tempord 0.1.4

Temporal orders and causal vector for physiological data analysis

tempord

tempord is a Python package for computing temporal order between pairs of time series signals based on paper:

M. Młyńczak, "Temporal orders and causal vector for physiological data analysis," 2020 42nd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Montreal, QC, Canada, 2020, pp. 750-753, doi: 10.1109/EMBC44109.2020.9176842.

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📦 Installation

You can install tempord from PyPI or clone the repository for development.

Option 1: Install from PyPI

pip install tempord

Option 2: Clone and install from source

1. Clone the repository

   git clone [e-mail]:mrosol/tempord.git
   cd tempord
   

2. Create a virtual environment (recommended)

   python -m venv .venv
   source .venv/bin/activate   # macOS / Linux
   # .\.venv\Scripts\activate  # Windows
   

3. Install required packages

   pip install -r requirements.txt
   

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⚙️ Usage

Import the main function from the tempord module and call it with a pandas.DataFrame containing your signals as columns.

Method: LM (linear regression, adjusted R²)

Measures how well one shifted signal predicts the other using adjusted R². Higher values indicate stronger linear dependence at a given shift.

from tempord import tempord
import pandas as pd

df = pd.DataFrame({'s1': signal1, 's2': signal2})

results = tempord(
    df,
    method="LM",
    modality="raw",              # use raw signal values
    thr=0.7,                     # skip time points where max R² < 0.7
    scaling=1,                   # 0=no scaling, 1=min-max, 2=z-score
    sig_length=10,               # window length in seconds
    max_shift_seconds=(-1, 1),   # backward/forward range in seconds
    fs=25,                       # sampling frequency (Hz)
    make_figure=True
)

Method: TD (time-series distance)

Measures dissimilarity between shifted windows using a distance metric. Lower values indicate greater similarity at a given shift. The td_type argument selects the metric.

Supported metrics: "euclidean", "manhattan", "chebyshev", "correlation", "cosine". A custom callable with signature f(a, b) -> float is also accepted.

results = tempord(
    df,
    method="TD",
    modality="raw",
    td_type="euclidean",         # distance metric
    thr=5.0,                     # skip time points where min distance > 5.0
    scaling=1,
    sig_length=10,
    max_shift_seconds=(-1, 1),
    fs=25,
    make_figure=True
)

Modality: phase

Setting modality="phase" converts each signal to its instantaneous phase before computing temporal order. Continuous signals use the Hilbert transform (zero-mean centred internally); binary signals use a cycle-linear phase. This is useful for oscillatory or binary rhythmic signals where amplitude is not informative.

results = tempord(
    df,
    method="LM",
    modality="phase",            # convert to instantaneous phase first
    thr=0.5,
    scaling=0,                   # phase signals typically need no additional scaling
    sig_length=10,
    max_shift_seconds=(-1, 1),
    fs=25,
    make_figure=True
)

Reading the results

results is a dict keyed by signal-pair tuples (e.g. ('s1', 's2')). Each value contains:

Key	Content
"Tempord"	DataFrame — parameter matrix (rows: shifts, columns: time points)
"Best"	DataFrame — shift at the extremum per time point (after threshold filtering)
"Fig"	matplotlib.Figure — heatmap with the extremum curve overlaid, or None

pair_result = results[('s1', 's2')]
fig = pair_result["Fig"]           # matplotlib figure
best_shifts = pair_result["Best"]  # DataFrame with columns "Points" and "Best"
param_matrix = pair_result["Tempord"]

Plotting and post-processing

The module provides helper functions used internally:

• get_causal_vector – extracts the shift at the extremum (max for LM, min for TD) for each time point, subject to the threshold.
• make_plot – draws a heatmap of the parameter matrix and overlays the extremum curve.

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📌 Notes

• Input signals must be numeric and of equal length. Windows or shifts that fall outside signal boundaries are skipped.
• For method="LM", the threshold applies to adjusted R² (higher = stronger correlation). For method="TD", the threshold applies to the minimum distance (lower = more similar). Pass thr=-1 to disable thresholding entirely.
• modality="phase" is most meaningful for oscillatory or binary rhythmic signals. For aperiodic signals the Hilbert-based phase may be unreliable.

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Contact

mail: [e-mail]