OMERO.server script to rename Images e.g. myimage_s1.tif to myimage_s001.tif to fix ordering in the clients.

Rename_Images.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

# See https://forum.image.sc/t/omero-screens-data-import/33466/10
# and https://forum.image.sc/t/upload-issue-with-metadata-ome-xml-companion-file/59290/9

import omero.scripts as scripts
from omero.gateway import BlitzGateway
import omero

from omero.rtypes import rstring, rlong

import re


def pad_zero(match):
    text = match.group(0)
    num = match.group('num')
    padded = "%03d" % int(num)
    return text.replace(num, padded)


def rename_images(conn, script_params):

    ids = script_params['IDs']
    prefix = script_params['Number_Prefix']

    p = re.compile(r'%s(?P<num>[0-9]+)' % prefix)

    images = []
    for dataset in conn.getObjects('Dataset', ids):
        images.extend(list(dataset.listChildren()))

    for image in images:
        name = image.getName()
        new_name = p.sub(pad_zero, name)
        image.setName(new_name)
        image.save()


def run_script():
    data_types = [rstring('Dataset')]

    client = scripts.client(
        'Rename_Images.py',
        """Renames e.g. myimage_s1.tif to myimage_s01.tif""",

        scripts.String(
            "Data_Type", optional=False, grouping="1",
            description="Choose source of images (only Dataset supported)",
            values=data_types, default="Dataset"),

        scripts.List(
            "IDs", optional=False, grouping="2",
            description="List of Dataset IDs").ofType(rlong(0)),

        scripts.String(
            "Number_Prefix", optional=False, grouping="3",
            description="E.g. '_s' to rename myimage_s1.tif to myimage_s01.tif"),
    )

    try:
        script_params = client.getInputs(unwrap=True)
        conn = BlitzGateway(client_obj=client)

        message = rename_images(conn, script_params)
        client.setOutput("Message", rstring(message))

    finally:
        client.closeSession()


if __name__ == "__main__":
    run_script()