R/joinEigenanatomy.R

In stnava/itkImageR: Examples using Rcpp to interface R and ITK

joinEigenanatomy <- function(datamatrix, mask, list_of_eanat_images, graphdensity = 0.65) {
  if (nargs() == 0) {
    print("Usage: ")
    print(args(joinEigenanatomy))
    return(1)
  }
  pckg <- try(require(igraph))
  if (!pckg) {
    getPckg("igraph")
  }
  library(igraph)
  decom2 <- imageListToMatrix(list_of_eanat_images, mask)
  myproj <- datamatrix %*% t(decom2)
  gg <- makeGraph(cor(myproj), graphdensity)
  communitymembership <- gg$walktrapcomm$membership
  newelist <- list()
  for (cl in 1:max(communitymembership)) {
    newe <- antsImageClone(mydecom$eigenanatomyimages[[1]])
    newe[mask > 0] <- 0
    templist <- mydecom$eigenanatomyimages[communitymembership == cl]
    for (eimg in templist) {
      newe[mask > 0] <- newe[mask > 0] + eimg[mask > 0]/sum(eimg[mask > 0])
      print(sum(newe > 0)/sum(mask > 0))
    }
    newe[mask > 0] <- newe[mask > 0]/sum(newe[mask > 0])
    newelist <- lappend(newelist, newe)
  }
  decom2 <- imageListToMatrix(newelist, mask)
  myproj <- datamatrix %*% t(decom2)
  colnames(myproj) <- paste("V", 1:ncol(myproj), sep = "")
  return(list(fusedlist = newelist, fusedproj = myproj, memberships = communitymembership))
}