def __init__(self, name, image, orientation=None, *args, **kwargs):
"""
Initialiser of an ROI by name and image object
:param str name: the name of this ROI
:param `omero.gateway._ImageWrapper` image: the associated image
"""
super(OMEROROI, self).__init__(*args, **kwargs)
if isinstance(name, str):
self.setName(name)
if isinstance(image, omero.gateway._ImageWrapper):
self.setImage(image)
self.__image = image
if orientation is not None:
directions = ['x', 'y', 'z']
try:
assert orientation in directions
except AssertionError:
print_date("Invalid orientation: {}; should be in {}".format(
orientation, ", ".join(directions)))
sys.exit(1)
self._orientation = orientation
# try to determine the orientation from the image name
else:
if re.match(r'.*\-front\..*$', image.name, re.IGNORECASE):
self._orientation = 'x'
elif re.match(r'.*\-side\..*$', image.name, re.IGNORECASE):
self._orientation = 'y'
elif re.match(r'.*\-top\..*$', image.name, re.IGNORECASE):
self._orientation = 'z'
else:
print_date(
"Unable to determine ROI orientation. Ensure image name has one of the form '*-front.*' (x), '*-side.*' (y) or '*-top.*' (z)."
)
sys.exit(1)
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
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)
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)
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 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)
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 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 __exit__(self, exc_type, exc_value, traceback): # @UnusedVariable
self.conn._closeSession()
if self.args.verbose:
print_date('Connection closed.')
self.connected = False