How to use the stardist.utils.path_absolute function in stardist

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github mpicbg-csbd / stardist / stardist / geometry / geom2d.py View on Github external
def _ocl_star_dist(a, n_rays=32):
    from gputools import OCLProgram, OCLArray, OCLImage
    (np.isscalar(n_rays) and 0 < int(n_rays)) or _raise(ValueError())
    n_rays = int(n_rays)
    src = OCLImage.from_array(a.astype(np.uint16,copy=False))
    dst = OCLArray.empty(a.shape+(n_rays,), dtype=np.float32)
    program = OCLProgram(path_absolute("kernels/stardist2d.cl"), build_options=['-D', 'N_RAYS=%d' % n_rays])
    program.run_kernel('star_dist', src.shape, None, dst.data, src)
    return dst.get()
github mpicbg-csbd / stardist / stardist / geometry / geom3d.py View on Github external
def _ocl_star_dist3D(lbl, rays, grid=(1,1,1)):
    from gputools import OCLProgram, OCLArray, OCLImage

    grid = _normalize_grid(grid,3)

    # if not all(g==1 for g in grid):
    #     raise NotImplementedError("grid not yet implemented for OpenCL version of star_dist3D()...")

    res_shape = tuple(s//g for s, g in zip(lbl.shape, grid))

    lbl_g = OCLImage.from_array(lbl.astype(np.uint16, copy=False))
    dist_g = OCLArray.empty(res_shape + (len(rays),), dtype=np.float32)
    rays_g = OCLArray.from_array(rays.vertices.astype(np.float32, copy=False))

    program = OCLProgram(path_absolute("kernels/stardist3d.cl"), build_options=['-D', 'N_RAYS=%d' % len(rays)])
    program.run_kernel('stardist3d', res_shape[::-1], None,
                       lbl_g, rays_g.data, dist_g.data,
                       np.int32(grid[0]),np.int32(grid[1]),np.int32(grid[2]))

    return dist_g.get()