Structured-light systems (SLSs) are widely used in active stereo vision to perform 3D modelling of a surface of interest. We propose a flexible method to calibrate SLSs projecting point patterns. The method is flexible in two respects. First, the calibration is independent of the number of points and their spatial distribution inside the pattern. Second, no positioning device is required since the projector geometry is determined in the camera coordinate system based on unknown positions of the calibration board. The projector optical center is estimated together with the 3D rays originating from the projector using a numerical optimization procedure. We study the 3D point reconstruction accuracy for two SLSs involving a laser based projector and a pico-projector, respectively, and for three point patterns. We finally illustrate the potential of our active vision system for a medical endoscopy application where a 3D cartography of the inspected organ (a large field of view surface also including image textures) can be reconstructed from a video acquisition using the laser based SLS.