--- a +++ b/ants/ops/smooth_image.py @@ -0,0 +1,73 @@ + + + +__all__ = ['smooth_image'] + +import math + +from ants.decorators import image_method +from ants.internal import get_lib_fn + +import ants + + +@image_method +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: + 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 = get_lib_fn('SmoothImage') + outimage = smooth_image_fn(image_float.pointer, sigma, sigma_in_physical_coordinates, max_kernel_width) + ants_outimage = ants.from_pointer(outimage) + return ants_outimage + else: + imagelist = ants.split_channels(image) + newimages = [] + for image in imagelist: + newimage = smooth_image(image, sigma, sigma_in_physical_coordinates, FWHM, max_kernel_width) + newimages.append(newimage) + return ants.merge_channels(newimages) +