Raw ALMA data files include autocorrelation outputs from the antennas which do not have atmospheric or instrumental effects subtracted.
In principle, a well-modeled astronomical source could be subtracted from the autocorrelations, leaving the atmospheric total power and instrumental effects.
The user would then be required to account for the instrumental effects to obtain an atmospheric measurement. Astronomical observations tend to tune away from the deepest atmospheric absorption, but it is present, particularly in the higher bands 7 and 9.