Mass reprojection of h5 files using gdal and bash tricks

Posted by: Gavin Fleming | in Uncategorised | 1 year, 3 months ago | Comments

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


if [ -n "$1" ]

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

    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>
    ">> ${args}_referenced.vrt

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

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


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


I copied the script and saved it as and made it executable in bash. I then ran the script as../ 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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