twolevel_subjectspace_resample.sh

#!/usr/bin/env bash

# Created by argbash-init v2.10.0
# ARG_HELP([Resampling from commonspace to subjectspace for twolevel_modelbuild.sh from optimized_antsMultivariateTemplateConstruction])
# ARG_OPTIONAL_SINGLE([output-dir],[],[Output directory for modelbuild],[output])
# ARG_OPTIONAL_SINGLE([walltime],[],[Walltime for short running stages (averaging, resampling)],[00:15:00])
# ARG_OPTIONAL_SINGLE([resample-input],[],[Files to be resampled into common space, structured the same as the input to twolevel_modelbuild.sh],[])
# ARG_OPTIONAL_SINGLE([resample-input-space],[],[Initial space of the input to be resampled (unbiased, final-target, or secondlevel for twolevel wrapper)],[final-target])
# ARG_TYPE_GROUP_SET([spacegroup],[SPACE],[resample-input-space],[unbiased,final-target,secondlevel])
# ARG_OPTIONAL_SINGLE([append-transforms],[],[Transform files which align modelbuild inputs to target-space, will be applied at the end of the transform chain, append with :1 to indicate applying the inverse],[])
# ARG_OPTIONAL_SINGLE([target-space],[],[Target space for each subject, structured the same as the input to modelbuild.sh. inputs is used if not specified.],[])
# ARG_OPTIONAL_BOOLEAN([debug],[],[Debug mode, print all commands to stdout],[])
# ARG_OPTIONAL_BOOLEAN([dry-run],[],[Dry run, don't run any commands, implies debug],[])
# ARG_POSITIONAL_SINGLE([inputs],[Input text files, one line per subject, comma separated scans per subject],[])
# ARG_LEFTOVERS([Arguments to be passed to subjectspace_resample.sh without validation])
# ARGBASH_SET_INDENT([  ])
# ARGBASH_GO()
# needed because of Argbash --> m4_ignore([
### START OF CODE GENERATED BY Argbash v2.10.0 one line above ###
# Argbash is a bash code generator used to get arguments parsing right.
# Argbash is FREE SOFTWARE, see https://argbash.dev for more info


die()
{
  local _ret="${2:-1}"
  test "${_PRINT_HELP:-no}" = yes && print_help >&2
  echo "$1" >&2
  exit "${_ret}"
}

# validators

spacegroup()
{
	local _allowed=("unbiased" "final-target" "secondlevel") _seeking="$1"
	for element in "${_allowed[@]}"
	do
		test "$element" = "$_seeking" && echo "$element" && return 0
	done
	die "Value '$_seeking' (of argument '$2') doesn't match the list of allowed values: 'unbiased', 'final-target' and 'secondlevel'" 4
}


begins_with_short_option()
{
  local first_option all_short_options='h'
  first_option="${1:0:1}"
  test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
}

# THE DEFAULTS INITIALIZATION - POSITIONALS
_positionals=()
_arg_leftovers=()
# THE DEFAULTS INITIALIZATION - OPTIONALS
_arg_output_dir="output"
_arg_walltime="00:15:00"
_arg_resample_input=
_arg_resample_input_space="final-target"
_arg_append_transforms=
_arg_target_space=
_arg_debug="off"
_arg_dry_run="off"


print_help()
{
  printf '%s\n' "Resampling from commonspace to subjectspace for twolevel_modelbuild.sh from optimized_antsMultivariateTemplateConstruction"
  printf 'Usage: %s [-h|--help] [--output-dir <arg>] [--walltime <arg>] [--resample-input <arg>] [--resample-input-space <SPACE>] [--append-transforms <arg>] [--target-space <arg>] [--(no-)debug] [--(no-)dry-run] <inputs> ... \n' "$0"
  printf '\t%s\n' "<inputs>: Input text files, one line per subject, comma separated scans per subject"
  printf '\t%s\n' "... : Arguments to be passed to subjectspace_resample.sh without validation"
  printf '\t%s\n' "-h, --help: Prints help"
  printf '\t%s\n' "--output-dir: Output directory for modelbuild (default: 'output')"
  printf '\t%s\n' "--walltime: Walltime for short running stages (averaging, resampling) (default: '00:15:00')"
  printf '\t%s\n' "--resample-input: Files to be resampled into common space, structured the same as the input to twolevel_modelbuild.sh (no default)"
  printf '\t%s\n' "--resample-input-space: Initial space of the input to be resampled (unbiased, final-target, or secondlevel for twolevel wrapper). Can be one of: 'unbiased', 'final-target' and 'secondlevel' (default: 'final-target')"
  printf '\t%s\n' "--append-transforms: Transform files which align modelbuild inputs to target-space, will be applied at the end of the transform chain, append with :1 to indicate applying the inverse (no default)"
  printf '\t%s\n' "--target-space: Target space for each subject, structured the same as the input to modelbuild.sh. inputs is used if not specified. (no default)"
  printf '\t%s\n' "--debug, --no-debug: Debug mode, print all commands to stdout (off by default)"
  printf '\t%s\n' "--dry-run, --no-dry-run: Dry run, don't run any commands, implies debug (off by default)"
}


parse_commandline()
{
  _positionals_count=0
  while test $# -gt 0
  do
    _key="$1"
    case "$_key" in
      -h|--help)
        print_help
        exit 0
        ;;
      -h*)
        print_help
        exit 0
        ;;
      --output-dir)
        test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
        _arg_output_dir="$2"
        shift
        ;;
      --output-dir=*)
        _arg_output_dir="${_key##--output-dir=}"
        ;;
      --walltime)
        test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
        _arg_walltime="$2"
        shift
        ;;
      --walltime=*)
        _arg_walltime="${_key##--walltime=}"
        ;;
      --resample-input)
        test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
        _arg_resample_input="$2"
        shift
        ;;
      --resample-input=*)
        _arg_resample_input="${_key##--resample-input=}"
        ;;
      --resample-input-space)
        test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
        _arg_resample_input_space="$(spacegroup "$2" "resample-input-space")" || exit 1
        shift
        ;;
      --resample-input-space=*)
        _arg_resample_input_space="$(spacegroup "${_key##--resample-input-space=}" "resample-input-space")" || exit 1
        ;;
      --append-transforms)
        test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
        _arg_append_transforms="$2"
        shift
        ;;
      --append-transforms=*)
        _arg_append_transforms="${_key##--append-transforms=}"
        ;;
      --target-space)
        test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
        _arg_target_space="$2"
        shift
        ;;
      --target-space=*)
        _arg_target_space="${_key##--target-space=}"
        ;;
      --no-debug|--debug)
        _arg_debug="on"
        test "${1:0:5}" = "--no-" && _arg_debug="off"
        ;;
      --no-dry-run|--dry-run)
        _arg_dry_run="on"
        test "${1:0:5}" = "--no-" && _arg_dry_run="off"
        ;;
      *)
        _last_positional="$1"
        _positionals+=("$_last_positional")
        _positionals_count=$((_positionals_count + 1))
        ;;
    esac
    shift
  done
}


handle_passed_args_count()
{
  local _required_args_string="'inputs'"
  test "${_positionals_count}" -ge 1 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require at least 1 (namely: $_required_args_string), but got only ${_positionals_count}." 1
}


assign_positional_args()
{
  local _positional_name _shift_for=$1
  _positional_names="_arg_inputs "
  _our_args=$((${#_positionals[@]} - 1))
  for ((ii = 0; ii < _our_args; ii++))
  do
    _positional_names="$_positional_names _arg_leftovers[$((ii + 0))]"
  done

  shift "$_shift_for"
  for _positional_name in ${_positional_names}
  do
    test $# -gt 0 || break
    eval "$_positional_name=\${1}" || die "Error during argument parsing, possibly an Argbash bug." 1
    shift
  done
}

parse_commandline "$@"
handle_passed_args_count
assign_positional_args 1 "${_positionals[@]}"

# OTHER STUFF GENERATED BY Argbash
# Validation of values


### END OF CODE GENERATED BY Argbash (sortof) ### ])
# [ <-- needed because of Argbash

set -uo pipefail
set -eE -o functrace

# shellcheck source=helpers.sh
source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/helpers.sh"

# Set magic variables for current file, directory, os, etc.
__file="${__dir}/$(basename "${BASH_SOURCE[${__b3bp_tmp_source_idx:-0}]}")"
__base="$(basename "${__file}" .sh)"
# shellcheck disable=SC2034,SC2015
__invocation="$(printf %q "${__file}")$( (($#)) && printf ' %q' "$@" || true)"

if [[ ${_arg_debug} == "off" ]]; then
  unset _arg_debug
fi

# Prefight check for required programs
preflight_check

# Setup a directory which contains all commands run
# for this invocation
mkdir -p ${_arg_output_dir}/secondlevel/jobs/${__datetime}

# Store the full command line for each run
echo ${__invocation} >${_arg_output_dir}/secondlevel/jobs/${__datetime}/invocation


mkdir -p ${_arg_output_dir}/secondlevel/commonspace-resampled

# Find transform files from resample-inputs to commonspace
if [[ ${_arg_resample_input_space} == "unbiased" ]]; then
  final_target_transforms=""
  real_outputdir="${_arg_output_dir}/subjectspace-resampled"
elif [[ ${_arg_resample_input_space} == "final-target" ]]; then
  inversewarp_to_final_target=${_arg_output_dir}/secondlevel/final-target/to_target_1InverseWarp.nii.gz
  if [[ -s ${inversewarp_to_final_target} ]]; then
    final_target_transforms="-t [${_arg_output_dir}/secondlevel/final-target/to_target_0GenericAffine.mat,1] -t ${inversewarp_to_final_target}"
  else
    fatal "Final target transform ${inversewarp_to_final_target} not found"
  fi
fi

info "Processing Two-Level Resampling"
i=1
while read -r subject_scans; do
  mkdir -p ${_arg_output_dir}/subjectspace-resampled/subject_${i}
  IFS=',' read -r -a scans <<<${subject_scans}
  # Save append-transforms for individual subjects
  if [[ -n ${_arg_append_transforms} ]]; then
    IFS=',' read -r -a transforms <<< $(sed "${i}q;d" ${_arg_append_transforms})
    append_transforms="--append-transforms ${_arg_output_dir}/subjectspace-resampled/subject_${i}/append_transforms.txt"
    printf "%s\n" "${transforms[@]}" > ${_arg_output_dir}/subjectspace-resampled/subject_${i}/append_transforms.txt
  else
    >${_arg_output_dir}/subjectspace-resampled/subject_${i}/append_transforms.txt
    append_transforms=""
  fi
  # Save target-space for individual subjects
  temp_target_space_file="${_arg_output_dir}/subjectspace-resampled/subject_${i}/target_space.txt"
  if [[ -n ${_arg_target_space} ]]; then
    IFS=',' read -r -a target_space <<< $(sed "${i}q;d" ${_arg_target_space})
    target_space_cmd="--target-space ${temp_target_space_file}"
    printf "%s\n" "${target_space[@]}" > ${temp_target_space_file}
  else
    >${temp_target_space_file}
    target_space_cmd=""
  fi


  info "Processing subject_${i}"

    if (( $(wc -l < ${_arg_output_dir}/firstlevel/subject_${i}/input_files.txt) > 1 )); then

    ${__dir}/subjectspace_resample.sh ${_arg_debug:+--debug} ${_arg_leftovers[@]+"${_arg_leftovers[@]}"} \
                                            --resample-input-space secondlevel \
                                            --output-dir ${_arg_output_dir}/firstlevel/subject_${i} \
                                            ${append_transforms} \
                                            --prepend-transforms "-t [${_arg_output_dir}/secondlevel/final/transforms/subject_${i}_0GenericAffine.mat,1] -t ${_arg_output_dir}/secondlevel/final/transforms/subject_${i}_1InverseWarp.nii.gz ${final_target_transforms}" \
                                            --resample-input ${_arg_resample_input} \
                                            ${target_space_cmd} \
                                            ${_arg_output_dir}/firstlevel/subject_${i}/input_files.txt
    fi

  ((++i))

done < ${_arg_inputs}

# ] <-- needed because of Argbash