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Merge pull request #669 from ankit-maverick/octagon
Adding Octagon structural element
This commit is contained in:
Johannes Schönberger
@@ -4,7 +4,8 @@ from .grey import (erosion, dilation, opening, closing, white_tophat,
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black_tophat, greyscale_erode, greyscale_dilate,
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greyscale_open, greyscale_close, greyscale_white_top_hat,
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greyscale_black_top_hat)
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from .selem import square, rectangle, diamond, disk, cube, octahedron, ball
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from .selem import (square, rectangle, diamond, disk, cube, octahedron, ball,
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octagon, star)
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from .ccomp import label
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from .watershed import watershed, is_local_maximum
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from ._skeletonize import skeletonize, medial_axis
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@@ -36,6 +37,7 @@ __all__ = ['binary_erosion',
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'cube',
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'octahedron',
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'ball',
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'octagon',
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'label',
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'watershed',
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'is_local_maximum',
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+119
-30
@@ -15,18 +15,18 @@ def square(width, dtype=np.uint8):
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Parameters
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----------
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width : int
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The width and height of the square
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The width and height of the square
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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A structuring element consisting only of ones, i.e. every
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pixel belongs to the neighborhood.
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A structuring element consisting only of ones, i.e. every
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pixel belongs to the neighborhood.
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"""
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return np.ones((width, width), dtype=dtype)
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@@ -41,21 +41,20 @@ def rectangle(width, height, dtype=np.uint8):
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Parameters
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----------
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width : int
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The width of the rectangle
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The width of the rectangle
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height : int
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The height of the rectangle
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The height of the rectangle
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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A structuring element consisting only of ones, i.e. every
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pixel belongs to the neighborhood.
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A structuring element consisting only of ones, i.e. every
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pixel belongs to the neighborhood.
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"""
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return np.ones((width, height), dtype=dtype)
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@@ -71,17 +70,19 @@ def diamond(radius, dtype=np.uint8):
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Parameters
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----------
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radius : int
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The radius of the diamond-shaped structuring element.
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The radius of the diamond-shaped structuring element.
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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"""
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half = radius
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(I, J) = np.meshgrid(range(0, radius * 2 + 1), range(0, radius * 2 + 1))
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@@ -98,16 +99,18 @@ def disk(radius, dtype=np.uint8):
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Parameters
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----------
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radius : int
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The radius of the disk-shaped structuring element.
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The radius of the disk-shaped structuring element.
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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"""
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L = np.linspace(-radius, radius, 2 * radius + 1)
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(X, Y) = np.meshgrid(L, L)
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@@ -125,18 +128,18 @@ def cube(width, dtype=np.uint8):
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Parameters
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----------
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width : int
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The width, height and depth of the cube
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The width, height and depth of the cube
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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A structuring element consisting only of ones, i.e. every
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pixel belongs to the neighborhood.
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A structuring element consisting only of ones, i.e. every
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pixel belongs to the neighborhood.
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"""
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return np.ones((width, width, width), dtype=dtype)
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@@ -153,17 +156,19 @@ def octahedron(radius, dtype=np.uint8):
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Parameters
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----------
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radius : int
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The radius of the octahedron-shaped structuring element.
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The radius of the octahedron-shaped structuring element.
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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"""
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# note that in contrast to diamond(), this method allows non-integer radii
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n = 2 * radius + 1
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@@ -184,16 +189,18 @@ def ball(radius, dtype=np.uint8):
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Parameters
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----------
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radius : int
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The radius of the ball-shaped structuring element.
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The radius of the ball-shaped structuring element.
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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"""
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n = 2 * radius + 1
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Z, Y, X = np.mgrid[ -radius:radius:n*1j,
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@@ -201,3 +208,85 @@ def ball(radius, dtype=np.uint8):
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-radius:radius:n*1j]
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s = X**2 + Y**2 + Z**2
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return np.array(s <= radius * radius, dtype=dtype)
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def octagon(m, n, dtype=np.uint8):
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"""
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Generates an octagon shaped structuring element with a given size of
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horizontal and vertical sides and a given height or width of slanted
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sides. The slanted sides are 45 or 135 degrees to the horizontal axis
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and hence the widths and heights are equal.
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Parameters
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----------
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m : int
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The size of the horizontal and vertical sides.
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n : int
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The height or width of the slanted sides.
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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"""
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from . import convex_hull_image
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selem = np.zeros((m + 2*n, m + 2*n))
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selem[0, n] = 1
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selem[n, 0] = 1
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selem[0, m + n -1] = 1
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selem[m + n - 1, 0] = 1
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selem[-1, n] = 1
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selem[n, -1] = 1
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selem[-1, m + n - 1] = 1
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selem[m + n - 1, -1] = 1
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selem = convex_hull_image(selem).astype(dtype)
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return selem
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def star(a, dtype=np.uint8):
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"""
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Generates a star shaped structuring element that has 8 vertices and is an
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overlap of square of size `2*a + 1` with its 45 degree rotated version.
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The slanted sides are 45 or 135 degrees to the horizontal axis.
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Parameters
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----------
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a : int
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Parameter deciding the size of the star structural element. The side
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of the square array returned is `2*a + 1 + 2*floor(a / 2)`.
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Other Parameters
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----------------
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dtype : data-type
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The data type of the structuring element.
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Returns
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-------
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selem : ndarray
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The structuring element where elements of the neighborhood
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are 1 and 0 otherwise.
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"""
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from . import convex_hull_image
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if a == 1:
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bfilter = np.zeros((3, 3), dtype)
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bfilter[:] = 1
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return bfilter
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m = 2 * a + 1
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n = a / 2
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selem_square = np.zeros((m + 2 * n, m + 2 * n))
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selem_square[n: m + n, n: m + n] = 1
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c = (m + 2 * n - 1) / 2
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selem_rotated = np.zeros((m + 2 * n, m + 2 * n))
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selem_rotated[0, c] = selem_rotated[-1, c] = selem_rotated[c, 0] = selem_rotated[c, -1] = 1
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selem_rotated = convex_hull_image(selem_rotated).astype(int)
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selem = selem_square + selem_rotated
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selem[selem > 0] = 1
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return selem.astype(dtype)
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@@ -66,6 +66,48 @@ class TestSElem():
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def test_selem_octahedron(self):
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self.strel_worker_3d("diamond-matlab-output.npz", selem.octahedron)
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def test_selem_octagon(self):
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expected_mask1 = np.array([[0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
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[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0]], dtype=np.uint8)
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actual_mask1 = selem.octagon(5, 3)
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expected_mask2 = np.array([[0, 1, 0],
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[1, 1, 1],
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[0, 1, 0]], dtype=np.uint8)
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actual_mask2 = selem.octagon(1, 1)
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assert_equal(expected_mask1, actual_mask1)
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assert_equal(expected_mask2, actual_mask2)
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def test_selem_star(self):
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expected_mask1 = np.array([[0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
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[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
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[0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0]], dtype=np.uint8)
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actual_mask1 = selem.star(4)
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expected_mask2 = np.array([[1, 1, 1],
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[1, 1, 1],
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[1, 1, 1]], dtype=np.uint8)
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actual_mask2 = selem.star(1)
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assert_equal(expected_mask1, actual_mask1)
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assert_equal(expected_mask2, actual_mask2)
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if __name__ == '__main__':
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np.testing.run_module_suite()
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