Py-GraSPI Documentation

Welcome to the documentation for Py-GraSPI.

About

Py-GraSPI (Graph-based Structure Property Identifier) is a Python package designed to compute a comprehensive set of descriptors for segmented microstructures using a graph-based approach. It leverages the igraph library to represent microstructures as graphs, enabling efficient computation of a wide range of descriptors with low computational overhead. Py-GraSPI is the Python implementation of the original GraSPI package, which was developed in C/C++. In addition to descriptor computation, Py-GraSPI offers tools for data conversion across various formats and for post-processing the raw outputs of the graph analysis.

In Brief

The Py-Graspi project provides tools for creating, filtering, and analyzing graphs, with benchmarks for runtime and memory performance.

Contents:

• Functionality
• Descriptors
• Inputs
• Installation
  • Simple Usage of Py-Graspi package
  • Manual Installation for Py-Graspi source code
  • Jupyter Notebook for Py-Graspi source code
• Example of Usage
  • Getting Started
  • Simple Example Usage
  • Command Line Usage
    • If input file is a .txt
    • If input file is a .graphe
    • Flags for command line functionality
• Graph-based representation of microstructure
• Basic Definitions
• API Overview
  • compute_descriptors()
  • descriptorsToTxt()
  • readDescriptorsFromTxt()
  • printDescriptors()
  • CC_descriptors()
  • shortest_path_descriptors()
  • filterGraph_metavertices()
  • generateGraph()
  • generateGraphAdj()
  • generateGraphGraphe()
  • adjList()
  • graphe_adjList()
  • adjvertexColors()
  • visualize()
  • connectedComponents()
  • filterGraph()
  • filterGraph_metavertices()
  • filterGraph_blue_red()
  • graph_data_class
    • graph_data_class.__init__()
    • graph_data_class.compute_shortest_paths()
• Advanced
  • To Run on DEBUG mode
  • Converting .plt files to .txt files
  • Translate Image File Into Rescaled .txt File
  • Example Visualization
  • 2D & 3D Morphologies Tests
  • Running Py-GraSPI on the Library of Morphologies
  • Tortuosity HeatMap Visualization
  • Jupyter NoteBook to Visualize HeatMap
  • Generate API Documentation
  • Update Py-Pi Package

Authors

• Olga Wodo – University at Buffalo

• Baskar Ganapathysubramanian – Iowa State University

• Jaroslaw Zola – University at Buffalo

Py-GraSPI has been developed collaboratively at the University at Buffalo and Iowa State University:

• Olga Wodo – University at Buffalo

• Baskar Ganapathysubramanian – Iowa State University

• Jaroslaw Zola – University at Buffalo

• Devyani Jivani – University at Buffalo

• Wenqi Zheng – University at Buffalo

• Michael Leung – University at Buffalo

• Kevin Martinez – University at Buffalo

• Jerry Zhou – University at Buffalo

• Qi Pan – University at Buffalo

• Julia Joseph – University at Buffalo

• Laibah Ahmed – University at Buffalo

• Donghwi Seo – University at Buffalo

For questions or inquiries, please contact: Olga Wodo – olgawodo@buffalo.edu