How do I check if an index is being used

The simplest solution to this is to use the mongodb inbuilt $indexStats aggregation stage, added in MongoDB 3.2.

Using the Mongo console:

db.collection.aggregate([ { $indexStats: { } } ])

Using PyMongo:

from pymongo import MongoClient
collection = MongoClient()[db_name][collection_name]
index_stats = collection.aggregate([{'$indexStats':{}}])

for index_info in index_stats:
    print index_info