Usage

Installation

To use Biobabel, first install it using pip:

$ pip install biobabel

Or you can install the latest development version directly from Github:

$ python -m pip install --upgrade "biobabel @ git+https://github.com/florisvanvugt/biobabel"

In both cases, omit the dollar sign when you copy-paste this into the terminal.

On Windows machines, some of the packages that biobabel depends on may require you to install Microsoft C++ Build Tools. If this is your case, when you run the above installation command, an error message will prompt you to install the build tools and includes a link from where you can download the tools. Re-run the biobabel installation after you have installed the build tools.

Basic usage

You would typically start by loading a physiology data file using the biobabel.load() function:

biobabel.load(fname, dialect=None)

Load physiology signal file.

fname : filename of the file to be read dialect : the file format. If None, the format is guessed

Example:

>>> import biobabel as bb
>>> bio = bb.load('tests/example.hdf5')

This loads the data into an object of the Biodata class, the core of the Biobabel logic.

>>> bio.print()
>>> bio.plot()
>>> bio.save('tests/new_filename.hdf5')

More complete overview of functionality in [Jupyter notebook](https://github.com/florisvanvugt/biobabel/blob/main/tests/Usage.ipynb).