An OMERO.script for adding metadata to images in OMERO

Add_Metadata.py

# See https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8397#p18758

import omero.scripts as scripts
import omero
from omero.gateway import BlitzGateway
from omero.model import InstrumentI, MicroscopeI, ObjectiveSettingsI, ObjectiveI
from omero.rtypes import rstring, rdouble, rlong


def add_metadata(conn, script_params):

    update_service = conn.getUpdateService()
    types_service = conn.getTypesService()

    for image in conn.getObjects("Image", script_params['IDs']):

        microscope = MicroscopeI()
        # optional parameters - check if they've been set...
        if 'Microscope_Manufacturer' in script_params:
            microscope.manufacturer = rstring(script_params['Microscope_Manufacturer'])
        if 'Microscope_Model' in script_params:
            microscope.model = rstring(script_params['Microscope_Model'])

        # Type is not optional param
        # Lookup the enumeration we need
        t = types_service.getEnumeration('MicroscopeType', script_params['Microscope_Type'])
        microscope.type = t

        instrument = InstrumentI()
        instrument.microscope = microscope

        # Objective and Objective Settings.
        objective = ObjectiveI()
        if 'Nominal_Magnification' in script_params:
            objective.nominalMagnification = rdouble(script_params['Nominal_Magnification'])
        # immersion and correction cannot be null
        i = types_service.getEnumeration('Immersion', script_params['Objective_Immersion'])
        objective.immersion = i
        c = types_service.getEnumeration('Correction', script_params['Objective_Correction'])
        objective.correction = c
        objective.instrument = instrument

        obj_settings = ObjectiveSettingsI()
        obj_settings.objective = objective

        # Update the omero.model.ImageI object from the image wrapper
        img = image._obj
        img.instrument = instrument
        img.objectiveSettings = obj_settings

        update_service.saveObject(img)


def run_script():
    """
    The main entry point of the script, as called by the client via the
    scripting service, passing the required parameters.
    """

    data_types = [rstring('Image')]
    microscope_types = [rstring('Upright'), rstring('Inverted'),
                        rstring('Dissection'), rstring('Electrophysiology'), rstring('Other')]
    immersion_enums = [rstring('Oil'), rstring('Water'), rstring('WaterDipping'),
                       rstring('Air'), rstring('Multi'), rstring('Glycerol'), 
                       rstring('Other'), rstring('Unknown')]
    # not all correction times listed
    correction_enums = [rstring('UV'), rstring('PlanApo'), rstring('PlanFluor'),
                       rstring('Other'), rstring('Unknown')]

    client = scripts.client(
        'Add_Metadata.py',
        """Add Acquisition Metadata to Images""",

        # provide 'Data_Type' and 'IDs' parameters so that webclient/Insight
        # auto-populates with currently selected images.
        scripts.String(
            "Data_Type", optional=False, grouping="01",
            description="The data you want to work with.", values=data_types,
            default="Image"),
        scripts.List(
            "IDs", optional=False, grouping="02",
            description="List of Image IDs").ofType(rlong(0)),

        # Optional microscope attributes
        scripts.String(
            "Microscope_Model", grouping="3",
            description="Microscope Model"),
        scripts.String(
            "Microscope_Manufacturer", grouping="3.1",
            description="Microscope Manufacturer"),

        # Non-optional microscope type
        scripts.String(
            "Microscope_Type", optional=False, grouping="3.2",
            values=microscope_types, description="Microscope Model"),

        # Objective
        scripts.String(
            "Objective_Immersion", grouping="5", optional=False,
            description="Objective Immersion", values=immersion_enums),
        # Use groupings to indent param in script UI
        scripts.Int("Nominal_Magnification", grouping="5.1"),
        scripts.String("Objective_Correction", grouping="5.2",
            optional=False, values=correction_enums),
    )

    try:
        conn = BlitzGateway(client_obj=client)

        script_params = client.getInputs(unwrap=True)
        print script_params

        # call the main script
        add_metadata(conn, script_params)

        # Return message to the client
        client.setOutput("Message", rstring("Metadata added"))

    finally:
        client.closeSession()


if __name__ == "__main__":
    run_script()