Пример #1
0
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
Пример #2
0
    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]