Using Python

Pulse Provides a Python API that uses a pybind11 interface to communicate with a Pulse Engine

We provide several example python files to demonstrate how to use our provided API

There are several ways to use our Python API:

pip install

We are currently still in the process of creating a PyPi package for Pulse that will allow you to pip install pulse on your local system.

Web Hosted Jupyter Notebooks

Binder provides a hosting service for browser based notebooks where you can view, run, and create new notebooks with out the need to install any packages or build any code. Click here to open our Binder Jupyter Notebooks

The environment provided, along with all notebooks are built from this repository

Building and Using Pulse Python Bindings

Ensure you have Python3 installed and available on your path.

Clone and follow the instructions to build the Pulse Physiology Engine. When configuring CMake, enable the Pulse_PYTHON_API

Using PyCharm

Once Pulse completes its build process, you can explore the provided Pulse API in PyCharm using these instructions

Updating your PYTHONPATH

You will need to add the following to our PYTHONPATH

From your Pulse source code directory, add the engine/src/python folder
From your Pulse build directory, add the 'build/install/bin` folder
- This contains the pybind11 object, for example on windows it is the PyPulse.cp37-win_amd64.pyd file
- Alternatively, you may copy this file to any folder already in your PYTHONPATH

Creating new patients in Pulse will require that files on disk are accessible. As explained here You may either:

Copy these directories to your application working directory
Set the location of the root directory using the set_data_root_dir method on the SEPatientConfiguration object

For any issues or questions using our Python API, contact us on our discourse forum