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7. Convert the result to GeoTIFF

Warning

Below guideline using CHIRPS data as example. If you are using IMERG, just replace text CHIRPS in the script or filename below with IMERG.

I need CDO to do a conversion of the result into GeoTIFF format, and CDO required the variable should be in time, lat, lon, while the output from SPI: java_xxxxx_spi_xxxxx_x_month.nc in lat, lon, time, you can check this via ncdump -h java_CHIRPS_spi_gamma_3_month.nc

  • Deactivate an active environment climate_indices then activate environment gis to start working on output conversion using CDO and GDAL.
conda deactivate && conda activate gis

  • Navigate your Terminal to folder Output_nc

  • Let's re-order the variables into time,lat,lon using ncpdq command from NCO and save the result to folder Output_TEMP

ncpdq -a time,lat,lon java_CHIRPS_spi_gamma_3_month.nc ../Output_TEMP/java_CHIRPS_spi_gamma_3_month_rev.nc

  • Navigate your Terminal to folder Output_TEMP

  • Check result and metadata to make sure everything is correct.

ncdump -h java_CHIRPS_spi_gamma_3_month_rev.nc

  • Then convert all SPI value into GeoTIFF with time dimension information as the filename using CDO and GDAL.

  • Navigate your Terminal to folder Output_TEMP, execute below script and save the result to folder Output_TIF

for t in `cdo showdate java_CHIRPS_spi_gamma_3_month_rev.nc`; do
    formatted_date=$(date -d $t +%Y%m%d)
    cdo seldate,$t java_CHIRPS_spi_gamma_3_month_rev.nc dummy.nc     
    gdal_translate -of GTiff -a_ullr 105.05 -5.05 116.25 -8.8 -a_srs EPSG:4326 -co COMPRESS=LZW -co PREDICTOR=1 dummy.nc ../Output_TIF/java_cli_chirps_spi3_${formatted_date}.tif
done

Note

If you are using IMERG or other data, or different area of interest, please make sure check the bounding box of the data <ulx> <uly> <lrx> <lry>. This -a_ullr assigns georeferenced bounds to the output file, ignoring what would have been derived from the source file.

FINISH

Congrats, now you are able to calculate SPI based on monthly rainfall in netCDF or GeoTIFF format.