def upload_image_from_file(file,
dataset_name,
project_name='',
attachments=(),
wait=-1):
attachments = list(attachments)
dataset_id = get_or_create_dataset_id(dataset_name, project_name)
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
r = file_import(cli._client, file, wait)
if r:
links = []
# TODO - doing this as iterable fileset for single file is weird
p = r.pixels[0]
image_id = p.image.id.val
logger.debug('Imported Image ID: %d' % image_id)
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(dataset_id, False)
link.child = omero.model.ImageI(image_id, False)
links.append(link)
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
if len(attachments) > 0:
# have to have loadedness -> True to link an annotation
image = conn.getObject("Image", image_id)
for attachment in attachments:
# TODO - add guess_mimetype / namespace here
upload_file_annotation(conn,
image,
attachment,
namespace='pyme.localizations')
return image_id
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 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 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():
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 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 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 main(argv):
parser = argparse.ArgumentParser()
# parser.addArgument('--session', type=int, help=(
# 'Connect with this session ID, default is to use or create a '
# 'session from the OMERO CLI'))
parser.add_argument(
'--dataset',
type=int,
help=(
'Add imported files to this Dataset ID (not valid when wait=-1)'))
parser.add_argument(
'--wait',
type=int,
default=-1,
help=('Wait for this number of seconds for each import to complete. '
'0: return immediately, -1: wait indefinitely (default)'))
parser.add_argument('path', nargs='+', help='Files or directories')
args = parser.parse_args(argv)
with cli_login() as cli:
conn = BlitzGateway(client_obj=cli._client)
if args.dataset and not conn.getObject('Dataset', args.dataset):
print('Dataset id not found: %s' % args.dataset)
sys.exit(1)
for fs_path in args.path:
print('Importing: %s' % fs_path)
rsp = full_import(cli._client, fs_path, args.wait)
if rsp:
links = []
for p in rsp.pixels:
print('Imported Image ID: %d' % p.image.id.val)
if args.dataset:
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(args.dataset, False)
link.child = omero.model.ImageI(p.image.id.val, False)
links.append(link)
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
def run(password, dataset_name, 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 Image where name='%s' \
AND details.owner.omeName=:username" % target
query_service = conn.getQueryService()
images = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(images) == 0:
print("No images with name %s found" % target)
continue
image_id = images[0].getId().getValue()
print('id', image_id)
dataset = omero.model.DatasetI()
dataset.setName(omero.rtypes.rstring(dataset_name))
dataset = conn.getUpdateService().saveAndReturnObject(dataset)
dataset_id = dataset.getId().getValue()
print(username, dataset_id)
link = omero.model.DatasetImageLinkI()
link.setParent(dataset)
link.setChild(omero.model.ImageI(image_id, False))
conn.getUpdateService().saveObject(link)
except Exception as exc:
print("Error while linking images: %s" % str(exc))
finally:
conn.close()
def get_or_create_dataset_id(dataset_name, project_name=''):
with cli_login(*LOGIN_ARGS) as cli:
conn = BlitzGateway(client_obj=cli._client)
# handle linking with project if given
if project_name != '':
# check if the dataset already exists within the project
project_id = get_or_create_project_id(conn, project_name)
# projects = conn.getContainerService().loadContainerHierarchy('Project',
# None, None)
project = conn.getObject("Project", project_id)
dataset_wrapper = project.findChildByName(dataset_name)
if dataset_wrapper != None:
return dataset_wrapper.getId()
# make a new dataset
dataset_id = create_dataset(conn, dataset_name)
# link it to the project
links = []
link = omero.model.ProjectDatasetLinkI()
link.parent = omero.model.ProjectI(project_id, False)
link.child = omero.model.DatasetI(dataset_id, False)
links.append(link)
conn.getUpdateService().saveArray(links, conn.SERVICE_OPTS)
return dataset_id
# no project specified, check if the dataset already exists
datasets = conn.getContainerService().loadContainerHierarchy(
'Dataset', None, None)
for d in datasets:
if d.getName().getValue() == dataset_name:
return d.getId().getValue()
# otherwise create a new dataset
return create_dataset(conn, dataset_name)
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 run(username, password, plate_id, host, port):
"""Run the script."""
# Create connection to training server
conn = BlitzGateway(username, password, host=host, port=port)
conn.connect()
# Create connection to IDR server
# NB: conn.connect() not working on IDR. Do it like this
idr_client = omero.client(host="idr.openmicroscopy.org", port=4064)
idr_client.createSession('public', 'public')
idr_conn = BlitzGateway(client_obj=idr_client)
# The plate we want to copy from IDR
idr_plate = idr_conn.getObject("Plate", plate_id)
plate_name = idr_plate.getName()
update_service = conn.getUpdateService()
plate = PlateI()
plate.name = rstring(plate_name)
plate = update_service.saveAndReturnObject(plate)
for idr_well in idr_plate.listChildren():
print("Well", idr_well.id, 'row', idr_well.row, 'col', idr_well.column)
# For each Well, get image and clone locally...
new_imgs = []
for idr_wellsample in idr_well.listChildren():
idr_image = idr_wellsample.getImage()
print("Image", idr_image.id)
image = copy_image(conn, idr_image)
new_imgs.append(image)
# link to Plate...
add_images_to_plate(update_service, plate, new_imgs,
idr_well.row, idr_well.column)
conn.close()
idr_conn.close()
def runScript():
"""
The main entry point of the script, as called by the client via the scripting service, passing the required parameters.
"""
orders = [rstring('T-Z-C'), rstring('T-C-Z'), rstring('Z-T-C'), rstring('Z-C-T'), rstring('C-Z-T'),
rstring('C-T-Z')]
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client('ExplodeImages.py',
'Explode multiplane/multitemporal images into multiple images, '
+ 'split based on channels, number of planes, and timestamps.',
scripts.String("Data_Type", optional=False, grouping="1",
description="The data you want to work with.", values=dataTypes,
default="Image"),
scripts.List("IDs", optional=False, grouping="1.1",
description="List of Dataset IDs or Image IDs").ofType(rlong(0)),
scripts.String("Storing_Dataset", optional=False, grouping="2",
description="Name of data set to store images", default='Explode'),
scripts.String("Base_Image_Path", grouping="2.1", description="Base name of image."),
scripts.String("Image_Order", grouping="2.2",
description="The order in which explosion information is displayed in"
+ " the image name. (T=time, Z=depth, C=color)",
values=orders, default="T-Z-C"),
version="1.0",
authors=["WebvalleyTeam 2013"],
institutions=["FBK"],
contact="*****@*****.**", )
try:
# process the list of args above.
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
# establish connection to omero
conn = BlitzGateway(client_obj=client)
#get objects
objects, logMessage = script_utils.getObjects(conn, scriptParams)
# gather all images
images = []
if (scriptParams["Data_Type"] == "Dataset"):
for dataSet in objects:
images.extend(list(dataSet.listChildren()))
if not images:
print "No images found in selected dataset."
else:
images = objects
datasetObj = omero.model.DatasetI()
datasetObj.setName(rstring(scriptParams["Storing_Dataset"]))
datasetObj = conn.getUpdateService().saveAndReturnObject(datasetObj)
savePlanes(images, conn, datasetObj, scriptParams)
finally:
client.closeSession()
""" FOR TRAINING PURPOSES ONLY! """ import omero from omero.rtypes import rdouble, rint, rstring 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() updateService = conn.getUpdateService() # Configuration # ================================================================= imageId = 27544 # Create ROI. # ================================================================= # We are using the core Python API and omero.model objects here, since ROIs are # not yet supported in the Python Blitz Gateway. # # In this example, we create an ROI with a rectangular shape and attach it to an # image. x = 50
def run():
"""
"""
dataTypes = [rstring("Plate")]
client = scripts.client(
"Manage_Plate_Acquisitions.py",
"Add or remove PlateAcquisition(s) in a given Plate",
scripts.String("Data_Type", optional=False, grouping="1",
description="The data type you want to work with.",
values=dataTypes,
default="Plate"),
scripts.List("IDs", optional=False, grouping="2",
description="List of Plate IDs").ofType(rlong(0)),
scripts.String("Mode", optional=False, grouping="3",
description="Select if you want to add or "
"remove PlateAcquisitions",
values=[rstring("Add"), rstring("Remove")],
default="Add"),
version="0.2",
authors=["Niko Klaric"],
institutions=["Glencoe Software Inc."],
contact="*****@*****.**",
)
try:
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
connection = BlitzGateway(client_obj=client)
updateService = connection.getUpdateService()
queryService = connection.getQueryService()
processedMessages = []
for plateId in scriptParams["IDs"]:
plateObj = connection.getObject("Plate", plateId)
if plateObj is None:
client.setOutput(
"Message",
rstring("ERROR: No Plate with ID %s" % plateId))
return
if scriptParams["Mode"] == "Add":
plateAcquisitionObj = PlateAcquisitionI()
plateAcquisitionObj.setPlate(PlateI(plateObj.getId(), False))
wellGrid = plateObj.getWellGrid()
for axis in wellGrid:
for wellObj in axis:
wellSampleList = wellObj.copyWellSamples()
plateAcquisitionObj.addAllWellSampleSet(wellSampleList)
plateAcquisitionObj = updateService.saveAndReturnObject(
plateAcquisitionObj)
plateAcquisitionId = plateAcquisitionObj.getId()._val
processedMessages.append(
"Linked new PlateAcquisition with ID %d"
" to Plate with ID %d." % (plateAcquisitionId, plateId))
else:
params = ParametersI()
params.addId(plateId)
queryString = """
FROM PlateAcquisition AS pa
LEFT JOIN FETCH pa.wellSample
LEFT OUTER JOIN FETCH pa.annotationLinks
WHERE pa.plate.id = :id
"""
plateAcquisitionList = queryService.findAllByQuery(
queryString, params, connection.SERVICE_OPTS)
if plateAcquisitionList:
updateList = []
for plate_acquisition in plateAcquisitionList:
for well_sample in plate_acquisition.copyWellSample():
well_sample.setPlateAcquisition(None)
updateList.append(well_sample)
updateService.saveArray(updateList)
plate_acquisition.clearWellSample()
plate_acquisition.clearAnnotationLinks()
plate_acquisition = updateService.saveAndReturnObject(
plate_acquisition)
updateService.deleteObject(plate_acquisition)
processedMessages.append(
"%d PlateAcquisition(s) removed from Plate with ID %d." %
(len(plateAcquisitionList), plateId))
client.setOutput("Message", rstring("No errors. %s" %
" ".join(processedMessages)))
finally:
client.closeSession()
# Configuration
# =================================================================
dataset_name = "MyDataset"
tag_name = "MyTag"
# Create Datasets
# =================================================================
object_array = list()
for i in xrange(3):
dataset = omero.model.DatasetI()
dataset.setName(rstring(dataset_name))
object_array.append(dataset)
conn.getUpdateService().saveArray(object_array)
# Create Tags
# =================================================================
object_array = list()
for i in xrange(3):
tag = omero.model.TagAnnotationI()
tag.setTextValue(rstring(tag_name))
tag.setDescription(rstring("%s %i" % (tag_name, i)))
object_array.append(tag)
conn.getUpdateService().saveArray(object_array)
# Find the datasets by name.
# =================================================================
else:
shapeTexts.append("")
if len(lengthsForImage) == 0:
print "No lines found on Image:", image.getName()
continue
imgAverage = sum(lengthsForImage) / len(lengthsForImage)
print "Average length of line for Image: %s is %s" % (image.getName(), imgAverage)
# Add the average as an annotation on each image.
lengthAnn = omero.model.DoubleAnnotationI()
lengthAnn.setDoubleValue(rdouble(imgAverage))
lengthAnn.setNs(rstring("imperial.training.demo.lineLengthAverage"))
link = omero.model.ImageAnnotationLinkI()
link.setParent(omero.model.ImageI(image.getId(), False))
link.setChild(lengthAnn)
conn.getUpdateService().saveAndReturnObject(link)
lengthsForImage = [] # reset for next image.
# Prepare data for adding to OMERO table.
data = [
omero.grid.LongColumn('imageId', '', imageIds),
omero.grid.RoiColumn('roidId', '', roiIds),
omero.grid.LongColumn('shapeId', '', shapeIds),
omero.grid.LongColumn('theZ', '', theZs),
omero.grid.LongColumn('theT', '', theTs),
omero.grid.DoubleColumn('lineLength', '', lineLengths),
omero.grid.StringColumn('shapeText', '', 64, shapeTexts),
]
table.addData(data)
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"""
print 'Created new Image:%s Name:"%s"' % (i.getId(), i.getName())
# Set the pixel size using units (new in 5.1.0)
# =================================================================
# Lengths are specified by value and a unit enumeration
# Here we set the pixel size X and Y to be 9.8 Angstroms
from omero.model.enums import UnitsLength
# Re-load the image to avoid update conflicts
i = conn.getObject("Image", i.getId())
u = omero.model.LengthI(9.8, UnitsLength.ANGSTROM)
p = i.getPrimaryPixels()._obj
p.setPhysicalSizeX(u)
p.setPhysicalSizeY(u)
conn.getUpdateService().saveObject(p)
# Create an Image from an existing image
# =================================================================
# We are going to create a new image by passing the method a 'generator' of 2D
# planes This will come from an existing image, by taking the average of 2
# channels.
zctList = []
image = conn.getObject('Image', imageId)
sizeZ, sizeC, sizeT = image.getSizeZ(), image.getSizeC(), image.getSizeT()
dataset = image.getParent()
pixels = image.getPrimaryPixels()
newSizeC = 1
def run():
"""
"""
dataTypes = [rstring("Plate")]
client = scripts.client(
"Manage_Plate_Acquisitions.py",
"Add or remove PlateAcquisition(s) in a given Plate",
scripts.String("Data_Type",
optional=False,
grouping="1",
description="The data type you want to work with.",
values=dataTypes,
default="Plate"),
scripts.List("IDs",
optional=False,
grouping="2",
description="List of Plate IDs").ofType(rlong(0)),
scripts.String("Mode",
optional=False,
grouping="3",
description="Select if you want to add or "
"remove PlateAcquisitions",
values=[rstring("Add"),
rstring("Remove")],
default="Add"),
version="0.2",
authors=["Niko Klaric"],
institutions=["Glencoe Software Inc."],
contact="*****@*****.**",
)
try:
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
connection = BlitzGateway(client_obj=client)
updateService = connection.getUpdateService()
queryService = connection.getQueryService()
processedMessages = []
for plateId in scriptParams["IDs"]:
plateObj = connection.getObject("Plate", plateId)
if plateObj is None:
client.setOutput(
"Message", rstring("ERROR: No Plate with ID %s" % plateId))
return
if scriptParams["Mode"] == "Add":
plateAcquisitionObj = PlateAcquisitionI()
plateAcquisitionObj.setPlate(PlateI(plateObj.getId(), False))
wellGrid = plateObj.getWellGrid()
for axis in wellGrid:
for wellObj in axis:
wellSampleList = wellObj.copyWellSamples()
plateAcquisitionObj.addAllWellSampleSet(wellSampleList)
plateAcquisitionObj = updateService.saveAndReturnObject(
plateAcquisitionObj)
plateAcquisitionId = plateAcquisitionObj.getId()._val
processedMessages.append(
"Linked new PlateAcquisition with ID %d"
" to Plate with ID %d." % (plateAcquisitionId, plateId))
else:
params = ParametersI()
params.addId(plateId)
queryString = """
FROM PlateAcquisition AS pa
LEFT JOIN FETCH pa.wellSample
LEFT OUTER JOIN FETCH pa.annotationLinks
WHERE pa.plate.id = :id
"""
plateAcquisitionList = queryService.findAllByQuery(
queryString, params, connection.SERVICE_OPTS)
if plateAcquisitionList:
updateList = []
for plate_acquisition in plateAcquisitionList:
for well_sample in plate_acquisition.copyWellSample():
well_sample.setPlateAcquisition(None)
updateList.append(well_sample)
updateService.saveArray(updateList)
plate_acquisition.clearWellSample()
plate_acquisition.clearAnnotationLinks()
plate_acquisition = updateService.saveAndReturnObject(
plate_acquisition)
updateService.deleteObject(plate_acquisition)
processedMessages.append(
"%d PlateAcquisition(s) removed from Plate with ID %d." %
(len(plateAcquisitionList), plateId))
client.setOutput(
"Message", rstring("No errors. %s" % " ".join(processedMessages)))
finally:
client.closeSession()
def CreatePlate(plateName, user, passwd):
import sys
sys.path.append('/home/cag3fr/omero_server/lib/python')
import Ice
import omero
from omero.gateway import BlitzGateway
import omero.scripts as scripts
import omero.util.script_utils as script_utils
from omero.rtypes import rint, rlong, rstring, robject, unwrap
import pandas as pd
import csv, operator
import fnmatch
import os
import math
# Dictionary of Well Number and Row/Column Number
Well96_to_RowCol = {
'A01': [0, 0],
'A02': [0, 1],
'A03': [0, 2],
'A04': [0, 3],
'A05': [0, 4],
'A06': [0, 5],
'A07': [0, 6],
'A08': [0, 7],
'A09': [0, 8],
'A10': [0, 9],
'A11': [0, 10],
'A12': [0, 11],
'B01': [1, 0],
'B02': [1, 1],
'B03': [1, 2],
'B04': [1, 3],
'B05': [1, 4],
'B06': [1, 5],
'B07': [1, 6],
'B08': [1, 7],
'B09': [1, 8],
'B10': [1, 9],
'B11': [1, 10],
'B12': [1, 11],
'C01': [2, 0],
'C02': [2, 1],
'C03': [2, 2],
'C04': [2, 3],
'C05': [2, 4],
'C06': [2, 5],
'C07': [2, 6],
'C08': [2, 7],
'C09': [2, 8],
'C10': [2, 9],
'C11': [2, 10],
'C12': [2, 11],
'D01': [3, 0],
'D02': [3, 1],
'D03': [3, 2],
'D04': [3, 3],
'D05': [3, 4],
'D06': [3, 5],
'D07': [3, 6],
'D08': [3, 7],
'D09': [3, 8],
'D10': [3, 9],
'D11': [3, 10],
'D12': [3, 11],
'E01': [4, 0],
'E02': [4, 1],
'E03': [4, 2],
'E04': [4, 3],
'E05': [4, 4],
'E06': [4, 5],
'E07': [4, 6],
'E08': [4, 7],
'E09': [4, 8],
'E10': [4, 9],
'E11': [4, 10],
'E12': [4, 11],
'F01': [5, 0],
'F02': [5, 1],
'F03': [5, 2],
'F04': [5, 3],
'F05': [5, 4],
'F06': [5, 5],
'F07': [5, 6],
'F08': [5, 7],
'F09': [5, 8],
'F10': [5, 9],
'F11': [5, 10],
'F12': [5, 11],
'G01': [6, 0],
'G02': [6, 1],
'G03': [6, 2],
'G04': [6, 3],
'G05': [6, 4],
'G06': [6, 5],
'G07': [6, 6],
'G08': [6, 7],
'G09': [6, 8],
'G10': [6, 9],
'G11': [6, 10],
'G12': [6, 11],
'H01': [7, 0],
'H02': [7, 1],
'H03': [7, 2],
'H04': [7, 3],
'H05': [7, 4],
'H06': [7, 5],
'H07': [7, 6],
'H08': [7, 7],
'H09': [7, 8],
'H10': [7, 9],
'H11': [7, 10],
'H12': [7, 11]
}
#Create plate in omero
conn = BlitzGateway(user, passwd, host="localhost", port=4064)
conn.connect()
updateService = conn.getUpdateService()
plate = omero.model.PlateI()
plate.name = omero.rtypes.RStringI(plateName)
plate.columnNamingConvention = rstring("number")
plate.rowNamingConvention = rstring("letter")
plate = updateService.saveAndReturnObject(plate)
plateId = plate.id.val
plate = conn.getObject("Plate", plateId)
conn.close()
filename = plateName + ".txt"
f = open(filename, "w")
f.write(str(plateId))
f.close()
def CreateWell(imageId, plateId, wellNum, user, passwd):
import sys
sys.path.append('/home/cag3fr/omero_server/lib/python')
import Ice
import omero
from omero.gateway import BlitzGateway
import omero.scripts as scripts
import omero.util.script_utils as script_utils
from omero.rtypes import rint, rlong, rstring, robject, unwrap
import pandas as pd
import csv, operator
import fnmatch
import os
import math
# Dictionary of Well Number and Row/Column Number
Well96_to_RowCol = {
'A01': [0, 0],
'A02': [0, 1],
'A03': [0, 2],
'A04': [0, 3],
'A05': [0, 4],
'A06': [0, 5],
'A07': [0, 6],
'A08': [0, 7],
'A09': [0, 8],
'A10': [0, 9],
'A11': [0, 10],
'A12': [0, 11],
'B01': [1, 0],
'B02': [1, 1],
'B03': [1, 2],
'B04': [1, 3],
'B05': [1, 4],
'B06': [1, 5],
'B07': [1, 6],
'B08': [1, 7],
'B09': [1, 8],
'B10': [1, 9],
'B11': [1, 10],
'B12': [1, 11],
'C01': [2, 0],
'C02': [2, 1],
'C03': [2, 2],
'C04': [2, 3],
'C05': [2, 4],
'C06': [2, 5],
'C07': [2, 6],
'C08': [2, 7],
'C09': [2, 8],
'C10': [2, 9],
'C11': [2, 10],
'C12': [2, 11],
'D01': [3, 0],
'D02': [3, 1],
'D03': [3, 2],
'D04': [3, 3],
'D05': [3, 4],
'D06': [3, 5],
'D07': [3, 6],
'D08': [3, 7],
'D09': [3, 8],
'D10': [3, 9],
'D11': [3, 10],
'D12': [3, 11],
'E01': [4, 0],
'E02': [4, 1],
'E03': [4, 2],
'E04': [4, 3],
'E05': [4, 4],
'E06': [4, 5],
'E07': [4, 6],
'E08': [4, 7],
'E09': [4, 8],
'E10': [4, 9],
'E11': [4, 10],
'E12': [4, 11],
'F01': [5, 0],
'F02': [5, 1],
'F03': [5, 2],
'F04': [5, 3],
'F05': [5, 4],
'F06': [5, 5],
'F07': [5, 6],
'F08': [5, 7],
'F09': [5, 8],
'F10': [5, 9],
'F11': [5, 10],
'F12': [5, 11],
'G01': [6, 0],
'G02': [6, 1],
'G03': [6, 2],
'G04': [6, 3],
'G05': [6, 4],
'G06': [6, 5],
'G07': [6, 6],
'G08': [6, 7],
'G09': [6, 8],
'G10': [6, 9],
'G11': [6, 10],
'G12': [6, 11],
'H01': [7, 0],
'H02': [7, 1],
'H03': [7, 2],
'H04': [7, 3],
'H05': [7, 4],
'H06': [7, 5],
'H07': [7, 6],
'H08': [7, 7],
'H09': [7, 8],
'H10': [7, 9],
'H11': [7, 10],
'H12': [7, 11]
}
conn = BlitzGateway(user, passwd, host="localhost", port=4064)
conn.connect()
image = conn.getObject("Image", int(imageId[6:]))
updateService = conn.getUpdateService()
well = omero.model.WellI()
well.plate = omero.model.PlateI(int(plateId), False)
wellRowCol = Well96_to_RowCol.get(wellNum)
well.column = rint(wellRowCol[1])
well.row = rint(wellRowCol[0])
ws = omero.model.WellSampleI()
ws.image = omero.model.ImageI(image.id, False)
ws.well = well
well.addWellSample(ws)
updateService.saveAndReturnObject(ws)
conn.close()
data1 = omero.grid.LongColumn('Uid', 'test Long', ids)
data2 = omero.grid.StringColumn('MyStringColumn', '', 64, strings)
data = [data1, data2]
table.addData(data)
orig_file = table.getOriginalFile()
table.close() # when we are done, close.
# Load the table as an original file
# ==================================
orig_file_id = orig_file.id.val
# ...so you can attach this data to an object e.g. Dataset
file_ann = omero.model.FileAnnotationI()
# use unloaded OriginalFileI
file_ann.setFile(omero.model.OriginalFileI(orig_file_id, False))
file_ann = conn.getUpdateService().saveAndReturnObject(file_ann)
link = omero.model.DatasetAnnotationLinkI()
link.setParent(omero.model.DatasetI(datasetId, False))
link.setChild(omero.model.FileAnnotationI(file_ann.getId().getValue(), False))
conn.getUpdateService().saveAndReturnObject(link)
# Table API
# =========
# .. seealso:: :javadoc:` OMERO Tables <slice2html/omero/grid/Table.html>`
open_table = resources.openTable(orig_file)
print("Table Columns:")
for col in open_table.getHeaders():
print(" ", col.name)
rowCount = open_table.getNumberOfRows()
class TestSavedMasks(ITest):
def setup_method(self):
self.conn = BlitzGateway(client_obj=self.client)
def save_and_return_masks(self, im, masks):
roi = omero.model.RoiI()
for mask in masks:
roi.addShape(mask)
us = self.conn.getUpdateService()
roi.setImage(im._obj)
roi = us.saveAndReturnObject(roi)
assert roi
rois = self.conn.getRoiService().findByImage(im.id, None)
assert len(rois.rois) == 1
shapes = rois.rois[0].copyShapes()
assert len(shapes) == len(masks)
assert all((type(mask) == omero.model.MaskI) for mask in shapes)
return shapes
@pytest.mark.parametrize('args', [{}, {
'rgba': (255, 128, 64, 128),
'z': 1,
'c': 2,
't': 3,
'text': 'test'
}])
def test_mask_from_binary_image(self, binary_image, args):
im = self.conn.createImageFromNumpySeq(iter([binary_image]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
mask = mask_from_binary_image(px, **args)
mask = self.save_and_return_masks(im, [mask])[0]
# The rest of this is more or less the same as the unit test
assert unwrap(mask.getWidth()) == 2
assert unwrap(mask.getHeight()) == 2
assert unwrap(mask.getX()) == 1
assert unwrap(mask.getY()) == 1
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8),
np.array([224], dtype=np.uint8))
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
def test_mask_from_binary_full_image(self):
binim = np.ones((4, 4), dtype=np.uint8)
im = self.conn.createImageFromNumpySeq(iter([binim]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
mask = mask_from_binary_image(px)
mask = self.save_and_return_masks(im, [mask])[0]
# The rest of this is more or less the same as the unit test
assert unwrap(mask.getWidth()) == 4
assert unwrap(mask.getHeight()) == 4
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8),
np.array([255, 255], dtype=np.uint8))
@pytest.mark.parametrize('args', [{}, {
'rgba': (255, 128, 64, 128),
'z': 1,
'c': 2,
't': 3,
'text': 'test'
}])
def test_masks_from_label_image(self, label_image, args):
im = self.conn.createImageFromNumpySeq(iter([label_image]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
masks = masks_from_label_image(px, **args)
masks = self.save_and_return_masks(im, masks)
# The rest of this is more or less the same as the unit test
expected = (
# w, h, x, y, bytes
(2, 2, 1, 1, np.array([224], dtype=np.uint8)),
(2, 3, 2, 0, np.array([72], dtype=np.uint8)),
)
assert len(masks) == 2
for i, mask in enumerate(masks):
assert unwrap(mask.getWidth()) == expected[i][0]
assert unwrap(mask.getHeight()) == expected[i][1]
assert unwrap(mask.getX()) == expected[i][2]
assert unwrap(mask.getY()) == expected[i][3]
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8),
expected[i][4])
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
@pytest.mark.parametrize('args', [{}, {
'rgba': (255, 128, 64, 128),
'z': 1,
'c': 2,
't': 3,
'text': 'test'
}])
def test_empty_mask_from_binary_image(self, args):
empty_binary_image = np.array([[0]], dtype=np.uint8)
raise_on_no_mask = False
im = self.conn.createImageFromNumpySeq(iter([empty_binary_image]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
mask = mask_from_binary_image(px,
raise_on_no_mask=raise_on_no_mask,
**args)
mask = self.save_and_return_masks(im, [mask])[0]
# The rest of this is more or less the same as the unit test
assert unwrap(mask.getWidth()) == 0
assert unwrap(mask.getHeight()) == 0
assert unwrap(mask.getX()) == 0
assert unwrap(mask.getY()) == 0
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8), [])
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
datasetByImageName = {}
df = pandas.read_csv(annoFile)
for index, row in df.iterrows():
if row["Image Name"] in datasetByImageName:
raise Exception(" !!! line %i : %s has already been added" %
(index, row["Image Name"]))
datasetByImageName[row["Image Name"]] = row["Dataset Name"]
datasetByName = {}
for imgName, dsName in datasetByImageName.iteritems():
if dsName not in existingDatasetsByName:
if dsName not in datasetByName:
dataset = omero.model.DatasetI()
dataset.setName(rstring(dsName))
dataset = conn.getUpdateService().saveAndReturnObject(dataset)
datasetByName[dsName] = dataset
datasetByImageName[imgName] = dataset
else:
datasetByImageName[imgName] = datasetByName[dsName]
else:
datasetByImageName[imgName] = existingDatasetsByName[dsName]
links = []
for ds in datasetByName.values():
link = omero.model.ProjectDatasetLinkI()
link.setParent(project._obj)
link.setChild(ds)
links.append(link)
if len(links) > 0:
conn.getUpdateService().saveAndReturnArray(links)
import omero
from omero.rtypes import rstring
from omero.gateway import BlitzGateway
from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
# Create a connection
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Create a new Dataset
# =================================================================
dataset = omero.model.DatasetI()
dataset.setName(rstring("New Dataset"))
dataset = conn.getUpdateService().saveAndReturnObject(dataset)
print("New dataset, Id:", dataset.getId().getValue())
dataset2 = omero.model.DatasetI()
dataset2.setName(rstring("New Dataset2"))
dataset2 = conn.getUpdateService().saveAndReturnObject(dataset2)
print("New dataset 2, Id:", dataset2.getId().getValue())
# How to annotate multiple Datasets
# =================================================================
# 1. you define objects you want to tag
dataset_list = [dataset, dataset2]
# 2. create a tag
tag = omero.model.TagAnnotationI()
tag.setTextValue(rstring("new tag"))
from omero.model.enums import UnitsLength
from omero.rtypes import rdouble, rint, rstring
from omero.gateway import BlitzGateway
from omero.gateway import ColorHolder
from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
from Parse_OMERO_Properties import imageId
imageId = int(imageId)
"""
start-code
"""
# Create a connection
# ===================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
updateService = conn.getUpdateService()
# Create ROI
# ==========
# We are using the core Python API and omero.model objects here, since ROIs
# are not yet supported in the Python Blitz Gateway.
#
# First we load our image and pick some parameters for shapes
x = 50
y = 200
width = 100
height = 50
image = conn.getObject("Image", imageId)
z = old_div(image.getSizeZ(), 2)
t = 0
userConn.connect()
for g in userConn.getGroupsMemberOf():
if g.getName() == "user":
continue
print " ", g.getName()
userConn.SERVICE_OPTS.setOmeroGroup(g.getId())
params = omero.sys.Parameters()
params.theFilter = omero.sys.Filter()
params.theFilter.ownerId = rlong(exp.getId())
tags = list( userConn.getObjects("TagAnnotation", params=params) )
for i in range( TAG_COUNT-len(tags) ):
t = TagAnnotationI()
newTagVal = "%s_%s_TEST" % (username, g.getName())
print "creating TAG:", newTagVal
t.textValue = wrap(str(newTagVal))
userConn.getUpdateService().saveObject(t, userConn.SERVICE_OPTS)
# for t in tags:
# print " TAG", t.getId(), t.getTextValue()
userConn.c.closeSession()
print "\n---- DOING ANNOTATING... ----\n"
# We want to Tag loads of stuff with OUR tags and Others' tags
for exp in allUsers:
username = exp.getOmeName()
if username not in USER_NAMES:
continue
print "\n\n------------ USER:"******"------------"
userConn = BlitzGateway(username, "ome")
userConn.connect()
"""
start-code
"""
# Create a connection
# ===================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Create a new Dataset
# ====================
datasetObj = omero.model.DatasetI()
datasetObj.setName(rstring("New Dataset"))
datasetObj = conn.getUpdateService().saveAndReturnObject(datasetObj)
datasetId = datasetObj.getId().getValue()
print "New dataset, Id:", datasetId
# Link to Project
# ===============
project = conn.getObject("Project", projectId)
if project is None:
import sys
sys.stderr.write("Error: Object does not exist.\n")
sys.exit(1)
link = omero.model.ProjectDatasetLinkI()
link.setParent(omero.model.ProjectI(project.getId(), False))
link.setChild(datasetObj)
conn.getUpdateService().saveObject(link)
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Configuration
# =================================================================
dataset_name = "MyDataset"
tag_name = "MyTag"
# Create Datasets
# =================================================================
object_array = list()
for i in xrange(3):
dataset = omero.model.DatasetI()
dataset.setName(rstring(dataset_name))
object_array.append(dataset)
conn.getUpdateService().saveArray(object_array)
# Create Tags
# =================================================================
object_array = list()
for i in xrange(3):
tag = omero.model.TagAnnotationI()
tag.setTextValue(rstring(tag_name))
tag.setDescription(rstring("%s %i" % (tag_name, i)))
object_array.append(tag)
conn.getUpdateService().saveArray(object_array)
# Find the datasets by name.
# =================================================================
datasets = conn.getObjects("Dataset", attributes={'name': dataset_name})
print "\nList Datasets:"
# Save channel names and colors
# =================================================================
print("Applying channel Names:", c_names, " Colors:", colors)
for i, c in enumerate(new_img.getChannels()):
lc = c.getLogicalChannel()
lc.setName(c_names[i])
lc.save()
r, g, b = colors[i]
# need to reload channels to avoid optimistic lock on update
c_obj = conn.getQueryService().get("Channel", c.getId())
c_obj.red = rint(r)
c_obj.green = rint(g)
c_obj.blue = rint(b)
c_obj.alpha = rint(255)
conn.getUpdateService().saveObject(c_obj)
new_img.resetRDefs() # reset based on colors above
# Apply pixel sizes from original image
# =================================================================
new_pix = conn.getQueryService().get("Pixels", new_img.getPixelsId())
new_pix.setPhysicalSizeX(pixels.getPhysicalSizeX())
new_pix.setPhysicalSizeY(pixels.getPhysicalSizeY())
new_pix.setPhysicalSizeZ(pixels.getPhysicalSizeZ())
conn.getUpdateService().saveObject(new_pix)
# Close connection:
# =================================================================
# When you are done, close the session to free up server resources.
conn.close()
import omero.callbacks
from omero.rtypes import rstring
from omero.gateway import BlitzGateway
from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
# Create a connection
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Create a new Project
# =================================================================
project = omero.model.ProjectI()
project.setName(rstring("New Project"))
project = conn.getUpdateService().saveAndReturnObject(project)
projectId = project.id.val
# Load the Project
# =================================================================
project = conn.getObject("Project", projectId)
if project is None:
import sys
sys.stderr.write("Error: Object does not exist.\n")
sys.exit(1)
print "\nProject:", project.getName()
# Delete Project
# =================================================================
import omero
import omero.callbacks
from omero.rtypes import rstring
from omero.gateway import BlitzGateway
from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
# Create a connection
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Create a new Project
# =================================================================
project = omero.model.ProjectI()
project.setName(rstring("New Project"))
project = conn.getUpdateService().saveAndReturnObject(project)
projectId = project.id.val
# Load the Project
# =================================================================
project = conn.getObject("Project", projectId)
if project is None:
import sys
sys.stderr.write("Error: Object does not exist.\n")
sys.exit(1)
print "\nProject:", project.getName()
# Delete Project
# =================================================================
# You can delete a number of objects of the same type at the same
def run(username, password, plate_id, host, port):
conn = BlitzGateway(username, password, host=host, port=port)
try:
conn.connect()
query_service = conn.getQueryService()
# Create a name for the Original File
tablename = "Channels_Min_Max_Intensity"
# Go through all wells in Plate, adding row for each
plate = conn.getObject("Plate", plate_id)
wellIds = []
rowData = []
chCount = 0
for well in plate._listChildren():
well = omero.gateway.WellWrapper(conn, well)
image = well.getImage()
if image is None:
continue
wellIds.append(well.id)
chCount = image.getSizeC()
row = []
print("well, image", well.id, image.id)
params = omero.sys.ParametersI()
params.addId(image.getPixelsId())
query = """select pixels from Pixels as pixels
left outer join fetch pixels.channels as channels
join fetch channels.statsInfo where pixels.id=:id"""
result = query_service.findAllByQuery(query, params)
row = []
for pix in result:
for ch in pix.iterateChannels():
si = ch.statsInfo
row.extend([si.globalMin.val, si.globalMax.val])
rowData.append(row)
print('wellIds', wellIds)
print('rowData', rowData)
# Now we know how many channels, we can make the table
col1 = omero.grid.WellColumn('Well', '', [])
columns = [col1]
colNames = []
for chIdx in range(chCount):
for name in ['Ch%sMin' % chIdx, 'Ch%sMax' % chIdx]:
colNames.append(name)
columns.append(omero.grid.LongColumn(name, '', []))
table = conn.c.sf.sharedResources().newTable(1, tablename)
table.initialize(columns)
# Add Data from above
data1 = omero.grid.WellColumn('Well', '', wellIds)
data = [data1]
for colIdx in range(len(rowData[0])):
colData = [r[colIdx] for r in rowData]
print("colData", len(colData))
name = colNames[colIdx]
data.append(omero.grid.LongColumn(name, '', colData))
print("Adding data: ", len(data))
table.addData(data)
table.close()
print("table closed...")
orig_file = table.getOriginalFile()
fileAnn = omero.model.FileAnnotationI()
fileAnn.ns = rstring(NAMESPACE)
fileAnn.setFile(omero.model.OriginalFileI(orig_file.id.val, False))
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = omero.model.PlateAnnotationLinkI()
link.setParent(omero.model.PlateI(plate_id, False))
link.setChild(omero.model.FileAnnotationI(fileAnn.id.val, False))
print("save link...")
conn.getUpdateService().saveAndReturnObject(link)
except Exception as exc:
print("Error while changing names: %s" % str(exc))
finally:
conn.close()
from Parse_OMERO_Properties import USERNAME, PASSWORD, HOST, PORT
from Parse_OMERO_Properties import projectId
"""
start-code
"""
# Create a connection
# ===================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Create a new Dataset
# ====================
datasetObj = omero.model.DatasetI()
datasetObj.setName(rstring("New Dataset"))
datasetObj = conn.getUpdateService().saveAndReturnObject(datasetObj)
datasetId = datasetObj.getId().getValue()
print "New dataset, Id:", datasetId
# Link to Project
# ===============
project = conn.getObject("Project", projectId)
if project is None:
import sys
sys.stderr.write("Error: Object does not exist.\n")
sys.exit(1)
link = omero.model.ProjectDatasetLinkI()
link.setParent(omero.model.ProjectI(project.getId(), False))
link.setChild(datasetObj)
conn.getUpdateService().saveObject(link)
parser.add_argument("--to-pass", default="omero")
parser.add_argument("source_image", type=int, help="input image")
parser.add_argument("target_image", type=int, help="output image")
ns = parser.parse_args()
image_id_src = ns.source_image
image_id_dst = ns.target_image
idr = BlitzGateway(ns.from_user, ns.from_pass, host=ns.from_host, secure=True)
local = BlitzGateway(ns.to_user, ns.to_pass, host=ns.to_host, secure=True)
idr.connect()
local.connect()
query_service = idr.getQueryService()
update_service = local.getUpdateService()
query = "FROM Mask WHERE roi.image.id = :id"
params = ParametersI()
params.addId(image_id_src)
count = 0
for mask_src in query_service.findAllByQuery(query, params):
mask_dst = MaskI()
mask_dst.x = mask_src.x
mask_dst.y = mask_src.y
mask_dst.width = mask_src.width
mask_dst.height = mask_src.height
mask_dst.theZ = mask_src.theZ
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# Configuration
# =================================================================
datasetId = 101
projectId = 51
# Create a new Dataset
# =================================================================
dataset = omero.model.DatasetI()
dataset.setName(rstring("New Dataset"))
dataset = conn.getUpdateService().saveAndReturnObject(dataset)
print "New dataset, Id:", dataset.getId().getValue()
dataset2 = omero.model.DatasetI()
dataset2.setName(rstring("New Dataset2"))
dataset2 = conn.getUpdateService().saveAndReturnObject(dataset2)
print "New dataset 2, Id:", dataset2.getId().getValue()
# How to annotate multiple Datasets
# =================================================================
# 1. you define objects you want to tag
dataset_list = [dataset, dataset2]
# 2. create a tag
tag = omero.model.TagAnnotationI()
else:
shapeTexts.append("")
if len(lengthsForImage) == 0:
print "No lines found on Image:", image.getName()
continue
imgAverage = sum(lengthsForImage) / len(lengthsForImage)
print "Average length of line for Image: %s is %s" % (image.getName(), imgAverage)
# Add the average as an annotation on each image.
lengthAnn = omero.model.DoubleAnnotationI()
lengthAnn.setDoubleValue(rdouble(imgAverage))
lengthAnn.setNs(rstring("imperial.training.demo.lineLengthAverage"))
link = omero.model.ImageAnnotationLinkI()
link.setParent(omero.model.ImageI(image.getId(), False))
link.setChild(lengthAnn)
conn.getUpdateService().saveAndReturnObject(link)
lengthsForImage = [] # reset for next image.
# Prepare data for adding to OMERO table.
data = [
omero.grid.LongColumn("imageId", "", imageIds),
omero.grid.RoiColumn("roidId", "", roiIds),
omero.grid.LongColumn("shapeId", "", shapeIds),
omero.grid.LongColumn("theZ", "", theZs),
omero.grid.LongColumn("theT", "", theTs),
omero.grid.DoubleColumn("lineLength", "", lineLengths),
omero.grid.StringColumn("shapeText", "", 64, shapeTexts),
]
table.addData(data)
"""Adds Image to Dataset (if not alreay in the Dataset).""",
# first parameter
scripts.Long("ImageId", optional=False),
# second parameter
scripts.Long("DatasetId", optional=False),
)
# we can now create our Blitz Gateway by wrapping the client object
conn = BlitzGateway(client_obj=client)
# get the parameters
imageId = unwrap(client.getInput("ImageId"))
datasetId = unwrap(client.getInput("DatasetId"))
try:
link = omero.model.DatasetImageLinkI()
link.setParent(omero.model.DatasetI(datasetId, False))
link.setChild(omero.model.ImageI(imageId, False))
conn.getUpdateService().saveObject(link)
message = "Added Image to Dataset"
except ValidationException:
message = "Could not add Image to Dataset - Already added"
# Return some value(s).
# Here, we return anything useful the script has produced.
# NB: The Insight and web clients will display the "Message" output.
client.setOutput("Message", rstring(message))
client.closeSession()
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()
datasets = query_service.findAllByQuery(query, params,
conn.SERVICE_OPTS)
if len(datasets) == 0:
print("No datasets with name %s found" % target)
continue
dataset_id = datasets[0].getId().getValue()
print('dataset', dataset_id)
params2 = omero.sys.ParametersI()
params2.addId(dataset_id)
query = "select l.child.id from DatasetImageLink l \
where l.parent.id = :id"
images = query_service.projection(query, params2,
conn.SERVICE_OPTS)
for k in range(0, len(images)):
image_id = images[k][0].getValue()
delta_t = 300
image = conn.getObject("Image", image_id)
params = omero.sys.ParametersI()
params.addLong('pid', image.getPixelsId())
query = "from PlaneInfo as Info where \
Info.theZ=0 and Info.theC=0 and pixels.id=:pid"
info_list = query_service.findAllByQuery(
query, params, conn.SERVICE_OPTS)
print('info_list', len(info_list))
if len(info_list) == 0:
print("Creating info...", image.getSizeT())
info_list = []
for t_index in range(image.getSizeT()):
print(' t', t_index)
info = PlaneInfoI()
info.theT = rint(t_index)
info.theZ = rint(0)
info.theC = rint(0)
info.pixels = PixelsI(image.getPixelsId(), False)
dt = t_index * delta_t
info.deltaT = TimeI(dt, UnitsTime.SECOND)
info_list.append(info)
else:
for info in info_list:
unwrap_t = unwrap(info.theT)
unwrap_z = unwrap(info.theZ)
print('theT %s, theZ %s' % (unwrap_t, unwrap_z))
t_index = info.theT.getValue()
dt = t_index * delta_t
info.deltaT = TimeI(dt, UnitsTime.SECOND)
print("Saving info_list", len(info_list))
conn.getUpdateService().saveArray(info_list)
except Exception as exc:
print("Error when setting the timestamps: %s" % str(exc))
finally:
conn.close()
# Save channel names and colors
# =================================================================
print "Applying channel Names:", cNames, " Colors:", colors
for i, c in enumerate(newImg.getChannels()):
lc = c.getLogicalChannel()
lc.setName(cNames[i])
lc.save()
r, g, b = colors[i]
# need to reload channels to avoid optimistic lock on update
cObj = conn.getQueryService().get("Channel", c.id)
cObj.red = rint(r)
cObj.green = rint(g)
cObj.blue = rint(b)
cObj.alpha = rint(255)
conn.getUpdateService().saveObject(cObj)
newImg.resetRDefs() # reset based on colors above
# Apply pixel sizes from original image
# =================================================================
newPix = conn.getQueryService().get("Pixels", newImg.getPixelsId())
physicalSizeX = pixels.getPhysicalSizeX()
if physicalSizeX is not None:
newPix.setPhysicalSizeX(rdouble(physicalSizeX))
physicalSizeY = pixels.getPhysicalSizeY()
if physicalSizeY is not None:
newPix.setPhysicalSizeY(rdouble(physicalSizeY))
