Flygon EX PK Psychic Protector damage calculation

[orangematt]

My Meganium MT with Crystal Shard Attacks the Defending Flygon PK with Fire Counterattack.

Would I calculate the damage with Weakness before my opponent activates Flygon EX's Poké-Body?

 

[PokePop]

The reduction from Psychic Protector comes after all damage calculations are done, so that is after W&R.