def datasets(self):
"""Returns 2 new OMERO Datasets with required fields set."""
dataset = omero.model.DatasetI()
dataset.name = rstring("A_%s" % self.uuid())
dataset2 = omero.model.DatasetI()
dataset2.name = rstring("B_%s" % self.uuid())
return self.update.saveAndReturnArray([dataset, dataset2])
def new_object(self, classname, name=None, description=None):
obj = classname()
if not name:
name = self.uuid()
obj.setName(rstring(name))
obj.setDescription(rstring(description))
return obj
def externalInfo():
o = ExternalInfoI()
o.entityId = rlong(123L)
o.entityType = rstring("test")
o.lsid = rstring("ABCDEF")
o.uuid = rstring("f90a1fd5-275c-4d14-82b3-87b5ef0f07de")
return o
def screens(self):
"""Returns 2 new OMERO Screens with required fields set."""
screen = omero.model.ScreenI()
screen.name = rstring("A_%s" % self.uuid())
screen2 = omero.model.ScreenI()
screen2.name = rstring("B_%s" % self.uuid())
return self.update.saveAndReturnArray([screen, screen2])
def new_user(self, group=None, perms=None, admin=False, system=False):
"""
admin: If user is to be an admin of the created group
system: If user is to be a system admin
"""
if not self.root:
raise Exception("No root client. Cannot create user")
adminService = self.root.getSession().getAdminService()
name = self.uuid()
# Create group if necessary
if not group:
g = self.new_group(perms=perms)
else:
g = group
# Create user
e = omero.model.ExperimenterI()
e.omeName = rstring(name)
e.firstName = rstring(name)
e.lastName = rstring(name)
e.ldap = rbool(False)
uid = adminService.createExperimenterWithPassword(e, rstring(name), g, [g, adminService.lookupGroup("user")])
e = adminService.lookupExperimenter(name)
if admin:
adminService.setGroupOwner(g, e)
if system:
adminService.addGroups(e, [omero.model.ExperimenterGroupI(0, False)])
return adminService.getExperimenter(uid)
def testGetSetMetaMap(self):
hdf = omero.tables.HdfStorage(self.hdfpath(), self.lock)
self.init(hdf, False)
hdf.add_meta_map({'a': rint(1)})
m1 = hdf.get_meta_map()
assert len(m1) == 3
assert m1['__initialized'].val > 0
assert m1['__version'] == rstring('2')
assert m1['a'] == rint(1)
with pytest.raises(omero.ApiUsageException) as exc:
hdf.add_meta_map({'b': rint(1), '__c': rint(2)})
assert exc.value.message == 'Reserved attribute name: __c'
assert hdf.get_meta_map() == m1
with pytest.raises(omero.ValidationException) as exc:
hdf.add_meta_map({'d': rint(None)})
assert exc.value.serverStackTrace.startswith('Unsupported type:')
assert hdf.get_meta_map() == m1
hdf.add_meta_map({}, replace=True)
m2 = hdf.get_meta_map()
assert len(m2) == 2
assert m2 == {
'__initialized': m1['__initialized'], '__version': rstring('2')}
hdf.add_meta_map({'__test': 1}, replace=True, init=True)
m3 = hdf.get_meta_map()
assert m3 == {'__test': rint(1)}
hdf.cleanup()
def runAsScript():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
print_duration(False) # start timer
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client(
'Images_From_ROIs.py',
"""Crop rectangular regions from slide scanner images.""",
scripts.String(
"Data_Type", optional=False, grouping="1",
description="Choose Images via their 'Dataset' or directly by "
" 'Image' IDs.", values=dataTypes, default="Image"),
scripts.List(
"IDs", optional=False, grouping="2",
description="List of Dataset IDs or Image IDs to "
" process.").ofType(rlong(0)),
scripts.String(
"Container_Name", grouping="3",
description="Option: put Images in new Dataset with this name",
default="From_ROIs"),
scripts.Bool(
"Email_Results", grouping="4", default=True,
description="E-mail the results"),
scripts.String("Email_address", grouping="4.1",
description="Specify e-mail address"),
version="5.0.2",
authors=["Daniel Matthews", "QBI"],
institutions = ["University of Queensland"],
contact = "*****@*****.**",
)
try:
parameterMap = client.getInputs(unwrap=True)
print parameterMap
# create a wrapper so we can use the Blitz Gateway.
conn = BlitzGateway(client_obj=client)
if parameterMap['Email_Results'] and not validate_email(conn, parameterMap):
client.setOutput("Message", rstring("No valid email address"))
return
robj, message = make_images_from_rois(conn, parameterMap)
client.setOutput("Message", rstring(message))
if robj is not None:
client.setOutput("Result", robject(robj))
finally:
client.closeSession()
print_duration()
def write_to_omero(self):
sf = self.client.getSession()
group = str(self.value_resolver.target_object.details.group.id.val)
sr = sf.sharedResources()
update_service = sf.getUpdateService()
name = 'bulk_annotations'
table = sr.newTable(1, name, {'omero.group': group})
if table is None:
raise MetadataError(
"Unable to create table: %s" % name)
original_file = table.getOriginalFile()
log.info('Created new table OriginalFile:%d' % original_file.id.val)
table.initialize(self.columns)
log.info('Table initialized with %d columns.' % (len(self.columns)))
table.addData(self.columns)
log.info('Added data column data.')
table.close()
file_annotation = FileAnnotationI()
file_annotation.ns = \
rstring('openmicroscopy.org/omero/bulk_annotations')
file_annotation.description = rstring(name)
file_annotation.file = OriginalFileI(original_file.id.val, False)
link = self.create_annotation_link()
link.parent = self.target_object
link.child = file_annotation
update_service.saveObject(link, {'omero.group': group})
def externalInfo():
o = ExternalInfoI()
o.entityId = rlong(123L)
o.entityType = rstring('test')
o.lsid = rstring('ABCDEF')
o.uuid = rstring('f90a1fd5-275c-4d14-82b3-87b5ef0f07de')
return o
def test1175(self):
uuid = self.root.sf.getAdminService().getEventContext().sessionUuid
update = self.root.sf.getUpdateService()
timeline = self.root.sf.getTimelineService()
# create dataset
ds = self.make_dataset(name='test1154-ds-%s' % (uuid),
client=self.root)
ds.unload()
# create tag
ann = omero.model.TagAnnotationI()
ann.textValue = rstring('tag-%s' % (uuid))
ann.setDescription(rstring('tag-%s' % (uuid)))
t_ann = omero.model.DatasetAnnotationLinkI()
t_ann.setParent(ds)
t_ann.setChild(ann)
update.saveObject(t_ann)
p = omero.sys.Parameters()
p.map = {}
f = omero.sys.Filter()
f.ownerId = rlong(0)
f.limit = rint(10)
p.theFilter = f
M = timeline.getMostRecentAnnotationLinks
res = M(None, ['TagAnnotation'], None, p)
assert len(res) > 0
# And now for #9609
res = M(None, ['TagAnnotation'], None, p, {"omero.group": "-1"})
assert len(res) > 0
def createTag(name, description=None):
print "Create Tag:", name
tag = TagAnnotationI()
tag.textValue = rstring(name)
if description is not None:
tag.description = rstring(description)
return tag
def create_original_file(self, content, client=None):
"""
Create an original file and upload it onto the server
"""
if client is None:
update = self.update
sf = self.sf
else:
update = client.sf.getUpdateService()
sf = client.sf
ofile = omero.model.OriginalFileI()
ofile.name = rstring("")
ofile.path = rstring("")
ofile = update.saveAndReturnObject(ofile)
rfs = sf.createRawFileStore()
try:
rfs.setFileId(ofile.id.val)
rfs.write(content, 0, len(content))
ofile = rfs.save()
assert len(content) == ofile.size.val
return ofile
finally:
rfs.close()
def runAsScript():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
printDuration(False) # start timer
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client(
'Images_From_ROIs.py',
"""Create new Images from the regions defined by Rectangle ROIs on \
other Images.
Designed to work with single-plane images (Z=1 T=1) with multiple ROIs per \
image.
If you choose to make an image stack from all the ROIs, this script \
assumes that all the ROIs on each Image are the same size.""",
scripts.String(
"Data_Type", optional=False, grouping="1",
description="Choose Images via their 'Dataset' or directly by "
" 'Image' IDs.", values=dataTypes, default="Image"),
scripts.List(
"IDs", optional=False, grouping="2",
description="List of Dataset IDs or Image IDs to "
" process.").ofType(rlong(0)),
scripts.String(
"Container_Name", grouping="3",
description="Option: put Images in new Dataset with this name"
" OR use this name for new Image stacks, if 'Make_Image_Stack')",
default="From_ROIs"),
scripts.Bool(
"Make_Image_Stack", grouping="4", default=False,
description="If true, make a single Image (stack) from all the"
" ROIs of each parent Image"),
version="4.2.0",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
parameterMap = client.getInputs(unwrap=True)
print parameterMap
# create a wrapper so we can use the Blitz Gateway.
conn = BlitzGateway(client_obj=client)
robj, message = makeImagesFromRois(conn, parameterMap)
client.setOutput("Message", rstring(message))
if robj is not None:
client.setOutput("Result", robject(robj))
finally:
client.closeSession()
printDuration()
def setUp(self):
AbstractPlateAnalysisCtx.DEFAULT_ORIGINAL_FILE_PROVIDER = \
FromFileOriginalFileProvider
original_files = list()
# Create our container images and an original file image map
images = list()
n_images = 0
for row in range(16):
for column in range(24):
well = WellI(n_images, True)
well.column = rint(column)
well.row = rint(row)
well_sample = WellSampleI(n_images, True)
well_sample.well = well
image = ImageI(n_images, True)
image.addWellSample(well_sample)
images.append(image)
original_file_image_map = dict()
# Our required original file format
format = rstring('Companion/InCell')
# Create original file representing the result file
o = OriginalFileI(1L, True)
o.name = rstring(self.RESULT_FILE)
o.path = rstring(os.path.join(self.ROOT, self.RESULT_FILE))
o.mimetype = format
original_files.append(o) #[1L] = o
original_file_image_map[1L] = image
sf = TestingServiceFactory()
self.analysis_ctx = InCellPlateAnalysisCtx(
images, original_files, original_file_image_map, 1L, sf)
def create_tag(self, name, description, text="tag"):
"""
Creates a new tag object. Returns the new tag object.
If either the name or description parameters are None, the user will be
prompted to input them.
The "text" parameter should be the text description to use upon user
input. For example, if we were creating a tag, this would be "tag"
(the default). If we were creating a tagset, this could be "tag set".
"""
if name is None:
name = raw_input("Please enter a name for this %s: " % text)
if description is None:
description = raw_input("Please enter a description for this %s: "
% text)
if name is not None and description is not None and name != '':
tag = TagAnnotationI()
tag.textValue = rstring(name)
if description is not None and len(description) > 0:
tag.description = rstring(description)
return tag
else:
self.ctx.err("Tag/tagset name cannot be 'None' or empty.")
sys.exit(1)
def testCreatAndUpdatePublicGroup(self):
# this is the test of creating public group and updating it
# including changes in #1434
uuid = self.uuid()
admin = self.root.sf.getAdminService()
# create group1
new_gr1 = ExperimenterGroupI()
new_gr1.name = rstring("group1_%s" % uuid)
new_gr1.ldap = rbool(False)
p = PermissionsI()
p.setUserRead(True)
p.setUserWrite(True)
p.setGroupRead(True)
p.setGroupWrite(True)
p.setWorldRead(False)
p.setWorldAnnotate(False)
p.setWorldWrite(False)
new_gr1.details.permissions = p
g1_id = admin.createGroup(new_gr1)
# update name of group1
gr1 = admin.getGroup(g1_id)
assert 'rwrw--' == str(gr1.details.permissions)
new_name = "changed_name_group1_%s" % uuid
gr1.name = rstring(new_name)
admin.updateGroup(gr1)
gr1_u = admin.getGroup(g1_id)
assert new_name == gr1_u.name.val
def test3136(self):
"""
Calls to updateGroup were taking too long
because the default value of permissions
returned by the server was triggering a
full changePermissions event.
"""
admin = self.root.sf.getAdminService()
group = self.new_group(perms="rw----")
# Change the name but not the permissions
group.name = rstring(self.uuid())
elapsed1, rv = self.timeit(admin.updateGroup, group)
# Now change the name and the permissions
group.name = rstring(self.uuid())
group.details.permissions = omero.model.PermissionsI("rwr---")
elapsed2, rv = self.timeit(admin.updateGroup, group)
# Locally this test always fails as the two times are
# the same order of magnitude. This may be an indication that
# the relevant ticket:
# http://trac.openmicroscopy.org/ome/ticket/3136
# is still valid. Does the ticket need re-opening
# or does the test condition need relaxing?
assert elapsed1 < (0.1 * elapsed2),\
"elapsed1=%s, elapsed2=%s" % (elapsed1, elapsed2)
def new_user(self, group = None, perms = None,
admin = False, system = False):
"""
admin: If user is to be an admin of the created group
system: If user is to be a system admin
"""
if not self.root:
raise exceptions.Exception("No root client. Cannot create user")
adminService = self.root.getSession().getAdminService()
name = self.uuid()
# Create group if necessary
if not group:
g = self.new_group(perms = perms)
group = g.name.val
else:
g, group = self.group_and_name(group)
# Create user
e = omero.model.ExperimenterI()
e.omeName = rstring(name)
e.firstName = rstring(name)
e.lastName = rstring(name)
uid = adminService.createUser(e, group)
e = adminService.lookupExperimenter(name)
if admin:
adminService.setGroupOwner(g, e)
if system:
adminService.addGroups(e, \
[omero.model.ExperimenterGroupI(0, False)])
return adminService.getExperimenter(uid)
def new_user(self, group = None, perms = None, admin = False):
if not self.root:
raise exceptions.Exception("No root client. Cannot create user")
admin = self.root.getSession().getAdminService()
name = self.uuid()
# Create group if necessary
if not group:
g = self.new_group(perms = perms)
group = g.name.val
else:
g, group = self.group_and_name(group)
# Create user
e = omero.model.ExperimenterI()
e.omeName = rstring(name)
e.firstName = rstring(name)
e.lastName = rstring(name)
uid = admin.createUser(e, group)
e = admin.lookupExperimenter(name)
if admin:
admin.setGroupOwner(g, e)
return admin.getExperimenter(uid)
def testChgrp11109(self):
"""
Place a plate in a single screen and attempt to move it.
"""
# One user in two groups
client, user = self.new_client_and_user(perms=PRIVATE)
admin = client.sf.getAdminService()
target_grp = self.new_group([user], perms=PRIVATE)
target_gid = target_grp.id.val
admin.getEventContext() # Refresh
update = client.sf.getUpdateService()
plate = PlateI()
plate.name = rstring("testChgrp11109")
screen = ScreenI()
screen.name = rstring("testChgrp11109")
link = screen.linkPlate(plate)
link = update.saveAndReturnObject(link)
# Now chgrp, should succeed
chgrp = Chgrp2(
targetObjects={"Plate": [link.child.id.val]}, groupId=target_gid)
self.doSubmit(chgrp, client)
# Check that the links have been destroyed
query = client.sf.getQueryService()
with pytest.raises(omero.ValidationException):
query.get("ScreenPlateLink", link.id.val, {"omero.group": "-1"})
def test_create_map_ann(self, ns, kw):
sess = MockSession()
self.mox.StubOutWithMock(sess.us, 'saveAndReturnObject')
map = {'a': rstring('1'), 'bb': rstring('cc')}
rid = 2
r = omero.model.MapAnnotationI()
if ns:
r.setNs(rstring(ns))
r.setMapValue(map)
r.setId(rlong(rid))
sess.us.saveAndReturnObject(mox.Func(
lambda o: o.getNs() == wrap(ns) and
o.getMapValue() == wrap(map).val)).AndReturn(r)
self.mox.ReplayAll()
ma = OmeroMetadata.MapAnnotations(sess, namespace=ns)
if kw:
assert ma.create_map_annkw(a='1', bb='cc') == rid
else:
assert ma.create_map_ann({'a': '1', 'bb': 'cc'}) == rid
self.mox.VerifyAll()
def getDatasetMap(self):
"""
Convert unique list of dataset names to a map
(dataset_name, dataset_object).
"""
dataset_map = {}
params = omero.sys.ParametersI()
params.add("pid", rlong(self.target_project_id))
for name in self.target_dataset_names:
params.add("dname", rstring(name))
dataset = self.query_service.findByQuery(
self.dataset_query, params)
if dataset is None:
print "Creating new datset"
dataset = omero.model.DatasetI()
dataset.setName(rstring(name))
dataset = \
self.update_service.saveAndReturnObject(dataset)
datasetId = dataset.getId().getValue()
print "\tNew dataset ID:", datasetId
link = omero.model.ProjectDatasetLinkI()
print "\tLinking dataset to:", self.target_project_id
link.parent = omero.model.ProjectI(
self.target_project_id, False)
link.child = omero.model.DatasetI(datasetId, False)
self.update_service.saveObject(link)
dataset = self.query_service.findByQuery(
self.dataset_query, params)
dataset_map[name] = dataset
return dataset_map
def test5793(self):
uuid = self.client.sf.getAdminService().getEventContext().sessionUuid
query = self.client.sf.getQueryService()
img = self.new_image(name="delete tagset test")
tag = omero.model.TagAnnotationI()
tag.textValue = rstring("tag %s" % uuid)
tag = self.client.sf.getUpdateService().saveAndReturnObject(tag)
img.linkAnnotation(tag)
img = self.client.sf.getUpdateService().saveAndReturnObject(img)
tagset = omero.model.TagAnnotationI()
tagset.textValue = rstring("tagset %s" % uuid)
tagset.linkAnnotation(tag)
tagset = self.client.sf.getUpdateService().saveAndReturnObject(tagset)
tag = tagset.linkedAnnotationList()[0]
command = omero.cmd.Delete("/Annotation", tagset.id.val, None)
handle = self.client.sf.submit(command)
self.waitOnCmd(self.client, handle)
assert not query.find("TagAnnotation", tagset.id.val)
assert tag.id.val == query.find("TagAnnotation", tag.id.val).id.val
def screen_plate_run_well(self):
"""
Returns a new OMERO Screen, linked Plate, linked Well, linked
WellSample, linked Image populate by an
L{test.integration.library.ITest} instance and
linked PlateAcquisition with all required fields set.
"""
screen = ScreenI()
screen.name = rstring(self.uuid())
plate = PlateI()
plate.name = rstring(self.uuid())
# Well A10 (will have two WellSamples)
well_a = WellI()
well_a.row = rint(0)
well_a.column = rint(9)
# Well A11 (will not have a WellSample)
well_b = WellI()
well_b.row = rint(0)
well_b.column = rint(10)
ws_a = WellSampleI()
image_a = self.new_image(name=self.uuid())
ws_a.image = image_a
ws_b = WellSampleI()
image_b = self.new_image(name=self.uuid())
ws_b.image = image_b
plate_acquisition = PlateAcquisitionI()
plate_acquisition.plate = plate
ws_a.plateAcquisition = plate_acquisition
ws_b.plateAcquisition = plate_acquisition
well_a.addWellSample(ws_a)
well_a.addWellSample(ws_b)
plate.addWell(well_a)
plate.addWell(well_b)
screen.linkPlate(plate)
return self.update.saveAndReturnObject(screen)
def plates(self):
"""Returns 2 new OMERO Plates with required fields set."""
plate = omero.model.PlateI()
plate.name = rstring("A_%s" % self.uuid())
plate2 = omero.model.PlateI()
plate2.name = rstring("B_%s" % self.uuid())
return self.update.saveAndReturnArray([plate, plate2])
def pix(self, x=10, y=10, z=10, c=3, t=50, client=None):
"""
Creates an int8 pixel of the given size in the database.
No data is written.
"""
image = self.new_image()
pixels = PixelsI()
pixels.sizeX = rint(x)
pixels.sizeY = rint(y)
pixels.sizeZ = rint(z)
pixels.sizeC = rint(c)
pixels.sizeT = rint(t)
pixels.sha1 = rstring("")
pixels.pixelsType = PixelsTypeI()
pixels.pixelsType.value = rstring("int8")
pixels.dimensionOrder = DimensionOrderI()
pixels.dimensionOrder.value = rstring("XYZCT")
image.addPixels(pixels)
if client is None:
client = self.client
update = client.sf.getUpdateService()
image = update.saveAndReturnObject(image)
pixels = image.getPrimaryPixels()
return pixels
def new_tag(self):
"""
Returns a new Tag objects
"""
tag = omero.model.TagAnnotationI()
tag.textValue = rstring(self.uuid())
tag.ns = rstring("pytest")
return self.sf.getUpdateService().saveAndReturnObject(tag)
def new_tag(request, itest, client):
"""
Returns a new Tag objects
"""
tag = omero.model.TagAnnotationI()
tag.textValue = rstring(itest.uuid())
tag.ns = rstring("pytest")
return client.getSession().getUpdateService().saveAndReturnObject(tag)
def project_with_datasets(project):
for dataset_id in range(1, 3):
o = DatasetI()
o.id = rlong(dataset_id)
o.name = rstring('dataset_name_%d' % dataset_id)
o.description = rstring('dataset_description_%d' % dataset_id)
project.linkDataset(o)
return project
def prep_directory(client, mrepo):
"""
Create an empty FS directory by performing an import and
then deleting the created fileset.
"""
from omero.cmd import Delete2, DoAll
from omero.grid import ImportSettings
from omero.model import ChecksumAlgorithmI
from omero.model import FilesetI
from omero.model import FilesetEntryI
from omero.model import UploadJobI
fs = FilesetI()
fs.linkJob(UploadJobI())
entry = FilesetEntryI()
entry.clientPath = rstring("README.txt")
fs.addFilesetEntry(entry)
settings = ImportSettings()
settings.checksumAlgorithm = ChecksumAlgorithmI()
settings.checksumAlgorithm.value = rstring("SHA1-160")
proc = mrepo.importFileset(fs, settings)
try:
tmp = create_path()
prx = proc.getUploader(0)
try:
tmp.write_text("THIS IS A PLACEHOLDER")
hash = client.sha1(tmp)
with open(tmp, "r") as source:
client.write_stream(source, prx)
finally:
prx.close()
tmp.remove()
handle = proc.verifyUpload([hash])
try:
req = handle.getRequest()
fs = req.activity.parent
finally:
handle.close()
dir = unwrap(mrepo.treeList(fs.templatePrefix.val))
oid = dir.items()[0][1].get("id")
ofile = client.sf.getQueryService().get("OriginalFile", oid)
delete1 = Delete2(targetObjects={"Fileset": [fs.id.val]})
delete2 = Delete2(targetObjects={"OriginalFile": [ofile.id.val]})
doall = DoAll()
doall.requests = [delete1, delete2]
cb = client.submit(doall)
cb.close(True)
finally:
proc.close()
return fs.templatePrefix.val
def dataset(self):
"""Returns a new OMERO Project with required fields set."""
dataset = DatasetI()
dataset.name = rstring(self.uuid())
return self.update.saveAndReturnObject(dataset)
ids = scriptParams["IDs"]
# dataType is 'Dataset' or 'Image' so we can use it directly in
# getObjects()
obs = conn.getObjects(dataType, ids) # generator of images or datasets
objects = list(obs)
return objects
if __name__ == "__main__":
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
dataTypes = [rstring('Dataset')] # only works on datasets
# Here we define the script name and description.
# Good practice to put url here to give users more guidance on how to run
# your script.
client = scripts.client(
'Key_Val_from_Description.py',
(" Adds key-value metadata pairs to images in a data set from "
" the description for a dataset or collections of datasets"
" k-v pairs taken from the dataset description"
" and by parsing the filename"
" Image IDs or by the Dataset IDs.\nSee"
" http://www.openmicroscopy.org/site/support/omero5.2/developers/"
"scripts/user-guide.html for the tutorial that uses this script."),
scripts.String("Data_Type",
optional=False,
def AddKeysToMatchingFiles(conn,
Id,
global_kv,
template,
file_keys,
spec_kv=None):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
dataset = conn.getObject("Dataset", Id)
# compile the regexp
if (template is not None):
template = "^{}$".format(template)
template = template.replace("*", "([^\s_\/]+)")
template = template.replace("?", "[^\s_\/]")
regexp = re.compile(template)
# add the metadata to the images
nimg = dataset.countChildren()
nimg_updated = 0
nkv_added = 0
for image in dataset.listChildren():
if (not (image.canAnnotate() and image.canLink())):
message = "You don't have permission to add annotations to {}".format(
image.getName())
client.setOutput("Message", rstring(message))
return
existing_kv = GetExistingMapAnnotions(image)
updated_kv = copy.deepcopy(existing_kv)
for key, vals in global_kv.items():
if key not in updated_kv: updated_kv[key] = set()
for val in vals:
updated_kv[key].add(val)
if (template is not None):
# apply the template to the file name
name = image.getName()
# this adds directory path to filename
# is probably better to extend name of file with path first
#path = os.path.dirname(image.getImportedImageFilePaths()['client_paths'][0])
#filename = path+"/"+name
filename = name
match = regexp.search(filename)
if (match is not None):
print("Match found", filename)
for i, val in enumerate(match.groups()):
i1 = i
if (i1 in file_keys):
key = file_keys[i1]
if key not in updated_kv: updated_kv[key] = set()
updated_kv[key].add(val)
if (spec_kv is not None):
for key, vals in spec_kv.items():
if key not in updated_kv: updated_kv[key] = set()
for val in vals:
updated_kv[key].add(val)
nold_i = sum(map(len, existing_kv.values()))
nnew_i = sum(map(len, updated_kv.values()))
nkv_added = nkv_added + (nnew_i + nold_i)
if (existing_kv != updated_kv):
RemoveMapAnnotations(conn, 'image', image.getId())
map_ann = omero.gateway.MapAnnotationWrapper(conn)
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
# namespace = "openmicroscopy.org/mapr/gene"
map_ann.setNs(namespace)
# convert the ordered dict to a list of lists
kv_list = []
for k, vset in updated_kv.items():
for v in vset:
kv_list.append([k, v])
map_ann.setValue(kv_list)
map_ann.save()
image.linkAnnotation(map_ann)
nimg_updated = nimg_updated + 1
return nimg_updated, nkv_added
def makeSingleImage(services, parameterMap, imageIds, dataset, colourMap):
"""
This takes the images specified by imageIds, sorts them in to Z,C,T
dimensions according to parameters in the parameterMap, assembles them
into a new Image, which is saved in dataset.
"""
if len(imageIds) == 0:
return
renderingEngine = services["renderingEngine"]
queryService = services["queryService"]
pixelsService = services["pixelsService"]
rawPixelStore = services["rawPixelStore"]
rawPixelStoreUpload = services["rawPixelStoreUpload"]
updateService = services["updateService"]
containerService = services["containerService"]
print "makeSingleImage: imageId count:", len(imageIds)
# Filter images by name if user has specified filter.
idNameMap = None
if "Filter_Names" in parameterMap:
filterString = parameterMap["Filter_Names"]
if len(filterString) > 0:
print "Filtering images for names containing '%s'" % filterString
idNameMap = getImageNames(queryService, imageIds)
imageIds = [
i for i in imageIds if idNameMap[i].find(filterString) > -1
]
imageId = imageIds[0]
# get pixels, with pixelsType, from the first image
query_string = "select p from Pixels p join fetch p.image i join "\
"fetch p.pixelsType pt where i.id='%d'" % imageId
pixels = queryService.findByQuery(query_string, None)
pixelsType = pixels.getPixelsType() # use the pixels type object we
# got from the first image.
# combined image will have same X and Y sizes...
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sourceZ = pixels.getSizeZ().getValue() # if we have a Z stack, use this
# in new image (don't combine Z)
# Now we need to find where our planes are coming from.
# imageMap is a map of destination:source, defined as (newX, newY,
# newZ):(imageId, z)
if "Manually_Define_Dimensions" in parameterMap and \
parameterMap["Manually_Define_Dimensions"]:
sizeZ, sizeC, sizeT, imageMap = manuallyAssignImages(
parameterMap, imageIds, sourceZ)
cNames = {}
else:
sizeZ, cNames, sizeT, imageMap = assignImagesByRegex(
parameterMap, imageIds, queryService, sourceZ, idNameMap)
sizeC = len(cNames)
print "sizeZ: %s sizeC: %s sizeT: %s" % (sizeZ, sizeC, sizeT)
if "Channel_Names" in parameterMap:
for c, name in enumerate(parameterMap["Channel_Names"]):
cNames[c] = name
imageName = "combinedImage"
description = "created from image Ids: %s" % imageIds
channelList = range(sizeC)
iId = pixelsService.createImage(sizeX, sizeY, sizeZ, sizeT, channelList,
pixelsType, imageName, description)
image = containerService.getImages("Image", [iId.getValue()], None)[0]
pixelsId = image.getPrimaryPixels().getId().getValue()
rawPixelStoreUpload.setPixelsId(pixelsId, True)
for theC in range(sizeC):
minValue = 0
maxValue = 0
for theZ in range(sizeZ):
for theT in range(sizeT):
if (theZ, theC, theT) in imageMap:
imageId, planeZ = imageMap[(theZ, theC, theT)]
print "Getting plane from Image ID:", imageId
query_string = "select p from Pixels p join fetch "\
"p.image i join fetch p.pixelsType pt where "\
"i.id='%d'" % imageId
pixels = queryService.findByQuery(query_string, None)
plane2D = getPlane(rawPixelStore, pixels, planeZ, 0, 0)
else:
print "Creating blank plane for theZ, theC, theT",\
theZ, theC, theT
plane2D = zeros((sizeY, sizeX))
print "Uploading plane: theZ: %s, theC: %s, theT: %s"\
% (theZ, theC, theT)
scriptUtil.uploadPlaneByRow(rawPixelStoreUpload, plane2D, theZ,
theC, theT)
minValue = min(minValue, plane2D.min())
maxValue = max(maxValue, plane2D.max())
print "Setting the min, max ", minValue, maxValue
pixelsService.setChannelGlobalMinMax(pixelsId, theC, float(minValue),
float(maxValue))
rgba = COLOURS["White"]
if theC in colourMap:
rgba = colourMap[theC]
print "Setting the Channel colour:", rgba
scriptUtil.resetRenderingSettings(renderingEngine, pixelsId, theC,
minValue, maxValue, rgba)
# rename new channels
pixels = renderingEngine.getPixels() # has channels loaded - (getting
# Pixels from image doesn't)
i = 0
for c in pixels.iterateChannels(): # c is an instance of
# omero.model.ChannelI
if i >= len(cNames):
break
lc = c.getLogicalChannel() # returns omero.model.LogicalChannelI
lc.setName(rstring(cNames[i]))
updateService.saveObject(lc)
i += 1
# put the image in dataset, if specified.
if dataset and dataset.canLink():
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(dataset.getId(), False)
link.child = omero.model.ImageI(image.id.val, False)
updateService.saveAndReturnObject(link)
else:
link = None
return image, link
class UserControl(UserGroupControl):
def _configure(self, parser):
self.exc = ExceptionHandler()
parser.add_login_arguments()
sub = parser.sub()
add = parser.add(sub, self.add, help="Add user")
add.add_argument("--ignore-existing",
action="store_true",
default=False,
help="Do not fail if user already exists")
add.add_argument("-m",
"--middlename",
help="Middle name, if available")
add.add_argument("-e", "--email")
add.add_argument("-i", "--institution")
# Capitalized since conflict with main values
add.add_argument("-a",
"--admin",
action="store_true",
help="Whether the user should be an admin")
add.add_argument("username", help="User's login name")
add.add_argument("firstname", help="User's first name")
add.add_argument("lastname", help="User's last name")
self.add_group_arguments(add, " to join")
password_group = add.add_mutually_exclusive_group()
password_group.add_argument("-P",
"--userpassword",
help="Password for user")
password_group.add_argument("--no-password",
action="store_true",
default=False,
help="Create user with empty password")
list = parser.add(sub,
self.list,
help="List information about all users")
info = parser.add(
sub, self.info,
"List information about the user(s). Default to the context user")
self.add_user_arguments(info)
for x in (list, info):
x.add_style_argument()
x.add_group_print_arguments()
x.add_user_sorting_arguments()
listgroups = parser.add(
sub, self.listgroups,
"List the groups of the user. Default to the context user")
self.add_user_arguments(listgroups)
listgroups.add_style_argument()
listgroups.add_user_print_arguments()
listgroups.add_group_sorting_arguments()
password = parser.add(sub, self.password, help="Set user's password")
password.add_argument("username",
nargs="?",
help="Username if not the current user")
email = parser.add(sub, self.email, help="List users' email addresses")
email.add_argument("-n",
"--names",
action="store_true",
default=False,
help="Print user names along with email addresses")
email.add_argument("-1",
"--one",
action="store_true",
default=False,
help="Print one user per line")
email.add_argument("-i",
"--ignore",
action="store_true",
default=False,
help="Ignore users without email addresses")
email.add_argument(
"--all",
action="store_true",
default=False,
help="Include all users, including deactivated accounts")
joingroup = parser.add(sub, self.joingroup, "Join one or more groups")
self.add_id_name_arguments(joingroup,
"user. Default to the current user")
group = self.add_group_arguments(joingroup, " to join")
group.add_argument("--as-owner",
action="store_true",
default=False,
help="Join the group(s) as an owner")
leavegroup = parser.add(sub, self.leavegroup,
"Leave one or more groups")
self.add_id_name_arguments(leavegroup,
"user. Default to the current user")
group = self.add_group_arguments(leavegroup, " to leave")
group.add_argument("--as-owner",
action="store_true",
default=False,
help="Leave the owner list of the group(s)")
for x in (email, password, list, add, joingroup, leavegroup):
x.add_login_arguments()
def format_name(self, exp):
record = ""
fn = _(exp.firstName)
mn = " "
if _(exp.middleName):
mn = " %s " % _(exp.middleName)
ln = _(exp.lastName)
record += "%s%s%s" % (fn, mn, ln)
return record
def email(self, args):
c = self.ctx.conn(args)
a = c.sf.getAdminService()
r = a.getSecurityRoles()
skipped = []
records = []
for exp in a.lookupExperimenters():
# Handle users without email
if not _(exp.email):
if not args.ignore:
skipped.append(exp)
continue
# Handle deactivated users
if not args.all:
groups = exp.linkedExperimenterGroupList()
group_ids = [x.id.val for x in groups]
if r.userGroupId not in group_ids:
continue
record = ""
if args.names:
record += '"%s"' % self.format_name(exp)
record += " <%s>" % _(exp.email)
else:
record += _(exp.email)
records.append(record)
if args.one:
for record in records:
self.ctx.out(record)
else:
self.ctx.out(", ".join(records))
if skipped:
self.ctx.err("Missing email addresses:")
for s in skipped:
self.ctx.err(self.format_name(s))
def password(self, args):
import omero
from omero.rtypes import rstring
client = self.ctx.conn(args)
own_name = self.ctx.get_event_context().userName
admin = client.sf.getAdminService()
# tickets 3202, 5841
own_pw = self._ask_for_password(" for your user (%s)" % own_name,
strict=False)
try:
client.sf.setSecurityPassword(own_pw)
self.ctx.out("Verified password.\n")
except omero.SecurityViolation, sv:
import traceback
self.ctx.die(456, "SecurityViolation: Bad credentials")
self.ctx.dbg(traceback.format_exc(sv))
if args.username:
try:
e = admin.lookupExperimenter(args.username)
except omero.ApiUsageException:
self.ctx.die(457, "Unknown user: %s" % args.username)
return # Never reached
self.ctx.out("Changing password for %s (id:%s)" %
(args.username, e.id.val))
else:
self.ctx.out("Changing password for %s" % own_name)
pw = self._ask_for_password(" to be set")
pw = rstring(pw)
if args.username:
admin.changeUserPassword(args.username, pw)
else:
admin.changePassword(pw)
self.ctx.out("Password changed")
def __init__(self, roicoord=ROICoordinate(), pointsList=(0, 0)):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
ShapeData.__init__(self)
self.points = rstring(self.listToString(pointsList))
self.setCoord(roicoord)
def processImage(conn, imageId, parameterMap):
"""
Process an image.
If imageStack is True, we make a Z-stack using one tile from each ROI (c=0)
Otherwise, we create a 5D image representing the ROI "cropping" the
original image. Image is put in a dataset if specified.
"""
createDataset = parameterMap['New_Dataset']
datasetName = parameterMap['New_Dataset_Name']
image = conn.getObject("Image", imageId)
if image is None:
return
parentDataset = image.getParent()
parentProject = parentDataset.getParent()
dataset = None
if not createDataset:
dataset = parentDataset
imageName = image.getName()
updateService = conn.getUpdateService()
pixels = image.getPrimaryPixels()
W = image.getSizeX()
H = image.getSizeY()
# note pixel sizes (if available) to set for the new images
physicalSizeX = pixels.getPhysicalSizeX()
physicalSizeY = pixels.getPhysicalSizeY()
physicalSizeZ = pixels.getPhysicalSizeZ()
# Store original channel details
cNames = []
emWaves = []
exWaves = []
for index, c in enumerate(image.getChannels()):
lc = c.getLogicalChannel()
cNames.append(str(c.getLabel()))
emWaves.append(lc.getEmissionWave())
exWaves.append(lc.getExcitationWave())
# x, y, w, h, zStart, zEnd, tStart, tEnd
rois = getRectangles(conn, image)
print "rois"
print rois
# Make a new 5D image per ROI
iIds = []
for index, r in enumerate(rois):
x, y, w, h, z1, z2, t1, t2 = r
# Bounding box
if x < 0:
x = 0
if y < 0:
y = 0
if x + w > W:
w = W - x
if y + h > H:
h = H - y
if parameterMap['Entire_Stack']:
if parameterMap['Z_Stack']:
z1 = 0
z2 = image.getSizeZ() - 1
if parameterMap['T_Stack']:
t1 = 0
t2 = image.getSizeT() - 1
print " ROI x: %s y: %s w: %s h: %s z1: %s z2: %s t1: %s t2: %s" % (
x, y, w, h, z1, z2, t1, t2)
# need a tile generator to get all the planes within the ROI
sizeZ = z2 - z1 + 1
sizeT = t2 - t1 + 1
sizeC = image.getSizeC()
zctTileList = []
tile = (x, y, w, h)
print "zctTileList..."
for z in range(z1, z2 + 1):
for c in range(sizeC):
for t in range(t1, t2 + 1):
zctTileList.append((z, c, t, tile))
def tileGen():
for i, t in enumerate(pixels.getTiles(zctTileList)):
yield t
print "sizeZ, sizeC, sizeT", sizeZ, sizeC, sizeT
description = """\
Created from Image ID: %d
Name: %s
x: %d y: %d w: %d h: %d""" % (imageId, imageName, x, y, w, h)
# make sure that script_utils creates a NEW rawPixelsStore
serviceFactory = conn.c.sf # noqa
newI = conn.createImageFromNumpySeq(tileGen(),
createImageName(imageName, index),
sizeZ=sizeZ,
sizeC=sizeC,
sizeT=sizeT,
description=description,
dataset=dataset)
iIds.append(newI.getId())
# Apply colors from the original image to the new one
if newI._prepareRenderingEngine():
renderingEngine = newI._re
# Apply the original channel names
newPixels = renderingEngine.getPixels()
for i, c in enumerate(newPixels.iterateChannels()):
lc = c.getLogicalChannel()
lc.setEmissionWave(emWaves[i])
lc.setExcitationWave(exWaves[i])
lc.setName(rstring(cNames[i]))
updateService.saveObject(lc)
renderingEngine.resetDefaultSettings(True)
# Apply the original pixel size - Get the object again to refresh state
newImg = conn.getObject("Image", newI.getId())
newPixels = newImg.getPrimaryPixels()
newPixels.setPhysicalSizeX(physicalSizeX)
newPixels.setPhysicalSizeY(physicalSizeY)
newPixels.setPhysicalSizeZ(physicalSizeZ)
newPixels.save()
if len(iIds) > 0 and createDataset:
# create a new dataset for new images
print "\nMaking Dataset '%s' of Images from ROIs of Image: %s" % (
datasetName, imageId)
dataset = omero.model.DatasetI()
dataset.name = rstring(datasetName)
desc = """\
Images in this Dataset are from ROIs of parent Image:
Name: %s
Image ID: %d""" % (imageName, imageId)
dataset.description = rstring(desc)
dataset = updateService.saveAndReturnObject(dataset)
for iid in iIds:
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(dataset.id.val, False)
link.child = omero.model.ImageI(iid, False)
updateService.saveObject(link)
if parentProject: # and put it in the current project
link = omero.model.ProjectDatasetLinkI()
link.parent = omero.model.ProjectI(parentProject.getId(), False)
link.child = omero.model.DatasetI(dataset.id.val, False)
updateService.saveAndReturnObject(link)
return len(iIds)
def processData(conn, scriptParams):
"""
For each Dataset, process each Image adding the length of each ROI line to
an OMERO.table.
Also calculate the average of all lines for each Image and add this as a
Double Annotation on Image.
"""
datasetIds = scriptParams['IDs']
for dataset in conn.getObjects("Dataset", datasetIds):
# first create our table...
# columns we want are: imageId, roiId, shapeId, theZ, theT,
# lineLength, shapetext.
columns = [
omero.grid.LongColumn('imageId', '', []),
omero.grid.RoiColumn('roidId', '', []),
omero.grid.LongColumn('shapeId', '', []),
omero.grid.LongColumn('theZ', '', []),
omero.grid.LongColumn('theT', '', []),
omero.grid.DoubleColumn('lineLength', '', []),
omero.grid.StringColumn('shapeText', '', 64, [])
]
# create and initialize the table
table = conn.c.sf.sharedResources().newTable(
1, "LineLengths%s" % str(random()))
table.initialize(columns)
# make a local array of our data (add it to table in one go)
imageIds = []
roiIds = []
shapeIds = []
theZs = []
theTs = []
lineLengths = []
shapeTexts = []
roiService = conn.getRoiService()
lengthsForImage = []
for image in dataset.listChildren():
result = roiService.findByImage(image.getId(), None)
for roi in result.rois:
for s in roi.copyShapes():
if type(s) == omero.model.LineI:
imageIds.append(image.getId())
roiIds.append(roi.getId().getValue())
shapeIds.append(s.getId().getValue())
theZs.append(s.getTheZ().getValue())
theTs.append(s.getTheT().getValue())
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
x = x1 - x2
y = y1 - y2
length = math.sqrt(math.pow(x, 2) + math.pow(y, 2))
lineLengths.append(length)
lengthsForImage.append(length)
if s.getTextValue():
shapeTexts.append(s.getTextValue().getValue())
else:
shapeTexts.append("")
if len(lengthsForImage) == 0:
print "No lines found on Image:", image.getName()
continue
imgAverage = sum(lengthsForImage) / len(lengthsForImage)
print ("Average length of line for Image: %s is %s"
% (image.getName(), imgAverage))
# Add the average as an annotation on each image.
lengthAnn = omero.model.DoubleAnnotationI()
lengthAnn.setDoubleValue(rdouble(imgAverage))
lengthAnn.setNs(
rstring("imperial.training.demo.lineLengthAverage"))
link = omero.model.ImageAnnotationLinkI()
link.setParent(omero.model.ImageI(image.getId(), False))
link.setChild(lengthAnn)
conn.getUpdateService().saveAndReturnObject(link)
lengthsForImage = [] # reset for next image.
# Prepare data for adding to OMERO table.
data = [
omero.grid.LongColumn('imageId', '', imageIds),
omero.grid.RoiColumn('roidId', '', roiIds),
omero.grid.LongColumn('shapeId', '', shapeIds),
omero.grid.LongColumn('theZ', '', theZs),
omero.grid.LongColumn('theT', '', theTs),
omero.grid.DoubleColumn('lineLength', '', lineLengths),
omero.grid.StringColumn('shapeText', '', 64, shapeTexts),
]
table.addData(data)
# get the table as an original file & attach this data to Dataset
orig_file = table.getOriginalFile()
fileAnn = omero.model.FileAnnotationI()
fileAnn.setFile(orig_file)
link = omero.model.DatasetAnnotationLinkI()
link.setParent(omero.model.DatasetI(dataset.getId(), False))
link.setChild(fileAnn)
# conn.getUpdateService().saveAndReturnObject(link)
a = array(lineLengths)
print "std", a.std()
print "mean", a.mean()
print "max", a.max()
print "min", a.min()
# lets retrieve all the lines that are longer than 2 standard
# deviations above mean
limit = a.mean() + (2 * a.std())
print "Retrieving all lines longer than: ", limit
rowCount = table.getNumberOfRows()
queryRows = table.getWhereList(
"lineLength > %s" % limit, variables={}, start=0, stop=rowCount,
step=0)
if len(queryRows) == 0:
print "No lines found"
else:
data = table.readCoordinates(queryRows)
for col in data.columns:
print "Query Results for Column: ", col.name
for v in col.values:
print " ", v
def attributes_by_attributes(conn,
name="Gene Symbol",
value="ASH2L",
ns="openmicroscopy.org/mapr/gene",
ns2="openmicroscopy.org/mapr/phenotype",
name2=None):
"""
Return a list of neighbours attributes
for given case insensitive attribute value.
"""
from omero.rtypes import rstring, rlist, unwrap
from omero.sys import ParametersI
params = ParametersI()
params.addString("value", value.lower())
q = ("select distinct new map( mv.value as value) "
"from Annotation as a "
"join a.mapValue as mv "
"where lower(mv.value) = :value {where_claus}")
where_claus = []
if name:
params.addString("name", name)
where_claus.append("and mv.name = :name")
q = q.format(**{'where_claus': " ".join(where_claus)})
values = [
v[0]['value']
for v in unwrap(conn.getQueryService().projection(q, params))
]
params = ParametersI()
valuelist = [rstring(unicode(v)) for v in values]
params.add('values', rlist(valuelist))
params.addString("ns", ns)
params.addString("ns2", ns2)
q = ("select distinct new map("
"mv.name as name, "
"mv.value as value, "
"mv2.name as name2, "
"mv2.value as value2) "
"from Image as i "
"join i.annotationLinks as ial "
"join i.annotationLinks as ial2 "
"join ial.child as a "
"join a.mapValue as mv "
"join ial2.child as a2 "
"join a2.mapValue as mv2 "
"where a.ns = :ns and a2.ns = :ns2 "
"and mv.value in (:values) {where_claus}")
where_claus = []
if name:
params.addString("name", name)
where_claus.append("and mv.name = :name")
if name2:
params.addString("name2", name2)
where_claus.append("and mv2.name = :name2")
q = q.format(**{'where_claus': " ".join(where_claus)})
res = {}
for r in unwrap(conn.getQueryService().projection(q, params)):
r = r[0]
try:
res[(r['name'], r['value'])].append((r['name2'], r['value2']))
except KeyError:
res[(r['name'], r['value'])] = [(r['name2'], r['value2'])]
return res
(theZ, theT, x, y, width, height)
# create an ROI, link it to Image
roi = omero.model.RoiI()
roi.setImage(image._obj
) # use the omero.model.ImageI that underlies the 'image' wrapper
# create a rectangle shape and add to ROI
rect = omero.model.RectI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(width)
rect.height = rdouble(height)
rect.theZ = rint(theZ)
rect.theT = rint(theT)
rect.textValue = rstring("test-Rectangle")
roi.addShape(rect)
# create an Ellipse shape and add to ROI
ellipse = omero.model.EllipseI()
ellipse.cx = rdouble(y)
ellipse.cy = rdouble(x)
ellipse.rx = rdouble(width)
ellipse.ry = rdouble(height)
ellipse.theZ = rint(theZ)
ellipse.theT = rint(theT)
ellipse.textValue = rstring("test-Ellipse")
roi.addShape(ellipse)
# Save the ROI (saves any linked shapes too)
r = updateService.saveAndReturnObject(roi)
def project(self):
"""Returns a new OMERO Project with required fields set."""
project = ProjectI()
project.name = rstring(self.uuid())
return self.update.saveAndReturnObject(project)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from omero.rtypes import rstring, rbool, rlong, rint
s = rstring("value")
b = rbool(True)
l = rlong(1)
i = rint(1)
def add(self, args):
email = args.email
login = args.username
first = args.firstname
middle = args.middlename
last = args.lastname
inst = args.institution
pasw = args.userpassword
import omero
from omero.rtypes import rbool, rstring
from omero_model_ExperimenterI import ExperimenterI as Exp
from omero_model_ExperimenterGroupI import ExperimenterGroupI as Grp
c = self.ctx.conn(args)
e = Exp()
e.omeName = rstring(login)
e.firstName = rstring(first)
e.lastName = rstring(last)
e.middleName = rstring(middle)
e.email = rstring(email)
e.institution = rstring(inst)
e.ldap = rbool(False)
# Fail-fast if no-password is passed and the server does not accept
# empty passwords
configService = c.getSession().getConfigService()
password_required = configService.getConfigValue(
"omero.security.password_required").lower()
if args.no_password and password_required != 'false':
self.ctx.die(
502, "Server does not allow user creation with empty"
" passwords")
# Check user existence
admin = c.getSession().getAdminService()
try:
usr = admin.lookupExperimenter(login)
if usr:
if args.ignore_existing:
self.ctx.out("User exists: %s (id=%s)" %
(login, usr.id.val))
return
else:
self.ctx.die(
3, "User exists: %s (id=%s)" % (login, usr.id.val))
except omero.ApiUsageException:
pass # Apparently no such user exists
[gid, groups] = self.list_groups(admin, args, use_context=False)
roles = admin.getSecurityRoles()
groups.append(Grp(roles.userGroupId, False))
if args.admin:
groups.append(Grp(roles.systemGroupId, False))
group = groups.pop(0)
try:
if args.no_password:
id = admin.createExperimenter(e, group, groups)
self.ctx.out("Added user %s (id=%s) without password" %
(login, id))
else:
if pasw is None:
pasw = self._ask_for_password(" for your new user (%s)" %
login,
strict=True)
id = admin.createExperimenterWithPassword(
e, rstring(pasw), group, groups)
self.ctx.out("Added user %s (id=%s) with password" %
(login, id))
except omero.ValidationException, ve:
# Possible, though unlikely after previous check
if self.exc.is_constraint_violation(ve):
self.ctx.die(66, "User already exists: %s" % login)
else:
self.ctx.die(67,
"Unknown ValidationException: %s" % ve.message)
def setFillSettings(self, colour):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
self.fillColour = rstring(colour)
# code) into the point indicated below.
# A more complete template, for 'real-world' scripts, is also included in this
# folder
# This script takes an Image ID as a parameter from the scripting service.
from omero.rtypes import rlong, rstring, unwrap
from omero.gateway import BlitzGateway
import omero
import omero.scripts as scripts
# Script definition
# Script name, description and 2 parameters are defined here.
# These parameters will be recognised by the Insight and web clients and
# populated with the currently selected Image(s)
dataTypes = [rstring('Project')]
client = scripts.client(
"Write_Data-4.py",
"""Downloads a named file annotation on a Project""",
# first parameter
scripts.String("Data_Type",
optional=False,
values=dataTypes,
default="Project"),
# second parameter
scripts.List("IDs", optional=False).ofType(rlong(0)),
scripts.String("File_Name", optional=False),
)
# we can now create our Blitz Gateway by wrapping the client object
conn = BlitzGateway(client_obj=client)
def testObjectCreationEqualsAndHash(self):
# RBool
true1 = rbool(True)
true2 = rbool(True)
false1 = rbool(False)
false2 = rbool(False)
assert true1 == true2
assert false1 == false2
assert true1.getValue()
assert not false1.getValue()
assert true1 == true2
assert true1 != false1
# RDouble
double_zero1 = rdouble(0.0)
double_zero2 = rdouble(0.0)
double_notzero1 = rdouble(1.1)
double_notzero1b = rdouble(1.1)
double_notzero2 = rdouble(2.2)
assert double_zero1.getValue() == 0.0
assert double_notzero1.getValue() == 1.1
assert double_zero1 == double_zero2
assert double_zero1 != double_notzero1
assert double_notzero1 == double_notzero1b
assert double_notzero1 != double_notzero2
# RFloat
float_zero1 = rfloat(0.0)
float_zero2 = rfloat(0.0)
float_notzero1 = rfloat(1.1)
float_notzero1b = rfloat(1.1)
float_notzero2 = rfloat(2.2)
assert float_zero1.getValue() == 0.0
assert float_notzero1.getValue() == 1.1
assert float_zero1 == float_zero2
assert float_zero1 != float_notzero1
assert float_notzero1 == float_notzero1b
assert float_notzero1 != float_notzero2
# RInt
int_zero1 = rint(0)
int_zero2 = rint(0)
int_notzero1 = rint(1)
int_notzero1b = rint(1)
int_notzero2 = rint(2)
assert int_zero1.getValue() == 0
assert int_notzero1.getValue() == 1
assert int_zero1 == int_zero2
assert int_zero1 != int_notzero1
assert int_notzero1 == int_notzero1b
assert int_notzero1 != int_notzero2
# RLong
long_zero1 = rlong(0)
long_zero2 = rlong(0)
long_notzero1 = rlong(1)
long_notzero1b = rlong(1)
long_notzero2 = rlong(2)
assert long_zero1.getValue() == 0
assert long_notzero1.getValue() == 1
assert long_zero1 == long_zero2
assert long_zero1 != long_notzero1
assert long_notzero1 == long_notzero1b
assert long_notzero1 != long_notzero2
# RTime
time_zero1 = rtime(0)
time_zero2 = rtime(0)
time_notzero1 = rtime(1)
time_notzero1b = rtime(1)
time_notzero2 = rtime(2)
assert time_zero1.getValue() == 0
assert time_notzero1.getValue() == 1
assert time_zero1 == time_zero2
assert time_zero1 != time_notzero1
assert time_notzero1 == time_notzero1b
assert time_notzero1 != time_notzero2
# RInternal
internal_null1 = rinternal(None)
internal_null2 = rinternal(None)
internal_notnull1 = rinternal(omero.grid.JobParams())
internal_notnull2 = rinternal(omero.grid.JobParams())
assert internal_null1 == internal_null2
assert internal_null1 == internal_null2
assert internal_null1 != internal_notnull2
assert internal_notnull1 == internal_notnull1
assert internal_notnull1 != internal_notnull2
# RObject
object_null1 = robject(None)
object_null2 = robject(None)
object_notnull1 = robject(omero.model.ImageI())
object_notnull2 = robject(omero.model.ImageI())
assert object_null1 == object_null2
assert object_null1 == object_null2
assert object_null1 != object_notnull2
assert object_notnull1 == object_notnull1
assert object_notnull1 != object_notnull2
# RString
string_null1 = rstring(None)
string_null2 = rstring(None)
string_notnull1 = rstring("str1")
string_notnull1b = rstring("str1")
string_notnull2 = rstring("str2")
assert string_null1 == string_null2
assert string_null1 == string_null2
assert string_null1 != string_notnull2
assert string_notnull1 == string_notnull1
assert string_notnull1 != string_notnull2
assert string_notnull1 == string_notnull1b
# RClass
class_null1 = rclass(None)
class_null2 = rclass(None)
class_notnull1 = rclass("str1")
class_notnull1b = rclass("str1")
class_notnull2 = rclass("str2")
assert class_null1 == class_null2
assert class_null1 == class_null2
assert class_null1 != class_notnull2
assert class_notnull1 == class_notnull1
assert class_notnull1 != class_notnull2
assert class_notnull1 == class_notnull1b
def copy_image_and_metadata(im, conn):
"""
Copy an image
im: The image
conn: The connection object, possibly on a different server
"""
sizeZ = im.getSizeZ()
sizeC = im.getSizeC()
sizeT = im.getSizeT()
zctList = [(z,c,t) for z in range(sizeZ) for c in range(sizeC)
for t in range(sizeT)]
def planeGen():
planes = im.getPrimaryPixels().getPlanes(zctList)
for p in planes:
yield p
d = im.getDescription()
newim = conn.createImageFromNumpySeq(
planeGen(), im.getName(), sizeZ=sizeZ, sizeC=sizeC, sizeT=sizeT)
#qs = conn.getQueryService()
#px = qs.get('Pixels', newim.getPrimaryPixels().id)
#params = omero.sys.Parameters()
#params.map = { 'id': wrap(px.id) }
#channels = qs.findAllByQuery(
# "SELECT c from Channel c "
# "join fetch c.pixels as p "
# "where p.id = :id", params)
us = conn.getUpdateService()
px_exc = [
'AnnotationLinksCountPerOwner',
'Channel',
'Image',
'PixelsFileMapsCountPerOwner',
'PixelsType',
'PrimaryChannel',
'RelatedTo',
'Sha1',
'SizeC',
'SizeT',
'SizeX',
'SizeY',
'SizeZ',
]
newim = conn.getObject('Image', newim.id)
newpx = newim.getPrimaryPixels()
copy_set_get(im.getPrimaryPixels()._obj, newpx._obj, exclude=px_exc)
newpx = us.saveAndReturnObject(newpx._obj)
ch_exc = [
'AnnotationLinksCountPerOwner',
'LogicalChannel',
'Pixels',
'StatsInfo',
]
lc_exc = ['DetectorSettings']
for c in xrange(sizeC):
newim = conn.getObject('Image', newim.id)
chsrc = im.getChannels()[c]
chdst = newim.getChannels()[c]
copy_set_get(chsrc._obj, chdst._obj, exclude=ch_exc)
us.saveAndReturnObject(chdst._obj)
lchsrc = chsrc.getLogicalChannel()
lchdst = chdst.getLogicalChannel()
copy_set_get(lchsrc._obj, lchdst._obj, exclude=lc_exc)
us.saveAndReturnObject(lchdst._obj)
desc = add_source_to_description(im, im.getDescription())
newim.setDescription(rstring(desc))
us.saveAndReturnObject(newim._obj)
return newim
def testPassThroughNoneAndRTypes(self):
"""
To prevent having to check for isintance(int,...) or
isintance(RInt,...) all over the place, the static methods
automatically check for acceptable
types and simply pass them through. Similarly, the primitive types all
check for None and return a null RType if necessary.
"""
# Bool
assert None == rbool(None)
assert rbool(True) == rbool(rbool(True))
assert rbool(True) == rbool(1)
assert rbool(False) == rbool(0)
# Double
assert None == rdouble(None)
assert rdouble(0.0) == rdouble(rdouble(0.0))
assert rdouble(0.0) == rdouble(rdouble(0))
assert rdouble(0.0) == rdouble(rdouble("0.0"))
pytest.raises(ValueError, lambda: rdouble("string"))
# Float
assert None == rfloat(None)
assert rfloat(0.0) == rfloat(rfloat(0.0))
assert rfloat(0.0) == rfloat(rfloat(0))
assert rfloat(0.0) == rfloat(rfloat("0.0"))
pytest.raises(ValueError, lambda: rfloat("string"))
# Long
assert None == rlong(None)
assert rlong(0) == rlong(rlong(0))
assert rlong(0) == rlong(rlong(0.0))
assert rlong(0) == rlong(rlong("0"))
pytest.raises(ValueError, lambda: rlong("string"))
# Time
assert None == rtime(None)
assert rtime(0) == rtime(rtime(0))
assert rtime(0) == rtime(rtime(0.0))
assert rtime(0) == rtime(rtime("0"))
pytest.raises(ValueError, lambda: rtime("string"))
# Int
assert None == rint(None)
assert rint(0) == rint(rint(0))
assert rint(0) == rint(rint(0.0))
assert rint(0) == rint(rint("0"))
pytest.raises(ValueError, lambda: rint("string"))
#
# Starting here handling of null is different.
#
# String
assert rstring("") == rstring(None)
assert rstring("a") == rstring(rstring("a"))
assert rstring("0") == rstring(0)
# Class
assert rclass("") == rclass(None)
assert rclass("c") == rclass(rclass("c"))
pytest.raises(ValueError, lambda: rclass(0))
# Internal
internal = omero.Internal()
assert rinternal(None) == rinternal(None)
assert rinternal(internal) == rinternal(rinternal(internal))
pytest.raises(ValueError, lambda: rinternal("string"))
# Object
obj = omero.model.ImageI()
assert robject(None) == robject(None)
assert robject(obj) == robject(robject(obj))
pytest.raises(ValueError, lambda: robject("string"))
#
# Same does not hold for collections
#
# Array
assert rarray([]) == rarray(None)
# assert rarray(obj) == rarray(rarray(obj))
# pytest.raises(ValueError, lambda : rarray("string"))
# List
assert rlist([]) == rlist(None)
# assert rlist(obj) == rlist(rlist(obj))
# pytest.raises(ValueError, lambda : rlist("string"))
# Set
assert rset([]) == rset(None)
# assert rset(obj) == rset(rset(obj))
# pytest.raises(ValueError, lambda : rset("string"))
# Map
assert rmap({}) == rmap(None)
green = np_array[::, ::, 1]
blue = np_array[::, ::, 2]
plane_gen = iter([red, green, blue])
plot_name = image.getName() + "_FRAP_plot"
i = conn.createImageFromNumpySeq(plane_gen, plot_name, sizeC=3,
dataset=image.getParent())
frap_plots.append(i)
else:
# If not plot, simply return input image
frap_plots.append(image)
return frap_plots
if __name__ == "__main__":
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client(
'Simple FRAP.py',
"""
This script does simple FRAP analysis using Ellipse ROIs previously
saved on images. If matplotlib is installed, data is plotted and new
OMERO images are created from the plots.
""",
scripts.String(
"Data_Type", optional=False, grouping="1",
description="Choose source of images",
values=dataTypes, default="Dataset"),
scripts.List(
"IDs", optional=False, grouping="2",
description="Dataset or Image IDs.").ofType(rlong(0)),
def __init__(self, roicoord=ROICoordinate(), pointsList=(0, 0)):
ShapeData.__init__(self)
self.points = rstring(self.listToString(pointsList))
self.setCoord(roicoord)
def AddMapAnnotations(conn, dtype, Id):
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
'''
* Reads information from the 'Dataset Details' field,
* constructs key-val data
* attaches it to the dataset and the images contained in it
'''
dataset = conn.getObject(dtype, int(Id))
if (not (dataset.canAnnotate() and dataset.canLink())):
message = "You don't have permission to add annotations to {}".format(
dataset.getName())
client.setOutput("Message", rstring(message))
return
description = dataset.getDescription().splitlines()
modes = {
"Summary": "default",
"global key-value": "global",
"filename key-value": "filename",
"end key-value": "default"
}
mode = 'default'
global_kv = OrderedDict() # stores the global key value pairs
file_keys = OrderedDict() # stores the 'slot' and key for the file keys
spec_kv = OrderedDict() # stores the file specific kv's
template = None
nimg_updated = 0
nkv_updated = 0
for line in description:
# 1. See if this is a mode string
match = re.search("^#\s*(\S+\s+\S+)", line.lower())
if (match is not None and match.group(1) in modes):
value = modes[match.group(1)]
# start a new filename block
if (mode != 'filename' and value == 'filename'):
file_keys = OrderedDict()
spec_kv = OrderedDict()
template = None
# end a filename block
if (mode == 'filename' and value != 'filename'):
print("Trigger parse fileanames")
print(spec_kv)
nimg_up, nadd = AddKeysToMatchingFiles(conn, Id, OrderedDict(),
template, file_keys,
spec_kv)
print("filename {} {}".format(nimg_up, nadd))
nimg_updated = nimg_updated + nimg_up
nkv_updated = nkv_updated + nadd
# end a global block
if (mode == 'global' and value != 'global'):
# Add globals to all the images
nimg_up, nadd = AddKeysToMatchingFiles(conn, Id, global_kv,
None, file_keys)
print("Global: {} {}".format(nimg_up, nadd))
nimg_updated = nimg_updated + nimg_up
nkv_updated = nkv_updated + nadd
mode = value
if (mode == 'default'):
pass
if (mode == 'global'):
# split the line for the kay value pair
match = re.search("^\s*(\S+)\s*:\s*(.*)", line)
if (match is not None):
key = match.group(1)
val = match.group(2)
if (key not in global_kv): global_kv[key] = set()
global_kv[key].add(val)
if (mode == 'filename'):
# the template
match = re.search("^\s*(\S+)\s+(\S+)", line)
if (match and (match.group(1).lower() == 'template')):
template = match.group(2)
print("New template {}".format(template))
# file templated kvs
# Start line
# | /----white space
# | |full stop|
# V V V V
match = re.search("^\s*(\d)\.\s+(\S+)", line)
# ^ ^
# position key
if (match is not None):
i = int(match.group(1)) - 1
file_keys[i] = match.group(2)
# file specific kvs
match = re.search("^\s*(\S+)\s*:\s*(\S+)", line)
if (match is not None):
key = match.group(1)
val = match.group(2)
if (key not in spec_kv): spec_kv[key] = set()
spec_kv[key].add(val)
# now add the key value pairs to the dataset
existing_kv = GetExistingMapAnnotions(dataset)
if (existing_kv != global_kv):
RemoveMapAnnotations(conn, 'dataset', dataset.getId())
map_ann = omero.gateway.MapAnnotationWrapper(conn)
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
# namespace = "openmicroscopy.org/mapr/gene"
map_ann.setNs(namespace)
# convert the ordered dict to a list of lists
kv_list = []
for k, vset in global_kv.items():
for v in vset:
kv_list.append([k, v])
map_ann.setValue(kv_list)
map_ann.save()
dataset.linkAnnotation(map_ann)
# add the metadata to the images
if (True):
#AddKeysToMatchingFiles( conn, Id, global_kv, template, file_keys )
return "Added a total of {} kv pairs to {}/{} files ".format(
nkv_updated, nimg_updated, len(list(dataset.listChildren())))
else:
nimg = dataset.countChildren()
nimg_updated = 0
nkv_tot = 0
for image in dataset.listChildren():
if (not (image.canAnnotate() and image.canLink())):
message = "You don't have permission to add annotations to {}".format(
image.getName())
client.setOutput("Message", rstring(message))
return
existing_kv = GetExistingMapAnnotions(image)
updated_kv = copy.deepcopy(global_kv)
if (template is not None):
# apply the template to the file name
name = image.getName()
path = os.path.dirname(
image.getImportedImageFilePaths()['client_paths'][0])
filename = path + "/" + name
match = regexp.search(filename)
if (match is not None):
for i, val in enumerate(match.groups()):
i1 = i + 1
if (i1 in file_keys):
key = file_keys[i1]
if key not in updated_kv: updated_kv[key] = set()
updated_kv[key].add(val)
print("existing_kv")
for k, v in existing_kv.items():
print(" {} : {}".format(k, v))
print("updated_kv")
for k, v in updated_kv.items():
print(" {} : {}".format(k, v))
print("Are they the same?", existing_kv == updated_kv)
if (existing_kv != updated_kv):
print("The key-values pairs are different")
RemoveMapAnnotations(conn, 'image', image.getId())
map_ann = omero.gateway.MapAnnotationWrapper(conn)
# namespace ="openmicroscopy.org/mapr/gene"
map_ann.setNs(namespace)
print("Namespace")
print(map_ann)
# convert the ordered dict to a list of lists
kv_list = []
for k, vset in updated_kv.items():
for v in vset:
kv_list.append([k, v])
map_ann.setValue(kv_list)
map_ann.save()
image.linkAnnotation(map_ann)
nimg_updated = nimg_updated + 1
nkv_tot = nkv_tot + len(updated_kv) - len(existing_kv)
return "Added a total of {} kv pairs to {}/{} files ".format(
nkv_tot, nimg_updated, nimg)
def setFillSettings(self, colour):
self.fillColour = rstring(colour)
def run_script():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
ckeys = COLOURS.keys()
ckeys.sort()
c_options = [rstring(col) for col in ckeys]
data_types = [rstring('Dataset'), rstring('Image')]
first_dim = [rstring('Time'), rstring('Channel'), rstring('Z')]
extra_dims = [
rstring(''),
rstring('Time'),
rstring('Channel'),
rstring('Z')
]
channel_regs = [rstring(r) for r in channel_regexes.keys()]
z_regs = [rstring(r) for r in z_regexes.keys()]
t_regs = [rstring(r) for r in time_regexes.keys()]
client = scripts.client(
'Combine_Images.py',
"""Combine several single-plane images (or Z-stacks) into one with \
greater Z, C, T dimensions.
See http://help.openmicroscopy.org/scripts.html""",
scripts.String(
"Data_Type",
optional=False,
grouping="1",
description="Use all the images in specified 'Datasets' or choose"
" individual 'Images'.",
values=data_types,
default="Image"),
scripts.List("IDs",
optional=False,
grouping="2",
description="List of Dataset IDs or Image IDs to "
"combine.").ofType(rlong(0)),
scripts.String(
"Filter_Names",
grouping="2.1",
description="Filter the images by names that contain this value"),
scripts.Bool(
"Auto_Define_Dimensions",
grouping="3",
default=True,
description="""Choose new dimensions with respect to the order of"
" the input images. See URL above."""),
scripts.String(
"Channel_Name_Pattern",
grouping="3.1",
default=DEFAULT_C_REGEX,
values=channel_regs,
description="""Auto-pick images by channel in the image name"""),
scripts.String(
"Z_Name_Pattern",
grouping="3.2",
default=DEFAULT_Z_REGEX,
values=z_regs,
description="""Auto-pick images by Z-index in the image name"""),
scripts.String(
"Time_Name_Pattern",
grouping="3.3",
default=DEFAULT_T_REGEX,
values=t_regs,
description="""Auto-pick images by T-index in the image name"""),
scripts.Bool(
"Manually_Define_Dimensions",
grouping="4",
default=False,
description="""Choose new dimensions with respect to the order of"
" the input images. See URL above."""),
scripts.String("Dimension_1",
grouping="4.1",
description="The first Dimension to change",
values=first_dim),
scripts.String(
"Dimension_2",
grouping="4.2",
values=extra_dims,
default="",
description="The second Dimension to change. Only specify this if"
" combining multiple dimensions."),
scripts.String(
"Dimension_3",
grouping="4.3",
values=extra_dims,
default="",
description="The third Dimension to change. Only specify this if"
" combining multiple dimensions."),
scripts.Int("Size_Z",
grouping="4.4",
description="Number of Z planes in new image",
min=1),
scripts.Int("Size_C",
grouping="4.5",
description="Number of channels in new image",
min=1),
scripts.Int("Size_T",
grouping="4.6",
description="Number of time-points in new image",
min=1),
scripts.List("Channel_Colours",
grouping="7",
description="List of Colors for channels.",
default="White",
values=c_options).ofType(rstring("")),
scripts.List(
"Channel_Names",
grouping="8",
description="List of Names for channels in the new image."),
version="4.2.0",
authors=["William Moore", "OME Team"],
institutions=["University of Dundee"],
contact="*****@*****.**",
)
try:
parameter_map = client.getInputs(unwrap=True)
conn = BlitzGateway(client_obj=client)
# create the combined image
images, message = combine_images(conn, parameter_map)
client.setOutput("Message", rstring(message))
if images:
if len(images) == 1:
client.setOutput("Combined_Image", robject(images[0]))
elif len(images) > 1:
client.setOutput("First_Image", robject(images[0]))
finally:
client.closeSession()
def make_single_image(services, parameter_map, image_ids, dataset, colour_map):
"""
This takes the images specified by image_ids, sorts them in to Z,C,T
dimensions according to parameters in the parameter_map, assembles them
into a new Image, which is saved in dataset.
"""
if len(image_ids) == 0:
return
rendering_engine = services["renderingEngine"]
query_service = services["queryService"]
pixels_service = services["pixelsService"]
raw_pixel_store = services["rawPixelStore"]
raw_pixel_store_upload = services["rawPixelStoreUpload"]
update_service = services["updateService"]
container_service = services["containerService"]
# Filter images by name if user has specified filter.
id_name_map = None
if "Filter_Names" in parameter_map:
filter_string = parameter_map["Filter_Names"]
if len(filter_string) > 0:
id_name_map = get_image_names(query_service, image_ids)
image_ids = [
i for i in image_ids if id_name_map[i].find(filter_string) > -1
]
image_id = image_ids[0]
# get pixels, with pixelsType, from the first image
query_string = "select p from Pixels p join fetch p.image i join "\
"fetch p.pixelsType pt where i.id='%d'" % image_id
pixels = query_service.findByQuery(query_string, None)
# use the pixels type object we got from the first image.
pixels_type = pixels.getPixelsType()
# combined image will have same X and Y sizes...
size_x = pixels.getSizeX().getValue()
size_y = pixels.getSizeY().getValue()
# if we have a Z stack, use this in new image (don't combine Z)
source_z = pixels.getSizeZ().getValue()
# Now we need to find where our planes are coming from.
# imageMap is a map of destination:source, defined as (newX, newY,
# newZ):(imageId, z)
if "Manually_Define_Dimensions" in parameter_map and \
parameter_map["Manually_Define_Dimensions"]:
size_z, size_c, size_t, image_map = manually_assign_images(
parameter_map, image_ids, source_z)
c_names = {}
else:
size_z, c_names, size_t, image_map = assign_images_by_regex(
parameter_map, image_ids, query_service, source_z, id_name_map)
size_c = len(c_names)
if "Channel_Names" in parameter_map:
for c, name in enumerate(parameter_map["Channel_Names"]):
c_names[c] = name
image_name = "combinedImage"
description = "created from image Ids: %s" % image_ids
channel_list = range(size_c)
iid = pixels_service.createImage(size_x, size_y, size_z, size_t,
channel_list, pixels_type, image_name,
description)
image = container_service.getImages("Image", [iid.getValue()], None)[0]
pixels_id = image.getPrimaryPixels().getId().getValue()
raw_pixel_store_upload.setPixelsId(pixels_id, True)
pixel_sizes = {'x': [], 'y': []}
for the_c in range(size_c):
min_value = 0
max_value = 0
for the_z in range(size_z):
for the_t in range(size_t):
if (the_z, the_c, the_t) in image_map:
image_id, plane_z = image_map[(the_z, the_c, the_t)]
query_string = "select p from Pixels p join fetch "\
"p.image i join fetch p.pixelsType pt where "\
"i.id='%d'" % image_id
pixels = query_service.findByQuery(query_string, None)
plane_2d = get_plane(raw_pixel_store, pixels, plane_z, 0,
0)
# Note pixels sizes (may be None)
pixel_sizes['x'].append(pixels.getPhysicalSizeX())
pixel_sizes['y'].append(pixels.getPhysicalSizeY())
else:
plane_2d = zeros((size_y, size_x))
script_utils.upload_plane_by_row(raw_pixel_store_upload,
plane_2d, the_z, the_c, the_t)
min_value = min(min_value, plane_2d.min())
max_value = max(max_value, plane_2d.max())
pixels_service.setChannelGlobalMinMax(pixels_id,
the_c, float(min_value),
float(max_value))
rgba = COLOURS["White"]
if the_c in colour_map:
rgba = colour_map[the_c]
script_utils.reset_rendering_settings(rendering_engine, pixels_id,
the_c, min_value, max_value,
rgba)
# rename new channels
pixels = rendering_engine.getPixels()
# has channels loaded - (getting Pixels from image doesn't)
i = 0
for c in pixels.iterateChannels():
# c is an instance of omero.model.ChannelI
if i >= len(c_names):
break
lc = c.getLogicalChannel() # returns omero.model.LogicalChannelI
lc.setName(rstring(c_names[i]))
update_service.saveObject(lc)
i += 1
# Set pixel sizes if known
pix_size_x = pick_pixel_sizes(pixel_sizes['x'])
pix_size_y = pick_pixel_sizes(pixel_sizes['y'])
if pix_size_x is not None or pix_size_y is not None:
# reload to avoid OptimisticLockException
pixels = services["queryService"].get('Pixels',
pixels.getId().getValue())
if pix_size_x is not None:
pixels.setPhysicalSizeX(pix_size_x)
if pix_size_y is not None:
pixels.setPhysicalSizeY(pix_size_y)
services["updateService"].saveObject(pixels)
# put the image in dataset, if specified.
if dataset and dataset.canLink():
link = omero.model.DatasetImageLinkI()
link.parent = omero.model.DatasetI(dataset.getId(), False)
link.child = omero.model.ImageI(image.getId().getValue(), False)
update_service.saveAndReturnObject(link)
else:
link = None
return image, link
def add(self, args):
email = args.email
login = args.username
first = args.firstname
middle = args.middlename
last = args.lastname
inst = args.institution
pasw = args.userpassword
import omero
from omero.rtypes import rstring
from omero_model_ExperimenterI import ExperimenterI as Exp
from omero_model_ExperimenterGroupI import ExperimenterGroupI as Grp
c = self.ctx.conn(args)
e = Exp()
e.omeName = rstring(login)
e.firstName = rstring(first)
e.lastName = rstring(last)
e.middleName = rstring(middle)
e.email = rstring(email)
e.institution = rstring(inst)
admin = c.getSession().getAdminService()
try:
usr = admin.lookupExperimenter(login)
if usr:
if args.ignore_existing:
self.ctx.out("User exists: %s (id=%s)"
% (login, usr.id.val))
return
else:
self.ctx.die(3, "User exists: %s (id=%s)"
% (login, usr.id.val))
except omero.ApiUsageException:
pass # Apparently no such user exists
groups = self.list_groups(admin, args)
roles = admin.getSecurityRoles()
groups.append(Grp(roles.userGroupId, False))
if args.admin:
groups.append(Grp(roles.systemGroupId, False))
group = groups.pop(0)
try:
if args.no_password:
id = admin.createExperimenter(e, group, groups)
self.ctx.out("Added user %s (id=%s) without password"
% (login, id))
else:
if pasw is None:
self._ask_for_password(" for your new user (%s)"
% login, strict=True)
id = admin.createExperimenterWithPassword(e, rstring(pasw),
group, groups)
self.ctx.out("Added user %s (id=%s) with password"
% (login, id))
except omero.ValidationException, ve:
# Possible, though unlikely after previous check
if self.exc.is_constraint_violation(ve):
self.ctx.die(66, "User already exists: %s" % login)
else:
self.ctx.die(67, "Unknown ValidationException: %s"
% ve.message)
def test_chgrp_old_container(self, dataset, credentials):
"""
Tests Admin moving user's Dataset to their Private group and
linking it to an existing Project there.
Bug from https://github.com/openmicroscopy/openmicroscopy/pull/3420
"""
django_client = self.get_django_client(credentials)
# user creates project in their target group
project = ProjectI()
projectName = "chgrp-target-%s" % self.client.getSessionId()
project.name = rstring(projectName)
ctx = {"omero.group": str(self.group2.id.val)}
project = self.sf.getUpdateService().saveAndReturnObject(project, ctx)
request_url = reverse('chgrp')
data = {
"group_id": self.group2.id.val,
"Dataset": dataset.id.val,
"target_id": "project-%s" % project.id.val,
}
rsp = post(django_client, request_url, data)
data = json.loads(rsp.content)
expected = {
"update": {
"childless": {
"project": [],
"orphaned": False,
"dataset": []
},
"remove": {
"project": [],
"plate": [],
"screen": [],
"image": [],
"dataset": [dataset.id.val]
}
}
}
assert data == expected
activities_url = reverse('activities_json')
data = get_json(django_client, activities_url)
# Keep polling activities until no jobs in progress
while data['inprogress'] > 0:
time.sleep(0.5)
data = get_json(django_client, activities_url)
# individual activities/jobs are returned as dicts within json data
for k, o in data.items():
if hasattr(o, 'values'): # a dict
if 'report' in o:
print o['report']
assert o['status'] == 'finished'
assert o['job_name'] == 'Change group'
assert o['to_group_id'] == self.group2.id.val
# Dataset should now be in new group, contained in Project
conn = BlitzGateway(client_obj=self.client)
userId = conn.getUserId()
conn.SERVICE_OPTS.setOmeroGroup('-1')
d = conn.getObject("Dataset", dataset.id.val)
assert d is not None
assert d.getDetails().group.id.val == self.group2.id.val
p = d.getParent()
assert p is not None
assert p.getName() == projectName
# Project owner should be current user
assert p.getDetails().owner.id.val == userId
assert p.getId() == project.id.val
def runAsScript():
"""
The main entry point of the script, as called by the client via the
scripting service, passing the required parameters.
"""
printDuration(False) # start timer
ckeys = COLOURS.keys()
ckeys.sort()
cOptions = [rstring(col) for col in ckeys]
dataTypes = [rstring('Screen')]
client = scripts.client(
'HCS _RenderSettings.py',
"""Sets the rendering settings for all images in a list of screens""",
scripts.String(
"Data_Type",
optional=False,
grouping="1",
description="Choose container of images (only Screen supported)",
values=dataTypes,
default="Screen"),
scripts.List("IDs",
optional=False,
grouping="2",
description="List of Screen IDs to process").ofType(
rlong(0)),
scripts.Bool("Reset_To_Imported",
grouping="3",
default=False,
description=
"Reset all rendering settings to original Imported values"
"Arguments below will be ignored"),
scripts.List("Channel_Colours",
grouping="4",
description="List of Colours for channels.",
default="White",
values=cOptions).ofType(rstring("")),
scripts.List(
"Channel_Names",
grouping="5",
description="List of Names for channels in the new image."),
version="0.0.1",
authors=["Damir Sudar"],
institutions=["Quantitative Imaging Systems LLC"],
contact="*****@*****.**",
)
try:
scriptParams = client.getInputs(unwrap=True)
print scriptParams
# wrap client to use the Blitz Gateway
conn = BlitzGateway(client_obj=client)
# set the desired rendering settings
message = set_rendersettings(conn, scriptParams)
client.setOutput("Message", rstring(message))
finally:
client.closeSession()
printDuration()
def run_script():
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
data_types = [rstring('Dataset')]
client = scripts.client(
'Create_Metadata_csv',
"""
This script reads the metadata attached data set and creates
a csv file attached to the Dataset
""",
scripts.String("Data_Type",
optional=False,
grouping="1",
description="Choose source of images",
values=data_types,
default="Dataset"),
scripts.List("IDs",
optional=False,
grouping="2",
description="Plate or Screen ID.").ofType(rlong(0)),
authors=["Christian Evenhuis"],
institutions=["MIF UTS"],
contact="*****@*****.**")
try:
# process the list of args above.
script_params = {}
for key in client.getInputKeys():
if client.getInput(key):
script_params[key] = client.getInput(key, unwrap=True)
# wrap client to use the Blitz Gateway
conn = BlitzGateway(client_obj=client)
print("connection made")
dataType = script_params["Data_Type"]
print(dataType)
ids = script_params["IDs"]
datasets = list(conn.getObjects(
dataType, ids)) # generator of images or datasets
print(ids)
print("datasets:")
print(datasets)
for ds in datasets:
# name of the file
csv_name = "{}_metadata_out.csv".format(ds.getName())
print(csv_name)
# remove the csv if it exists
for ann in ds.listAnnotations():
if (isinstance(ann, omero.gateway.FileAnnotationWrapper)):
if (ann.getFileName() == csv_name):
# if the name matches delete it
try:
delete = Delete2(targetObjects={
'FileAnnotation': [int(ann.getId())]
})
handle = conn.c.sf.submit(delete)
conn.c.waitOnCmd(handle,
loops=10,
ms=500,
failonerror=True,
failontimeout=False,
closehandle=False)
print("Deleted existing csv")
except Exception, ex:
print("Failed to delete existing csv: {}".format(
ex.message))
else:
print("No exisiting file")
# filename key multiple vals
# assemble the metadata into an OrderedDict of ( OrderedDict of Sets )
file_names = [img.getName() for img in list(ds.listChildren())]
kv_dict = OrderedDict()
for img in ds.listChildren():
fn = img.getName()
kv_dict[fn] = GetExistingMapAnnotions(img)
# attach the data
mess = attach_csv_file(conn, ds, kv_dict)
print(mess)
mess = "done"
client.setOutput("Message", rstring(mess))
def save_web_figure(request, conn=None, **kwargs):
"""
Saves 'figureJSON' in POST as an original file. If 'fileId' is specified
in POST, then we update that file. Otherwise create a new one with
name 'figureName' from POST.
"""
update = conn.getUpdateService()
if not request.method == 'POST':
return HttpResponse("Need to use POST")
figure_json = request.POST.get('figureJSON')
if figure_json is None:
return HttpResponse("No 'figureJSON' in POST")
# See https://github.com/will-moore/figure/issues/16
figure_json = figure_json.encode('utf8')
image_ids = []
first_img_id = None
try:
json_data = json.loads(figure_json)
for panel in json_data['panels']:
image_ids.append(panel['imageId'])
if len(image_ids) > 0:
first_img_id = long(image_ids[0])
# remove duplicates
image_ids = list(set(image_ids))
# pretty-print json
figure_json = json.dumps(json_data, sort_keys=True,
indent=2, separators=(',', ': '))
except Exception:
pass
file_id = request.POST.get('fileId')
if 'figureName' in json_data and len(json_data['figureName']) > 0:
figure_name = json_data['figureName']
else:
n = datetime.now()
# time-stamp name by default: WebFigure_2013-10-29_22-43-53.json
figure_name = "Figure_%s-%s-%s_%s-%s-%s.json" % \
(n.year, n.month, n.day, n.hour, n.minute, n.second)
# we store json in description field...
description = {}
if first_img_id is not None:
# We duplicate the figure name here for quicker access when
# listing files
# (use this instead of file name because it supports unicode)
description['name'] = figure_name
description['imageId'] = first_img_id
if 'baseUrl' in panel:
description['baseUrl'] = panel['baseUrl']
desc = json.dumps(description)
if file_id is None:
# Create new file
# Try to set Group context to the same as first image
curr_gid = conn.SERVICE_OPTS.getOmeroGroup()
conn.SERVICE_OPTS.setOmeroGroup('-1')
i = conn.getObject("Image", first_img_id)
if i is not None:
gid = i.getDetails().getGroup().getId()
conn.SERVICE_OPTS.setOmeroGroup(gid)
else:
# Don't leave as -1
conn.SERVICE_OPTS.setOmeroGroup(curr_gid)
file_size = len(figure_json)
f = StringIO()
f.write(figure_json)
# Can't use unicode for file name
figure_name = unicodedata.normalize(
'NFKD', figure_name).encode('ascii', 'ignore')
orig_file = conn.createOriginalFileFromFileObj(
f, '', figure_name, file_size, mimetype="application/json")
fa = omero.model.FileAnnotationI()
fa.setFile(omero.model.OriginalFileI(orig_file.getId(), False))
fa.setNs(wrap(JSON_FILEANN_NS))
fa.setDescription(wrap(desc))
fa = update.saveAndReturnObject(fa, conn.SERVICE_OPTS)
file_id = fa.getId().getValue()
else:
# Update existing Original File
conn.SERVICE_OPTS.setOmeroGroup('-1')
# Following seems to work OK with group -1 (regardless of group ctx)
fa = conn.getObject("FileAnnotation", file_id)
if fa is None:
return Http404("Couldn't find FileAnnotation of ID: %s" % file_id)
conn.SERVICE_OPTS.setOmeroGroup(fa.getDetails().group.id.val)
# Update description
fa._obj.setDescription(wrap(desc))
update.saveAndReturnObject(fa._obj, conn.SERVICE_OPTS)
orig_file = fa._obj.file
# Update name and size
orig_file.setName(rstring(figure_name))
size = len(figure_json)
orig_file.setSize(rlong(size))
orig_file = update.saveAndReturnObject(
orig_file, conn.SERVICE_OPTS)
# upload file
raw_file_store = conn.createRawFileStore()
raw_file_store.setFileId(orig_file.getId().getValue(),
conn.SERVICE_OPTS)
raw_file_store.write(figure_json, 0, size, conn.SERVICE_OPTS)
raw_file_store.truncate(size, conn.SERVICE_OPTS) # ticket #11751
# Once #11928 is fixed, these last 2 lines can be replaced with
# rawFileStore.close(conn.SERVICE_OPTS)
raw_file_store.save(conn.SERVICE_OPTS)
raw_file_store.close()
# Link file annotation to all images (remove from any others)
link_to_images = False # Disabled for now
if link_to_images:
current_links = conn.getAnnotationLinks("Image", ann_ids=[file_id])
for l in current_links:
if l.getParent().getId().getValue() not in image_ids:
# remove old link
update.deleteObject(l._obj, conn.SERVICE_OPTS)
else:
# we don't need to create links for these
image_ids.remove(l.getParent().getId().getValue())
# create new links if necessary
links = []
if len(image_ids) > 0:
for i in conn.getObjects("Image", image_ids):
if not i.canAnnotate():
continue
link = omero.model.ImageAnnotationLinkI()
link.parent = omero.model.ImageI(i.getId(), False)
link.child = omero.model.FileAnnotationI(file_id, False)
links.append(link)
# Don't want to fail at this point due to strange permissions combo
try:
update.saveArray(links, conn.SERVICE_OPTS)
except Exception:
pass
return HttpResponse(str(file_id))
class UserControl(UserGroupControl):
def _configure(self, parser):
self.exc = ExceptionHandler()
parser.add_login_arguments()
sub = parser.sub()
add = parser.add(sub, self.add, help="Add user")
add.add_argument(
"--ignore-existing", action="store_true", default=False,
help="Do not fail if user already exists")
add.add_argument(
"-m", "--middlename", help="Middle name, if available")
add.add_argument("-e", "--email")
add.add_argument("-i", "--institution")
# Capitalized since conflict with main values
add.add_argument(
"-a", "--admin", action="store_true",
help="Whether the user should be an admin")
add.add_argument("username", help="User's login name")
add.add_argument("firstname", help="User's given name")
add.add_argument("lastname", help="User's surname name")
self.add_group_arguments(add, "join", "the group as an owner")
password_group = add.add_mutually_exclusive_group()
password_group.add_argument(
"-P", "--userpassword", help="Password for user")
password_group.add_argument(
"--no-password", action="store_true", default=False,
help="Create user with empty password")
list = parser.add(sub, self.list, help="List current users")
printgroup = list.add_mutually_exclusive_group()
printgroup.add_argument(
"--long", action="store_true", default=True,
help="Print comma-separated list of all groups (default)")
printgroup.add_argument(
"--count", action="store_true", default=False,
help="Print count of all groups")
sortgroup = list.add_mutually_exclusive_group()
sortgroup.add_argument(
"--sort-by-id", action="store_true", default=True,
help="Sort users by ID (default)")
sortgroup.add_argument(
"--sort-by-login", action="store_true", default=False,
help="Sort users by login")
sortgroup.add_argument(
"--sort-by-first-name", action="store_true", default=False,
help="Sort users by first name")
sortgroup.add_argument(
"--sort-by-last-name", action="store_true", default=False,
help="Sort users by last name")
sortgroup.add_argument(
"--sort-by-email", action="store_true", default=False,
help="Sort users by email")
password = parser.add(
sub, self.password, help="Set user's password")
password.add_argument(
"username", nargs="?", help="Username if not the current user")
email = parser.add(
sub, self.email, help="List users' email addresses")
email.add_argument(
"-n", "--names", action="store_true", default=False,
help="Print user names along with email addresses")
email.add_argument(
"-1", "--one", action="store_true", default=False,
help="Print one user per line")
email.add_argument(
"-i", "--ignore", action="store_true", default=False,
help="Ignore users without email addresses")
joingroup = parser.add(sub, self.joingroup, "Join one or more groups")
self.add_user_arguments(joingroup)
group = self.add_group_arguments(joingroup, "join")
group.add_argument(
"--as-owner", action="store_true", default=False,
help="Join the group(s) as an owner")
leavegroup = parser.add(
sub, self.leavegroup, "Leave one or more groups")
self.add_user_arguments(leavegroup)
group = self.add_group_arguments(leavegroup, "leave")
group.add_argument(
"--as-owner", action="store_true", default=False,
help="Leave the owner list of the group(s)")
for x in (email, password, list, add, joingroup, leavegroup):
x.add_login_arguments()
def add_user_arguments(self, parser):
group = parser.add_mutually_exclusive_group()
group.add_argument(
"--id", help="ID of the user. Default to the current user")
group.add_argument(
"--name", help="Name of the user. Default to the current user")
def add_group_arguments(self, parser, action="join", owner_desc=""):
group = parser.add_argument_group('Group arguments')
group.add_argument(
"group_id_or_name", metavar="group", nargs="*",
help="ID or name of the group(s) to %s" % action)
group.add_argument(
"--group-id", metavar="group", nargs="+",
help="ID of the group(s) to %s" % action)
group.add_argument(
"--group-name", metavar="group", nargs="+",
help="Name of the group(s) to %s" % action)
return group
def format_name(self, exp):
record = ""
fn = _(exp.firstName)
mn = " "
if _(exp.middleName):
mn = " %s " % _(exp.middleName)
ln = _(exp.lastName)
record += "%s%s%s" % (fn, mn, ln)
return record
def email(self, args):
c = self.ctx.conn(args)
a = c.sf.getAdminService()
skipped = []
records = []
for exp in a.lookupExperimenters():
# Handle users without email
if not _(exp.email):
if not args.ignore:
skipped.append(exp)
continue
record = ""
if args.names:
record += '"%s"' % self.format_name(exp)
record += " <%s>" % _(exp.email)
else:
record += _(exp.email)
records.append(record)
if args.one:
for record in records:
self.ctx.out(record)
else:
self.ctx.out(", ".join(records))
if skipped:
self.ctx.err("Missing email addresses:")
for s in skipped:
self.ctx.err(self.format_name(s))
def password(self, args):
import omero
from omero.rtypes import rstring
client = self.ctx.conn(args)
own_name = self.ctx._event_context.userName
admin = client.sf.getAdminService()
# tickets 3202, 5841
own_pw = self._ask_for_password(" for your user (%s)"
% own_name, strict=False)
try:
client.sf.setSecurityPassword(own_pw)
self.ctx.out("Verified password.\n")
except omero.SecurityViolation, sv:
import traceback
self.ctx.die(456, "SecurityViolation: Bad credentials")
self.ctx.dbg(traceback.format_exc(sv))
if args.username:
self.ctx.out("Changing password for %s" % args.username)
else:
self.ctx.out("Changing password for %s" % own_name)
pw = self._ask_for_password(" to be set")
pw = rstring(pw)
if args.username:
admin.changeUserPassword(args.username, pw)
else:
admin.changePassword(pw)
self.ctx.out("Password changed")
