"gdal2xyz generates the csv file, but excel fails to open all the rows!"

Ah, so you now have a new csv file having a huge number of lines that have a
value of zero in the third column? You could delete these unwanted lines
using awk:

awk.exe "$3!=0" FS=, infile.csv > thinned.csv

Awk comes with Linux, but there are versions for Windows too.

Good luck, Nick.

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