niinote

#!/usr/bin/env bash
set -euo pipefail

#
# run 3dNotes to annotate output ($1) of a cmd ($@)
#
# 20200110WF: init
cmd=$(basename $0)
[ $# -lt 2 ] && \
  echo "USAGE: $cmd output cmd\nEXAMPLE: $cmd betted.nii.gz bet input.nii.gz betted.nii.gz" && \
  exit 1

export AFNI_NO_OBLIQUE_WARNING="YES" # 3dNotes likes to complain. silence it

output="$1"; shift
# ext used if there are spaces in output name
! [[ "$output" =~ nii(.gz)$ ]] && echo "unknown extention. need nii or nii.gz!" >&2 && exit 1
ext=$BASH_REMATCH

#eval "$@" || exit $?
arg="$(printf "%q " "$@")"
# arg="$(printf "%q " "$*")"  # all a giant quote
eval "$arg" || exit $?
arg="$*"
[ ! -r "$output" ] &&
   echo "# ERROR: no expected output '$output'! but successfully ran cmd $arg" >&2 &&
   exit 1

# 3dNotes does not like writting to a prefix with spaces
MOVEBACK=""
if [[ "$(basename "$output")"  =~ " " ]]; then
   echo "# WARNING! '$output' has a space! WHY? moving to and from temp for 3dNotes" >&2
   MOVEBACK="$output"
   output=$(mktemp /tmp/XXXXX.$ext)
   mv "$MOVEBACK" "$output"
fi

3dNotes -h "'${arg//\'/\"}'" "$output" || exit $?
[ -n "$MOVEBACK" ] && mv "$output" "$MOVEBACK"
exit 0