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The linear wave and geostrophic (vortex) solutions are shown to be a complete basis for physical variables $(u,v,w,ρ)$ in a rotating non-hydrostatic Boussinesq model with arbitrary stratification. As a consequence, the fluid can be unambiguously separated into linear wave and geostrophic components at each instant in time, without the need for temporal filtering. The fluid can then be diagnosed for temporal changes in wave and geostrophic coefficients at each unique wavenumber and mode, including those that inevitably occur due to nonlinear interactions. We demonstrate that this methodology can be used to determine which physical interactions cause the transfer of energy between modes by projecting the nonlinear equations of motion onto the wave-vortex basis. In the particular example given, we show that an eddy in geostrophic balance superimposed with inertial oscillations at the surface transfers energy from the inertial oscillations to internal gravity wave modes. This approach can be applied more generally to determine which mechanisms are involved in energy transfers between wave and vortices, including their respective scales. Finally, we show that the nonlinear equations of motion expressed in a wave-vortex basis are computationally efficient for certain problems. In cases where stratification profiles vary strongly with depth, this approach may be an attractive alternative to traditional spectral models for rotating Boussinesq flow.