Visa to Japan

From Wikivisa

I am spanish living in the uk since the 5th of may 1999.I want to apply for a (6 months or one year) student visa go to Japan.Can I apply from an embassy in the uk or do I need to apply from my own country? I heard that a student visa takes around two or three months is that correct? And also is it allowed to apply for the student visa already staying in Japan on a tourist 90 days visa or you must apply from a foreing country? When you apply for a student visa does the embassy keep your passport? Thank you!!!