def create_containers(self, cli, project, dataset):
"""
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
dsId = None
if project is not None:
# We need to find or create a project
# This is not nice but we really shouldn't be dealing with large numbers of objects here
plist = list(conn.getObjects("Project", attributes={'name': project}, params=params))
if len(plist) == 0:
# Create project and dataset then link
p = self.create_project(conn, project)
d = self.create_dataset(conn, dataset)
dsId = d.id.val
self.link_dataset(conn, p.id.val, dsId)
else:
# Pick the first, it's as good as any
p = plist[0]
print "Using existing Project:", project
# Since Project already exists check children for dataset
for c in p.listChildren():
if c.getName() == dataset:
d = c
dsId = d.getId()
# No existing child dataset so create one and link
if d is None:
d = self.create_dataset(conn, dataset)
dsId = d.id.val
self.link_dataset(conn, p.getId(), dsId)
else:
print "Using existing Dataset:", dataset
else:
# There may be more than one dataset with the same name
# This is not nice but we really shouldn't be dealing with large numbers of objects here
dlist = list(conn.getObjects("Dataset", attributes={'name': dataset}, params=params))
if len(dlist) != 0:
# We want one without a parent, the first will do
for c in dlist:
if len(c.listParents()) == 0:
d = c
dsId = d.getId()
if d is None:
dsId = self.create_dataset(conn, dataset).id.val
else:
print "Using existing Dataset:", dataset
return dsId
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 connect_to_omero(user, password, host, port=4064):
conn = BlitzGateway(user, password, host=host, port=port)
print conn.connect()
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
return conn
def connect_to_omero(user, password, host, port=4064):
conn = BlitzGateway(user, password, host=host, port=port)
print conn.connect()
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
return conn
def testExperimenterListParents(self):
"""Test listParents() for Experimenter in ExperimenterGroup."""
client, exp = self.new_client_and_user()
conn = BlitzGateway(client_obj=client)
userGroupId = conn.getAdminService().getSecurityRoles().userGroupId
exp = conn.getUser()
groups = exp.listParents()
assert len(groups) == 2
gIds = [g.id for g in groups]
assert userGroupId in gIds
# ExperimenterGroup has no parent
assert len(groups[0].listParents()) == 0
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_as_script():
"""
Main entry point of the script, as called via the scripting service.
"""
client = scripts.client(
'Export_Tree_Hierarchy.py',
'Trigger an update of the symlink tree hierarchy on the sciCORE '
'cluster filesystem.',
authors = ["Niko Ehrenfeuchter"],
institutions = ["IMCF, University of Basel"],
contact = "*****@*****.**",
)
try:
# wrap client to use the Blitz Gateway
conn = BlitzGateway(client_obj=client)
username = conn.getUser().getName()
markdir = os.path.join(os.environ['HOME'], '.omero_tree_export_usernames')
if not os.path.exists(markdir):
# do not create the marker directory, send back an error message
# instead - the directory has to exist, otherwise the wrapper
# daemon is not running!
message = "ERROR: Marker directory '%s' missing!" % markdir
client.setOutput("Message", rstring(message))
raise IOError("directory '%s' missing!" % markdir)
filename = os.path.join(markdir, username)
if os.path.exists(filename):
message = ("WARNING: a request for username '%s' is already "
"existing! Please contact an administrator if this "
"request does not get processed soon!" % username)
else:
message = "Requested update for username '%s'." % username
with open(filename, 'a') as out:
out.write('%s' % username)
client.setOutput("Message", rstring(message))
finally:
# Cleanup
client.closeSession()
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
# Using secure connection.
# =============================================================
# By default, once we have logged in, data transfer is not encrypted (faster)
# To use a secure connection, call setSecure(True):
# conn.setSecure(True) # <--------- Uncomment this
# Current session details
# =============================================================
# By default, you will have logged into your 'current' group in OMERO. This
# can be changed by switching group in the OMERO.insight or OMERO.web clients.
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
print "Other Members of current group:"
for exp in conn.listColleagues():
print " ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()
)
sys.exit(1)
# Using secure connection.
# =============================================================
# By default, once we have logged in, data transfer is not encrypted (faster)
# To use a secure connection, call setSecure(True):
# conn.setSecure(True) # <--------- Uncomment this
# Current session details
# =============================================================
# By default, you will have logged into your 'current' group in OMERO. This
# can be changed by switching group in the OMERO insight or web clients.
user = conn.getUser()
print "Current user:"******" ID:", user.getId()
print " Username:"******" Full Name:", user.getFullName()
print "Member of:"
for g in conn.getGroupsMemberOf():
print " ID:", g.getName(), " Name:", g.getId()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
print "Other Members of current group:"
for exp in conn.listColleagues():
print " ID:", exp.getId(), exp.getOmeName(
), " Name:", exp.getFullName()
def run_script():
dataTypes = [rstring('Project'), rstring('Dataset')]
# TODO: enable attaching to images
dataTypes_attach = [rstring('Dataset'), rstring('Project')]
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
client = scripts.client(
'Remote_Import.py',
"""Remote import from dedicated workstations:
* Import the content of the OMERO_ImportData/<username>/ folder on the selected workstation.
* Appends files with the specified suffix to the Project or Dataset.
* The scanned subfolder depth is 10
---------------------------------------------------------------
INPUT:
---------------------------------------------------------------
Select PROJECT as TARGET for import : : A Dataset object is created for each subdirectory on OMERO_ImportData/<username>/
Select DATASET as TARGET for import : : All images (also images in subdirectories) are imported into this Dataset
""",
scripts.String(
PARAM_WS,
optional=False,
grouping="1",
description="Choose a workstation where you want to import from",
values=WORKSTATION_NAMES),
scripts.String(PARAM_DATATYPE,
optional=True,
grouping="2",
description="Choose kind of destination object.",
values=dataTypes),
scripts.Long(
PARAM_ID,
optional=False,
grouping="3",
description=
"ID of destination object. Please select only ONE object."),
scripts.Bool(
PARAM_SKIP_EXISTING,
grouping="4",
description=
"skip files that are already uploaded (checked 'import from' path).",
default=False),
scripts.Bool(PARAM_ATTACH,
grouping="5",
description="Attach containing non image files",
default=False),
scripts.String(PARAM_DEST_ATTACH,
grouping="5.1",
description="Object to that should be attach",
values=dataTypes_attach,
default="Dataset"),
scripts.String(
PARAM_ATTACH_FILTER,
grouping="5.2",
description=
"Filter files by given file extension (for example txt, pdf). Separated by ','."
),
namespaces=[omero.constants.namespaces.NSDYNAMIC],
version="1.1.0",
authors=["Susanne Kunis", "CellNanOs"],
institutions=["University of Osnabrueck"],
contact="*****@*****.**",
) # noqa
try:
params = client.getInputs(unwrap=True)
if os.path.exists(MOUNT_PATH):
conn = BlitzGateway(client_obj=client)
datapath = checkWorkstation(conn, params.get(PARAM_WS), MOUNT_PATH,
conn.getUser().getName())
if datapath:
robj, message = remoteImport(conn, params, datapath)
else:
message = "No data available on %s for user" % (
params.get(PARAM_WS))
robj = None
client.setOutput("Message", rstring(message))
if robj is not None:
client.setOutput("Result", robject(robj._obj))
else:
client.setOutput(
"ERROR", rstring("No such Mount directory: %s" % MOUNT_PATH))
finally:
client.closeSession()
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 """%s%s:%s Name:"%s" (owner=%s)""" % (
" " * indent,
obj.OMERO_CLASS,
obj.getId(),
obj.getName(),
obj.getOwnerOmeName())
# List all Projects available to the user currently logged in
# ===========================================================
# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is False, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
my_expId = conn.getUser().getId()
for project in conn.listProjects(my_expId):
print_obj(project)
for dataset in project.listChildren():
print_obj(dataset, 2)
for image in dataset.listChildren():
print_obj(image, 4)
# Retrieve the datasets owned by the user currently logged in
# ===========================================================
# Here we create an omero.sys.ParametersI instance which we
# can use to filter the results that are returned. If we did
# not pass the params argument to getObjects, then all Datasets
# in the current group would be returned.
print "\nList Datasets:"
def run():
"""
Launch (remote) Priism ER deconvolution job on a list of images.
Results imported back into dataset of origin for each image.
"""
# Build GUI dialog for user to choose images & update parameters
client = script.client(
"ER_Deconvolution.py", "ER deconvolution",
script.String(
"Data_Type", optional=False,
grouping="1", values=[rstring('Image')], default="Image"),
script.List(
"IDs", optional=False,
description="image IDs (must have original .dv file!)",
grouping='2').ofType(rlong(0)),
script.Int(
"alpha", optional=False,
description='regularization parameter "alpha" - try 1000-10000',
grouping='3', default=job['par.alpha'], min=0),
script.Float(
"lambda f", optional=False,
description='smoothing parameter "lambda f" - try 0.1-1.0',
grouping='4', default=job['par.lamf'], min=0.0, max=1.0),
script.Int(
"iterations", optional=False,
description="number of iterations - try 10-100",
grouping='5', default=job['par.niter'], min=0),
version="0.99",
authors=["Graeme Ball"],
institutions=["Dundee Imaging Facility"],
contact="*****@*****.**"
)
try:
tempdir = None
input_image_ids = [int(n) for n in client.getInput("IDs", unwrap=True)]
job['par.alpha'] = client.getInput("alpha", unwrap=True)
job['par.lamf'] = client.getInput("lambda f", unwrap=True)
job['par.niter'] = client.getInput("iterations", unwrap=True)
conn = BlitzGateway(client_obj=client)
user = str(conn.getUser().getName())
group = str(conn.getGroupFromContext().getName())
sid = client.getSessionId()
# export images (must be .dv!) to shared / temp storage
tempdir = mktempdir(user, TEMP)
inputs = []
for iid in input_image_ids:
try:
path = export_original_dvfile(conn, iid, tempdir)
image = conn.getObject("Image", iid)
fail(image is None, "No such image, ID=%d" % iid)
did = image.getParent().getId()
#did = image.getDataset().getId()
inputs.append({'imageID': iid, 'path': path, 'datasetID': did})
except RuntimeError as e:
print "Fail: " + str(e)
jobs = []
for inp in inputs:
command = dict(job) # copy
command['inputs'] = [inp] # only 1 input image for this job
jobs.append(json.dumps([command])) # only 1 command for this job
# N.B. '.jobs' file format more flexible than needed here
# write jobs definition file (1 line json string per job)
jobs_filepath = os.path.join(tempdir, jobs_filename)
with open(jobs_filepath, 'w') as f:
f.writelines(["%s\n" % j for j in jobs])
# poll filesystem, checking for results
client.enableKeepAlive(KEEPALIVE_PULSE)
results_filepath = os.path.join(tempdir, results_filename)
result_count = 0 # results .json file grows as results appear
import_count = 0 # ensure we only attempt to import each result once
tstart = time.time()
while result_count < len(inputs) and (time.time() - tstart) < TIMEOUT:
fail(not conn.isConnected(), "Connection lost!")
alive_filepath = os.path.join(tempdir, alive_check_filename)
with open(alive_filepath, 'w') as f:
f.write("%f\n%d" % (time.time(), RESULTS_POLL_PULSE))
time.sleep(RESULTS_POLL_PULSE)
if os.path.exists(results_filepath):
with open(results_filepath, 'r') as fr:
results = fr.readlines() # 1 line json string per result
new_results = results[import_count:]
import_count += import_results(new_results, user, group,
sid, conn)
result_count = len(results)
if result_count < len(inputs):
print "Job timed out after %d seconds, %d results imported" % \
(TIMEOUT, import_count)
finally:
if tempdir is not None and tempdir.startswith(TEMP):
if os.path.exists(tempdir):
shutil.rmtree(tempdir) # we checked 'tempdir' is sane first!
client.closeSession()
print """%s%s:%s Name:"%s" (owner=%s)""" % (\
" " * indent,
obj.OMERO_CLASS,\
obj.getId(),\
obj.getName(),\
obj.getOwnerOmeName())
# List all Projects available to me, and their Datasets and Images:
# =================================================================
# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is Fale, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
my_expId = conn.getUser().getId()
for project in conn.listProjects(my_expId):
print_obj(project)
for dataset in project.listChildren():
print_obj(dataset, 2)
for image in dataset.listChildren():
print_obj(image, 4)
# Retrieve the datasets owned by the user currently logged in:
# =================================================================
# Here we create an omero.sys.ParametersI instance which we
# can use to filter the results that are returned. If we did
# not pass the params argument to getObjects, then all Datasets
# in the current group would be returned.
print "\nList Datasets:"
print "=" * 50
class OMEROConnection(object):
def __init__(self, args, configs):
self.args = args
self.configs = configs
self.connect_with = self.configs['CONNECT_WITH']
self.host = self.configs['OMERO_{}_HOST'.format(self.connect_with)]
self.user = self.configs['OMERO_{}_USER'.format(self.connect_with)]
self.password = self.configs['OMERO_{}_PASSWORD'.format(
self.connect_with)]
self.port = self.configs['OMERO_{}_PORT'.format(self.connect_with)]
def __enter__(self):
from omero.gateway import BlitzGateway # @UnresolvedImport
self.conn = BlitzGateway(host=self.host,
username=self.user,
passwd=self.password,
port=self.port)
self.connected = self.conn.connect()
# failed to connect
if not self.connected:
print_date(
"Unable to connect to host '{}' on port {} using user '{}'".
format(self.host, self.port, self.user))
print_date("Check that server is up")
sys.exit(1)
# keepalive
self.conn.c.enableKeepAlive(5)
self.omero_user = self.conn.getUser()
self.userId = self.omero_user.getId()
self.updateService = self.conn.getUpdateService()
self.roiService = self.conn.getRoiService()
return self
def __exit__(self, exc_type, exc_value, traceback): # @UnusedVariable
self.conn._closeSession()
if self.args.verbose:
print_date('Connection closed.')
self.connected = False
def list(self):
"""List images or ROIs
:return int count: the number of images/ROIs
"""
if self.args.images:
print_date("Listing images...")
images = self.images()
if self.args.summary:
pass
else:
print_date("Structuring output...")
image_view = ImageView(images)
print(image_view)
return len(images)
elif self.args.rois:
print_date("Listing ROIs...")
rois = self.rois()
if self.args.summary:
pass
else:
print_date("Structuring output...")
roi_view = ROIView(rois)
print(roi_view)
return len(rois)
@property
def projects(self):
if self.args.project is not None:
projects = self.conn.searchObjects(["Project"], self.args.project)
return projects
else:
return self.conn.listProjects(self.userId)
def datasets(self, project=None):
"""List the datasets associated with the current user
:param project: a project
:param bool in_project: are these datasets contained within a project?
"""
datasets = list()
if self.args.dataset is not None:
datasets += self.conn.searchObjects(["Dataset"], self.args.dataset)
else:
if project is not None:
projects = self.conn.searchObjects(["Project"], project)
for p in projects:
datasets += p.listChildren()
else:
params = omero.sys.ParametersI() # @UndefinedVariable
params.exp(self.userId)
datasets += self.conn.getObjects("Dataset", params=params)
return datasets
def images(self, project=None, dataset=None):
"""The list of images associated with the current user
If the image ID is specified only the required image is returned. (The project and dataset are ignored.)
Otherwise:
- If a project object is provided all images in all datasets in the project are returned. (The dataset is ignored.)
- If a project object and dataset object are provided then only those images in the project and dataset are return.
- If no project object is provided but a dataset object is provided then only those images in the dataset are returned.
:param str project: OMERO project name
:param str dataset: OMERO dataset name
:return list images: a list of OMERO ``Image`` objects
"""
# assertions
images = list()
print_date("Retrieving images...")
if self.args.image_id is not None:
try:
assert isinstance(self.args.image_id, int) or isinstance(
self.args.image_id, long)
except AssertionError:
print_date("Invalid type for image ID: {}".format(
type(self.args.image_id)))
sys.exit(1)
image = self.getImage(self.args.image_id)
if image is not None:
images.append(image)
elif self.args.image_name is not None:
images = self.conn.searchObjects(["Image"], self.args.image_name)
else:
if project is not None: # project specified
print_date(
"Searching for images in project '{}'".format(project))
# get all projects matching
projects = self.conn.searchObjects(["Project"], project)
# get all datasets in projects matching
datasets_in_projects = dict()
for p in projects:
for d in p.listChildren():
datasets_in_projects[d.getName()] = d
print_date("Found {} datasets in project '{}'".format(
len(datasets_in_projects), project))
# dataset specified
if dataset is not None:
print_date(
"Searching for images in dataset '{}'".format(dataset))
if dataset in datasets_in_projects.keys():
images += datasets_in_projects[dataset].listChildren()
else: # dataset not specified
print_date(
"Searching for images in all {} datasets".format(
len(datasets_in_projects)))
for dataset in datasets_in_projects.keys():
images += datasets_in_projects[dataset].listChildren()
else: # project not specified
# dataset specified
if dataset is not None:
print_date(
"Searching for images in dataset '{}'".format(dataset))
datasets = self.conn.searchObjects(["Dataset"], dataset)
for dataset in datasets:
images += dataset.listChildren()
else:
datasets = self.datasets()
print_date(
"Searching for images in all {} datasets".format(
len(datasets)))
for dataset in datasets:
images += dataset.listChildren()
print_date("Found {} image(s).".format(len(images)))
return images
def getImage(self, image_id):
"""Get the image with the image ID specified on the command line
:param int image_id: command line arguments
:return image: an image
:rtype image: ``OMEROImage``
"""
return self.conn.getObject("Image", image_id)
def rois(self, project=None, dataset=None):
"""Get an iterator over the ROIs associated with the specified image ID
:param int image_id: image ID
"""
rois = list()
print_date("Retrieving ROIs...")
if self.args.image_id is not None:
return self.getROIs(self.args.image_id)
else:
for image in self.images(project, dataset):
if image.getROICount() > 0:
rois.append((image, self.getROIs(image.getId())))
roi_count = sum(map(lambda r: len(r[1]), rois))
print_date("Found {:,} ROIs in {:,} images.".format(
roi_count, len(rois)))
return rois
def getROIs(self, image_id):
result = self.roiService.findByImage(image_id, None)
return result.rois
def attachRois(self, omero_rois):
"""Attach the rois from the iterable"""
non_rois = filter(lambda r: not isinstance(r, OMEROROI), omero_rois)
try:
assert len(non_rois) == 0
except AssertionError:
print_date("Found {:,} non-ROI objects".format(len(non_rois)))
return 1
for roi in omero_rois:
self.saveRoi(roi)
return os.EX_OK
# save
def saveRoi(self, roi):
"""Save the given ROI
:param roi: an ROI object
:type roi: `omero.model.Roi`
"""
import Ice
try:
self.updateService.saveObject(roi)
except Ice.MemoryLimitException as e: # @UndefinedVariable
print_date(str(e))
sys.exit(1)
# delete
def deleteRoi(self, roi_id):
"""
Delete the given ROI
:param roi: an ROI object
:type roi: `omero.model.Roi`
"""
from omero.callbacks import CmdCallbackI # @UnresolvedImport
handle = self.conn.deleteObjects("Roi", [roi_id],
deleteAnns=True,
deleteChildren=True)
callback = CmdCallbackI(self.conn.c, handle)
while not callback.block(500):
if self.args.verbose:
print_date(".", newline=False, incl_date=False)
time.sleep(2)
callback.close(True)
class Omero(Observable):
"""Run a process for a pipeline
Run a process from data in an Experiment and save the
results in new ProcessedDataset in the experiment
Parameters
----------
host
Adresse of the Omero server
port
Port used to communicate with the server
username
Username to authenticate to the database
password
User password
"""
def __init__(self, host: str, port: int, username: str, password: str):
Observable.__init__(self)
self.conn = None
self._host = host
self._connect(host, port, username, password)
def close(self):
self.conn.close()
def _connect(self, host: str, port: int, username: str, password: str):
self.conn = BlitzGateway(username,
password,
host=host,
port=port,
secure=True)
rv = self.conn.connect()
if not rv:
print("Unable to connect to the Omero database")
else:
user = self.conn.getUser()
print("Current user:"******" ID:", user.getId())
print(" Username:"******" Full Name:", user.getFullName())
def import_dataset(self, experiment: Experiment, omero_dataset_id: int):
dataset = self.conn.getObject("Dataset", omero_dataset_id)
image_count = dataset.countChildren()
k = 0
for image in dataset.listChildren():
k += 1
self.notify_observers(
100 * k / image_count,
'import image ' + str(k) + '/' + str(image_count))
self._import_image(experiment, image)
self.notify_observers(100, 'Done')
def import_image(self, experiment: Experiment, omero_image_id: int):
image = self.conn.getObject("Image", omero_image_id)
self._import_image(experiment, image)
def _import_image(self, experiment: Experiment, image):
# read metadata from omero
rawdatasetdir = os.path.dirname(experiment.md_uri)
filename = os.path.join(rawdatasetdir, 'data', image.getName())
author = image.getAuthor()
date = image.getDate().strftime('%Y-%m-%d %I:%M %S %p')
extension = os.path.splitext(image.getName())[1][1:]
tags = dict()
for ann in image.listAnnotations():
if ann.OMERO_TYPE == omero.model.MapAnnotationI:
for kv in ann.getValue():
tags[kv[0]] = kv[1]
# print('readed tags:')
# print('\t author:', author)
# print('\t date:', date)
# print('\t extension:', extension)
# print('\t tags:', tags)
# write metadata to the experiment
experiment.import_data(
filename,
image.getName(),
author=author,
format=extension,
date=date,
tags=tags,
copy=False,
)
# register tag to experiment if not exists
for tag in tags:
experiment.set_tag(tag, False)
# copy image
channel = 0
imageData = _get_data(image, channel)
tif = TIFF.open(filename, mode='w')
for t in range(imageData.shape[0]):
for z in range(imageData.shape[1]):
tif.write_image(imageData[t, z, :, :])
tif.close()
"""
print("""%s%s:%s Name:"%s" (owner=%s)""" %
(" " * indent, obj.OMERO_CLASS, obj.getId(), obj.getName(),
obj.getOwnerOmeName()))
# List all Projects owned by the user currently logged in
# =======================================================
# By default this returns Projects from all owners across
# all groups. We can filter by group and owner using the
# optional opts dict (new in 5.3.0)
# We also order by name and use 'limit' and 'offset',
# to load the first 5 Projects
print("\nList Projects:")
print("=" * 50)
my_exp_id = conn.getUser().getId()
default_group_id = conn.getEventContext().groupId
for project in conn.getObjects("Project",
opts={
'owner': my_exp_id,
'group': default_group_id,
'order_by': 'lower(obj.name)',
'limit': 5,
'offset': 0
}):
print_obj(project)
assert project.getDetails().getOwner().id == my_exp_id
# We can get Datasets with listChildren, since we have the Project already.
# Or conn.getObjects("Dataset", opts={'project', id}) if we have Project ID
for dataset in project.listChildren():
print_obj(dataset, 2)