Ninjas in fiction are usually very dramatic, highly visible acrobats, dressed in black pajamas and ski masks, who kill people with weapons like nunchakus, throwing stars, etc.
To the best of my knowledge, historically real ninjas tended to dress like people of different social groups, usually low-status ones (servants, peasants, bakers, fisher-people, etc.), and to fight with things like farming implements.
I can't seem to find a single film that attempted to depict ninjas in a more realistic and historically-accurate way. Was there ever any movie or TV show about, or with, this type of relatively realistic ninja?