dda-py 0.5.0

Python bindings for DDA (Delay Differential Analysis)

dda-py

Python bindings for DDA (Delay Differential Analysis). The package supports the historical run_DDA_AsciiEdf binary and the pure-Rust ddalab engine. Provide the executable used by the API you call; neither backend is bundled in the Python wheel.

Package Layout

Implementation modules are grouped by responsibility:

dda_py/
├── core/             # result types, model encoding, and variant metadata
├── backends/
│   ├── native/       # request validation, execution, and output parsing
│   ├── legacy.py     # compatibility with the original tuple-returning API
│   └── rust.py       # pure-Rust ddalab backend
├── workflows/        # array, batch, and BIDS entry points
├── analysis/         # statistics, CCD calibration, selection, and motifs
└── visualization/    # optional plotting support

Public symbols remain available from dda_py. Historical module paths such as dda_py.api, dda_py.runner, and dda_py.results are maintained as compatibility aliases.

Installation

pip install dda-py

Optional dependencies:

pip install 'dda-py[mne]'        # MNE-Python integration
pip install 'dda-py[pandas]'     # DataFrame export
pip install 'dda-py[matplotlib]' # Plotting
pip install 'dda-py[scipy]'      # Window comparison statistics
pip install 'dda-py[mne-bids]'   # BIDS dataset integration
pip install 'dda-py[all]'        # All optional deps

Quick Start (High-Level API)

import numpy as np
from dda_py import run_st

# Analyze a numpy array (n_channels x n_samples)
data = np.random.randn(3, 10000)
result = run_st(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)

print(result.coefficients.shape)   # (3, n_windows, 3)
print(result.n_channels)           # 3
print(result.n_windows)            # depends on data length
print(result.to_dataframe().head())

MNE-Python Integration

import mne
from dda_py import run_st

raw = mne.io.read_raw_edf("data.edf", preload=True)
result = run_st(raw, delays=(7, 10), wl=200, ws=100)
# sfreq is extracted automatically from the MNE Raw object

Cross-Timeseries Analysis

from dda_py import run_ct

data = np.random.randn(4, 10000)  # 4 channels
result = run_ct(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)
print(result.n_pairs)              # 6 (all unique pairs)
print(result.pair_labels)          # ['ch0-ch1', 'ch0-ch2', ...]

Dynamical Ergodicity

from dda_py import run_de

data = np.random.randn(2, 10000)
result = run_de(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)
print(result.ergodicity.shape)     # (n_windows,)

Directed and Synchronization Analyses

from dda_py import run_cd, run_sy

directed = run_cd(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)
print(directed.pair_labels)  # ordered labels such as "ch0->ch1"

synchrony = run_sy(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)
print(synchrony.synchronization.shape)  # (n_channels, n_windows)

Pure-Rust Backend and Advanced CCD Variants

Set DDALAB_BINARY_PATH or pass rust_binary= to expose every variant implemented by dda-rs, including CCD, CCDLOG, CCDPR2, CCDSIG, CCDSTAB, TRCCD, and MVCCD.

from dda_py import run_rust

result = run_rust(
    data,
    sfreq=256.0,
    variants=["CCDLOG", "CCDPR2"],
    channels=[0, 1, 2],
    cd_pairs=[(0, 1)],
    variant_configs={
        "CCDLOG": {
            "conditioning_channels": [2],
            "conditioning_strategy": "all_selected",
        }
    },
    wl=200,
    ws=100,
)

ccdlog = result["CCDLOG"]
print(ccdlog.q_matrix.shape)

run_rust_file() provides the same interface for existing ASCII files. Rust channel and pair indices are 0-based; the historical run_DDA() interface remains 1-based.

CCD Statistics and Network Motifs

The normalized CCD statistics and null-calibration helpers from dda-rs are available directly in NumPy:

from dda_py import CcdStatConfig, CcdStatistic, compute_ccd_statistic

stat = compute_ccd_statistic(
    y,
    baseline_design,
    source_design,
    CcdStatConfig(statistic=CcdStatistic.PARTIAL_R2),
)
print(stat.value, stat.diagnostics)

Use transform_cd_to_network_motifs() to convert a directed CD matrix into normalized adjacency matrices at 25%, 50%, and 75% of the analyzed interval.

Plotting

Requires pip install 'dda-py[matplotlib]'.

from dda_py import run_st, plot_coefficients, plot_heatmap, plot_errors, plot_model

result = run_st(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)

# Coefficient time series per channel
fig = plot_coefficients(result, use_time=True, sfreq=256.0)

# Heatmap (channels x windows) for a single coefficient
fig = plot_heatmap(result, coeff_index=0, cmap="RdBu_r")

# Reconstruction errors over time
fig = plot_errors(result)

# Visualize the model space grid with selected terms highlighted
fig = plot_model([1, 2, 10], num_delays=2, polynomial_order=4)

All plotting functions accept an optional ax parameter to draw into an existing matplotlib axes, and return a matplotlib.figure.Figure.

from dda_py import run_de, plot_ergodicity

result = run_de(data, sfreq=256.0, delays=(7, 10), wl=200, ws=100)
fig = plot_ergodicity(result, use_time=True, sfreq=256.0)

Batch Processing

Process multiple files in one call:

from dda_py import run_batch, collect_results

# Run DDA on a list of files
results = run_batch(
    ["subj01.edf", "subj02.edf", "subj03.edf"],
    variant="st",
    sfreq=256.0,
    delays=(7, 10),
    wl=200,
    ws=100,
    progress=True,  # shows progress bar (uses tqdm if installed)
)

# Stack results into a single GroupResult for group analysis
group = collect_results(results, labels=["subj01", "subj02", "subj03"])
print(group.coefficients.shape)    # (3, n_channels, n_windows, n_coeffs)
print(group.mean_over_windows())   # (3, n_channels, n_coeffs)
print(group.to_dataframe().head())

Statistics

Group-level statistical analysis between two groups of DDA results.

Permutation Test

from dda_py import permutation_test

result = permutation_test(
    group_a=results_patients,
    group_b=results_controls,
    n_permutations=10000,
    seed=42,
)

print(result.p_value)              # (n_channels, n_coeffs)
print(result.observed_stat)        # (n_channels, n_coeffs)
print(result.to_dataframe())

Effect Size

from dda_py import compute_effect_size

effect = compute_effect_size(results_patients, results_controls)
print(effect.cohens_d)             # (n_channels, n_coeffs)
print(effect.to_dataframe())

Window Comparison

Requires pip install 'dda-py[scipy]'. Compare baseline vs test windows within a single recording:

from dda_py import compare_windows

comp = compare_windows(
    result,
    baseline_windows=slice(0, 10),
    test_windows=slice(10, 20),
    method="ttest",  # or "ranksum"
)
print(comp.p_value)
print(comp.baseline_mean)
print(comp.test_mean)

BIDS Integration

Requires pip install 'dda-py[mne-bids]'. Discover and analyze recordings from a BIDS dataset:

from dda_py import find_recordings, run_bids

# List available recordings
recordings = find_recordings("/path/to/bids", datatype="eeg", task="rest")
for rec in recordings:
    print(rec.label)  # e.g. "sub-01_ses-01_task-rest_run-01"

# Run DDA on all matching recordings
results = run_bids(
    "/path/to/bids",
    variant="st",
    datatype="eeg",
    task="rest",
    delays=(7, 10),
    wl=200,
    ws=100,
)
# returns {"sub-01_task-rest": STResult, "sub-02_task-rest": STResult, ...}

Low-Level API

For full control over the DDA binary, use the direct file API. Channel indices are 1-based to match the DDA binary and the Julia bindings.

from dda_py import run_DDA

result = run_DDA(
    file_path="data.edf",
    channels=[1, 2, 3],
    flavors=["ST", "CT"],
    binary_path="/path/to/run_DDA_AsciiEdf",
    WL=200,
    WS=100,
    WL_CT=2,
    WS_CT=2,
    delays=[7, 10],
    model=[1, 2, 10],
    derivative_points=4,
    order=4,
    out_fn="results/run1",
)

print(result.ST)
print(result.CT)

Structure Selection

structure_selection runs explicit candidate -MODEL and -TAU combinations through the same binary-facing API and returns the ST candidate with the lowest error.

from dda_py import structure_selection

selection = structure_selection(
    file_path="data.ascii",
    channels=[1, 2],
    binary_path="/path/to/run_DDA_AsciiEdf",
    candidate_models=[[1, 2, 6], [1, 2, 10]],
    candidate_delays=[[7, 10], [10, 20]],
    derivative_points=4,
    order=3,
    WL=3000,
    WS=200,
    input_format="ascii",
)

print(selection.best_model)
print(selection.best_delays)
print(selection.best_score)

Model Encoding

Visualize what DDA model indices mean:

from dda_py import visualize_model_space, decode_model_encoding

# Show all monomials for 2 delays, polynomial order 4
print(visualize_model_space(2, 4, highlight_encoding=[1, 2, 10]))

# Decode model [1, 2, 10] to equation
print(decode_model_encoding([1, 2, 10], num_delays=2, polynomial_order=4, format="text"))
# dx/dt = a_1 x_1 + a_2 x_2 + a_3 x_1^4

CLI

dda --file data.edf --channels 1 2 3 --flavors ST --wl 200 --ws 100
dda --file data.edf --channels 1 2 3 --flavors ST CT --delays 7 10 --ct-wl 2 --ct-ws 2 -o results.json

Variants

• ST - Single Timeseries
• CT - Cross Timeseries
• CD - Cross Dynamical
• DE - Dynamical Ergodicity
• SY - Synchrony

License

MIT