I am looking for a simple tool with which I can assign vertices to specific points in my original image, and then assign new locations for some/all of these vertices and have it transform the image accordingly by stretching/squashing the image sections between and around the vertices.

Does anyone know of a (preferably free) tool that can do this simply on large res images (6000x4000 pixels... I have plenty of memory).

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In the end I solved the problem by using ImageMagick and a manually crafted file of coordinate transformations. The result wasn't perfect, but it did give me the required amount of precise control.

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