mad-datasets 0.4.0

Helper to access to open-source gait datasets used by MaD-Lab

mad-datasets

Helper to access to open-source gait datasets of the MaD-Lab (and maybe externals in the future).

The aim of this package is to ensure that all datasets can be loaded in a similar fashion and all data (and annotations) are in the same format (i.e. the same sensor orientations, units, etc.). This should allow to easily run the same algorithm across multiple datasets.

:warning: While this makes it easier to work with the datasets, the coordinate system and other data information provided with the dataset might not match the format you get when using this library!

All datasets APIs are built using the tpcp.Dataset interface. For available datasets see the table below.

Usage

Install the package from Pip

pip install mad-datasets

Then download/obtain the dataset that you are planning to use (see below). The best way to get started is to then check the example for the respective dataset on the documentation page.

Datasets

Dataset	Info Link	Download
EgaitSegmentationValidation2014	https://www.mad.tf.fau.de/research/activitynet/digital-biobank/	Email to data owner (see info link)
EgaitParameterValidation2013	https://www.mad.tf.fau.de/research/activitynet/digital-biobank/	Email to data owner (see info link)
StairAmbulationHealthy2021	https://osf.io/sgbw7/	https://osf.io/download/5ueq6/
SensorPositionDataset2019	https://zenodo.org/record/5747173	https://zenodo.org/record/5747173

Testing

The /tests directory contains a set of tests to check the functionality of the library. However, most tests rely on the existence of the respective datasets in certain folders outside the library. Therefore, the tests can only be run locally and not on the CI server.

To run them locally, make sure datasets are downloaded into the correct folders and then run poe test.

Documentation (build instructions)

Like the tests, the documentation requires the datasets to be downloaded into the correct folders to execute the examples. Therefore, we can not build the docs automatically on RTD. Instead we host the docs via github pages. The HTML source can be found in the gh-pages branch of this repo.

To make the deplowment as easy as possible, we "mounted" the gh-pages branch as a submodule in the docs/_build/html folder. Hence, before you attempt to build the docs, you need to initialize the submodule.

git submodule update --init --recursive

After that you can run poe docs to build the docs and then poe upload_docs to push the changes to the gh-pages branch. We will always just update a single commit on the gh-pages branch to keep the effective file size small.

**WARNING: ** Don't delete the docs/_build folder manually or by running the sphinx make file! This will delete the submodule and might cause issues. The poe task is configured to clean all relevant files in the docs/_build folder before each run.

After an update of the documentation, you will see that you also need to make a commit in the main repo, as the commit hash of the docs submodule has changed.

To make sure you don't forget to update the docs, the poe prepare_release task will also build and upload the docs automatically.