The performance of free electron laser x-ray light sources, and systems for ultrafast electron diffraction and ultrafast electron microscopy, is limited by the brightness of the electron sources used. The intrinsic emittance, or equivalently, the mean transverse energy (MTE) of electrons emitted from the photocathode determines the maximum possible brightness in such systems. With ongoing improvements in photocathode design and synthesis, we are now at a point where the physical and chemical surface roughness of the cathode can become a limiting factor. Here we show how measurements of the spatially dependent variations in height and surface potential can be used to compute the electron beam mean transverse energy (MTE), one of the key determining factors in evaluation of brightness.