Hi,

I am setting up a database to manage computer vision training data, and I would appreciate your feedback on my current schema and approach.

Current setup

The data consists of images (not stored in the database, I only store their paths as strings), annotations (equivalent to a labelling operation performed by a human operator on one image), and labels (their geometries are stored directly in the database).
Initially, I used separate collections for images, annotations, and labels, as shown below:

# Images collection:
{
    "_id": ObjectId('10'),
    "image_name": "DSC04799",
    "path": "/path/to/DSC04799.tif"
},
...

# Annotations collection:
{
    "_id": ObjectId('11'),
    "class": "Cat",
    "version": 1,
    "image_id": ObjectId('10'),
},
...

# Labels collection:
{
    "_id": ObjectId('12'),
    "geometry": [1, 2, 3, ...],
    "annotation_id": ObjectId('11'),
},
...

After reading the MongoDB documentation on embedding vs. referencing, I decided to switch to a single “images” collection with embedded annotations and labels::

{
    "_id": ObjectId('10'),
    "image_name": "DSC04799",
    "path": "/path/to/DSC04799.tif"
    "annotations":[
        {
            "_id": ObjectId('11'),
            "class": "Cat",
            "version": 1,
            "labels": [
                {
                    "_id": ObjectId('12'),
                    "geometry": [1, 2, 3, ...],
                },
                ...
            ]
        },
        ...
    ]
},
...

Code snippets

When using the previous schema, before inserting a new annotation I could easily check if it was already existing in the database(with pymongo):

annotation_doc = annotations_collection.find_one(
    {"image_id": image_id, "class": class, "version": version}
)
if annotation_doc is None:
    annotation_id = annotations_collection.insert_one(
        {"_id": ObjectId(), "image_id": image_id, "class": class, "version": version, "labels": labels}
    )

After the schema change, the equivalent operation became more complex:

# Look for annotation in DB, and insert it if not already present
pipeline = [
    {"$match": {"_id": image_id}},
    {"$unwind": "$annotations"},
    {"$match": {"annotations.class": class, "annotations.version": version}},
    {"$project": {"_id": "$annotations._id"}},
]
cursor = images_collection.aggregate(pipeline)
try:
    annotation_id = next(cursor)["_id"]
except StopIteration:
    annotation_id = images_collection.update_one(
        {"_id": image_id},
        {"$push": {"annotations": {"_id": ObjectId(), "class": class, "version": version, "labels": labels}},
    )

Concerns and questions

Since switching to the new schema, I find the queries more complex, and I’m wondering if I’m on the right track. Are these complex queries typical of MongoDB, or am I facing a learning curve?

I’m also curious about the pros and cons of using embedding in this scenario. Does the updated schema seem appropriate for my use case? Should I consider going back to separate collections?

Thank you for your help and guidance!