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This has to do with C-ordering versus Fortran ordering, also known as https://en.wikipedia.org/wiki/Row-major_order

This bug appears with the following parameters:

d.addPairwiseGaussian(sxy=3, compat=0)
d.addPairwiseBilateral(sxy=3, srgb=5, rgbim=img, compat=50)

And this is confirmed by this other Python wrapper for densecrf:

see the order (D, W, H) at this line:
https://github.com/mbickel/DenseInferenceWrapper/blob/master/denseinference/lib/libDenseCRF/densecrf.cpp#L139

while the original 2D code is (H,W).

adding Python example for dense inference adapted from the original C++ example (http://www.philkr.net/home/densecrf)