sweetsourcod
The sweet source coding library (Python and C++)
Science Score: 67.0%
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✓CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Repository
The sweet source coding library (Python and C++)
Basic Info
- Host: GitHub
- Owner: martiniani-lab
- License: other
- Language: C
- Default Branch: master
- Homepage: https://github.com/martiniani-lab/sweetsourcod
- Size: 276 KB
Statistics
- Stars: 12
- Watchers: 6
- Forks: 4
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
SweetSourCod
The sweet source-coding library
This library is a collection of methods to estimate the entropy of sequences by data compression (source coding).
Examples of the use of this library can be found in
S. Martiniani, P. Chaikin, D. Levine, "Quantifying hidden order out of equilibrium", Phys. Rev. X 9, 011031 (2019)
S. Martiniani, Y. Lemberg, P. Chaikin, D. Levine, "Correlation lengths in the language of computable information", Phys. Rev. Lett. 125, 170601 (2020)
A. Cavagna, P. M. Chaikin, D. Levine, S. Martiniani, A. Puglisi, and M. Viale, "Vicsek model by time-interlaced compression: A dynamical computable information density", Phys. Rev. E 103, 062141 (2021)
S. Ro, B. Guo, A. Shih, T. Phan, R. Austin, D. Levine, P. Chaikin, and S. Martiniani, "Model-Free Measurement of Local Entropy Production and Extractable Work in Active Matter", Phys. Rev. Lett. 129, 220601 (2022)
Description
The library implements/wraps a number of algorithms and utilities:
LZ77, Lempel-Ziv 77 pattern matching code. Wraps the kkp2 algorithm performing LZ77 factorization in O(n).
LZ78, Lempel-Ziv 78 incremental parsing rule.
Cross-parsing complexity, for computing KL divergence.
Block Entropy, Shannon entropy for blocks of a given size.
Block Sorting (Burrows-Wheeler Transform) based entropy estimator.
Wraps a range of compression algorithms readily available in Python (after reducing the sequence to its minimal binary representation)
- deflate
- bzip2
- lzma
- zstd
- brotli
- zopfli
run-length encoding
Hilbert curve, Hilbert-Peano space filling curve for optimal compression of higher dimensional sequences on a square grid.
Gosper curve, space filling curve for optimal compression of higher dimensional sequences on an hexagonal grid.
Installation
You can install the library in place by running
shell
python setup.py build_ext -i
Owner
- Name: Martiniani Lab
- Login: martiniani-lab
- Kind: organization
- Location: Minneapolis, MN
- Repositories: 4
- Profile: https://github.com/martiniani-lab
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Martiniani"
given-names: "Stefano"
orcid: "https://orcid.org/0000-0003-2028-2175"
- family-names: "Guo"
given-names: "Buming"
orcid: "https://orcid.org/0000-0003-2581-7933"
title: "Sweetsourcod"
version: 1.0.0
# doi: 10.5281/zenodo.1234
# date-released: 2017-12-18
url: "https://github.com/martiniani-lab/sweetsourcod"
preferred-citation:
type: article
authors:
- family-names: "Martiniani"
given-names: "Stefano"
orcid: "https://orcid.org/0000-0003-2028-2175"
- family-names: "Chaikin"
given-names: "Paul"
orcid: "https://orcid.org/0000-0001-9864-0089"
- family-names: "Levine"
given-names: "Dov"
orcid: "https://orcid.org/0000-0001-8241-8168"
doi: "10.1103/PhysRevX.9.011031"
journal: "Physical Review X"
# month:
start: 220601 # First page number
# end: 10 # Last page number
title: "Quantifying Hidden Order out of Equilibrium"
# issue:
volume: 9
year: 2019
GitHub Events
Total
- Issues event: 1
- Watch event: 4
- Issue comment event: 1
- Push event: 2
Last Year
- Issues event: 1
- Watch event: 4
- Issue comment event: 1
- Push event: 2
Dependencies
- backports.lzma *
- bitarray *
- brotli *
- cython *
- numba *
- numpy *
- requests >=2.20.0
- zopfli *
- zstd *
- backports.lzma ==0.0.14
- bitarray ==0.9.3
- brotli ==1.0.7
- certifi ==2020.12.5
- chardet ==3.0.4
- cython ==0.29.10
- enum34 ==1.1.10
- funcsigs ==1.0.2
- idna ==2.8
- llvmlite ==0.32.1
- numba ==0.44.0
- numpy ==1.16.4
- requests ==2.22.0
- singledispatch ==3.6.1
- six ==1.15.0
- urllib3 ==1.25.8
- zopfli ==0.1.6
- zstd ==1.4.0.0
- numpy *