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Merge pull request #1298 from pratapvardhan/morph-selem
Morph selem ellipse structuring element
This commit is contained in:
Johannes Schönberger
+90
-44
@@ -5,18 +5,18 @@
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import numpy as np
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from scipy import ndimage
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from skimage import draw
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def square(width, dtype=np.uint8):
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"""
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Generates a flat, square-shaped structuring element. Every pixel
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along the perimeter has a chessboard distance no greater than radius
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(radius=floor(width/2)) pixels.
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"""Generates a flat, square-shaped structuring element.
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Every pixel along the perimeter has a chessboard distance
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no greater than radius (radius=floor(width/2)) pixels.
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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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@@ -34,17 +34,17 @@ def square(width, dtype=np.uint8):
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def rectangle(width, height, dtype=np.uint8):
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"""
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Generates a flat, rectangular-shaped structuring element of a
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given width and height. Every pixel in the rectangle belongs
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to the neighboorhood.
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"""Generates a flat, rectangular-shaped structuring element.
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Every pixel in the rectangle generated for a given width and given height
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belongs to the neighboorhood.
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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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@@ -62,11 +62,11 @@ def rectangle(width, height, dtype=np.uint8):
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def diamond(radius, dtype=np.uint8):
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"""
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Generates a flat, diamond-shaped structuring element of a given
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radius. A pixel is part of the neighborhood (i.e. labeled 1) if
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the city block/manhattan distance between it and the center of the
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neighborhood is no greater than radius.
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"""Generates a flat, diamond-shaped structuring element.
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A pixel is part of the neighborhood (i.e. labeled 1) if
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the city block/manhattan distance between it and the center of
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the neighborhood is no greater than radius.
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Parameters
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----------
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@@ -92,8 +92,8 @@ def diamond(radius, dtype=np.uint8):
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def disk(radius, dtype=np.uint8):
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"""
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Generates a flat, disk-shaped structuring element of a given radius.
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"""Generates a flat, disk-shaped structuring element.
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A pixel is within the neighborhood if the euclidean distance between
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it and the origin is no greater than radius.
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@@ -118,16 +118,60 @@ def disk(radius, dtype=np.uint8):
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return np.array((X ** 2 + Y ** 2) <= radius ** 2, dtype=dtype)
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def cube(width, dtype=np.uint8):
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def ellipse(width, height, dtype=np.uint8):
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"""Generates a flat, ellipse-shaped structuring element.
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Every pixel along the perimeter of ellipse satisfies
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the equation ``(x/width+1)**2 + (y/height+1)**2 = 1``.
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Parameters
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----------
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width : int
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The width of the ellipse-shaped structuring element.
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height : int
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The height of the ellipse-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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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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Examples
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--------
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>>> from skimage.morphology import selem
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>>> selem.ellipse(5, 3)
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array([[0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 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, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0]], dtype=uint8)
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"""
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Generates a cube-shaped structuring element (the 3D equivalent of
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a square). Every pixel along the perimeter has a chessboard distance
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selem = np.zeros((2 * height + 1, 2 * width + 1), dtype=dtype)
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rows, cols = draw.ellipse(height, width, height + 1, width + 1)
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selem[rows, cols] = 1
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return selem
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def cube(width, dtype=np.uint8):
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""" Generates a cube-shaped structuring element.
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This is the 3D equivalent of a square.
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Every pixel along the perimeter has a chessboard distance
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no greater than radius (radius=floor(width/2)) pixels.
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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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@@ -145,12 +189,12 @@ def cube(width, dtype=np.uint8):
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def octahedron(radius, dtype=np.uint8):
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"""
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Generates a octahedron-shaped structuring element of a given radius
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(the 3D equivalent of a diamond). A pixel is part of the
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neighborhood (i.e. labeled 1) if the city block/manhattan distance
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between it and the center of the neighborhood is no greater than
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radius.
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"""Generates a octahedron-shaped structuring element.
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This is the 3D equivalent of a diamond.
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A pixel is part of the neighborhood (i.e. labeled 1) if
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the city block/manhattan distance between it and the center of
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the neighborhood is no greater than radius.
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Parameters
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----------
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@@ -179,11 +223,11 @@ def octahedron(radius, dtype=np.uint8):
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def ball(radius, dtype=np.uint8):
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"""
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Generates a ball-shaped structuring element of a given radius (the
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3D equivalent of a disk). A pixel is within the neighborhood if the
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euclidean distance between it and the origin is no greater than
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radius.
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"""Generates a ball-shaped structuring element.
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This is the 3D equivalent of a disk.
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A pixel is within the neighborhood if the euclidean distance between
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it and the origin is no greater than radius.
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Parameters
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----------
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@@ -210,10 +254,11 @@ def ball(radius, dtype=np.uint8):
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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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"""Generates an octagon shaped structuring element.
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For a given size of (m) horizontal and vertical sides
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and a given (n) height or width of slanted sides octagon is generated.
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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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@@ -250,9 +295,10 @@ def octagon(m, n, dtype=np.uint8):
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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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"""Generates a star shaped structuring element.
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Start has 8 vertices and is an overlap of square of size `2*a + 1`
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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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@@ -298,9 +344,9 @@ def star(a, dtype=np.uint8):
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def _default_selem(ndim):
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"""
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Generates a cross-shaped structuring element (connectivity=1). This is the
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default structuring element (selem) if no selem was specified.
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"""Generates a cross-shaped structuring element (connectivity=1).
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This is the default structuring element (selem) if no selem was specified.
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Parameters
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----------
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@@ -102,6 +102,25 @@ class TestSElem():
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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_ellipse(self):
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"""Test ellipse structuring elements"""
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expected_mask1 = np.array([[0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 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, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0]], dtype=np.uint8)
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actual_mask1 = selem.ellipse(5, 3)
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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.ellipse(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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assert_equal(expected_mask1, selem.ellipse(3, 5).T)
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assert_equal(expected_mask2, selem.ellipse(1, 1).T)
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def test_selem_star(self):
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"""Test star structuring elements"""
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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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