diff --git a/.github/workflows/test-and-lint.yml b/.github/workflows/test-and-lint.yml index 93619de2..d33d28e8 100644 --- a/.github/workflows/test-and-lint.yml +++ b/.github/workflows/test-and-lint.yml @@ -32,7 +32,7 @@ jobs: poetry install - name: Testing with coverage run: | - poetry run pytest ngmt/test/ --cov=ngmt --cov-report=xml + poetry run pytest kielmat/test/ --cov=kielmat --cov-report=xml - name: Upload coverage to Codecov uses: codecov/codecov-action@v2 env: diff --git a/.gitignore b/.gitignore index 978072f7..f60aafe8 100644 --- a/.gitignore +++ b/.gitignore @@ -1,13 +1,14 @@ # See: https://git-scm.com/docs/gitignore __pycache__/ projects/ -/ngmt.egg-info -ngmt/datasets/_* +/kielmat.egg-info +# from before the package was renamed +/ngmt.egg-info my_messy_code/mytestconde.py /my_messy_code/* -ngmt/examples_gait_sqeuence.py +kielmat/examples_gait_sqeuence.py examples/data @@ -21,3 +22,7 @@ examples/data # local changelog generator create_changelog.py changelog.yml + +# example data +kiemat/datasets/_* +ngmt/datasets/_* diff --git a/CHANGELOG.md b/CHANGELOG.md index 5a4e58b1..17b29cde 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,35 +6,35 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [0.0.4] -Forth release of NGMT for for JOSS publication. +Forth release of KielMAT for for JOSS publication. ### Fixed -- Gait sequence detection with datetime [[#61]](https://github.com/neurogeriatricskiel/NGMT/pull/61) +- Gait sequence detection with datetime [[#61]](https://github.com/neurogeriatricskiel/KielMAT/pull/61) ### Changed -- Reworked documentation [[#60]](https://github.com/neurogeriatricskiel/NGMT/pull/60) +- Reworked documentation [[#60]](https://github.com/neurogeriatricskiel/KielMAT/pull/60) ## [0.0.3] - 2024-02-27 -Third unofficial release of NGMT for testing purposes. +Third unofficial release of KielMAT for testing purposes. ### Added -- Pyarrow as dependency [[ADD]](https://github.com/neurogeriatricskiel/NGMT/commit/22e401a5519cc9adde37b5c752a361a07d8166ac) -- Testing coverage [[ADD]](https://github.com/neurogeriatricskiel/NGMT/commit/f6a919100e7a9d7319a4af77592a78bd6949bb69) +- Pyarrow as dependency [[ADD]](https://github.com/neurogeriatricskiel/KielMAT/commit/22e401a5519cc9adde37b5c752a361a07d8166ac) +- Testing coverage [[ADD]](https://github.com/neurogeriatricskiel/KielMAT/commit/f6a919100e7a9d7319a4af77592a78bd6949bb69) ### Fixed -- Existing algorithms adapted to new dataclass structure [[FIX]](https://github.com/neurogeriatricskiel/NGMT/commit/3adf7756d9998b36454dccc86d9e2283200d72ed) +- Existing algorithms adapted to new dataclass structure [[FIX]](https://github.com/neurogeriatricskiel/KielMAT/commit/3adf7756d9998b36454dccc86d9e2283200d72ed) ## [0.0.2] - 2024-01-22 -Second unofficial release of NGMT for testing purposes. +Second unofficial release of KielMAT for testing purposes. ### Added -- Physical acitivity monitoring algorithm [[#29]](https://github.com/neurogeriatricskiel/NGMT/commit/a8d9067cde00f0c9a0dba8b7fc623ba4eeb32d0a) +- Physical acitivity monitoring algorithm [[#29]](https://github.com/neurogeriatricskiel/KielMAT/commit/a8d9067cde00f0c9a0dba8b7fc623ba4eeb32d0a) ## [0.0.1] - 2023-11-21 -This is the first unofficial release of NGMT. +This is the first unofficial release of KielMAT. Therefore, we do not have a proper changelog for this release. ### Added diff --git a/README.md b/README.md index 36ae2c45..f98ce10c 100644 --- a/README.md +++ b/README.md @@ -1,44 +1,46 @@ -[![codecov](https://codecov.io/gh/neurogeriatricskiel/NGMT/graph/badge.svg?token=L578RHZ699)](https://codecov.io/gh/neurogeriatricskiel/NGMT) -[![build docs](https://github.com/neurogeriatricskiel/NGMT/actions/workflows/mkdocs.yml/badge.svg)](https://github.com/neurogeriatricskiel/NGMT/actions/workflows/mkdocs.yml) +[![codecov](https://codecov.io/gh/neurogeriatricskiel/KielMAT/graph/badge.svg?token=L578RHZ699)](https://codecov.io/gh/neurogeriatricskiel/KielMAT) +[![build docs](https://github.com/neurogeriatricskiel/KielMAT/actions/workflows/mkdocs.yml/badge.svg)](https://github.com/neurogeriatricskiel/KielMAT/actions/workflows/mkdocs.yml) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) -![GitHub issues](https://img.shields.io/github/issues-raw/neurogeriatricskiel/NGMT) -![GitHub contributors](https://img.shields.io/github/contributors/neurogeriatricskiel/NGMT) -[![lint-and-test](https://github.com/neurogeriatricskiel/NGMT/actions/workflows/test-and-lint.yml/badge.svg)](https://github.com/neurogeriatricskiel/NGMT/actions/workflows/test-and-lint.yml) -![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ngmt) +![GitHub issues](https://img.shields.io/github/issues-raw/neurogeriatricskiel/KielMAT) +![GitHub contributors](https://img.shields.io/github/contributors/neurogeriatricskiel/KielMAT) +[![lint-and-test](https://github.com/neurogeriatricskiel/KielMAT/actions/workflows/test-and-lint.yml/badge.svg)](https://github.com/neurogeriatricskiel/KielMAT/actions/workflows/test-and-lint.yml) +![PyPI - Python Version](https://img.shields.io/pypi/pyversions/kielmat) -![NGMTLogo](ngmt_logo_transBG.png) +![KielMATLogo](kielmat_logo_transBG.png) -Welcome to the NeuroGeriatricsMotionToolbox (NGMT). We are a Python based toolbox for processing motion data. +Welcome to the KielMotionAnalysisToolbox (KielMAT). We are a Python based toolbox for processing motion data. -The toolbox is aimed at motion researchers who want to use python based open source software to process their data. -We have implemented validated algorithms in modules to process motion data, such as: - - Gait sequence detection (GSD) - - Inital contact detection (ICD) - - Physical activity monitoring (PAM) - - Postural transition detection (SSD) - - More to follow ... +The toolbox is aimed at motion researchers who want to use Python-based open-source software to process their data. We have implemented validated algorithms in modules to process motion data, as shown in the table below: + +| Module | Description | Data | +|--------------------------------|------------------------------------------------|----------------------------------------| +| Gait sequence detection (GSD) | Detects gaits | 3D accelerations from the lower back | +| Initial contact detection (ICD)| Detects initial contact during gait | 3D accelerations from the lower back | +| Postural transition detection (SSD) | Detects sit-to-stand and stand-to-sit movements | 3D accelerations and gyroscope from the lower back | +| Physical activity monitoring (PAM) | Monitors physical activity levels | 3D accelerations from the wrist | +| More to follow... | Additional modules to be added | | The idea is that various motion data can be loaded into our dedicated dataclass which rely on principles from the [Motion-BIDS](https://bids-specification.readthedocs.io/en/latest/modality-specific-files/motion.html) standard. ## Data classes ### Data classes: conceptual framework -Motion data is recorded with many different systems and modalities, each with their own proprietary data format. NGMT deals with this by organizing both data and metadata in a [BIDS-like format](https://bids-specification.readthedocs.io/en/stable/modality-specific-files/motion.html). The BIDS format suggests that [motion recording data](https://bids-specification.readthedocs.io/en/stable/modality-specific-files/motion.html#motion-recording-data) from a single tracking system is organized in a single `*_tracksys-