Tomokane used electrical impulses to read Miyabi's emotions.
Tomokane can apparently read Miyabi's emotions, which are extremely subtlely expressed, if at all. It is unknown if the others can do this too, but if not, there's still an explanation: we've already seen her detect that her brother's brain was "signaling" for help, and she apparently was able to locate him on a campus that has been described as "maze-like". Therefore, when she thought Miyabi looked happy, she wasn't reading Miyabi's face, but electrical impulses. Miyabi is a Time Lord.
Some of the other girls have gone off thinking she might be an alien, she seems to have many odd things needed at the moment hiding in her uniform, she might even be travelling to the different eras to learn the art knowledge when no one is looking. She is also referred to as The Professor which can sometimes be a Doctor.- Tomokane could also have been her companion for a few journeys while the other girls are not looking and they got into an encounter with Weeping Angels. This could play a reason why she thought the measuring of the plaster with the pencil was instead for shooting it in case it started moving.
- The Doctor, the Master, the Professor... Theme Naming supports this hypothesis.
