R/getANTsRData.R

In muschellij2/atropos: Core Software Infrastructure for 'ANTsR'

#' getANTsRData
#'
#' Downloads antsr test data
#'
#' @param fileid one of the permitted file ids or pass "show" to list all
#'   valid possibilities. Note that most require internet access to download.
#' @param usefixedlocation directory to which you download files
#' @param verbose optional boolean
#' @param method Method to be used for downloading files,
#' passed to \code{\link{download.file}}
#' @param quiet If \code{TRUE}, suppress status messages 
#' (if any), and the progress bar.
#' @return filename string
#' @author Avants BB
#' @examples
#'
#' fi <- getANTsRData( "r16" )
#'
#' @export getANTsRData
getANTsRData <- function(fileid, 
                         usefixedlocation = FALSE, 
                         verbose=FALSE,
                         method = ifelse( 
                           Sys.info()['sysname'] == 'Linux',
                           'wget', 'auto'),
                         quiet = FALSE) {
  myusage <- "usage: getANTsRData(fileid = whatever , usefixedlocation = TRUE )"
  if (missing(fileid)) {
    print(myusage)
    return(NULL)
  }
  validlist = c("r16", "r27", "r30", "r62", "r64", "r85", "r64","nki", "pcasl",
                "ch2","ch2a","ch2b","finn","finncsv",
                "mni","mnia","mnib","mnit","mninat","mnijhu1","mnijhu2","mnidfn","mniyeo",
                "atroposseg","simple","fmrinetworks",
                "rsbold", "rsboldmask", "rsboldseg", "rsboldpts", "decslice", "dtislice",
                "adfmri", "population", "surf", "blob", "rand", "show",
                "multi_component_image")
  if (  sum( validlist == fileid ) == 0 )
    stop("no data with that id - try show to get list of valid ids")
  if ( fileid == "show" )
    return( validlist )
  if ( fileid == "population" )
  {
    ilist = list(
      antsImageRead( getANTsRData("r16") ),
      antsImageRead( getANTsRData("r27") ),
      antsImageRead( getANTsRData("r64") ) )
    return( ilist )
  }
  
  maketmpimg <- function(  ) {
    img = makeImage( c(256,256), voxval = rnorm( 256^2, 100, 3 ),
                     pixeltype = "unsigned char" )
    tfn = tempfile( fileext = ".jpg")
    antsImageWrite( img,  tfn )
    return( tfn )
  }
  
  if ( fileid == "simple" ) {
    x = system.file("extdata", "simple.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/simple.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x  )
  }
  if ( fileid == "r16" ) {
    x = system.file("extdata", "r16slice.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/r16slice.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  if ( fileid == "r27" ) {
    x = system.file("extdata", "r27slice.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/r27slice.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  if ( fileid == "r30" ) {
    x = system.file("extdata", "r30slice.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/r30slice.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  if ( fileid == "r62" ) {
    x = system.file("extdata", "r62slice.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/r62slice.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  if ( fileid == "r64" ) {
    x = system.file("extdata", "r64slice.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/r64slice.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  if ( fileid == "r85" ) {
    x = system.file("extdata", "r85slice.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = paste(path.package("atropos"),
                                     "/extdata/r85slice.jpg",sep="")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  if ( fileid == "rand" ) {
    x = system.file("extdata", "rand.jpg", package="atropos")
    if ( nchar( x ) == 0 ) x = maketmpimg()
    return(  x )
  }
  
  if ( fileid == "multi_component_image") {
    fname = system.file("extdata", "multi_component_image.nii.gz", 
                        package = "atropos")  
    return(fname)
  }
  
  # ch2b = brodmann ch2a = aal mnib = brodmann mnia = all mnit = tracts
  
  myurl <- switch(fileid,
                  KK = "http://placid.nlm.nih.gov/download?items=10766",
                  ADNI = "http://placid.nlm.nih.gov/download?folders=238",
                  K1 = "http://www.nitrc.org/frs/downloadlink.php/2201",
                  BT = "http://placid.nlm.nih.gov/download?items=10767",
                  AB = "http://placid.nlm.nih.gov/download?items=10753",
                  ch2 = "https://ndownloader.figshare.com/files/3888853",
                  ch2b = "https://ndownloader.figshare.com/files/3676050",
                  ch2a = "https://ndownloader.figshare.com/files/3674664",
                  finn = "https://ndownloader.figshare.com/files/4249681",
                  finncsv = "https://ndownloader.figshare.com/files/4454071",
                  mni = "https://ndownloader.figshare.com/files/3674667",
                  mnib = "https://ndownloader.figshare.com/files/3676050",
                  mnia = "https://ndownloader.figshare.com/files/3674664",
                  mnit = "http://placid.nlm.nih.gov/download?items=11660",
                  mninat = "https://ndownloader.figshare.com/files/3676062",
                  mnijhu1 = "https://ndownloader.figshare.com/files/3676056",
                  mnijhu2 = "https://ndownloader.figshare.com/files/3676059",
                  mnidfn = "https://ndownloader.figshare.com/files/3676047",
                  mniyeo = "https://ndownloader.figshare.com/files/4863193",
                  # nki = "http://files.figshare.com/1363201/NKI.zip",
                  nki = "https://ndownloader.figshare.com/files/3133826",
                  pcasl = "http://files.figshare.com/1862041/101_pcasl.nii.gz",
                  pcaslseg = "http://files.figshare.com/1862040/101_seg.nii.gz",
                  atroposseg = "http://files.figshare.com/1893339/atroposseg.nii",
                  rsbold = "https://ndownloader.figshare.com/files/2119176",
                  rsboldmask = "https://ndownloader.figshare.com/files/2119177",
                  rsboldseg = "https://ndownloader.figshare.com/files/2119178",
                  rsboldpts = "http://files.figshare.com/2126379/bold_rois.csv",
                  decslice = "https://ndownloader.figshare.com/files/2156224",
                  dtislice = "https://ndownloader.figshare.com/files/2157786" ,
                  fmrinetworks = "https://ndownloader.figshare.com/files/3639108",
                  adfmri      = "https://ndownloader.figshare.com/files/4901371",
                  surf        = paste0("https://github.com/stnava/antsSurf/blob/", 
                                       "master/ADNI_137_S_0158_MR_MPR__GradWarp_", 
                                       "_N3__Scaled_Br_20070306171702344_S20209_", 
                                       "I42985BrainSegmentation.nii.gz?raw=true"),
                  blob      = paste0("https://github.com/stnava/antsSurf/blob/", 
                                     "master/blob.nii.gz?raw=true")
  )
  
  myext <- ".nii.gz"
  if (fileid == "ADNI" | fileid == "K1" | fileid == "nki" |
      fileid == "fmrinetworks")
    myext <- ".zip"
  tdir <- tempdir()  # for temporary storage
  tfn <- tempfile( pattern = "antsr", tmpdir = tdir, fileext = myext )  # for temporary storage
  if (usefixedlocation == TRUE) {
    tdir <- system.file( package = "ANTsR" )  # for a fixed location
    tfn <- paste( tdir, "/html/", fileid, myext, sep = "" )  # for a fixed location
  }
  if ( ! file.exists( tfn ) )
  {
    download.file( myurl, tfn, method = method )
  }
  if ( fileid == "fmrinetworks" )
  {
    inms = c(
      "IFG_middle_temporal",
      "anterior_cingulate_precun","auditory",
      "default", "left_executive",
      "left_right_exec_combined_network",
      "motor", "parietal_association_cortex",
      "posterior_default","right_executive",
      "salience","supplementary_motor","visual")
    selinds = c(4,1,2,3,6,7,8,11,12,13)
    unzip( tfn , exdir = tdir )
    flist = Sys.glob( paste(tdir,"/rsfmrinetwork_*nii.gz",sep='') )
    ilist = imageFileNames2ImageList( flist )
    if ( verbose )
    {
      lochelp="Map the mni template to your image then transform these
      network files to the individual space.\n"
      cat( lochelp )
    }
    return( list(
      networkNames=inms[selinds],
      images=ilist[selinds] ) )
  }
  if ( fileid == "surf" | fileid == "blob" |fileid == "ADNI" | fileid == "K1" |
       fileid == "nki" ) {
    return(tfn)
  }
  # could use md5sum
  mymd5 <- switch(fileid,
                  KK = "397a773658558812e91c03bbb29334bb", 
                  BT = "eb1f8ee2bba81fb80fed77fb459600f0",
                  AB = "d38b04c445772db6e4ef3d2f34787d67", 
                  ch2 = "501c45361cf92dadd007bee55f02e053",
                  ch2b = "5db6c10eb8aeabc663d10e010860465f",
                  mnit = "dab456335a4bfa2b3bc31e9882699ee9", 
                  pcasl = "e59716ae76a853465efacf3cfb53bc58",
                  pcaslseg = "3872d709475ee2d51d90aa7f4df5af8f",
                  atroposseg = "f40680bd1de0592c9fa9e380bd9e29be",
                  rsbold = "dfba022d1f715c00e042a79c6250eb16",
                  rsboldmask = "15c9c6b38ce8e7f69fd4b64c110a17b4",
                  rsboldseg = "d50ceabc2bffbf12cee8b16e2216bfbc",
                  rsboldpts = "9eefc8d78fae07bfc0b5ef2da45b5d39",
                  decslice = "08f41703ac7398319c6dba66701c0653",
                  dtislice = "fd9bf3f50bad39833ec78b8dd3677df0")
  
  if (!is.null(mymd5))
    if (tools::md5sum(tfn) != mymd5) {
      stop("checksum failure")
    }
  return(tfn)
  }