nikeshbajaj/spkit

Signal Processing Toolkit, including ML models with visualization

Signal Processing toolkit

Links: Homepage | Documentation | Github | PyPi - project | _ Installation: pip install spkit

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Installation

Requirement: numpy, matplotlib, scipy.stats, scikit-learn, seaborn

with pip

pip install spkit

update with pip

pip install spkit --upgrade

New in 0.0.9.5:

MEA Processing Toolkit

• sp.mea

Geometrical Functions

• sp.gemetry

More on signal processing

• sp.core

Statistics

• sp.stats

For updated list of contents and documentation check github or Documentation

List of all functions

Signal Processing Techniques

Information Theory functions

for real valued signals

• Entropy

  • Shannon entropy
  • Rényi entropy of order α, Collision entropy,
  • Joint entropy
  • Conditional entropy
  • Mutual Information
  • Cross entropy
  • Kullback–Leibler divergence
  • Spectral Entropy
  • Approximate Entropy
  • Sample Entropy
  • Permutation Entropy
  • SVD Entropy

• Plot histogram with optimal bin size

• Computation of optimal bin size for histogram using FD-rule

• Compute bin_width with various statistical measures

• Plot Venn Diagram- joint distribuation and normalized entropy values

Dispersion Entropy --for time series (physiological signals)

• Dispersion Entropy (Advanced) - for time series signal
  • Dispersion Entropy
  • Dispersion Entropy - multiscale
  • Dispersion Entropy - multiscale - refined

Matrix Decomposition

• SVD
• ICA using InfoMax, Extended-InfoMax, FastICA & Picard

Continuase Wavelet Transform

• Gauss wavelet
• Morlet wavelet
• Gabor wavelet
• Poisson wavelet
• Maxican wavelet
• Shannon wavelet

Discrete Wavelet Transform

• Wavelet filtering
• Wavelet Packet Analysis and Filtering

Basic Filtering

• Removing DC/ Smoothing for multi-channel signals
• Bandpass/Lowpass/Highpass/Bandreject filtering for multi-channel signals

Biomedical Signal Processing

MEA Processing Toolkit

Artifact Removal Algorithm

• ATAR Algorithm Automatic and Tunable Artifact Removal Algorithm for EEG from artical
• ICA based Algorith

Analysis and Synthesis Models

• DFT Analysis & Synthesis
• STFT Analysis & Synthesis
• Sinasodal Model - Analysis & Synthesis
  • to decompose a signal into sinasodal wave tracks
• f0 detection

Ramanajum Methods for period estimation

• Period estimation for a short length sequence using Ramanujam Filters Banks (RFB)
• Minizing sparsity of periods

Fractional Fourier Transform

• Fractional Fourier Transform
• Fast Fractional Fourier Transform

Machine Learning models - with visualizations

• Logistic Regression
• Naive Bayes
• Decision Trees
• DeepNet (to be updated)

Linear Feedback Shift Register

• pylfsr

Cite As

@software{nikesh_bajaj_2021_4710694,
  author       = {Nikesh Bajaj},
  title        = {Nikeshbajaj/spkit: 0.0.9.4},
  month        = apr,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {0.0.9.4},
  doi          = {10.5281/zenodo.4710694},
  url          = {https://doi.org/10.5281/zenodo.4710694}
}

Contacts:

• Nikesh Bajaj
• https://nikeshbajaj.in
• n.bajaj[AT]qmul.ac.uk, n.bajaj[AT]imperial[dot]ac[dot]uk

Imperial College London

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spkit's Issues

Import error python 2.7

For independent python 2.7 version, import error was reported.

IndexError: index 2048 is out of bounds for axis 0 with size 2048

Hi. Thanks for your great job!
I try to run your code (Generating Dynamic Spatio-Spectral Map) and have this error:
--> ax2.set_xlim([tx[i],tx[i+3*N]])
IndexError: index 2048 is out of bounds for axis 0 with size 2048

Also I have no interactive wiget.

blackmanharris import needs to be changed

should be changed to scipy.signal.windows in the following files.
spkit/core/fractional_processes.py
spkit/core/advance_techniques.py

May be other files.

what is TopoMap pos parameter?

I've seen this TopoMap in example but pos parameter is not init.. how can I use this?

.

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no spkit.cwt

Dear Nikeshbajaj, your toolkit is beautiful, but i have a little problem with spkit.cwt.
When import this, then an error: No module named 'spkit.cwt'

But the installation process it's ok.

thanks for any response
Tomas

Relative path importing

As pointed out by @mk-ling

To be fixed: relative path of 'core' and others too

Message:
First of all, thx for the contribution, I appreciate it. However, when I tried to import spkit from my project path(which also have a package named "core"), the import statements in spkit(eg. from core import xxx) locates to the "core" package in my project instead of the one in spkit. So I'd suggest to use relative import in such places that might have ambiguities(just like what numpy did if you look at their code). Other than this, spkit has been very helpful. Again, thx for the contribution from you guys.

Originally posted by @mk-ling in #7

IndexError: out of bounds for axis 0

@mkhazova reported:

• using code here https://spkit.github.io/examples/gen_topo

it throws Index error:

index 4704 is out of bounds for axis 0 with size 4675

which was in the code, not resolved before.