mirror of
https://github.com/wassname/scikit-image.git
synced 2026-07-12 20:45:35 +08:00
Fixed doctest problem
This commit is contained in:
Julius Bier Kirkegaard
@@ -1,233 +1,233 @@
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import warnings
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import numpy as np
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from skimage import img_as_float
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import scipy
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import scipy.linalg
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from scipy.interpolate import RectBivariateSpline, interp2d
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from skimage.filters import sobel
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def active_contour(image, snake, alpha=0.01, beta=0.1,
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w_line=0, w_edge=1, gamma=0.01,
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bc='periodic', max_px_move=1.0,
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max_iterations=2500, convergence=0.1):
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"""Active contour model.
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Active contours by fitting snakes to features of images. Supports single
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and multichannel 2D images. Snakes can be periodic (for segmentation) or
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have fixed and/or free ends.
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Parameters
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----------
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image : (N, M) or (N, M, 3) ndarray
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Input image.
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snake : (N, 2) ndarray
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Initialisation coordinates of snake. For periodic snakes, it should
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not include duplicate endpoints.
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alpha : float, optional
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Snake length shape parameter. Higher values makes snake contract
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faster.
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beta : float, optional
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Snake smoothness shape parameter. Higher values makes snake smoother.
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w_line : float, optional
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Controls attraction to brightness. Use negative values to attract to
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dark regions.
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w_edge : float, optional
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Controls attraction to edges. Use negative values to repel snake from
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edges.
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gamma : float, optional
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Explicit time stepping parameter.
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bc : {'periodic', 'free', 'fixed'}, optional
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Boundary conditions for worm. 'periodic' attaches the two ends of the
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snake, 'fixed' holds the end-points in place, and'free' allows free
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movement of the ends. 'fixed' and 'free' can be combined by parsing
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'fixed-free', 'free-fixed'. Parsing 'fixed-fixed' or 'free-free'
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yields same behaviour as 'fixed' and 'free', respectively.
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max_px_move : float, optional
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Maximum pixel distance to move per iteration.
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max_iterations : int, optional
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Maximum iterations to optimize snake shape.
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convergence: float, optional
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Convergence criteria.
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Returns
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-------
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snake : (N, 2) ndarray
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Optimised snake, same shape as input parameter.
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References
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----------
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.. [1] Kass, M.; Witkin, A.; Terzopoulos, D. "Snakes: Active contour
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models". International Journal of Computer Vision 1 (4): 321
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(1988).
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Examples
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--------
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>>> from skimage.draw import circle_perimeter
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>>> from skimage.filters import gaussian_filter
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Create and smooth image:
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>>> img = np.zeros((100, 100))
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>>> rr, cc = circle_perimeter(35, 45, 25)
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>>> img[rr, cc] = 1
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>>> img = gaussian_filter(img, 2)
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Initiliaze spline:
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>>> s = np.linspace(0, 2*np.pi,100)
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>>> init = 50*np.array([np.cos(s), np.sin(s)]).T+50
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Fit spline to image:
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>>> snake = active_contour(img, init, w_edge=0, w_line=1) #doctest: +SKIP
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>>> int(np.mean(np.sqrt((45-snake[:, 0])**2 +
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(35-snake[:, 1])**2))) #doctest: +SKIP
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25
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"""
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scipy_version = list(map(int, scipy.__version__.split('.')))
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new_scipy = scipy_version[0] > 0 or \
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(scipy_version[0] == 0 and scipy_version[1] >= 14)
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if not new_scipy:
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raise NotImplementedError('You are using an old version of scipy. '
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'Active contours is implemented for scipy versions '
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'0.14.0 and above.')
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max_iterations = int(max_iterations)
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if max_iterations <= 0:
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raise ValueError("max_iterations should be >0.")
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convergence_order = 10
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valid_bcs = ['periodic', 'free', 'fixed', 'free-fixed',
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'fixed-free', 'fixed-fixed', 'free-free']
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if bc not in valid_bcs:
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raise ValueError("Invalid boundary condition.\n"+
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"Should be one of: "+", ".join(valid_bcs)+'.')
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img = img_as_float(image)
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RGB = img.ndim == 3
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# Find edges using sobel:
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if w_edge != 0:
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if RGB:
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edge = [sobel(img[:, :, 0]), sobel(img[:, :, 1]),
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sobel(img[:, :, 2])]
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else:
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edge = [sobel(img)]
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for i in range(3 if RGB else 1):
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edge[i][0, :] = edge[i][1, :]
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edge[i][-1, :] = edge[i][-2, :]
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edge[i][:, 0] = edge[i][:, 1]
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edge[i][:, -1] = edge[i][:, -2]
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else:
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edge = [0]
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# Superimpose intensity and edge images:
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if RGB:
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img = w_line*np.sum(img, axis=2) \
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+ w_edge*sum(edge)
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else:
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img = w_line*img + w_edge*edge[0]
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# Interpolate for smoothness:
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if new_scipy:
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intp = RectBivariateSpline(np.arange(img.shape[1]),
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np.arange(img.shape[0]), img.T, kx=2, ky=2, s=0)
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else:
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intp = np.vectorize(interp2d(np.arange(img.shape[1]),
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np.arange(img.shape[0]), img, kind='cubic', copy=False,
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bounds_error=False, fill_value=0))
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x, y = snake[:, 0].copy(), snake[:, 1].copy()
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xsave = np.empty((convergence_order, len(x)))
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ysave = np.empty((convergence_order, len(x)))
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# Build snake shape matrix for Euler equation
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n = len(x)
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a = np.roll(np.eye(n), -1, axis=0) \
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+ np.roll(np.eye(n), -1, axis=1) \
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- 2*np.eye(n) # second order derivative, central difference
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b = np.roll(np.eye(n), -2, axis=0) \
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+ np.roll(np.eye(n), -2, axis=1) \
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- 4*np.roll(np.eye(n), -1, axis=0) \
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- 4*np.roll(np.eye(n), -1, axis=1) \
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+ 6*np.eye(n) # fourth order derivative, central difference
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A = -alpha*a + beta*b
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# Impose boundary conditions different from periodic:
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sfixed = False
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if bc.startswith('fixed'):
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A[0, :] = 0
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A[1, :] = 0
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A[1, :3] = [1, -2, 1]
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sfixed = True
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efixed = False
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if bc.endswith('fixed'):
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A[-1, :] = 0
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A[-2, :] = 0
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A[-2, -3:] = [1, -2, 1]
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efixed = True
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sfree = False
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if bc.startswith('free'):
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A[0, :] = 0
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A[0, :3] = [1, -2, 1]
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A[1, :] = 0
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A[1, :4] = [-1, 3, -3, 1]
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sfree = True
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efree = False
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if bc.endswith('free'):
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A[-1, :] = 0
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A[-1, -3:] = [1, -2, 1]
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A[-2, :] = 0
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A[-2, -4:] = [-1, 3, -3, 1]
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efree = True
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# Only one inversion is needed for implicit spline energy minimization:
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inv = scipy.linalg.inv(A+gamma*np.eye(n))
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# Explicit time stepping for image energy minimization:
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for i in range(max_iterations):
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if new_scipy:
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fx = intp(x, y, dx=1, grid=False)
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fy = intp(x, y, dy=1, grid=False)
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else:
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fx = intp(x, y, dx=1)
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fy = intp(x, y, dy=1)
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if sfixed:
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fx[0] = 0
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fy[0] = 0
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if efixed:
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fx[-1] = 0
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fy[-1] = 0
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if sfree:
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fx[0] *= 2
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fy[0] *= 2
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if efree:
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fx[-1] *= 2
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fy[-1] *= 2
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xn = np.dot(inv, gamma*x + fx)
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yn = np.dot(inv, gamma*y + fy)
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# Movements are capped to max_px_move per iteration:
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dx = max_px_move*np.tanh(xn-x)
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dy = max_px_move*np.tanh(yn-y)
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if sfixed:
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dx[0] = 0
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dy[0] = 0
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if efixed:
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dx[-1] = 0
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dy[-1] = 0
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x[:] += dx
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y[:] += dy
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# Convergence criteria needs to compare to a number of previous
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# configurations since oscillations can occur.
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j = i%(convergence_order+1)
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if j < convergence_order:
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xsave[j, :] = x
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ysave[j, :] = y
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else:
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dist = np.min(np.max(np.abs(xsave-x[None, :])
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+ np.abs(ysave-y[None, :]), 1))
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if dist < convergence:
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break
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return np.array([x, y]).T
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import warnings
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import numpy as np
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from skimage import img_as_float
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import scipy
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import scipy.linalg
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from scipy.interpolate import RectBivariateSpline, interp2d
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from skimage.filters import sobel
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def active_contour(image, snake, alpha=0.01, beta=0.1,
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w_line=0, w_edge=1, gamma=0.01,
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bc='periodic', max_px_move=1.0,
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max_iterations=2500, convergence=0.1):
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"""Active contour model.
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Active contours by fitting snakes to features of images. Supports single
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and multichannel 2D images. Snakes can be periodic (for segmentation) or
|
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have fixed and/or free ends.
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Parameters
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----------
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image : (N, M) or (N, M, 3) ndarray
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Input image.
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snake : (N, 2) ndarray
|
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Initialisation coordinates of snake. For periodic snakes, it should
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not include duplicate endpoints.
|
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alpha : float, optional
|
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Snake length shape parameter. Higher values makes snake contract
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faster.
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beta : float, optional
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Snake smoothness shape parameter. Higher values makes snake smoother.
|
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w_line : float, optional
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Controls attraction to brightness. Use negative values to attract to
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dark regions.
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w_edge : float, optional
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Controls attraction to edges. Use negative values to repel snake from
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edges.
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gamma : float, optional
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Explicit time stepping parameter.
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bc : {'periodic', 'free', 'fixed'}, optional
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Boundary conditions for worm. 'periodic' attaches the two ends of the
|
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snake, 'fixed' holds the end-points in place, and'free' allows free
|
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movement of the ends. 'fixed' and 'free' can be combined by parsing
|
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'fixed-free', 'free-fixed'. Parsing 'fixed-fixed' or 'free-free'
|
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yields same behaviour as 'fixed' and 'free', respectively.
|
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max_px_move : float, optional
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Maximum pixel distance to move per iteration.
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max_iterations : int, optional
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Maximum iterations to optimize snake shape.
|
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convergence: float, optional
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Convergence criteria.
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Returns
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-------
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snake : (N, 2) ndarray
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Optimised snake, same shape as input parameter.
|
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|
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References
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----------
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.. [1] Kass, M.; Witkin, A.; Terzopoulos, D. "Snakes: Active contour
|
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models". International Journal of Computer Vision 1 (4): 321
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(1988).
|
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|
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Examples
|
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--------
|
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>>> from skimage.draw import circle_perimeter
|
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>>> from skimage.filters import gaussian_filter
|
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|
||||
Create and smooth image:
|
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|
||||
>>> img = np.zeros((100, 100))
|
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>>> rr, cc = circle_perimeter(35, 45, 25)
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>>> img[rr, cc] = 1
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>>> img = gaussian_filter(img, 2)
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|
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Initiliaze spline:
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|
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>>> s = np.linspace(0, 2*np.pi,100)
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>>> init = 50*np.array([np.cos(s), np.sin(s)]).T+50
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Fit spline to image:
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>>> snake = active_contour(img, init, w_edge=0, w_line=1) #doctest: +SKIP
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>>> dist = np.sqrt((45-snake[:, 0])**2 +(35-snake[:, 1])**2) #doctest: +SKIP
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>>> int(np.mean(dist)) #doctest: +SKIP
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25
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"""
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scipy_version = list(map(int, scipy.__version__.split('.')))
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new_scipy = scipy_version[0] > 0 or \
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(scipy_version[0] == 0 and scipy_version[1] >= 14)
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if not new_scipy:
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raise NotImplementedError('You are using an old version of scipy. '
|
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'Active contours is implemented for scipy versions '
|
||||
'0.14.0 and above.')
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max_iterations = int(max_iterations)
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if max_iterations <= 0:
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raise ValueError("max_iterations should be >0.")
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convergence_order = 10
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valid_bcs = ['periodic', 'free', 'fixed', 'free-fixed',
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'fixed-free', 'fixed-fixed', 'free-free']
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if bc not in valid_bcs:
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raise ValueError("Invalid boundary condition.\n"+
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"Should be one of: "+", ".join(valid_bcs)+'.')
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img = img_as_float(image)
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RGB = img.ndim == 3
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# Find edges using sobel:
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if w_edge != 0:
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if RGB:
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edge = [sobel(img[:, :, 0]), sobel(img[:, :, 1]),
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sobel(img[:, :, 2])]
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else:
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edge = [sobel(img)]
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for i in range(3 if RGB else 1):
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edge[i][0, :] = edge[i][1, :]
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edge[i][-1, :] = edge[i][-2, :]
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edge[i][:, 0] = edge[i][:, 1]
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edge[i][:, -1] = edge[i][:, -2]
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else:
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edge = [0]
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|
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# Superimpose intensity and edge images:
|
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if RGB:
|
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img = w_line*np.sum(img, axis=2) \
|
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+ w_edge*sum(edge)
|
||||
else:
|
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img = w_line*img + w_edge*edge[0]
|
||||
|
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# Interpolate for smoothness:
|
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if new_scipy:
|
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intp = RectBivariateSpline(np.arange(img.shape[1]),
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np.arange(img.shape[0]), img.T, kx=2, ky=2, s=0)
|
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else:
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intp = np.vectorize(interp2d(np.arange(img.shape[1]),
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np.arange(img.shape[0]), img, kind='cubic', copy=False,
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bounds_error=False, fill_value=0))
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x, y = snake[:, 0].copy(), snake[:, 1].copy()
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xsave = np.empty((convergence_order, len(x)))
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ysave = np.empty((convergence_order, len(x)))
|
||||
|
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# Build snake shape matrix for Euler equation
|
||||
n = len(x)
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||||
a = np.roll(np.eye(n), -1, axis=0) \
|
||||
+ np.roll(np.eye(n), -1, axis=1) \
|
||||
- 2*np.eye(n) # second order derivative, central difference
|
||||
b = np.roll(np.eye(n), -2, axis=0) \
|
||||
+ np.roll(np.eye(n), -2, axis=1) \
|
||||
- 4*np.roll(np.eye(n), -1, axis=0) \
|
||||
- 4*np.roll(np.eye(n), -1, axis=1) \
|
||||
+ 6*np.eye(n) # fourth order derivative, central difference
|
||||
A = -alpha*a + beta*b
|
||||
|
||||
# Impose boundary conditions different from periodic:
|
||||
sfixed = False
|
||||
if bc.startswith('fixed'):
|
||||
A[0, :] = 0
|
||||
A[1, :] = 0
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||||
A[1, :3] = [1, -2, 1]
|
||||
sfixed = True
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efixed = False
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||||
if bc.endswith('fixed'):
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A[-1, :] = 0
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A[-2, :] = 0
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A[-2, -3:] = [1, -2, 1]
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efixed = True
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sfree = False
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if bc.startswith('free'):
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A[0, :] = 0
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A[0, :3] = [1, -2, 1]
|
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A[1, :] = 0
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A[1, :4] = [-1, 3, -3, 1]
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sfree = True
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efree = False
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if bc.endswith('free'):
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||||
A[-1, :] = 0
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||||
A[-1, -3:] = [1, -2, 1]
|
||||
A[-2, :] = 0
|
||||
A[-2, -4:] = [-1, 3, -3, 1]
|
||||
efree = True
|
||||
|
||||
# Only one inversion is needed for implicit spline energy minimization:
|
||||
inv = scipy.linalg.inv(A+gamma*np.eye(n))
|
||||
|
||||
# Explicit time stepping for image energy minimization:
|
||||
for i in range(max_iterations):
|
||||
if new_scipy:
|
||||
fx = intp(x, y, dx=1, grid=False)
|
||||
fy = intp(x, y, dy=1, grid=False)
|
||||
else:
|
||||
fx = intp(x, y, dx=1)
|
||||
fy = intp(x, y, dy=1)
|
||||
if sfixed:
|
||||
fx[0] = 0
|
||||
fy[0] = 0
|
||||
if efixed:
|
||||
fx[-1] = 0
|
||||
fy[-1] = 0
|
||||
if sfree:
|
||||
fx[0] *= 2
|
||||
fy[0] *= 2
|
||||
if efree:
|
||||
fx[-1] *= 2
|
||||
fy[-1] *= 2
|
||||
xn = np.dot(inv, gamma*x + fx)
|
||||
yn = np.dot(inv, gamma*y + fy)
|
||||
|
||||
# Movements are capped to max_px_move per iteration:
|
||||
dx = max_px_move*np.tanh(xn-x)
|
||||
dy = max_px_move*np.tanh(yn-y)
|
||||
if sfixed:
|
||||
dx[0] = 0
|
||||
dy[0] = 0
|
||||
if efixed:
|
||||
dx[-1] = 0
|
||||
dy[-1] = 0
|
||||
x[:] += dx
|
||||
y[:] += dy
|
||||
|
||||
# Convergence criteria needs to compare to a number of previous
|
||||
# configurations since oscillations can occur.
|
||||
j = i%(convergence_order+1)
|
||||
if j < convergence_order:
|
||||
xsave[j, :] = x
|
||||
ysave[j, :] = y
|
||||
else:
|
||||
dist = np.min(np.max(np.abs(xsave-x[None, :])
|
||||
+ np.abs(ysave-y[None, :]), 1))
|
||||
if dist < convergence:
|
||||
break
|
||||
|
||||
return np.array([x, y]).T
|
||||
|
||||
Reference in New Issue
Block a user