smartem-decisions
Smart data collection system for cryo-electron microscopy at Diamond Light Source.
Installation
SmartEM Agent (data collection)
pip install smartem-decisions[agent]
Windows executable: Download the latest smartem-agent-windows-vX.Y.Z.exe from GitHub Releases.
SmartEM Backend (API server)
pip install smartem-decisions[backend]
All components
pip install smartem-decisions[all]
Usage
Agent
Watch a directory for EPU output and send data to the backend:
# Basic usage
smartem-agent watch /path/to/epu/output --api-url http://localhost:8000
# Dry run (no API calls)
smartem-agent watch /path/to/epu/output --dry-run
# Verbose output
smartem-agent watch /path/to/epu/output -vv
Parse EPU data without watching:
smartem-agent parse dir /path/to/epu/output
smartem-agent parse session /path/to/EpuSession.dm
smartem-agent parse atlas /path/to/Atlas.dm
Backend
Start the API server and message consumer:
# HTTP API server
python -m smartem_backend.api_server
# Message queue consumer
python -m smartem_backend.consumer -v
Components
| Package | Description |
|---|---|
smartem_agent |
Data collection agent that monitors EPU output |
smartem_backend |
Core backend with HTTP API and message queue processing |
smartem_common |
Shared schemas, types, and utilities |
Installation Extras
| Extra | Description |
|---|---|
[agent] |
Agent dependencies (watchdog, lxml) |
[backend] |
Backend dependencies (FastAPI, SQLAlchemy, Pika) |
[common] |
Core schemas only (Pydantic) |
[images] |
Image processing (Pillow, mrcfile, tifffile) |
[dev] |
Development tools (pytest, ruff, pyright) |
[all] |
All dependencies |
Development
# Install with dev dependencies
pip install -e ".[dev]"
# Run tests
pytest
# Lint
ruff check src/
ruff format --check src/
# Type check
pyright
Documentation
Links
- PyPI: https://pypi.org/project/smartem-decisions/
- Repository: https://github.com/DiamondLightSource/smartem-decisions
- Issues: https://github.com/DiamondLightSource/smartem-decisions/issues
- Changelog: GitHub Releases
License
Apache-2.0
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