Kartoza - Mass reprojection of h5 Files using Gdal and Bash Tricks

FOSSGIS

The author obtained HDF (Hierarchical Data Format) h5 files that displayed incorrectly in QGIS due to lack of georeferencing.

Mass Reprojection of h5 Files ¶

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.

Explore Kartoza

Mass reprojection of h5 Files using Gdal and Bash Tricks

Kartoza - Mass reprojection of h5 Files using Gdal and Bash Tricks

FOSSGIS

Mass Reprojection of h5 Files ¶

Want to Learn More?