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I have a bunch of aerial photographs (>70 covering over 10000km2) that are tiled from which I want to build a VRT and ultimately export multiple (~2000) tiny sections (~300m x 300m) distributed around the whole territory using gdal_translate. That should be fairly easy, however I have some tiles that are represented twice (for 2 differents years) where the difference is in the NODATA. Here is a simple example:

Image 1:enter image description here

Image 2:enter image description here

When I build the VRT using:

"C:\Mrnmicro\Applic\gdal\1.11.1\gdalbuildvrt.exe" -srcnodata "0" -overwrite  "C:\Users\ferba1\Desktop\jeter\testvrt\mosai.vrt" "C:\Users\ferba1\Desktop\jeter\testvrt\*.jp2"

I get a nice result:enter image description here

However, if I try to export the two squares using gdal_translate:

C:\Mrnmicro\Applic\gdal\1.11.1\gdal_translate.exe" -projwin 273000 5246300 273300 5246000 -of "GTiff" "C:\Users\ferba1\Desktop\jeter\testvrt\mosai.vrt" "C:\Users\ferba1\Desktop\jeter\testvrt\nord.tif
C:\Mrnmicro\Applic\gdal\1.11.1\gdal_translate.exe" -projwin 278000 5238300 278400 5238000 -of "GTiff" "C:\Users\ferba1\Desktop\jeter\testvrt\mosai.vrt" "C:\Users\ferba1\Desktop\jeter\testvrt\sud.tif

The red square is all nodata while the blue square is ok. Is there a way that gdal_translate on a vrt with no data like that better deal with missing data when I have overlapping images?

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After lots of trials, I've found the problem. It wasn't in the vrt creation like I though first. The problem was caused by the .jp2 format from LizardTech which made gdal fail on a third of my images.

I had to convert all my images to geoTiff which is a way better format. I had to use ArcGIS for that because gdal_translate failed on all images which ever driver I used (OpenJPEG or gdal_ECW_JP2ECW).

After the convertion, my initial code work perfectly.

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