drkostas / tda_examples

Exploratory code on topological data analysis

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TDA Playground

GitHub license

Table of Contents

About

A playground for topological data analysis.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.

Prerequisites

You need to have a machine with Python > 3.6 and any Bash based shell (e.g. zsh) installed.

$ python3.8 -V
Python 3.8.5

$ echo $SHELL
/usr/bin/zsh

Installing, Testing, Building

All the installation steps are being handled by the Makefile:

$ make install

Running the code locally

In order to run the code, you will only need to change the yml file if you need to, and either run its file directly or invoke its console script.

If you don't need to change yml file, skip to Execution Options.

Modifying the Configuration

There are already two configured yml files (confs/default.yml, confs/default_print_only.yml) with the following structure:

tda:
  - config:
      results_folder: res/rips_full_with_polygons_dgm2
      cutoff_min: 0.45
      cutoff_step: 0.1
      cutoff_lim: 7.1
      show_fig: False
      save_fig: True
      create_gif: False
      points:
        - x: 0.0
          y: 0.0
        - x: 0.0
          y: 1.0
        - x: 1.0
          y: 0.0
        - x: 1.0
          y: 1.0
        - x: 4.0
          y: 4.0
        - x: 4.0
          y: 5.414213562373095
        - x: 5.414213562373095
          y: 4.0
        - x: 5.414213562373095
          y: 5.414213562373095
    type: rips

Execution Options

First, make sure you are in the correct virtual environment:

$ conda activate tda_playground

$ which python
/home/drkostas/anaconda3/envs/tda_playground/bin/python

TDA Playground play.py

Now, in order to run the code you can either call the main.py directly, or invoke the tda_playground_main console script.

$ python tda_playground/play.py --help

For example:

$ python tda_playground/play.py -c confs/default.yml -l logs/default.log

TDA Playground Jupyter

Run:

$ jupyter notebook

And open playground.ipynb

TODO

Read the TODO to see the current task list.

License

This project is licensed under the MIT License - see the LICENSE file for details.

About

Exploratory code on topological data analysis


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Language:HTML 48.7%Language:Jupyter Notebook 42.9%Language:Python 6.6%Language:Cython 1.6%Language:Makefile 0.1%