scikit-image/scikit-image

f8c0573 Oct 17, 2018
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 import numpy as np from scipy import ndimage as ndi def profile_line(image, src, dst, linewidth=1, order=1, mode='constant', cval=0.0): """Return the intensity profile of an image measured along a scan line. Parameters ---------- image : numeric array, shape (M, N[, C]) The image, either grayscale (2D array) or multichannel (3D array, where the final axis contains the channel information). src : 2-tuple of numeric scalar (float or int) The start point of the scan line. dst : 2-tuple of numeric scalar (float or int) The end point of the scan line. The destination point is *included* in the profile, in contrast to standard numpy indexing. linewidth : int, optional Width of the scan, perpendicular to the line order : int in {0, 1, 2, 3, 4, 5}, optional The order of the spline interpolation to compute image values at non-integer coordinates. 0 means nearest-neighbor interpolation. mode : {'constant', 'nearest', 'reflect', 'mirror', 'wrap'}, optional How to compute any values falling outside of the image. cval : float, optional If `mode` is 'constant', what constant value to use outside the image. Returns ------- return_value : array The intensity profile along the scan line. The length of the profile is the ceil of the computed length of the scan line. Examples -------- >>> x = np.array([[1, 1, 1, 2, 2, 2]]) >>> img = np.vstack([np.zeros_like(x), x, x, x, np.zeros_like(x)]) >>> img array([[0, 0, 0, 0, 0, 0], [1, 1, 1, 2, 2, 2], [1, 1, 1, 2, 2, 2], [1, 1, 1, 2, 2, 2], [0, 0, 0, 0, 0, 0]]) >>> profile_line(img, (2, 1), (2, 4)) array([ 1., 1., 2., 2.]) >>> profile_line(img, (1, 0), (1, 6), cval=4) array([ 1., 1., 1., 2., 2., 2., 4.]) The destination point is included in the profile, in contrast to standard numpy indexing. For example: >>> profile_line(img, (1, 0), (1, 6)) # The final point is out of bounds array([ 1., 1., 1., 2., 2., 2., 0.]) >>> profile_line(img, (1, 0), (1, 5)) # This accesses the full first row array([ 1., 1., 1., 2., 2., 2.]) """ perp_lines = _line_profile_coordinates(src, dst, linewidth=linewidth) if image.ndim == 3: pixels = [ndi.map_coordinates(image[..., i], perp_lines, order=order, mode=mode, cval=cval) for i in range(image.shape[2])] pixels = np.transpose(np.asarray(pixels), (1, 2, 0)) else: pixels = ndi.map_coordinates(image, perp_lines, order=order, mode=mode, cval=cval) intensities = pixels.mean(axis=1) return intensities def _line_profile_coordinates(src, dst, linewidth=1): """Return the coordinates of the profile of an image along a scan line. Parameters ---------- src : 2-tuple of numeric scalar (float or int) The start point of the scan line. dst : 2-tuple of numeric scalar (float or int) The end point of the scan line. linewidth : int, optional Width of the scan, perpendicular to the line Returns ------- coords : array, shape (2, N, C), float The coordinates of the profile along the scan line. The length of the profile is the ceil of the computed length of the scan line. Notes ----- This is a utility method meant to be used internally by skimage functions. The destination point is included in the profile, in contrast to standard numpy indexing. """ src_row, src_col = src = np.asarray(src, dtype=float) dst_row, dst_col = dst = np.asarray(dst, dtype=float) d_row, d_col = dst - src theta = np.arctan2(d_row, d_col) length = int(np.ceil(np.hypot(d_row, d_col) + 1)) # we add one above because we include the last point in the profile # (in contrast to standard numpy indexing) line_col = np.linspace(src_col, dst_col, length) line_row = np.linspace(src_row, dst_row, length) # we subtract 1 from linewidth to change from pixel-counting # (make this line 3 pixels wide) to point distances (the # distance between pixel centers) col_width = (linewidth - 1) * np.sin(-theta) / 2 row_width = (linewidth - 1) * np.cos(theta) / 2 perp_rows = np.array([np.linspace(row_i - row_width, row_i + row_width, linewidth) for row_i in line_row]) perp_cols = np.array([np.linspace(col_i - col_width, col_i + col_width, linewidth) for col_i in line_col]) return np.array([perp_rows, perp_cols])