kmeansSegmentation: k means image segmentation.

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

k means image segmentation.

Description

k means image segmentation that is a wrapper around atropos

Usage

kmeansSegmentation(img, k, kmask = NULL, mrf = 0.1, verbose = FALSE, ...)

Arguments

img	input image
k	integer number of classes
kmask	segment inside this mask
mrf	smoothness, higher is smoother
verbose	boolean
...	additional arguments to pass to atropos

Value

segmentation and probability images

Note

This function will likely give different results on multiple runs.

Author(s)

Brian B. Avants

Examples

fi <- antsImageRead(getANTsRData("r16"), 2)
orig <- antsImageClone(fi)
fi <- n3BiasFieldCorrection(fi, 4)
seg <- kmeansSegmentation(fi, 3)
seg2 <- kmeansSegmentation(fi, 3)
arr1 <- as.array(seg$segmentation)
arr2 <- as.array(seg2$segmentation)
testthat::expect_equal(arr1, arr2)

set.seed(2)
# 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 )
orig <- antsImageRead(getANTsRData("r16"), 2)
seg <- kmeansSegmentation(orig, 3, use_random_seed = TRUE)
seg2 <- kmeansSegmentation(orig, 3, use_random_seed = TRUE)
arr1 <- as.array(seg$segmentation)
arr2 <- as.array(seg2$segmentation)
tab <- table(arr1, arr2)
tab
identical(arr1, arr2)
seg <- kmeansSegmentation(orig, 3, use_random_seed = FALSE)
seg2 <- kmeansSegmentation(orig, 3, use_random_seed = FALSE)
arr1 <- as.array(seg$segmentation)
arr2 <- as.array(seg2$segmentation)
tab <- table(arr1, arr2)
tab

stnava/ANTsR documentation built on April 13, 2025, 4:10 a.m.