Finds the brightest point in a plane and draws an ellipse around it. Useful for generating test ROIs.

add_ellipse_per_channel.py

import omero
from omero.rtypes import rdouble, rint
import omero.grid
from omero.gateway import BlitzGateway
import numpy as np

USERNAME = "user"
PASSWORD = "password"
HOST = "merge-ci-devspace.openmicroscopy.org"
PORT = 4064

plate_id = 13855
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

updateService = conn.getUpdateService()

plate = conn.getObject("Plate", plate_id)

# Channels we want to analyse - 1 ROI created per channel
channels = [0]

print(plate.name)
for well in plate._listChildren():
    well = omero.gateway.WellWrapper(conn, well)
    image = well.getImage()
    pix = image.getPrimaryPixels()
    print(image.name, well.row, well.column)
    size_x = image.getSizeX()
    size_y = image.getSizeY()
    for c in channels:
        plane = pix.getPlane(theZ=0, theC=c, theT=0)
        max_pixel = plane.max()
        min_pixel = plane.min()
        mean_pixel = (max_pixel + min_pixel) / 2
        y = np.argmax(plane) // size_x
        x = np.argmax(plane) % size_x
        cx = x
        cy = y

        # walk away from max_pixel until below mean_pixel
        # in x direction...
        while(x < size_x and plane[y][x] > mean_pixel):
            x += 1
        x_end = x
        x = cx
        while(x > 0 and plane[y][x] > mean_pixel):
            x -= 1
        cx = (x_end + x) // 2
        rx = x_end - cx

        # and y
        while(y < size_y and plane[y][cx] > mean_pixel):
            y += 1
        y_end = y
        y = cy
        while(y > 0 and plane[y][cx] > mean_pixel):
            y -= 1
        cy = (y_end + y) / 2
        ry = y_end - cy

        print('xy', cx, rx, cy, ry)

        ellipse = omero.model.EllipseI()
        ellipse.x = rdouble(cx)
        ellipse.y = rdouble(cy)
        ellipse.radiusX = rdouble(rx)
        ellipse.radiusY = rdouble(ry)
        ellipse.theZ = rint(0)
        ellipse.theT = rint(0)
        ellipse.theC = rint(c)

        roi = omero.model.RoiI()
        roi.setImage(image._obj)
        roi.addShape(ellipse)
        updateService.saveAndReturnObject(roi)

conn.close()