def create_mask(
binim, rgba=None, z=None, c=None, t=None, text=None,
raise_on_no_mask=False):
"""
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 Exception("Invalid binary image")
else:
if raise_on_no_mask:
raise Exception("No mask found")
x0 = 0
w = 0
y0 = 0
h = 0
submask = []
mask = MaskI()
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 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]