Source code for ants.utils.smooth_image

 

__all__ = ['smooth_image']

import math

from .. import utils
from ..core import ants_image as iio



def _smooth_image_helper(image, sigma, sigma_in_physical_coordinates=True, FWHM=False, max_kernel_width=70):
    outimage = image.clone()
    if not isinstance(sigma, (tuple,list)):
        sigma = [sigma]

    if isinstance(sigma, (tuple, list)) and ((len(sigma) != image.dimension) and (len(sigma) != 1)):
        raise ValueError('Length of sigma must be either 1 or the dimensionality of input image')

    image_float = image.clone('float')
    if FWHM:
        sigma = [s/2.355 for s in sigma]

    max_kernel_width = int(math.ceil(max_kernel_width))

    smooth_image_fn = utils.get_lib_fn('SmoothImage%iD'%image.dimension)
    outimage = smooth_image_fn(image_float.pointer, sigma, sigma_in_physical_coordinates, max_kernel_width)
    ants_outimage = iio.ANTsImage(pixeltype='float', dimension=image.dimension,
                                components=image.components, pointer=outimage)
    return ants_outimage


def smooth_image(image, sigma, sigma_in_physical_coordinates=True, FWHM=False, max_kernel_width=32):
    """
    Smooth an image

    ANTsR function: `smoothImage`

    Arguments
    ---------
    image   
        Image to smooth
    
    sigma   
        Smoothing factor. Can be scalar, in which case the same sigma is applied to each dimension, or a vector of length dim(inimage) to specify a unique smoothness for each dimension.
    
    sigma_in_physical_coordinates : boolean  
        If true, the smoothing factor is in millimeters; if false, it is in pixels.
    
    FWHM : boolean    
        If true, sigma is interpreted as the full-width-half-max (FWHM) of the filter, not the sigma of a Gaussian kernel.
    
    max_kernel_width : scalar    
        Maximum kernel width
    
    Returns
    -------
    ANTsImage
    
    Example
    -------
    >>> import ants
    >>> image = ants.image_read( ants.get_ants_data('r16'))
    >>> simage = ants.smooth_image(image, (1.2,1.5))
    """
    if image.components == 1:
        return _smooth_image_helper(image, sigma, sigma_in_physical_coordinates, FWHM, max_kernel_width)
    else:
        imagelist = utils.split_channels(image)
        newimages = []
        for image in imagelist:
            newimage = _smooth_image_helper(image, sigma, sigma_in_physical_coordinates, FWHM, max_kernel_width)
            newimages.append(newimage)
        return utils.merge_channels(newimages)