KartozaI 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.
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