R/rapidlyInspectImageData.R

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

#' Simple rapidlyInspectImageData function.
#'
#' rapidlyInspectImageData collects basic statistics over a dataset and returns them
#' in a dataframe.
#'
#' @param myfiles input list of filenames
#' @return matrix is output
#' @author Avants BB
#' @examples
#' \dontrun{
#' fnl <- c(
#'   getANTsRData("r16"),
#'   getANTsRData("r27"),
#'   getANTsRData("r62"),
#'   getANTsRData("r64"),
#'   getANTsRData("r85")
#' )
#' mm <- rapidlyInspectImageData(fnl)
#' }
#'
#' @export rapidlyInspectImageData
rapidlyInspectImageData <- function(myfiles) {
  if (nargs() == 0) {
    print(args(rapidlyInspectImageData))
    return(1)
  }
  if (!usePkg("moments")) {
    print("Need moments package")
    return(NULL)
  }
  measnames <- c("mean1", "mean2", "sd1", "sd2", "kurt1", "kurt2")
  nmeas <- length(measnames)
  nfn <- length(myfiles)
  mymat <- matrix(rep(0, nfn * nmeas), nrow = nfn)
  colnames(mymat) <- measnames
  for (i in 1:nfn) {
    img <- antsImageRead(myfiles[i])
    if (img@components > 1) img <- splitChannels(img) %>% antsAverageImages(verbose = FALSE)
    thresh <- mean(img[img > min(img)])
    mymat[i, 1] <- thresh
    mymat[i, 2] <- mean(img[img > thresh])
    mymat[i, 3] <- sd(img[img > min(img)])
    mymat[i, 4] <- sd(img[img > thresh])
    mymat[i, 5] <- moments::kurtosis(img[img > min(img)])
    mymat[i, 6] <- moments::kurtosis(img[img > thresh])
  }
  rownames(mymat) <- myfiles
  return(mymat)
}