will-moore

"""
See http://lists.openmicroscopy.org.uk/pipermail/ome-users/2017-February/006362.html
and
https://forum.image.sc/t/use-python-to-export-figures-from-omero/46520
"""

from omero.rtypes import wrap
from omero.gateway import BlitzGateway
import omero

will-moore

# select obj, minIndex(ws), maxIndex(ws)  from Plate as obj join fetch obj.wells wells left outer join fetch wells.wellSamples ws where obj.id in (:ids) group by obj.id


2017-01-23 16:50:16,095 INFO  [ome.services.sessions.state.SessionCache] (2-thread-5) Synchronizing session cache. Count = 4
2017-01-23 16:50:16,095 INFO  [        ome.services.util.ServiceHandler] (2-thread-5)  Executor.doWork -- ome.services.sessions.SessionManagerImpl.reload[5e9cdf94-4184-40ee-a3da-9c5693f55812]
2017-01-23 16:50:16,095 INFO  [        ome.services.util.ServiceHandler] (2-thread-5)  Args:	[null, InternalSF@33779587]
2017-01-23 16:50:16,108 INFO  [         ome.security.basic.EventHandler] (2-thread-5)  Auth:	user=0,group=0,event=null(Sessions),sess=d30fd532-ae16-47a0-a3cc-5dbb3a9b3a91
2017-01-23 16:50:16,116 INFO  [                 org.perf4j.TimingLogger] (2-thread-5) start[1485190216095] time[20] tag[omero.call.success.ome.services.sessions.SessionManagerImpl$6.doWork]
2017-01-23 16:50:16,116 INFO  [        ome.services.u

will-moore

# query is
select obj , minIndex(ws), maxIndex(ws)  from Plate as obj join fetch obj.wells wells left outer join fetch wells.wellSamples ws where obj.id in (:ids)


2017-01-23 15:54:27,130 INFO  [                 org.perf4j.TimingLogger] (.Server-83) start[1485186867124] time[6] tag[omero.call.exception]
2017-01-23 15:54:27,133 WARN  [        ome.services.util.ServiceHandler] (.Server-83) InvalidDataAccessResourceUsageException thrown.

org.springframework.dao.InvalidDataAccessResourceUsageException: could not execute query; SQL [select plate0_.id as col_0_0_, min(wellsample2_.well_index) as col_1_0_, max(wellsample2_.well_index) as col_2_0_, wells1_.id as id143_1_, wellsample2_.id as id146_2_, plate0_.id as id109_0_, wells1_.id as id143_1_, wellsample2_.id as id146_2_, plate0_.columnNamingConvention as columnNa2_109_0_, plate0_.columns as columns109_0_, plate0_.defaultSample as defaultS4_109_0_, plate0_.description as descript5_109_0_, plate0_.creation_id as creation17_109_0_, plate0_.external_id as external

will-moore

//      When the BBC micro:bit runs.
function onStart(  ) {
	microbit.draw(Pattern("01000.01100.01110.01100.01000"));
	wait(200);
	
}

function onPressA(  ) {
	/* create variables to keep track of
	  

will-moore

# Pearson coefficient described at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074624/

# Start with
# $ omero shell --login

conn = omero.gateway.BlitzGateway(client_obj=client)
i = conn.getObject("Image", 62137)
p = i.getPrimaryPixels()

# get 2D planes and reshape to 1D array

will-moore

from omero.gateway import BlitzGateway
from PIL import Image

conn = BlitzGateway("user-3", "ome", host="eel.openmicroscopy.org", port=4064)
# Image is a 'fake' bio-formats image (grey intensity gradient)
imageId = 25501

conn.connect()

will-moore

import requests
session = requests.Session()

BASE_URL = "https://test.openmicroscopy.org/omero/"
# BASE_URL = "http://localhost:4080/"

login_url = BASE_URL + "webclient/login/"
r = session.get(login_url)
token = r.cookies['csrftoken']

will-moore

import requests

session = requests.Session()

# Start by getting supported versions from the base url...
r = session.get('http://localhost:4080/webgateway/api/')
# we get a list of versions
versions = r.json()
print 'Versions', versions

will-moore

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

import omero.scripts as scripts
from omero.gateway import BlitzGateway
from omero.rtypes import rstring, rlong
import numpy

try:
    from PIL import Image  # see ticket:2597

will-moore

# Alternatively start with omero shell, instead of first 2 lines below, do this:
# $ bin/omero shell --login
#  conn = omero.gateway.BlitzGateway(client_obj=client)
conn = BlitzGateway("will", "ome", host="localhost", port=4064)
conn.connect()
updateService = conn.getUpdateService()
roiService = conn.getRoiService()
from omero.rtypes import rstring

imageId = 3731