def screen_plates(self, user1):
"""Return Screen with Plates and an orphaned Plate."""
# Create and name all the objects
screen = ScreenI()
screen.name = rstring('screen')
for i in range(5):
plate1 = PlateI()
plate1.name = rstring('Plate%s' % i)
screen.linkPlate(plate1)
# Create single orphaned Plate
plate = PlateI()
plate.name = rstring('plate')
screen = get_update_service(user1).saveAndReturnObject(screen)
plate = get_update_service(user1).saveAndReturnObject(plate)
# Add well to first plate
plates = screen.linkedPlateList()
plates.sort(cmp_name_insensitive)
plate_id = plates[0].id.val
well = WellI()
well.column = rint(0)
well.row = rint(0)
well.plate = PlateI(plate_id, False)
image = self.create_test_image(size_x=5,
size_y=5,
session=user1[0].getSession())
ws = WellSampleI()
ws.image = ImageI(image.id, False)
ws.well = well
well.addWellSample(ws)
well = get_update_service(user1).saveAndReturnObject(well)
return screen, plate
def create_plate_wells(self, user1, rows, cols, plateacquisitions=1):
"""Return Plate with Wells."""
updateService = get_update_service(user1)
plate = PlateI()
plate.name = rstring('plate')
plate = updateService.saveAndReturnObject(plate)
# PlateAcquisitions for plate
plate_acqs = []
for p in range(plateacquisitions):
plate_acq = PlateAcquisitionI()
plate_acq.name = rstring('plateacquisition_%s' % p)
plate_acq.description = rstring('plateacquisition_description')
plate_acq.maximumFieldCount = rint(3)
plate_acq.startTime = rtime(1)
plate_acq.endTime = rtime(2)
plate_acq.plate = PlateI(plate.id.val, False)
plate_acq = updateService.saveAndReturnObject(plate_acq)
plate_acqs.append(plate_acq)
# Create Wells for plate
ref_frame = UnitsLength.REFERENCEFRAME
for row in range(rows):
for col in range(cols):
# create Well
well = WellI()
well.column = rint(col)
well.row = rint(row)
well.plate = PlateI(plate.id.val, False)
# Only wells in first Column have well-samples etc.
if col == 0:
# Have 3 images/well-samples per plateacquisition
# (if no plateacquisitions, create 3 well-samples without)
for p in range(max(1, plateacquisitions)):
for i in range(3):
image = self.create_test_image(
size_x=5, size_y=5,
session=user1[0].getSession())
ws = WellSampleI()
ws.image = ImageI(image.id, False)
ws.well = well
ws.posX = LengthI(i * 10, ref_frame)
ws.posY = LengthI(i, ref_frame)
if p < len(plate_acqs):
ws.setPlateAcquisition(
PlateAcquisitionI(plate_acqs[p].id.val,
False))
well.addWellSample(ws)
updateService.saveObject(well)
return plate
def image_well_plate(self):
"""
Returns a new OMERO Project, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set.
"""
plate = PlateI()
plate.name = rstring(self.uuid())
plate = self.update.saveAndReturnObject(plate)
well = WellI()
well.plate = plate
well = self.update.saveAndReturnObject(well)
image = self.new_image(name=self.uuid())
ws = WellSampleI()
ws.image = image
ws.well = well
well.addWellSample(ws)
ws = self.update.saveAndReturnObject(ws)
return plate, well, ws.image
def image_well_plate(self):
"""
Returns a new OMERO Project, linked Dataset and linked Image populated
by an L{test.integration.library.ITest} instance with required fields
set.
"""
plate = PlateI()
plate.name = rstring(self.uuid())
plate = self.update.saveAndReturnObject(plate)
well = WellI()
well.plate = plate
well = self.update.saveAndReturnObject(well)
image = self.new_image(name=self.uuid())
ws = WellSampleI()
ws.image = image
ws.well = well
well.addWellSample(ws)
ws = self.update.saveAndReturnObject(ws)
return plate, well, ws.image
