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Merge pull request #848 from ahojnnes/warps
Speed up warps by inlining interpolation functions
This commit is contained in:
Stefan van der Walt
@@ -123,9 +123,6 @@ Library:
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Extension: skimage.transform._warps_cy
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Sources:
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skimage/transform/_warps_cy.pyx
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Extension: skimage._shared.interpolation
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Sources:
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skimage/_shared/interpolation.pyx
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Extension: skimage.segmentation._felzenszwalb_cy
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Sources:
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skimage/segmentation/_felzenszwalb_cy.pyx
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@@ -1,27 +1,331 @@
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#cython: cdivision=True
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#cython: boundscheck=False
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#cython: nonecheck=False
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#cython: wraparound=False
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from libc.math cimport ceil, floor
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cdef double nearest_neighbour_interpolation(double* image, Py_ssize_t rows,
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Py_ssize_t cols, double r,
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double c, char mode,
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double cval)
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cdef double bilinear_interpolation(double* image, Py_ssize_t rows, Py_ssize_t cols,
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double r, double c, char mode,
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double cval)
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cdef inline Py_ssize_t round(double r):
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return <Py_ssize_t>((r + 0.5) if (r > 0.0) else (r - 0.5))
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cdef double quadratic_interpolation(double x, double[3] f)
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cdef double biquadratic_interpolation(double* image, Py_ssize_t rows, Py_ssize_t cols,
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double r, double c, char mode,
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double cval)
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cdef double cubic_interpolation(double x, double[4] f)
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cdef double bicubic_interpolation(double* image, Py_ssize_t rows, Py_ssize_t cols,
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double r, double c, char mode,
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double cval)
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cdef inline double nearest_neighbour_interpolation(double* image, Py_ssize_t rows,
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Py_ssize_t cols, double r,
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double c, char mode,
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double cval):
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"""Nearest neighbour interpolation at a given position in the image.
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cdef double get_pixel2d(double* image, Py_ssize_t rows, Py_ssize_t cols, Py_ssize_t r,
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Py_ssize_t c, char mode, double cval)
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Parameters
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----------
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image : double array
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Input image.
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rows, cols : int
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Shape of image.
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r, c : double
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Position at which to interpolate.
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mode : {'C', 'W', 'R', 'N'}
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
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cval : double
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Constant value to use for constant mode.
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cdef double get_pixel3d(double* image, Py_ssize_t rows, Py_ssize_t cols, Py_ssize_t dims,
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Py_ssize_t r, Py_ssize_t c, Py_ssize_t d, char mode, double cval)
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Returns
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-------
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value : double
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Interpolated value.
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cdef Py_ssize_t coord_map(Py_ssize_t dim, Py_ssize_t coord, char mode)
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"""
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return get_pixel2d(image, rows, cols, round(r), round(c), mode, cval)
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cdef inline double bilinear_interpolation(double* image, Py_ssize_t rows,
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Py_ssize_t cols, double r, double c,
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char mode, double cval):
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"""Bilinear interpolation at a given position in the image.
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Parameters
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----------
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image : double array
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Input image.
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rows, cols : int
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Shape of image.
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r, c : double
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Position at which to interpolate.
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mode : {'C', 'W', 'R', 'N'}
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
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cval : double
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Constant value to use for constant mode.
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Returns
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-------
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value : double
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Interpolated value.
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"""
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cdef double dr, dc
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cdef Py_ssize_t minr, minc, maxr, maxc
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minr = <Py_ssize_t>floor(r)
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minc = <Py_ssize_t>floor(c)
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maxr = <Py_ssize_t>ceil(r)
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maxc = <Py_ssize_t>ceil(c)
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dr = r - minr
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dc = c - minc
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top = (1 - dc) * get_pixel2d(image, rows, cols, minr, minc, mode, cval) \
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+ dc * get_pixel2d(image, rows, cols, minr, maxc, mode, cval)
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bottom = (1 - dc) * get_pixel2d(image, rows, cols, maxr, minc, mode, cval) \
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+ dc * get_pixel2d(image, rows, cols, maxr, maxc, mode, cval)
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return (1 - dr) * top + dr * bottom
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cdef inline double quadratic_interpolation(double x, double[3] f):
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"""Quadratic interpolation.
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Parameters
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----------
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x : double
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Position in the interval [-1, 1].
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f : double[4]
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Function values at positions [-1, 0, 1].
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Returns
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-------
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value : double
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Interpolated value.
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"""
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return f[1] - 0.25 * (f[0] - f[2]) * x
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cdef inline double biquadratic_interpolation(double* image, Py_ssize_t rows,
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Py_ssize_t cols, double r, double c,
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char mode, double cval):
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"""Biquadratic interpolation at a given position in the image.
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Parameters
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----------
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image : double array
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Input image.
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rows, cols : int
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Shape of image.
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r, c : double
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Position at which to interpolate.
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mode : {'C', 'W', 'R', 'N'}
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
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cval : double
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Constant value to use for constant mode.
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Returns
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-------
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value : double
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Interpolated value.
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"""
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cdef Py_ssize_t r0 = round(r)
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cdef Py_ssize_t c0 = round(c)
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if r < 0:
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r0 -= 1
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if c < 0:
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c0 -= 1
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# scale position to range [-1, 1]
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cdef double xr = (r - r0) - 1
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cdef double xc = (c - c0) - 1
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if r == r0:
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xr += 1
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if c == c0:
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xc += 1
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cdef double fc[3], fr[3]
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cdef Py_ssize_t pr, pc
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# row-wise cubic interpolation
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for pr in range(r0, r0 + 3):
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for pc in range(c0, c0 + 3):
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fc[pc - c0] = get_pixel2d(image, rows, cols, pr, pc, mode, cval)
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fr[pr - r0] = quadratic_interpolation(xc, fc)
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# cubic interpolation for interpolated values of each row
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return quadratic_interpolation(xr, fr)
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cdef inline double cubic_interpolation(double x, double[4] f):
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"""Cubic interpolation.
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Parameters
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----------
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x : double
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Position in the interval [0, 1].
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f : double[4]
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Function values at positions [0, 1/3, 2/3, 1].
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Returns
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-------
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value : double
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Interpolated value.
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"""
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return \
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f[1] + 0.5 * x * \
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(f[2] - f[0] + x * \
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(2.0 * f[0] - 5.0 * f[1] + 4.0 * f[2] - f[3] + x * \
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(3.0 * (f[1] - f[2]) + f[3] - f[0])))
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cdef inline double bicubic_interpolation(double* image, Py_ssize_t rows,
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Py_ssize_t cols, double r, double c,
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char mode, double cval):
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"""Bicubic interpolation at a given position in the image.
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Parameters
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----------
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image : double array
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Input image.
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rows, cols : int
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Shape of image.
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r, c : double
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Position at which to interpolate.
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mode : {'C', 'W', 'R', 'N'}
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
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cval : double
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Constant value to use for constant mode.
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Returns
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-------
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value : double
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Interpolated value.
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"""
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cdef Py_ssize_t r0 = <Py_ssize_t>r - 1
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cdef Py_ssize_t c0 = <Py_ssize_t>c - 1
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if r < 0:
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r0 -= 1
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if c < 0:
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c0 -= 1
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# scale position to range [0, 1]
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cdef double xr = (r - r0) / 3
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cdef double xc = (c - c0) / 3
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cdef double fc[4], fr[4]
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cdef Py_ssize_t pr, pc
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# row-wise cubic interpolation
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for pr in range(r0, r0 + 4):
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for pc in range(c0, c0 + 4):
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fc[pc - c0] = get_pixel2d(image, rows, cols, pr, pc, mode, cval)
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fr[pr - r0] = cubic_interpolation(xc, fc)
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# cubic interpolation for interpolated values of each row
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return cubic_interpolation(xr, fr)
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cdef inline double get_pixel2d(double* image, Py_ssize_t rows, Py_ssize_t cols,
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Py_ssize_t r, Py_ssize_t c, char mode, double cval):
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"""Get a pixel from the image, taking wrapping mode into consideration.
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Parameters
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----------
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image : double array
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Input image.
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rows, cols : int
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Shape of image.
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r, c : int
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Position at which to get the pixel.
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mode : {'C', 'W', 'R', 'N'}
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
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cval : double
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Constant value to use for constant mode.
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Returns
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-------
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value : double
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Pixel value at given position.
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"""
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if mode == 'C':
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if (r < 0) or (r > rows - 1) or (c < 0) or (c > cols - 1):
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return cval
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else:
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return image[r * cols + c]
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else:
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return image[coord_map(rows, r, mode) * cols + coord_map(cols, c, mode)]
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cdef inline double get_pixel3d(double* image, Py_ssize_t rows, Py_ssize_t cols,
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Py_ssize_t dims, Py_ssize_t r, Py_ssize_t c, Py_ssize_t d,
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char mode, double cval):
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"""Get a pixel from the image, taking wrapping mode into consideration.
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Parameters
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----------
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image : double array
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Input image.
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rows, cols, dims : int
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Shape of image.
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r, c, d : int
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Position at which to get the pixel.
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mode : {'C', 'W', 'R', 'N'}
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
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cval : double
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Constant value to use for constant mode.
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Returns
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-------
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value : double
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Pixel value at given position.
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"""
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if mode == 'C':
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if (r < 0) or (r > rows - 1) or (c < 0) or (c > cols - 1):
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return cval
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else:
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return image[r * cols * dims + c * dims + d]
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else:
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return image[coord_map(rows, r, mode) * cols * dims
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+ coord_map(cols, c, mode) * dims
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+ d]
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cdef inline Py_ssize_t coord_map(Py_ssize_t dim, Py_ssize_t coord, char mode):
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"""
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Wrap a coordinate, according to a given mode.
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Parameters
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----------
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dim : int
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Maximum coordinate.
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coord : int
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Coord provided by user. May be < 0 or > dim.
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mode : {'W', 'R', 'N'}
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Whether to wrap or reflect the coordinate if it
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falls outside [0, dim).
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"""
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dim = dim - 1
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if mode == 'R': # reflect
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if coord < 0:
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# How many times times does the coordinate wrap?
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if <Py_ssize_t>(-coord / dim) % 2 != 0:
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return dim - <Py_ssize_t>(-coord % dim)
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else:
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return <Py_ssize_t>(-coord % dim)
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elif coord > dim:
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if <Py_ssize_t>(coord / dim) % 2 != 0:
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return <Py_ssize_t>(dim - (coord % dim))
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else:
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return <Py_ssize_t>(coord % dim)
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elif mode == 'W': # wrap
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if coord < 0:
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return <Py_ssize_t>(dim - (-coord % dim))
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elif coord > dim:
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return <Py_ssize_t>(coord % dim)
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elif mode == 'N': # nearest
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if coord < 0:
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return 0
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elif coord > dim:
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return dim
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return coord
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@@ -1,331 +0,0 @@
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#cython: cdivision=True
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#cython: boundscheck=False
|
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#cython: nonecheck=False
|
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#cython: wraparound=False
|
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from libc.math cimport ceil, floor
|
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|
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cdef inline Py_ssize_t round(double r):
|
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return <Py_ssize_t>((r + 0.5) if (r > 0.0) else (r - 0.5))
|
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|
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|
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cdef inline double nearest_neighbour_interpolation(double* image, Py_ssize_t rows,
|
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Py_ssize_t cols, double r,
|
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double c, char mode,
|
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double cval):
|
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"""Nearest neighbour interpolation at a given position in the image.
|
||||
|
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Parameters
|
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----------
|
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image : double array
|
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Input image.
|
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rows, cols : int
|
||||
Shape of image.
|
||||
r, c : double
|
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Position at which to interpolate.
|
||||
mode : {'C', 'W', 'R', 'N'}
|
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Wrapping mode. Constant, Wrap, Reflect or Nearest.
|
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cval : double
|
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Constant value to use for constant mode.
|
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|
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Returns
|
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-------
|
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value : double
|
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Interpolated value.
|
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|
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"""
|
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|
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return get_pixel2d(image, rows, cols, round(r), round(c), mode, cval)
|
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|
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|
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cdef inline double bilinear_interpolation(double* image, Py_ssize_t rows,
|
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Py_ssize_t cols, double r, double c,
|
||||
char mode, double cval):
|
||||
"""Bilinear interpolation at a given position in the image.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
image : double array
|
||||
Input image.
|
||||
rows, cols : int
|
||||
Shape of image.
|
||||
r, c : double
|
||||
Position at which to interpolate.
|
||||
mode : {'C', 'W', 'R', 'N'}
|
||||
Wrapping mode. Constant, Wrap, Reflect or Nearest.
|
||||
cval : double
|
||||
Constant value to use for constant mode.
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Interpolated value.
|
||||
|
||||
"""
|
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cdef double dr, dc
|
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cdef Py_ssize_t minr, minc, maxr, maxc
|
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|
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minr = <Py_ssize_t>floor(r)
|
||||
minc = <Py_ssize_t>floor(c)
|
||||
maxr = <Py_ssize_t>ceil(r)
|
||||
maxc = <Py_ssize_t>ceil(c)
|
||||
dr = r - minr
|
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dc = c - minc
|
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top = (1 - dc) * get_pixel2d(image, rows, cols, minr, minc, mode, cval) \
|
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+ dc * get_pixel2d(image, rows, cols, minr, maxc, mode, cval)
|
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bottom = (1 - dc) * get_pixel2d(image, rows, cols, maxr, minc, mode, cval) \
|
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+ dc * get_pixel2d(image, rows, cols, maxr, maxc, mode, cval)
|
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return (1 - dr) * top + dr * bottom
|
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|
||||
|
||||
cdef inline double quadratic_interpolation(double x, double[3] f):
|
||||
"""Quadratic interpolation.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : double
|
||||
Position in the interval [-1, 1].
|
||||
f : double[4]
|
||||
Function values at positions [-1, 0, 1].
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Interpolated value.
|
||||
|
||||
"""
|
||||
return f[1] - 0.25 * (f[0] - f[2]) * x
|
||||
|
||||
|
||||
cdef inline double biquadratic_interpolation(double* image, Py_ssize_t rows,
|
||||
Py_ssize_t cols, double r, double c,
|
||||
char mode, double cval):
|
||||
"""Biquadratic interpolation at a given position in the image.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
image : double array
|
||||
Input image.
|
||||
rows, cols : int
|
||||
Shape of image.
|
||||
r, c : double
|
||||
Position at which to interpolate.
|
||||
mode : {'C', 'W', 'R', 'N'}
|
||||
Wrapping mode. Constant, Wrap, Reflect or Nearest.
|
||||
cval : double
|
||||
Constant value to use for constant mode.
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Interpolated value.
|
||||
|
||||
"""
|
||||
|
||||
cdef Py_ssize_t r0 = round(r)
|
||||
cdef Py_ssize_t c0 = round(c)
|
||||
if r < 0:
|
||||
r0 -= 1
|
||||
if c < 0:
|
||||
c0 -= 1
|
||||
# scale position to range [-1, 1]
|
||||
cdef double xr = (r - r0) - 1
|
||||
cdef double xc = (c - c0) - 1
|
||||
if r == r0:
|
||||
xr += 1
|
||||
if c == c0:
|
||||
xc += 1
|
||||
|
||||
cdef double fc[3], fr[3]
|
||||
|
||||
cdef Py_ssize_t pr, pc
|
||||
|
||||
# row-wise cubic interpolation
|
||||
for pr in range(r0, r0 + 3):
|
||||
for pc in range(c0, c0 + 3):
|
||||
fc[pc - c0] = get_pixel2d(image, rows, cols, pr, pc, mode, cval)
|
||||
fr[pr - r0] = quadratic_interpolation(xc, fc)
|
||||
|
||||
# cubic interpolation for interpolated values of each row
|
||||
return quadratic_interpolation(xr, fr)
|
||||
|
||||
|
||||
cdef inline double cubic_interpolation(double x, double[4] f):
|
||||
"""Cubic interpolation.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : double
|
||||
Position in the interval [0, 1].
|
||||
f : double[4]
|
||||
Function values at positions [0, 1/3, 2/3, 1].
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Interpolated value.
|
||||
|
||||
"""
|
||||
return \
|
||||
f[1] + 0.5 * x * \
|
||||
(f[2] - f[0] + x * \
|
||||
(2.0 * f[0] - 5.0 * f[1] + 4.0 * f[2] - f[3] + x * \
|
||||
(3.0 * (f[1] - f[2]) + f[3] - f[0])))
|
||||
|
||||
|
||||
cdef inline double bicubic_interpolation(double* image, Py_ssize_t rows,
|
||||
Py_ssize_t cols, double r, double c,
|
||||
char mode, double cval):
|
||||
"""Bicubic interpolation at a given position in the image.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
image : double array
|
||||
Input image.
|
||||
rows, cols : int
|
||||
Shape of image.
|
||||
r, c : double
|
||||
Position at which to interpolate.
|
||||
mode : {'C', 'W', 'R', 'N'}
|
||||
Wrapping mode. Constant, Wrap, Reflect or Nearest.
|
||||
cval : double
|
||||
Constant value to use for constant mode.
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Interpolated value.
|
||||
|
||||
"""
|
||||
|
||||
cdef Py_ssize_t r0 = <Py_ssize_t>r - 1
|
||||
cdef Py_ssize_t c0 = <Py_ssize_t>c - 1
|
||||
if r < 0:
|
||||
r0 -= 1
|
||||
if c < 0:
|
||||
c0 -= 1
|
||||
# scale position to range [0, 1]
|
||||
cdef double xr = (r - r0) / 3
|
||||
cdef double xc = (c - c0) / 3
|
||||
|
||||
cdef double fc[4], fr[4]
|
||||
|
||||
cdef Py_ssize_t pr, pc
|
||||
|
||||
# row-wise cubic interpolation
|
||||
for pr in range(r0, r0 + 4):
|
||||
for pc in range(c0, c0 + 4):
|
||||
fc[pc - c0] = get_pixel2d(image, rows, cols, pr, pc, mode, cval)
|
||||
fr[pr - r0] = cubic_interpolation(xc, fc)
|
||||
|
||||
# cubic interpolation for interpolated values of each row
|
||||
return cubic_interpolation(xr, fr)
|
||||
|
||||
|
||||
cdef inline double get_pixel2d(double* image, Py_ssize_t rows, Py_ssize_t cols,
|
||||
Py_ssize_t r, Py_ssize_t c, char mode, double cval):
|
||||
"""Get a pixel from the image, taking wrapping mode into consideration.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
image : double array
|
||||
Input image.
|
||||
rows, cols : int
|
||||
Shape of image.
|
||||
r, c : int
|
||||
Position at which to get the pixel.
|
||||
mode : {'C', 'W', 'R', 'N'}
|
||||
Wrapping mode. Constant, Wrap, Reflect or Nearest.
|
||||
cval : double
|
||||
Constant value to use for constant mode.
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Pixel value at given position.
|
||||
|
||||
"""
|
||||
if mode == 'C':
|
||||
if (r < 0) or (r > rows - 1) or (c < 0) or (c > cols - 1):
|
||||
return cval
|
||||
else:
|
||||
return image[r * cols + c]
|
||||
else:
|
||||
return image[coord_map(rows, r, mode) * cols + coord_map(cols, c, mode)]
|
||||
|
||||
|
||||
cdef inline double get_pixel3d(double* image, Py_ssize_t rows, Py_ssize_t cols,
|
||||
Py_ssize_t dims, Py_ssize_t r, Py_ssize_t c, Py_ssize_t d,
|
||||
char mode, double cval):
|
||||
"""Get a pixel from the image, taking wrapping mode into consideration.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
image : double array
|
||||
Input image.
|
||||
rows, cols, dims : int
|
||||
Shape of image.
|
||||
r, c, d : int
|
||||
Position at which to get the pixel.
|
||||
mode : {'C', 'W', 'R', 'N'}
|
||||
Wrapping mode. Constant, Wrap, Reflect or Nearest.
|
||||
cval : double
|
||||
Constant value to use for constant mode.
|
||||
|
||||
Returns
|
||||
-------
|
||||
value : double
|
||||
Pixel value at given position.
|
||||
|
||||
"""
|
||||
if mode == 'C':
|
||||
if (r < 0) or (r > rows - 1) or (c < 0) or (c > cols - 1):
|
||||
return cval
|
||||
else:
|
||||
return image[r * cols * dims + c * dims + d]
|
||||
else:
|
||||
return image[coord_map(rows, r, mode) * cols * dims
|
||||
+ coord_map(cols, c, mode) * dims
|
||||
+ d]
|
||||
|
||||
|
||||
cdef inline Py_ssize_t coord_map(Py_ssize_t dim, Py_ssize_t coord, char mode):
|
||||
"""
|
||||
Wrap a coordinate, according to a given mode.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
dim : int
|
||||
Maximum coordinate.
|
||||
coord : int
|
||||
Coord provided by user. May be < 0 or > dim.
|
||||
mode : {'W', 'R', 'N'}
|
||||
Whether to wrap or reflect the coordinate if it
|
||||
falls outside [0, dim).
|
||||
|
||||
"""
|
||||
dim = dim - 1
|
||||
if mode == 'R': # reflect
|
||||
if coord < 0:
|
||||
# How many times times does the coordinate wrap?
|
||||
if <Py_ssize_t>(-coord / dim) % 2 != 0:
|
||||
return dim - <Py_ssize_t>(-coord % dim)
|
||||
else:
|
||||
return <Py_ssize_t>(-coord % dim)
|
||||
elif coord > dim:
|
||||
if <Py_ssize_t>(coord / dim) % 2 != 0:
|
||||
return <Py_ssize_t>(dim - (coord % dim))
|
||||
else:
|
||||
return <Py_ssize_t>(coord % dim)
|
||||
elif mode == 'W': # wrap
|
||||
if coord < 0:
|
||||
return <Py_ssize_t>(dim - (-coord % dim))
|
||||
elif coord > dim:
|
||||
return <Py_ssize_t>(coord % dim)
|
||||
elif mode == 'N': # nearest
|
||||
if coord < 0:
|
||||
return 0
|
||||
elif coord > dim:
|
||||
return dim
|
||||
|
||||
return coord
|
||||
@@ -14,12 +14,9 @@ def configuration(parent_package='', top_path=None):
|
||||
config.add_data_dir('tests')
|
||||
|
||||
cython(['geometry.pyx'], working_path=base_path)
|
||||
cython(['interpolation.pyx'], working_path=base_path)
|
||||
cython(['transform.pyx'], working_path=base_path)
|
||||
|
||||
config.add_extension('geometry', sources=['geometry.c'])
|
||||
config.add_extension('interpolation', sources=['interpolation.c'],
|
||||
include_dirs=[get_numpy_include_dirs()])
|
||||
config.add_extension('transform', sources=['transform.c'],
|
||||
include_dirs=[get_numpy_include_dirs()])
|
||||
|
||||
|
||||
Reference in New Issue
Block a user