suppressPackageStartupMessages(library("optparse"))
# Make option list
option_list <- list(
make_option(c("-i", "--input"), type="character", default=NULL, help="Input 4D functional image (required)", metavar="file"),
make_option(c("-r", "--roi"), type="character", default=NULL, help="3D image with ROIs (required)", metavar="file"),
make_option(c("-m", "--mask"), type="character", default=NULL, help="3D brain mask (optional)", metavar="file"),
make_option("--outtype", type="character", default="nifti", help="Type of output: nifti or text (default: %default)", metavar="option"),
make_option("--overwrite", action="store_true", default=FALSE, help="Overwrite output if it already exists"),
make_option(c("-v", "--verbose"), action="store_true", default=TRUE, help="Print extra output [default]"),
make_option(c("-q", "--quiet"), action="store_false", dest="verbose", help="Print little output")
)
# Make class/usage
parser <- OptionParser(usage = "%prog [options] outfile",
option_list=option_list,
add_help_option=TRUE)
# Parse
parser_out <- parse_args(parser, positional_arguments = TRUE)
args <- parser_out$args
opts <- parser_out$options
# Check options/arguments
if (length(args) != 1) {
print_help(parser)
quit(save="no", status=1)
}
saved_opts <- list(args=args, opts=opts)
tryCatch({
# load connectir
suppressWarnings(suppressPackageStartupMessages(library("connectir")))
# set output
opts$outfile <- args[1]
if (opts$outtype == "text") {
opts$outfile <- paste(rmext(opts$outfile), "txt", sep=".")
} else if (opts$outtype == "nifti") {
opts$outfile <- paste(rmext(opts$outfile), "nii.gz", sep=".")
} else {
vstop("unrecognized output type '%s'; must be text or nifti", opts$outtype)
}
###
# Check Inputs
###
vcat(opts$verbose, "Checking options")
if (is.null(opts$input))
stop("Must specify input (-i/--input)")
if (is.null(opts$roi))
stop("Must specify roi (-r/--roi)")
if (!file.exists(opts$input))
vstop("Input '%s' doesn't exist", opts$input)
if (!file.exists(opts$roi))
vstop("ROI file '%s' doesn't exist", opts$roi)
if (!is.null(opts$mask) && !file.exists(opts$mask))
vstop("Mask '%s' doesn't exist", opts$mask)
if (file.exists(opts$outfile) && !opts$overwrite)
vstop("Output '%s' already exists (consider using --overwrite)", opts$outfile)
###
# Setup
###
vcat(opts$verbose, "Setup inputs")
input <- abspath(opts$input)
roi <- abspath(opts$roi)
if (!is.null(opts$mask))
mask <- abspath(opts$mask)
else
mask <- NULL
outfile <- abspath(opts$outfile)
outtype <- opts$outtype
overwrite <- opts$overwrite
verbose <- opts$verbose
###
# Run IT!
###
start.time <- Sys.time()
roi_mean_wrapper(input, roi, mask,
out_file=outfile, outtype=outtype, overwrite=overwrite,
verbose=verbose)
end.time <- Sys.time()
vcat(verbose, "Done! Total computation time: %.1f minutes\n",
as.numeric(end.time-start.time, units="mins"))
}, warning = function(ex) {
cat("\nA warning was detected: \n")
cat(ex$message, "\n\n")
cat("Called by: \n")
print(ex$call)
cat("\nSaving options...\n")
save(saved_opts, file="called_options.rda")
}, error = function(ex) {
cat("\nAn error was detected: \n")
cat(ex$message, "\n\n")
cat("Called by: \n")
print(ex$call)
cat("\nSaving options...\n")
save(saved_opts, file="called_options.rda")
}, interrupt = function(ex) {
cat("\nSaving options...\n")
save(saved_opts, file="called_options.rda")
cat("\nKill signal sent. Trying to clean up...\n")
rm(list=ls())
gc(FALSE)
cat("...success\n")
}, finally = {
cat("\nRemoving everything from memory\n")
rm(list=ls())
gc(FALSE)
cat("...sucesss\n")
})
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