censor_1d

#!/usr/bin/env bash
set -euo pipefail
trap 'e=$?; [ $e -ne 0 ] && echo "$0 exited in error"' EXIT

#  20210219WF  init
# make fd censor file

usage(){
   cat <<HEREDOC
USAGE:
 $(basename $0) [-prefix fd_cen] [-colidx 0] [-thres 0.5] /path/to/*/motion_info/fd.txt

SYNOPSIS:
 - create 1d files with one value per line:
    1 when below thres         (\$x <  \$thres)
    0 when at or above thres   (\$x >= \$thres)
 - mnemonic: "censor*data will have 0 where censored"
 - "\$prefix_\$thres.1d" is output, saved in the same directory as input

OPTIONS:
 -prefix - what to name the file [fd_cen]
 -thres  - threshold to use      [0.5]
 -colidx - column idx (0-based)  [0] (first column)
 -help   - this help
 -n      - set DRYRUN=1; dont write files, but echo what would happen

ENV.:
    DRYRUN=1  show dont touch, same as -n

NOTES:
  see "fd_calc" and afni's "1deval" for generating input to censor_1d
HEREDOC
}
env|grep -q ^DRYRUN=. && DRYRUN=echo || DRYRUN=
writeto(){ [ -z "$DRYRUN" ] && cat > "$1" && return; cat; echo "# would write to $1"; }

[ $# -eq 0 ] && usage && exit 1

THRES=0.5
prefix=fd_cen
colidx=0
while [ $# -gt 0 ]; do
   case "$1" in
      -n|-dryrun)  DRYRUN="echo"; shift 1;;
      -prefix) prefix="$2"; shift 2;;
      -colidx) colidx="$2"; shift 2;;
      -thres)  THRES="$2"; shift 2;;
      -h*)  usage; exit;;
      -*)  echo "UNKNOWN '$1'"; usage; exit 1;;
      *) [ ! -r "$1" ] && echo "'$1' is not a file!" && exit 1; break;;
   esac
done

for fd in "$@"; do
   [ ! -r "$1" ] && echo "'$1' is not a file!" && continue
   dn="$(dirname "$fd")"
   out="$dn/${prefix}_$THRES.1d"
   [ "$out" == "$fd" ] && echo "ERROR: input and output are the same! ('$fd')" && exit 1
   [ -r "$out" ] && continue
   echo "# writing $out"
   $DRYRUN perl -slane 'print $F[$colidx]>=$thres?0:1' -- -thres=$THRES -colidx=$colidx < "$fd" |writeto "$out"
done