Script to process OMERO Polygons, creating a Point at the centre of each Polygon (with Polygon ID as Point label)

rois_to_centre_points.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import omero
from omero.rtypes import rdouble, rint, rstring, unwrap
from omero.gateway import BlitzGateway

USERNAME = 'username'
PASSWORD = 'password'
HOST = 'localhost'
PORT = 4064

image_id = 160872

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
updateService = conn.getUpdateService()

# We have a helper function for creating an ROI and linking it to new shapes
def create_roi(i_id, shapes):
    # create an ROI, link it to Image
    roi = omero.model.RoiI()
    # use the omero.model.ImageI that underlies the 'image' wrapper
    roi.setImage(omero.model.ImageI(i_id, False))
    for shape in shapes:
        roi.addShape(shape)
    # Save the ROI (saves any linked shapes too)
    return updateService.saveAndReturnObject(roi)

def create_point(i_id, x, y, text, z, t):
    # create an ROI with single point shape
    point = omero.model.PointI()
    point.x = rdouble(x)
    point.y = rdouble(y)
    if z is not None:
        point.theZ = rint(z)
    if t is not None:
        point.theT = rint(t)
    point.textValue = rstring(text)
    create_roi(i_id, [point])


# Process Shapes (ONLY Polygons supported) to find centre point and
# create a Point for each, with the Polygon ID as the Point label
roi_service = conn.getRoiService()
result = roi_service.findByImage(image_id, None)
for roi in result.rois:
    print "ROI:  ID:", roi.getId().getValue()
    for s in roi.copyShapes():
        shape_id = s.getId().getValue()
        the_t = unwrap(s.getTheT())
        the_z = unwrap(s.getTheZ())
        cx = None
        cy = None
        print s.__class__.__name__
        if type(s) == omero.model.RectangleI:
            min_x = s.getX().getValue()
            min_y = s.getY().getValue()
            max_x = min_x + s.getWidth().getValue()
            max_y = min_y + s.getHeight().getValue()
            cx = (min_x + max_x) / 2
            cy = (min_y + max_y) / 2
        elif type(s) == omero.model.LabelI:
            cx = s.getX().getValue()
            cy = s.getY().getValue()
        elif type(s) == omero.model.LineI:
            min_x = s.getX1().getValue()
            min_y = s.getX2().getValue()
            max_x = s.getY1().getValue()
            max_y = s.getY2().getValue()
            cx = (min_x + max_x) / 2
            cy = (min_y + max_y) / 2
        elif type(s) == omero.model.PolygonI or type(s) == omero.model.PolylineI:
            # find bounding box and centre
            points = s.getPoints().val.split(" ");
            try:
                x_coords = [float(p.split(",")[0]) for p in points if len(p) > 0]
                y_coords = [float(p.split(",")[1]) for p in points if len(p) > 0]
                min_x = min(x_coords)
                max_x = max(x_coords)
                min_y = min(y_coords)
                max_y = max(y_coords)
                cx = (min_x + max_x) / 2
                cy = (min_y + max_y) / 2
            except ValueError:
                print "Invalid points", points

        print 'xy', cx, cy, 'z', the_z, 't', the_t
        if cx is not None and cy is not None:
            # Create Point with shape_id as text
            create_point(image_id, cx, cy, shape_id, the_z, the_t)

conn.close()