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#' Resample a GIFTI file (with its ROI)
#'
#' Perform spatial resampling of GIFTI data on the cortical surface (metric
#' and label), or of GIFTI surface geometry data itself.
#'
#' @param original_fname The GIFTI file to resample.
#' @param target_fname Where to save the resampled file.
#' @param hemisphere \code{"left"} (default) or \code{"right"}. An error will
#' occur if the hemisphere indicated in the GIFTI metadata does not match.
#' @param file_type \code{"metric"}, \code{"label"}, \code{"surf"}, or \code{NULL}
#' (default) to infer from \code{original_fname}.
#' @param original_res The resolution of the original file. If \code{NULL}
#' (default), infer from the file. Alternatively, provide
#' \code{sphere_original_fname} which will override \code{original_res}.
#'
#' In general, \code{original_res} should be used when the original file is
#' in registration with the spheres created by the Workbench command
#' \code{-surface-create-sphere}, and \code{sphere_original_fname} should be
#' used when it is not compatible.
#' @param resamp_res Target resolution for resampling (number of
#' cortical surface vertices per hemisphere). Alternatively, provide
#' \code{sphere_target_fname} which will override \code{resamp_res}.
#'
#' In general, \code{resamp_res} should be used when the target file will be
#' in registration with the spheres created by the Workbench command
#' \code{-surface-create-sphere}, and \code{sphere_target_fname} should be
#' used when it is not compatible.
#' @param resamp_method \code{"barycentric"} (default) or \code{"adaptive"}
#' resampling. These options correspond to the Workbench command options
#' \code{"BARYCENTRIC"} and \code{"ADAP_BARY_AREA"}, respectively.
#'
#' While adaptive resampling is recommended for metric or label
#' data, it requires that \code{area_original_fname} be provided.
#' @param area_original_fname,area_target_fname File paths to the surfaces to
#' use for vertex area correction during adaptive resampling. (Ignored if
#' resampling with the barycentric method.) \code{area_original_fname} should
#' match the current resolution of the data, and \code{area_target_fname}
#' should match \code{resamp_res}. If \code{area_target_fname} is not provided,
#' \code{area_original_fname} will be resampled with the barycentric method,
#' and the result will be used as \code{area_target_fname}.
#' @param ROIcortex_original_fname The name of the ROI file corresponding to
#' \code{original_fname}. Leave as \code{NULL} (default) if this doesn't exist
#' or shouldn't be resampled.
#' @param ROIcortex_target_fname The name of the resampled ROI file. Only
#' applicable if \code{ROIcortex_original_fname} is provided.
#' @param sphere_original_fname,sphere_target_fname File paths to the sphere
#' surfaces in the original and target resolutions. If possible, the simpler
#' arguments \code{original_res} and \code{resamp_res} can be used instead. But
#' those depend on the surface being compatible with that created by
#' \code{-surface-create-sphere}, which isn't always true. Therefore
#' \code{sphere_original_fname} and \code{sphere_target_fname} can be used if
#' needed.
#' @param read_dir Directory to append to the path of every file name in
#' \code{original_fname} and \code{ROIcortex_original_fname}. If \code{NULL}
#' (default), do not append any directory to the path.
#' @param write_dir Directory to append to the path of every file name in
#' \code{target_fname} and \code{ROIcortex_target_fname}. If \code{NULL}
#' (default), do not append any directory to the path.
#'
#' @return The resampled GIFTI file name, invisibly
#'
#' @importFrom gifti readgii
#'
#' @family gifting
#' @export
#'
#' @section Connectome Workbench:
#' This function interfaces with the \code{"-metric-resample"}, \code{"-label-resample"},
#' and/or \code{"-surface-resample"} Workbench commands, depending on the input.
#'
resample_gifti <- function(
original_fname, target_fname, hemisphere=c("left", "right"),
file_type=NULL, original_res=NULL,
resamp_res=NULL, resamp_method=c("barycentric", "adaptive"),
area_original_fname=NULL, area_target_fname=NULL,
ROIcortex_original_fname=NULL, ROIcortex_target_fname=NULL,
sphere_original_fname=NULL, sphere_target_fname=NULL,
read_dir=NULL, write_dir=NULL) {
# ----------------------------------------------------------------------------
# Check arguments. -----------------------------------------------------------
# ----------------------------------------------------------------------------
# File type
if (is.null(file_type)) {
if (grepl("func.gii", original_fname, fixed=TRUE)) {
file_type <- "metric"
} else if (grepl("label.gii", original_fname, fixed=TRUE)) {
file_type <- "label"
} else if (grepl("surf.gii", original_fname, fixed=TRUE)) {
file_type <- "surface"
} else {
stop(paste(
"Could not infer file type of ", original_fname,
". Please set the file_type argument."
))
}
}
file_type <- match.arg(file_type, c("metric", "label", "surface"))
# Original & target file names
original_fname <- format_path(original_fname, read_dir, mode=4)
stopifnot(file.exists(original_fname))
target_fname <- format_path(target_fname, write_dir, mode=2)
# Hemisphere
hemisphere <- match.arg(hemisphere, c("left", "right"))
if (file_type == "surface") {
surf <- make_surf(original_fname, hemisphere)
}
# Original ROI & target ROI file names
do_ROI <- !is.null(ROIcortex_original_fname)
if (do_ROI) {
ROIcortex_original_fname <- format_path(
ROIcortex_original_fname, read_dir, mode=4
)
stopifnot(file.exists(ROIcortex_original_fname))
if (is.null(ROIcortex_target_fname)) {
ROIcortex_target_fname <- cifti_component_suffix(
paste0("ROIcortex", switch(hemisphere, left="L", right="R")),
switch(file_type, metric="func", label="func", surface="surf")
)
}
ROIcortex_target_fname <- format_path(
ROIcortex_target_fname, write_dir, mode=2
)
}
# Check resamp_method and area files
resamp_method <- match.arg(resamp_method, c("barycentric", "adaptive"))
if (resamp_method == "adaptive") {
if (is.null(area_original_fname)) {
stop("Adaptive sampling requires `area_original_fname`.")
}
}
# Compatible args
if (do_ROI & file_type=="surface") {
stop("do_ROI AND file_type=='surface', but surface files do not use ROI.")
}
# ----------------------------------------------------------------------------
# Spheres & Area surface. ----------------------------------------------------
# ----------------------------------------------------------------------------
# Spheres
tdir <- tempdir()
if (is.null(sphere_original_fname)) {
# Check `original_res`
if (is.null(original_res)) {
gii <- readgii(original_fname)
original_res <- switch(file_type,
metric = nrow(gii$data[[1]]),
label = nrow(gii$data[[1]]),
surface = nrow(gii$data$pointset)
)
}
stopifnot(is.numeric(original_res) && original_res > 0)
sphereL_original_fname <- format_path(paste0("sphereL_", original_res, ".surf.gii"), tdir, mode=2)
sphereR_original_fname <- format_path(paste0("sphereR_", original_res, ".surf.gii"), tdir, mode=2)
write_spheres(sphereL_original_fname, sphereR_original_fname, original_res)
sphere_original_fname <- switch(hemisphere,
left = sphereL_original_fname,
right = sphereR_original_fname
)
# Check that the sphere is of compatible resolution.
sphere_original_res <- nrow(readgii(sphere_original_fname)$data$pointset)
if (sphere_original_res != original_res) {
stop(paste(
"Unable to create sphere with matching resolution to input GIFTI.",
"Please provide `sphere_original_fname` (and `sphere_target_fname`)",
"instead of `original_res` (and `resamp_res`)."
))
}
}
if (is.null(sphere_target_fname)) {
# Check `resamp_res`.
if (is.null(resamp_res)) {
stop("Provide either `sphere_target_fname` or `resamp_res`.")
}
stopifnot(is.numeric(resamp_res) && resamp_res > 0)
sphereL_target_fname <- format_path(paste0("sphereL_", resamp_res, ".surf.gii"), tdir, mode=2)
sphereR_target_fname <- format_path(paste0("sphereR_", resamp_res, ".surf.gii"), tdir, mode=2)
write_spheres(sphereL_target_fname, sphereR_target_fname, resamp_res)
sphere_target_fname <- switch(hemisphere,
left = sphereL_target_fname,
right = sphereR_target_fname
)
}
# Area surface for adaptive resampling
if (resamp_method == "adaptive") {
if (is.null(area_target_fname)) {
area_target_fname <- paste0(
tempfile(), "_area_target_", hemisphere, ".surf.gii"
)
resample_gifti(
original_fname=area_original_fname,
target_fname=area_target_fname,
hemisphere=hemisphere,
file_type="surf",
original_res=original_res,
resamp_res=resamp_res,
sphere_original_fname=sphere_original_fname,
sphere_target_fname=sphere_target_fname
)
}
}
# ----------------------------------------------------------------------------
# Make and run command. ------------------------------------------------------
# ----------------------------------------------------------------------------
resamp_method_wb <- switch(resamp_method,
adaptive="ADAP_BARY_AREA",
barycentric="BARYCENTRIC"
)
if (file_type=="surface" && resamp_res>original_res) {
ciftiTools_warn("Upsampling a surface is not recommended, if avoidable.")
}
cmd_name <- switch(file_type,
metric="-metric-resample",
label="-label-resample",
surface="-surface-resample"
)
cmd <- paste(
cmd_name,
sys_path(original_fname), sys_path(sphere_original_fname),
sys_path(sphere_target_fname), resamp_method_wb, sys_path(target_fname)
)
if (resamp_method_wb=="ADAP_BARY_AREA") {
cmd <- paste(
cmd,
ifelse(endsWith(area_original_fname, "shape.gii"), "-area-metrics", "-area-surfs"),
sys_path(area_original_fname),
sys_path(area_target_fname)
)
}
if (do_ROI) {
cmd <- paste(
cmd,
"-current-roi", sys_path(ROIcortex_original_fname),
"-valid-roi-out", sys_path(ROIcortex_target_fname)
)
}
run_wb_cmd(cmd)
if (do_ROI) {
out <- c(target_fname, ROIcortex_target_fname)
names(out) <- c(file_type, "ROI")
} else {
out <- target_fname
names(out) <- file_type
}
invisible(out)
}
#' Generate GIFTI sphere surface files
#'
#' This function generates a pair of GIFTI vertex-matched left and right spheres
#' in the target resolution. These are required for resampling CIFTI and GIFTI
#' files.
#'
#' @param sphereL_fname File path to left-hemisphere spherical GIFTI to be
#' created
#' @param sphereR_fname File path to right-hemisphere spherical GIFTI to be
#' created
#' @inheritParams resamp_res_Param_required
#' @param write_dir (Optional) directory to place the sphere files in. If
#' \code{NULL} (default), do not append any directory to the sphere file paths.
#'
#' @return The names of the written sphere files, invisibly
#'
#' @keywords internal
#'
write_spheres <- function(
sphereL_fname, sphereR_fname, resamp_res,
write_dir=NULL) {
sphereL_fname <- format_path(sphereL_fname, write_dir, mode=2)
sphereR_fname <- format_path(sphereR_fname, write_dir, mode=2)
resamp_res <- format(resamp_res, scientific=FALSE)
# Make left
run_wb_cmd(
paste("-surface-create-sphere", resamp_res[1], sys_path(sphereL_fname)),
)
# Make right
if (length(resamp_res)==1 || length(unique(resamp_res))==1) {
run_wb_cmd(
paste("-surface-flip-lr", sys_path(sphereL_fname), sys_path(sphereR_fname)),
)
} else {
sphereR_temp <- paste0(tempfile(), ".surf.gii")
run_wb_cmd(
paste("-surface-create-sphere", resamp_res[2], sphereR_temp),
)
run_wb_cmd(
paste("-surface-flip-lr", sphereR_temp, sys_path(sphereR_fname)),
)
}
# Set structure
run_wb_cmd(
paste("-set-structure", sys_path(sphereL_fname), "CORTEX_LEFT"),
)
run_wb_cmd(
paste("-set-structure", sys_path(sphereR_fname), "CORTEX_RIGHT"),
)
invisible(list(sphereL_fname=sphereL_fname, sphereR_fname=sphereR_fname))
}
#' @rdname resample_gifti
#' @export
resampleGIfTI <- function(
original_fname, target_fname, hemisphere,
file_type=NULL, original_res=NULL, resamp_res,
ROIcortex_original_fname=NULL, ROIcortex_target_fname=NULL,
read_dir=NULL, write_dir=NULL){
resample_gifti(
original_fname, target_fname, hemisphere,
file_type, original_res, resamp_res,
ROIcortex_original_fname, ROIcortex_target_fname,
read_dir, write_dir
)
}
#' @rdname resample_gifti
#' @export
resamplegii <- function(
original_fname, target_fname, hemisphere,
file_type=NULL, original_res=NULL, resamp_res,
ROIcortex_original_fname=NULL, ROIcortex_target_fname=NULL,
read_dir=NULL, write_dir=NULL){
resample_gifti(
original_fname, target_fname, hemisphere,
file_type, original_res, resamp_res,
ROIcortex_original_fname, ROIcortex_target_fname,
read_dir, write_dir
)
}
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