def get_images(gateway, datasets, orphaned=True):
"""Return all image ids and image names for provided dataset ids"""
browse = gateway.getFacility(BrowseFacility)
experimenter = gateway.getLoggedInUser()
ctx = SecurityContext(experimenter.getGroupId())
images = []
for dataset_id in datasets:
ids = ArrayList(1)
ids.add(Long(dataset_id))
j = browse.getImagesForDatasets(ctx, ids).iterator()
while j.hasNext():
image = j.next()
images.append({
'Image Id': String.valueOf(image.getId()),
'Image Name': image.getName(),
'Dataset Id': dataset_id,
'Dataset Name': datasets[dataset_id],
})
if orphaned:
orphans = browse.getOrphanedImages(
ctx, ctx.getExperimenter()) # need to pass user id (long)
for image in orphans:
images.append({
'Image Id': String.valueOf(image.getId()),
'Image Name': image.getName(),
'Dataset Id': -1,
'Dataset Name': '<Orphaned>',
})
return images
def uploadImage(path, gateway):
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
sessionKey = gateway.getSessionId(user)
config = ImportConfig()
config.email.set("")
config.sendFiles.set('true')
config.sendReport.set('false')
config.contOnError.set('false')
config.debug.set('false')
config.hostname.set(HOST)
config.sessionKey.set(sessionKey)
config.targetClass.set("omero.model.Dataset")
config.targetId.set(datasetId)
loci.common.DebugTools.enableLogging("DEBUG")
store = config.createStore()
reader = OMEROWrapper(config)
library = ImportLibrary(store,reader)
errorHandler = ErrorHandler(config)
library.addObserver(LoggingImportMonitor())
candidates = ImportCandidates (reader, path, errorHandler)
reader.setMetadataOptions(DefaultMetadataOptions(MetadataLevel.ALL))
success = library.importCandidates(config, candidates)
return success
def upload_image(gateway, path, host, dataset_id):
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
session_key = gateway.getSessionId(user)
str2d = Array.newInstance(String,[1])
str2d[0] = path
config = ImportConfig()
config.email.set("")
config.sendFiles.set('true')
config.sendReport.set('false')
config.contOnError.set('false')
config.debug.set('false')
config.hostname.set(host)
config.sessionKey.set(session_key)
config.targetClass.set("omero.model.Dataset")
config.targetId.set(dataset_id)
loci.common.DebugTools.enableLogging("DEBUG")
store = config.createStore()
reader = OMEROWrapper(config)
library = ImportLibrary(store,reader)
error_handler = ErrorHandler(config)
library.addObserver(LoggingImportMonitor())
candidates = ImportCandidates(reader, str2d, error_handler)
reader.setMetadataOptions(DefaultMetadataOptions(MetadataLevel.ALL))
print('Importing image: ' + str2d[0])
success = library.importCandidates(config, candidates)
return success
def create_table(gatway):
currentGroupId = gateway.getLoggedInUser().getGroupId()
ctx = SecurityContext(currentGroupId)
fac = gateway.getFacility(TablesFacility)
table_name = "TablesDemo:%s" % str(random.randint(1, 1000))
col1 = omero.grid.LongColumn('Uid', 'testLong', [])
col2 = omero.grid.StringColumn('MyStringColumnInit', '', 64, [])
columns = [col1, col2]
resources = gateway.getSharedResources(ctx)
repository_id = resources.repositories().descriptions[0].getId().getValue()
table = resources.newTable(repository_id, table_name)
table.initialize(columns)
# Add data to the table
ids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
strings = [
"one", "two", "three", "four", "five", "six", "seven", "eight", "nine",
"ten"
]
data1 = omero.grid.LongColumn('Uid', 'test Long', ids)
data2 = omero.grid.StringColumn('MyStringColumn', '', 64, strings)
data = [data1, data2]
table.addData(data)
table.close()
return table
def download_image(gateway, image_id, path):
"Download the files composing the image"
transfer = gateway.getFacility(TransferFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
return transfer.downloadImage(ctx, path, Long(image_id))
def _get_images_browser(gateway, dataset_id, group_id):
browse = gateway.getFacility(BrowseFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(group_id)
ids = ArrayList(1)
val = Long(dataset_id)
ids.add(val)
images = browse.getImagesForDatasets(ctx, ids)
return images.iterator()
def getImageIds(gateway, datasetId):
browse = gateway.getFacility(BrowseFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
ids = ArrayList(1)
val = Long(datasetId)
ids.add(val)
images = browse.getImagesForDatasets(ctx, ids)
j = images.iterator()
imageIds = []
while j.hasNext():
image = j.next()
imageIds.append(String.valueOf(image.getId()))
def get_groups(gateway):
"""Retrieves the groups for the user"""
currentGroupId = gateway.getLoggedInUser().getGroupId()
ctx = SecurityContext(currentGroupId)
adminService = gateway.getAdminService(ctx, True)
uid = adminService.lookupExperimenter(username)
groups = []
for g in sorted(adminService.getMemberOfGroupIds(uid)):
groupname = str(adminService.getGroup(g).getName().getValue())
groups.append({
'Id': g,
'Name': groupname,
})
if g == currentGroupId:
currentGroup = groupname
return groups, currentGroup
def add_image_tag(gateway, tag_text, image_id, description=None):
"""Adds a tag to an image"""
data_manager = gateway.getFacility(DataManagerFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
# Arrange the data
tag_data = TagAnnotationData(tag_text)
if description:
tag_data.setTagDescription(description)
# Link the data to the image
link = ImageAnnotationLinkI()
link.setChild(tag_data.asAnnotation())
link.setParent(ImageI(image_id, False))
return data_manager.saveAndReturnObject(ctx, link)
def get_image_ids(gateway, dataset_id):
"""Return all image ids for given dataset"""
browse = gateway.getFacility(BrowseFacility)
experimenter = gateway.getLoggedInUser()
ctx = SecurityContext(experimenter.getGroupId())
images = []
ids = ArrayList(1)
ids.add(Long(dataset_id))
j = browse.getImagesForDatasets(ctx, ids).iterator()
while j.hasNext():
image = j.next()
images.append({
'Image Id': String.valueOf(image.getId()),
'Image Name': image.getName(),
'Dataset Id': dataset_id,
})
return images
def get_projects_datasets(gateway):
"""Retrieves the projects and datasets for the user"""
results = []
proj_dict = {}
ds_dict = {}
groupid = gateway.getLoggedInUser().getGroupId()
ctx = SecurityContext(groupid)
containerService = gateway.getPojosService(ctx)
# Read datasets in all projects
projects = containerService.loadContainerHierarchy(
"Project", None,
None) # allowed: 'Project", "Dataset", "Screen", "Plate"
for p in projects: # omero.model.ProjectI
p_id = p.getId().getValue()
p_name = p.getName().getValue()
proj_dict[p_id] = p_name
for d in p.linkedDatasetList():
ds_id = d.getId().getValue()
ds_name = d.getName().getValue()
results.append({
'Project Id': p_id,
'Project Name': p_name,
'Dataset Id': ds_id,
'Dataset Name': ds_name,
'Group Id': groupid,
})
ds_dict[ds_id] = ds_name
# read datasets not linked to any project
ds_in_proj = [p['Dataset Id'] for p in results]
ds = containerService.loadContainerHierarchy("Dataset", None, None)
for d in ds: # omero.model.ProjectI
ds_id = d.getId().getValue()
ds_name = d.getName().getValue()
if ds_id not in ds_in_proj:
ds_dict[ds_id] = ds_name
results.append({
'Project Id': '--',
'Project Name': '--',
'Dataset Id': ds_id,
'Dataset Name': ds_name,
'Group Id': groupid,
})
return results, proj_dict, ds_dict
def _add_table(gateway, table_parameters, table_data, table_name, target):
"""Appends a table to a target object"""
# Verify consistency of tables
if len(table_parameters) != len(table_data):
raise Exception('Table parameters and data do not have the same length')
columns = []
for i in range(len(table_parameters)):
columns.append(TableDataColumn(table_parameters[i][0],
i,
table_parameters[i][1]))
if len(table_parameters[i]) == 3:
columns[-1].setDescription(table_parameters[i][2])
table = TableData(columns, table_data)
facility = gateway.getFacility(TablesFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
facility.addTable(ctx, target, table_name, table)
def _get_available_tables(gateway, target):
facility = gateway.getFacility(TablesFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(user.getGroupId())
return facility.getAvailableTables(ctx, target)
def _data_manager_generator(gateway, group_id):
data_manager = gateway.getFacility(DataManagerFacility)
user = gateway.getLoggedInUser()
ctx = SecurityContext(group_id)
return data_manager, ctx
# use the appropriate target DataObject and attach the MapAnnotationData object to it
if target_type == "Project":
target_obj = ProjectData(ProjectI(target_id, False))
elif target_type == "Dataset":
target_obj = DatasetData(DatasetI(target_id, False))
elif target_type == "Image":
target_obj = browse.getImage(ctx, long(target_id))
table_facility = gateway.getFacility(TablesFacility)
table_facility.addTable(ctx, target_obj, "Table_from_Fiji", table_data)
# Main code
gateway = connect(group_id, username, password, server, port)
currentGroupId = gateway.getLoggedInUser().getGroupId()
ctx = SecurityContext(currentGroupId)
# 1. Create a Omero Table obkect, upload, and link it to target object
table = create_table(gateway)
link_table_to_object(gateway, table, target_id, target_type)
# 2. Create a ImageJ ResultsTable, convert it into Omero table object, upload and link it to target object
imp = IJ.openImage("http://imagej.nih.gov/ij/images/blobs.gif")
IJ.run(imp, "8-bit", "")
# white might be required depending on the version of Fiji
IJ.run(imp, "Auto Threshold", "method=MaxEntropy stack")
IJ.run(imp, "Analyze Particles...",
"size=10-Infinity pixel display clear add stack")
IJ.run(
"Set Measurements...", "area mean standard modal min centroid center \
perimeter bounding fit shape feret's integrated median skewness \
