| docs | ||
| openflexure_microscope | ||
| tests | ||
| utilities | ||
| .gitignore | ||
| poetry.lock | ||
| pyproject.toml | ||
| README.md | ||
| readthedocs.yaml | ||
OpenFlexure Microscope Software
Installation
Easy
- Run
curl -LSs get.openflexure.org/microscope |sudo bash - Follow on-screen prompts
Manual
User
- (Recommended) create a virtual environment
pip3 install virtualenvmkdir ~/.openflexurepython3 -m virtualenv ~/.openflexure/envmicroscope- Activate with
source /.openflexure/envmicroscope/bin/activate
- Install non-python dependencies with
sudo apt-get install libatlas-base-dev libjasper-dev libjpeg-dev - Users: Install module by running
pip install openflexure-microscope==1.0.0b5 - Developers: Install Poetry, clone this repo, and
poetry installfrom inside the repo.
Usage
Running the web API in Gunicorn (port 5000)
- Ensure Gunicorn is installed to the current environment (
pip install gunicorn) - Run
gunicorn --threads 5 --workers 1 --graceful-timeout 3 --bind 0.0.0.0:5000 openflexure_microscope.api.app:app
REST(ish) API
The Flask app serves a (reasonably) RESTful web API. For most user-facing functionality, this is the preferred interface. API documentation, with example requests, is available here.
Developer notes
Build-system
As of 1.0.0b0, we're using Poetry to manage dependencies, build, and distribute the package. All package information and dependencies are found in pyproject.toml, in line with PEP 518. If you're developing this package, make use of poetry.lock to ensure you're using the latest locked dependency list.
Microscope plugins
The Microscope module, and Flask app, both support plugins for extending lower-level functionality not well suited to web API calls. This plugin system is still in fairly early development, and is not yet properly documented. The current documentation can be found here.
Running tests through the PTVSD remote debugger (port 3000)
- From the openflexure-microscope-software directory, run
python3 -m ptvsd --host 0.0.0.0 --port 3000 --wait tests/test_camera.py
Credits
Video streaming
Based on supporting code for the article video streaming with Flask and its follow-up Flask Video Streaming Revisited.