Dear Mohamad,

I think Even is right, and it is the bowtie-effect. The file you are trying
to warp is still a 'swath', therefore it still contains the bowtie-effect.
You can see that the right side of the image looks worse, the viewing angles
are greatest at that edge, and the overlap between sensor scans is at its
largest. At nadir, more to the left of the image, it already looks much
better. I don't know the MCTK, but that image also doesn't look great,
although better.

You could use dedicated tools such as MRTSwath to resample the image to a
regular grid. Or use something like PyResample (if you work with Python).

https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath

https://github.com/pytroll/pyresample (part of PyTroll:
http://www.pytroll.org/)

Once you have a regular grid, all GDAL tools and function will work fine.

Gdalwarp and the other utilities will work directly with the higher level
MODIS products, which are gridded to a sinusoidal grid. 


Regards,
Rutger




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