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I have 2000+ 1x1km TIF DEMs which need to be subtracted from the same amount of 1x1km TIF DOMs. The result should be 2000+ normalised TIFs containing the heights above Ground.

Which method could I use to iterate through each DOM and subtract the correct DEM? I am unsure about how to match the correct DOMs and DEMs.

If there's a tile number or something like that you could use that to group by, otherwise mosaic them all (the DEM's and the DOM's) and then subtract both mosaics.

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