Python script for to generate an OMERO.table on a Plate from channel min/max values

channelIntensityToTable.py

import omero
from omero.rtypes import rstring
import omero.grid
from omero.gateway import BlitzGateway

USERNAME = "will"
PASSWORD = "ome"
HOST = "localhost"
PORT = 4064

screenId = 4304
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
tablename = "Channels_Min_Mex_Intensity"

# Go through all wells in all Plates, adding row for each
screen = conn.getObject("Screen", screenId)
wellIds = []
rowData = []
chCount = 1
for plate in screen.listChildren():
    print plate.name
    for well in plate._listChildren():
        well = omero.gateway.WellWrapper(conn, well)
        image = well.getImage()
        if image is None:
            continue
        wellIds.append(well.id)
        # chCount = image.getSizeC()
        row = []
        print "well, image", well.id, image.id
        for ch in image.getChannels():
            row.append(long(ch.getWindowMin()))
            row.append(long(ch.getWindowMax()))
        rowData.append(row)

    print 'wellIds', wellIds
    print 'rowData', rowData


# Now we know how many channels, we can make the table
col1 = omero.grid.WellColumn('Well', '', [])
columns = [col1]
colNames = []
for chIdx in range(chCount):
    for name in ['Ch%sMin' % chIdx, 'Ch%sMax' % chIdx]:
        colNames.append(name)
        columns.append(omero.grid.LongColumn(name, '', []))

table = conn.c.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)


# Add Data from above
data1 = omero.grid.WellColumn('Well', '', wellIds)
data = [data1]
for colIdx in range(chCount * 2):
    colData = [r[colIdx] for r in rowData]
    print "colData", len(colData)
    name = colNames[colIdx]
    data.append(omero.grid.LongColumn(name, '', colData))

print "Adding data: ", len(data)
table.addData(data)
orig_file = table.getOriginalFile()
table.close()

print "table closed..."
fileAnn = omero.model.FileAnnotationI()
fileAnn.ns = rstring('openmicroscopy.org/omero/bulk_annotations')
fileAnn.setFile(omero.model.OriginalFileI(orig_file.id.val, False))
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = omero.model.ScreenAnnotationLinkI()
link.setParent(omero.model.ScreenI(screenId, False))
link.setChild(omero.model.FileAnnotationI(fileAnn.id.val, False))

print "save link..."
conn.getUpdateService().saveAndReturnObject(link)

conn._closeSession()