def test5756Wrapped(self):
"""
Accessing deleted image in share seems to have changed.
This tests what happens using BlitzGateway wrappers.
"""
new_group = self.new_group()
new_client, new_user = self.new_client_and_user(new_group)
share = new_client.sf.getShareService()
query = new_client.sf.getQueryService()
update = new_client.sf.getUpdateService()
image = self.make_image(client=new_client)
objects = [image]
share_id = share.createShare("", None, objects, [], [], True)
new_context = omero.model.ShareI(share_id, False)
old_context = new_client.sf.setSecurityContext(new_context)
image = query.get("Image", image.id.val)
from omero.gateway import ImageWrapper, BlitzGateway
conn = BlitzGateway(client_obj=new_client)
wrapper = ImageWrapper(conn=conn, obj=image)
new_client.sf.setSecurityContext(old_context)
update.deleteObject(image)
new_client.sf.setSecurityContext(new_context)
with pytest.raises(IndexError):
wrapper.__loadedHotSwap__()
def test5756Wrapped(self):
"""
Accessing deleted image in share seems to have changed.
This tests what happens using BlitzGateway wrappers.
"""
share = self.client.sf.getShareService()
query = self.client.sf.getQueryService()
update = self.client.sf.getUpdateService()
image = self.new_image()
image = update.saveAndReturnObject(image)
objects = [image]
self.share_id = share.createShare("", None, objects, [], [], True)
new_context = omero.model.ShareI(self.share_id, False)
old_context = self.client.sf.setSecurityContext(new_context)
image = query.get("Image", image.id.val)
from omero.gateway import ImageWrapper, BlitzGateway
conn = BlitzGateway(client_obj = self.client)
wrapper = ImageWrapper(conn = conn, obj = image)
self.client.sf.setSecurityContext(old_context)
update.deleteObject(image)
self.client.sf.setSecurityContext(new_context)
with pytest.raises(IndexError):
wrapper.__loadedHotSwap__()
def load_omero_channel(image: ImageWrapper, channel: ChannelWrapper,
c_index: int) -> LayerData:
data = get_data_lazy(image, c_index=c_index)
color = channel.getColor().getRGB()
color = [r / 256 for r in color]
cmap = Colormap([[0, 0, 0], color])
scale = None
# FIXME: still getting size mismatch sometimes is there a getNDim()?
if image.getSizeZ() > 1:
size_x = image.getPixelSizeX()
size_z = image.getPixelSizeZ()
if size_x is not None and size_z is not None:
if image.getSizeC() > 1:
scale = [1, size_z / size_x, 1, 1]
else:
scale = [size_z / size_x, 1, 1]
meta = {
"blending": "additive",
"colormap": ("from_omero", cmap),
"scale": scale,
"name": channel.getLabel(),
"visible": channel.isActive(),
"contrast_limits": [channel.getWindowStart(),
channel.getWindowEnd()],
}
# contrast limits range ... not accessible from plugin interface
# win_min = channel.getWindowMin()
# win_max = channel.getWindowMax()
return (data, meta)
def get_data_lazy(image: ImageWrapper, c_index: int = 0) -> da.Array:
"""Get n-dimensional dask array, with delayed reading from OMERO image."""
size_z = image.getSizeZ()
size_t = image.getSizeT()
size_x = image.getSizeX()
size_y = image.getSizeY()
pixels = image.getPrimaryPixels()
@delayed
@timer
def get_plane(plane_name):
z, c, t = [int(n) for n in plane_name.split(",")]
p = pixels.getPlane(z, c, t)
return p
dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
plane_names = [
f"{z},{c_index},{t}" for t in range(size_t) for z in range(size_z)
]
lazy_arrays = [get_plane(pn) for pn in plane_names]
dask_arrays = [
da.from_delayed(delayed_reader, shape=(size_y, size_x), dtype=dtype)
for delayed_reader in lazy_arrays
]
# Stack into one large dask.array
if size_z == 1 or size_t == 1:
return da.stack(dask_arrays, axis=0)
z_stacks = []
for t in range(size_t):
z_stacks.append(
da.stack(dask_arrays[t * size_z:(t + 1) * size_z], axis=0))
stack = da.stack(z_stacks, axis=0)
return stack
def listRois(conn, eid=None, limit=10):
"""
List the most recently created ROIs, optionally filtering by owner.
Returns a list of RecentObjects wrapping the linked Images.
"""
queryService = conn.getQueryService()
params = omero.sys.ParametersI()
f = omero.sys.Filter()
f.limit = rint(limit)
params.theFilter = f
if eid is not None:
params.map["eid"] = rlong(long(eid))
eidSelect = "where roi.details.owner.id=:eid "
else:
eidSelect = ""
query = "select roi from Roi as roi " \
"join fetch roi.image as image " \
"join fetch roi.details.owner " \
"join fetch roi.details.creationEvent as event %s" \
"order by event desc" % eidSelect
rois = queryService.findAllByQuery(query, params)
return [RecentEvent(ImageWrapper(conn, r.image), r) for r in rois]
def test5756Wrapped(self):
"""
Accessing deleted image in share seems to have changed.
This tests what happens using BlitzGateway wrappers.
"""
share = self.client.sf.getShareService()
query = self.client.sf.getQueryService()
update = self.client.sf.getUpdateService()
image = self.new_image()
image = update.saveAndReturnObject(image)
objects = [image]
self.share_id = share.createShare("", None, objects, [], [], True)
new_context = omero.model.ShareI(self.share_id, False)
old_context = self.client.sf.setSecurityContext(new_context)
image = query.get("Image", image.id.val)
from omero.gateway import ImageWrapper, BlitzGateway
conn = BlitzGateway(client_obj=self.client)
wrapper = ImageWrapper(conn=conn, obj=image)
self.client.sf.setSecurityContext(old_context)
update.deleteObject(image)
self.client.sf.setSecurityContext(new_context)
self.assertRaises(IndexError, wrapper.__loadedHotSwap__)
def get_omero_metadata(image: ImageWrapper) -> Dict:
"""Get metadata from OMERO as a Dict to pass to napari."""
channels = image.getChannels()
colors = []
for ch in channels:
# use current rendering settings from OMERO
color = ch.getColor().getRGB()
color = [r / 256 for r in color]
colors.append(Colormap([[0, 0, 0], color]))
contrast_limits = [[ch.getWindowStart(),
ch.getWindowEnd()] for ch in channels]
visibles = [ch.isActive() for ch in channels]
names = [ch.getLabel() for ch in channels]
scale = None
# Setting z-scale causes issues with Z-slider.
# See https://github.com/tlambert03/napari-omero/pull/15
# if image.getSizeZ() > 1:
# size_x = image.getPixelSizeX()
# size_z = image.getPixelSizeZ()
# if size_x is not None and size_z is not None:
# scale = [1, size_z / size_x, 1, 1]
return {
'channel_axis': 1,
'colormap': colors,
'contrast_limits': contrast_limits,
'name': names,
'visible': visibles,
'scale': scale,
}
def wrapped_image():
image = ImageI()
image.id = rlong(1L)
image.description = rstring('description')
image.name = rstring('name')
image.acquisitionDate = rtime(1000) # In milliseconds
image.details.owner = ExperimenterI(1L, False)
creation_event = EventI()
creation_event.time = rtime(2000) # In milliseconds
image.details.creationEvent = creation_event
return ImageWrapper(conn=MockConnection(), obj=image)
def get_data_lazy(image: ImageWrapper) -> da.Array:
"""Get 5D dask array, with delayed reading from OMERO image."""
nt, nc, nz, ny, nx = [getattr(image, f'getSize{x}')() for x in 'TCZYX']
pixels = image.getPrimaryPixels()
dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
get_plane = delayed(timer(lambda idx: pixels.getPlane(*idx)))
def get_lazy_plane(zct):
return da.from_delayed(get_plane(zct), shape=(ny, nx), dtype=dtype)
# 5D stack: TCZXY
t_stacks = []
for t in range(nt):
c_stacks = []
for c in range(nc):
z_stack = []
for z in range(nz):
z_stack.append(get_lazy_plane((z, c, t)))
c_stacks.append(da.stack(z_stack))
t_stacks.append(da.stack(c_stacks))
return da.stack(t_stacks)
def testGetROICount(self):
"""
Test no ROI couting method
"""
# Create group with two member and one image
group = self.new_group(perms="rwrw--")
owner = self.new_client(group=group) # Owner of share
member = self.new_client(group=group) # Member of group
img = self.createTestImage(session=owner.sf)
from omero.gateway import ImageWrapper, BlitzGateway
conn = BlitzGateway(client_obj=owner)
# Test no ROI count
wrapper = ImageWrapper(conn, img)
assert wrapper.getROICount() == 0
# Test ROI shape
roi1 = omero.model.RoiI()
roi1.addShape(omero.model.RectI())
roi1.addShape(omero.model.RectI())
roi1.setImage(img)
roi1 = owner.sf.getUpdateService().saveAndReturnObject(roi1)
roi2 = omero.model.RoiI()
roi2.addShape(omero.model.RectI())
roi2.addShape(omero.model.EllipseI())
roi2.setImage(img)
roi2 = owner.sf.getUpdateService().saveAndReturnObject(roi2)
wrapper = ImageWrapper(conn, img)
assert wrapper.getROICount() == 2
assert wrapper.getROICount("Rect") == 2
assert wrapper.getROICount("Ellipse") == 1
assert wrapper.getROICount("Line") == 0
assert wrapper.getROICount(["Rect", "Ellipse"]) == 2
# Test ROI permissions
roi3 = omero.model.RoiI()
roi3.addShape(omero.model.EllipseI())
roi3.setImage(img)
roi3 = member.sf.getUpdateService().saveAndReturnObject(roi3)
assert wrapper.getROICount() == 3
assert wrapper.getROICount(filterByCurrentUser=True) == 2
assert wrapper.getROICount("Ellipse") == 2
assert wrapper.getROICount("Ellipse", None) == 2
assert wrapper.getROICount("Ellipse", 1) == 1
assert wrapper.getROICount("Ellipse", True) == 1
assert wrapper.getROICount("Rect") == 2
assert wrapper.getROICount("Rect", None) == 2
assert wrapper.getROICount("Rect", 1) == 2
assert wrapper.getROICount("Rect", True) == 2
# Member gateway
conn = BlitzGateway(client_obj=member)
wrapper = ImageWrapper(conn, img)
assert wrapper.getROICount() == 3
assert wrapper.getROICount(filterByCurrentUser=True) == 1
assert wrapper.getROICount("Ellipse") == 2
assert wrapper.getROICount("Ellipse", None) == 2
assert wrapper.getROICount("Ellipse", 1) == 1
assert wrapper.getROICount("Ellipse", True) == 1
assert wrapper.getROICount("Rect") == 2
assert wrapper.getROICount("Rect", None) == 2
assert wrapper.getROICount("Rect", 1) == 0
assert wrapper.getROICount("Rect", True) == 0
def testGetROICount(self):
"""
Test no ROI couting method
"""
# Create group with two member and one image
group = self.new_group(perms="rwrw--")
owner = self.new_client(group=group) # Owner of share
member = self.new_client(group=group) # Member of group
img = self.createTestImage(session=owner.sf)
from omero.gateway import ImageWrapper, BlitzGateway
conn = BlitzGateway(client_obj=owner)
# Test no ROI count
wrapper = ImageWrapper(conn, img)
assert wrapper.getROICount() == 0
# Test ROI shape
roi1 = omero.model.RoiI()
roi1.addShape(omero.model.RectangleI())
roi1.addShape(omero.model.RectangleI())
roi1.setImage(img)
roi1 = owner.sf.getUpdateService().saveAndReturnObject(roi1)
roi2 = omero.model.RoiI()
roi2.addShape(omero.model.RectangleI())
roi2.addShape(omero.model.EllipseI())
roi2.setImage(img)
roi2 = owner.sf.getUpdateService().saveAndReturnObject(roi2)
wrapper = ImageWrapper(conn, img)
assert wrapper.getROICount() == 2
assert wrapper.getROICount("Rectangle") == 2
assert wrapper.getROICount("Ellipse") == 1
assert wrapper.getROICount("Line") == 0
assert wrapper.getROICount(["Rectangle", "Ellipse"]) == 2
# Test ROI permissions
roi3 = omero.model.RoiI()
roi3.addShape(omero.model.EllipseI())
roi3.setImage(img)
roi3 = member.sf.getUpdateService().saveAndReturnObject(roi3)
assert wrapper.getROICount() == 3
assert wrapper.getROICount(filterByCurrentUser=True) == 2
assert wrapper.getROICount("Ellipse") == 2
assert wrapper.getROICount("Ellipse", None) == 2
assert wrapper.getROICount("Ellipse", 1) == 1
assert wrapper.getROICount("Ellipse", True) == 1
assert wrapper.getROICount("Rectangle") == 2
assert wrapper.getROICount("Rectangle", None) == 2
assert wrapper.getROICount("Rectangle", 1) == 2
assert wrapper.getROICount("Rectangle", True) == 2
# Member gateway
conn = BlitzGateway(client_obj=member)
wrapper = ImageWrapper(conn, img)
assert wrapper.getROICount() == 3
assert wrapper.getROICount(filterByCurrentUser=True) == 1
assert wrapper.getROICount("Ellipse") == 2
assert wrapper.getROICount("Ellipse", None) == 2
assert wrapper.getROICount("Ellipse", 1) == 1
assert wrapper.getROICount("Ellipse", True) == 1
assert wrapper.getROICount("Rectangle") == 2
assert wrapper.getROICount("Rectangle", None) == 2
assert wrapper.getROICount("Rectangle", 1) == 0
assert wrapper.getROICount("Rectangle", True) == 0
def load_image_wrapper(image: ImageWrapper) -> List[LayerData]:
return [
load_omero_channel(image, channel, c)
for c, channel in enumerate(image.getChannels())
]