ngmt 0.0.1

The NeuroGeriatricMotionToolbox (NGMT) is a Python-based toolbox for processing motion data.

NGMT

Welcome to the NeuroGeriatricMotionToolbox (NGMT). We are a Python based toolbox for processing motion data.

The toolbox is currently under development and is not yet ready for use.

The toolbox is aimed at a wide variety of motion researchers who want to use open souce software to process their data. We have implemented a wide variety of functions to process motion data, such as:

• Gait sequence detection (GSD)
• Inital contact detection (ICD)
• More to follow ...

The idea is that various motion data can be loaded into our dedicated dataclasses which rely on principles from the Motion-BIDS standard.

Relation of data classes

classDiagram
    class RawData {
        FilePath: str
        FileName: str
    }

    class FileInfo {
        SubjectID: str
        TaskName: str
        DatasetName: str
        FilePath: str
    }

    class ChannelData {
        name: List[str]
        component: List[str]
        ch_type: List[str]
        tracked_point: List[str]
        units: List[str]
        get_channel_units()
    }

    class EventData {
        name: List[str]
        onset: List[float]
        duration: List[float]
        trial_type: Optional[List[str]] = None
    }

    class RecordingData {
        name: str
        data: np.ndarray
        sampling_frequency: float
        times: np.1darray
        channels: ChannelData
        start_time: float
        pick_channel_types()
    }

    class MotionData {
        data: List[RecordingData]
        times: np.ndarray  # Can be a 1D array representing timestamps
        info: List[FileInfo]
        synchronise_recordings(self, systems: List[RecordingData]):
    }

    RecordingData --> MotionData: raw data with same sampling rate
    ChannelData --> RecordingData: info per channel
    EventData --> RecordingData: info about potential events
    FileInfo --> MotionData: indent on disk
    FileInfo --> ChannelData: info per channel 
    FileInfo --> RecordingData: raw time series data
    FileInfo --> EventData: Include events if available in raw data
    RawData --> FileInfo: Get info from file

This is the planned class structure for motion data. Data from any file format can ultimately be imported into the MotionData class. The MotionData object contains a FileInfo object. The FileInfo object contains information about the file, such as the subject ID, the task name, the project name and the file path. The MotionData class also contains a list of RecordingData objects.

Each RecordingData object contains the raw data, the sampling rate, the time stamps and the channel info (ChannelData) of a tracking system. It is up to the user how to group the source data into a tracking system. The RecordingData object can also contain information about events. The EventData objects stores information about events such as onset or duration.

The ChannelData object is used to store the channel name, the channel type, the channel units and the tracked point.

Documentation

The full documentation can be found here.

Installation

After the first release, the toolbox can be installed via pip

For now, the toolbox can be installed via the following steps:

1. Clone the repository
2. Create a virtual environment
3. Install the requirements
4. Install the toolbox

For now please install the toolbox by cloning and install via poerty

git clone https://github.com/neurogeriatricskiel/NGMT.git
cd NGMT
poetry install

Authors

Masoud Abedinifar, Clint Hansen, Walter Maetzler, Robbin Romijnders & Julius Welzel