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Merge pull request #568 from ahojnnes/circle

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ENH: Faster version of circle and ellipse drawing.
This commit is contained in:
Stefan van der Walt
2013-05-27 13:11:38 -07:00
parent 03119e37b4 a12e557849
commit ba354dde4d
3 changed files with 237 additions and 116 deletions
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skimage/draw/__init__.py
+3 -4
View File
@@ -1,5 +1,5 @@
from ._draw import line, polygon, ellipse, ellipse_perimeter, \
circle, circle_perimeter, set_color, bresenham
from .draw import circle, ellipse, set_color
from ._draw import line, polygon, ellipse_perimeter, circle_perimeter
__all__ = ['line',
'polygon',
@@ -7,5 +7,4 @@ __all__ = ['line',
'ellipse_perimeter',
'circle',
'circle_perimeter',
'set_color',
'bresenham']
'set_color']
skimage/draw/_draw.pyx
+78 -112
View File
@@ -8,7 +8,6 @@ import numpy as np
cimport numpy as cnp
from libc.math cimport sqrt
from skimage._shared.geometry cimport point_in_polygon
from skimage._shared.utils import deprecated
def line(Py_ssize_t y, Py_ssize_t x, Py_ssize_t y2, Py_ssize_t x2):
@@ -28,6 +27,24 @@ def line(Py_ssize_t y, Py_ssize_t x, Py_ssize_t y2, Py_ssize_t x2):
May be used to directly index into an array, e.g.
``img[rr, cc] = 1``.
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)
"""
cdef cnp.ndarray[cnp.intp_t, ndim=1, mode="c"] rr, cc
@@ -74,9 +91,6 @@ def line(Py_ssize_t y, Py_ssize_t x, Py_ssize_t y2, Py_ssize_t x2):
return rr, cc
bresenham = deprecated('skimage.draw.line')(line)
def polygon(y, x, shape=None):
"""Generate coordinates of pixels within polygon.
@@ -87,7 +101,7 @@ def polygon(y, x, shape=None):
x : (N,) ndarray
X-coordinates of vertices of polygon.
shape : tuple, optional
image shape which is used to determine maximum extents of output pixel
Image shape which is used to determine maximum extents of output pixel
coordinates. This is useful for polygons which exceed the image size.
By default the full extents of the polygon are used.
@@ -98,6 +112,26 @@ def polygon(y, x, shape=None):
May be used to directly index into an array, e.g.
``img[rr, cc] = 1``.
Examples
--------
>>> from skimage.draw import polygon
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> x = np.array([1, 7, 4, 1])
>>> y = np.array([1, 2, 8, 1])
>>> rr, cc = polygon(y, x)
>>> 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, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 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, 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]], dtype=uint8)
"""
cdef Py_ssize_t nr_verts = x.shape[0]
@@ -133,82 +167,6 @@ def polygon(y, x, shape=None):
return np.array(rr, dtype=np.intp), np.array(cc, dtype=np.intp)
def ellipse(double cy, double cx, double yradius, double xradius, shape=None):
"""Generate coordinates of pixels within ellipse.
Parameters
----------
cy, cx : double
Centre coordinate of ellipse.
yradius, xradius : double
Minor and major semi-axes. ``(x/xradius)**2 + (y/yradius)**2 = 1``.
shape : tuple, optional
image shape which is used to determine maximum extents of output pixel
coordinates. This is useful for ellipses which exceed the image size.
By default the full extents of the ellipse are used.
Returns
-------
rr, cc : ndarray of int
Pixel coordinates of ellipse.
May be used to directly index into an array, e.g.
``img[rr, cc] = 1``.
"""
cdef Py_ssize_t minr = int(max(0, cy - yradius))
cdef Py_ssize_t maxr = int(math.ceil(cy + yradius))
cdef Py_ssize_t minc = int(max(0, cx - xradius))
cdef Py_ssize_t maxc = int(math.ceil(cx + xradius))
# make sure output coordinates do not exceed image size
if shape is not None:
maxr = min(shape[0] - 1, maxr)
maxc = min(shape[1] - 1, maxc)
cdef Py_ssize_t r, c
# output coordinate arrays
cdef list rr = list()
cdef list cc = list()
for r in range(minr, maxr+1):
for c in range(minc, maxc+1):
if sqrt(((r - cy) / yradius)**2 + ((c - cx) / xradius)**2) < 1:
rr.append(r)
cc.append(c)
return np.array(rr, dtype=np.intp), np.array(cc, dtype=np.intp)
def circle(double cy, double cx, double radius, shape=None):
"""Generate coordinates of pixels within circle.
Parameters
----------
cy, cx : double
Centre coordinate of circle.
radius: double
Radius of circle.
shape : tuple, optional
image shape which is used to determine maximum extents of output pixel
coordinates. This is useful for circles which exceed the image size.
By default the full extents of the circle are used.
Returns
-------
rr, cc : ndarray of int
Pixel coordinates of circle.
May be used to directly index into an array, e.g.
``img[rr, cc] = 1``.
Notes
-----
This function is a wrapper for skimage.draw.ellipse()
"""
return ellipse(cy, cx, radius, radius, shape)
def circle_perimeter(Py_ssize_t cy, Py_ssize_t cx, Py_ssize_t radius,
method='bresenham'):
"""Generate circle perimeter coordinates.
@@ -223,7 +181,6 @@ def circle_perimeter(Py_ssize_t cy, Py_ssize_t cx, Py_ssize_t radius,
bresenham : Bresenham method
andres : Andres method
Returns
-------
rr, cc : (N,) ndarray of int
@@ -241,8 +198,27 @@ def circle_perimeter(Py_ssize_t cy, Py_ssize_t cx, Py_ssize_t radius,
References
----------
.. [1] J.E. Bresenham, "Algorithm for computer control of a digital
plotter", 4 (1965) 25-30.
.. [2] E. Andres, "Discrete circles, rings and spheres", 18 (1994) 695-706.
plotter", 4 (1965) 25-30.
.. [2] E. Andres, "Discrete circles, rings and spheres",
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)
"""
@@ -311,6 +287,24 @@ def ellipse_perimeter(Py_ssize_t cy, Py_ssize_t cx, Py_ssize_t yradius,
.. [1] J. Kennedy "A fast Bresenham type algorithm for
drawing ellipses".
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)
"""
# If both radii == 0, return the center to avoid infinite loop in 2nd set
@@ -373,31 +367,3 @@ def ellipse_perimeter(Py_ssize_t cy, Py_ssize_t cx, Py_ssize_t yradius,
ychange += twobsquared
return np.array(py, dtype=np.intp) + cy, np.array(px, dtype=np.intp) + cx
def set_color(img, coords, color):
"""Set pixel color in the image at the given coordinates.
Coordinates that exceed the shape of the image will be ignored.
Parameters
----------
img : (M, N, D) ndarray
Image
coords : ((P,) ndarray, (P,) ndarray)
Coordinates of pixels to be colored.
color : (D,) ndarray
Color to be assigned to coordinates in the image.
Returns
-------
img : (M, N, D) ndarray
The updated image.
"""
rr, cc = coords
rr_inside = np.logical_and(rr >= 0, rr < img.shape[0])
cc_inside = np.logical_and(cc >= 0, cc < img.shape[1])
inside = np.logical_and(rr_inside, cc_inside)
img[rr[inside], cc[inside]] = color
skimage/draw/draw.py
+156
View File
@@ -0,0 +1,156 @@
# coding: utf-8
import numpy as np
def _coords_inside_image(rr, cc, shape):
mask = (rr >= 0) & (rr < shape[0]) & (cc >= 0) & (cc < shape[1])
return rr[mask], cc[mask]
def ellipse(cy, cx, yradius, xradius, shape=None):
"""Generate coordinates of pixels within ellipse.
Parameters
----------
cy, cx : double
Centre coordinate of ellipse.
yradius, xradius : double
Minor and major semi-axes. ``(x/xradius)**2 + (y/yradius)**2 = 1``.
shape : tuple, optional
Image shape which is used to determine maximum extents of output pixel
coordinates. This is useful for ellipses which exceed the image size.
By default the full extents of the ellipse are used.
Returns
-------
rr, cc : ndarray of int
Pixel coordinates of ellipse.
May be used to directly index into an array, e.g.
``img[rr, cc] = 1``.
Examples
--------
>>> from skimage.draw import ellipse
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = ellipse(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, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 0],
[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, 0, 0, 0, 0, 0, 0, 0, 0, 0]], dtype=uint8)
"""
dr = 1 / float(yradius)
dc = 1 / float(xradius)
r, c = np.ogrid[-1:1:dr, -1:1:dc]
rr, cc = np.nonzero(r ** 2 + c ** 2 < 1)
rr.flags.writeable = True
cc.flags.writeable = True
rr += cy - yradius
cc += cx - xradius
if shape is not None:
_coords_inside_image(rr, cc, shape)
return rr, cc
def circle(cy, cx, radius, shape=None):
"""Generate coordinates of pixels within circle.
Parameters
----------
cy, cx : double
Centre coordinate of circle.
radius: double
Radius of circle.
shape : tuple, optional
Image shape which is used to determine maximum extents of output pixel
coordinates. This is useful for circles which exceed the image size.
By default the full extents of the circle are used.
Returns
-------
rr, cc : ndarray of int
Pixel coordinates of circle.
May be used to directly index into an array, e.g.
``img[rr, cc] = 1``.
Notes
-----
This function is a wrapper for skimage.draw.ellipse()
Examples
--------
>>> from skimage.draw import circle
>>> img = np.zeros((10, 10), dtype=np.uint8)
>>> rr, cc = circle(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)
"""
return ellipse(cy, cx, radius, radius, shape)
def set_color(img, coords, color):
"""Set pixel color in the image at the given coordinates.
Coordinates that exceed the shape of the image will be ignored.
Parameters
----------
img : (M, N, D) ndarray
Image
coords : ((P,) ndarray, (P,) ndarray)
Coordinates of pixels to be colored.
color : (D,) ndarray
Color to be assigned to coordinates in the image.
Returns
-------
img : (M, N, D) ndarray
The updated image.
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)
"""
rr, cc = coords
rr, cc = _coords_inside_image(rr, cc, img.shape)
img[rr, cc] = color