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Exercise 3a: Study phenology from MODIS NDVI time series (forest vector)

In this exercise the following tools will be used:

  • pktools: pkcreatect, pkndvi, pkgetmask, pkextract, pkstatogr
  • bash: for loop, redirection (»)
  • awk: basic

Create directory for this exercise

mkdir -p ${OUTPUTDIR}/exercise3

Remove old output

rm -f ${OUTPUTDIR}/exercise3/forest_ndvi_mean_stdev.txt

Extract NDVI time series from forest in Cornwall (mean value for each polygon)

for MONTH in 01 02 03 04 05 06 07 08 09 10 11 12;do
	echo "create NDVI image for month $MONTH"
	pkndvi -min 0 -max 100 -dst_s 100 -r ndvi -ot Byte -b 0 -b 1 -i ${MODIS250DIR}/2006${MONTH}-MODIS250_CW.tif -o ${OUTPUTDIR}/exercise3/2006${MONTH}-MODIS250_CW_NDVI.tif
	echo "create NDVI mask (values smaller than 0.5 should not be forested)"
	pkgetmask -i ${OUTPUTDIR}/exercise3/2006${MONTH}-MODIS250_CW_NDVI.tif -o ${OUTPUTDIR}/exercise3/2006${MONTH}-MODIS250_CW_MASK.tif -min 50 -max 100 -data 1 -nodata 0
    rm -f ${OUTPUTDIR}/exercise3/forest_modis_${MONTH}.shp
    echo "extract NDVI for month $MONTH"
    pkextract -i ${OUTPUTDIR}/exercise3/2006${MONTH}-MODIS250_CW_NDVI.tif -s ${OUTPUTDIR}/exercise1/cornwall_forest_3035.shp -m ${OUTPUTDIR}/exercise3/2006${MONTH}-MODIS250_CW_MASK.tif -msknodata 0 -o ${OUTPUTDIR}/exercise3/forest_modis_${MONTH}.shp -r mean -polygon -bn NDVI --ftype Integer
    echo "calculate statistics using pkstatogr"
    pkstatogr -i ${OUTPUTDIR}/exercise3/forest_modis_${MONTH}.shp -n NDVI -mean -stdev| awk '{print $4,$6}' >> ${OUTPUTDIR}/exercise3/forest_ndvi_mean_stdev.txt
wiki/exercise3a.txt · Last modified: 2020/07/17 06:39 (external edit)