gmt-fork/share/tools/ncdeflate

#!/usr/bin/env bash
#
#
# Copyright (c) 1991-2021 by the GMT Team (https://www.generic-mapping-tools.org/team.html)
# See LICENSE.TXT file for copying and redistribution conditions.
#
# Compresses all variables in the given netcdf files with the
# specified deflation level.

function usage () {
  echo "usage: $(basename $0) [-d n] [-o dir] [-s] file [file ...]"  >&2
  echo "  [-d n]    set compression level (0=min, 9=max, default=3)" >&2
  echo "  [-o dir]  output directory" >&2
  echo "  [-s]      add shuffle option to deflation compression" >&2
  echo "  [-v]      be verbose" >&2
  echo "  [-x s]    add suffix \"s\" to output filename" >&2
  exit 1
}

# set defaults
NC_DEFLATE=3
NC_SHUFFLE=
NC_SUFFIX=""
NC_VERBOSE=0
OUTDIR=""

# handle filenames with spaces
IFS=$'\n'

# test if nccopy in PATH
if ! which nccopy >/dev/null 2>&1; then
  echo "$(basename $0): cannot find nccopy." >&2
  exit 1
fi

# find compatible stat command
if stat -f%z "$0" >/dev/null 2>&1; then
  # BSD
  STAT=stat
  STATOPT="-f%z"
elif stat -c%s "$0" >/dev/null 2>&1; then
  # GNU
  STAT=stat
  STATOPT="-c%s"
elif gstat -c%s "$0" >/dev/null 2>&1; then
  # GNU
  STAT=gstat
else
  echo "$(basename $0): no compatible stat command found." >&2
  exit 1
fi

function file1_greater_file2 () {
  # return TRUE if 1st file is larger than the 2nd
  size1=$($STAT $STATOPT "$1")
  size2=$($STAT $STATOPT "$2")
  if [ "$size1" -gt "$size2" ]; then
    # compression ratio
    NC_RATIO=$((100 - ${size2} * 100 / ${size1}))
    return 0
  fi
  NC_RATIO="NA"
  return 1
}

# parse command line args
while getopts ":d:o:svx:" opt; do
  case $opt in
    d)
    NC_DEFLATE="$OPTARG"
    ;;
    o)
    OUTDIR="$OPTARG"
    ;;
    s)
    NC_SHUFFLE="-s"
    ;;
    v)
    NC_VERBOSE=TRUE
    ;;
    x)
    NC_SUFFIX="$OPTARG"
    ;;
    \?)
    echo "Invalid option: -$OPTARG" >&2
    usage
    ;;
    :)
    echo "Option -$OPTARG requires an argument." >&2
    usage
    ;;
  esac
done

# test if 0 <= NC_DEFLATE <= 9
test "$NC_DEFLATE" -ge 0 -a "$NC_DEFLATE" -le 9 || usage

# remove options from $@
shift $((OPTIND-1))

test -z "$1" && usage

for file in $@; do
  if ! [ -f "$file" ]; then
    echo "$file: not found" >&2
    continue
  fi

  # set default chunking
  NC_CHUNK="-c$(ncdump -h "$file" | awk '/^dimensions:/ { getline ; while (match($0,"^\t")) {printf "%s/128,", $1; getline } } END {print "/"}')"

  # compress file
  if [ "$NC_VERBOSE" = "TRUE" ]; then
    echo -n "$(basename "${file}")... " >&2
  fi
  if [ "$NC_DEFLATE" -gt 0 ]; then
    nccopy -k 3 -d $NC_DEFLATE $NC_SHUFFLE $NC_CHUNK "$file" "${file}.$$.tmp" || continue
  else
    # write classic
    nccopy -k 1 "$file" "${file}.$$.tmp" || continue
  fi

  # check compressed file size
  if [ "$NC_DEFLATE" -eq 0 ] || file1_greater_file2 "$file" "${file}.$$.tmp" ; then
    # if no compression or if compressed file is smaller than original file:
    # replace original file with compressed/decompressed file
    if [ "${OUTDIR}" ]; then
      mv -f "${file}.$$.tmp" "${OUTDIR}/$(basename ${file})${NC_SUFFIX}"
    else
      mv -f "${file}.$$.tmp" "${file}${NC_SUFFIX}"
    fi

    if [ "$NC_VERBOSE" = "TRUE" ]; then
      if [ "$NC_DEFLATE" -eq 0 ]; then
        echo "done." >&2
      else
        echo "ratio: ${NC_RATIO}%." >&2
      fi
    fi
  else
    # keep original file and remove compressed file
    rm -f "${file}.$$.tmp"
    # copy original file
    if [ "${OUTDIR}" ]; then
      cp -f "${file}" "${OUTDIR}/$(basename ${file})${NC_SUFFIX}"
   fi

    if [ "$NC_VERBOSE" = "TRUE" ]; then
      echo "could not reduce file size. already compressed?" >&2
    fi
  fi
done

exit 0