R/zzzz_NiftiMatrix.R

In neuroconductor/NiftiArray: HDF5 Delayed Array for Nifti Objects

#' "niftiImage" class
#'
#' @name niftiImage-class
#' @aliases niftiImage
#' @family niftiImage
#'
setOldClass("niftiImage")



# write to current dump
.as_NiftiArray <- function(from) writeNiftiArray(from)

#' @aliases coerce,ANY,NiftiArray-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("ANY", "NiftiArray", .as_NiftiArray)

#' @aliases coerce,DelayedArray,NiftiArray-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("DelayedArray", "NiftiArray", .as_NiftiArray)

#' @aliases coerce,DelayedMatrix,NiftiMatrix-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs(
  "DelayedMatrix", "NiftiMatrix",
  function(from) as(as(from, "NiftiArray"), "NiftiMatrix"))


#' @aliases coerce,HDF5Array,NiftiArray-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("HDF5Array", "NiftiArray", .as_NiftiArray)

#' @aliases coerce,HDF5Array,NiftiMatrix-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs(
  "HDF5Array",
  "NiftiMatrix",
  function(from) as(as(from, "NiftiArray"), "NiftiMatrix"))

#' @aliases coerce,HDF5Matrix,NiftiMatrix-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs(
  "HDF5Matrix", "NiftiMatrix",
  function(from) as(as(from, "NiftiArray"), "NiftiMatrix"))


#' @importMethodsFrom DelayedArray matrixClass
#' @rdname NiftiMatrix
#' @aliases matrixClass,NiftiArray-method
#' @name matrixClass
#' @param x Typically a DelayedArray object.
setMethod("matrixClass", "NiftiArray", function(x) "NiftiMatrix")

#' @aliases coerce,NiftiArray,NiftiMatrix-method
#' @importMethodsFrom methods coerce
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("NiftiArray", "NiftiMatrix", function(from) {
  # from = res[[1]]
  dfrom = dim(from)
  if (is_extendible(from)) {
    dfrom = dfrom[-length(dfrom)]
  }
  nd = length(dfrom)
  if ( (nd > 4 && dfrom[5] > 1) ||
      nd > 5) {
    stop(paste0("NiftiMatrix from NiftiArray not ",
                "defined for > 4 dimensions!"))
  }
  dfrom = c(dfrom, rep(1L, max(4 - nd, 0)))
  out_dim = c(prod(dfrom[seq(3)]), dfrom[seq(4, length(dfrom))])
  out_dim = as.integer(out_dim)
  if (nd > 2) {
    hdr = nifti_header(from)
    if (utils::packageVersion("HDF5Array") >= package_version("1.13.3")) {
      #   # 1.13.3
      #   # stop("Not implemented yet!")
      dim(from) = dfrom
      from = writeNiftiArray(from, header = hdr, extendible = FALSE)
      # does not give resshaped niftimatrix
      mat <- ReshapedNiftiArray(
        filepath = from@seed@filepath,
        name = from@seed@name,
        dim = out_dim,
        header = hdr)
      # mat = as(mat, "NiftiMatrix")
      return(mat)
    } else {
      mat = matrix(from, ncol = dfrom[4])
      mat = writeNiftiArray(mat, header = hdr, extendible = FALSE)
      return(mat)
    }
  } else {
    new("NiftiMatrix", from)
  }
})


#' @aliases coerce,NiftiArrayList,NiftiMatrix-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("NiftiArrayList", "NiftiMatrix", function(from) {
  verbose = attr(from, "verbose")
  if (is.null(verbose)) {
    verbose = FALSE
  }
  applier = lapply
  if (verbose) {
    if (requireNamespace("pbapply", quietly = TRUE)) {
      applier = pbapply::pblapply
    }
  }
  hdr = nifti_header(from[[1]])
  from = applier(from, function(x) {
    as(x, "NiftiMatrix")
  })
  from = do.call(DelayedArray::acbind, args = from)
  writeNiftiArray(from, header = hdr, extendible = FALSE)
})


#' @aliases coerce,numeric,NiftiMatrix-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("numeric", "NiftiMatrix", function(from) {
  from = matrix(from, ncol = 1)
  as(as(from, "NiftiArray"), "NiftiMatrix")
})

#' @rdname NiftiArray
#' @aliases coerce,numeric,NiftiArray-method
#' @export
#' @name coerce
setAs("numeric", "NiftiArray",
      function(from) as(as(from, "NiftiMatrix"), "NiftiArray")
)

#' @aliases coerce,NiftiArray,niftiImage-method
#' @rdname NiftiArray
#' @name coerce
#' @importFrom RNifti updateNifti
#' @export
setAs("NiftiArray", "niftiImage", function(from) {
  hdr = nifti_header(from)
  out_img = RNifti::updateNifti(as.array(from), template = hdr)
  out_img
})

#' @aliases coerce,ReshapedNiftiArray,niftiImage-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("ReshapedNiftiArray", "niftiImage", function(from) {
  hdr = nifti_header(from)
  out_img = RNifti::updateNifti(as.array(from), template = hdr)
  out_img
})

#' @aliases coerce,ReshapedNiftiMatrix,NiftiArray-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("ReshapedNiftiMatrix", "NiftiArray", function(from) {
  extendible = from@seed@extendible
  x = NiftiArray(from@seed@filepath,
                 extendible = extendible,
                 name = from@seed@name,
                 header_name = from@seed@header_name,
                 header = nifti_header(from))
  if (extendible) {
    dim(x) = dim(x)[-length(dim(x))]
  }
  x
  # hdr = nifti_header(from)
  # d = hdr$dim
  # d = d[ 2:(2 + d[1] - 1)]
  # arr = array(as.array(from), dim = d)
  #
  # out_img = RNifti::updateNifti(arr, template = hdr)
  # out_img
})

#' @aliases coerce,ReshapedHDF5Matrix,niftiImage-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("ReshapedHDF5Matrix", "niftiImage", function(from) {
  hdr = nifti_header(from)
  d = hdr$dim
  d = d[ 2:(2 + d[1] - 1)]
  arr = array(as.array(from), dim = d)
  out_img = RNifti::updateNifti(arr, template = hdr)
  out_img
})

# #' @aliases coerce,ReshapedNiftiMatrix,niftiImage-method
# #' @rdname NiftiArray
# #' @name coerce
# #' @export
# setAs("ReshapedNiftiMatrix", "niftiImage", function(from) {
#   hdr = nifti_header(from)
#   d = hdr$dim
#   d = d[ 2:(2 + d[1] - 1)]
#   arr = array(as.array(from), dim = d)
#   out_img = RNifti::updateNifti(arr, template = hdr)
#   out_img
# })

#' @aliases coerce,NiftiMatrix,niftiImage-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("NiftiMatrix", "niftiImage", function(from) {
  as(as(from, "NiftiArray"), "niftiImage")
})

#' @aliases coerce,ReshapedNiftiMatrix,niftiImage-method
#' @rdname NiftiArray
#' @name coerce
#' @export
setAs("ReshapedNiftiMatrix", "niftiImage", function(from) {
  as(as(from, "NiftiArray"), "niftiImage")
})


#' @aliases coerce,NiftiMatrix,NiftiArray-method
#' @rdname NiftiArray
#' @export
#' @name coerce
setAs("NiftiMatrix", "NiftiArray", function(from) {
  hdr = nifti_header(from)
  extendible = hdr$extendible
  if (is.null(extendible)) {
    extendible = FALSE
  }
  d = hdr$dim
  d = d[ 2:(2 + d[1] - 1)]
  mat = array(from, dim = d)
  writeNiftiArray(mat, header = hdr, extendible = extendible)
})  # no-op

#' @rdname NiftiArray
#' @aliases coerce,ANY,NiftiMatrix-method
#' @export
#' @name coerce
setAs("ANY", "NiftiMatrix",
      function(from) as(as(from, "NiftiArray"), "NiftiMatrix")
)

#' @rdname NiftiArray
#' @aliases coerce,NiftiArrayList,NiftiArray-method
#' @export
#' @name coerce
setAs(
  "NiftiArrayList", "NiftiArray",
  function(from) {
    ndims = lapply(from, dim)
    ndims = vapply(ndims, length, FUN.VALUE = integer(1))
    stopifnot(all(ndims == ndims[1]))
    ndims = unique(ndims)
    hdr = nifti_header(from[[1]])
    extendible = hdr$extendible
    if (is.null(extendible)) {
      extendible = FALSE
    }

    verbose = attr(from, "verbose")
    if (is.null(verbose)) {
      verbose = FALSE
    }
    applier = lapply
    if (verbose) {
      if (requireNamespace("pbapply", quietly = TRUE)) {
        applier = pbapply::pblapply
      }
    }

    # Adapted from
    # https://support.bioconductor.org/p/107051/
    from = applier(from, function(x) {
      dim(x) = c(dim(x), 1L)
      x = DelayedArray::aperm(x, perm = (ndims + 1):1)
      x
    })
    # 1 for
    if (verbose) {
      message("Binding data together")
    }
    res = do.call(DelayedArray::arbind, args = from)
    res = aperm(res, (ndims + 1):1)
    hdr$dim[ndims + 1 + 1] = dim(res)[ndims + 1]
    hdr$pixdim[ndims + 1 + 1] = 1
    if (verbose) {
      message("Running writeNiftiArray")
    }
    res = writeNiftiArray(res, header = hdr, verbose = verbose,
                          extendible = extendible)
    res
  })