tests/testthat/test-Atropos.R

In neuroconductor-devel/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

context("segmenting image")

test_that("image can be segmented with atropos", {
          img <- antsImageRead( getANTsRData( "r16" ) , 2)
          mask <- antsImageClone(img)
          mask[img>10] <- 1
          mask[img<=10] <- 0
          nvox <- sum(as.array(mask))
          segs1<-atropos( d = img@dimension, a = img, m = "[0.2,1x1]",
            c = "[5,0]",  i = "kmeans[3]", x =mask)
          testcsf = abs( sum( segs1$segmentation == 1 ) - 2330 ) < 100
          testgm = abs( sum( segs1$segmentation == 2 ) - 7333 ) < 100
          testwm = abs( sum( segs1$segmentation == 3 ) - 8518 ) < 100
          expect_true( testcsf & testgm & testwm )
})
#todo : other segmentation approaches of atropos