def index(request):
conn = BlitzGateway(OMERO_USER,OMERO_PASSWORD,host=os.environ['OMEROHOST'])
if not conn.connect():
return HttpResponseServerError("Could not connect to Omero server")
projects = []
thumbnails = {}
for project in conn.listProjects():
can_get_rois = False
p = {'id':project.id,
'name':project.name,
'datasets':[]
}
for dataset in project.listChildren():
ds = {'id':dataset.id,
'name':dataset.name,
'images':[]
}
for image in dataset.listChildren():
#if image.getROICount() > 0:
img_meta = image.simpleMarshal()
if dataset.name != 'ROI_images' and len(img_from_roi.getRectangles(conn,image)) >0:
img_meta['can_get_rois'] = True
ds['images'].append(img_meta)
size_x = image.getSizeX()
size_y = image.getSizeY()
if size_x*0.005 > 256:
thumbnails[image.id] = image.getThumbnail(size=(size_x*0.005,size_y*0.005))
else:
thumbnails[image.id] = image.getThumbnail(size=(size_x*0.1,size_y*0.1))
p['datasets'].append(ds)
projects.append(p)
conn.close()
return render(request, 'exportml/index.html',{'projects':projects,'thumbnails':thumbnails})
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"""
" " * 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:"
print "=" * 50
" " * 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
perm_string = str(group_perms)
permission_names = {
'rw----': 'PRIVATE',
'rwr---': 'READ-ONLY',
'rwra--': 'READ-ANNOTATE',
'rwrw--': 'READ-WRITE'} # Not exposed in 4.4.0 clients
print "Permissions: %s (%s)" % (permission_names[perm_string], perm_string)
# By default, any query applies to ALL data that we can access in our Current
# group.
# This will be determined by group permissions e.g. in Read-Only or
# Read-Annotate groups, this will include other users' data See
# :doc:`/sysadmins/server-permissions`.
projects = conn.listProjects() # may include other users' data
for p in projects:
print p.getName(), "Owner: ", p.getDetails().getOwner().getFullName()
# Will return None if Image is not in current group
image = conn.getObject("Image", imageId)
print "Image: ", image
# 'Cross-group' querying, use '-1'
# ===============================
conn.SERVICE_OPTS.setOmeroGroup('-1')
image = conn.getObject("Image", imageId) # Will query across all my groups
print "Image: ", image,
if image is not None:
print "Group: ", image.getDetails().getGroup().getName(),
print image.details.group.id.val # access groupId without loading group
perm_string = str(group_perms)
permission_names = {
'rw----': 'PRIVATE',
'rwr---': 'READ-ONLY',
'rwra--': 'READ-ANNOTATE',
'rwrw--': 'READ-WRITE'
} # Not exposed in 4.4.0 clients
print "Permissions: %s (%s)" % (permission_names[perm_string], perm_string)
# By default, any query applies to ALL data that we can access in our Current
# group.
# This will be determined by group permissions e.g. in Read-Only or
# Read-Annotate groups, this will include other users' data See
# :doc:`/sysadmins/server-permissions`.
projects = conn.listProjects() # may include other users' data
for p in projects:
print p.getName(), "Owner: ", p.getDetails().getOwner().getFullName()
# Will return None if Image is not in current group
image = conn.getObject("Image", imageId)
print "Image: ", image
# 'Cross-group' querying, use '-1'
# ===============================
conn.SERVICE_OPTS.setOmeroGroup('-1')
image = conn.getObject("Image", imageId) # Will query across all my groups
print "Image: ", image,
if image is not None:
print "Group: ", image.getDetails().getGroup().getName(),
print image.details.group.id.val # access groupId without loading group
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
for project in conn.listProjects(only_owned=True):
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
import sys
import omero
from omero.gateway import BlitzGateway
conn = BlitzGateway('root', 'omero-root-password', host='192.168.1.22')
if not conn.connect():
sys.exit(1)
projects = []
for project in conn.listProjects():
has_images = False
p = {'id': project.id, 'name': project.name, 'datasets': []}
for dataset in project.listChildren():
ds = {'id': dataset.id, 'name': dataset.name, 'images': []}
for image in dataset.listChildren():
if image.getROICount() > 0:
ds['images'].append(image.simpleMarshal())
has_images = True
p['datasets'].append(ds)
if has_images:
projects.append(p)
for p in projects:
print(p)
'''roi_service = conn.getRoiService()
result = roi_service.findByImage(image.getId(), None)
for roi in result.rois:
for s in roi.copyShapes():
#prints way too much info, would be good for ragged shapes
#print roi_service.getPoints(s.getId().getValue())
#print s
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)
