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 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(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()
conn.connect()
NAMESPACE = "openmicroscopy.org/omero/bulk_annotations"
MAP_KEY = "Channels"
# TO BE MODIFIED
project_id = 4501
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
key_values = ann.getValue()
channels_value = [kv[1] for kv in key_values if kv[0] == MAP_KEY]
if len(channels_value) == 0:
print " No Key-Value found for key:", MAP_KEY
channels = channels_value[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)
ch1 = channel_name
elif channel_info.strip().startswith("Ch2"):
ch2 = channel_name
elif channel_info.strip().startswith("Ch3"):
ch3 = channel_name
if not (ch1 and ch2 and ch3):
print("Channel name missing for row {}".format(index))
channel_names[key] = {1: ch1, 2: ch2, 3: ch3}
conn = BlitzGateway(os.environ.get('OMERO_USER', 'xxx'),
os.environ.get('OMERO_PASSWORD', 'xxx'),
host=host,
port=port)
conn.connect()
screen = conn.getObject("Screen", sys.argv[2])
for pl in screen.listChildren():
n_fields = pl.getNumberOfFields()
for well in pl.listChildren():
print("Processing {} - {}".format(pl.getName(), well.getWellPos()))
for field in range(n_fields[0], n_fields[1] + 1):
ws = well.getWellSample(field)
key = "{},{}".format(pl.getName(), well.getWellPos())
if ws and ws.getImage() and key in channel_names:
img = well.getImage()
conn.setChannelNames("Image", [img.getId()],
channel_names[key],
channelCount=None)
conn.close()
