CT/liver/scripts/download_data.sh

#!/usr/bin/env bash
set -euo pipefail

PROJECT_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
DATA_ROOT="${DATA_ROOT:-${PROJECT_ROOT}/data}"
RAW_ROOT="${RAW_ROOT:-${DATA_ROOT}/raw}"
EXTRACTED_ROOT="${EXTRACTED_ROOT:-${DATA_ROOT}/extracted}"
MANIFEST_ROOT="${MANIFEST_ROOT:-${PROJECT_ROOT}/manifests}"
LOG_ROOT="${LOG_ROOT:-${PROJECT_ROOT}/logs}"

WAW_RAW="${RAW_ROOT}/waw_tace"
WAW_EXTRACTED="${EXTRACTED_ROOT}/waw_tace"
MSD_RAW="${RAW_ROOT}/msd_liver"
MSD_EXTRACTED="${EXTRACTED_ROOT}/msd_liver"
HCC_RAW="${RAW_ROOT}/hcc_tace_seg"
HCC_EXTRACTED="${EXTRACTED_ROOT}/hcc_tace_seg"

HCC_TCIA_MANIFEST="${HCC_TCIA_MANIFEST:-}"
NBIA_RETRIEVER="${NBIA_RETRIEVER:-nbia-data-retriever}"

usage() {
  cat <<'EOF'
Usage:
  scripts/download_data.sh [command]

Commands:
  all             Download WAW-TACE and MSD Task03 Liver. HCC-TACE-Seg runs only if HCC_TCIA_MANIFEST is set.
  waw-tace        Download WAW-TACE from Zenodo.
  extract-waw-tace
                  Extract WAW-TACE zip files into data/extracted/waw_tace.
  msd-liver       Download MSD Task03 Liver from the MONAI mirror.
  hcc-tace-seg    Download HCC-TACE-Seg from TCIA using NBIA Data Retriever and a .tcia manifest.
  layout          Create and print the planned project data layout.

Environment variables:
  DATA_ROOT            Override data root. Default: <project>/data
  HCC_TCIA_MANIFEST    Path to the HCC-TACE-Seg .tcia manifest downloaded from TCIA.
  NBIA_RETRIEVER       NBIA Data Retriever CLI path. Default: nbia-data-retriever

Examples:
  scripts/download_data.sh layout
  scripts/download_data.sh waw-tace
  scripts/download_data.sh extract-waw-tace
  scripts/download_data.sh msd-liver
  HCC_TCIA_MANIFEST=/path/to/HCC-TACE-Seg.tcia scripts/download_data.sh hcc-tace-seg
  scripts/download_data.sh all
EOF
}

require_cmd() {
  local cmd="$1"
  if ! command -v "${cmd}" >/dev/null 2>&1; then
    echo "Missing required command: ${cmd}" >&2
    exit 1
  fi
}

mkdir_layout() {
  mkdir -p \
    "${WAW_RAW}" "${WAW_EXTRACTED}" \
    "${MSD_RAW}" "${MSD_EXTRACTED}" \
    "${HCC_RAW}" "${HCC_EXTRACTED}" \
    "${DATA_ROOT}/processed/waw_tace" \
    "${DATA_ROOT}/processed/msd_liver" \
    "${DATA_ROOT}/processed/hcc_tace_seg" \
    "${MANIFEST_ROOT}" \
    "${LOG_ROOT}"
}

print_layout() {
  mkdir_layout
  cat <<EOF
Project root:
  ${PROJECT_ROOT}

Raw downloads:
  ${WAW_RAW}
  ${MSD_RAW}
  ${HCC_RAW}

Extracted data:
  ${WAW_EXTRACTED}
  ${MSD_EXTRACTED}
  ${HCC_EXTRACTED}

Processed data, generated later by preprocessing scripts:
  ${DATA_ROOT}/processed/waw_tace
  ${DATA_ROOT}/processed/msd_liver
  ${DATA_ROOT}/processed/hcc_tace_seg

Project manifests and logs:
  ${MANIFEST_ROOT}
  ${LOG_ROOT}
EOF
}

download_file() {
  local url="$1"
  local output="$2"
  local log_file="$3"

  echo "Downloading: ${output}"
  wget -c --show-progress "${url}" -O "${output}" 2>&1 | tee -a "${log_file}"
}

download_waw_tace() {
  require_cmd wget
  require_cmd tee
  mkdir_layout

  local log_file="${LOG_ROOT}/download_waw_tace.log"
  echo "Writing WAW-TACE downloads to ${WAW_RAW}"

  download_file "https://zenodo.org/records/12741586/files/clinical_data_wawtace_v2_15_07_2024.xlsx?download=1" "${WAW_RAW}/clinical_data_wawtace_v2_15_07_2024.xlsx" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/ct_hcc_metadata_v2.csv?download=1" "${WAW_RAW}/ct_hcc_metadata_v2.csv" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/ct_scans_1_4_wawtace_09_05_24.zip?download=1" "${WAW_RAW}/ct_scans_1_4_wawtace_09_05_24.zip" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/ct_scans_2_4_wawtace_09_05_24.zip?download=1" "${WAW_RAW}/ct_scans_2_4_wawtace_09_05_24.zip" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/ct_scans_3_4_wawtace_09_05_24.zip?download=1" "${WAW_RAW}/ct_scans_3_4_wawtace_09_05_24.zip" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/ct_scans_4_4_wawtace_09_05_24.zip?download=1" "${WAW_RAW}/ct_scans_4_4_wawtace_09_05_24.zip" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/organ_masks_wawtace_09_05_2024.zip?download=1" "${WAW_RAW}/organ_masks_wawtace_09_05_2024.zip" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/tumor_masks_wawtace_v1_08_05_2024.zip?download=1" "${WAW_RAW}/tumor_masks_wawtace_v1_08_05_2024.zip" "${log_file}"
  download_file "https://zenodo.org/records/12741586/files/radiomics_data_wawtace_09_05_2024.xlsx?download=1" "${WAW_RAW}/radiomics_data_wawtace_09_05_2024.xlsx" "${log_file}"

  echo "WAW-TACE raw download finished."
  echo "To extract: scripts/download_data.sh extract-waw-tace"
}

extract_waw_tace() {
  require_cmd unzip
  mkdir_layout

  local found_zip=0
  local zip_file

  for zip_file in "${WAW_RAW}"/*.zip; do
    if [[ ! -f "${zip_file}" ]]; then
      continue
    fi
    found_zip=1
    echo "Extracting ${zip_file} to ${WAW_EXTRACTED}"
    unzip -n "${zip_file}" -d "${WAW_EXTRACTED}"
  done

  if [[ "${found_zip}" -eq 0 ]]; then
    echo "No WAW-TACE zip files found in ${WAW_RAW}" >&2
    exit 1
  fi

  echo "WAW-TACE extraction finished."
}

download_msd_liver() {
  require_cmd wget
  require_cmd tar
  require_cmd tee
  mkdir_layout

  local log_file="${LOG_ROOT}/download_msd_liver.log"
  local archive="${MSD_RAW}/Task03_Liver.tar"

  download_file "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task03_Liver.tar" "${archive}" "${log_file}"

  if [[ -d "${MSD_EXTRACTED}/Task03_Liver" ]]; then
    echo "Skip existing extracted MSD data: ${MSD_EXTRACTED}/Task03_Liver"
    return
  fi

  echo "Extracting MSD Task03 Liver to ${MSD_EXTRACTED}"
  tar -xf "${archive}" -C "${MSD_EXTRACTED}"
  echo "MSD Task03 Liver finished."
}

download_hcc_tace_seg() {
  require_cmd tee
  mkdir_layout

  if [[ -z "${HCC_TCIA_MANIFEST}" ]]; then
    cat >&2 <<EOF
HCC_TCIA_MANIFEST is not set.

Download the HCC-TACE-Seg .tcia manifest from TCIA first:
  https://www.cancerimagingarchive.net/collection/hcc-tace-seg/

Then run:
  HCC_TCIA_MANIFEST=/path/to/HCC-TACE-Seg.tcia scripts/download_data.sh hcc-tace-seg
EOF
    exit 1
  fi

  if [[ ! -f "${HCC_TCIA_MANIFEST}" ]]; then
    echo "Manifest not found: ${HCC_TCIA_MANIFEST}" >&2
    exit 1
  fi

  if ! command -v "${NBIA_RETRIEVER}" >/dev/null 2>&1; then
    cat >&2 <<EOF
NBIA Data Retriever CLI not found: ${NBIA_RETRIEVER}

Install NBIA Data Retriever, or set NBIA_RETRIEVER to the full executable path, for example:
  NBIA_RETRIEVER=/opt/nbia-data-retriever/bin/nbia-data-retriever HCC_TCIA_MANIFEST=/path/to/HCC-TACE-Seg.tcia scripts/download_data.sh hcc-tace-seg
EOF
    exit 1
  fi

  local log_file="${LOG_ROOT}/download_hcc_tace_seg.log"
  echo "Downloading HCC-TACE-Seg to ${HCC_RAW}"
  "${NBIA_RETRIEVER}" --cli "${HCC_TCIA_MANIFEST}" -d "${HCC_RAW}" --agree-to-license -v 2>&1 | tee -a "${log_file}"
  echo "HCC-TACE-Seg raw download finished."
}

download_all() {
  download_waw_tace
  download_msd_liver

  if [[ -n "${HCC_TCIA_MANIFEST}" ]]; then
    download_hcc_tace_seg
  else
    echo "Skip HCC-TACE-Seg: set HCC_TCIA_MANIFEST to enable TCIA download."
  fi
}

main() {
  local command="${1:-all}"

  case "${command}" in
    all)
      download_all
      ;;
    waw-tace)
      download_waw_tace
      ;;
    extract-waw-tace)
      extract_waw_tace
      ;;
    msd-liver)
      download_msd_liver
      ;;
    hcc-tace-seg)
      download_hcc_tace_seg
      ;;
    layout)
      print_layout
      ;;
    -h|--help|help)
      usage
      ;;
    *)
      echo "Unknown command: ${command}" >&2
      usage >&2
      exit 1
      ;;
  esac
}

main "$@"