One often reoccuring problem though, is when photographing scenes with waves. You often cannot get a believable line of waves, cf the example
1. I see stitching error in the example; that needs to be corrected before the waves.
2. Your example is not a really bad case; it can be much worse.
Anyway, one has to use a product, which allows for manual intervention between warping and blending (PTAssembler, PTGui, Hugin). The "stitcher"does not create a pano but warps the individual sources, which will be blended together by a special program, like Enblend and Smartblend. Both processes can be performed, and the tangible areas repaired afterwards through overlaying by corrections created from the output of the warping process.
One possible solution is to cut a region over the seam from the overlapping warped frames and making a masked transition between them, usually from left to right. The problem is, that the result will be muddy; if the waves were clear, this is very noticable.
The other solution is the zig-zagging; much more labour. The result can be excellent, though it does not always work. The condition is, that the overlapping frames' darkness must match - but that should always be so (I never let the stitcher adjust the darkness). Larger but very regular waves can not be repaired this way.
1. The initial state, after blending:
2. One of the two adjacent warped, unblended frames is copied over the other, with 50% opacity to show the overlapping areas:
3. Most of the overlapping water surface is selected (here with polygonal lasso), the selection inverted and deleted from both layers (the background layer has to be copied for this). The opacity of the top layer can be restored now. (I named the two layers "LeftSide" respectively "RightSide", in order to avoid mixing them up.):
4. Now, the zig-zag selection: start in one corner, go accross close to the other edge, and back, of course somewhat lower (if started in the upper corner):
The starting point dictates, from which layer what has to be kept. I started at the left edge; I delete the selection from the right side frame and keep the selection from the left side frame (by inverting the selection and deleting it).
The selection from the left side frame is narrowing towards the right, the selection from the right side frame is narrowing towards the left.
The resulting layers are:
5. The right side needs to be cleaned up a bit:
6. and the image flattened (for convenience I selected both layers before flattening):
7. Now this selection will be copied over the blended pano, aligned and merged; that's easy.
Here is the final pano (after having repeated this process for most of the seams; one of them is not repaired):
(The horizontally posterization of the sky is due to the downsized graduation; the original sky was ugly, homogenous gray, I replaced it. There is no posterization in the full size.)