Create masks in OMERO.

Create_mask.py

import omero
from omero.rtypes import rint, rdouble
from omero.gateway import ColorHolder
from omero.gateway import BlitzGateway

import numpy
import struct
import math


def create_mask(mask_bytes, bytes_per_pixel):
    if bytes_per_pixel == 2:
        divider = 16.0
        format_string = "H"  # Unsigned short
        byte_factor = 0.5
    elif bytes_per_pixel == 1:
        divider = 8.0
        format_string = "B"  # Unsiged char
        byte_factor = 1
    else:
        message = "Format %s not supported"
        raise ValueError(message)
    steps = math.ceil(len(mask_bytes) / divider)
    mask = []
    for i in range(long(steps)):
        binary = mask_bytes[
            i * int(divider):i * int(divider) + int(divider)]
        format = str(int(byte_factor * len(binary))) + format_string
        binary = struct.unpack(format, binary)
        s = ""
        for bit in binary:
            s += str(bit)
        mask.append(int(s, 2))
    return bytearray(mask)


def create_mask_roi(
    update_service, mask_bytes, omero_image, x, y, width, height, color
):
    # Create new ROI
    roi = omero.model.RoiI()
    mask = omero.model.MaskI()
    # Set position
    mask.setTheC(rint(0))
    mask.setTheZ(rint(0))
    mask.setTheT(rint(0))
    mask.setX(rdouble(mask_position_x))
    mask.setY(rdouble(mask_position_y))
    mask.setWidth(rdouble(mask_width))
    mask.setHeight(rdouble(mask_height))
    mask.setFillColor(rint(color.getInt()))
    mask.setBytes(mask_bytes)
    roi.addShape(mask)
    roi.setImage(omero_image._obj)
    roi = update_service.saveAndReturnObject(roi)
    return roi.getId().getValue()

# Define mask's fill color
fill_color = ColorHolder()
fill_color.setRed(255)
fill_color.setBlue(0)
fill_color.setGreen(0)
fill_color.setAlpha(100)
# Define mask position and size
mask_position_x = 50
mask_position_y = 50
mask_width = 100
mask_height = 100
# Create [0, 1] mask
mask_array = numpy.random.randint(0, 2, mask_width * mask_height)
# Set correct number of bytes per value
mask_array = mask_array.astype(numpy.uint8)
# Convert the mask to bytes
mask_array = mask_array.tobytes()
# Pack the bytes to a bit mask
mask_packed = create_mask(mask_array, 1)

# Connect to the server
blitz = BlitzGateway("USERNAME", "PASSWORD", host="HOST", port="PORT")
blitz.connect()
# Define image you'd like to attach the mask to
image_id = 1
# Get the image from the server
omero_image = blitz.getObject("Image", image_id)
# Get the update service
update_service = blitz.getUpdateService()
# Attach the mask to the image
roi_id = create_mask_roi(
    update_service, mask_packed, omero_image, mask_position_x, mask_position_y,
    mask_width, mask_height, fill_color)