Mass reprojection of h5 Files using Gdal and Bash Tricks

I recently got hold of h5 files (Hierarchical Data Format (HDF)) and I tried to load them into QGIS and they were drawing in the wrong places.This was because they were not georeferenced. I set out to georeference them using GDAL. Since I was dealing with many h5 files I searched for an automated way to georeference them and could not find one complete solution hence I decided to do it myself with the help of Tim Sutton.

The following script is the one I used to automate georeferencing h5 files in Ubuntu 16.04.

#!/usr/bin/env bash

  


FILENAME=$1

  


  


if [ -n "$1" ]

then

    FILENAME=$1

fi

  


  


if [[ "$FILENAME" == *h5 ]];

then

  


    LIST="chla cyanobacteria cyanobacteria_high_risk flag_cloud vegetation"

  


    for args in $LIST; do

  


    gdal_translate -a_srs "EPSG:4326" -mask 1 -of VRT HDF5:"${FILENAME}"://bands/${args} ${args}.vrt

  


    gdal_translate -a_srs "EPSG:4326" -mask 1 -of VRT HDF5:"${FILENAME}"://bands/longitude lon.vrt

    gdal_translate -a_srs "EPSG:4326" -mask 1 -of VRT HDF5:"${FILENAME}"://bands/latitude lat.vrt

  


    LINES=`cat ${args}.vrt | wc -l`

    BOTTOMLINES=`echo "$LINES-2" | bc`

    head -2 ${args}.vrt > ${args}_referenced.vrt

    echo "

       <metadata domain="GEOLOCATION">

         <mdi key="X_DATASET">lon.vrt</mdi>

         <mdi key="X_BAND">1</mdi>

         <mdi key="Y_DATASET">lat.vrt</mdi>

         <mdi key="Y_BAND">1</mdi>

         <mdi key="PIXEL_OFFSET">0</mdi>

         <mdi key="LINE_OFFSET">0</mdi>

         <mdi key="PIXEL_STEP">1</mdi>

         <mdi key="LINE_STEP">1</mdi>

       </metadata>

    ">> ${args}_referenced.vrt

  


    tail -${BOTTOMLINES} ${args}.vrt >> ${args}_referenced.vrt

  


    gdalwarp -dstalpha -geoloc -t_srs EPSG:4326 ${args}_referenced.vrt ${FILENAME%.*}_${args}.tif

  


  


    done

else

    :

fi

  


find . -name "*.vrt" -type f -delete

I copied the script and saved it as reproject_h5.sh and made it executable in bash. I then ran the script as../reproject_h5.sh MER_FSG.h5 You can also run the script by looping through a text file that contains filenames for the h5 rasters.