Signal Processing Toolkit - Documentation!

Important

Version: 0.0.9.6 | Released on 27/05/2023

Authors:

Nikesh Bajaj, Jesús Requena Carrión

Home:

https://spkit.github.io

New in 0.0.9.6

• MEA: Multi-Electrode Arrays Processing

• Geomatrical Functions

• Differential Entropy, Transfer Entropy,

• Signal differentiation, spatial filters

• Homepage spkit - https://spkit.github.io

Getting started

• Installation
• Links:

Information Theory

• Information Theory for Real-Valued signals
  • Entropy of real-valued signal (~ IID)
    • View in Jupyter-Notebook
    • Shannan entropy
    • Rényi entropy (e.g. Collision Entropy)
    • Mutual Information & Joint Entropy
    • Conditional entropy
    • Cross entropy & Kullback–Leibler divergence
  • Entropy of real-valued signal (~ non-IID)
    • Spectral Entropy
    • Approximate Entropy
    • Sample Entropy
    • Singular Value Decomposition Entropy
    • Permutation Entropy
    • Dispersion Entropy
  • EEG Signal
    • View in Jupyter-Notebook
    • Single Channel
    • Multi-Channels (cross)

Dispersion Entropy (time-series, physiological signals)

• Dispersion Entropy
  • Backgorund
  • An Example
    • Important Note: Log base
  • Embedding diamension 4
  • Dispersion Entropy with sliding window
  • Dispersion Entropy multiscale
  • Multiscale-refined Dispersion Entropy
  • View in Jupyter-Notebook for details

EEG Artifact Removal Algorithms

• ATAR - Automatic and Tunable Artifact Removal Algorithm for EEG
  • Notebook
    • View in Jupyter-Notebook
  • (1) Soft Thresholding (𝛽=0.1) - a quick example
  • (2) Linear Attenuation
  • (3) Elimination
  • Tuning 𝛽 with ‘soft’ : Controlling the aggressiveness
  • Tuning 𝛽 with ‘elim’
  • Tuning 𝛽 with ‘linAtten’
  • Other Settings
    • wavelet function
    • upper and lower bounds: \(k_1\) and \(k_2\)
    • IPR - Interpercentile range
    • constant threshold (θ=300), (not adaptive)
    • fixing threshold (θα=300), not using ipr method to adaptively change threshold
    • window length (5 sec)
• Blind Source Seperation - ICA Based Artifact Removal
  • Notebook
    • View in Jupyter-Notebook
  • A quick example
  • With smallar segment

Multi-Electrode Arrays Processing: MEA

• Multi-Electrode Arrays Processing
  • Backgorund
  • Complete Analysis of a recording
  • Step-wise Analysis
  • 1. Read HDF File
  • 2. Stim Localisation
  • 3. Alignment of Stim Cycles
  • 4. Averaging Cycles or Selecting one
  • 5. Activation Time
  • 6. Repolarisation Time (optional)
  • 7. APD (if RT is computed)
  • 8. Extracting EGM
  • 9. EGM Feature Extraction
  • 10. Identifying BAD Channels/electrodes
  • 11. Creating Feature Matrix
  • 12. Interpolation
  • 13. Conduction Velocity
  • Plots and Figures
  • Extracting EGM
  • EGM Processing & Feature Extractions
  • Conduction and Activation Map

Complex Continuous Wavelet Transform

• Complex Wavelets
  • Notebook
    • View in Jupyter-Notebook
  • A quick example to compare different wavelets
  • Gauss wavelet
    • Plot wavelet functions
    • With a range of scale parameters
    • Signal Analysis - EEG
    • Scalogram with default parameters
    • With a range of frequency and Q
    • With a plot of analysis wavelets
    • Speech
    • Audio
  • Morlet wavelet
  • Gabor wavelet
  • Poisson wavelet
    • #Type 1 (n)
    • #Type 2
    • #Type 3 (n)
  • Maxican wavelet
  • Shannon wavelet

Ramanujan Filter Banks for Period Estimation

• Ramanujan Filter Banks
  • Period estimation using RFB - (spkit version 0.0.9.4)
  • Single pattern with period of 10
  • Multiple pattern with periods of 3,7 and 10

Analysis and Synthesis Models

• Analysis and Synthesis Models
• DFT: Analysis and Synthesis
  • Analysis and Synthesis
  • Plot figures
  • Effect of windowing
  • No windowing
  • View in Jupyter-Notebook
• STFT: Analysis and Synthesis
  • Analysis and Synthesis
  • Plot figures:
  • View in Jupyter-Notebook
• FRFT: Fractional Fourier Transform
  • Analysis and Synthesis
  • Plot figures
  • View in Jupyter-Notebook-1
  • View in Jupyter-Notebook-2
• Sinasodal Model: Analysis and Synthesis
  • Analysis and Synthesis
  • Plots
  • Residual
  • Audio output
    • Original Audio
    • Reconstructed Audio
    • Residual Audio - hissing sound
  • View in Jupyter-Notebook-1
  • View in Jupyter-Notebook-2

DFT and STFT for Analysis and Synthesis of signals

#TODO

Fractional Fourier Transform

• Fractional Fourier Transform
  • View in Jupyter-Notebook
    • Fractional Fourier Transform
    • Fast Fractional Fourier Transform

Filtering

• Signal Filtering
  • Removing DC component (removing drift) - using IIR
  • Removing DC component (removing drift) - using Savitzky-Golay filter
  • Filtering frequency components - using IIR (butterworth) filter
  • Wavelet Filtering
  • Wavelet Filtering - on smaller windows

Wavelet Filtering

• Wavelet Filtering
  • Background
  • Example
  • View in Jupyter-Notebook for details and more examples

Independent Component Analysis

• Independent Component Analysis - ICA
  • View in Jupyter-Notebook

EEG Topographic Maps (Spatio-Temporal/Spectral)

• EEG Topographic Maps
  • Spatio-Temporal Map
  • Spatio-Spectral Map
  • Spatio-Spectro-Temporal Map

Machine Learning

• Machine Learning
  • New Updates
    • Decision Tree - View Notebooks
  • Logistic Regression
    • View more examples in Notebooks
    • Binary Class
    • Multi Class - with polynomial features
  • Naive Bayes
    • View more examples in Notebooks
  • Decision Trees
    • View more examples in Notebooks
    • Depth Analysis
    • Plottng tree while training

Basic-utilities

• Periodogram
• A quick stats of an array
• Compute statistical outliers

LFSR

• Link to pylfsr documentation
  • Example: 5 bit LFSR with x^5 + x^2 + 1
  • Check out full documentation of LFSR**

API Doc

• API docs
  • Entropy Functions

ChangeLog

• ChangeLog

Contacts

• Contacts