changed folder name to avoid accidental running during test

misc/generate_random_prediction_test.py

@@ -0,0 +1,39 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+from shared.data_store import connect_minio
+from shared.database import connect_mongodb
+from shared.database.classes import VisualCommunication
+from shared.utils import check_env, setup_logging
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongodb()
+    # get list of image paths
+    test_dir = Path(__file__).parent
+    img_dir = test_dir / 'imgs'
+    img_path_list = [path for path in img_dir.glob('*.jpeg') if path.is_file()]
+    print(img_path_list)
+    # instantiate data object
+    vis_com_list = [
+        VisualCommunication.from_file(path, minio_client=minio_client)
+        for path in img_path_list
+    ]
+    # generate random predictions
+    for vis_com in vis_com_list:
+        vis_com.generate_random_prediction()
+    for vis_com in vis_com_list:
+        print(vis_com)

misc/get_visual_communication_test.py

@@ -0,0 +1,28 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+from shared.data_store import connect_minio
+from shared.database import connect_mongodb, get_visual_communication
+from shared.utils import check_env, setup_logging
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongodb()
+    # get visual communication
+    vis_com = get_visual_communication(collection)
+    print(repr(vis_com))
+    image = vis_com.get_image(minio_client=minio_client)
+    image.show()

misc/image_download_test.py

@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+from shared.database import connect_mongodb
+from shared.database.classes import VisualCommunication
+
+if __name__ == '__main__':
+    # prepare env vars
+    env_path = Path(__file__).parent.parent / 'local.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    os.environ['MONGO_HOST'] = 'localhost'
+    # connect to database
+    collection, db, client = connect_mongodb()
+    print(client.server_info())
+    # download images
+    data = None
+    for data in collection.find().limit(3):
+        if data is None:
+            print('no document found')
+            break
+        vis_com: VisualCommunication = VisualCommunication.model_validate(data)
+        print(repr(vis_com))
+    if data is not None:
+        print(vis_com.image)
+        print(vis_com.model_dump())

misc/image_upload_test.py

@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from dotenv import load_dotenv
+from pymongo.errors import DuplicateKeyError
+
+from shared.data_store import connect_minio
+from shared.database import connect_mongodb
+from shared.database.classes import VisualCommunication
+from shared.utils import check_env, setup_logging
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongodb()
+    # get list of image paths
+    test_dir = Path(__file__).parent
+    img_dir = test_dir / 'imgs'
+    img_path_list = [path for path in img_dir.glob('*.jpeg') if path.is_file()]
+    print(img_path_list)
+    # instantiate data object
+    vis_com_list = [
+        VisualCommunication.from_file(path, minio_client=minio_client)
+        for path in img_path_list
+    ]
+    for vis_com in vis_com_list:
+        print(repr(vis_com))
+    # upload images
+    for vis_com in vis_com_list:
+        try:
+            result = collection.insert_one(vis_com.model_dump())
+        except DuplicateKeyError as exc:
+            print('ignoring:\n', exc)
+        else:
+            print(f"inserted document: {result}")

misc/image_upload_to_server_test.py

@@ -0,0 +1,49 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from dotenv import load_dotenv
+from pymongo.errors import DuplicateKeyError
+
+from shared.data_store import connect_minio
+from shared.database import VisualCommunication, connect_mongodb
+from shared.utils import check_env, setup_logging
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongodb()
+    # get list of image paths
+    ext_img_dir = Path('/Volumes/BW-PSSD/Mixed Methods/')
+    assert ext_img_dir.exists()
+    img_path_list = [
+        path
+        for path in ext_img_dir.glob(
+            '*.jpg',
+        )
+        if path.is_file()
+    ]
+    print(f"found {len(img_path_list)} images")
+    # create visual communication objects
+    vis_com_list = [
+        VisualCommunication.from_file(path, minio_client=minio_client)
+        for path in img_path_list
+    ]
+    print(f"created {len(vis_com_list)} visual communication objects")
+    # upload images
+    for vis_com in vis_com_list:
+        try:
+            result = collection.insert_one(vis_com.model_dump())
+        except DuplicateKeyError as exc:
+            print('ignoring:\n', exc)
+        else:
+            print(f"inserted document: {result}")

misc/model_io_test.py

@@ -0,0 +1,34 @@
+"""Test that a model can be saved and loaded again."""
+
+from pathlib import Path
+
+import torch
+from dotenv import load_dotenv
+from torchinfo import summary
+
+from model.src.models import VisualCommunicationModel
+from shared.data_store import connect_minio, put_model
+from shared.utils import setup_logging
+
+DEVICE = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # setup logging
+    setup_logging()
+    # connect to minio
+    client = connect_minio()
+    # instantiate model
+    model = VisualCommunicationModel().to(DEVICE)
+    # show model weights
+    summary(model)
+    # put buffer in minio bucket
+    hash_str = put_model(
+        client=client,
+        model=model,
+    )
+    print(f"hash string: {hash_str}")
+    print('saved to Minio')

misc/model_outputs_from_annotation_test.py

@@ -0,0 +1,11 @@
+from __future__ import annotations
+
+from shared.dto import ModelData
+
+if __name__ == '__main__':
+    # instantiate data object
+    vis_com_list = [ModelData.from_random() for i in range(3)]
+    # generate random predictions
+    [vis_com.from_random() for vis_com in vis_com_list]
+    for vis_com in vis_com_list:
+        print(vis_com)

misc/new_model_to_minio_test.py

@@ -0,0 +1,32 @@
+"""Definition of function to generate a new randomly initialized model and save
+it in Minio datastore."""
+
+from pathlib import Path
+
+from dotenv import load_dotenv
+from torchinfo import summary
+
+from model.src.models import VisualCommunicationModel
+from shared.data_store import connect_minio, put_model
+from shared.utils import setup_logging
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # setup logging
+    setup_logging()
+    # connect to minio
+    client = connect_minio()
+    # instantiate model
+    model = VisualCommunicationModel(download_resnet_weights=True)
+    # show model weights
+    summary(model)
+    # put buffer in minio bucket
+    hash_str = put_model(
+        client=client,
+        model=model,
+    )
+    print(f"hash string: {hash_str}")
+    print('saved to Minio')

misc/prediction_upload_test.py

@@ -0,0 +1,45 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+from shared.data_store import connect_minio
+from shared.database import connect_mongodb, upsert_prediction
+from shared.database.classes import VisualCommunication
+from shared.utils import check_env, setup_logging
+
+if __name__ == '__main__':
+    # load in env file
+    env_path = Path(__file__).parent.parent / 'server.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    # ensure env vars set
+    check_env()
+    # setup logging
+    setup_logging()
+    # connect to minIO
+    minio_client = connect_minio()
+    # connect to MongoDB
+    collection, db, client = connect_mongodb()
+    # get list of image paths
+    test_dir = Path(__file__).parent
+    img_dir = test_dir / 'imgs'
+    img_path_list = [path for path in img_dir.glob('*.jpeg') if path.is_file()]
+    # instantiate data object
+    vis_com_list = [
+        VisualCommunication.from_file(path, minio_client=minio_client)
+        for path in img_path_list
+    ]
+    # generate random predictions
+    for vis_com in vis_com_list:
+        vis_com.generate_random_prediction()
+    # upload visual communication
+    for vis_com in vis_com_list:
+        if vis_com.prediction is None:
+            continue
+        upsert_prediction(
+            collection=collection,
+            vis_com_name=vis_com.name,
+            predictions=vis_com.prediction,
+        )

misc/total_annotated_test.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+from shared.database import connect_mongodb, count_documents
+
+if __name__ == '__main__':
+    # prepare env vars
+    env_path = Path(__file__).parent.parent / 'local.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    os.environ['MONGO_HOST'] = 'localhost'
+    # connect to database
+    collection, db, client = connect_mongodb()
+    # get visual communication
+    num_docs = count_documents(
+        collection=collection,
+        only_with_annotation=True,
+    )
+    print(f"number of annotated  documents in database: {num_docs}")

misc/total_documents_test.py

@@ -0,0 +1,23 @@
+from __future__ import annotations
+
+import os
+from pathlib import Path
+
+from dotenv import load_dotenv
+
+from shared.database import connect_mongodb, count_documents
+
+if __name__ == '__main__':
+    # prepare env vars
+    env_path = Path(__file__).parent.parent / 'local.env'
+    assert env_path.exists()
+    load_dotenv(env_path)
+    os.environ['MONGO_HOST'] = 'localhost'
+    # connect to database
+    collection, db, client = connect_mongodb()
+    # get visual communication
+    num_docs = count_documents(
+        collection=collection,
+        only_with_annotation=False,
+    )
+    print(f"total number of documents in database: {num_docs}")