Merge: fileBased -> groupBased

[ax3l]

I recently needed a small script that converted our usual "fileBased" iterationEncoding to a single "groupBased" file (in HDF5).

Next time I need it I will rewrite it in pure python so it's more portable. (Actually, I tried pure bash but needed a small in-file manipulation which I found no CLI tool for).

Nevertheless, here it is already:

#!/usr/bin/env bash
#
# Copyright 2017 Axel Huebl
#
# Use under the ISC software license.
#

# needs input argument parsing & help

dumps=($(ls h5/*_*.h5))
first=0

for d in ${dumps[@]};
do
    if [ $first -eq 0 ]
    then
        # includes copy of / attributes from first file
        cp $d simData.h5
        first=1
    else
        step=$(echo $d | sed 's/.\+_\([0-9]\+\)\.h5/\1/')
        h5copy -i $d -s "/data/$step" \
               -o simData.h5 -d "/data/$step"
    fi
done

# that might not be necessary if your files already had compression enabled
h5repack -i simData.h5 -o simData.h5.gz -f GZIP=1 && \
    mv simData.h5.gz simData.h5

# change attributes:
#   "/iterationEncoding" -> "groupBased"
#   "/iterationFormat" -> "/data/%T/"
python -c 'import h5py; import numpy as np; f=h5py.File("simData.h5", "a"); f.attrs["iterationEncoding"] = np.string_("groupBased"); f.attrs["iterationFormat"] = np.string_("/data/%T/"); f.close()'