Higra: Hierarchical Graph Analysis
Higra is a C++/Python library for efficient sparse graph analysis with a special focus on hierarchical methods. Some of the main features are:
- efficient methods and data structures to handle the dual representations of hierarchical clustering: trees (dendrograms) and saliency maps (ultrametric distances);
- hierarchical clusterings: quasi-flat zone hierarchy, hierarchical watersheds, agglomerative clustering (single-linkage, average-linkage, complete-linkage, exponential-linkage, Ward, or user provided linkage rule), constrained connectivity hierarchy;
- component trees: min and max trees;
- manipulate and explore hierarchies: simplification, accumulators, cluster extraction, various attributes (size, volume, dynamics, perimeter, compactness, moments, etc.), horizontal and non-horizontal cuts, hierarchies alignment;
- optimization on hierarchies: optimal cuts, energy hierarchies;
- algorithms on graphs: accumulators, vertices and clusters dissimilarities, region adjacency graphs, minimum spanning trees and forests, watershed cuts;
- assessment: supervised assessment of graph clusterings and hierarchical clusterings;
- image toolbox: special methods for grid graphs, tree of shapes, hierarchical clustering methods dedicated to image analysis, optimization of Mumford-Shah energy.
Higra is thought for modularity, performance and seamless integration with classical data analysis pipelines. The data structures (graphs and trees) are decoupled from data (vertex and edge weights ) which are simply arrays (xtensor arrays in C++ and numpy arrays in Python).
Installation
The Python package can be installed with Pypi:
pip install higra
Supported systems:
- Python 3.10, 3.11, 3.12, 3.13, 3.14
- Linux 64 bits (x86_64), macOS (x86_64 & ARM), Windows 64 bits (x86_64) (requires Visual C++ Redistributable for Visual Studio 2015)
Documentation
Demonstration and tutorials
A collection of demonstration notebooks is available in the documentation. Notebooks are stored in a dedicated repository Higra-Notebooks.
Code samples
This example demonstrates the construction of a single-linkage hierarchical clustering and its simplification by a cluster size criterion.
This example demonstrates the use of hierarchical clustering for image filtering.
Developing C++ extensions
While Higra provides many vectorized operators to implement algorithms efficiently in Python, it is possible that some operations cannot be done efficiently in Python. In such case, the Higra-cppextension-cookiecutter enables to easily setup and generate c++ extension using Higra with Python bindings.
License and how-to cite
The license Cecill-B is fully compatible with BSD-like licenses (BSD, X11, MIT) with an attribution requirement.
The recommended way to give attribution is by citing the following presentation article:
B. Perret, G. Chierchia, J. Cousty, S.J. F. Guimarães, Y. Kenmochi, L. Najman, Higra: Hierarchical Graph Analysis, SoftwareX, Volume 10, 2019. DOI: 10.1016/j.softx.2019.100335
Bibtex
@article{PCCGKN:softwarex2019,
title = "Higra: Hierarchical Graph Analysis",
journal = "SoftwareX",
volume = "10",
pages = "1--6",
year = "2019",
issn = "2352-7110",
doi = "10.1016/j.softx.2019.100335",
author = "B. Perret and G. Chierchia and J. Cousty and S.J. F. Guimar\~{a}es and Y. Kenmochi and L. Najman",
}
Third-party libraries
Higra bundles several third-party libraries (inside the lib folder):
- pybind11 helps to create Python bindings of c++ methods and classes - BSD-style license
- xtensor (with xtl, xsimd, and xtensor-python provides
numpylike arrays for c++ with seamless integration with Python - all under the BSD-3-Clause license - Catch2 is a unit test framework - Boost Software License 1.0
1 maintainer
Release files for higra 0.6.13
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 162.2 MB
Release files / higra-0.6.13-cp314-cp314t-win_amd64.whl
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Release files / higra-0.6.13-cp314-cp314-win_amd64.whl
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Release files / higra-0.6.13-cp314-cp314-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
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Release files / higra-0.6.13-cp314-cp314-macosx_11_0_arm64.whl
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| Download URL | higra-0.6.13-cp310-cp310-win_amd64.whl |
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