import warnings from skimage import img_as_ubyte from .misc import default_fallback from . import cmorph __all__ = ['erosion', 'dilation', 'opening', 'closing', 'white_tophat', 'black_tophat'] @default_fallback def erosion(image, selem=None, out=None, shift_x=False, shift_y=False): """Return greyscale morphological erosion of an image. Morphological erosion sets a pixel at (i,j) to the minimum over all pixels in the neighborhood centered at (i,j). Erosion shrinks bright regions and enlarges dark regions. Parameters ---------- image : ndarray Image array. selem : ndarray, optional The neighborhood expressed as a 2-D array of 1's and 0's. If None, use cross-shaped structuring element (connectivity=1). out : ndarrays, optional The array to store the result of the morphology. If None is passed, a new array will be allocated. shift_x, shift_y : bool, optional shift structuring element about center point. This only affects eccentric structuring elements (i.e. selem with even numbered sides). Returns ------- eroded : uint8 array The result of the morphological erosion. Examples -------- >>> # Erosion shrinks bright regions >>> import numpy as np >>> from skimage.morphology import square >>> bright_square = np.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=np.uint8) >>> erosion(bright_square, square(3)) array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]], dtype=uint8) """ if image is out: raise NotImplementedError("In-place erosion not supported!") image = img_as_ubyte(image) selem = img_as_ubyte(selem) return cmorph._erode(image, selem, out=out, shift_x=shift_x, shift_y=shift_y) @default_fallback def dilation(image, selem=None, out=None, shift_x=False, shift_y=False): """Return greyscale morphological dilation of an image. Morphological dilation sets a pixel at (i,j) to the maximum over all pixels in the neighborhood centered at (i,j). Dilation enlarges bright regions and shrinks dark regions. Parameters ---------- image : ndarray Image array. selem : ndarray, optional The neighborhood expressed as a 2-D array of 1's and 0's. If None, use cross-shaped structuring element (connectivity=1). out : ndarray, optional The array to store the result of the morphology. If None, is passed, a new array will be allocated. shift_x, shift_y : bool, optional shift structuring element about center point. This only affects eccentric structuring elements (i.e. selem with even numbered sides). Returns ------- dilated : uint8 array The result of the morphological dilation. Examples -------- >>> # Dilation enlarges bright regions >>> import numpy as np >>> from skimage.morphology import square >>> bright_pixel = np.array([[0, 0, 0, 0, 0], ... [0, 0, 0, 0, 0], ... [0, 0, 1, 0, 0], ... [0, 0, 0, 0, 0], ... [0, 0, 0, 0, 0]], dtype=np.uint8) >>> dilation(bright_pixel, square(3)) 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) """ if image is out: raise NotImplementedError("In-place dilation not supported!") image = img_as_ubyte(image) selem = img_as_ubyte(selem) return cmorph._dilate(image, selem, out=out, shift_x=shift_x, shift_y=shift_y) @default_fallback def opening(image, selem=None, out=None): """Return greyscale morphological opening of an image. The morphological opening on an image is defined as an erosion followed by a dilation. Opening can remove small bright spots (i.e. "salt") and connect small dark cracks. This tends to "open" up (dark) gaps between (bright) features. Parameters ---------- image : ndarray Image array. selem : ndarray, optional The neighborhood expressed as a 2-D array of 1's and 0's. If None, use cross-shaped structuring element (connectivity=1). out : ndarray, optional The array to store the result of the morphology. If None is passed, a new array will be allocated. Returns ------- opening : uint8 array The result of the morphological opening. Examples -------- >>> # Open up gap between two bright regions (but also shrink regions) >>> import numpy as np >>> from skimage.morphology import square >>> bad_connection = np.array([[1, 0, 0, 0, 1], ... [1, 1, 0, 1, 1], ... [1, 1, 1, 1, 1], ... [1, 1, 0, 1, 1], ... [1, 0, 0, 0, 1]], dtype=np.uint8) >>> opening(bad_connection, square(3)) array([[0, 0, 0, 0, 0], [1, 1, 0, 1, 1], [1, 1, 0, 1, 1], [1, 1, 0, 1, 1], [0, 0, 0, 0, 0]], dtype=uint8) """ h, w = selem.shape shift_x = True if (w % 2) == 0 else False shift_y = True if (h % 2) == 0 else False eroded = erosion(image, selem) out = dilation(eroded, selem, out=out, shift_x=shift_x, shift_y=shift_y) return out @default_fallback def closing(image, selem=None, out=None): """Return greyscale morphological closing of an image. The morphological closing on an image is defined as a dilation followed by an erosion. Closing can remove small dark spots (i.e. "pepper") and connect small bright cracks. This tends to "close" up (dark) gaps between (bright) features. Parameters ---------- image : ndarray Image array. selem : ndarray, optional The neighborhood expressed as a 2-D array of 1's and 0's. If None, use cross-shaped structuring element (connectivity=1). out : ndarray, optional The array to store the result of the morphology. If None, is passed, a new array will be allocated. Returns ------- closing : uint8 array The result of the morphological closing. Examples -------- >>> # Close a gap between two bright lines >>> import numpy as np >>> from skimage.morphology import square >>> broken_line = np.array([[0, 0, 0, 0, 0], ... [0, 0, 0, 0, 0], ... [1, 1, 0, 1, 1], ... [0, 0, 0, 0, 0], ... [0, 0, 0, 0, 0]], dtype=np.uint8) >>> closing(broken_line, square(3)) array([[0, 0, 0, 0, 0], [0, 0, 0, 0, 0], [1, 1, 1, 1, 1], [0, 0, 0, 0, 0], [0, 0, 0, 0, 0]], dtype=uint8) """ h, w = selem.shape shift_x = True if (w % 2) == 0 else False shift_y = True if (h % 2) == 0 else False dilated = dilation(image, selem) out = erosion(dilated, selem, out=out, shift_x=shift_x, shift_y=shift_y) return out @default_fallback def white_tophat(image, selem=None, out=None): """Return white top hat of an image. The white top hat of an image is defined as the image minus its morphological opening. This operation returns the bright spots of the image that are smaller than the structuring element. Parameters ---------- image : ndarray Image array. selem : ndarray, optional The neighborhood expressed as a 2-D array of 1's and 0's. If None, use cross-shaped structuring element (connectivity=1). out : ndarray, optional The array to store the result of the morphology. If None is passed, a new array will be allocated. Returns ------- opening : uint8 array The result of the morphological white top hat. Examples -------- >>> # Subtract grey background from bright peak >>> import numpy as np >>> from skimage.morphology import square >>> bright_on_grey = np.array([[2, 3, 3, 3, 2], ... [3, 4, 5, 4, 3], ... [3, 5, 9, 5, 3], ... [3, 4, 5, 4, 3], ... [2, 3, 3, 3, 2]], dtype=np.uint8) >>> white_tophat(bright_on_grey, square(3)) array([[0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 1, 5, 1, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0]], dtype=uint8) """ if image is out: raise NotImplementedError("Cannot perform white top hat in place.") out = opening(image, selem, out=out) out = image - out return out @default_fallback def black_tophat(image, selem=None, out=None): """Return black top hat of an image. The black top hat of an image is defined as its morphological closing minus the original image. This operation returns the dark spots of the image that are smaller than the structuring element. Note that dark spots in the original image are bright spots after the black top hat. Parameters ---------- image : ndarray Image array. selem : ndarray, optional The neighborhood expressed as a 2-D array of 1's and 0's. If None, use cross-shaped structuring element (connectivity=1). out : ndarray, optional The array to store the result of the morphology. If None is passed, a new array will be allocated. Returns ------- opening : uint8 array The result of the black top filter. Examples -------- >>> # Change dark peak to bright peak and subtract background >>> import numpy as np >>> from skimage.morphology import square >>> dark_on_grey = np.array([[7, 6, 6, 6, 7], ... [6, 5, 4, 5, 6], ... [6, 4, 0, 4, 6], ... [6, 5, 4, 5, 6], ... [7, 6, 6, 6, 7]], dtype=np.uint8) >>> black_tophat(dark_on_grey, square(3)) array([[0, 0, 0, 0, 0], [0, 0, 1, 0, 0], [0, 1, 5, 1, 0], [0, 0, 1, 0, 0], [0, 0, 0, 0, 0]], dtype=uint8) """ if image is out: raise NotImplementedError("Cannot perform white top hat in place.") out = closing(image, selem, out=out) out = out - image return out