3dNotes_each

#!/usr/bin/env bash
#
# run 3dNotes for each file argument
# 3dNotes alone will only work on one file
#
# 20220308WF - init
#
[ -v DRYRUN ] && DRYRUN=echo || DRYRUN=
warn(){ echo "$@" >&2; }

add_noop() { cat; }
add_f() { sed "s;^;${1//;/_}\t;";}
_3dNotes_each() {
  prepend_func=add_noop
  while [[ $# -gt 0 && "$1" =~ ^- ]]; do
     case $1 in
        -f) prepend_func=add_f; shift;;
        -h) echo "USAGE: $0 [-f] file.nii.gz file2.nii.gz -- maybe-more-files.nii.gz"; exit ;;
        --) shift; break;;
     esac
  done
  
  for f in "$@"; do
     echo "# $f"
     (3dNotes "$f" || :) | $prepend_func "$f"
  done
  return 0
}

# if not sourced (testing), run as command
if ! [[ "$(caller)" != "0 "* ]]; then
  set -euo pipefail
  trap 'e=$?; [ $e -ne 0 ] && echo "$0 exited in error $e"' EXIT
  _3dNotes_each "$@"
  exit $?
fi

####
# testing with bats. use like
#   bats ./3dNotes_each --verbose-run
####
if  [[ "$(caller)" =~ /bats.*/preprocessing.bash ]]; then
@test "emtpy does nothing" {
   run _3dNotes_each
}
@test "can run with bad file" {
   run _3dNotes_each FILEDNE.nii.gz
   [[ "$output" =~ FILEDNE.nii.gz ]] 
}
fi