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tsdf

A package to read, modify and write TSDF data in Python.

https://github.com/biomarkersparkinson/tsdf

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.0%) to scientific vocabulary

Keywords

data-format python time-series
Last synced: 6 months ago · JSON representation ·

Repository

A package to read, modify and write TSDF data in Python.

Basic Info
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 0
  • Open Issues: 19
  • Releases: 6
Topics
data-format python time-series
Created about 3 years ago · Last pushed 8 months ago
Metadata Files
Readme Contributing License Citation Security

README.md

tsdf

| Badges | | |:----:|----| | Packages and Releases | Latest release PyPI Static Badge | | Build Status | Python package | | DOI | DOI | | License | GitHub license | | Fairness | fair-software.eu OpenSSF Best Practices |

A package (documentation) to load TSDF data (specification) into Python.

Overview

The tsdf package is a comprehensively documented reference implementation of the Time Series Data Format (TSDF) standard [1]. TSDF simplifies data storage and exchange of multi-channel digital sensor data, thereby promoting interpretability and reproducibility of scientific results. Sensor measurements and timestamps are stored as raw tabular binary array files. To ensure unambiguous reconstruction, binary array files are accompanied by human-readable JavaScript Object Notation (JSON) metadata files, which contain a set of mandatory fields limited to essential sensor measurement information.

The tsdf Python package implements functions for reading and writing TSDF files. It guarantees formatting and metadata consistency. It enforces usage of the essential metadata such as study identification, time frame, data channel descriptions and data attributes corresponding to the binary data.

Installation

Using pip

The package is available in PyPi and requires Python 3.10 or higher. It can be installed using:

bash $ pip install tsdf

Usage

See our extended tutorials.

Development

Running tests

bash poetry install poetry run pytest

Building the documentation

We use Sphinx to build the documentation. Use this command to build the documentation locally:

bash poetry run make html --directory docs

Contributing

We welcome contributions! Please see our Contributing Guidelines for more details on coding standards, how to get started, and the submission process.

Code of Conduct

To ensure a welcoming and respectful community, all contributors and participants are expected to adhere to our Code of Conduct. By participating in this project, you agree to abide by its terms.

License

This package was created by Pablo Rodríguez, Peter Kok and Vedran Kasalica. It is licensed under the terms of the Apache License 2.0 license.

Credits

  • The TSDF data format was created by Kasper Claes, Valentina Ticcinelli, Reham Badawy, Yordan P. Raykov, Luc J.W. Evers, Max A. Little.
  • This package was created with cookiecutter and the py-pkgs-cookiecutter template.

Owner

  • Name: Digital Biomarkers for Parkinson's disease
  • Login: biomarkersParkinson
  • Kind: organization
  • Location: Netherlands

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: tsdf
abstract: >
  The tsdf package is a comprehensively documented2 reference implementation of the Time Series Data Format (TSDF) 
  standard [1](https://arxiv.org/abs/2211.11294). TSDF simplifies data storage and exchange of multi-channel digital 
  sensor data, thereby promoting interpretability and reproducibility of scientific results. Sensor measurements and 
  timestamps are stored as raw tabular binary array files. To ensure unambiguous reconstruction, binary array files are 
  accompanied by human-readable JavaScript Object Notation (JSON) metadata files, which contain a set of mandatory fields 
  limited to essential sensor measurement information.

The tsdf Python package implements functions for reading and writing TSDF files. It guarantees formatting and metadata consistency. It enforces usage of the essential metadata such as study identification, time frame, data channel descriptions and data attributes corresponding to the binary data.'
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Peter
    family-names: Kok
    email: p.kok@esciencecenter.nl
    affiliation: Netherlands eScience Center
    orcid: 'https://orcid.org/0000-0002-6630-7326'
  - given-names: Vedran
    family-names: Kasalica
    email: v.kasalica@esciencecenter.nl
    affiliation: Netherlands eScience Center
    orcid: 'https://orcid.org/0000-0002-0097-1056'
  - given-names: Pablo
    family-names: Rodríguez-Sánchez
    email: p.rodriguez-sanchez@esciencecenter.nl
    affiliation: Netherlands eScience Center
    orcid: 'https://orcid.org/0000-0002-2855-940X'
identifiers:
  - type: doi
    value: 10.5281/zenodo.7867900
repository-code: 'https://github.com/biomarkersParkinson/tsdf'
url: 'https://biomarkersparkinson.github.io/tsdf/'
license: Apache-2.0

GitHub Events

Total
  • Issues event: 12
  • Delete event: 4
  • Issue comment event: 8
  • Push event: 8
  • Pull request review comment event: 2
  • Pull request review event: 5
  • Pull request event: 7
  • Create event: 4
Last Year
  • Issues event: 12
  • Delete event: 4
  • Issue comment event: 8
  • Push event: 8
  • Pull request review comment event: 2
  • Pull request review event: 5
  • Pull request event: 7
  • Create event: 4

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 2,064 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 8
  • Total maintainers: 5
pypi.org: tsdf

A Python library that provides methods for encoding and decoding TSDF (Time Series Data Format) data, which allows you to easily create, manipulate and serialize TSDF files in your Python code.

  • Versions: 8
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2,064 Last month
Rankings
Dependent packages count: 7.2%
Average: 20.3%
Dependent repos count: 33.4%
Maintainers (5)
kretep PabRod VKasalica erikpost lucevers
Last synced: 7 months ago

Dependencies

.github/workflows/python-package.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
poetry.lock pypi
  • 133 dependencies
pyproject.toml pypi
  • flatten-json ^0.1.13
  • mkdocs ^1.4.2
  • mkdocs-jupyter ^0.22.0
  • mypy ^1.0.1
  • numpy ^1.24.1
  • python ^3.9