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constraints will drive the reconstruction to the desired solution you set using constraints.
This is especially useful when you, say, get a sparse point cloud and you see that there are some wrongly placed cameras. You can then set control points and re-run the reconstruction/optimize camera paremeters to guide zephyr to the desired solution - and if you want the solution to also have specific coordinates (e.g. from a GPS device) you can set them as well.
Controls are what their name says - just a control. It will not be considered when reconstructing as a constraint, but will still tell you which is the residual between the computed coordinate and your expected coordinate, so that you are able to measure accuracy/errors.
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