def run_as_program():
"""
Testing function to allow the script to be called outside of the OMERO
scripting environment. The connection details and image ID must be valid.
"""
import getpass
HOST = 'localhost'
PORT = 4064
USERNAME = raw_input("OMERO username: "******"OMERO password: "******"OMERO host (%s): " % HOST)
if h:
HOST = h
p = raw_input("OMERO port (%d): " % PORT)
if p:
PORT = p
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
params = {}
params[PARAM_IDS] = [1]
params[PARAM_DATATYPE] = "Image"
params[PARAM_ALL_IMAGES] = True
params[PARAM_READABLE] = True
(count, ok) = run(conn, params)
print (summary(count, ok))
def run(username, password, host, port):
full_names = ["Francis Crick",
"Linda Buck",
"Charles Darwin",
"Marie Curie",
"Alexander Fleming",
"Rosalind Franklin",
"Robert Hooke",
"Jane Goodall",
"Gregor Mendel",
"Barbara McClintock",
"Louis Pasteur",
"Ada Lovelace",
"Linus Pauling",
"Frances Kelsey",
"Maurice Wilkins",
"Florence Nightingale",
"John Sulston",
"Elizabeth Blackwell",
"Richard Dawkins",
"Caroline Dean",
"Stephen Reicher",
"Wendy Barclay",
"Paul Nurse",
"Jennifer Doudna",
"Adrian Thomas",
"Ann Clarke",
"Oswald Avery",
"Liz Sockett",
"Erwin Chargaff",
"Tracey Rogers",
"Ronald Fisher",
"Rachel Carson",
"William Harvey",
"Nettie Stevens",
"Jeffrey Hall",
"Youyou Tu",
"Michael Rosbash",
"Carol Greider",
"Yoshinori Ohsumi",
"Rosalyn Yalow"]
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
admin_service = conn.getAdminService()
for i, full_name in enumerate(full_names):
username = '******' % (i + 1)
print username, full_name
exp = admin_service.lookupExperimenter(username)
names = full_name.split(" ")
exp.firstName = rstring(names[0])
exp.lastName = rstring(names[1])
admin_service.updateExperimenter(exp)
except Exception as exc:
print "Error while renaming users: %s" % str(exc)
finally:
conn.close()
def run_as_program():
"""
Testing function to allow the script to be called outside of the OMERO
scripting environment. The connection details and image ID must be valid.
"""
import getpass
HOST = 'localhost'
PORT = 4064
USERNAME = raw_input("OMERO username: "******"OMERO password: "******"OMERO host (%s): " % HOST)
if h:
HOST = h
p = raw_input("OMERO port (%d): " % PORT)
if p:
PORT = p
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
conn.keepAlive()
params = create_script_defaults()
params[PARAM_DATATYPE] = 'Image'
params[PARAM_IDS] = [51]
# params[PARAM_DATATYPE] = 'Dataset'
# params[PARAM_IDS] = [2]
params[PARAM_UPLOAD_RESULTS] = True
params[PARAM_EMAIL_RESULTS] = True
params[PARAM_EMAIL] = ADMIN_EMAIL
count = run(conn, params)
if count >= 0:
print ("Processed %d image%s" %
(count, count != 1 and 's' or ''))
def main(argv):
parser = make_parser()
args = parser.parse_args(argv[1:])
if not args.out_file:
args.out_file = "map_screen_%d.tsv" % args.screen_id
passwd = getpass.getpass()
conn = BlitzGateway(
args.user, passwd, host=args.host, port=args.port, group=args.group
)
conn.connect()
screen = conn.getObject("Screen", args.screen_id)
print "writing to %s" % args.out_file
print "SCREEN: %s" % screen.name
with open(args.out_file, "w") as fo:
fo.write("PLATE\tSERIES\tWELL\tFIELD\tImageID\tWellID\n")
for p in screen.listChildren():
rows = []
print " plate: %s" % p.name
for w in p.listChildren():
n_fields = sum(1 for _ in w.listChildren())
for i in xrange(n_fields):
img = w.getImage(i)
well_tag = "%s%02d" % (LETTERS[w.row], w.column + 1)
rows.append((
p.name, img.getSeries(), well_tag, i + 1, img.id, w.id
))
rows.sort(key=itemgetter(1))
rows.sort()
for r in rows:
fo.write("%s\t%d\t%s\t%d\t%d\t%d\n" % r)
def run(name, password, dataset_name, anntype, ns, host, port):
conn = BlitzGateway(name, password, host=host, port=port)
try:
conn.connect()
datasets = conn.getObjects("Dataset",
attributes={"name": dataset_name})
for dataset in datasets:
print dataset.getId()
ann_ids = []
given_type = None
if anntype == "map":
given_type = omero.model.MapAnnotationI
if anntype == "file":
given_type = omero.model.FileAnnotationI
if ns == "none":
ns = None
for image in dataset.listChildren():
for a in image.listAnnotations(ns):
if a.OMERO_TYPE == given_type:
print a.getId(), a.OMERO_TYPE, a.ns
ann_ids.append(a.id)
# Delete the annotations link to the dataset
for a in dataset.listAnnotations(ns):
if a.OMERO_TYPE == given_type:
print a.getId(), a.OMERO_TYPE, a.ns
ann_ids.append(a.id)
if len(ann_ids) > 0:
print "Deleting %s annotations..." % len(ann_ids)
conn.deleteObjects('Annotation', ann_ids, wait=True)
except Exception as exc:
print "Error while deleting annotations: %s" % str(exc)
finally:
conn.close()
def connect():
conn = BlitzGateway('public', 'public',
host='ws://idr.openmicroscopy.org/omero-ws',
secure=True)
conn.connect()
conn.c.enableKeepAlive(60)
return conn
def run(username, password, project_id, host, port):
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
project = conn.getObject("Project", project_id)
for dataset in project.listChildren():
print("\n\nDataset", dataset.id, dataset.name)
for image in dataset.listChildren():
print("Image", image.id, image.name)
ann = image.getAnnotation(NAMESPACE)
if ann is None:
print(" No annotation found")
continue
keys = ann.getValue()
values = [kv[1] for kv in keys if kv[0] == MAP_KEY]
if len(values) == 0:
print(" No Key-Value found for key:", MAP_KEY)
channels = values[0].split("; ")
print("Channels", channels)
name_dict = {}
for c, ch_name in enumerate(channels):
name_dict[c + 1] = ch_name.split(":")[1]
conn.setChannelNames("Image", [image.id],
name_dict,
channelCount=None)
except Exception as exc:
print("Error while changing names: %s" % str(exc))
finally:
conn.close()
def run(datasetname, password, host, port):
conn = BlitzGateway('trainer-1', password, host=host, port=port)
conn.connect()
try:
trainer_dataset = conn.getObject("Dataset",
attributes={'name': datasetname},
opts={'owner': conn.getUserId()})
# Create {name: [tag_id, tag_id]} for images in Dataset
image_tag_links = {}
image_ratings = {}
for image in trainer_dataset.listChildren():
tag_ids = []
for ann in image.listAnnotations():
if ann.OMERO_TYPE.__name__ == 'TagAnnotationI':
tag_ids.append(ann.id)
elif ann.ns == RATING_NS:
image_ratings[image.getName()] = ann.longValue
if len(tag_ids) > 0:
image_tag_links[image.getName()] = tag_ids
# print image_tag_links
print('image_ratings', image_ratings)
link_tags(conn, datasetname, image_tag_links, image_ratings)
finally:
conn.close()
def test_unicode_password(self):
with pytest.raises(Ice.ConnectionRefusedException):
gateway = BlitzGateway(
username='******', passwd=u'ążźćółę',
host='localhost', port=65535
)
gateway.connect()
def test_unicode_password(self):
with pytest.raises(Ice.ConnectionRefusedException):
gateway = BlitzGateway(username='******',
passwd=u'ążźćółę',
host='localhost',
port=65535)
gateway.connect()
def main():
try:
conn = BlitzGateway(username, password, host=server, port=4064)
conn.connect() #Returns True when connected
updateService = conn.getUpdateService()
from omero.rtypes import rdouble, rint, rstring
images = conn.getObjects("Image",
opts={
'owner': owner_id,
'dataset': datasetID
})
for image in images:
imageId = image.getId()
roi_service = conn.getRoiService()
result = roi_service.findByImage(imageId, None)
for roi in result.rois:
print("ROI: ID:", roi.getId().getValue())
for s in roi.copyShapes():
if type(s) == omero.model.EllipseI:
ctr_x = s.getX().getValue()
ctr_y = s.getY().getValue()
x, y, w, h = rect_roi_frm_ctr(image, ctr_x, ctr_y,
width, height)
MAX_GFP = max_proj(image, max_ch, x, y, w, h)
BFZ9 = load_stack_plane(image, slc_ch, slc, x, y, w, h)
hstk = np.stack((MAX_GFP, BFZ9), axis=0)
tmp_str = 'output_' + str(imageId) + '_' + str(
roi.getId().getValue()) + '.tif'
output_hyperstack(hstk, tmp_str)
finally:
if conn:
conn.close()
def main(argv):
parser = make_parser()
args = parser.parse_args(argv[1:])
if not args.out_file:
args.out_file = "map_screen_%d.tsv" % args.screen_id
passwd = getpass.getpass()
conn = BlitzGateway(args.user,
passwd,
host=args.host,
port=args.port,
group=args.group)
conn.connect()
screen = conn.getObject("Screen", args.screen_id)
print "writing to %s" % args.out_file
print "SCREEN: %s" % screen.name
with open(args.out_file, "w") as fo:
fo.write("PLATE\tSERIES\tWELL\tFIELD\tImageID\tWellID\n")
for p in screen.listChildren():
rows = []
print " plate: %s" % p.name
for w in p.listChildren():
n_fields = sum(1 for _ in w.listChildren())
for i in xrange(n_fields):
img = w.getImage(i)
well_tag = "%s%02d" % (LETTERS[w.row], w.column + 1)
rows.append((p.name, img.getSeries(), well_tag, i + 1,
img.id, w.id))
rows.sort(key=itemgetter(1))
rows.sort()
for r in rows:
fo.write("%s\t%d\t%s\t%d\t%d\t%d\n" % r)
def testChgrpAsync(self):
"""
Try to reproduce "race condition" bugs seen in web #8037 (fails to reproduce)
"""
image = self.image
ctx = self.gateway.getAdminService().getEventContext()
uuid = ctx.sessionUuid
self.loginAsAdmin()
gid = self.gateway.createGroup("chgrp-test-%s" % uuid, member_Ids=[ctx.userId], perms=COLLAB)
self.loginAsAuthor()
original_group = ctx.groupId
self.assertNotEqual(None, self.gateway.getObject("Image", image.id))
# Do the Chgrp
rsp = self.doChange("Image", image.getId(), gid, return_complete=False)
while rsp.getResponse() is None:
# while waiting, try various things to reproduce race condition seen in web.
img = self.gateway.getObject("Image", image.id)
c = BlitzGateway()
c.connect(sUuid=uuid)
#self.gateway.setGroupForSession(gid)
# Image should no-longer be available in current group
self.assertEqual(None, self.gateway.getObject("Image", image.id), "Image should not be available in original group")
# Switch to new group - confirm that image is there.
self.gateway.setGroupForSession(gid)
img = self.gateway.getObject("Image", image.id)
self.assertNotEqual(None, img, "Image should be available in new group")
self.assertEqual(img.getDetails().getGroup().id, gid, "Image group.id should match new group")
def run(username, password, idr_obj, local_obj, host, port):
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
# Project:1
if ':' not in idr_obj or ':' not in local_obj:
print('Objects must be: %s' % obj_help)
return
dtype = idr_obj.split(':')[0]
idr_id = idr_obj.split(':')[1]
localtype = local_obj.split(':')[0]
if dtype != localtype:
print("Object types must match")
return
local_id = local_obj.split(':')[1]
if dtype == 'Project':
annotate_project(conn, local_id, idr_id)
elif dtype == 'Plate':
plate = conn.getObject('Plate', local_id)
annotate_plate(conn, plate, idr_id)
elif dtype == 'Screen':
annotate_screen(conn, local_id, idr_id)
else:
print("Only supports Project, Screen or Plate")
finally:
conn.close()
def run(name, password, dataset_name, dataset_id, host, port):
conn = BlitzGateway(name, password, host=host, port=port)
try:
conn.connect()
roi_service = conn.getRoiService()
datasets = []
if dataset_id >= 0:
datasets.append(conn.getObject("Dataset", dataset_id))
else:
datasets = conn.getObjects("Dataset",
attributes={"name": dataset_name})
for dataset in datasets:
print(dataset.getId())
for image in dataset.listChildren():
result = roi_service.findByImage(image.getId(), None,
conn.SERVICE_OPTS)
if result is not None:
roi_ids = [roi.id.val for roi in result.rois]
if len(roi_ids) > 0:
print("Deleting %s ROIs..." % len(roi_ids))
conn.deleteObjects("Roi", roi_ids, wait=True)
except Exception as exc:
print("Error while deleting Rois: %s" % str(exc))
finally:
conn.close()
def run(password, project_name, dataset_name, host, port):
for user_number in range(1, 41):
username = "******" % user_number
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
project = ProjectI()
project.setName(rstring(project_name))
update_service = conn.getUpdateService()
project = update_service.saveAndReturnObject(project)
ds = conn.getObject("Dataset",
attributes={'name': dataset_name},
opts={'owner': conn.getUserId()})
if ds is None:
print("No dataset with name %s found" % dataset_name)
continue
dataset_id = ds.getId()
print(username, dataset_id)
link = ProjectDatasetLinkI()
link.setParent(ProjectI(project.getId().getValue(), False))
link.setChild(DatasetI(dataset_id, False))
conn.getUpdateService().saveObject(link)
except Exception as exc:
print("Error while creating project: %s" % str(exc))
finally:
conn.close()
def run(password, target, host, port):
for user_number in range(1, 51):
username = "******" % user_number
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
ds = conn.getObject("Dataset",
attributes={'name': target},
opts={'owner': conn.getUserId()})
if ds is None:
print("No dataset with name %s found" % target)
continue
print("Dataset", ds.getId())
conn.setChannelNames("Dataset", [ds.getId()], {
1: "H2B",
2: "nuclear lamina"
})
except Exception as exc:
print("Error while changing the channel names: %s" % str(exc))
finally:
# Close connection for each user when done
conn.close()
def create_containers(self, cli, project, dataset):
"""
Creates containers with names provided if they don't exist already.
Returns Dataset ID.
"""
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway(host='localhost')
conn.connect(sUuid = sessionId)
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = wrap(conn.getUser().getId())
d = None
dsId = None
if project is not None:
# We need to find or create a project
# This is not nice but we really shouldn't be dealing with large numbers of objects here
plist = list(conn.getObjects("Project", attributes={'name': project}, params=params))
if len(plist) == 0:
# Create project and dataset then link
p = self.create_project(conn, project)
d = self.create_dataset(conn, dataset)
dsId = d.id.val
self.link_dataset(conn, p.id.val, dsId)
else:
# Pick the first, it's as good as any
p = plist[0]
print "Using existing Project:", project
# Since Project already exists check children for dataset
for c in p.listChildren():
if c.getName() == dataset:
d = c
dsId = d.getId()
# No existing child dataset so create one and link
if d is None:
d = self.create_dataset(conn, dataset)
dsId = d.id.val
self.link_dataset(conn, p.getId(), dsId)
else:
print "Using existing Dataset:", dataset
else:
# There may be more than one dataset with the same name
# This is not nice but we really shouldn't be dealing with large numbers of objects here
dlist = list(conn.getObjects("Dataset", attributes={'name': dataset}, params=params))
if len(dlist) != 0:
# We want one without a parent, the first will do
for c in dlist:
if len(c.listParents()) == 0:
d = c
dsId = d.getId()
if d is None:
dsId = self.create_dataset(conn, dataset).id.val
else:
print "Using existing Dataset:", dataset
return dsId
def run(password, target, host, port):
for i in range(1, 51):
username = "******" % i
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
params = omero.sys.ParametersI()
params.addString('username', username)
query = "from Dataset where name='%s' \
AND details.owner.omeName=:username" % target
query_service = conn.getQueryService()
dataset = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(dataset) == 0:
print("No dataset with name %s found" % target)
continue
dataset_id = dataset[0].getId().getValue()
print('dataset', dataset_id)
dataset = conn.getObject("Dataset", dataset_id)
kvp_sets = [
[["mitomycin-A", "0mM"], ["PBS", "10mM"],
["incubation (mins)", "20"], ["temperature", "37"],
["Organism", "H**o sapiens"]],
[["mitomycin-A", "20mM"], ["PBS", "10mM"],
["incubation (mins)", "10"], ["temperature", "40"],
["Organism", "H**o sapiens"]],
[["mitomycin-A", "10microM"], ["PBS", "10mM"],
["incubation (mins)", "5"], ["temperature", "37"],
["Organism", "H**o sapiens"]],
[["mitomycin-A", "0mM"], ["PBS", "10mM"],
["incubation (mins)", "2"], ["temperature", "68"],
["Organism", "H**o sapiens"]],
]
for count, image in enumerate(dataset.listChildren()):
key_value_data = kvp_sets[count % 4]
map_ann = omero.gateway.MapAnnotationWrapper(conn)
# Use 'client' namespace to allow editing in Insight & web
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
map_ann.setNs(namespace)
map_ann.setValue(key_value_data)
map_ann.save()
# NB: only link a client map annotation to a single object
image.linkAnnotation(map_ann)
print('linking to image', image.getName())
except Exception as exc:
print("Error while setting key-value pairs: %s" % str(exc))
finally:
conn.close()
def run(password, admin_name, target, tag, host, port):
for i in range(1, 51):
username = "******" % i
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
updateService = conn.getUpdateService()
ds = conn.getObject("Dataset",
attributes={'name': target},
opts={'owner': conn.getUserId()})
if ds is None:
print("No dataset with name %s found" % target)
continue
params = omero.sys.ParametersI()
params.addString('username', admin_name)
query = "from TagAnnotation where textvalue='%s' \
AND details.owner.omeName=:username" % tag
query_service = conn.getQueryService()
tags = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(tags) == 0:
print("No tag with name %s found" % tag)
continue
tag_id = tags[0].id.getValue()
print(tag_id)
links = []
for image in ds.listChildren():
name = image.getName()
if name in images_to_tag:
# Check first that the image is not tagged
params = omero.sys.ParametersI()
params.addLong('parent', image.id)
params.addLong('child', tag_id)
query = "select link from ImageAnnotationLink as link \
where link.parent.id=:parent \
AND link.child.id=:child"
values = query_service.findAllByQuery(
query, params, conn.SERVICE_OPTS)
if len(values) == 0:
link = ImageAnnotationLinkI()
link.parent = ImageI(image.id, False)
link.child = TagAnnotationI(tag_id, False)
links.append(link)
else:
print("Tag %s already linked to %s" % (tag, name))
if len(links) > 0:
updateService.saveArray(links)
except Exception as exc:
print("Error when tagging the images: %s" % str(exc))
finally:
conn.close()
def get_image(image_id):
from OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
conn = BlitzGateway(USERNAME, PASSWORD, port=PORT, host=HOST)
conn.connect()
conn.SERVICE_OPTS.setOmeroGroup('-1')
if (image_id):
image = conn.getObject("Image", image_id)
return image
else:
return None
def run(args):
username = args.username
password = args.password
project_id = args.project_id
host = args.server
port = args.port
use_stain = args.use_stain
add_map_anns = args.add_map_anns
token_index = 0 if use_stain else 1
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
project = conn.getObject("Project", project_id)
for dataset in project.listChildren():
print("\n\nDataset", dataset.id, dataset.name)
for image in dataset.listChildren():
print("Image", image.id, image.name)
ann = image.getAnnotation(NAMESPACE)
if ann is None:
print(" No annotation found")
continue
keys = ann.getValue()
values = [kv[1] for kv in keys if kv[0] == MAP_KEY]
if len(values) == 0:
print(" No Key-Value found for key:", MAP_KEY)
channels = values[0].split("; ")
print("Channels", channels)
name_dict = {}
key_value_pairs = []
for c, ch_name in enumerate(channels):
tokens = ch_name.split(":")
if add_map_anns and len(tokens) > 1:
key_value_pairs.extend(
[["Ch%s_Stain" % c, tokens[0]],
["Ch%s_Label" % c, tokens[1]]]
)
if len(tokens) > token_index:
label = tokens[token_index]
else:
label = ch_name
name_dict[c + 1] = label
conn.setChannelNames("Image", [image.id], name_dict,
channelCount=None)
if len(key_value_pairs) > 0:
create_map_ann(conn, image, key_value_pairs)
except Exception as exc:
print("Error while changing names: %s" % str(exc))
finally:
conn.close()
def connect(hostname, username, password):
"""
Connect to an OMERO server
:param hostname: Host name
:param username: User
:param password: Password
:return: Connected BlitzGateway
"""
conn = BlitzGateway(username, password, host=hostname, secure=True)
conn.connect()
conn.c.enableKeepAlive(60)
return conn
def create_containers(cli, dataset, project=None):
"""
Creates containers with names provided if they don't exist already.
Returns Dataset ID.
"""
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway(host='localhost')
conn.connect(sUuid=sessionId)
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = wrap(conn.getUser().getId())
d = None
prId = None
if project is not None:
p = conn.getObject("Project",
attributes={'name': project},
params=params)
if p is None:
print "Creating Project:", project
p = omero.model.ProjectI()
p.name = wrap(project)
prId = conn.getUpdateService().saveAndReturnObject(p).id.val
else:
print "Using Project:", project, p
prId = p.getId()
# Since Project already exists, check children for Dataset
for c in p.listChildren():
if c.getName() == dataset:
d = c
if d is None:
d = conn.getObject("Dataset",
attributes={'name': dataset},
params=params)
if d is None:
print "Creating Dataset:", dataset
d = omero.model.DatasetI()
d.name = wrap(dataset)
dsId = conn.getUpdateService().saveAndReturnObject(d).id.val
if prId is not None:
print "Linking Project-Dataset..."
link = omero.model.ProjectDatasetLinkI()
link.child = omero.model.DatasetI(dsId, False)
link.parent = omero.model.ProjectI(prId, False)
conn.getUpdateService().saveObject(link)
else:
print "Using Dataset:", dataset, d
dsId = d.getId()
return dsId
def run(password, project_name, dataset_name, host, port):
for user_number in range(1, 51):
username = "******" % user_number
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
params = omero.sys.ParametersI()
params.addString('username', username)
# make sure only one result is returned by query
params.page(0, 1)
query = "from Project where name='%s' \
AND details.owner.omeName=:username \
ORDER BY id DESC" % project_name
service = conn.getQueryService()
pr_list = service.findAllByQuery(query, params, conn.SERVICE_OPTS)
if pr_list is None:
print("No project with name %s found" % project_name)
continue
project_id = pr_list[0].getId().getValue()
print(username, project_id)
params = omero.sys.ParametersI()
params.addString('username', username)
# make sure only one result is returned by query
params.page(0, 1)
query = "from Dataset where name='%s' \
AND details.owner.omeName=:username \
ORDER BY id DESC" % dataset_name
service = conn.getQueryService()
ds_list = service.findAllByQuery(query, params, conn.SERVICE_OPTS)
if ds_list is None:
print("No dataset with name %s found" % dataset_name)
continue
dataset_id = ds_list[0].getId().getValue()
print(username, dataset_id)
link = ProjectDatasetLinkI()
link.setParent(ProjectI(project_id, False))
link.setChild(DatasetI(dataset_id, False))
conn.getUpdateService().saveObject(link)
except Exception as exc:
print("Error while linking to project: %s" % str(exc))
finally:
conn.close()
def connect_to_omero(user, password, host, port=4064):
conn = BlitzGateway(user, password, host=host, port=port)
print conn.connect()
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
return conn
def JoinSession(conn):
try:
LogWriter.logDebug("Connect To:" + str(conn.host) + " " +
str(conn.port) + " " + str(conn._getSessionId()))
connection = BlitzGateway('OMERO.script',
host=conn.host,
port=conn.port)
connection.connect(sUuid=conn._getSessionId())
return connection
except Exception as inst:
LogWriter.logError("Connecting own session failed " +
str(inst.message))
LogWriter.logError(traceback.format_exc())
return None
def getOmeroConn():
try:
conn = BlitzGateway("root",
omero_rootpass,
host="localhost",
port="4064")
conn.connect()
return conn
except Exception as e:
logging.error(
"Something went wrong when getting OMERO-connection, is server up? Somethimes it takes 30 sek to start."
)
logging.error("Exception: " + str(e))
raise e
def connect_to_omero(user, password, host, port=4064):
conn = BlitzGateway(user, password, host=host, port=port)
print conn.connect()
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
return conn
def main(argv):
parser = argparse.ArgumentParser()
parser.add_argument('username2', help='Target server Username')
parser.add_argument('password2', help='Target server Password')
parser.add_argument('server2', help='Target server')
parser.add_argument('source',
help=('Copy ROIs FROM this: Image:ID or Dataset:ID'))
parser.add_argument('target',
help=('Copy ROIs TO this: Image:ID or Dataset:ID'))
args = parser.parse_args(argv)
with cli_login() as cli:
conn = BlitzGateway(client_obj=cli._client)
conn.SERVICE_OPTS.setOmeroGroup(-1)
conn2 = BlitzGateway(args.username2,
args.password2,
port=4064,
host=args.server2)
conn2.connect()
source_images = []
target_image_ids = []
source = args.source
source_id = int(source.split(":")[1])
target = args.target
target_id = int(target.split(":")[1])
if source.startswith('Image:'):
source_images.append(conn.getObject('Image', source_id))
target_image_ids.append(target_id)
elif source.startswith('Dataset:'):
dataset = conn.getObject('Dataset', source_id)
target_dataset = conn2.getObject('Dataset', target_id)
ids_by_name = image_ids_by_name(target_dataset)
for image in dataset.listChildren():
if image.name in ids_by_name:
source_images.append(image)
target_image_ids.append(ids_by_name[image.name])
else:
print("Source needs to be Image:ID or Dataset:ID")
print("Processing", source_images)
print("...to target images:", target_image_ids)
for image, to_target_id in zip(source_images, target_image_ids):
process_image(conn, conn2, image, to_target_id)
conn2.close()
def run(password, target, host, port):
for i in range(1, 51):
username = "******" % i
print(username)
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
params = omero.sys.ParametersI()
params.addString('username', username)
query = "from Dataset where name='%s' \
AND details.owner.omeName=:username" % target
service = conn.getQueryService()
dataset = service.findAllByQuery(query, params, conn.SERVICE_OPTS)
if len(dataset) == 0:
print("No dataset with name %s found" % target)
continue
dataset_obj = dataset[0]
datasetId = dataset[0].getId().getValue()
print('dataset', datasetId)
params2 = omero.sys.ParametersI()
params2.addId(dataset_obj.getId())
query = "select l.child.id from DatasetImageLink \
l where l.parent.id = :id"
images = service.projection(query, params2, conn.SERVICE_OPTS)
values = []
for k in range(0, len(images)):
image_id = images[k][0].getValue()
image = conn.getObject("Image", image_id)
u = omero.model.LengthI(0.33, UnitsLength.MICROMETER)
p = image.getPrimaryPixels()._obj
p.setPhysicalSizeX(u)
p.setPhysicalSizeY(u)
values.append(p)
if len(images) > 0:
conn.getUpdateService().saveArray(values)
except Exception as exc:
print("Error during calibration: %s" % str(exc))
finally:
conn.close()
def main(md_path, admin_user, server, port):
# load metadata
md_path = pathlib.Path(md_path)
if not md_path.is_file():
logging.error('file does not exist, check md argument')
return
try:
with open(md_path, 'r') as f:
md = json.load(f)
except json.JSONDecodeError as err:
logging.error(f'Unable to load json: {err}')
return
annotation_md = md['data']
# set up connection
password = getpass(f'Enter password for {admin_user}: ')
conn = BlitzGateway(admin_user, password, host=server, port=port)
conn.connect()
group_id = get_group_id(conn, md['OMERO_group'])
conn.SERVICE_OPTS.setOmeroGroup(group_id)
# loop through metadata and annotate
print('New Annotations:')
for md in annotation_md:
project = str(md.pop('project'))
dataset = str(md.pop('dataset'))
filename = md.pop('filename')
ns = CURRENT_MD_NS
dataset_ids = find_datasets(conn, project, dataset)
im_id_array = []
for did in dataset_ids:
im_id_array.append(get_image_ids(conn, dataset=did))
im_ids = [im_id for sublist in im_id_array for im_id in sublist]
im_ids = filter_by_filename(conn, im_ids, filename)
# im_ids = [im_id for sublist in im_id_array
# for im_id in sublist
# if image_has_imported_filename(conn, im_id, filename)]
if len(im_ids) == 0:
print(f"Cannot annotate {project} / {dataset} / {filename}"
" because it can not be found")
else:
map_ann_id = post_map_annotation(conn, "Image", im_ids, md, ns)
print(map_ann_id)
conn.close()
print('Complete!')
def connect( server, port, username, password ):
'''
Helper method that connects to an OMERO.searcher server.
@param server
@param port
@param username
@param password
@returns connection
'''
try:
conn = BlitzGateway( username, password, host=server, port=int(port))
conn.connect()
return conn
except:
return None
def index(request):
conn = BlitzGateway(OMERO_USER,OMERO_PASSWORD,host=os.environ['OMEROHOST'])
if not conn.connect():
return HttpResponseServerError("Could not connect to Omero server")
projects = []
thumbnails = {}
for project in conn.listProjects():
can_get_rois = False
p = {'id':project.id,
'name':project.name,
'datasets':[]
}
for dataset in project.listChildren():
ds = {'id':dataset.id,
'name':dataset.name,
'images':[]
}
for image in dataset.listChildren():
#if image.getROICount() > 0:
img_meta = image.simpleMarshal()
if dataset.name != 'ROI_images' and len(img_from_roi.getRectangles(conn,image)) >0:
img_meta['can_get_rois'] = True
ds['images'].append(img_meta)
size_x = image.getSizeX()
size_y = image.getSizeY()
if size_x*0.005 > 256:
thumbnails[image.id] = image.getThumbnail(size=(size_x*0.005,size_y*0.005))
else:
thumbnails[image.id] = image.getThumbnail(size=(size_x*0.1,size_y*0.1))
p['datasets'].append(ds)
projects.append(p)
conn.close()
return render(request, 'exportml/index.html',{'projects':projects,'thumbnails':thumbnails})
def main(args):
parser = argparse.ArgumentParser()
parser.add_argument('id', help="The id of the project.")
parser.add_argument('--username', default="demo")
parser.add_argument('--server', default="localhost")
parser.add_argument('--port', default=4064)
args = parser.parse_args(args)
password = getpass.getpass()
# Create a connection
try:
conn = BlitzGateway(args.username, password, host=args.server,
port=args.port)
conn.connect()
load_images(conn, args.id)
finally:
conn.close()
def get_coordinates_list(index_ligne,imageId, large, delta_x,z):
conn = BlitzGateway('tbacoyannis','d33pl34rn1ng',port=4064,host='chinensis.polytechnique.fr')
connected = conn.connect()
image = conn.getObject("Image", imageId)
pixels = image.getPrimaryPixels() # get raw pixels information
size_x= image.getSizeX()
size_y= image.getSizeY()
size_z = image.getSizeZ()
size_c = image.getSizeC()
size_t = image.getSizeT()
nb_fenetres=np.arange(size_x/delta_x)
index=nb_fenetres
x=(index*delta_x)+delta_x
#x=x[22:-22]
y=((index_ligne*delta_x)+delta_x)*np.ones(len(x)) #(index))
index_colonne=index+2
index_lignee=(2+index_ligne)*np.ones(len(x))
Tuple_Coord=(x,y,index_lignee, index_colonne)
conn._closeSession()
return(Tuple_Coord)
def main(group, admin_user, server, port):
password = getpass(f'Enter password for {admin_user}: ')
conn = BlitzGateway(admin_user, password, host=server, port=port)
conn.connect()
group_id = get_group_id(conn, group)
conn.SERVICE_OPTS.setOmeroGroup(group_id)
image_ids = get_image_ids(conn, across_groups=False)
with open("omeroImages2Import.tsv", 'w') as f:
f.write('omero_id\timage_file\timage_name\n')
for im_id in image_ids:
im_o, _ = get_image(conn, im_id, no_pixels=True)
imp_filename = Path(get_original_filepaths(conn, im_id)[0]).name
image_name = im_o.getName()
out_string = f'{im_id}\t{imp_filename}\t{image_name}\n'
f.write(out_string)
conn.close()
def connect_to_omero(uname, passwd):
conn = BlitzGateway(uname, passwd, host=HOST, port=PORT)
connected = conn.connect()
if not connected:
sys.stderr.write("Error : Connection not available, please check your user name and password.\n")
return None
return conn
class OMEConnect(widgets.VBox):
"""OMERO database connection widget
"""
def __init__(self, host="localhost", port=4064):
"""Connects to an omero database.
Parameters
----------
host: str, the omero server host (default localhost)
port: int, the connection port (default 4064)
"""
self.host = host
self.port = port
self.logbox = widgets.Text(description="OME loggin")
self.pwdbox = widgets.Password(description="OME password")
self.gobtn = widgets.Button(description="Let me in")
self.gobtn.on_click(self.on_go_clicked)
self.out = widgets.Output()
super().__init__((self.logbox, self.pwdbox, self.gobtn, self.out))
self.conn = None
def on_go_clicked(self, b):
self.out.clear_output()
if self.conn is not None:
self.conn.close()
self.conn = BlitzGateway(self.logbox.value,
self.pwdbox.value,
host=self.host,
port=self.port)
self.conn.connect()
if self.conn.isConnected():
with self.out:
print("Logging successful!\n")
display(
Image(
"https://media.giphy.com/media/Azwmdv1NTSe9W/giphy.gif"
))
sleep(3)
self.out.clear_output()
else:
with self.out:
("sorry, connection failed, try again?")
self.logbox.value = ""
self.pwdbox.value = ""
def create_containers(cli, dataset, project=None):
"""
Creates containers with names provided if they don't exist already.
Returns Dataset ID.
"""
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway()
conn.connect(sUuid = sessionId)
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = wrap(conn.getUser().getId())
d = None
prId = None
if project is not None:
p = conn.getObject("Project", attributes={'name': project}, params=params)
if p is None:
print "Creating Project:", project
p = omero.model.ProjectI()
p.name = wrap(project)
prId = conn.getUpdateService().saveAndReturnObject(p).id.val
else:
print "Using Project:", project, p
prId = p.getId()
# Since Project already exists, check children for Dataset
for c in p.listChildren():
if c.getName() == dataset:
d = c
if d is None:
d = conn.getObject("Dataset", attributes={'name': dataset}, params=params)
if d is None:
print "Creating Dataset:", dataset
d = omero.model.DatasetI()
d.name = wrap(dataset)
dsId = conn.getUpdateService().saveAndReturnObject(d).id.val
if prId is not None:
print "Linking Project-Dataset..."
link = omero.model.ProjectDatasetLinkI()
link.child = omero.model.DatasetI(dsId, False)
link.parent = omero.model.ProjectI(prId, False)
conn.getUpdateService().saveObject(link)
else:
print "Using Dataset:", dataset, d
dsId = d.getId()
return dsId
def connect_to_omero():
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
connected = conn.connect()
if not connected:
import sys
sys.stderr.write("Error : Connection not available, please check your user name and password.\n")
return None
return conn
def omero_login(user, passwd, host, port):
"""Establish the connection to an OMERO server.
Parameters
==========
user : str - OMERO user name (e.g. "demo_user_01")
passwd : str - OMERO user password
host : str - OMERO server hostname to connect to
port : int - OMERO server port number (e.g. 4064)
Returns
=======
conn : omero.gateway._BlitzGateway - OMERO connection object
"""
conn = BlitzGateway(user, passwd, host=host, port=port, secure=True,
useragent="HRM-OMERO.connector")
conn.connect()
return conn
def temporary_connection():
temp_client = omero.client()
omeroProperties = temp_client.getProperties().getPropertiesForPrefix('omero')
# Configuration
HOST = omeroProperties.get('omero.host', 'localhost')
PORT = omeroProperties.get('omero.port', 4064)
USERNAME = omeroProperties.get('omero.user')
PASSWORD = omeroProperties.get('omero.pass')
temp_conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
connected = temp_conn.connect()
return temp_client,temp_conn
def connect_base():
"""Establish the base connection to OMERO.
Returns the connection in the context defined in localconfig.
"""
# establish the base connection with an admin account
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
if su_conn.connect() is False:
raise RuntimeError('Connection to OMERO failed, check settings!')
log.debug("Successfully connected to OMERO.")
return su_conn
def create_screen(self, cli, screen):
"""
Creates screen with name provided if it doesn't exist already.
Returns Screen ID.
"""
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway(host='localhost')
conn.connect(sUuid = sessionId)
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = wrap(conn.getUser().getId())
slist = list(conn.getObjects("Screen", attributes={'name': screen}, params=params))
if len(slist) == 0:
print "Creating Screen:", screen
s = ScreenI()
s.name = wrap(screen.encode('ascii','ignore'))
scrId = conn.getUpdateService().saveAndReturnObject(s).id.val
else:
scrId = slist[0].getId()
print "Using Screen:", screen
return scrId
def group_exists(self, user, group):
if not self.user_exists(user):
return False
else:
if group in self.known_users[user]:
print "in Group:", group
return True
try:
try:
conn = BlitzGateway(user, "ome", host='localhost')
conn.connect()
groups = conn.getGroupsMemberOf()
except:
return False
if group in [g.name for g in groups]:
print "in Group:", group
self.known_users[user].append(group)
return True
else:
print "is not in Group:", group, "- ignoring."
return False
finally:
conn.seppuku()
def user_exists(self, user):
if user in self.known_users.keys():
print "User:"******"root", "omero", host='localhost')
conn.connect()
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
u = conn.getObject("Experimenter", attributes={'omeName': user}, params=params)
except:
print "Error getting user - ignoring."
return False
if u is None:
print "User:"******"does not exist - ignoring."
return False
else:
print "User:", user,
self.known_users[user] = []
return True
finally:
conn.seppuku()
class ScriptsManager(object):
def __init__(self, user="******", pwd="omero", host="localhost", port=4064):
self.conn = BlitzGateway(user, pwd, host=host, port=port)
result = self.conn.connect()
if not result:
raise RuntimeError("Cannot connect to <{0}>".format(host)+
" with user <{0}>.".format(user))
self.svc = self.conn.getScriptService()
def list(self):
return self.svc.getScripts()
def delete(self, id):
try:
self.svc.deleteScript(id)
except Exception, e:
raise RuntimeError("Failed to delete script: "+
"{0} ({1})".format(id, e))
def connect_as_user(username):
"""Establish a connection to OMERO with a given user context.
To establish a connection as a specific user without knowing their
credential, a two-stage process is required: first the bsae connection is
created with an admin user, then this existing connection is switched over
to a (non-privileged) user account.
Returns the connection in the user's context.
"""
# establish the base connection with an admin account
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
if su_conn.connect() is False:
raise RuntimeError('Connection to OMERO failed, check settings!')
# now switch to the requested user
conn = su_conn.suConn(username)
if conn.connect() is False:
raise RuntimeError('User switching in OMERO failed, check settings!')
log.debug("Successfully connected to OMERO.")
return conn
def new_connection(self, user, passw, host):
conn = BlitzGateway(user, passw, host=host)
conn.connect()
return conn
#
# Copyright (C) 2011 University of Dundee & Open Microscopy Environment.
# All Rights Reserved.
# Use is subject to license terms supplied in LICENSE.txt
#
from sys import argv
import omero
from omero.gateway import BlitzGateway
from Connect_To_OMERO import USERNAME, PASSWORD, HOST, PORT
# Create a connection
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Configuration
# =================================================================
script, imageId = argv
# Reitrieve an image by Image ID:
# =================================================================
image = conn.getObject("Image", imageId)
print "\nImage:%s" % imageId
print "=" * 50
class Omg(object):
"""
OMERO gateway that wraps Blitz gateway and CLI, intended for
scripting and interactive work.
Attributes
----------
conn : Blitz gateway connection
"""
def __init__(self, conn=None, user=None, passwd=None,
server=SERVER, port=PORT, skey=None):
"""
Requires active Blitz connection OR username plus password or sesskey
"""
if conn is None and (user is None or (passwd is None and skey is None)):
raise ValueError("Bad parameters," + self.__init__.__doc__)
if conn is not None:
if conn.isConnected():
self.conn = conn
else:
raise ValueError("Cannot initialize with closed connection!")
else:
if passwd is not None:
self.conn = BlitzGateway(user, passwd, host=server, port=port)
self.conn.connect()
else:
self.conn = BlitzGateway(user, host=server, port=port)
self.conn.connect(skey)
if self.conn.isConnected():
self._server = self.conn.host
self._port = self.conn.port
self._user = self.conn.getUser().getName()
self._key = self.conn.getSession().getUuid().getValue()
print("Connected to {0} (port {1}) as {2}, session key={3}".format(
self._server, self._port, self._user, self._key))
else:
print("Failed to open connection :-(")
def ls(self):
"""
Print groups, then projects/datasets/images for current group.
"""
print("Groups for {0}:-".format(self.conn.getUser().getName()))
for gid, gname in self._ls_groups():
print(" {0} ({1})".format(gname, str(gid)))
curr_grp = self.conn.getGroupFromContext()
gid, gname = curr_grp.getId(), curr_grp.getName()
print("\nData for current group, {0} ({1}):-".format(gname, gid))
for pid, pname in self._ls_projects():
print(" Project: {0} ({1})".format(pname, str(pid)))
for did, dname in self._ls_datasets(pid):
print(" Dataset: {0} ({1})".format(dname, str(did)))
for iid, iname in self._ls_images(did):
print(" Image: {0} ({1})".format(iname, str(iid)))
# TODO, list orphaned Datasets and Images
def _ls_groups(self):
"""list groups (id, name) this session is a member of"""
groups = self.conn.getGroupsMemberOf()
return [(group.getId(), group.getName()) for group in groups]
def _ls_projects(self):
"""list projects (id, name) in the current session group"""
projs = self.conn.listProjects(self.conn.getUserId())
return [(proj.getId(), proj.getName()) for proj in projs]
def _ls_datasets(self, proj_id):
"""list datasets (id, name) within the project id given"""
dsets = self.conn.getObject("Project", proj_id).listChildren()
return [(dset.getId(), dset.getName()) for dset in dsets]
def _ls_images(self, dset_id):
"""list images (id, name) within the dataset id given"""
imgs = self.conn.getObject("Dataset", dset_id).listChildren()
return [(img.getId(), img.getName()) for img in imgs]
def chgrp(self, group_id):
"""
Change group for this session to the group_id given.
"""
self.conn.setGroupForSession(group_id)
def get(self, im_id, get_att=True):
"""
Download the specified image as an OME-TIFF to current directory,
with attachments also downloaded to folder: img_path + '_attachments'
Return : path to downloaded image
"""
img = self.conn.getObject("Image", oid=im_id)
img_name = self._unique_name(img.getName(), im_id)
img_path = os.path.join(os.getcwd(), img_name)
img_file = open(str(img_path + ".ome.tiff"), "wb")
fsize, blockgen = img.exportOmeTiff(bufsize=65536)
for block in blockgen:
img_file.write(block)
img_file.close()
fa_type = omero.model.FileAnnotationI
attachments = [ann for ann in img.listAnnotations()
if ann.OMERO_TYPE == fa_type]
if get_att and len(attachments) > 0:
att_dir = img_path + "_attachments"
os.mkdir(att_dir)
def download_attachment(att, att_dir):
"""download OMERO file annotation to att_dir"""
att_file = open(os.path.join(att_dir, att.getFileName()), "wb")
for att_chunk in att.getFileInChunks():
att_file.write(att_chunk)
att_file.close()
for att in attachments:
download_attachment(att, att_dir)
return img_path
def _unique_name(self, img_name, im_id):
"""Make unique name combining a file basename & OMERO Image id"""
path_and_base, ext = os.path.splitext(img_name)
base = os.path.basename(path_and_base) # name in OMERO can has path
return "{0}_{1}".format(base, str(im_id))
def dget(self, dataset_id):
"""
Download an entire OMERO Dataset to the current directory.
"""
downloads = []
wdir = os.getcwd()
dset_name = self.conn.getObject("Dataset", dataset_id).getName()
dset_path = os.path.join(wdir, dset_name + "_D" + str(dataset_id))
os.mkdir(dset_path)
os.chdir(dset_path)
for img_id, img_name in self._ls_images(dataset_id):
downloads.append(self.get(img_id))
os.chdir(wdir)
return downloads
def pget(self, project_id):
"""
Download an entire OMERO Project to the current directory.
"""
downloads = []
wdir = os.getcwd()
proj_name = self.conn.getObject("Project", project_id).getName()
proj_path = os.path.join(wdir, proj_name + "_P" + str(project_id))
os.mkdir(proj_path)
os.chdir(proj_path)
for dset_id, dset_name in self._ls_datasets(project_id):
downloads.extend(self.dget(dset_id))
os.chdir(wdir)
return downloads
def put(self, filename, name=None, dataset=None):
"""
Import filename using OMERO CLI, optionally with a specified name
to a specified dataset (dataset_id).
Return : OMERO image Id
"""
cli = omero.cli.CLI()
cli.loadplugins()
import_args = ["import"]
import_args.extend(["-s", str(self._server)])
import_args.extend(["-k", str(self._key)])
if dataset is not None:
import_args.extend(["-d", str(dataset)])
if name is not None:
import_args.extend(["-n", str(name)])
clio = "cli.out"
clie = "cli.err"
import_args.extend(["---errs=" + clie, "---file=" + clio, "--"])
import_args.append(filename)
cli.invoke(import_args, strict=True)
pix_id = int(open(clio, 'r').read().rstrip())
im_id = self.conn.getQueryService().get("Pixels", pix_id).image.id.val
os.remove(clio)
os.remove(clie)
return im_id
def describe(self, im_id, description):
"""
Append to image description.
"""
img = self.conn.getObject("Image", oid=im_id)
old_description = img.getDescription() or ""
img.setDescription(old_description + "\n" + description)
img.save()
def attach(self, im_id, attachments):
"""
Attach a list of files to an image.
"""
img = self.conn.getObject("Image", oid=im_id)
for attachment in attachments.split():
fann = self.conn.createFileAnnfromLocalFile(attachment)
img.linkAnnotation(fann)
img.save()
# TODO: ls_tags() and tag() methods?
def mkp(self, project_name, description=None):
"""
Make new OMERO project in current group, returning the new project Id.
"""
# see: omero/lib/python/omeroweb/webclient/controller/container.py
proj = omero.model.ProjectI()
proj.name = omero.rtypes.rstring(str(project_name))
if description is not None and description != "":
proj.description = omero.rtypes.rstring(str(description))
return self._save_and_return_id(proj)
def mkd(self, dataset_name, project_id=None, description=None):
"""
Make new OMERO dataset, returning the new dataset Id.
"""
dset = omero.model.DatasetI()
dset.name = omero.rtypes.rstring(str(dataset_name))
if description is not None and description != "":
dset.description = omero.rtypes.rstring(str(description))
if project_id is not None:
l_proj_dset = omero.model.ProjectDatasetLinkI()
proj = self.conn.getObject("Project", project_id)
l_proj_dset.setParent(proj._obj)
l_proj_dset.setChild(dset)
dset.addProjectDatasetLink(l_proj_dset)
return self._save_and_return_id(dset)
def _save_and_return_id(self, obj):
"""Save new omero object and return id assgined to it"""
# see: OmeroWebGateway.saveAndReturnId
# in: lib/python/omeroweb/webclient/webclient_gateway.py
u_s = self.conn.getUpdateService()
res = u_s.saveAndReturnObject(obj, self.conn.SERVICE_OPTS)
res.unload()
return res.id.val
def im(self, im_id):
"""
Return an Im object for the image id specified.
"""
img = self.conn.getObject("Image", im_id)
# build pixel np.ndarray
nx, ny = img.getSizeX(), img.getSizeY()
nz, nt, nc = img.getSizeZ(), img.getSizeT(), img.getSizeC()
planes = [(z, c, t) for c in range(nc)
for t in range(nt)
for z in range(nz)]
pix_gen = img.getPrimaryPixels().getPlanes(planes)
pix = np.array([i for i in pix_gen]).reshape((nc, nt, nz, ny, nx))
# initialize Im using pix and extracted metadata
meta = self._extract_meta(img, im_id)
return Im(pix=pix, meta=meta)
def _extract_meta(self, img, im_id):
"""Extract metadata attributes from OMERO Blitz gateway Image"""
meta = {}
meta['name'] = self._unique_name(img.getName(), im_id)
meta['description'] = img.getDescription()
def _extract_ch_info(ch):
"""extract core metadata for for channel, return as dict"""
ch_info = {'label': ch.getLabel()}
ch_info['ex_wave'] = ch.getExcitationWave()
ch_info['em_wave'] = ch.getEmissionWave()
ch_info['color'] = ch.getColor().getRGB()
return ch_info
meta['channels'] = [_extract_ch_info(ch) for ch in img.getChannels()]
meta['pixel_size'] = {'x': img.getPixelSizeX(),
'y': img.getPixelSizeY(),
'z': img.getPixelSizeZ(),
'units': "um"}
tag_type = omero.model.TagAnnotationI
tags = [ann for ann in img.listAnnotations()
if ann.OMERO_TYPE == tag_type]
meta['tags'] = {tag.getValue() + " (" + str(tag.getId()) + ")":
tag.getDescription() for tag in tags}
fa_type = omero.model.FileAnnotationI
attachments = [ann for ann in img.listAnnotations()
if ann.OMERO_TYPE == fa_type]
meta['attachments'] = [att.getFileName() + " (" + str(att.getId()) +
")" for att in attachments]
user_id = self.conn.getUser().getName() + " (" + \
str(self.conn.getUser().getId()) + ") @" + self.conn.host
meta_ext = {}
meta_ext['user_id'] = user_id
meta['meta_ext'] = meta_ext
# TODO: ROIs, display settings?
# objective: Image.loadOriginalMetadata()[1][find 'Lens ID Number'][1],
return meta
def imput(self, im, dataset_id=None):
"""
Create a new OMERO Image using an Im object, returning new image id.
"""
# see: omero/lib/python/omero/util/script_utils.py
# see: omero/lib/python/omeroweb/webclient/webclient_gateway.py
# see: https://gist.github.com/will-moore/4141708
if not isinstance(im, Im):
raise TypeError("first imput argument must be of type Im")
nc, nt, nz, ny, nx = im.shape
ch_nums = range(nc)
q_s = self.conn.getQueryService()
p_s = self.conn.getPixelsService()
c_s = self.conn.getContainerService()
u_s = self.conn.getUpdateService()
pu_s = self.conn.c.sf.createRawPixelsStore()
q_ptype = "from PixelsType as p where p.value='{0}'".format(
str(im.dtype))
pixelsType = q_s.findByQuery(q_ptype, None)
im_id = p_s.createImage(nx, ny, nz, nt, ch_nums, pixelsType,
im.name, im.description)
img_i = c_s.getImages("Image", [im_id.getValue()], None)[0]
img = self.conn.getObject("Image", im_id.getValue())
pix_id = img_i.getPrimaryPixels().getId().getValue()
pu_s.setPixelsId(pix_id, True)
for c in range(nc):
for t in range(nt):
for z in range(nz):
plane = im.pix[c, t, z, :, :]
script_utils.uploadPlaneByRow(pu_s, plane, z, c, t)
l_dset_im = omero.model.DatasetImageLinkI()
dset = self.conn.getObject("Dataset", dataset_id)
l_dset_im.setParent(dset._obj)
l_dset_im.setChild(img._obj)
self._update_meta(im, im_id)
u_s.saveObject(l_dset_im, self.conn.SERVICE_OPTS)
return im_id.getValue()
def _update_meta(self, im, im_id):
"""Set OMERO Image metadata using Im metadata"""
if e.errno != errno.EEXIST:
raise
HOST = "lincs-omero.hms.harvard.edu"
PORT = 4064
GROUP = "Public"
# Read username and password.
print "Connecting to OMERO server: %s:%d" % (HOST, PORT)
username = getpass._raw_input("Username: "******"Error: Connection not available, please check your " "username and password.")
sys.exit(1)
else:
print "Login successful.\n"
# Set our default group so we can see the data.
# (I thought I had to do this, but now I am not sure it's needed.
# -JLM 2013/12/04)
try:
group = next(g for g in conn.listGroups() if g.getName() == GROUP)
except StopIteration:
print >> sys.stderr, "Error: could not find group '%s'" % GROUP
conn.setGroupForSession(group.getId())
import omero
import omero.cli
from omero.gateway import BlitzGateway
from omero.rtypes import wrap, rlong, rdouble, rint, rstring
from omero.model import DatasetI, ProjectI, TagAnnotationI
# Only these people will be logged in to do Tagging, Comments etc
# We will still create Tags for ALL users so they're available for others to use.
USER_NAMES = ["user-10", "user-11", "user-12"]
# USER_NAMES = ["user-7", "user-8", "user-9", "user-10", "user-11", "user-12"]
conn = BlitzGateway('root', 'omero', host='localhost')
conn.connect()
conn.SERVICE_OPTS.setOmeroGroup(-1)
# ---- CONFIGURATION ----
TAG_COUNT = 1 # Number of tags each user should use (link)
TAG_TARGETS = ['Project', 'Dataset', 'Image', "Screen", "Plate"]
ROI_COUNT = 3
allUsers = []
for exp in conn.getObjects("Experimenter"):
n = exp.getName()
if n not in ["root", "guest"]:
print n
allUsers.append(exp)
def use_connection(self, cli, host):
sessionId = cli._event_context.sessionUuid
conn = BlitzGateway(host=host)
conn.connect(sUuid = sessionId)
return conn
PORT = 4064
USER = "******"
# PASS = '******'
# PASS = '******'
SU_USER = "******"
SU_PASS = "******"
try:
from localconfig import USER, SU_USER, SU_PASS, MANAGED_REPO
except ImportError:
print "Using hard-coded configuration values!"
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
if su_conn.connect() is False:
raise RuntimeError("Connection to OMERO failed, check settings!")
conn = su_conn.suConn(USER)
if conn.connect() is False:
raise RuntimeError("User switching in OMERO failed, check settings!")
su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
su_conn.connect()
conn = su_conn.suConn(USER)
conn.connect()
# projs = [ x for x in conn.listProjects() ]
projs = [x for x in conn.listProjects(eid=conn.getUserId())]
for proj in projs: