175 lines
6.9 KiB
Python
175 lines
6.9 KiB
Python
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from warnings import warn
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import numpy as np
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from scipy import ndimage as ndi
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from .._shared.utils import _validate_interpolation_order
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def profile_line(image, src, dst, linewidth=1,
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order=None, mode=None, cval=0.0,
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*, reduce_func=np.mean):
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"""Return the intensity profile of an image measured along a scan line.
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Parameters
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----------
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image : ndarray, shape (M, N[, C])
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The image, either grayscale (2D array) or multichannel
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(3D array, where the final axis contains the channel
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information).
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src : array_like, shape (2, )
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The coordinates of the start point of the scan line.
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dst : array_like, shape (2, )
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The coordinates of the end point of the scan
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line. The destination point is *included* in the profile, in
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contrast to standard numpy indexing.
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linewidth : int, optional
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Width of the scan, perpendicular to the line
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order : int in {0, 1, 2, 3, 4, 5}, optional
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The order of the spline interpolation, default is 0 if
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image.dtype is bool and 1 otherwise. The order has to be in
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the range 0-5. See `skimage.transform.warp` for detail.
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mode : {'constant', 'nearest', 'reflect', 'mirror', 'wrap'}, optional
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How to compute any values falling outside of the image.
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cval : float, optional
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If `mode` is 'constant', what constant value to use outside the image.
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reduce_func : callable, optional
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Function used to calculate the aggregation of pixel values
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perpendicular to the profile_line direction when `linewidth` > 1.
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If set to None the unreduced array will be returned.
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Returns
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-------
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return_value : array
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The intensity profile along the scan line. The length of the profile
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is the ceil of the computed length of the scan line.
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Examples
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--------
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>>> x = np.array([[1, 1, 1, 2, 2, 2]])
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>>> img = np.vstack([np.zeros_like(x), x, x, x, np.zeros_like(x)])
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>>> img
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array([[0, 0, 0, 0, 0, 0],
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[1, 1, 1, 2, 2, 2],
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[1, 1, 1, 2, 2, 2],
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[1, 1, 1, 2, 2, 2],
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[0, 0, 0, 0, 0, 0]])
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>>> profile_line(img, (2, 1), (2, 4))
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array([1., 1., 2., 2.])
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>>> profile_line(img, (1, 0), (1, 6), cval=4)
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array([1., 1., 1., 2., 2., 2., 4.])
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The destination point is included in the profile, in contrast to
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standard numpy indexing.
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For example:
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>>> profile_line(img, (1, 0), (1, 6)) # The final point is out of bounds
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array([1., 1., 1., 2., 2., 2., 0.])
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>>> profile_line(img, (1, 0), (1, 5)) # This accesses the full first row
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array([1., 1., 1., 2., 2., 2.])
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For different reduce_func inputs:
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>>> profile_line(img, (1, 0), (1, 3), linewidth=3, reduce_func=np.mean)
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array([0.66666667, 0.66666667, 0.66666667, 1.33333333])
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>>> profile_line(img, (1, 0), (1, 3), linewidth=3, reduce_func=np.max)
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array([1, 1, 1, 2])
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>>> profile_line(img, (1, 0), (1, 3), linewidth=3, reduce_func=np.sum)
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array([2, 2, 2, 4])
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The unreduced array will be returned when `reduce_func` is None or when
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`reduce_func` acts on each pixel value individually.
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>>> profile_line(img, (1, 2), (4, 2), linewidth=3, order=0,
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... reduce_func=None)
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array([[1, 1, 2],
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[1, 1, 2],
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[1, 1, 2],
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[0, 0, 0]])
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>>> profile_line(img, (1, 0), (1, 3), linewidth=3, reduce_func=np.sqrt)
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array([[1. , 1. , 0. ],
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[1. , 1. , 0. ],
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[1. , 1. , 0. ],
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[1.41421356, 1.41421356, 0. ]])
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"""
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order = _validate_interpolation_order(image.dtype, order)
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if mode is None:
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warn("Default out of bounds interpolation mode 'constant' is "
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"deprecated. In version 0.19 it will be set to 'reflect'. "
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"To avoid this warning, set `mode=` explicitly.",
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FutureWarning, stacklevel=2)
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mode = 'constant'
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perp_lines = _line_profile_coordinates(src, dst, linewidth=linewidth)
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if image.ndim == 3:
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pixels = [ndi.map_coordinates(image[..., i], perp_lines,
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prefilter=order > 1,
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order=order, mode=mode,
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cval=cval) for i in
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range(image.shape[2])]
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pixels = np.transpose(np.asarray(pixels), (1, 2, 0))
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else:
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pixels = ndi.map_coordinates(image, perp_lines, prefilter=order > 1,
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order=order, mode=mode, cval=cval)
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# The outputted array with reduce_func=None gives an array where the
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# row values (axis=1) are flipped. Here, we make this consistent.
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pixels = np.flip(pixels, axis=1)
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if reduce_func is None:
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intensities = pixels
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else:
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try:
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intensities = reduce_func(pixels, axis=1)
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except TypeError: # function doesn't allow axis kwarg
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intensities = np.apply_along_axis(reduce_func, arr=pixels, axis=1)
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return intensities
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def _line_profile_coordinates(src, dst, linewidth=1):
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"""Return the coordinates of the profile of an image along a scan line.
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Parameters
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----------
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src : 2-tuple of numeric scalar (float or int)
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The start point of the scan line.
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dst : 2-tuple of numeric scalar (float or int)
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The end point of the scan line.
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linewidth : int, optional
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Width of the scan, perpendicular to the line
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Returns
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-------
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coords : array, shape (2, N, C), float
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The coordinates of the profile along the scan line. The length of the
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profile is the ceil of the computed length of the scan line.
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Notes
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-----
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This is a utility method meant to be used internally by skimage functions.
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The destination point is included in the profile, in contrast to
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standard numpy indexing.
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"""
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src_row, src_col = src = np.asarray(src, dtype=float)
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dst_row, dst_col = dst = np.asarray(dst, dtype=float)
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d_row, d_col = dst - src
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theta = np.arctan2(d_row, d_col)
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length = int(np.ceil(np.hypot(d_row, d_col) + 1))
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# we add one above because we include the last point in the profile
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# (in contrast to standard numpy indexing)
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line_col = np.linspace(src_col, dst_col, length)
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line_row = np.linspace(src_row, dst_row, length)
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# we subtract 1 from linewidth to change from pixel-counting
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# (make this line 3 pixels wide) to point distances (the
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# distance between pixel centers)
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col_width = (linewidth - 1) * np.sin(-theta) / 2
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row_width = (linewidth - 1) * np.cos(theta) / 2
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perp_rows = np.array([np.linspace(row_i - row_width, row_i + row_width,
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linewidth) for row_i in line_row])
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perp_cols = np.array([np.linspace(col_i - col_width, col_i + col_width,
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linewidth) for col_i in line_col])
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return np.array([perp_rows, perp_cols])
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