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vent-plotting

Ventilator data processing. This repository maintains the ventplotting Python package.

Installation

Install the Python packages listed in ventplotting/requirements.txt:

pip3 install -r ventplotting/requirements.txt

Notebooks

Jupyter notebooks are found in notebooks/. To run them properly, start Jupyter (or even better, JupyterLab) from the repository directory:

jupyter-lab

Notebooks are designed to be run from start to finish via the "Restart and Run All Cells..." menu command from within Jupyter.

For optimal development experience, first install the Python packages listed in notebooks/requirements.txt:

pip3 install -r notebooks/requirements.txt

and also install each extension listed in notebooks/labextensions.txt with the following command format for each extension listed (where @jupyterlab/celltags should be replaced with the extension as listed in notebooks/labextensions.txt):

jupyter labextension install @jupyterlab/celltags

Some notebooks are to be manually run, while other notebooks are automatically and parametrically generated (using Papermill) by manual execution of other notebooks. Specifically:

  • notebooks/example_plotting.ipynb: manually run, demonstrates plotting of raw measurements and control settings.
  • notebooks/plotting_template.ipynb: a template for automatic notebook generation and execution, plots a single file specified by its parameters.
  • notebooks/solenoid pinch valve only.ipynb: a notebook which automatically generates and runs notebooks for the solenoid pinch valve only dataset collection. The resulting notebooks are found at notebooks/solenoid pinch valve only/.

Dataset Auto-Downloading

By default, notebooks will look for data in the ../vent-data directory (relative to the repository directory). For example, if the repository directory is /home/lietk12/Projects/mp/vent4us/vent-plotting/, then the notebooks will look for datasets in /home/lietk12/Projects/mp/vent4us/vent-data/.