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I am using FWtools for pre processing of time-series MODIS data, I want to mosaic series of two scenes. But I don't know the batch code for gdalwarp.

I am using windows.

Kindly help me out.

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It is not completely clear to me what you are trying to do, but if you simply want to mosaic two images using gdalwarp, this should work:

gdalwarp input1.tif input2.tif output.tiff

If your data is in one of the FAST formats, GDAL can handle the conversion too.

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if you want to mosaic two tiles, you can use gdalwarp. Another option is to build a VRT (virtual dataset) that does the temporal stacking AND the mosaicking. You can either convert the resulting VRT to say a GeoTIFF, or if you are using GDAL-aware tools, use it as a normal raster dataset.

I have a blog entry that describes how to do just that in great detail.

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