Using the OMERO query service to search for images based on metadata.

Metadata_Query.py

# DEMO of how to use code example at https://gist.github.com/will-moore/5782494#file-metadata_search-py-L13

import omero
from omero.rtypes import rint, wrap, rdouble, unwrap
from omero.gateway import BlitzGateway

conn = BlitzGateway('will', 'ome', host='localhost', port=4064)
conn.connect()



def searchImages(conn, scriptParams):
    """
    Here we build our hql query and get the results from the queryService
    """
 
    # Script has defaults for some parameters, so we know these are filled
    minSizeC = "Min_Channel_Count" in scriptParams and scriptParams["Min_Channel_Count"] or 1
    minSizeZ = "Min_Size_Z" in scriptParams and scriptParams["Min_Size_Z"] or 1
    minSizeT = "Min_Size_T" in scriptParams and scriptParams["Min_Size_T"] or 1
    # For others, we check if specified
    channelNames = "Channel_Names" in scriptParams and scriptParams["Channel_Names"] or []
    nominalMagnification = "Magnification" in scriptParams and scriptParams["Magnification"] or None
    lensNA = "Lens_NA" in scriptParams and scriptParams["Lens_NA"] or None
    excitationWave = "Excitation_Wavelength" in scriptParams and scriptParams["Excitation_Wavelength"] or None
    objectiveModel = "Objective_Model" in scriptParams and scriptParams["Objective_Model"] or None
 
    qs = conn.getQueryService()
    params = omero.sys.Parameters()
    params.map = {}
    clauses = []
 
    query = "select i from Image i left outer join i.pixels as pixels"
 
    if minSizeZ > 1 or minSizeC > 1 or minSizeT > 1:
        # We have already joined pixels
        if minSizeZ > 1:
            params.map["sizeZ"] = rint(minSizeZ)
            clauses.append("pixels.sizeZ>=:sizeZ")
        if minSizeC > 1:
            params.map["sizeC"] = rint(minSizeC)
            clauses.append("pixels.sizeC>=:sizeC")
        if minSizeT > 1:
            params.map["sizeT"] = rint(minSizeT)
            clauses.append("pixels.sizeT>=:sizeT")
 
    if len(channelNames) > 0 or excitationWave is not None:
        query = query + " left outer join pixels.channels as c join c.logicalChannel as lc"
        if len(channelNames) > 0:
            params.map["cNames"] = wrap(channelNames)
            clauses.append("lc.name in (:cNames)")
        if excitationWave is not None:
            params.map["exWave"] = rdouble(excitationWave)
            clauses.append("lc.excitationWave=:exWave")
 
 
    if nominalMagnification is not None or lensNA is not None or objectiveModel is not None:
        query += " join i.objectiveSettings as objS join objS.objective as ob"
        if nominalMagnification is not None:
            params.map["nomMag"] = rdouble(nominalMagnification)
            clauses.append("ob.nominalMagnification=:nomMag")
        if lensNA is not None:
            params.map["lensNA"] = rdouble(lensNA)
            clauses.append("ob.lensNA=:lensNA")
        if objectiveModel is not None:
            params.map["objectiveModel"] = wrap(objectiveModel)
            clauses.append("ob.model=:objectiveModel")
 
    query = query + " where " + " and ".join(clauses)
 
    print "Searh parameters map:", unwrap(params.map)
    print query
 
    imgs = qs.findAllByQuery(query, params)
    return imgs



searchParams = {"Magnification": 100,
	"Min_Channel_Count": 3}
for i in searchImages(conn, searchParams):
	print i.id.val, i.name.val


searchParams = {"Magnification": 40}
for i in searchImages(conn, searchParams):
	print i.id.val, i.name.val


searchParams = {"Excitation_Wavelength": 490, "Lens_NA": 1.4}
for i in searchImages(conn, searchParams):
	print i.id.val, i.name.val


searchParams = {"Channel_Names": ["DAPI", "GFP"]}
for i in searchImages(conn, searchParams):
	print i.id.val, i.name.val