def test_empty_mask_from_binary_image(self, args, raise_on_no_mask):
empty_binary_image = np.array([[0]])
if raise_on_no_mask:
with pytest.raises(NoMaskFound):
mask = mask_from_binary_image(
empty_binary_image,
raise_on_no_mask=raise_on_no_mask,
**args)
else:
mask = mask_from_binary_image(empty_binary_image,
raise_on_no_mask=raise_on_no_mask,
**args)
assert unwrap(mask.getWidth()) == 0
assert unwrap(mask.getHeight()) == 0
assert unwrap(mask.getX()) == 0
assert unwrap(mask.getY()) == 0
assert np.array_equal(mask.getBytes(), [])
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
def test_mask_from_binary_image(self, binary_image, args):
im = self.conn.createImageFromNumpySeq(iter([binary_image]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
mask = mask_from_binary_image(px, **args)
mask = self.save_and_return_masks(im, [mask])[0]
# The rest of this is more or less the same as the unit test
assert unwrap(mask.getWidth()) == 2
assert unwrap(mask.getHeight()) == 2
assert unwrap(mask.getX()) == 1
assert unwrap(mask.getY()) == 1
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8),
np.array([224], dtype=np.uint8))
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
def create_rois(im, labels):
"""
Create single-Z masks for all labels and Zs.
Combine all Zs for a given label into one ROI.
"""
nz = im.getSizeZ()
assert im.getSizeT() == 1
if not all(
np.equal(
labels.shape,
[im.getSizeZ(), im.getSizeY(),
im.getSizeX()])):
raise ValueError(
'Incompatible ZYX dimensions image:{} labels:{}'.format(
[im.getSizeZ(), im.getSizeY(),
im.getSizeX()], labels.shape))
rois = []
ulabels = np.unique(labels)
for n in range(1, len(ulabels)):
print('Creating ROI index {}'.format(n))
roi = omero.model.RoiI()
roi.setName(rstring(n))
for z in range(nz):
try:
mask = mask_from_binary_image(labels[z] == ulabels[n],
rgba=RGBA,
z=z)
roi.addShape(mask)
except NoMaskFound:
pass
rois.append(roi)
return rois
def test_empty_mask_from_binary_image(self, args):
empty_binary_image = np.array([[0]], dtype=np.uint8)
raise_on_no_mask = False
im = self.conn.createImageFromNumpySeq(iter([empty_binary_image]),
"omero-rois-integration")
# Reload
im = self.conn.getObject("Image", im.id)
px = im.getPrimaryPixels().getPlane()
mask = mask_from_binary_image(px,
raise_on_no_mask=raise_on_no_mask,
**args)
mask = self.save_and_return_masks(im, [mask])[0]
# The rest of this is more or less the same as the unit test
assert unwrap(mask.getWidth()) == 0
assert unwrap(mask.getHeight()) == 0
assert unwrap(mask.getX()) == 0
assert unwrap(mask.getY()) == 0
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8), [])
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == "test"
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None
def test_mask_from_binary_full_image(self, binary_image):
binim = np.ones((4, 4))
mask = mask_from_binary_image(binim)
assert unwrap(mask.getWidth()) == 4
assert unwrap(mask.getHeight()) == 4
assert np.array_equal(mask.getBytes(),
np.array([255, 255], dtype=np.uint8))
def test_mask_from_binary_full_image(self):
binim = np.ones((4, 4), dtype=np.uint8)
im = self.conn.createImageFromNumpySeq(iter([binim]),
'omero-rois-integration')
# Reload
im = self.conn.getObject('Image', im.id)
px = im.getPrimaryPixels().getPlane()
mask = mask_from_binary_image(px)
mask = self.save_and_return_masks(im, [mask])[0]
# The rest of this is more or less the same as the unit test
assert unwrap(mask.getWidth()) == 4
assert unwrap(mask.getHeight()) == 4
assert np.array_equal(np.frombuffer(mask.getBytes(), np.uint8),
np.array([255, 255], dtype=np.uint8))
def create_mask(mask_path, x_offset, y_offset, t, text):
try:
mask_data = imread(mask_path)
mask_data = np.invert(mask_data)
h, w = mask_data.shape[0], mask_data.shape[1]
mask = mask_from_binary_image(mask_data,
rgba=(255, 255, 255, 128),
t=t,
text=text)
mask.setX(rdouble(mask.getX().getValue() + x_offset - w / 2))
mask.setY(rdouble(mask.getY().getValue() + y_offset - h / 2))
roi = omero.model.RoiI()
roi.addShape(mask)
return roi
except Exception as e:
print(f"Mask creation failed for {mask_path}")
print(e)
return None
def test_mask_from_binary_image(self, binary_image, args):
mask = mask_from_binary_image(binary_image, **args)
assert unwrap(mask.getWidth()) == 2
assert unwrap(mask.getHeight()) == 2
assert unwrap(mask.getX()) == 1
assert unwrap(mask.getY()) == 1
assert np.array_equal(mask.getBytes(), np.array([224], dtype=np.uint8))
if args:
assert unwrap(mask.getTheZ()) == 1
assert unwrap(mask.getTheC()) == 2
assert unwrap(mask.getTheT()) == 3
assert unwrap(mask.getTextValue()) == 'test'
else:
assert unwrap(mask.getTheZ()) is None
assert unwrap(mask.getTheC()) is None
assert unwrap(mask.getTheT()) is None
assert unwrap(mask.getTextValue()) is None