folderize.py

#!/usr/bin/env python

# Copyright (C) 2016 Open Microscopy Environment & University of Dundee.
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

# author: [email protected]

from omero.gateway import BlitzGateway
from omero.cmd import FindChildren
from omero.callbacks import CmdCallbackI
from omero.model import FolderI, RoiI, FolderRoiLinkI
from omero.rtypes import rstring, unwrap
from omero.sys import ParametersI

from random import choice

import logging

# create logger
logger = logging.getLogger('folderize')
logger.setLevel(logging.INFO)

# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)

# create formatter
formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')

# add formatter to ch
ch.setFormatter(formatter)

# add ch to logger
logger.addHandler(ch)

# set up connection

conn = BlitzGateway('demo', 'ome',
                    host='orca-3.openmicroscopy.org', port=24064, secure=True)
status = conn.connect()

if status:
    logger.info("Connection established")
else:
    logger.warn("Connection failed")
    exit()

updateService = conn.getUpdateService()

# find ROI proxies

roi_query = "select r.id from Roi r"
p = conn.getQueryService().projection(roi_query, ParametersI())
roi_ids = [unwrap(row)[0] for row in p]


rois = [RoiI(roi_id, False) for roi_id in roi_ids]

logger.info("Found %g ROIs" % len(rois))

# create folder proxies

folders = list()

for i in range(12):
    folder = FolderI()
    folder.name = rstring('folder #%d' % (i+1))
    folders.append(folder)

folders = [FolderI(folder_.id.val, False)
           for folder_ in updateService.saveAndReturnArray(folders)]
logger.info("Created %s folders" % len(folders))

# put ROIs in folders

links = list()
for roi in rois:
    link = FolderRoiLinkI()
    link.parent = choice(folders)
    link.child = roi
    links.append(link)

# For large amount of ROIs it is necessary to divide into batches else the
# update call throws and Ice.MemorySizeLimit exception
batches = 50000
sublinks = [links[i:i + batches] for i in range(0, len(links), batches)]

logger.info("Saving %s links in batches of %s" % (len(links), batches))
for i in range(len(sublinks)):
    updateService.saveAndReturnArray(sublinks[i])
    logger.info("Linked %s ROIs to folders - %s/%s" % (
        len(sublinks[i]), i, len(sublinks)))

conn._closeSession()

# to see the resulting ROI counts, adjust the plate ID in this query,

'''
bin/omero hql "SELECT parent.name, COUNT(id) FROM FolderRoiLink
  WHERE child.image IN
    (SELECT image FROM WellSample WHERE well.plate.id = 244)
  GROUP BY parent.name"
'''

folderize_genesymbol.py

#!/usr/bin/env python

# Copyright (C) 2016 Open Microscopy Environment & University of Dundee.
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.


from omero.gateway import BlitzGateway
from omero.model import FolderI, RoiI, FolderRoiLinkI
from omero.rtypes import rstring, unwrap
from omero.sys import ParametersI

import logging


# create logger
logger = logging.getLogger('folderize_genesymbol')
logger.setLevel(logging.INFO)

# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.INFO)

# create formatter
formatter = logging.Formatter('%(asctime)s - %(levelname)s - %(message)s')

# add formatter to ch
ch.setFormatter(formatter)

# add ch to logger
logger.addHandler(ch)

# set up connection

conn = BlitzGateway('demo', 'demo',
                    host='orca-3.openmicroscopy.org', port=24064, secure=True)
status = conn.connect()

if status:
    logger.info("Connection established")
else:
    logger.warn("Connection failed")
    exit()

updateService = conn.getUpdateService()

# Find ROI proxies
logger.info("Fetching ROIs associated to images with Gene Symbols")
roi_query = ("select distinct mv.value, r.id from Roi r "
             "join r.image i "
             "join i.annotationLinks al "
             "join al.child ma "
             "join ma.mapValue mv "
             "where mv.name = 'Gene Symbol'")
p = conn.getQueryService().projection(roi_query, ParametersI())
genes = [unwrap(row)[0] for row in p]
rois = [unwrap(row)[1] for row in p]
unique_genes = set(genes)

logger.info("Found %g ROIs associated to %g gene symbols" % (
    len(rois), len(set(genes))))

# Create folders per gene

# Initializes top folder
topfolder = FolderI()
topfolder.name = rstring('Genes')

objects = []
for gene in unique_genes:
    folder = FolderI()
    folder.name = rstring(gene)
    folder.setParentFolder(topfolder)
    objects.append(folder)

logger.info("Creating folders for each unique gene")
folders = updateService.saveAndReturnArray(objects)
logger.info("Created %s folders" % len(folders))

# Create dictionary of gene folders for linking
genefolders = {}
for folder in folders:
    genefolders[folder.name.val] = FolderI(folder.id.val, False)

# Create array of Folder-ROI lonks
links = []
for i in range(len(rois)):
    link = FolderRoiLinkI()
    link.parent = genefolders[genes[i]]
    link.child = RoiI(rois[i], False)
    links.append(link)

# For large amount of ROIs it is necessary to divide into batches else the
# update call throws and Ice.MemorySizeLimit exception
batches = 50000
sublinks = [links[i:i + batches] for i in range(0, len(links), batches)]

logger.info("Saving %s links in batches of %s" % (len(links), batches))
for i in range(len(sublinks)):
    updateService.saveAndReturnArray(sublinks[i])
    logger.info("Linked %s ROIs to folders - %s/%s" % (
        len(sublinks[i]), i, len(sublinks)))

conn._closeSession()