R/antsApplyTransforms.R

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

antsApplyTransforms <- function(fixed = NA, moving = NA, transformlist = "", interpolator = "Linear", imagetype = 0, 
  ...) {
  numargs <- nargs()
  if (typeof(fixed) == "list") {
    .Call("antsApplyTransforms", int_antsProcessArguments(c(fixed, "-z", 1, "--float", 0)), PACKAGE = "itkImageR")
    return(0)
  }
  if (missing(fixed) | missing(moving) | missing(transformlist)) {
    cat(" warpedimg<-antsApplyTransforms( fixed=img1 , moving=img2 , transformlist=list(\"my0GenericAffine.mat\",\"my1Warp.nii.gz\") ) ")
    cat("\n\n")
    cat("For full mode: use standard ants call as in antsApplyTransforms full mode ... \n\n")
    cat(" antsApplyTransforms(\"-d\",\"2\",\"-i\",\"r64slice.nii.gz\",\"-o\",\"temp.nii.gz\",\"-r\",\"r16slice.nii.gz\",\"-t\",\"./Z0GenericAffine.mat\") \n")
    cat("for full help: \n")
    cat("use .Call( \"antsApplyTransforms\", int_antsProcessArguments( c(list(\"--help\")) ), PACKAGE=\"itkImageR\" );\n\n")
    return(0)
  }
  args <- list(fixed, moving, transformlist, interpolator, ...)
  if (!is.character(fixed)) {
    if (fixed@class[[1]] == "antsImage" & moving@class[[1]] == "antsImage") {
      ttexists <- TRUE
      for (i in 1:length(transformlist)) {
        if (!file.exists(transformlist[i])) 
          ttexists <- FALSE
      }
      if (ttexists) {
        inpixeltype <- fixed@pixeltype
        fixed <- antsImageClone(fixed, "double")
        moving <- antsImageClone(moving, "double")
        warpedmovout <- antsImageClone(moving, "double")
        f <- fixed
        m <- moving
        wmo <- warpedmovout
        mytx <- list()
        for (i in c(1:length(transformlist))) {
          ismat <- FALSE
          if (i == 1 & length(transformlist) > 1) {
          if (length(grep(".mat", transformlist[i])) == 1) {
            ismat <- TRUE
            print("treating this as an inverse transform")
          }
          }
          if (!ismat) 
          mytx <- list(mytx, "-t", transformlist[i]) else mytx <- list(mytx, "-t", paste("[", transformlist[i], ",1]", sep = ""))
        }
        args <- list(d = fixed@dimension, i = m, o = wmo, r = f, n = interpolator, unlist(mytx))
        myargs <- int_antsProcessArguments(c(args))
        for (jj in c(1:length(myargs))) {
          if (!is.na(myargs[jj])) {
          if (myargs[jj] == "-") {
            myargs2 <- rep(NA, (length(myargs) - 1))
            myargs2[1:(jj - 1)] <- myargs[1:(jj - 1)]
            myargs2[jj:(length(myargs) - 1)] <- myargs[(jj + 1):(length(myargs))]
            myargs <- myargs2
          }
          }
        }
        .Call("antsApplyTransforms", c(myargs, "-z", 1, "--float", 0, "-e", imagetype), PACKAGE = "itkImageR")
        gc()
        return(antsImageClone(warpedmovout, inpixeltype))
      }
      if (!ttexists) 
        cat("Problem in arg list \n see usage by calling antsApplyTransforms() w/o arguments \n")
    }
    return(0)
  }
  # if ( Sys.info()['sysname'] == 'XXX' ) { mycmd<-antsrParseListToString( c(args) ) system(
  # paste('antsApplyTransforms ', mycmd$mystr ) ) return( antsImageRead( mycmd$outimg, as.numeric(mycmd$outdim)
  # ) ) }
  .Call("antsApplyTransforms", int_antsProcessArguments(c(args, "-z", 1, "--float", 0, "-e", imagetype)), PACKAGE = "itkImageR")
  gc()  # trigger garbage collection
}


antsrParseListToString <- function(mylist, outimg = NA, outdim = NA) {
  mystr <- ""
  len <- length(mylist)
  outimg <- ""
  outdim <- 11
  for (x in 1:len) {
    if (class(mylist[[x]])[1] == "antsImage") {
      tfn <- paste(tempdir(), "img", x, ".nii.gz", sep = "")
      antsImageWrite(mylist[[x]], tfn)
      mystr <- paste(mystr, tfn)
      outdim <- mylist[[x]]@dimension
      if (typeof(mylist[[x - 1]]) == "character") {
        if (mylist[[x - 1]] == "-o") 
          outimg <- tfn
      }
      if (typeof(mylist[[x - 1]]) != "S4") 
        if (mylist[[x - 1]] == "-o") 
          outimg <- tfn
    } else mystr <- paste(mystr, toString(mylist[[x]]))
  }
  mystr <- sub(",", " ", mystr)
  mystr <- sub(" - ", " ", mystr)
  mystr <- sub("-t,", "-t ", mystr)
  mystr <- sub(", ", " ", mystr)
  return(list(mystr = mystr, outimg = outimg, outdim = outdim))
}

antsrParseListToString2 <- function(mylist, outimg = NA, outdim = NA) {
  mystr <- ""
  outimg <- ""
  outdim <- 11
  len <- length(mylist)
  for (x in 1:len) {
    mystr <- paste(mystr, " -", names(mylist)[x], " ", sep = "")
    if (class(mylist[[x]])[1] == "antsImage") {
      tfn <- paste(tempdir(), "img", x, ".nii.gz", sep = "")
      antsImageWrite(mylist[[x]], tfn)
      mystr <- paste(mystr, tfn)
      outdim <- mylist[[x]]@dimension
      if (names(mylist)[x] == "o") 
        outimg <- tfn
    } else mystr <- paste(mystr, toString(mylist[[x]]))
  }
  mystr <- sub(",", " ", mystr)
  mystr <- sub(" - ", " ", mystr)
  mystr <- sub("-t,", "-t ", mystr)
  mystr <- sub(", ", " ", mystr)
  return(list(mystr = mystr, outimg = outimg, outdim = outdim))
}