Nothing
mritc <- function(intarr, mask, method=c("EM", "ICM", "HMRFEM", "MCMC",
"MCMCsub", "PVHMRFEM", "MCMCsubbias")){
if (length(dim(intarr)) != 3)
stop("The intensity values of an MR image has to be in a 3D array.")
if(length(dim(mask)) != 3)
stop("The 'mask' has to be of dimension 3.")
if(! all(unique(as.vector(mask)) %in% 0:1))
stop("The value of mask has to be either 1 or 0.")
if(all(mask==0))
stop("All voxels are outside the mask.")
method <- match.arg(method)
y <- intarr[mask == 1]
if(method == "MCMCsub") sub <- TRUE
else sub <- FALSE
mrispatial <- makeMRIspatial(mask, nnei=6, sub)
if(method=="MCMCsubbias"){
mrispatial26 <- makeMRIspatial(mask, nnei=26, sub=FALSE, bias=TRUE)
}
init <- initOtsu(y, 2)
prop <- init$prop
mu <- init$mu
sigma <- init$sigma
result <- switch(method,
EM = mritc.em(y, prop, mu, sigma, verbose=TRUE),
ICM = mritc.icm(y, mrispatial$neighbors, mrispatial$blocks,
mu=mu, sigma=sigma, verbose=TRUE),
HMRFEM = mritc.hmrfem(y, mrispatial$neighbors, mrispatial$blocks,
mu=mu, sigma=sigma, verbose=TRUE),
MCMC = mritc.bayes.nobias(y, mrispatial$neighbors, mrispatial$blocks,
mrispatial$sub, mrispatial$subvox,
spatialMat=diag(1,3), beta=0.7, mu, sigma,
niter=100, verbose=TRUE),
MCMCsub = mritc.bayes.nobias(y, mrispatial$neighbors, mrispatial$blocks,
mrispatial$sub, mrispatial$subvox,
spatialMat=matrix(c(2,0,-1,0,2,0,-1,0,2), nrow=3),
beta=0.3, mu, sigma, niter=100, verbose=TRUE),
MCMCsubbias = mritc.bayes.bias(y, mrispatial$neighbors,
mrispatial$blocks, mrispatial$subvox,
mrispatial26$neighbors, mrispatial26$blocks,
mrispatial26$weineighbors, mrispatial26$weights,
spatialMat=matrix(c(2,0,-1,0,2,0,-1,0,2), nrow=3),
beta=0.3, mu, sigma, niter=1000, verbose=TRUE),
PVHMRFEM = mritc.pvhmrfem(y, mrispatial$neighbors, mrispatial$blocks,
mu=mu, sigma=sigma, verbose=TRUE))
class(result) <- "mritc"
result$method <- method
result$mask <- mask
result
}
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