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#' Write a \code{"xifti"} object to GIFTI and NIFTI files
#'
#' Write metric or label GIFTIs for the cortical surface data and NIFTIs for the
#' subcortical labels and mask in a \code{"xifti"} object. Each present
#' brainstructure will be written; if a brainstructure is absent the
#' corresponding file is not written.
#'
#' @inheritParams xifti_Param
#' @inheritParams separate_cifti_files
#' @inheritParams verbose_Param_FALSE
#'
#' @return List of written files
#' @importFrom RNifti writeNifti
#'
#' @family writing
#' @export
#'
write_xifti2 <- function(
xifti,
brainstructures=NULL,
cortexL_fname=NULL, cortexR_fname=NULL,
subcortVol_fname=NULL, subcortLabs_fname=NULL,
ROI_brainstructures="all",
ROIcortexL_fname=NULL, ROIcortexR_fname=NULL,
ROIsubcortVol_fname=NULL, write_dir=NULL,
verbose=FALSE) {
# [DEV NOTE] This function is written in a similar way to `separate_cifti`.
# If making changes here, consider making parallel changes there.
# [TO DO] write label GIFTI from dlabel CIFTI?
# Check `xifti`.
stopifnot(is.xifti(xifti))
# Get numerical intent. Use scalar file if no intent is present.
if (is.null(xifti$meta$cifti$intent)) { xifti$meta$cifti$intent <- 3006 }
intent_cifti <- xifti$meta$cifti$intent
# Check which brainstructures are present.
bs_present <- c("left", "right", "subcortical")[!vapply(xifti$data, is.null, FALSE)]
# Reconcile `brainstructures` with `bs_present`.
# Get output files: which ones to write, and their names.
x <- separate_cifti_files(
bs_present=bs_present,
intent = intent_cifti,
brainstructures=brainstructures,
cortexL_fname=cortexL_fname, cortexR_fname=cortexR_fname,
subcortVol_fname=subcortVol_fname, subcortLabs_fname=subcortLabs_fname,
ROI_brainstructures=ROI_brainstructures,
ROIcortexL_fname=ROIcortexL_fname, ROIcortexR_fname=ROIcortexR_fname,
ROIsubcortVol_fname=ROIsubcortVol_fname,
write_dir=write_dir
)
do <- x$do; ROI_do <- x$ROI_do; sep_fnames <- x$sep_fnames; rm(x)
if (all(!do)) { message("Nothing to write."); return(invisible(NULL)) }
# Check for and modify multiple columns with different label tables.
if (intent_cifti == 3007) {
intent_gii <- "label"
data_type <- "INT32"
label_table <- xifti$meta$cifti$labels
# [TO DO] check if this is actually necessary
if (length(label_table) > 1) {
if (length(unique(label_table)) > 1) {
warning(paste(
"CIFTI files support a different label table for each column,",
"but GIFTI & NIFTI files only support a single label table. Writing",
"the `xifti` requires exporting to GIFTI & NIFTI files.",
"Using the label table for the first column."
))
}
}
label_table <- label_table[[1]]
col_names <- names(xifti$meta$cifti$labels)
} else if (intent_cifti == 3006) {
col_names <- xifti$meta$cifti$names
intent_gii <- data_type <- label_table <- NULL
} else {
intent_gii <- data_type <- label_table <- col_names <- NULL
}
# Left cortex
if (do["left"]){
if (verbose) {cat("Writing left cortex.\n")}
# Add back medial wall.
if (is.null(xifti$meta$cortex$medial_wall_mask$left)) {
mwall <- rep(TRUE, nrow(xifti$data$cortex_left))
} else {
mwall <- xifti$meta$cortex$medial_wall_mask$left
}
cdat <- unmask_cortex(xifti$data$cortex_left, mwall)
# `NA` values create another variable level without a Key--bad!
if (!is.null(intent_gii) && intent_gii=="label" && ROI_do["left"]) {
cdat[!mwall] <- cdat[mwall][1]
}
# Write data and ROI.
write_metric_gifti(
cdat, sep_fnames["cortexL"], "left", data_type = data_type,
intent=intent_gii, label_table = label_table, col_names = col_names
)
if (ROI_do["left"]) {
write_metric_gifti(
as.numeric(mwall), sep_fnames["ROIcortexL"],
"left", data_type = "FLOAT32"
)
}
}
# Right cortex
if (do["right"]){
if (verbose) {cat("Writing right cortex.\n")}
# Add back medial wall.
if (is.null(xifti$meta$cortex$medial_wall_mask$right)) {
mwall <- rep(TRUE, nrow(xifti$data$cortex_right))
} else {
mwall <- xifti$meta$cortex$medial_wall_mask$right
}
cdat <- unmask_cortex(xifti$data$cortex_right, mwall)
# `NA` values create another variable level without a Key--bad!
if (!is.null(intent_gii) && intent_gii=="label" && ROI_do["right"]) {
cdat[!mwall] <- cdat[mwall][1]
}
# Write data and ROI.
write_metric_gifti(
cdat, sep_fnames["cortexR"], "right", data_type = data_type,
intent=intent_gii, label_table = label_table, col_names = col_names
)
if (ROI_do["right"]) {
write_metric_gifti(
as.numeric(mwall), sep_fnames["ROIcortexR"],
"right", data_type = "FLOAT32"
)
}
}
## Subcortex: unmask to get volumetric array.
if (do["subVol"] | do["subLab"]) {
if (verbose) {cat("Writing subcortical data and labels.\n")}
# Handle case where just one of these files are requested.
sep_fnames2 <- sep_fnames
if (is.na(sep_fnames2["subcortVol"])) {
sep_fnames2["subcortVol"] <- tempfile(fileext=".subVol.nii")
}
if (is.na(sep_fnames2["subcortLabs"])) {
sep_fnames2["subcortLabs"] <- tempfile(fileext=".subLab.nii")
}
write_subcort_nifti(
xifti$data$subcort,
xifti$meta$subcort$labels,
xifti$meta$subcort$mask,
xifti$meta$subcort$trans_mat,
xifti$meta$subcort$trans_units,
xifti$meta$cifti$names,
label_table,
sep_fnames2["subcortVol"],
sep_fnames2["subcortLabs"],
sep_fnames["ROIsubcortVol"],
fill=0
)
}
invisible(sep_fnames)
}
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