Before it was a stage of an inner process, calcination was a bench operation that a working alchemist performed on a substance with a fire.
What the word describes
Calcinatio means reducing a material to a dry powder by prolonged heating in an open vessel. The name is the same root as calcium and as quicklime, and the paradigm case is burning limestone until what remains is a friable white residue that behaves quite differently from the stone that went in. The operation is real chemistry, it was performed, and its products were examined.
That practical layer is easy to lose when the operations are presented only as psychological stages, and losing it makes the historical texts unreadable, since they are full of instructions about vessel, fuel and duration that only make sense as instructions.
Where the number seven comes from
A fixed sequence of exactly seven operations, numbered and matched to the seven planets, is a modern arrangement rather than a medieval or early modern one. The historical texts do not agree on how many operations there are. George Ripley's Compound of Alchymy, written in the fifteenth century, sets out twelve gates. Other authors give other counts, and the operations named here appear among their lists in varying order and with varying company.
The atlas records the seven-step scheme because it is the one in general circulation, and records here that it is a tidying of a much less tidy record.