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 add_point(us, img, x, y, z):
""" Adds a point ROI to the given image
Args:
us The UpdateService
img The image (ImageWrapper)
x x (in pixels)
y y (in pixels)
z z plane index
"""
p = omero.model.PointI()
p.x = rdouble(x)
p.y = rdouble(y)
p.theZ = rint(z)
ch = ColorHolder.fromRGBA(r, g, b, a)
p.setStrokeColor(rint(ch.getInt()))
roi = omero.model.RoiI()
roi.setImage(img._obj)
roi.addShape(p)
us.saveAndReturnObject(roi)
mask_x = 50 mask_y = 50 mask_h = 100 mask_w = 100 # Create [0, 1] mask mask_array = numpy.fromfunction(lambda x, y: (x * y) % 2, (mask_w, mask_h)) # Set correct number of bytes per value mask_array = mask_array.astype(numpy.uint8) # Convert the mask to bytes mask_array = mask_array.tostring() # Pack the bytes to a bit mask mask_packed = create_mask(mask_array, 1) # Define mask's fill color mask_color = ColorHolder() mask_color.setRed(255) mask_color.setBlue(0) mask_color.setGreen(0) mask_color.setAlpha(100) # create an ROI with a single mask mask = omero.model.MaskI() mask.setTheC(rint(0)) mask.setTheZ(rint(0)) mask.setTheT(rint(0)) mask.setX(rdouble(mask_x)) mask.setY(rdouble(mask_y)) mask.setWidth(rdouble(mask_w)) mask.setHeight(rdouble(mask_h)) mask.setFillColor(rint(mask_color.getInt()))
def testShapeColors(self, color):
"""Test create an ROI with various shapes & colors set."""
color_holder = ColorHolder()
color_holder.setRed(color[0])
color_holder.setGreen(color[1])
color_holder.setBlue(color[2])
color_holder.setAlpha(color[3])
colorInt = color_holder.getInt()
assert colorInt == color[4]
img = self.new_image("testCreateRois")
img = self.update.saveAndReturnObject(img)
roi = omero.model.RoiI()
roi.setImage(img)
rect = omero.model.RectangleI()
rect.x = rdouble(5)
rect.y = rdouble(5)
rect.width = rdouble(100)
rect.height = rdouble(100)
rect.fillColor = rint(colorInt)
rect.strokeColor = rint(colorInt)
rect.theZ = rint(0)
rect.theT = rint(0)
rect.textValue = rstring("test-Rectangle")
roi.addShape(rect)
ellipse = omero.model.EllipseI()
ellipse.x = rdouble(50.0)
ellipse.y = rdouble(35.5)
ellipse.radiusX = rdouble(2000)
ellipse.radiusY = rdouble(300.04)
ellipse.fillColor = rint(colorInt)
ellipse.strokeColor = rint(colorInt)
ellipse.theZ = rint(1)
ellipse.theT = rint(2)
ellipse.textValue = rstring("test-Ellipse")
roi.addShape(ellipse)
line = omero.model.LineI()
line.x1 = rdouble(0)
line.x2 = rdouble(500.9)
line.y1 = rdouble(-100)
line.y2 = rdouble(201.0)
line.theZ = rint(-1)
line.theT = rint(1)
line.strokeColor = rint(colorInt)
line.fillColor = rint(colorInt)
line.textValue = rstring("test-Line")
roi.addShape(line)
point = omero.model.PointI()
point.x = rdouble(1000)
point.y = rdouble(0)
point.strokeColor = rint(colorInt)
point.fillColor = rint(colorInt)
point.textValue = rstring("test-Point")
roi.addShape(point)
new_roi = self.update.saveAndReturnObject(roi)
roi_service = self.client.sf.getRoiService()
result = roi_service.findByImage(img.id.val, None)
assert result is not None
shapeCount = 0
for roi in result.rois:
assert roi.id.val == new_roi.id.val
for s in roi.copyShapes():
assert s.getFillColor().val == colorInt
assert s.getStrokeColor().val == colorInt
shapeCount += 1
# Check we found 4 shapes
assert shapeCount == 4