#!/bin/bash

function help_exit
{
    cat <<-EOF
List subject IDs in SUBJECT_DIR.
Usage: $(basename $0) [OPTIONS] SUBJECT_DIR

Options:
    -c, --cross         Only cross-sectional stream
    -b, --base          Only base stream
    -l, --long          Only longitudinal stream
    -d, --done          Only subject IDs with scripts/recon-all.done
    -e, --error         Only subject IDs with scripts/recon-all.error
    -r, --running       Only subject IDs with scripts/IsRunning.?h
    -f, --full-path     Prepend full absolute path
    -n, --count         Print number of subjects found
    -h, --help          Show this help text

EOF
    exit 0
}

function err_exit
{
    echo "ERROR: $@" && exit 1
}

# Parse arguments.
[[ $# -eq 0 ]] && help_exit
positional=()
while [[ $# -gt 0 ]]; do
    case "$1" in
        -c|--cross)
            stream="c" && shift
        ;;
        -b|--base)
            stream="b" && shift
        ;;
        -l|--long)
            stream="l" && shift
        ;;
        -d|--done)
            state="d" && shift
        ;;
        -e|--error)
            state="e" && shift
        ;;
        -r|--running)
            state="r" && shift
        ;;
        -f|--full-path)
            full_path=1 && shift
        ;;
        -n|--count)
            count=1 && shift
        ;;
        -h|--help)
            help_exit
        ;;
        -*)
            err_exit "unknown flag \"$1\""
        ;;
        *)
            positional+=("$1") && shift
        ;;
    esac
done
set -- "${positional[@]}" 
sd=$(echo "$1" | sed -e 's,/\+$,,') # Trailing slashes.
if [[ $# -ne 1 ]]; then
    err_exit "number of positional arguments is not 1"
elif [[ ! -d $sd ]]; then
    err_exit "SUBJECTS_DIR \"$sd\" not found"
fi

# Find subjects processed with stream.
cmd="find \"$sd/\" -mindepth 1 -maxdepth 1 ! -type f ! -name fsaverage"
if [[ -z $stream ]]; then
    cmd="$cmd -exec test -e '{}/mri/orig' \; -print"
elif [[ $stream == c ]]; then
    cmd="$cmd -exec test -e '{}/mri/orig/001.mgz' \; -print"
elif [[ $stream == b ]]; then
    cmd="$cmd -exec test -e '{}/base-tps' \; -print"
elif [[ $stream == l ]]; then
    cmd="$cmd -name '*.long.*'"
fi
subj=$(eval $cmd)

# Filter subject state.
[[ -n $full_path ]] && path=$(cd "$sd" && pwd -P)/
out=()
for s in $subj; do
    d="$s/scripts"
    if [[ $state == d && ! -e "$d/recon-all.done" ]]; then
        continue
    elif [[ $state == e && ! -e "$d/recon-all.error" ]]; then
        continue
    elif [[ $state == r && ! -e "$d/IsRunning.lh" && \
            ! -e "$d/IsRunning.rh" ]]; then
        continue
    fi
    out+=("${path}${s##*/}") # Basename only.
done

# Print output.
if [[ -n $count ]]; then
    echo ${#out[@]}
else
    printf '%s\n' "${out[@]}"
fi