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 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(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 test_numpy_to_image(self):
client = self.new_client()
image = self.create_test_image(100, 100, 2, 3, 4, client.getSession())
conn = BlitzGateway(client_obj=client)
image = conn.getObject("Image", image.id.val)
pixels = image.getPrimaryPixels()
channel_min_max = []
for c in image.getChannels():
min_c = c.getWindowMin()
max_c = c.getWindowMax()
channel_min_max.append((min_c, max_c))
z = image.getSizeZ() / 2
t = 0
c = 0
try:
for min_max in channel_min_max:
plane = pixels.getPlane(z, c, t)
i = scriptUtil.numpy_to_image(plane, min_max, int32)
assert i is not None
try:
# check if the image can be handled.
i.load()
assert True
except IOError:
assert False
c += 1
finally:
conn.close()
def get_file_contents(client, original_file_id):
"""Returns Original File contents as a string."""
conn = BlitzGateway(client_obj=client)
orig_file = conn.getObject("OriginalFile", original_file_id)
text = "".join(orig_file.getFileInChunks())
conn.close()
return text
def check_file_annotation(client,
file_annotation,
parent_type="Image",
is_linked=True,
file_name=None):
"""
Check validity of file annotation. If hasFileAnnotation, check the size,
name and number of objects linked to the original file.
"""
assert file_annotation is not None
orig_file = file_annotation.getValue().getFile()
assert orig_file.getSize().getValue() > 0
assert orig_file.getName().getValue() is not None
id = file_annotation.getValue().getId().getValue()
assert id > 0
conn = BlitzGateway(client_obj=client)
wrapper = conn.getObject("FileAnnotation", id)
name = None
if file_name is not None:
name = wrapper.getFile().getName()
links = sum(1 for i in wrapper.getParentLinks(parent_type))
conn.close()
if is_linked:
assert links == 1
else:
assert links == 0
if file_name is not None:
assert name == file_name
def check(self):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
for experiment in self.m["experiments"]:
self.check_object(gateway, experiment, "Project")
for experiment in self.m["screens"]:
self.check_object(gateway, experiment, "Screen")
if "map" in self.m:
if self.m["experiments"]:
study_type = "Project"
else:
study_type = "Screen"
self.check_object(gateway, self.m, study_type)
finally:
if cli:
cli.close()
gateway.close()
def check(obj):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
remote_obj = gateway.getObject(
obj.type, attributes={"name": obj.name})
errors = []
if remote_obj.description != obj.description:
errors.append("current:%s\nexpected:%s" % (
remote_obj.description, obj.description))
for al in remote_obj._getAnnotationLinks(
ns="openmicroscopy.org/omero/client/mapAnnotation"):
mapValue = al.child.mapValue
kv_pairs = [(m.name, m.value) for m in mapValue]
for i in range(len(kv_pairs)):
if kv_pairs[i] != obj.map[i]:
errors.append(
"current:%s\nexpected:%s" % (kv_pairs[i], obj.map[i]))
if not errors:
log.info("No annotations mismatch detected")
else:
for e in errors:
log.info("Found some annotations mismatch")
print e
finally:
if cli:
cli.close()
gateway.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 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():
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 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 check(self):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
for experiment in self.m["experiments"]:
self.check_object(gateway, experiment, "Project")
for experiment in self.m["screens"]:
self.check_object(gateway, experiment, "Screen")
if "map" in self.m:
if self.m["experiments"]:
study_type = "Project"
else:
study_type = "Screen"
self.check_object(gateway, self.m, study_type)
finally:
if cli:
cli.close()
gateway.close()
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 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 test_get_objects(self):
client = self.new_client()
image = self.create_test_image(100, 100, 1, 1, 1, client.getSession())
conn = BlitzGateway(client_obj=client)
params = {}
params["Data_Type"] = "Image"
params["IDs"] = [image.id.val]
objects, message = scriptUtil.get_objects(conn, params)
assert objects[0].id == image.id.val
assert message is ''
conn.close()
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 make_roi_images(request,image_id):
conn = BlitzGateway(OMERO_USER,OMERO_PASSWORD,host=os.environ['OMEROHOST'])
if not conn.connect():
return HttpResponseServerError("Could not connect to Omero server")
parameterMap = {'Data_Type':'Image',
'IDs':[long(image_id)],
'New_Dataset':True,
'New_Dataset_Name':'ROI_images',
'Entire_Stack':False
}
msg = img_from_roi.makeImagesFromRois(conn,parameterMap)
conn.close()
return render(request, 'exportml/gen_roi_message.html', {'messages':msg})
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 run_as_script():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
data_types = [rstring('Dataset')]
client = scripts.client(
'Shapes_To_Table.py',
("This script processes images, measuring the length of ROI Lines and"
" saving the results to an OMERO.table."),
scripts.String(
"Data_Type",
optional=False,
grouping="1",
description="Choose source of images (only Dataset supported)",
values=data_types,
default="Dataset"),
scripts.List("IDs",
optional=False,
grouping="2",
description="List of Dataset IDs to convert to new"
" Plates.").ofType(rlong(0)),
version="4.3.2",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
# process the list of args above.
script_params = {}
for key in client.getInputKeys():
if client.getInput(key):
script_params[key] = client.getInput(key, unwrap=True)
print(script_params)
# wrap client to use the Blitz Gateway
conn = BlitzGateway(client_obj=client)
# process images in Datasets
message = process_data(conn, script_params)
if message is not None:
client.setOutput("Message", rstring(message))
else:
client.setOutput("Message", rstring("No datasets found"))
finally:
conn.close()
def connection_test(username, password, host=HOST, port=PORT, secure=False):
print(f'connecting to {host}:{port} secure={secure}')
conn = BlitzGateway(username,
password,
host=host,
port=port,
secure=secure)
try:
connected = conn.connect()
conn.close()
return connected
except:
conn.close()
return False
def test_populate_metadata_for_screen(self):
sid = super(TestImportScripts, self).get_script(populate_metadata)
assert sid > 0
client, user = self.new_client_and_user()
update_service = client.getSession().getUpdateService()
plates = self.import_plates(client, plate_cols=3, plate_rows=1)
plate = plates[0]
name = plate.name.val
screen = omero.model.ScreenI()
screen.name = omero.rtypes.rstring("test_for_screen")
spl = omero.model.ScreenPlateLinkI()
spl.setParent(screen)
spl.setChild(plate)
spl = update_service.saveAndReturnObject(spl)
screen_id = spl.getParent().id.val
assert screen_id > 0
assert spl.getChild().id.val == plate.id.val
cvs_file = create_path("test_screen", ".csv")
# create a file annotation
with open(cvs_file.abspath(), 'w+') as f:
f.write("Well,Plate, Well Type, Facility-Salt-Batch-ID\n")
f.write("A01,%s,Treatment,FOOL10041-101-2\n" % name)
f.write("A02,%s,Control,\n" % name)
f.write("A03,%s,Treatment,FOOL10041-101-2\n" % name)
conn = BlitzGateway(client_obj=client)
fa = conn.createFileAnnfromLocalFile(cvs_file, mimetype="text/csv")
assert fa is not None
assert fa.id > 0
link = omero.model.ScreenAnnotationLinkI()
link.setParent(omero.model.ScreenI(screen_id, False))
link.setChild(omero.model.FileAnnotationI(fa.id, False))
link = update_service.saveAndReturnObject(link)
assert link.id.val > 0
# run the script
screen_ids = []
screen_ids.append(spl.getParent().id)
args = {
"Data_Type": omero.rtypes.rstring("Screen"),
"IDs": omero.rtypes.rlist(screen_ids),
"File_Annotation": omero.rtypes.rstring(str(fa.id))
}
message = run_script(client, sid, args, "Message")
assert message is not None
assert message.getValue().startswith('Table data populated')
conn.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 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 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 check(self, update=False):
from omero.cli import CLI
from omero.gateway import BlitzGateway
cli = CLI()
cli.loadplugins()
cli.onecmd('login -q')
try:
gateway = BlitzGateway(client_obj=cli.get_client())
self.check_study(gateway, update=update)
finally:
if cli:
cli.close()
gateway.close()
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 check_file_annotation(client, file_annotation,
parent_type="Image", link_count=0):
"""
Check validity of file annotation. If hasFileAnnotation, check the size,
name and number of objects linked to the original file.
"""
assert file_annotation is not None
id = file_annotation.getId().getValue()
assert id > 0
orig_file = file_annotation.getFile()
assert orig_file.getSize().getValue() > 0
assert orig_file.getName().getValue() is not None
conn = BlitzGateway(client_obj=client)
wrapper = conn.getObject("FileAnnotation", id)
links = sum(1 for i in wrapper.getParentLinks(parent_type))
conn.close()
assert links == link_count
