maskImage: Mask input image by mask image.

In muschellij2/atropos: Core Software Infrastructure for 'ANTsR'

Description

Mask an input image by a mask image. If the mask image has multiple labels, it is possible to specify which label(s) to mask at.

Usage

maskImage(img.in, img.mask, level = 1, binarize = FALSE)

Arguments

img.in	Input image.
img.mask	Mask or label image.
level	Level(s) at which to mask image. If vector or list of values, output image is non-zero at all locations where label image matches any of the levels specified.
binarize	binarize the output image?

Value

An object of type antsImage.

Author(s)

Kandel BM and Avants B.

Examples

myimg <- antsImageRead(getANTsRData("r16"))
mask <- getMask(myimg)
myimg.mask <- maskImage(myimg, mask, 3)
testthat::expect_equal(sum(myimg.mask), 0)
myimg.mask <- maskImage(myimg, mask)
testthat::expect_equal(sum(myimg.mask), 3295494)
# set below for slower but numerically repeatable results
# these should be set in .Renviron not by sys calls
# Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)
seg <- kmeansSegmentation(myimg, 3)
myimg.mask <- maskImage(myimg, seg$segmentation, c(1,3))
check = myimg * (seg$segmentation == 1 | seg$segmentation == 3)
testthat::expect_equal(myimg.mask, check)
myimg.mask <- maskImage(myimg, seg$segmentation, c(1,3), binarize = TRUE)
coerce_mask(myimg.mask, error = TRUE) # no error

muschellij2/atropos documentation built on May 4, 2019, 3:17 p.m.