remove-duplicates.js

var result = db.measurements.aggregate({
    "$group": {
        "_id": {
            "sensor": "$sensor._id",
            "user": "$user",
            "time": "$time",
            "geom": "$geometry"
        },
        "tracks": { "$addToSet": "$track" }
    }
}, { 
    "$match": { "tracks.1": { "$exists": true} }
}, { 
    "$group": { "_id": "$tracks" }
}, {
    "$group": { 
        "_id": 1,
        "tracks": {
            "$addToSet": "$_id"
        }
    }
}).result[0].tracks

for (var i = 0; i < result.length; ++i) {
    var tracksWithLength = [];
    for (var j = 0; j < result[i].length; ++j) {
        tracksWithLength[j] =  {
            track: result[i][j],
            length: db.measurements.count({ track: result[i][j] })
        }
    }
    tracksWithLength.sort(function(a, b){ return a.length - b.length })
    for (j = 1; j < tracksWithLength.length; ++j) {
        db.measurements.remove({
            track: tracksWithLength[j].track
        })
        db.tracks.remove({
            _id: tracksWithLength[j].track.getId()
        })
    }
}

var tracks = db.tracks.aggregate({ "$group": { "_id": 1, "tracks": { "$addToSet": "$_id" } } }).result[0].tracks
for (var i = 0; i < tracks.length; ++i) {
    var count = db.measurements.count({
        track: DBRef("tracks", tracks[i])
    });
    print(tracks[i] + ": " + count)
    if (count == 0) {
        db.tracks.remove({ "_id": tracks[i] })
    }
}