def mask():
o = MaskI()
populate_shape(o)
o.x = rdouble(0.0)
o.y = rdouble(0.0)
o.width = rdouble(1.0)
o.height = rdouble(2.0)
o.id = rlong(8L)
return o
def mask(identity_transform):
o = MaskI()
populate_shape(o, identity_transform)
o.x = rdouble(0.0)
o.y = rdouble(0.0)
o.width = rdouble(1.0)
o.height = rdouble(2.0)
o.id = rlong(8)
return o
def __init__(self, maskShape=None):
ShapeData.__init__(self)
if(maskShape is None):
self.setValue(MaskI())
self.setX(0)
self.setY(0)
self.setWidth(0)
self.setHeight(0)
self.setBytes(None)
else:
self.setValue(maskShape)
def make_mask(x, y, h, w):
mask = MaskI()
mask.x = rdouble(x)
mask.y = rdouble(y)
mask.height = rdouble(h)
mask.width = rdouble(w)
mask.bytes = make_circle(h, w)
roi = RoiI()
roi.description = rstring("created by overlapping-masks.py")
roi.addShape(mask)
roi.image = image
roi = update_service.saveAndReturnObject(roi)
print(f"Roi:{roi.id.val}")
def shapes(self):
"""Create a bunch of unsaved Shapes."""
rect = RectangleI()
rect.x = rdouble(10)
rect.y = rdouble(20)
rect.width = rdouble(30)
rect.height = rdouble(40)
# Only save theT, not theZ
rect.theT = rint(0)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
# ellipse without saving theZ & theT
ellipse = EllipseI()
ellipse.x = rdouble(33)
ellipse.y = rdouble(44)
ellipse.radiusX = rdouble(55)
ellipse.radiusY = rdouble(66)
ellipse.textValue = rstring("test-Ellipse")
line = LineI()
line.x1 = rdouble(200)
line.x2 = rdouble(300)
line.y1 = rdouble(400)
line.y2 = rdouble(500)
line.textValue = rstring("test-Line")
point = PointI()
point.x = rdouble(1)
point.y = rdouble(1)
point.theZ = rint(1)
point.theT = rint(1)
point.textValue = rstring("test-Point")
polygon = PolygonI()
polygon.theZ = rint(5)
polygon.theT = rint(5)
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 200,200, 250,75"
polygon.points = rstring(points)
mask = MaskI()
mask.setTheC(rint(0))
mask.setTheZ(rint(0))
mask.setTheT(rint(0))
mask.setX(rdouble(100))
mask.setY(rdouble(100))
mask.setWidth(rdouble(500))
mask.setHeight(rdouble(500))
mask.setTextValue(rstring("test-Mask"))
mask.setBytes(None)
return [rect, ellipse, line, point, polygon, mask]
def mask_from_binary_image(binim,
rgba=None,
z=None,
c=None,
t=None,
text=None,
raise_on_no_mask=True):
"""
Create a mask shape from a binary image (background=0)
:param numpy.array binim: Binary 2D array, must contain values [0, 1] only
:param rgba int-4-tuple: Optional (red, green, blue, alpha) colour
:param z: Optional Z-index for the mask
:param c: Optional C-index for the mask
:param t: Optional T-index for the mask
:param text: Optional text for the mask
:param raise_on_no_mask: If True (default) throw an exception if no mask
found, otherwise return an empty Mask
:return: An OMERO mask
:raises NoMaskFound: If no labels were found
:raises InvalidBinaryImage: If the maximum labels is greater than 1
"""
# Find bounding box to minimise size of mask
xmask = binim.sum(0).nonzero()[0]
ymask = binim.sum(1).nonzero()[0]
if any(xmask) and any(ymask):
x0 = min(xmask)
w = max(xmask) - x0 + 1
y0 = min(ymask)
h = max(ymask) - y0 + 1
submask = binim[y0:(y0 + h), x0:(x0 + w)]
if not np.array_equal(np.unique(submask),
[0, 1]) and not np.array_equal(
np.unique(submask), [1]):
raise InvalidBinaryImage()
else:
if raise_on_no_mask:
raise NoMaskFound()
x0 = 0
w = 0
y0 = 0
h = 0
submask = []
mask = MaskI()
# BUG in older versions of Numpy:
# https://github.com/numpy/numpy/issues/5377
# Need to convert to an int array
# mask.setBytes(np.packbits(submask))
mask.setBytes(np.packbits(np.asarray(submask, dtype=int)))
mask.setWidth(rdouble(w))
mask.setHeight(rdouble(h))
mask.setX(rdouble(x0))
mask.setY(rdouble(y0))
if rgba is not None:
ch = ColorHolder.fromRGBA(*rgba)
mask.setFillColor(rint(ch.getInt()))
if z is not None:
mask.setTheZ(rint(z))
if c is not None:
mask.setTheC(rint(c))
if t is not None:
mask.setTheT(rint(t))
if text is not None:
mask.setTextValue(rstring(text))
return mask
def createBaseType(self):
return MaskI()
def createBaseType(self):
warnings.warn("This module is deprecated as of OMERO 5.3.0",
DeprecationWarning)
return MaskI()
idr.connect()
local.connect()
query_service = idr.getQueryService()
update_service = local.getUpdateService()
query = "FROM Mask WHERE roi.image.id = :id"
params = ParametersI()
params.addId(image_id_src)
count = 0
for mask_src in query_service.findAllByQuery(query, params):
mask_dst = MaskI()
mask_dst.x = mask_src.x
mask_dst.y = mask_src.y
mask_dst.width = mask_src.width
mask_dst.height = mask_src.height
mask_dst.theZ = mask_src.theZ
mask_dst.theC = mask_src.theC
mask_dst.theT = mask_src.theT
mask_dst.bytes = mask_src.bytes
mask_dst.fillColor = mask_src.fillColor
mask_dst.transform = mask_src.transform
roi_dst = RoiI()
roi_dst.description = rstring(
"created by copy-masks script for original mask #{}".format(
mask_src.id.val))
roi_dst.image = ImageI(image_id_dst, False)