skimage.draw#

skimage.draw.bezier_curve

Generate Bezier curve coordinates.

skimage.draw.circle_perimeter

Generate circle perimeter coordinates.

skimage.draw.circle_perimeter_aa

Generate anti-aliased circle perimeter coordinates.

skimage.draw.disk

Generate coordinates of pixels within circle.

skimage.draw.ellipse

Generate coordinates of pixels within ellipse.

skimage.draw.ellipse_perimeter

Generate ellipse perimeter coordinates.

skimage.draw.ellipsoid

Generates ellipsoid with semimajor axes aligned with grid dimensions on grid with specified spacing.

skimage.draw.ellipsoid_stats

Calculates analytical surface area and volume for ellipsoid with semimajor axes aligned with grid dimensions of specified spacing.

skimage.draw.line

Generate line pixel coordinates.

skimage.draw.line_aa

Generate anti-aliased line pixel coordinates.

skimage.draw.line_nd

Draw a single-pixel thick line in n dimensions.

skimage.draw.polygon

Generate coordinates of pixels inside a polygon.

skimage.draw.polygon2mask

Create a binary mask from a polygon.

skimage.draw.polygon_perimeter

Generate polygon perimeter coordinates.

skimage.draw.random_shapes

Generate an image with random shapes, labeled with bounding boxes.

skimage.draw.rectangle

Generate coordinates of pixels within a rectangle.

skimage.draw.rectangle_perimeter

Generate coordinates of pixels that are exactly around a rectangle.

skimage.draw.set_color

Set pixel color in the image at the given coordinates.
skimage.draw.bezier_curve(r0, c0, r1, c1, r2, c2, weight, shape=None)[source]#

Generate Bezier curve coordinates.

Parameters:
r0, c0int

Coordinates of the first control point.

r1, c1int

Coordinates of the middle control point.

r2, c2int

Coordinates of the last control point.

weightdouble

Middle control point weight, it describes the line tension.

shapetuple, optional

Image shape which is used to determine the maximum extent of output pixel coordinates. This is useful for curves that exceed the image size. If None, the full extent of the curve is used.

Returns:
rr, cc(N,) ndarray of int

Indices of pixels that belong to the Bezier curve. May be used to directly index into an array, e.g. img[rr, cc] = 1.

Notes

The algorithm is the rational quadratic algorithm presented in reference [1].

References

[1]

A Rasterizing Algorithm for Drawing Curves, A. Zingl, 2012 http://members.chello.at/easyfilter/Bresenham.pdf

Examples

>>> import numpy as np
>>> from skimage.draw import bezier_curve
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = bezier_curve(1, 5, 5, -2, 8, 8, 2)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
       [0, 0, 0, 1, 1, 0, 0, 0, 0, 0],
       [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 1, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)

Shapes

Shapes
skimage.draw.circle_perimeter(r, c, radius, method='bresenham', shape=None)[source]#

Generate circle perimeter coordinates.

Parameters:
r, cint

Centre coordinate of circle.

radiusint

Radius of circle.

method{‘bresenham’, ‘andres’}, optional

bresenham : Bresenham method (default) andres : Andres method

shapetuple, optional

Image shape which is used to determine the maximum extent of output pixel coordinates. This is useful for circles that exceed the image size. If None, the full extent of the circle is used. Must be at least length 2. Only the first two values are used to determine the extent of the input image.

Returns:
rr, cc(N,) ndarray of int

Bresenham and Andres’ method: Indices of pixels that belong to the circle perimeter. May be used to directly index into an array, e.g. img[rr, cc] = 1.

Notes

Andres method presents the advantage that concentric circles create a disc whereas Bresenham can make holes. There is also less distortions when Andres circles are rotated. Bresenham method is also known as midpoint circle algorithm. Anti-aliased circle generator is available with circle_perimeter_aa.

References

[1]

J.E. Bresenham, “Algorithm for computer control of a digital plotter”, IBM Systems journal, 4 (1965) 25-30.

[2]

E. Andres, “Discrete circles, rings and spheres”, Computers & Graphics, 18 (1994) 695-706.

Examples

>>> from skimage.draw import circle_perimeter
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = circle_perimeter(4, 4, 3)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
       [0, 0, 1, 0, 0, 0, 1, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 1, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 1, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 1, 0, 0],
       [0, 0, 1, 0, 0, 0, 1, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)

Shapes

Shapes

Circular and Elliptical Hough Transforms

Circular and Elliptical Hough Transforms
skimage.draw.circle_perimeter_aa(r, c, radius, shape=None)[source]#

Generate anti-aliased circle perimeter coordinates.

Parameters:
r, cint

Centre coordinate of circle.

radiusint

Radius of circle.

shapetuple, optional

Image shape which is used to determine the maximum extent of output pixel coordinates. This is useful for circles that exceed the image size. If None, the full extent of the circle is used. Must be at least length 2. Only the first two values are used to determine the extent of the input image.

Returns:
rr, cc, val(N,) ndarray (int, int, float)

Indices of pixels (rr, cc) and intensity values (val). img[rr, cc] = val.

Notes

Wu’s method draws anti-aliased circle. This implementation doesn’t use lookup table optimization.

Use the function draw.set_color to apply circle_perimeter_aa results to color images.

References

[1]

X. Wu, “An efficient antialiasing technique”, In ACM SIGGRAPH Computer Graphics, 25 (1991) 143-152.

Examples

>>> from skimage.draw import circle_perimeter_aa
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc, val = circle_perimeter_aa(4, 4, 3)
>>> img[rr, cc] = val * 255
>>> img
array([[  0,   0,   0,   0,   0,   0,   0,   0,   0,   0],
       [  0,   0,  60, 211, 255, 211,  60,   0,   0,   0],
       [  0,  60, 194,  43,   0,  43, 194,  60,   0,   0],
       [  0, 211,  43,   0,   0,   0,  43, 211,   0,   0],
       [  0, 255,   0,   0,   0,   0,   0, 255,   0,   0],
       [  0, 211,  43,   0,   0,   0,  43, 211,   0,   0],
       [  0,  60, 194,  43,   0,  43, 194,  60,   0,   0],
       [  0,   0,  60, 211, 255, 211,  60,   0,   0,   0],
       [  0,   0,   0,   0,   0,   0,   0,   0,   0,   0],
       [  0,   0,   0,   0,   0,   0,   0,   0,   0,   0]], dtype=uint8)

>>> from skimage import data, draw
>>> image = data.chelsea()
>>> rr, cc, val = draw.circle_perimeter_aa(r=100, c=100, radius=75)
>>> draw.set_color(image, (rr, cc), [1, 0, 0], alpha=val)

Shapes

Shapes
skimage.draw.disk(center, radius, *, shape=None)[source]#

Generate coordinates of pixels within circle.

Parameters:
centertuple

Center coordinate of disk.

radiusdouble

Radius of disk.

shapetuple, optional

Image shape as a tuple of size 2. Determines the maximum extent of output pixel coordinates. This is useful for disks that exceed the image size. If None, the full extent of the disk is used. The shape might result in negative coordinates and wraparound behaviour.

Returns:
rr, ccndarray of int

Pixel coordinates of disk. May be used to directly index into an array, e.g. img[rr, cc] = 1.

Examples

>>> import numpy as np
>>> from skimage.draw import disk
>>> shape = (4, 4)
>>> img = np.zeros(shape, dtype=np.uint8)
>>> rr, cc = disk((0, 0), 2, shape=shape)
>>> img[rr, cc] = 1
>>> img
array([[1, 1, 0, 0],
       [1, 1, 0, 0],
       [0, 0, 0, 0],
       [0, 0, 0, 0]], dtype=uint8)
>>> img = np.zeros(shape, dtype=np.uint8)
>>> # Negative coordinates in rr and cc perform a wraparound
>>> rr, cc = disk((0, 0), 2, shape=None)
>>> img[rr, cc] = 1
>>> img
array([[1, 1, 0, 1],
       [1, 1, 0, 1],
       [0, 0, 0, 0],
       [1, 1, 0, 1]], dtype=uint8)
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = disk((4, 4), 5)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
       [0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
       [1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [0, 1, 1, 1, 1, 1, 1, 1, 0, 0],
       [0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)

Shapes

Shapes

Shape Index

Shape Index
skimage.draw.ellipse(r, c, r_radius, c_radius, shape=None, rotation=0.0)[source]#

Generate coordinates of pixels within ellipse.

Parameters:
r, cdouble

Centre coordinate of ellipse.

r_radius, c_radiusdouble

Minor and major semi-axes. (r/r_radius)**2 + (c/c_radius)**2 = 1.

shapetuple, optional

Image shape which is used to determine the maximum extent of output pixel coordinates. This is useful for ellipses which exceed the image size. By default the full extent of the ellipse are used. Must be at least length 2. Only the first two values are used to determine the extent.

rotationfloat, optional (default 0.)

Set the ellipse rotation (rotation) in range (-PI, PI) in contra clock wise direction, so PI/2 degree means swap ellipse axis

Returns:
rr, ccndarray of int

Pixel coordinates of ellipse. May be used to directly index into an array, e.g. img[rr, cc] = 1.

Notes

The ellipse equation:

((x * cos(alpha) + y * sin(alpha)) / x_radius) ** 2 +
((x * sin(alpha) - y * cos(alpha)) / y_radius) ** 2 = 1

Note that the positions of ellipse without specified shape can have also, negative values, as this is correct on the plane. On the other hand using these ellipse positions for an image afterwards may lead to appearing on the other side of image, because image[-1, -1] = image[end-1, end-1]

>>> rr, cc = ellipse(1, 2, 3, 6)
>>> img = np.zeros((6, 12), dtype=np.uint8)
>>> img[rr, cc] = 1
>>> img
array([[1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1],
       [1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1],
       [1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1],
       [1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1]], dtype=uint8)

Examples

>>> from skimage.draw import ellipse
>>> img = np.zeros((10, 12), dtype=np.uint8)
>>> rr, cc = ellipse(5, 6, 3, 5, rotation=np.deg2rad(30))
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0],
       [0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0],
       [0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
       [0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
       [0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)

Shapes

Shapes

Approximate and subdivide polygons

Approximate and subdivide polygons

Masked Normalized Cross-Correlation

Masked Normalized Cross-Correlation

Corner detection

Corner detection

Measure region properties

Measure region properties
skimage.draw.ellipse_perimeter(r, c, r_radius, c_radius, orientation=0, shape=None)[source]#

Generate ellipse perimeter coordinates.

Parameters:
r, cint

Centre coordinate of ellipse.

r_radius, c_radiusint

Minor and major semi-axes. (r/r_radius)**2 + (c/c_radius)**2 = 1.

orientationdouble, optional

Major axis orientation in clockwise direction as radians.

shapetuple, optional

Image shape which is used to determine the maximum extent of output pixel coordinates. This is useful for ellipses that exceed the image size. If None, the full extent of the ellipse is used. Must be at least length 2. Only the first two values are used to determine the extent of the input image.

Returns:
rr, cc(N,) ndarray of int

Indices of pixels that belong to the ellipse perimeter. May be used to directly index into an array, e.g. img[rr, cc] = 1.

References

[1]

A Rasterizing Algorithm for Drawing Curves, A. Zingl, 2012 http://members.chello.at/easyfilter/Bresenham.pdf

Examples

>>> from skimage.draw import ellipse_perimeter
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = ellipse_perimeter(5, 5, 3, 4)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 1, 1, 0, 0],
       [0, 0, 1, 0, 0, 0, 0, 0, 1, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 1],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 1],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 1],
       [0, 0, 1, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 1, 1, 1, 1, 1, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)

Note that the positions of ellipse without specified shape can have also, negative values, as this is correct on the plane. On the other hand using these ellipse positions for an image afterwards may lead to appearing on the other side of image, because image[-1, -1] = image[end-1, end-1]

>>> rr, cc = ellipse_perimeter(2, 3, 4, 5)
>>> img = np.zeros((9, 12), dtype=np.uint8)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1],
       [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0],
       [0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0],
       [1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0]], dtype=uint8)

Shapes

Shapes

Circular and Elliptical Hough Transforms

Circular and Elliptical Hough Transforms
skimage.draw.ellipsoid(a, b, c, spacing=(1.0, 1.0, 1.0), levelset=False)[source]#

Generates ellipsoid with semimajor axes aligned with grid dimensions on grid with specified spacing.

Parameters:
afloat

Length of semimajor axis aligned with x-axis.

bfloat

Length of semimajor axis aligned with y-axis.

cfloat

Length of semimajor axis aligned with z-axis.

spacingtuple of floats, length 3

Spacing in (x, y, z) spatial dimensions.

levelsetbool

If True, returns the level set for this ellipsoid (signed level set about zero, with positive denoting interior) as np.float64. False returns a binarized version of said level set.

Returns:
ellip(N, M, P) array

Ellipsoid centered in a correctly sized array for given spacing. Boolean dtype unless levelset=True, in which case a float array is returned with the level set above 0.0 representing the ellipsoid.

Marching Cubes

Marching Cubes
skimage.draw.ellipsoid_stats(a, b, c)[source]#

Calculates analytical surface area and volume for ellipsoid with semimajor axes aligned with grid dimensions of specified spacing.

Parameters:
afloat

Length of semimajor axis aligned with x-axis.

bfloat

Length of semimajor axis aligned with y-axis.

cfloat

Length of semimajor axis aligned with z-axis.

Returns:
volfloat

Calculated volume of ellipsoid.

surffloat

Calculated surface area of ellipsoid.

skimage.draw.line(r0, c0, r1, c1)[source]#

Generate line pixel coordinates.

Parameters:
r0, c0int

Starting position (row, column).

r1, c1int

End position (row, column).

Returns:
rr, cc(N,) ndarray of int

Indices of pixels that belong to the line. May be used to directly index into an array, e.g. img[rr, cc] = 1.

Notes

Anti-aliased line generator is available with line_aa.

Examples

>>> from skimage.draw import line
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = line(1, 1, 8, 8)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 1, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)

Shapes

Shapes

Straight line Hough transform

Straight line Hough transform
skimage.draw.line_aa(r0, c0, r1, c1)[source]#

Generate anti-aliased line pixel coordinates.

Parameters:
r0, c0int

Starting position (row, column).

r1, c1int

End position (row, column).

Returns:
rr, cc, val(N,) ndarray (int, int, float)

Indices of pixels (rr, cc) and intensity values (val). img[rr, cc] = val.

References

[1]

A Rasterizing Algorithm for Drawing Curves, A. Zingl, 2012 http://members.chello.at/easyfilter/Bresenham.pdf

Examples

>>> from skimage.draw import line_aa
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc, val = line_aa(1, 1, 8, 8)
>>> img[rr, cc] = val * 255
>>> img
array([[  0,   0,   0,   0,   0,   0,   0,   0,   0,   0],
       [  0, 255,  74,   0,   0,   0,   0,   0,   0,   0],
       [  0,  74, 255,  74,   0,   0,   0,   0,   0,   0],
       [  0,   0,  74, 255,  74,   0,   0,   0,   0,   0],
       [  0,   0,   0,  74, 255,  74,   0,   0,   0,   0],
       [  0,   0,   0,   0,  74, 255,  74,   0,   0,   0],
       [  0,   0,   0,   0,   0,  74, 255,  74,   0,   0],
       [  0,   0,   0,   0,   0,   0,  74, 255,  74,   0],
       [  0,   0,   0,   0,   0,   0,   0,  74, 255,   0],
       [  0,   0,   0,   0,   0,   0,   0,   0,   0,   0]], dtype=uint8)

Shapes

Shapes
skimage.draw.line_nd(start, stop, *, endpoint=False, integer=True)[source]#

Draw a single-pixel thick line in n dimensions.

The line produced will be ndim-connected. That is, two subsequent pixels in the line will be either direct or diagonal neighbors in n dimensions.

Parameters:
startarray-like, shape (N,)

The start coordinates of the line.

stoparray-like, shape (N,)

The end coordinates of the line.

endpointbool, optional

Whether to include the endpoint in the returned line. Defaults to False, which allows for easy drawing of multi-point paths.

integerbool, optional

Whether to round the coordinates to integer. If True (default), the returned coordinates can be used to directly index into an array. False could be used for e.g. vector drawing.

Returns:
coordstuple of arrays

The coordinates of points on the line.

Examples

>>> lin = line_nd((1, 1), (5, 2.5), endpoint=False)
>>> lin
(array([1, 2, 3, 4]), array([1, 1, 2, 2]))
>>> im = np.zeros((6, 5), dtype=int)
>>> im[lin] = 1
>>> im
array([[0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0],
       [0, 1, 0, 0, 0],
       [0, 0, 1, 0, 0],
       [0, 0, 1, 0, 0],
       [0, 0, 0, 0, 0]])
>>> line_nd([2, 1, 1], [5, 5, 2.5], endpoint=True)
(array([2, 3, 4, 4, 5]), array([1, 2, 3, 4, 5]), array([1, 1, 2, 2, 2]))
skimage.draw.polygon(r, c, shape=None)[source]#

Generate coordinates of pixels inside a polygon.

Parameters:
r(N,) array_like

Row coordinates of the polygon’s vertices.

c(N,) array_like

Column coordinates of the polygon’s vertices.

shapetuple, optional

Image shape which is used to determine the maximum extent of output pixel coordinates. This is useful for polygons that exceed the image size. If None, the full extent of the polygon is used. Must be at least length 2. Only the first two values are used to determine the extent of the input image.

Returns:
rr, ccndarray of int

Pixel coordinates of polygon. May be used to directly index into an array, e.g. img[rr, cc] = 1.

See also

polygon2mask

Create a binary mask from a polygon.

Notes

This function ensures that rr and cc don’t contain negative values. Pixels of the polygon that whose coordinates are smaller 0, are not drawn.

Examples

>>> import skimage as ski
>>> r = np.array([1, 2, 8])
>>> c = np.array([1, 7, 4])
>>> rr, cc = ski.draw.polygon(r, c)
>>> img = np.zeros((10, 10), dtype=int)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
       [0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])

If the image shape is defined and vertices / points of the polygon are outside this coordinate space, only a part (or none at all) of the polygon’s pixels is returned. Shifting the polygon’s vertices by an offset can be used to move the polygon around and potentially draw an arbitrary sub-region of the polygon.

>>> offset = (2, -4)
>>> rr, cc = ski.draw.polygon(r - offset[0], c - offset[1], shape=img.shape)
>>> img = np.zeros((10, 10), dtype=int)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])

Shapes

Shapes
skimage.draw.polygon2mask(image_shape, polygon)[source]#

Create a binary mask from a polygon.

Parameters:
image_shapetuple of size 2

The shape of the mask.

polygon(N, 2) array_like

The polygon coordinates of shape (N, 2) where N is the number of points. The coordinates are (row, column).

Returns:
mask2-D ndarray of type ‘bool’

The binary mask that corresponds to the input polygon.

See also

polygon

Generate coordinates of pixels inside a polygon.

Notes

This function does not do any border checking. Parts of the polygon that are outside the coordinate space defined by image_shape are not drawn.

Examples

>>> import skimage as ski
>>> image_shape = (10, 10)
>>> polygon = np.array([[1, 1], [2, 7], [8, 4]])
>>> mask = ski.draw.polygon2mask(image_shape, polygon)
>>> mask.astype(int)
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 1, 1, 1, 1, 1, 1, 0, 0],
       [0, 0, 1, 1, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 1, 1, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])

If vertices / points of the polygon are outside the coordinate space defined by image_shape, only a part (or none at all) of the polygon is drawn in the mask.

>>> offset = np.array([[2, -4]])
>>> ski.draw.polygon2mask(image_shape, polygon - offset).astype(int)
array([[0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 1, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 1, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 1],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
skimage.draw.polygon_perimeter(r, c, shape=None, clip=False)[source]#

Generate polygon perimeter coordinates.

Parameters:
r(N,) ndarray

Row coordinates of vertices of polygon.

c(N,) ndarray

Column coordinates of vertices of polygon.

shapetuple, optional

Image shape which is used to determine maximum extents of output pixel coordinates. This is useful for polygons that exceed the image size. If None, the full extents of the polygon is used. Must be at least length 2. Only the first two values are used to determine the extent of the input image.

clipbool, optional

Whether to clip the polygon to the provided shape. If this is set to True, the drawn figure will always be a closed polygon with all edges visible.

Returns:
rr, ccndarray of int

Pixel coordinates of polygon. May be used to directly index into an array, e.g. img[rr, cc] = 1.

Examples

>>> from skimage.draw import polygon_perimeter
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = polygon_perimeter([5, -1, 5, 10],
...                            [-1, 5, 11, 5],
...                            shape=img.shape, clip=True)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 1, 1, 1, 0, 0, 0],
       [0, 0, 0, 1, 0, 0, 0, 1, 0, 0],
       [0, 0, 1, 0, 0, 0, 0, 0, 1, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 1],
       [1, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       [1, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       [1, 0, 0, 0, 0, 0, 0, 0, 0, 1],
       [0, 1, 1, 0, 0, 0, 0, 0, 0, 1],
       [0, 0, 0, 1, 0, 0, 0, 1, 1, 0],
       [0, 0, 0, 0, 1, 1, 1, 0, 0, 0]], dtype=uint8)
skimage.draw.random_shapes(image_shape, max_shapes, min_shapes=1, min_size=2, max_size=None, num_channels=3, shape=None, intensity_range=None, allow_overlap=False, num_trials=100, rng=None, *, channel_axis=-1)[source]#

Generate an image with random shapes, labeled with bounding boxes.

The image is populated with random shapes with random sizes, random locations, and random colors, with or without overlap.

Shapes have random (row, col) starting coordinates and random sizes bounded by min_size and max_size. It can occur that a randomly generated shape will not fit the image at all. In that case, the algorithm will try again with new starting coordinates a certain number of times. However, it also means that some shapes may be skipped altogether. In that case, this function will generate fewer shapes than requested.

Parameters:
image_shapetuple

The number of rows and columns of the image to generate.

max_shapesint

The maximum number of shapes to (attempt to) fit into the shape.

min_shapesint, optional

The minimum number of shapes to (attempt to) fit into the shape.

min_sizeint, optional

The minimum dimension of each shape to fit into the image.

max_sizeint, optional

The maximum dimension of each shape to fit into the image.

num_channelsint, optional

Number of channels in the generated image. If 1, generate monochrome images, else color images with multiple channels. Ignored if multichannel is set to False.

shape{rectangle, circle, triangle, ellipse, None} str, optional

The name of the shape to generate or None to pick random ones.

intensity_range{tuple of tuples of uint8, tuple of uint8}, optional

The range of values to sample pixel values from. For grayscale images the format is (min, max). For multichannel - ((min, max),) if the ranges are equal across the channels, and ((min_0, max_0), … (min_N, max_N)) if they differ. As the function supports generation of uint8 arrays only, the maximum range is (0, 255). If None, set to (0, 254) for each channel reserving color of intensity = 255 for background.

allow_overlapbool, optional

If True, allow shapes to overlap.

num_trialsint, optional

How often to attempt to fit a shape into the image before skipping it.

rng{numpy.random.Generator, int}, optional

Pseudo-random number generator. By default, a PCG64 generator is used (see numpy.random.default_rng()). If rng is an int, it is used to seed the generator.

channel_axisint or None, optional

If None, the image is assumed to be a grayscale (single channel) image. Otherwise, this parameter indicates which axis of the array corresponds to channels.

New in version 0.19: channel_axis was added in 0.19.

Returns:
imageuint8 array

An image with the fitted shapes.

labelslist

A list of labels, one per shape in the image. Each label is a (category, ((r0, r1), (c0, c1))) tuple specifying the category and bounding box coordinates of the shape.

Other Parameters:
random_seedDEPRECATED

Deprecated in favor of rng.

Deprecated since version 0.21.

Examples

>>> import skimage.draw
>>> image, labels = skimage.draw.random_shapes((32, 32), max_shapes=3)
>>> image 
array([
   [[255, 255, 255],
    [255, 255, 255],
    [255, 255, 255],
    ...,
    [255, 255, 255],
    [255, 255, 255],
    [255, 255, 255]]], dtype=uint8)
>>> labels 
[('circle', ((22, 18), (25, 21))),
 ('triangle', ((5, 6), (13, 13)))]

Random Shapes

Random Shapes
skimage.draw.rectangle(start, end=None, extent=None, shape=None)[source]#

Generate coordinates of pixels within a rectangle.

Parameters:
starttuple

Origin point of the rectangle, e.g., ([plane,] row, column).

endtuple

End point of the rectangle ([plane,] row, column). For a 2D matrix, the slice defined by the rectangle is [start:(end+1)]. Either end or extent must be specified.

extenttuple

The extent (size) of the drawn rectangle. E.g., ([num_planes,] num_rows, num_cols). Either end or extent must be specified. A negative extent is valid, and will result in a rectangle going along the opposite direction. If extent is negative, the start point is not included.

shapetuple, optional

Image shape used to determine the maximum bounds of the output coordinates. This is useful for clipping rectangles that exceed the image size. By default, no clipping is done.

Returns:
coordsarray of int, shape (Ndim, Npoints)

The coordinates of all pixels in the rectangle.

Notes

This function can be applied to N-dimensional images, by passing start and end or extent as tuples of length N.

Examples

>>> import numpy as np
>>> from skimage.draw import rectangle
>>> img = np.zeros((5, 5), dtype=np.uint8)
>>> start = (1, 1)
>>> extent = (3, 3)
>>> rr, cc = rectangle(start, extent=extent, shape=img.shape)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0],
       [0, 1, 1, 1, 0],
       [0, 1, 1, 1, 0],
       [0, 1, 1, 1, 0],
       [0, 0, 0, 0, 0]], dtype=uint8)

>>> img = np.zeros((5, 5), dtype=np.uint8)
>>> start = (0, 1)
>>> end = (3, 3)
>>> rr, cc = rectangle(start, end=end, shape=img.shape)
>>> img[rr, cc] = 1
>>> img
array([[0, 1, 1, 1, 0],
       [0, 1, 1, 1, 0],
       [0, 1, 1, 1, 0],
       [0, 1, 1, 1, 0],
       [0, 0, 0, 0, 0]], dtype=uint8)

>>> import numpy as np
>>> from skimage.draw import rectangle
>>> img = np.zeros((6, 6), dtype=np.uint8)
>>> start = (3, 3)
>>>
>>> rr, cc = rectangle(start, extent=(2, 2))
>>> img[rr, cc] = 1
>>> rr, cc = rectangle(start, extent=(-2, 2))
>>> img[rr, cc] = 2
>>> rr, cc = rectangle(start, extent=(-2, -2))
>>> img[rr, cc] = 3
>>> rr, cc = rectangle(start, extent=(2, -2))
>>> img[rr, cc] = 4
>>> print(img)
[[0 0 0 0 0 0]
 [0 3 3 2 2 0]
 [0 3 3 2 2 0]
 [0 4 4 1 1 0]
 [0 4 4 1 1 0]
 [0 0 0 0 0 0]]
skimage.draw.rectangle_perimeter(start, end=None, extent=None, shape=None, clip=False)[source]#

Generate coordinates of pixels that are exactly around a rectangle.

Parameters:
starttuple

Origin point of the inner rectangle, e.g., (row, column).

endtuple

End point of the inner rectangle (row, column). For a 2D matrix, the slice defined by inner the rectangle is [start:(end+1)]. Either end or extent must be specified.

extenttuple

The extent (size) of the inner rectangle. E.g., (num_rows, num_cols). Either end or extent must be specified. Negative extents are permitted. See rectangle to better understand how they behave.

shapetuple, optional

Image shape used to determine the maximum bounds of the output coordinates. This is useful for clipping perimeters that exceed the image size. By default, no clipping is done. Must be at least length 2. Only the first two values are used to determine the extent of the input image.

clipbool, optional

Whether to clip the perimeter to the provided shape. If this is set to True, the drawn figure will always be a closed polygon with all edges visible.

Returns:
coordsarray of int, shape (2, Npoints)

The coordinates of all pixels in the rectangle.

Examples

>>> import numpy as np
>>> from skimage.draw import rectangle_perimeter
>>> img = np.zeros((5, 6), dtype=np.uint8)
>>> start = (2, 3)
>>> end = (3, 4)
>>> rr, cc = rectangle_perimeter(start, end=end, shape=img.shape)
>>> img[rr, cc] = 1
>>> img
array([[0, 0, 0, 0, 0, 0],
       [0, 0, 1, 1, 1, 1],
       [0, 0, 1, 0, 0, 1],
       [0, 0, 1, 0, 0, 1],
       [0, 0, 1, 1, 1, 1]], dtype=uint8)

>>> img = np.zeros((5, 5), dtype=np.uint8)
>>> r, c = rectangle_perimeter(start, (10, 10), shape=img.shape, clip=True)
>>> img[r, c] = 1
>>> img
array([[0, 0, 0, 0, 0],
       [0, 0, 1, 1, 1],
       [0, 0, 1, 0, 1],
       [0, 0, 1, 0, 1],
       [0, 0, 1, 1, 1]], dtype=uint8)
skimage.draw.set_color(image, coords, color, alpha=1)[source]#

Set pixel color in the image at the given coordinates.

Note that this function modifies the color of the image in-place. Coordinates that exceed the shape of the image will be ignored.

Parameters:
image(M, N, D) ndarray

Image

coordstuple of ((P,) ndarray, (P,) ndarray)

Row and column coordinates of pixels to be colored.

color(D,) ndarray

Color to be assigned to coordinates in the image.

alphascalar or (N,) ndarray

Alpha values used to blend color with image. 0 is transparent, 1 is opaque.

Examples

>>> from skimage.draw import line, set_color
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = line(1, 1, 20, 20)
>>> set_color(img, (rr, cc), 1)
>>> img
array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 1, 0, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 1, 0],
       [0, 0, 0, 0, 0, 0, 0, 0, 0, 1]], dtype=uint8)