My question is: as these lenses have a different field of view, i guess that the automatically generated flight plan wont work anymore as the field of view of this lens is smaller. with the stock camera i get good results using 90% overlap.
Is it possible to tell Pix4d Mapper that the cameras field of view has changed so i get 90% overlap again?
As you already mentioned, when changing the lens the difference in the field of view needs to be taken into account in order to get the correct overlap between images.
When using Pix4Dcapture for performing automated missions the default camera, in your case default Phantom 4 camera, will be taken into account for calculating the flight parameters as we are not able to automatically detect that the lens was changed.
There is a possibility to define a custom camera on the iOS version of the app, but it can only be used for cameras that can be triggered independently, e.g. by defining a timelapse or trigger interval in the camera itself. Unfortunately, this is not the case for DJI cameras.
As a side note, when using the camera model not included in our database we first recommend acquiring a good dataset that can be used for calibrating the lens as described here: How to calibrate a Perspective Lens Camera.
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