Fetch pixel data of an image at specific resolution (level) from omero server

read_omero_image_level_region.py

# ref https://forum.image.sc/t/omero-py-how-to-get-tiles-at-different-zoom-level-pyramidal-image/

import numpy as np
from omero.gateway import BlitzGateway
from omero.model import enums as omero_enums
import omero

def connect_hms_omero(session_id):
    SESSION_ID = session_id
    HOST = 'omero-app.hms.harvard.edu'

    conn = BlitzGateway(SESSION_ID, SESSION_ID, host=HOST, port=4064)
    conn.connect()
    return conn

def connect_idr():
    autocfg = [
        "--Ice.Default.Router=OMERO.Glacier2/router:wss -p 443 -h @omero.host@ -r /omero-ws",
        "--omero.user=public",
        "--omero.pass=public"
    ]
    HOST = 'idr.openmicroscopy.org'
    c = omero.client(host=HOST, args=autocfg)
    c.createSession()
    c.enableKeepAlive(300)
    return BlitzGateway(client_obj=c)

conn = connect_hms_omero('4819a822-2416-4cf5-a6df-d43bf1752045')

PIXEL_TYPES = {
    omero_enums.PixelsTypeint8: np.int8,
    omero_enums.PixelsTypeuint8: np.uint8,
    omero_enums.PixelsTypeint16: np.int16,
    omero_enums.PixelsTypeuint16: np.uint16,
    omero_enums.PixelsTypeint32: np.int32,
    omero_enums.PixelsTypeuint32: np.uint32,
    omero_enums.PixelsTypefloat: np.float32,
    omero_enums.PixelsTypedouble: np.float64,
}

IMAGE_ID = 1362653
# IMAGE_ID =9826019
image = conn.getObject("image", IMAGE_ID)
print('image', image.name)

pixels = image.getPrimaryPixels()
dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)

pix = image._conn.c.sf.createRawPixelsStore()
pid = image.getPixelsId()
# level 0 is the highest level of the pyramid
level = 3
z, c, t, x, y = (0, 0, 0, 0, 0)

try:
    pix.setPixelsId(pid, False)

    # Get info on number of levels and sizes in (W, H)
    level_sizes = [(r.sizeX, r.sizeY) for r in pix.getResolutionDescriptions()][::-1]
    print(level_sizes)

    pix.setResolutionLevel(level)
    print(pix.getTileSize())
    w, h = level_sizes[level]
    # Maximum allowed is 256000000 bytes (see Ice.MessageSizeMax)
    tile = pix.getTile(z, c, t, x, y, w, h)
finally:
    pix.close()

tile = np.frombuffer(tile, dtype=np.dtype(dtype).newbyteorder('>'))
tile = tile.reshape((h, w))

import tifffile
tifffile.imsave('omero_test.tif', tile)