#!/bin/bash -e

# Usage: dfm2h5 <list of header files>
#
# This script converts DFM output consisting of binary files and 
# associated header files to to HDF5.
#
# EXAMPLES
# Convert all DFM data in a directory
#   dfm2h5 *.hdr
# See the contents of an HDF5 file
#   h5dump 0100001.h5
#
# HDF5 INSTALL
# Obtain sources from ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current/src
#   gunzip hdf5-1.6.1.tar.gz
#   tar xvf hdf5-1.6.1.tar
#   cd hdf5-1.6.1
#   make check
#   make install
# This will install in /usr/local/
# To change this default see release_docs/INSTALL
# You also may want to install HDF4 and the h4h5tools to convert
# to HDF4 for applications that do not yet support HDF5
#
# MATLAB
# HDF5 support was added to Matlab for version 6.5.1 although
# it does not function properly yet.  Eventually you should be
# able to read an HDF5 file with to following command:
#   data = hdf5read('0100001.h5','/dataset0')
#
# Geoffrey Ely gely@ucsd.edu

while getopts d opt; do
  case $opt in
  d) deleteout="yes" ;;
  esac
done
shift `expr $OPTIND - 1`

for file in "$@"; do
  echo $file
  base="${file%.hdr}"
  set `cat $file`
  dims="${1},$(( ${4} - ${2} + 1 )),$(( ${7} - ${5} + 1 )),$(( ${10} - ${8} + 1 ))"
  outsep=${19}
  if [ "${outsep}" = "T" ]; then
    for (( i=${11}; i<=${13}; i=$i+${12} )); do
      num=`printf "%05d" $i`
      [ "$deleteout" = "yes" ] && rm -f "${base}${num}.h5"
      h5import "${base}${num}.bin" -d "$dims" -o "${base}${num}.h5"
      hdfimport "${base}${num}.bin" -o "${base}${num}.hdf"
    done
  else
    dims="$dims,$(( ( ${13} - ${11} ) / ${12} + 1 ))"
    [ "$deleteout" = "yes" ] && rm -f "${base}mux.h5"
    h5import "${base}mux.bin" -d "$dims" -o "${base}mux.h5"
  fi
done