Why do I see a dip in amplitude when I create a phase change?

Several of the WaveShaper units allow changing the phase of the filter as a function of the wavelength. These phase changes may – in case they are large and step like changes – introduce a variation of the transmission.

The reason is shown in the graphics below. The WaveShaper has a typical optical transfer function with a width (FWHM) of about 10 to 11 GHz (for most models). When switching from one phase (for example 0) to a different phase (for example pi: 3.14), some signal components which carry an opposite sign do overlap and therefore cause cancellation as indicated by the notch of the black transmission curve.