def setup_method(self, method):
self.clis = []
self.sess = self.create_client_session(self.user)
self.name = UserAccount.uuid()
ns = UserAccount.uuid()
self.ft_space = ns + '/features'
self.ann_space = ns + '/source'
class TableStoreTestHelper(object):
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user(perms='rwra--')
def teardown_class(self):
self.ua.close()
def setup_method(self, method):
self.clis = []
self.sess = self.create_client_session(self.user)
self.name = UserAccount.uuid()
ns = UserAccount.uuid()
self.ft_space = ns + '/features'
self.ann_space = ns + '/source'
def teardown_method(self, method):
for cli in self.clis:
cli.closeSession()
def create_user_same_group(self):
g = self.sess.getAdminService().getDefaultGroup(self.user.id.val)
return self.ua.new_user(group=g)
def create_client_session(self, user):
cli = omero.client()
self.clis.append(cli)
un = unwrap(user.getOmeName())
sess = cli.createSession(un, un)
return sess
class TableStoreTestHelper(object):
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user(perms="rwra--")
def teardown_class(self):
self.ua.close()
def setup_method(self, method):
self.clis = []
self.sess = self.create_client_session(self.user)
self.name = UserAccount.uuid()
ns = UserAccount.uuid()
self.ft_space = ns + "/features"
self.ann_space = ns + "/source"
def teardown_method(self, method):
for cli in self.clis:
cli.closeSession()
def create_user_same_group(self):
g = self.sess.getAdminService().getDefaultGroup(self.user.id.val)
return self.ua.new_user(group=g)
def create_client_session(self, user):
cli = omero.client()
self.clis.append(cli)
un = unwrap(user.getOmeName())
sess = cli.createSession(un, un)
return sess
def setup_method(self, method):
self.clis = []
self.sess = self.create_client_session(self.user)
self.name = UserAccount.uuid()
ns = UserAccount.uuid()
self.ft_space = ns + "/features"
self.ann_space = ns + "/source"
def setup_method(self, method):
self.cli = omero.client()
un = unwrap(self.user.getOmeName())
self.sess = self.cli.createSession(un, un)
self.fsmeta = {'fsname': 'a'}
ns = UserAccount.uuid()
self.nsc = ns + '/c'
self.nsr = ns + '/r'
def setup_method(self, method):
self.cli = omero.client()
un = unwrap(self.user.getOmeName())
self.sess = self.cli.createSession(un, un)
self.fsmeta = {'fsname': 'a', 'version': '1'}
self.rowmetas = [{'id': '1'}, {'id': '2'}]
self.valuess = [[1.0, 2.0], [-1.0, -2.0]]
self.ns = UserAccount.uuid()
self.nsc = self.ns + '/featureset'
self.nsr = self.ns + '/sample'
def test_create_map_ann(self):
ns = UserAccount.uuid()
ma = OmeroMetadata.MapAnnotations(self.sess, namespace=ns)
d = {'a': '1', 'bb': 'cc'}
aid = ma.create_map_ann({'a': '1', 'bb': 'cc'})
params = omero.sys.ParametersI()
params.addLong('id', aid)
mr = self.sess.getQueryService().findByQuery(
'from MapAnnotation ann join fetch ann.mapValue where id=:id',
params)
assert unwrap(mr.getNs()) == ns
assert unwrap(mr.getMapValue()) == d
def test_query_by_map_ann(self, projection):
ns = UserAccount.uuid()
ma = OmeroMetadata.MapAnnotations(self.sess, namespace=ns)
d1 = {'a': '1', 'bb': 'cc'}
d1f = {'bb': 'cc'}
d2 = {'a': '1', 'bb': 'd'}
d2f = {'bb': 'd'}
m1 = omero.model.MapAnnotationI()
m1.setNs(wrap(ns))
m1.setMapValue(wrap(d1).val)
m2 = omero.model.MapAnnotationI()
m2.setNs(wrap(ns))
m2.setMapValue(wrap(d2).val)
m1 = self.sess.getUpdateService().saveAndReturnObject(m1)
m2 = self.sess.getUpdateService().saveAndReturnObject(m2)
rs = ma.query_by_map_ann(d1, projection)
assert len(rs) == 1
if projection:
if projection is True:
assert rs.values()[0] == d1
else:
assert rs.values()[0] == d1f
else:
assert unwrap(rs[0].getNs()) == ns
assert unwrap(rs[0].getMapValue()) == d1
rs = ma.query_by_map_ann({'a': '1'}, projection)
assert len(rs) == 2
if projection:
rmv1, rmv2 = rs.values()
if projection is True:
self.assert_equal_any_order((rmv1, rmv2), (d1, d2))
else:
self.assert_equal_any_order((rmv1, rmv2), (d1f, d2f))
else:
assert unwrap(rs[0].getNs()) == ns
assert unwrap(rs[1].getNs()) == ns
rmv1 = unwrap(rs[0].getMapValue())
rmv2 = unwrap(rs[1].getMapValue())
self.assert_equal_any_order((rmv1, rmv2), (d1, d2))
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user()
class TestMapAnnotations(object):
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user()
def teardown_class(self):
self.ua.close()
def setup_method(self, method):
self.cli = omero.client()
un = unwrap(self.user.getOmeName())
self.sess = self.cli.createSession(un, un)
def teardown_method(self, method):
self.cli.closeSession()
@staticmethod
def assert_equal_any_order(a, b):
assert ((a[0] == b[0] and a[1] == b[1]) or
(a[0] == b[1] and a[1] == b[0]))
def test_create_map_ann(self):
ns = UserAccount.uuid()
ma = OmeroMetadata.MapAnnotations(self.sess, namespace=ns)
d = {'a': '1', 'bb': 'cc'}
aid = ma.create_map_ann({'a': '1', 'bb': 'cc'})
params = omero.sys.ParametersI()
params.addLong('id', aid)
mr = self.sess.getQueryService().findByQuery(
'from MapAnnotation ann join fetch ann.mapValue where id=:id',
params)
assert unwrap(mr.getNs()) == ns
assert unwrap(mr.getMapValue()) == d
@pytest.mark.parametrize('projection', [True, False, ('bb',)])
def test_query_by_map_ann(self, projection):
ns = UserAccount.uuid()
ma = OmeroMetadata.MapAnnotations(self.sess, namespace=ns)
d1 = {'a': '1', 'bb': 'cc'}
d1f = {'bb': 'cc'}
d2 = {'a': '1', 'bb': 'd'}
d2f = {'bb': 'd'}
m1 = omero.model.MapAnnotationI()
m1.setNs(wrap(ns))
m1.setMapValue(wrap(d1).val)
m2 = omero.model.MapAnnotationI()
m2.setNs(wrap(ns))
m2.setMapValue(wrap(d2).val)
m1 = self.sess.getUpdateService().saveAndReturnObject(m1)
m2 = self.sess.getUpdateService().saveAndReturnObject(m2)
rs = ma.query_by_map_ann(d1, projection)
assert len(rs) == 1
if projection:
if projection is True:
assert rs.values()[0] == d1
else:
assert rs.values()[0] == d1f
else:
assert unwrap(rs[0].getNs()) == ns
assert unwrap(rs[0].getMapValue()) == d1
rs = ma.query_by_map_ann({'a': '1'}, projection)
assert len(rs) == 2
if projection:
rmv1, rmv2 = rs.values()
if projection is True:
self.assert_equal_any_order((rmv1, rmv2), (d1, d2))
else:
self.assert_equal_any_order((rmv1, rmv2), (d1f, d2f))
else:
assert unwrap(rs[0].getNs()) == ns
assert unwrap(rs[1].getNs()) == ns
rmv1 = unwrap(rs[0].getMapValue())
rmv2 = unwrap(rs[1].getMapValue())
self.assert_equal_any_order((rmv1, rmv2), (d1, d2))
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user(perms='rwra--')
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user()
class TestUtils(object):
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user()
def teardown_class(self):
self.ua.close()
def setup_method(self, method):
self.cli = omero.client()
un = unwrap(self.user.getOmeName())
self.sess = self.cli.createSession(un, un)
def teardown_method(self, method):
self.cli.closeSession()
def create_image(self):
szx, szy, szz, szc, szt = 4, 5, 6, 7, 8
def planegen():
for count in xrange(szz * szc * szt):
yield numpy.ones((szy, szx), numpy.uint16) * count
conn = omero.gateway.BlitzGateway(client_obj=self.cli)
im = conn.createImageFromNumpySeq(planegen(), __name__, szz, szc, szt)
return im._obj
@pytest.mark.parametrize('robject', [True, False])
def test_create_roi_for_plane(self, robject):
im = self.create_image()
r = utils.create_roi_for_plane(
self.sess, unwrap(im.getId()), 2, 4, 6, robject=robject)
if not robject:
p = omero.sys.ParametersI()
p.addId(r)
r = self.sess.getQueryService().findByQuery(
'FROM Roi r JOIN FETCH r.shapes where r.id=:id', p)
assert r.getImage().getId() == im.getId()
assert r.sizeOfShapes() == 1
s = r.getShape(0)
assert unwrap(s.getX()) == 0
assert unwrap(s.getY()) == 0
assert unwrap(s.getWidth()) == 4
assert unwrap(s.getHeight()) == 5
assert unwrap(s.getTheZ()) == 2
assert unwrap(s.getTheC()) == 4
assert unwrap(s.getTheT()) == 6
@pytest.mark.parametrize('projection', [True, False])
def test_find_rois_for_plane(self, projection):
def getIds(objs, robject=True):
if robject:
return sorted(unwrap(o.getId()) for o in objs)
return sorted(objs)
im = self.create_image()
iid = unwrap(im.getId())
r1 = utils.create_roi_for_plane(
self.sess, unwrap(im.getId()), 2, 3, 4, robject=True)
r2 = utils.create_roi_for_plane(
self.sess, unwrap(im.getId()), 2, 4, 6, robject=True)
r3 = utils.create_roi_for_plane(
self.sess, unwrap(im.getId()), 2, 4, 8, robject=True)
r3.getShape(0).setWidth(rdouble(1))
r3 = self.sess.getUpdateService().saveAndReturnObject(r3)
r4 = utils.create_roi_for_plane(
self.sess, unwrap(im.getId()), 2, 4, 8, robject=True)
r4.addShape(omero.model.RectI())
r4 = self.sess.getUpdateService().saveAndReturnObject(r4)
rs = utils.find_rois_for_plane(self.sess, iid=iid, z=1000)
assert rs == []
rs = utils.find_rois_for_plane(
self.sess, iid=iid, fullplane=True, projection=projection)
assert getIds(rs, not projection) == getIds([r1, r2])
rs = utils.find_rois_for_plane(
self.sess, iid=iid, singleshape=False, projection=projection)
assert getIds(rs, not projection) == getIds([r1, r2, r4])
rs = utils.find_rois_for_plane(
self.sess, iid=iid, fullplane=False, projection=projection)
assert getIds(rs, not projection) == getIds([r1, r2, r3])
rs = utils.find_rois_for_plane(
self.sess, iid=iid, c=4, fullplane=False, singleshape=False,
projection=projection)
assert getIds(rs, not projection) == getIds([r2, r3, r4])
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user(perms="rwra--")
class TestFeatureSetTableStore(object):
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user()
def teardown_class(self):
self.ua.close()
def setup_method(self, method):
self.cli = omero.client()
un = unwrap(self.user.getOmeName())
self.sess = self.cli.createSession(un, un)
self.fsmeta = {'fsname': 'a'}
ns = UserAccount.uuid()
self.nsc = ns + '/c'
self.nsr = ns + '/r'
def teardown_method(self, method):
self.cli.closeSession()
@pytest.mark.parametrize('exists', [True, False])
def test_get_table(self, exists):
store = FeatureSetTableStoreProxy(
self.sess, self.nsc, self.nsr, self.fsmeta)
if exists:
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
table = store.get_table()
assert table and table == store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
else:
with pytest.raises(OmeroTablesFeatureStore.NoTableMatchException):
store.get_table()
def test_new_table(self):
tcols = [
omero.grid.LongArrayColumn('Integers', '', 1),
omero.grid.LongArrayColumn('Longs', '', 2),
omero.grid.DoubleArrayColumn('Floats', '', 3),
omero.grid.StringColumn('String', '', 4),
]
desc = [
(int, 'Integers', 1),
(long, 'Longs', 2),
(float, 'Floats', 3),
(str, 'String', 4),
]
store = FeatureSetTableStoreProxy(
self.sess, self.nsc, self.nsr, self.fsmeta)
store.new_table(desc)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
tid = unwrap(store.table.getOriginalFile().getId())
params = omero.sys.ParametersI()
params.addString('ns', self.nsc)
ann = self.sess.getQueryService().findByQuery(
'from MapAnnotation ann join fetch ann.mapValue where ann.ns=:ns',
params)
assert unwrap(ann.getNs()) == self.nsc
m = unwrap(ann.getMapValue())
assert len(m) == 2
assert m['fsname'] == 'a'
assert m['_tableid'] == str(tid)
store.close()
def test_open_table(self):
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
store = FeatureSetTableStoreProxy(
self.sess, self.nsc, self.nsr, self.fsmeta)
store.open_table(tid)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
def test_store1(self):
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
store = OmeroTablesFeatureStore.FeatureSetTableStore(
self.sess, self.nsc, self.nsr, self.fsmeta)
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.table.getNumberOfRows() == 0
rowmeta = {'objectid': 4}
values = [[1, 2], [-1.0]]
store.store1(rowmeta, values)
assert store.table.getNumberOfRows() == 1
data = store.table.readCoordinates([0])
assert data.columns[0].values == [values[0]]
assert data.columns[1].values == [values[1]]
params = omero.sys.ParametersI()
params.addString('ns', self.nsr)
ann = self.sess.getQueryService().findAllByQuery(
'from MapAnnotation ann join fetch ann.mapValue where ann.ns=:ns',
params)
assert len(ann) == 1
ann = ann[0]
assert unwrap(ann.getNs()) == self.nsr
m = unwrap(ann.getMapValue())
assert len(m) == 3
assert m['objectid'] == '4'
assert m['_tableid'] == str(tid)
assert m['_offset'] == '0'
store.close()
def test_store(self):
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
store = OmeroTablesFeatureStore.FeatureSetTableStore(
self.sess, self.nsc, self.nsr, self.fsmeta)
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.table.getNumberOfRows() == 0
rowmetas = [{'objectid': 4}, {'objectid': 5}]
valuess = [([1, 2], [-1.0]), ([3, 4], [-2.0])]
store.store(rowmetas, valuess)
assert store.table.getNumberOfRows() == 2
data = store.table.readCoordinates([0, 1])
assert data.columns[0].values == [valuess[0][0], valuess[1][0]]
assert data.columns[1].values == [valuess[0][1], valuess[1][1]]
params = omero.sys.ParametersI()
params.addString('ns', self.nsr)
ann = self.sess.getQueryService().findAllByQuery(
'from MapAnnotation ann join fetch ann.mapValue where ann.ns=:ns',
params)
assert len(ann) == 2
ann1 = ann[0]
ann2 = ann[1]
assert unwrap(ann1.getNs()) == self.nsr
m1 = unwrap(ann1.getMapValue())
assert len(m1) == 3
assert m1['objectid'] == '4'
assert m1['_tableid'] == str(tid)
assert m1['_offset'] == '0'
assert unwrap(ann2.getNs()) == self.nsr
m2 = unwrap(ann2.getMapValue())
assert len(m2) == 3
assert m2['objectid'] == '5'
assert m2['_tableid'] == str(tid)
assert m2['_offset'] == '1'
store.close()
def test_fetch(self):
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
store = OmeroTablesFeatureStore.FeatureSetTableStore(
self.sess, self.nsc, self.nsr, self.fsmeta)
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
assert store.table.getNumberOfRows() == 0
rowmetas = [{'objectid': '4'}, {'objectid': '5'}]
valuess = [([1, 2], [-1.0]), ([3, 4], [-2.0])]
store.store(rowmetas, valuess)
rowquery = {'objectid': '4'}
ra, rv = store.fetch(rowquery)
assert len(ra) == 1
assert len(rv) == 1
assert ra[0]['objectid'] == '4'
assert rv[0] == valuess[0]
rowquery = {'objectid': ['4', '5']}
ra, rv = store.fetch(rowquery)
# Could be either way round
assert len(ra) == 2
assert len(rv) == 2
assert compare_2_2([ra[0]['objectid'], ra[1]['objectid']], ['4', '5'])
assert compare_2_2(rv, valuess)
store.close()
class TestFeatureTableStore(object):
def setup_class(self):
self.ua = UserAccount()
self.user = self.ua.new_user()
def teardown_class(self):
self.ua.close()
def setup_method(self, method):
self.cli = omero.client()
un = unwrap(self.user.getOmeName())
self.sess = self.cli.createSession(un, un)
self.fsmeta = {'fsname': 'a', 'version': '1'}
self.rowmetas = [{'id': '1'}, {'id': '2'}]
self.valuess = [[1.0, 2.0], [-1.0, -2.0]]
self.ns = UserAccount.uuid()
self.nsc = self.ns + '/featureset'
self.nsr = self.ns + '/sample'
def teardown_method(self, method):
self.cli.closeSession()
def test_create_feature_set(self):
fts = OmeroTablesFeatureStore.FeatureTableStore(
self.sess, namespace=self.ns, cachesize=1)
with pytest.raises(OmeroTablesFeatureStore.NoTableMatchException):
store = fts.get_feature_set(self.fsmeta)
col_desc = [(int, 'x', 1)]
fts.create_feature_set(self.fsmeta, col_desc)
store = fts.get_feature_set(self.fsmeta)
expected_cols = [omero.grid.LongArrayColumn('x', '', 1)]
TableStoreHelper.assert_coltypes_equal(store.cols, expected_cols)
with pytest.raises(OmeroTablesFeatureStore.TooManyTablesException):
fts.create_feature_set(self.fsmeta, col_desc)
fts.close()
def test_get_feature_set(self):
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
fts = OmeroTablesFeatureStore.FeatureTableStore(
self.sess, namespace=self.ns, cachesize=1)
store = fts.get_feature_set(self.fsmeta)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
fts.close()
def test_store_fetch(self):
tid, tcols = TableStoreHelper.create_table(
self.sess, self.nsc, self.fsmeta)
fts = OmeroTablesFeatureStore.FeatureTableStore(
self.sess, namespace=self.ns, cachesize=1)
rowmetas = [{'objectid': 4}, {'objectid': 5}]
valuess = [([1, 2], [-1.0]), ([3, 4], [-2.0])]
fts.store(self.fsmeta, rowmetas, valuess)
assert len(fts.fss) == 1
store = fts.get_feature_set(self.fsmeta)
assert store.table
TableStoreHelper.assert_coltypes_equal(store.cols, tcols)
rowquery = {'objectid': ['4', '5']}
ra, rv = store.fetch(rowquery)
# Could be either way round
assert len(ra) == 2
assert len(rv) == 2
assert compare_2_2([ra[0]['objectid'], ra[1]['objectid']], ['4', '5'])
assert compare_2_2(rv, valuess)
fts.close()