        pixels = img.find(NS + "Pixels")
        sizeX = int(pixels.attrib["SizeX"])
        sizeY = int(pixels.attrib["SizeY"])
        phyX = float(pixels.attrib["PhysicalSizeX"])
        phyY = float(pixels.attrib["PhysicalSizeY"])
        unitX = pixels.attrib["PhysicalSizeXUnit"]
        unitY = pixels.attrib["PhysicalSizeYUnit"]
        plane = pixels.find(NS + "Plane")
        posX = int(plane.attrib.get("PositionX", ""))//1000000
        posY = int(plane.attrib.get("PositionY", ""))//1000000
        print(f'{name:20}\t{sizeX:5d}\t{sizeY:5d}\t{phyX:>4.2f}{unitX}\t{phyY:>4.2f}{unitY}\t{posX:10d}\t{posY:10d}')