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I try to merge some multiband rasterfiles (Sentinel 2 data) with Rasterio into a single rasterfile but the result is incorrect. The files are too big to fit in my RAM completely, but I have enough SWAP and I don't get a Error Message. Any ideas, what could have gone wrong?

My code:

import rasterio
from rasterio.merge import merge
import glob

files = glob.glob("../data_multiband/*.tif")
mosaic = []
for file in files:
    tmp = rasterio.open(file)
    mosaic.append(tmp)
mosaic, out_trans = merge(mosaic)
out_meta = tmp.meta.copy()
out_meta.update({"driver": "GTiff",
                 "height": mosaic.shape[1],
                 "width": mosaic.shape[2],
                 "transform": out_trans})
with rasterio.open("../data_merged/test.tif", "w", **out_meta) as dest:
    dest.write(mosaic)

That is how the result looks:

enter image description here

As you can see (red marks) some rasterfiles occur two times. The one on the left side are wrong. Thats how the original files look:

enter image description here

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  • RAM performance is measured in nanoseconds, swap speed in milliseconds; the three orders of magnitude difference is an indicator that you really don't want to rely on swap for this (1 sec of RAM ~= 16.6 minutes of swap)
    – Vince
    Oct 2, 2020 at 12:40
  • does it work when you use only two input images? If yes try to add ass many images as possible and see where the error occurs.
    – til_b
    Oct 5, 2020 at 22:16

2 Answers 2

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I solved the problem. The files have the same crs, but are in different zones. Reprojecting solved it

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You may want to use gdalwarp (or gdal.Warp if using Python) for this. This will allow you to merge and reproject in one go. Often a good idea to set x/y resolution when reprojecting in case GDAL ends giving you something like 9.34 m rather than 10 m

gdalwarp  -t_srs "EPSG:XXXX" -tr X Y in1.tif in2.tif out.tif

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