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
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 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 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()
class OMEROConnectionManager:
''' Basic management of an OMERO Connection. Methods which make use of
a connection will attempt to connect if connect was not already
successfuly executed '''
def __init__(self, config_file=None):
# Set the connection as not established
self.conn = None
self.SUUID = None
self.HOST = None
self.PORT = None
self.USERNAME = None
self.PASSWORD = None
# If config_file not specified, first see if there's an active OMERO
# CLI session.
if config_file is None:
store = SessionsStore()
session_props = store.get_current()
self.HOST, self.USERNAME, self.SUUID, self.PORT = session_props
# config_file specified, or no active session. Continue with reading
# connection params from the config file.
if config_file is not None or self.SUUID is None:
# Normalize file path.
if config_file is None:
config_file = '~/.omero/config'
config_file = os.path.expanduser(config_file)
# Check config file exists.
if not (os.path.exists(config_file)
and os.path.isfile(config_file)):
sys.stderr.write('No active OMERO CLI session and '
'configuration file {} does not '
'exist\n'.format(config_file))
sys.exit(1)
# Check permisisons on config file.
if os.stat(config_file).st_mode & 0077:
sys.stderr.write('Configuration file contains private '
'credentials and must not be accessible by '
'other users. Please run:\n\n'
' chmod 600 {}\n\n'.format(config_file))
sys.exit(1)
# Read the credentials file.
config = ConfigParser.RawConfigParser()
config.read(config_file)
self.HOST = config.get('OMEROCredentials', 'host')
self.PORT = config.getint('OMEROCredentials', 'port')
self.USERNAME = config.get('OMEROCredentials', 'username')
self.PASSWORD = config.get('OMEROCredentials', 'password')
def connect(self):
''' Create an OMERO Connection '''
# If connection already established just return it
if self.conn is not None:
return self.conn
# Initialize the connection. At least HOST and PORT will be defined,
# but USERNAME and PASSWORD may be None if we are connecting to an
# existing session via its uuid.
self.conn = BlitzGateway(username=self.USERNAME,
passwd=self.PASSWORD,
host=self.HOST,
port=self.PORT)
# Connect. If USERNAME and PASSWORD are None then SUUID must be
# defined.
connected = self.conn.connect(sUuid=self.SUUID)
# Check that the connection was established
if not connected:
sys.stderr.write('Error: Connection not available, '
'please check your user name and password.\n')
sys.exit(1)
return self.conn
def disconnect(self):
''' Terminate the OMERO Connection '''
self.conn.seppuku(softclose=True)
self.conn = None
def hql_query(self, query, params=None):
''' Execute the given HQL query and return the results. Optionally
accepts a parameters object.
For conveniance, will unwrap the OMERO types '''
# Connect if not already connected
if self.conn is None:
self.connect()
if params is None:
params = ParametersI()
# Set OMERO Group to -1 to query across all available data
self.conn.SERVICE_OPTS.setOmeroGroup(-1)
# Get the Query Service
qs = self.conn.getQueryService()
# Execute the query
rows = qs.projection(query, params, self.conn.SERVICE_OPTS)
# Unwrap the query results
unwrapped_rows = []
for row in rows:
unwrapped_row=[]
for column in row:
if column is None:
unwrapped_row.append(None)
else:
unwrapped_row.append(column.val)
unwrapped_rows.append(unwrapped_row)
return unwrapped_rows
def __del__(self):
self.disconnect()
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"""
class OMEROConnectionManager(object):
''' Basic management of an OMERO Connection. Methods which make use of
a connection will attempt to connect if connection was not already
successfuly executed '''
def __init__(self, config_file=Path.home() / '.omero' / 'config'):
self.config_file = config_file
# Set the connection as not established
self.conn = None
def connect(self):
''' Create an OMERO Connection '''
# If connection already established just return it
if self.conn is not None:
return self.conn
params = get_params_from_session()
if params is None:
params = get_params_from_config_file(self.config_file)
# Initialize the connection. At least HOST and PORT will be defined,
# but USERNAME and PASSWORD may be None if we are connecting to an
# existing session via its uuid.
self.conn = BlitzGateway(username=params.get('username'),
passwd=params.get('password'),
host=params['host'],
port=params['port'])
# Connect. If USERNAME and PASSWORD are None then SUUID must be
# defined.
connected = self.conn.connect(sUuid=params.get('suuid'))
# Check that the connection was established
if not connected:
sys.stderr.write('Error: Connection not available, '
'please check your user name and password.\n')
sys.exit(1)
return self.conn
def disconnect(self):
''' Terminate the OMERO Connection '''
if self.conn:
self.conn.seppuku(softclose=True)
self.conn = None
def hql_query(self, query, params=None):
''' Execute the given HQL query and return the results. Optionally
accepts a parameters object.
For conveniance, will unwrap the OMERO types '''
# Connect if not already connected
if self.conn is None:
self.connect()
if params is None:
params = ParametersI()
# Set OMERO Group to -1 to query across all available data
self.conn.SERVICE_OPTS.setOmeroGroup(-1)
# Get the Query Service
qs = self.conn.getQueryService()
# Execute the query
rows = qs.projection(query, params, self.conn.SERVICE_OPTS)
# Unwrap the query results
unwrapped_rows = []
for row in rows:
unwrapped_row = []
for column in row:
if column is None:
unwrapped_row.append(None)
else:
unwrapped_row.append(column.val)
unwrapped_rows.append(unwrapped_row)
return unwrapped_rows
def __del__(self):
self.disconnect()
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()
parser = argparse.ArgumentParser(
description="generate fake masks that overlap"
)
parser.add_argument("--to-host", default="localhost")
parser.add_argument("--to-user", default="root")
parser.add_argument("--to-pass", default="omero")
parser.add_argument("target_image", type=int, help="output image")
ns = parser.parse_args()
image_id_dst = ns.target_image
local = BlitzGateway(ns.to_user, ns.to_pass, host=ns.to_host, secure=True)
local.connect()
query_service = local.getQueryService()
update_service = local.getUpdateService()
query = "FROM Image WHERE id = :id"
params = ParametersI()
params.addId(image_id_dst)
count = 0
image = query_service.findByQuery(query, params)
def make_circle(h, w):
x = np.arange(0, w)
y = np.arange(0, h)
arr = np.zeros((y.size, x.size), dtype=bool)
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()
HOST = config.get('OMERODetails', 'host')
PORT = config.getint('OMERODetails', 'port')
USERNAME = config.get('OMERODetails', 'username')
PASSWORD = config.get('OMERODetails', 'password')
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
connected = conn.connect()
if not connected:
import sys
sys.stderr.write("Error: Connection not available, please check your user name and password.\n")
sys.exit(1)
session = conn.getSession()
queryService = conn.getQueryService()
params = Parameters()
ldapSearch = LDAPSearch(ldap_details)
# Check users
query = "from Experimenter"
experimenters = queryService.findAllByQuery(query, params)
print('Experimenters')
for experimenter in experimenters:
output = '%s' %experimenter.omeName.getValue()
if experimenter.email and experimenter.email.getValue().strip() != '':
output = output + ', %s ' %experimenter.email.getValue()
if len(ldapSearch.userSearch(experimenter.omeName.getValue())) == 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()
# Suggests OMERO.cli commands to fix the idr0004 field-image mapping. # author: [email protected] from omero.gateway import BlitzGateway from omero.rtypes import wrap from omero.sys import ParametersI import os conn = BlitzGateway(os.environ.get('IDR_USER', 'root'), os.environ.get('IDR_PASSWORD', 'omero'), host=os.environ.get('IDR_HOST', 'localhost')) conn.connect() conn.setGroupForSession(3) # Public query_service = conn.getQueryService() # Find the plates of idr0004. query = """ SELECT child.id FROM ScreenPlateLink WHERE parent.name LIKE :name """ params = ParametersI() params.add('name', wrap('idr0004-%')) rows = query_service.projection(query, params) plate_ids = [row[0].val for row in rows]
c_names = []
colors = []
for ch in img.getChannels():
c_names.append(ch.getLabel())
colors.append(ch.getColor().getRGB())
# 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)
parser.add_argument("--to-user", default="root")
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
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_set1 = [["mitomycin-A", "0mM"], ["PBS", "10mM"],
["incubation", "10min"], ["temperature", "37"],
["Organism", "H**o sapiens"]]
kvp_set2 = [["mitomycin-A", "20mM"], ["PBS", "10mM"],
["incubation", "10min"], ["temperature", "37"],
["Organism", "H**o sapiens"]]
kvp_set3 = [["mitomycin-A", "10microM"], ["PBS", "10mM"],
["incubation", "5min"], ["temperature", "37"],
["Organism", "H**o sapiens"]]
kvp_set4 = [["mitomycin-A", "0mM"], ["PBS", "10mM"],
["incubation", "5min"], ["temperature", "68"],
["Organism", "H**o sapiens"]]
images_kvp_order = [('A10.pattern1.tif', kvp_set1),
('A10.pattern2.tif', kvp_set2),
('A10.pattern5.tif', kvp_set2),
('A1.pattern1.tif', kvp_set4),
('A1.pattern2.tif', kvp_set1),
('A5.pattern1.tif', kvp_set3),
('A5.pattern2.tif', kvp_set2),
('A5.pattern3.tif', kvp_set2),
('A5.pattern4.tif', kvp_set2),
('A6.pattern1.tif', kvp_set3),
('A6.pattern2.tif', kvp_set2),
('A6.pattern3.tif', kvp_set2),
('B12.pattern1.tif', kvp_set1),
('B12.pattern2.tif', kvp_set1),
('B12.pattern3.tif', kvp_set1),
('B12.pattern4.tif', kvp_set3),
('B12.pattern5.tif', kvp_set3),
('C4.pattern1.tif', kvp_set2),
('C4.pattern2.tif', kvp_set2),
('C4.pattern3.tif', kvp_set2),
('C4.pattern4.tif', kvp_set2),
('C4.pattern5.tif', kvp_set2),
('C4.pattern6.tif', kvp_set2),
('C4.pattern7.tif', kvp_set3),
('C4.pattern8.tif', kvp_set3),
('C4.pattern9.tif', kvp_set1),
('C4.pattern.tif', kvp_set1),
('E4.pattern5.tif', kvp_set3),
('E4.pattern6.tif', kvp_set1),
('E4.pattern7.tif', kvp_set3),
('E4.pattern8.tif', kvp_set3),
('E4.pattern9.tif', kvp_set1)]
images_kvp_order = dict(images_kvp_order)
for image in dataset.listChildren():
if image.getName() in images_kvp_order:
print images_kvp_order[image.getName()]
key_value_data = images_kvp_order[image.getName()]
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()
colors = []
for ch in image.getChannels():
cNames.append(ch.getLabel())
colors.append(ch.getColor().getRGB())
# 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))
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()
Used after import of SPW data to provide spatial settings on well
samples. Tested by spw_test.
"""
import argparse
import omero
from omero.gateway import BlitzGateway
from omero.model.enums import UnitsLength
parser = argparse.ArgumentParser()
parser.add_argument('host', help='OMERO host')
parser.add_argument('port', help='OMERO port')
parser.add_argument('key', help='OMERO session key')
parser.add_argument('plateId', help='Plate ID to process', type=int)
args = parser.parse_args()
conn = BlitzGateway(host=args.host, port=args.port)
conn.connect(args.key)
update = conn.getUpdateService()
plate = conn.getObject('Plate', args.plateId)
r = UnitsLength.REFERENCEFRAME
cols = 3
for well in plate.listChildren():
for i, ws in enumerate(well.listChildren()):
x = i % cols
y = i / cols
ws = conn.getQueryService().get('WellSample', ws.id)
ws.posY = omero.model.LengthI(y, r)
ws.posX = omero.model.LengthI(x, r)
update.saveObject(ws)
