OMERO script to rename Image Channels

Rename_Channels.py

import omero.scripts as scripts
from omero.gateway import BlitzGateway
from omero.rtypes import rstring, rlong


def renameChannels(conn, parameterMap):
    
    updateService = conn.getUpdateService()

    channel_names = parameterMap["Channel_Names"].split(",")
    channel_names = [ name.strip() for name in channel_names]

    ids = parameterMap["IDs"]
    images = []
    if parameterMap["Data_Type"] == "Dataset":
        for ds in conn.getObjects("Dataset", ids):
            images.extend( list(ds.listChildren()) )
    else:
        images = list( conn.getObjects("Image", ids) )

    for image in images:
        for n, c in zip(channel_names, image.getChannels()):
            lc = c._obj.getLogicalChannel()            # returns omero.model.LogicalChannelI
            lc.setName(rstring(n))
            updateService.saveObject(lc)


if __name__ == "__main__":

    dataTypes = [rstring('Dataset'),rstring('Image')]
    
    client = scripts.client('Rename_Channels.py', """Rename image Channels""",
    
    scripts.String("Data_Type", optional=False, grouping="1",
        description="Use all the images in specified 'Datasets' or choose individual 'Images'.",
        values=dataTypes, default="Image"),
        
    scripts.List("IDs", optional=False, grouping="2",
        description="List of Dataset IDs or Image IDs to combine.").ofType(rlong(0)),
        
    scripts.String("Channel_Names", optional=False, grouping="3",
        description="Add Channel names separated by commas. E.g. 'DAPI, FITC, Red'")
    )

    try:
        session = client.getSession()

        # process the list of args above.
        parameterMap = {}
        for key in client.getInputKeys():
            if client.getInput(key):
                parameterMap[key] = client.getInput(key).getValue()

        print parameterMap
        
        conn = BlitzGateway(client_obj=client)
        
        # renameChannels...
        renameChannels(conn, parameterMap)

        client.setOutput("Message", rstring("Channels Renamed!"))

    finally:
        client.closeSession()