R/writeNormalizedPopulationData.R

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

#' Save normalized population data to a directory or h5 file
#'
#' This function simplifies the steps of saving a population (image) analysis
#' into an efficient hdf5 file, using the h5 library or to a directory.  The
#' population image data is stored as a matrix.  Along with the matrix will be a
#' data frame with population demographics. The number of matrix columns will be
#' defined by a mask that the user should also supply.  Finally, a boolean
#' vector should be passed in that matches the images to the demographics. This
#' function cannot check if the matching between demographics and images is
#' correct and, as such, the user should take care in creating the inputs.
#' WARNING: when using h5, the demographics file will currently be cast to a data.matrix so
#' one should not reuse this file as the reference demographics file.
#'
#' @param demographics data frame that identifies the variables of interest.
#' @param imageMat a matrix that stores the normalized image data.
#' @param imageMask mask with number of non-zero entries defining the matrix columns.
#' @param imageBoolean a vector of booleans with length equal to the number of
#' rows in the demographics data frame and number of true values equal to the
#' number of rows in the image matrix.
#' @param filename output filename for hdf5 file (if .h5) or directory name.
#' @return successOrFailure boolean
#' @author Avants BB
#' @examples
#' # read below will test out writing as well
#' \dontrun{
#' ilist <- getANTsRData("population")
#' mask <- getMask(ilist[[1]])
#' imat <- imageListToMatrix(ilist, mask)
#' demog <- data.frame(
#'   id = c("A", "B", "C", NA),
#'   age = c(11, 7, 18, 22), sex = c("M", "M", "F", "F")
#' )
#' ibool <- c(TRUE, TRUE, TRUE, FALSE)
#' tfn <- tempfile(fileext = ".h5")
#' if (usePkg("hdf5r")) {
#'   demographics <- demog
#'   imageMat <- imat
#'   imageMask <- mask
#'   imageBoolean <- ibool
#'   filename <- tfn
#'   writeNormalizedPopulationData(
#'     demog, imat, mask, ibool,
#'     tfn
#'   )
#' }
#' }
#' @export writeNormalizedPopulationData
writeNormalizedPopulationData <- function(
    demographics,
    imageMat,
    imageMask,
    imageBoolean,
    filename) {
  outputToDir <- length(grep("h5", filename)) == 0
  if (!outputToDir) {
    if (!usePkg("hdf5r")) {
      stop("Please install package hdf5r in order to use this function.")
    }
  }
  if (sum(imageMask > 0.5) != ncol(imageMat)) {
    stop("stopping because sum( imageMask > 0.5 ) != ncol( imageMat )")
  }
  if (sum(imageBoolean) != nrow(imageMat)) {
    stop("stopping because sum( imageBoolean ) != nrow( imageMat )")
  }
  if (length(imageBoolean) != nrow(demographics)) {
    stop("stopping because length( imageBoolean ) != nrow( demographics )")
  }
  if (file.exists(filename)) {
    stop("stopping because file.exists( filename )")
  }
  if (outputToDir) {
    dir.create(filename, showWarnings = TRUE, recursive = FALSE, mode = "0777")
    write.csv(demographics, paste(filename, "/demog.csv", sep = ""), row.names = FALSE)
    haveImageDf <- data.frame(haveImage = imageBoolean)
    write.csv(haveImageDf, paste(filename, "/haveImage.csv", sep = ""), row.names = FALSE)
    antsImageWrite(imageMask, paste(filename, "/imageMask.nii.gz", sep = ""))
    antsImageWrite(as.antsImage(imageMat), paste(filename, "/imageMat.mha", sep = ""))
    return(TRUE)
  }
  file <- hdf5r::h5file(filename)
  file$create_group("antsrpopdata")
  # file[["antsrpopdata/demographics"]] <- data.matrix( demographics )
  file[["antsrpopdata/demographics"]] <- demographics
  # hdf5r::h5attr(file[["antsrpopdata/demographics"]], "colnames") <- colnames(demographics)
  file[["antsrpopdata/imageMat"]] <- imageMat
  file[["antsrpopdata/imageMask"]] <- as.array(imageMask)
  hdf5r::h5attr(file[["antsrpopdata/imageMask"]], "spacing") <- antsGetSpacing(imageMask)
  hdf5r::h5attr(file[["antsrpopdata/imageMask"]], "direction") <- antsGetDirection(imageMask)
  hdf5r::h5attr(file[["antsrpopdata/imageMask"]], "origin") <- antsGetOrigin(imageMask)
  file[["antsrpopdata/imageBoolean"]] <- imageBoolean
  file[["antsrpopdata/filename"]] <- filename
  hdf5r::h5close(file)
  return(TRUE)
}




#' Read normalized population from h5 file or directory
#'
#' This function reads a file created by \code{writeNormalizedPopulationData}.
#'
#' @param filename input filename for hdf5 file.
#' @return list containing demographics, imageMat, imageMask and imageBoolean
#' @author Avants BB
#' @examples
#' tfn <- system.file("extdata", "normpop.h5", package = "ANTsR")
#' if (file.exists(tfn)) {
#'   dlist <- readNormalizedPopulationData(tfn)
#' }
#' \dontrun{
#' ilist <- getANTsRData("population")
#' mask <- getMask(ilist[[1]])
#' imat <- imageListToMatrix(ilist, mask)
#' demog <- data.frame(age = c(11, 7, 18, 22), sex = c("M", "M", "F", "F"))
#' ibool <- c(TRUE, TRUE, TRUE, FALSE)
#' tfn <- tempfile(fileext = ".h5")
#' if (usePkg("hdf5r")) writeNormalizedPopulationData(demog, imat, mask, ibool, tfn)
#' if (usePkg("hdf5r")) {
#'   dlist <- readNormalizedPopulationData(tfn)
#'   all.equal(dlist$demographics, demog)
#'   all.equal(dlist$imageMat, imat)
#'   all.equal(as.array(dlist$imageMask), as.array(mask))
#'   all.equal(dlist$imageBool, ibool)
#' }
#' }
#' @export readNormalizedPopulationData
readNormalizedPopulationData <- function(filename) {
  outputToDir <- length(grep("h5", filename)) == 0
  if (!outputToDir) {
    if (!usePkg("hdf5r")) {
      stop("Please install package hdf5r in order to use this function.")
    }
  }
  if (outputToDir) {
    if (!dir.exists(filename)) {
      stop(paste(filename, "directory does not exist."))
    }
    demographics <- read.csv(paste(filename, "/demog.csv", sep = ""))
    imageBoolean <- read.csv(paste(filename, "/haveImage.csv", sep = ""))$haveImage
    imageMask <- antsImageRead(paste(filename, "/imageMask.nii.gz", sep = ""))
    imageMat <- as.matrix(antsImageRead(paste(filename, "/imageMat.mha", sep = "")))
  } else {
    file <- hdf5r::h5file(filename)
    demog <- file[["antsrpopdata/demographics"]]
    demographics <- demog$read()
    # hdf5r::h5attr( demog, "colnames" )
    # colnames( demographics ) <- hdf5r::h5attr( demog, "colnames" )
    temp <- file[["antsrpopdata/imageMat"]]
    imageMat <- temp$read()
    temp <- file[["antsrpopdata/imageMask"]]
    imageMask <- as.antsImage(temp$read())
    k <- antsSetSpacing(imageMask, hdf5r::h5attr(temp, "spacing"))
    k <- antsSetOrigin(imageMask, hdf5r::h5attr(temp, "origin"))
    k <- antsSetDirection(imageMask, hdf5r::h5attr(temp, "direction"))
    temp <- file[["antsrpopdata/imageBoolean"]]
    imageBoolean <- temp$read()
    hdf5r::h5close(file)
  }
  return(
    list(
      demographics   = data.frame(demographics),
      imageMat       = imageMat,
      imageMask      = imageMask,
      imageBoolean   = imageBoolean
    )
  )
}