visiannot 0.3.1

Graphical user interface for visualization and annotation of video and signal data

ViSiAnnoT

ViSiAnnoT (Video Signal Annotation Tool) is a package that provides a graphical user interface for the visualization and annotation of video and signal data.

The main features are:

• Simultaneous visualization of several videos

• Simultaneous visualization of several signals

  • Regularly sampled or not
  • Zoom on signals
  • Plot thresholds on signals
  • Plot temporal intervals on signals

• Combined visualization of videos and signals

• Management of long recordings (split in several files)

  • Automatic synchronization between the different modalities
  • Tools for fast navigation

• Multi-label annotation of temporal events

• Multi-label image extraction

• Configuration via a graphical user interface

Documentation

Documentation is hosted on ReadTheDocs.

Installation

Pip

The easiest way is to install ViSiAnnoT with pip:

$ pip install visiannot

You may need to call pip3 instead.

From source

You may install ViSiAnnoT from source:

$ git clone https://github.com/RphWbr/visiannot
$ cd visiannot
$ pip install .

Depedencies

ViSiAnnoT requires Python 3.6+.

It is cross-platform and has been tested on Windows 7/10, Ubuntu 16/18/20 and MacOS Mojave/Catalina.

The following packages are required and are automatically installed with pip:

• configobj (saving and loading configuration files)
• opencv-python
• h5py
• numpy
• PyQt5 (GUI creation)
• pyqtgraph (video and signal plots)
• pytz (used for date-time comparison)
• scipy
• tinytag

Run ViSiAnnoT

Once it is installed, you can launch ViSiAnnoT with the following command line::

$ python3 -m visiannot

First, the configuration GUI will open, see dedicated user guide. Then the ViSiAnnoT GUI will open, see dedicated user guide.

In order to familiarize with ViSiAnnoT, an example of dataset is provided on GitHub. You may download or clone this repository on your computer.

Support

This package is developed at the LTSI Lab, INSERM-1099, located at Université Rennes 1, France.

For any enquiry, please send an email to [e-mail].

If you encounter a bug, feel free to raise an issue on GitHub.

License

Copyright Université Rennes 1 / INSERM (2018)

Contributor: Raphaël Weber

[e-mail]

This software is a computer program whose purpose is to to provide a graphical user interface for the visualization and annotation of video and signal data.

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info".

As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability.

In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.

Using ViSiAnnoT in a scientific publication

If you use ViSiAnnoT in a scientific publication, we would appreciate citations to the following paper:

CAILLEAU, Léa, WEBER, Raphael, CABON, Sandie, et al. Quiet Sleep Organization of Very Preterm Infants Is Correlated With Postnatal Maturation. Frontiers in Pediatrics, 2020, vol. 8, p. 613.

Bibtex entry::

@article{cailleau2020quiet,
title={Quiet sleep organization of very preterm infants is correlated with postnatal maturation},
author={Cailleau, L{\'e}a and Weber, Raphael and Cabon, Sandie and Flamant, Cyril and Rou{\'e}, Jean-Michel and Favrais, G{\'e}raldine and Gascoin, G{\'e}raldine and Thollot, Aurore and Por{\'e}e, Fabienne and Pladys, Patrick},
journal={Frontiers in Pediatrics},
volume={8},
pages={613},
year={2020},
publisher={Frontiers}
}

Acknowledgment

The initial development of ViSiAnnoT was made possible by a funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 689260 (Digi-NewB project).