I tried to reproject MODIS L2 data(AQUA_MODIS.20200227T052500.L2.OC.nc) to geotiff using Python, tired GCP but the result was a little misplaced. Also found that part of the lat and lon of the data is not monotonically increasing(see the picture attached), why is this and how should I deal with it while reprojecting?
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If you want to map MODIS L2 data, I would suggest downloading Seadas and the Science software and using the program "mapgen" to bin and map the data to almost any projection you would like.