A method to calibrate a polarizer in polarized optical system at any angle of incidence, by decoupling the calibration from a polarization effect of the system, by providing a calibration apparatus that includes a substrate having a polarizer disposed on a surface thereof, with an indicator on the substrate for indicating a polarization orientation of the polarizer, loading the calibration apparatus in the polarized optical system with the indicator in a desired position, determining an initial angle between the polarization orientation and a reference of the polarized optical system, acquiring spectra using the polarized optical system at a plurality of known angles between the polarization orientation and the reference of the polarized optical system, using the spectra to plot a curve indicating an angle of the polarizer in the polarized optical system, and when the angle of the polarizer is outside of a desired range, adjusting the angle of the polarizer, and repeating the steps of acquiring the spectra, and plotting a curve indicating the angle of the polarizer.