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