BIDS input

.gitignore

@@ -1,3 +1,5 @@
 output/
 logs/
 .qbatch/
+.vscode
+*.csv

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "antsRegistration_affine_SyN"]
 	path = antsRegistration_affine_SyN
 	url = https://github.com/CoBrALab/antsRegistration_affine_SyN.git
+[submodule "libBIDS.sh"]
+	path = libBIDS.sh
+	url = https://github.com/CoBrALab/libBIDS.sh.git

helpers.sh

@@ -9,7 +9,7 @@ __datetime=$(date -u +%F_%H-%M-%S-UTC)
 ### BASH HELPER FUNCTIONS ###
 # Stolen from https://github.com/kvz/bash3boilerplate"
 
-if [[ ${_arg_dry_run} == "on" || ${_arg_debug} == "on" ]]; then
+if [[ ${_arg_dry_run:-off} == "on" || ${_arg_debug:-off} == "on" ]]; then
   LOG_LEVEL=7
 else
   LOG_LEVEL=6

modelbuild_input_from_bids.sh

@@ -0,0 +1,181 @@
+#!/bin/bash
+#
+# ARG_OPTIONAL_SINGLE([suffix],[],[BIDS file suffix to construct inputs with],[T1w])
+# ARG_OPTIONAL_SINGLE([derivatives],[],[Derivatives sub-path to use (for preprocessed data)],[NA])
+
+# ARG_OPTIONAL_REPEATED([column-filter],[],[Use to filter other BIDS entity types])
+
+# ARG_OPTIONAL_SINGLE([masks],[],[Generate brain masks file],[])
+
+# ARG_POSITIONAL_SINGLE([input_bids],[Path to BIDS dataset top-level directory],[])
+# ARG_POSITIONAL_SINGLE([output],[CSV filename to save],[])
+# ARG_HELP([Helper script to parse a BIDS-formatted dataset and generate an input.csv for modelbuild.sh])
+# ARGBASH_SET_INDENT([  ])
+# ARGBASH_GO()
+# needed because of Argbash --> m4_ignore([
+### START OF CODE GENERATED BY Argbash v2.11.0 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}"
+}
+
+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=()
+# THE DEFAULTS INITIALIZATION - OPTIONALS
+_arg_suffix="T1w"
+_arg_derivatives="NA"
+_arg_column_filter=()
+_arg_masks=
+
+print_help() {
+  printf '%s\n' "Helper script to parse a BIDS-formatted dataset and generate an input.csv for modelbuild.sh"
+  printf 'Usage: %s [--suffix <arg>] [--derivatives <arg>] [--column-filter <arg>] [--masks <arg>] [-h|--help] <input_bids> <output>\n' "$0"
+  printf '\t%s\n' "<input_bids>: Path to BIDS dataset top-level directory"
+  printf '\t%s\n' "<output>: CSV filename to save"
+  printf '\t%s\n' "--suffix: BIDS file suffix to construct inputs with (default: 'T1w')"
+  printf '\t%s\n' "--derivatives: Derivatives sub-path to use (for preprocessed data) (default: 'NA')"
+  printf '\t%s\n' "--column-filter: Use to filter other BIDS entity types (empty by default)"
+  printf '\t%s\n' "--masks: Generate brain masks file (no default)"
+  printf '\t%s\n' "-h, --help: Prints help"
+}
+
+parse_commandline() {
+  _positionals_count=0
+  local _key
+  while test $# -gt 0; do
+    _key="$1"
+    case "$_key" in
+    --suffix)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_suffix="$2"
+      shift
+      ;;
+    --suffix=*)
+      _arg_suffix="${_key##--suffix=}"
+      ;;
+    --derivatives)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_derivatives="$2"
+      shift
+      ;;
+    --derivatives=*)
+      _arg_derivatives="${_key##--derivatives=}"
+      ;;
+    --column-filter)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_column_filter+=("$2")
+      shift
+      ;;
+    --column-filter=*)
+      _arg_column_filter+=("${_key##--column-filter=}")
+      ;;
+    --masks)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_masks="$2"
+      shift
+      ;;
+    --masks=*)
+      _arg_masks="${_key##--masks=}"
+      ;;
+    -h | --help)
+      print_help
+      exit 0
+      ;;
+    -h*)
+      print_help
+      exit 0
+      ;;
+    *)
+      _last_positional="$1"
+      _positionals+=("$_last_positional")
+      _positionals_count=$((_positionals_count + 1))
+      ;;
+    esac
+    shift
+  done
+}
+
+handle_passed_args_count() {
+  local _required_args_string="'input_bids' and 'output'"
+  test "${_positionals_count}" -ge 2 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require exactly 2 (namely: $_required_args_string), but got only ${_positionals_count}." 1
+  test "${_positionals_count}" -le 2 || _PRINT_HELP=yes die "FATAL ERROR: There were spurious positional arguments --- we expect exactly 2 (namely: $_required_args_string), but got ${_positionals_count} (the last one was: '${_last_positional}')." 1
+}
+
+assign_positional_args() {
+  local _positional_name _shift_for=$1
+  _positional_names="_arg_input_bids _arg_output "
+
+  shift "$_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
+
+### END OF CODE GENERATED BY Argbash (sortof) ### ])
+# [ <-- needed because of Argbash
+
+set -uo pipefail
+set -eE -o functrace
+
+# Load up helper scripts and define helper variables
+# shellcheck source=helpers.sh
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/helpers.sh"
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/libBIDS.sh/libBIDS.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' "$@" || true)"
+
+bids_table=$(libBIDSsh_parse_bids_to_csv "${_arg_input_bids}")
+
+# Prefix filters with the proper option
+_column_filter_args=()
+for filter in "${_arg_column_filter[@]}"; do
+  _column_filter_args+=("-r" "$filter")
+done
+
+filtered_image_table=$(libBIDSsh_csv_filter "${bids_table}" \
+  -r "suffix:${_arg_suffix}" \
+  -r "extension:(nii|nii.gz)" \
+  -r "derivatives:${_arg_derivatives}" \
+  "${_column_filter_args[@]}")
+
+declare -A row
+while libBIDSsh_csv_iterator "$filtered_image_table" row "subject" "session"; do
+  printf "%s\n" "${row[path]}"
+done >"${_arg_output}"
+
+if [[ -n "${_arg_masks}" ]]; then
+  filtered_mask_table=$(libBIDSsh_csv_filter "${bids_table}" \
+    -r "suffix:mask" \
+    -r "extension:(nii|nii.gz)" \
+    -r "derivatives:${_arg_derivatives}" \
+    "${_column_filter_args[@]}")
+  declare -A row
+  while libBIDS_csv_iterator "$filtered_mask_table" row "subject" "session"; do
+    printf "%s\n" "${row[path]}"
+  done >"${_arg_masks}"
+fi
+
+# ] <-- needed because of Argbash

twolevel_modelbuild_input_from_bids.sh

@@ -0,0 +1,192 @@
+#!/bin/bash
+#
+# ARG_OPTIONAL_SINGLE([suffix],[],[BIDS file suffix to construct inputs with],[T1w])
+# ARG_OPTIONAL_SINGLE([derivatives],[],[Derivatives sub-path to use (for preprocessed data)],[NA])
+
+# ARG_OPTIONAL_REPEATED([column-filter],[],[Use to filter other BIDS entity types])
+
+# ARG_OPTIONAL_SINGLE([masks],[],[Generate brain masks file],[])
+
+# ARG_POSITIONAL_SINGLE([input_bids],[Path to BIDS dataset top-level directory],[])
+# ARG_POSITIONAL_SINGLE([output],[CSV filename to save],[])
+# ARG_HELP([Helper script to parse a BIDS-formatted dataset and generate an input.csv for modelbuild.sh])
+# ARGBASH_SET_INDENT([  ])
+# ARGBASH_GO()
+# needed because of Argbash --> m4_ignore([
+### START OF CODE GENERATED BY Argbash v2.11.0 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}"
+}
+
+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=()
+# THE DEFAULTS INITIALIZATION - OPTIONALS
+_arg_suffix="T1w"
+_arg_derivatives="NA"
+_arg_column_filter=()
+_arg_masks=
+
+print_help() {
+  printf '%s\n' "Helper script to parse a BIDS-formatted dataset and generate an input.csv for modelbuild.sh"
+  printf 'Usage: %s [--suffix <arg>] [--derivatives <arg>] [--column-filter <arg>] [--masks <arg>] [-h|--help] <input_bids> <output>\n' "$0"
+  printf '\t%s\n' "<input_bids>: Path to BIDS dataset top-level directory"
+  printf '\t%s\n' "<output>: CSV filename to save"
+  printf '\t%s\n' "--suffix: BIDS file suffix to construct inputs with (default: 'T1w')"
+  printf '\t%s\n' "--derivatives: Derivatives sub-path to use (for preprocessed data) (default: 'NA')"
+  printf '\t%s\n' "--column-filter: Use to filter other BIDS entity types (empty by default)"
+  printf '\t%s\n' "--masks: Generate brain masks file (no default)"
+  printf '\t%s\n' "-h, --help: Prints help"
+}
+
+parse_commandline() {
+  _positionals_count=0
+  local _key
+  while test $# -gt 0; do
+    _key="$1"
+    case "$_key" in
+    --suffix)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_suffix="$2"
+      shift
+      ;;
+    --suffix=*)
+      _arg_suffix="${_key##--suffix=}"
+      ;;
+    --derivatives)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_derivatives="$2"
+      shift
+      ;;
+    --derivatives=*)
+      _arg_derivatives="${_key##--derivatives=}"
+      ;;
+    --column-filter)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_column_filter+=("$2")
+      shift
+      ;;
+    --column-filter=*)
+      _arg_column_filter+=("${_key##--column-filter=}")
+      ;;
+    --masks)
+      test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
+      _arg_masks="$2"
+      shift
+      ;;
+    --masks=*)
+      _arg_masks="${_key##--masks=}"
+      ;;
+    -h | --help)
+      print_help
+      exit 0
+      ;;
+    -h*)
+      print_help
+      exit 0
+      ;;
+    *)
+      _last_positional="$1"
+      _positionals+=("$_last_positional")
+      _positionals_count=$((_positionals_count + 1))
+      ;;
+    esac
+    shift
+  done
+}
+
+handle_passed_args_count() {
+  local _required_args_string="'input_bids' and 'output'"
+  test "${_positionals_count}" -ge 2 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require exactly 2 (namely: $_required_args_string), but got only ${_positionals_count}." 1
+  test "${_positionals_count}" -le 2 || _PRINT_HELP=yes die "FATAL ERROR: There were spurious positional arguments --- we expect exactly 2 (namely: $_required_args_string), but got ${_positionals_count} (the last one was: '${_last_positional}')." 1
+}
+
+assign_positional_args() {
+  local _positional_name _shift_for=$1
+  _positional_names="_arg_input_bids _arg_output "
+
+  shift "$_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
+
+### END OF CODE GENERATED BY Argbash (sortof) ### ])
+# [ <-- needed because of Argbash
+
+set -uo pipefail
+set -eE -o functrace
+
+# Load up helper scripts and define helper variables
+# shellcheck source=helpers.sh
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/helpers.sh"
+source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/libBIDS.sh/libBIDS.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' "$@" || true)"
+
+bids_table=$(libBIDSsh_parse_bids_to_csv "${_arg_input_bids}")
+
+# Prefix filters with the proper option
+_column_filter_args=()
+for filter in "${_arg_column_filter[@]}"; do
+  _column_filter_args+=("-r" "$filter")
+done
+
+filtered_image_table=$(libBIDSsh_csv_filter "${bids_table}" \
+  -r "suffix:${_arg_suffix}" \
+  -r "extension:(nii|nii.gz)" \
+  -r "derivatives:${_arg_derivatives}" \
+  "${_column_filter_args[@]}")
+
+declare -a subjects
+declare -A row
+libBIDSsh_csv_column_to_array "$filtered_image_table" "subject" subjects true true
+for subject in "${subjects[@]}"; do
+  while libBIDSsh_csv_iterator "$(libBIDSsh_csv_filter "${filtered_image_table}" -r "subject:${subject}")" row "subject" "session"; do
+    printf "%s," "${row[path]}"
+  done
+  printf "\n"
+done >"${_arg_output}"
+
+if [[ -n "${_arg_masks}" ]]; then
+  filtered_mask_table=$(libBIDSsh_csv_filter "${bids_table}" \
+    -r "suffix:mask" \
+    -r "extension:(nii|nii.gz)" \
+    -r "derivatives:${_arg_derivatives}" \
+    "${_column_filter_args[@]}")
+
+  declare -a subjects
+  declare -A row
+  libBIDSsh_csv_column_to_array "$filtered_mask_table" "subject" subjects true true
+  for subject in "${subjects[@]}"; do
+    while libBIDSsh_csv_iterator "$(libBIDSsh_csv_filter "${filtered_mask_table}" -r "subject:${subject}")" row "subject" "session"; do
+      printf "%s," "${row[path]}"
+    done
+    printf "\n"
+  done >"${_arg_masks}"
+fi
+
+# ] <-- needed because of Argbash