add-intended-for

#!/usr/bin/env bash
#
# 20221020WF - init. lncd "habit" project
# 20231110WF - into lncdtools
# 20231221WF - takes multiple patterns
#

usage(){
   cat <<HEREDOC
'add-intended-for' adds an element like
  'IntendedFor': ['sub-1/ses-1/func/sub-1_ses-1_task-rest_bold.nii.gz']
 to the json files matching \`-fmap 'pattern.json'\`

 IntendedFor is used by fmriprep's susceptibility distortion correction (SDC).

USAGE:
  $(basename "$0") -fmap '*PA_run-1_epi.json' [-for '*_bold.nii.gz'] [-for '*dwi.nii.gz']  subj-1/ses-1/ [subj-2/ses-1/ ...]

OPTIONS:
  -help    this message

  -fmap    pattern to find fmap json file. where to insert IntendedFor

  -for     pattern to find bold or dwi file(s).
           default is '*_bold.nii.gz'. An alternative: '*dwi.nii.gz'
           Can repeat "-for 'pattern.nii.gz'" 
           to put multiple patterns into the 'IntendedFor' array

  -me_okay include multiecho files in search.
           default is to exclude all files matching '*echo-*'

  sesdir   any number of session dirs 
           each should be session root dir with fmap/, func/ +/- dwi/
           repeat for as many sessions as needed. Consider using a glob

NOTE:
  * skips files where 'IntendedFor' already exists
  * test with 'DRYRUN=1 add-intended-for ...'

HEREDOC
}

#shellcheck disable=SC2089 # intentionally not an array
FIND_EXCLUDE=" -not -name *echo-*"

csv_niifiles(){
   local sesdir="$1"; shift
   #local boldpat="${1:?need at least one bold or dwi file pattern}"
   local find_names
   # build a list of acceptable names
   find_names=$(printf " -iname %s -or" "$@"|sed 's/-or$//')
   # shellcheck disable=SC2086,SC2090 # sending multiple args in ea. var
   (cd "$sesdir" &&
    find func/ dwi/ \( $find_names \) $FIND_EXCLUDE ) |
    sed 's/^\|$/"/g'|
    paste -sd,
}
find_se_file(){
   local sesdir="${1:?find_se_file requires session dir}"
   local pattern="${2:?find_se_file requires a json pattern}"
   mapfile -t sefiles < <(find "$sesdir/fmap" -name "$pattern") 
   if [[ -z "${sefiles[*]}" || ! -r "${sefiles[0]}" ]]; then
      warn "no like '$sesdir/fmap/$pattern'?" 
      exit 1
   fi
   [ ${#sefiles[@]} -gt 1 ] && warn ">1 match for '$pattern' found: ${sefiles[*]}"
   printf "%s\n" "${sefiles[@]}"
}

add_intended_for(){
   local sefile forfilescsv str
   sefile="$1"; shift
   forfilescsv="$1"; shift
   # (DANGER) inline replace on
   # matching files without an 'IntendedFor' line
   str="\"IntendedFor\": [$forfilescsv],"
   grep -L IntendedFor "$sefile" |
      xargs -r dryrun sed "s;{;{\n$str;" -i || :
   return 0
}

_intendedFor() {
  local boldpatt=()
  local sepatt=""
  local sesdirs=()
  [ $# -eq 0 ] && usage && exit 1
  while [ $# -gt 0 ]; do
     case "$1" in
        -for|-bold|-dwi) boldpatt=("${boldpatt[@]}" "$2"); shift 2;;
        -fmap) sepatt="$2"; shift 2;;
        -me_okay) FIND_EXCLUDE=""; shift 1;;
        -help) usage; exit 0;;
        *) sesdirs+=("$1"); shift 1;;
     esac
  done
  [ -z "${boldpatt[*]}" ] && boldpatt=('*_bold.nii.gz')

  # check inputs
  [ -z "$sepatt" ] &&
     echo "ERROR: no -fmap pattern; see -help" &&
     exit 1
  ! [[ "$sepatt" =~ .json$ ]] &&
     echo "-fmap pattern must end with .json" &&
     exit 2

  for sesdir in "${sesdirs[@]}"; do
     mapfile -t sefiles < <(find_se_file "$sesdir" "$sepatt")
     for sefile in "${sefiles[@]}"; do
        forfilescsv=$(csv_niifiles "$sesdir" "${boldpatt[@]}")
        [ -z "$forfilescsv" ] &&
           warn "no matching files in $sesdir/{func,dwi}/ matching ${boldpatt[*]}" && return 1
        add_intended_for "$sefile" "$forfilescsv" || :
     done
  done
  return 0
}

# if not sourced (testing), run as command
eval "$(iffmain "_intendedFor")"