"""extrema.py - local minima and maxima This module provides functions to find local maxima and minima of an image. Here, local maxima (minima) are defined as connected sets of pixels with equal gray level which is strictly greater (smaller) than the gray level of all pixels in direct neighborhood of the connected set. In addition, the module provides the related functions h-maxima and h-minima. Soille, P. (2003). Morphological Image Analysis: Principles and Applications (2nd ed.), Chapter 6. Springer-Verlag New York, Inc. """ import numpy as np from ..util import dtype_limits, invert, crop from .._shared.utils import warn from . import greyreconstruct, _util from ._extrema_cy import _local_maxima def _add_constant_clip(image, const_value): """Add constant to the image while handling overflow issues gracefully. """ min_dtype, max_dtype = dtype_limits(image, clip_negative=False) if const_value > (max_dtype - min_dtype): raise ValueError("The added constant is not compatible" "with the image data type.") result = image + const_value result[image > max_dtype-const_value] = max_dtype return(result) def _subtract_constant_clip(image, const_value): """Subtract constant from image while handling underflow issues. """ min_dtype, max_dtype = dtype_limits(image, clip_negative=False) if const_value > (max_dtype-min_dtype): raise ValueError("The subtracted constant is not compatible" "with the image data type.") result = image - const_value result[image < (const_value + min_dtype)] = min_dtype return(result) def h_maxima(image, h, selem=None): """Determine all maxima of the image with height >= h. The local maxima are defined as connected sets of pixels with equal grey level strictly greater than the grey level of all pixels in direct neighborhood of the set. A local maximum M of height h is a local maximum for which there is at least one path joining M with a higher maximum on which the minimal value is f(M) - h (i.e. the values along the path are not decreasing by more than h with respect to the maximum's value) and no path for which the minimal value is greater. Parameters ---------- image : ndarray The input image for which the maxima are to be calculated. h : unsigned integer The minimal height of all extracted maxima. selem : ndarray, optional The neighborhood expressed as an n-D array of 1's and 0's. Default is the ball of radius 1 according to the maximum norm (i.e. a 3x3 square for 2D images, a 3x3x3 cube for 3D images, etc.) Returns ------- h_max : ndarray The maxima of height >= h. The resulting image is a binary image, where pixels belonging to the selected maxima take value 1, the others take value 0. See also -------- skimage.morphology.extrema.h_minima skimage.morphology.extrema.local_maxima skimage.morphology.extrema.local_minima References ---------- .. [1] Soille, P., "Morphological Image Analysis: Principles and Applications" (Chapter 6), 2nd edition (2003), ISBN 3540429883. Examples -------- >>> import numpy as np >>> from skimage.morphology import extrema We create an image (quadratic function with a maximum in the center and 4 additional constant maxima. The heights of the maxima are: 1, 21, 41, 61, 81 >>> w = 10 >>> x, y = np.mgrid[0:w,0:w] >>> f = 20 - 0.2*((x - w/2)**2 + (y-w/2)**2) >>> f[2:4,2:4] = 40; f[2:4,7:9] = 60; f[7:9,2:4] = 80; f[7:9,7:9] = 100 >>> f = f.astype(np.int) We can calculate all maxima with a height of at least 40: >>> maxima = extrema.h_maxima(f, 40) The resulting image will contain 3 local maxima. """ # Check for h value that is larger then range of the image. If this # is True then there are no h-maxima in the image. if h > np.ptp(image): return np.zeros(image.shape, dtype=np.uint8) # Check for floating point h value. For this to work properly # we need to explicitly convert image to float64. # # FIXME: This could give incorrect results if image is int64 and # has a very high dynamic range. The dtype of image is # changed to float64, and different integer values could # become the same float due to rounding. # # >>> ii64 = np.iinfo(np.int64) # >>> a = np.array([ii64.max, ii64.max - 2]) # >>> a[0] == a[1] # False # >>> b = a.astype(np.float64) # >>> b[0] == b[1] # True # if np.issubdtype(type(h), np.floating) and \ np.issubdtype(image.dtype, np.integer): if ((h % 1) != 0): warn('possible precision loss converting image to ' 'floating point. To silence this warning, ' 'ensure image and h have same data type.', stacklevel=2) image = image.astype(np.float_) else: h = image.dtype.type(h) if (h == 0): raise ValueError("h = 0 is ambiguous, use local_maxima() " "instead?") if np.issubdtype(image.dtype, np.floating): # The purpose of the resolution variable is to allow for the # small rounding errors that inevitably occur when doing # floating point arithmetic. We want shifted_img to be # guaranteed to be h less than image. If we only subtract h # there may be pixels were shifted_img ends up being # slightly greater than image - h. # # The resolution is scaled based on the pixel values in the # image because floating point precision is relative. A # very large value of 1.0e10 will have a large precision, # say +-1.0e4, and a very small value of 1.0e-10 will have # a very small precision, say +-1.0e-16. # resolution = 2 * np.finfo(image.dtype).resolution * np.abs(image) shifted_img = image - h - resolution else: shifted_img = _subtract_constant_clip(image, h) rec_img = greyreconstruct.reconstruction(shifted_img, image, method='dilation', selem=selem) residue_img = image - rec_img return (residue_img >= h).astype(np.uint8) def h_minima(image, h, selem=None): """Determine all minima of the image with depth >= h. The local minima are defined as connected sets of pixels with equal grey level strictly smaller than the grey levels of all pixels in direct neighborhood of the set. A local minimum M of depth h is a local minimum for which there is at least one path joining M with a deeper minimum on which the maximal value is f(M) + h (i.e. the values along the path are not increasing by more than h with respect to the minimum's value) and no path for which the maximal value is smaller. Parameters ---------- image : ndarray The input image for which the minima are to be calculated. h : unsigned integer The minimal depth of all extracted minima. selem : ndarray, optional The neighborhood expressed as an n-D array of 1's and 0's. Default is the ball of radius 1 according to the maximum norm (i.e. a 3x3 square for 2D images, a 3x3x3 cube for 3D images, etc.) Returns ------- h_min : ndarray The minima of depth >= h. The resulting image is a binary image, where pixels belonging to the selected minima take value 1, the other pixels take value 0. See also -------- skimage.morphology.extrema.h_maxima skimage.morphology.extrema.local_maxima skimage.morphology.extrema.local_minima References ---------- .. [1] Soille, P., "Morphological Image Analysis: Principles and Applications" (Chapter 6), 2nd edition (2003), ISBN 3540429883. Examples -------- >>> import numpy as np >>> from skimage.morphology import extrema We create an image (quadratic function with a minimum in the center and 4 additional constant maxima. The depth of the minima are: 1, 21, 41, 61, 81 >>> w = 10 >>> x, y = np.mgrid[0:w,0:w] >>> f = 180 + 0.2*((x - w/2)**2 + (y-w/2)**2) >>> f[2:4,2:4] = 160; f[2:4,7:9] = 140; f[7:9,2:4] = 120; f[7:9,7:9] = 100 >>> f = f.astype(np.int) We can calculate all minima with a depth of at least 40: >>> minima = extrema.h_minima(f, 40) The resulting image will contain 3 local minima. """ if h > np.ptp(image): return np.zeros(image.shape, dtype=np.uint8) if np.issubdtype(type(h), np.floating) and \ np.issubdtype(image.dtype, np.integer): if ((h % 1) != 0): warn('possible precision loss converting image to ' 'floating point. To silence this warning, ' 'ensure image and h have same data type.', stacklevel=2) image = image.astype(np.float_) else: h = image.dtype.type(h) if (h == 0): raise ValueError("h = 0 is ambiguous, use local_minima() " "instead?") if np.issubdtype(image.dtype, np.floating): resolution = 2 * np.finfo(image.dtype).resolution * np.abs(image) shifted_img = image + h + resolution else: shifted_img = _add_constant_clip(image, h) rec_img = greyreconstruct.reconstruction(shifted_img, image, method='erosion', selem=selem) residue_img = rec_img - image return (residue_img >= h).astype(np.uint8) def local_maxima(image, selem=None, connectivity=None, indices=False, allow_borders=True): """Find local maxima of n-dimensional array. The local maxima are defined as connected sets of pixels with equal gray level (plateaus) strictly greater than the gray levels of all pixels in the neighborhood. Parameters ---------- image : ndarray An n-dimensional array. selem : ndarray, optional A structuring element used to determine the neighborhood of each evaluated pixel (``True`` denotes a connected pixel). It must be a boolean array and have the same number of dimensions as `image`. If neither `selem` nor `connectivity` are given, all adjacent pixels are considered as part of the neighborhood. connectivity : int, optional A number used to determine the neighborhood of each evaluated pixel. Adjacent pixels whose squared distance from the center is less than or equal to `connectivity` are considered neighbors. Ignored if `selem` is not None. indices : bool, optional If True, the output will be a tuple of one-dimensional arrays representing the indices of local maxima in each dimension. If False, the output will be a boolean array with the same shape as `image`. allow_borders : bool, optional If true, plateaus that touch the image border are valid maxima. Returns ------- maxima : ndarray or tuple[ndarray] If `indices` is false, a boolean array with the same shape as `image` is returned with ``True`` indicating the position of local maxima (``False`` otherwise). If `indices` is true, a tuple of one-dimensional arrays containing the coordinates (indices) of all found maxima. Warns ----- UserWarning If `allow_borders` is false and any dimension of the given `image` is shorter than 3 samples, maxima can't exist and a warning is shown. See Also -------- skimage.morphology.local_minima skimage.morphology.h_maxima skimage.morphology.h_minima Notes ----- This function operates on the following ideas: 1. Make a first pass over the image's last dimension and flag candidates for local maxima by comparing pixels in only one direction. If the pixels aren't connected in the last dimension all pixels are flagged as candidates instead. For each candidate: 2. Perform a flood-fill to find all connected pixels that have the same gray value and are part of the plateau. 3. Consider the connected neighborhood of a plateau: if no bordering sample has a higher gray level, mark the plateau as a definite local maximum. Examples -------- >>> from skimage.morphology import local_maxima >>> image = np.zeros((4, 7), dtype=int) >>> image[1:3, 1:3] = 1 >>> image[3, 0] = 1 >>> image[1:3, 4:6] = 2 >>> image[3, 6] = 3 >>> image array([[0, 0, 0, 0, 0, 0, 0], [0, 1, 1, 0, 2, 2, 0], [0, 1, 1, 0, 2, 2, 0], [1, 0, 0, 0, 0, 0, 3]]) Find local maxima by comparing to all neighboring pixels (maximal connectivity): >>> local_maxima(image) array([[False, False, False, False, False, False, False], [False, True, True, False, False, False, False], [False, True, True, False, False, False, False], [ True, False, False, False, False, False, True]]) >>> local_maxima(image, indices=True) (array([1, 1, 2, 2, 3, 3]), array([1, 2, 1, 2, 0, 6])) Find local maxima without comparing to diagonal pixels (connectivity 1): >>> local_maxima(image, connectivity=1) array([[False, False, False, False, False, False, False], [False, True, True, False, True, True, False], [False, True, True, False, True, True, False], [ True, False, False, False, False, False, True]]) and exclude maxima that border the image edge: >>> local_maxima(image, connectivity=1, allow_borders=False) array([[False, False, False, False, False, False, False], [False, True, True, False, True, True, False], [False, True, True, False, True, True, False], [False, False, False, False, False, False, False]]) """ image = np.asarray(image, order="C") if image.size == 0: # Return early for empty input if indices: # Make sure that output is a tuple of 1 empty array per dimension return np.nonzero(image) else: return np.zeros(image.shape, dtype=np.bool) if allow_borders: # Ensure that local maxima are always at least one smaller sample away # from the image border image = _util._fast_pad(image, image.min()) # Array of flags used to store the state of each pixel during evaluation. # See _extrema_cy.pyx for their meaning flags = np.zeros(image.shape, dtype=np.uint8) _util._set_border_values(flags, value=3) if any(s < 3 for s in image.shape): # Warn and skip if any dimension is smaller than 3 # -> no maxima can exist & structuring element can't be applied warn( "maxima can't exist for an image with any dimension smaller 3 " "if borders aren't allowed", stacklevel=3 ) else: selem = _util._resolve_neighborhood(selem, connectivity, image.ndim) neighbor_offsets = _util._offsets_to_raveled_neighbors( image.shape, selem, center=((1,) * image.ndim) ) try: _local_maxima(image.ravel(), flags.ravel(), neighbor_offsets) except TypeError: if image.dtype == np.float16: # Provide the user with clearer error message raise TypeError("dtype of `image` is float16 which is not " "supported, try upcasting to float32") else: raise # Otherwise raise original message if allow_borders: # Revert padding performed at the beginning of the function flags = crop(flags, 1) else: # No padding was performed but set edge values back to 0 _util._set_border_values(flags, value=0) if indices: return np.nonzero(flags) else: return flags.view(np.bool) def local_minima(image, selem=None, connectivity=None, indices=False, allow_borders=True): """Find local minima of n-dimensional array. The local minima are defined as connected sets of pixels with equal gray level (plateaus) strictly smaller than the gray levels of all pixels in the neighborhood. Parameters ---------- image : ndarray An n-dimensional array. selem : ndarray, optional A structuring element used to determine the neighborhood of each evaluated pixel (``True`` denotes a connected pixel). It must be a boolean array and have the same number of dimensions as `image`. If neither `selem` nor `connectivity` are given, all adjacent pixels are considered as part of the neighborhood. connectivity : int, optional A number used to determine the neighborhood of each evaluated pixel. Adjacent pixels whose squared distance from the center is less than or equal to `connectivity` are considered neighbors. Ignored if `selem` is not None. indices : bool, optional If True, the output will be a tuple of one-dimensional arrays representing the indices of local minima in each dimension. If False, the output will be a boolean array with the same shape as `image`. allow_borders : bool, optional If true, plateaus that touch the image border are valid minima. Returns ------- minima : ndarray or tuple[ndarray] If `indices` is false, a boolean array with the same shape as `image` is returned with ``True`` indicating the position of local minima (``False`` otherwise). If `indices` is true, a tuple of one-dimensional arrays containing the coordinates (indices) of all found minima. See Also -------- skimage.morphology.local_maxima skimage.morphology.h_maxima skimage.morphology.h_minima Notes ----- This function operates on the following ideas: 1. Make a first pass over the image's last dimension and flag candidates for local minima by comparing pixels in only one direction. If the pixels aren't connected in the last dimension all pixels are flagged as candidates instead. For each candidate: 2. Perform a flood-fill to find all connected pixels that have the same gray value and are part of the plateau. 3. Consider the connected neighborhood of a plateau: if no bordering sample has a smaller gray level, mark the plateau as a definite local minimum. Examples -------- >>> from skimage.morphology import local_minima >>> image = np.zeros((4, 7), dtype=int) >>> image[1:3, 1:3] = -1 >>> image[3, 0] = -1 >>> image[1:3, 4:6] = -2 >>> image[3, 6] = -3 >>> image array([[ 0, 0, 0, 0, 0, 0, 0], [ 0, -1, -1, 0, -2, -2, 0], [ 0, -1, -1, 0, -2, -2, 0], [-1, 0, 0, 0, 0, 0, -3]]) Find local minima by comparing to all neighboring pixels (maximal connectivity): >>> local_minima(image) array([[False, False, False, False, False, False, False], [False, True, True, False, False, False, False], [False, True, True, False, False, False, False], [ True, False, False, False, False, False, True]]) >>> local_minima(image, indices=True) (array([1, 1, 2, 2, 3, 3]), array([1, 2, 1, 2, 0, 6])) Find local minima without comparing to diagonal pixels (connectivity 1): >>> local_minima(image, connectivity=1) array([[False, False, False, False, False, False, False], [False, True, True, False, True, True, False], [False, True, True, False, True, True, False], [ True, False, False, False, False, False, True]]) and exclude minima that border the image edge: >>> local_minima(image, connectivity=1, allow_borders=False) array([[False, False, False, False, False, False, False], [False, True, True, False, True, True, False], [False, True, True, False, True, True, False], [False, False, False, False, False, False, False]]) """ return local_maxima( image=invert(image), selem=selem, connectivity=connectivity, indices=indices, allow_borders=allow_borders )