DynamicAnnotationDB
DynamicAnnotationDB (DADB) is an interface layer for creating, modifying and interacting with PostgreSQL databases used to store spatial point annotations and segmentation data defined by a chunkedgraph.
Features
- Create and manage PostgreSQL databases for annotation storage
- Handle spatial point annotations with PostGIS integration
- Support for segmentation data linked to annotations
- Dynamic schema generation and validation
- CRUD operations for annotations and segmentation data
- Reference annotation support with table linking
- Built-in versioning and tracking of modifications
Installation
You can install DynamicAnnotationDB using pip:
pip install DynamicAnnotationDB
Or install from source:
git clone https://github.com/CAVEconnectome/DynamicAnnotationDB
cd DynamicAnnotationDB
pip install -e .
Quick Start
Here's a basic example of using DynamicAnnotationDB:
from dynamicannotationdb import DynamicAnnotationInterface
# Connect to database
sql_uri = "postgresql://postgres:postgres@localhost:5432"
aligned_volume = "my_annotations"
interface = DynamicAnnotationInterface(sql_uri, aligned_volume)
# Create a new annotation table
table_name = "synapse_annotations"
interface.annotation.create_table(
table_name=table_name,
schema_type="synapse",
description="Synapse annotations for dataset X",
user_id="user@example.com",
voxel_resolution_x=4.0,
voxel_resolution_y=4.0,
voxel_resolution_z=40.0
)
# Insert annotations
annotations = [{
"pre_pt": {"position": [121, 123, 1232]},
"ctr_pt": {"position": [128, 143, 1232]},
"post_pt": {"position": [235, 187, 1232]},
"size": 1
}]
annotation_ids = interface.annotation.insert_annotations(table_name, annotations)
Key Components
The interface consists of several key components:
- Annotation Client: Handle CRUD operations for annotation data
- Segmentation Client: Manage segmentation data linked to annotations
- Schema Client: Generate and validate dynamic schemas
- Database Client: Core database operations and metadata management
Documentation
Full documentation is available at dynamicannotationdb.readthedocs.io.
Features in Detail
Dynamic Schema Support
DADB uses EMAnnotationSchemas to define table structures:
# Create a table with a specific schema
interface.annotation.create_table(
table_name="my_table",
schema_type="synapse",
description="Description",
user_id="user@example.com",
voxel_resolution_x=4.0,
voxel_resolution_y=4.0,
voxel_resolution_z=40.0
)
Segmentation Support
Link segmentation data to annotations:
# Create a segmentation table
seg_table = interface.segmentation.create_segmentation_table(
table_name="my_table",
schema_type="synapse",
segmentation_source="seg_source"
)
# Insert linked data
interface.segmentation.insert_linked_annotations(
table_name="my_table",
pcg_table_name="seg_source",
annotations=[...]
)
Reference Tables
Create tables that reference other annotations:
# Create a reference table
interface.annotation.create_table(
table_name="reference_table",
schema_type="reference_type",
description="Reference annotations",
user_id="user@example.com",
voxel_resolution_x=4.0,
voxel_resolution_y=4.0,
voxel_resolution_z=40.0,
table_metadata={
"reference_table": "target_table",
"track_target_id_updates": True
}
)
Development
Requirements
- Python 3.7+
- PostgreSQL with PostGIS extension
- Docker (optional, for testing)
Testing
Run tests with pytest:
# Install test requirements
pip install -r test_requirements.txt
# Run tests (requires a PostgreSQL with PostGIS extension running)
pytest
# Run tests with a temporary Docker PostgreSQL instance (preferred local testing method)
pytest --docker=true
License
This project is licensed under the MIT License - see the LICENSE file for details.
Support
For support, please open an issue on the GitHub repository.
4 maintainers
Metadata
4 maintainers
Release files for DynamicAnnotationDB 5.15.0
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