def make_well_sample(x_pos=None, y_pos=None): ws = WellSampleI() image = itest.new_image(name=itest.uuid()) ws.image = image if x_pos is not None: ws.posX = LengthI(x_pos, UnitsLength.REFERENCEFRAME) if y_pos is not None: ws.posY = LengthI(y_pos, UnitsLength.REFERENCEFRAME) return ws
def screen_with_plates(screen): for plate_id in range(5, 7): o = PlateI() o.id = rlong(plate_id) o.name = rstring('plate_name_%d' % plate_id) o.description = rstring('plate_description_%d' % plate_id) o.columnNamingConvention = rstring('number') o.rowNamingConvention = rstring('letter') o.columns = rint(12) o.rows = rint(8) o.defaultSample = rint(0) o.externalIdentifier = rstring('external_identifier_%d' % plate_id) o.status = rstring('status_%d' % plate_id) o.wellOriginX = LengthI(0.1, UnitsLength.REFERENCEFRAME) o.wellOriginY = LengthI(1.1, UnitsLength.REFERENCEFRAME) screen.linkPlate(o) for well_id in range(7, 9): well = WellI() well.id = rlong(well_id) well.column = rint(2) well.row = rint(1) well.externalDescription = \ rstring('external_description_%d' % well_id) well.externalIdentifier = \ rstring('external_identifier_%d' % well_id) well.type = rstring('the_type') well.alpha = rint(0) well.red = rint(255) well.green = rint(0) well.blue = rint(0) well.status = rstring('the_status') o.addWell(well) plateacquisition = PlateAcquisitionI() plateacquisition.id = rlong(well_id) plateacquisition.name = rstring( 'plateacquisition_name_%d' % well_id) plateacquisition.description = rstring( 'plateacquisition_description_%d' % well_id) plateacquisition.maximumFieldCount = rint(1) plateacquisition.startTime = rtime(1L) plateacquisition.endTime = rtime(2L) for wellsample_id in range(9, 11): wellsample = WellSampleI() wellsample.setPlateAcquisition(plateacquisition) wellsample.id = rlong(wellsample_id) wellsample.posX = LengthI(1.0, UnitsLength.REFERENCEFRAME) wellsample.posY = LengthI(2.0, UnitsLength.REFERENCEFRAME) wellsample.timepoint = rtime(1L) wellsample.image = create_image(1L) well.addWellSample(wellsample) return screen
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