segment {bioimagetools}

Segmentation of 3D images using EM algorithms

Description

Segmentation of 3D images using EM algorithms

Usage

segment(
  img,
  nclust,
  beta,
  z.scale = 0,
  method = "cem",
  varfixed = TRUE,
  maxit = 30,
  mask = array(TRUE, dim(img)),
  priormu = rep(NA, nclust),
  priormusd = rep(NULL, nclust),
  min.eps = 10^{
     -7
 },
  inforce.nclust = FALSE,
  start = NULL,
  silent = FALSE
)

Arguments

img

is a 3d array representing an image.

nclust

is the number of clusters/classes to be segmented.

beta

is a matrix of size nclust x nclust, representing the prior weight of classes neighboring each other.

z.scale

ratio of voxel dimension in x/y direction and z direction. Will be multiplied on beta for neighboring voxel in z direction.

method

only "cem" classification EM algorithm implemented.

varfixed

is a logical variable. If TRUE, the variance is equal in each class.

maxit

is the maximum number of iterations.

mask

is a logical array, representing the voxels to be used in the segmentation.

priormu

is a vector with mean of the normal prior of the expected values of all classes. Default is NA, which represents no prior assumption.

priormusd

is a vector with standard deviations of the normal prior of the expected values of all classes.

min.eps

stop criterion. Minimal change in sum of squared estimate of mean in order to stop.

inforce.nclust

if TRUE enforces number of clusters to be nclust. Otherwise classes might be removed during algorithm.

start

not used

silent

if TRUE, function remains silent during running time

Value

A list with "class": 3d array of class per voxel; "mu" estimated means; "sigma": estimated standard deviations.

Examples

## Not run: 
original<-array(1,c(300,300,50))
for (i in 1:5)original[(i*60)-(0:20),,]<-original[(i*60)-(0:20),,]+1
for (i in 1:10)original[,(i*30)-(0:15),]<-original[,(i*30)-(0:15),]+1
original[,,26:50]<-4-aperm(original[,,26:50],c(2,1,3))

img<-array(rnorm(300*300*50,original,.2),c(300,300,50))
img<-img-min(img)
img<-img/max(img)

try1<-segment(img,3,beta=0.5,z.scale=.3)
print(sum(try1$class!=original)/prod(dim(original)))

beta<-matrix(rep(-.5,9),nrow=3)
beta<-beta+1.5*diag(3)
try2<-segment(img,3,beta,z.scale=.3)
print(sum(try2$class!=original)/prod(dim(original)))

par(mfrow=c(2,2))
img(original)
img(img)
img(try1$class)
img(try2$class)

## End(Not run)