R/write_cifti_from_separate.R

In mandymejia/ciftiTools: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

#' Write a CIFTI file from NIFTI and GIFTI files
#'
#' Make a CIFTI file from component NIFTI/GIFTI files using the
#'  \code{-cifti-create-...} Connectome Workbench commands.
#'
#' Every provided component will be included. The ROIs are only used if the
#'  corresponding cortex is provided. Either both or none of the subcortical
#'  NIFTIs should be provided.
#'
#' @param cifti_fname Path to the CIFTI to write.
#' @param cortexL_fname The left cortex file.
#' @param ROIcortexL_fname The left cortex ROI file.
#' @param cortexR_fname The right cortex file.
#' @param ROIcortexR_fname The right cortex ROI file.
#' @param subcortVol_fname The subcortical data file.
#' @param subcortLabs_fname The subcortical labels file.
#' @param timestep If a dense time series ("dtseries.nii") file is being written,
#'  this is the time between measurements. If \code{NULL}, use the Connectome
#'  Workbench default (1.0).
#' @param timestart If a dense time series ("dtseries.nii") file is being written,
#'  this is starting time. If \code{NULL}, use the Connectome Workbench default
#'  (0.0).
#' @param names For "dscalar.nii" or "dlabel.nii", these are the column names.
#'
#' @keywords internal
#'
write_cifti_from_separate <- function(
  cifti_fname,
  cortexL_fname=NULL, ROIcortexL_fname=NULL,
  cortexR_fname=NULL, ROIcortexR_fname=NULL,
  subcortVol_fname=NULL, subcortLabs_fname=NULL,
  timestep=NULL, timestart=NULL, names=NULL){

  # Determine what kind of CIFTI is being written.
  # Must be one of the following after the check in `cifti_info`
  cifti_extn <- get_cifti_extn(cifti_fname)
  if (!(cifti_extn %in% c("dtseries.nii", "dscalar.nii", "dlabel.nii"))) {
    ciftiTools_warn("`cifti_fname` does not end in a CIFTI extension (*.nii). Writing a dscalar.\n")
    cifti_extn <- "dscalar.nii"
  }

  create_cmd <- switch(cifti_extn,
    "dtseries.nii" = "-cifti-create-dense-timeseries",
    "dscalar.nii" = "-cifti-create-dense-scalar",
    "dlabel.nii" = "-cifti-create-label"
  )

  what <- switch(cifti_extn,
    "dtseries.nii" = "metric",
    "dscalar.nii" = "metric",
    "dlabel.nii" = "label"
  )

  # TO-DO: adjust GIFTI/NIFTI written files accordingly?

  cmd <- paste(create_cmd, sys_path(cifti_fname))

  # Volume
  if (!is.null(subcortVol_fname)){
    cmd <- paste(
      cmd, "-volume", sys_path(subcortVol_fname), sys_path(subcortLabs_fname)
    )
  }

  # Left
  if (!is.null(cortexL_fname)) {
    cmd <- paste(cmd, paste0("-left-", what), sys_path(cortexL_fname))
    if (!is.null(ROIcortexL_fname)) {
      cmd <- paste(cmd, "-roi-left", sys_path(ROIcortexL_fname))
    }
  }

  # Right
  if (!is.null(cortexR_fname)) {
    cmd <- paste(cmd, paste0("-right-", what), sys_path(cortexR_fname))
    if (!is.null(ROIcortexR_fname)) {
      cmd <- paste(cmd, "-roi-right", sys_path(ROIcortexR_fname))
    }
  }

  # Metadata
  if (create_cmd == "-cifti-create-dense-timeseries") {
    if (!is.null(timestep)) { cmd <- paste(cmd, "-timestep", timestep) }
    if (!is.null(timestart)) { cmd <- paste(cmd, "-timestart", timestart) }
  }

  # Warning for dlabel:
  #   WARNING: label file '[the file]' contains data array with data type other than int32
  #   --> all values are 0 ???
  #   WARNING about conflicting key values from activations xifti. ignore?
  run_wb_cmd(cmd, ignore.stderr=TRUE)

  # ADD BACK NAMES
  if (!is.null(names)) {
    cmd <- paste(
      "-set-map-names",
      sys_path(cifti_fname),
      paste("-map", seq(length(names)), shQuote(names), collapse=" ")
    )
    run_wb_cmd(cmd, ignore.stderr=TRUE)
  }

  invisible(cifti_fname)
}