Methods and systems for detecting spectrophotometer misalignment

This application generally relates to methods and systems for detecting spectrophotometer misalignment. In particular, the application may characterize the noise of a spectral measurement relative to a reference substrate known to exhibit a generally linear (flat) spectral output over a known spectrum. From the spectral measurement, a linear regression may be performed on a portion of the spectral output to determine a best fit line and a correlation of determination ("R-squared value") may be determined correlated the measured data to the best fit line. Finally, the R squared value may be compared to a predetermined threshold R squared value to determine if the sensor is misaligned beyond an acceptable amount. If so, an alert may be generated.