cubicalripser / cubicalripser_2dim

calculator of persistence pair for 2 dimensional pixel data

CubicalRipser_2dim : calculator of persistence pair for 2 dimensional pixel data

copyright by Takeki Sudo and Kazushi Ahara, Meiji University, 2018

description

C++ system for computation of Cubical persistence pairs Copyright 2018 Takeki Sudo and Kazushi Ahara, Meiji University. CubicalRipser is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CubicalRipser is deeply depending on 'Ripser', software for Vietoris-Rips persitence pairs by Ulrich Bauer, 2015-2016. We appreciate Ulrich very much. We rearrange his codes of Ripser and add some new ideas for optimization on it and modify it for calculation of a Cubical filtration. This part of CubicalRiper is a calculator of cubical persistence pairs for 2 dimensional pixel data. The input data format conforms to that of DIPHA and of PERSEUS.

how to make and execute

To make an exe file,

% make

To execute CubicalRipser,

% CR2 [option] [input_filename]

option:

--help   

   print options

--format     

    use the specified file format for the input. Options are:
  
    dipha          (pixel data in DIPHA file format; default
   
    perseus        (pixel data in Perseus file format)

--threshold <t>  

    compute cubical complexes up to birth time <t>

--method 

    method to compute the persistent homology of the cubical complexes. Options are:

        link_find      (calculating the 0-dim PP, use 'link_find' algorithm; default)

        compute_pairs  (calculating the 0-dim PP, use 'compute_pairs' algorithm)

--output [output_filename] 

    name of file that will contain the persistence diagram. If the input_filename ends '.csv' then CR2 
outputs a CSV file. Otherwise, output file is DIPHA diagram file.

--print

    print persistence pairs on your console.

about speed

In 2 and 3 dimensional case, we believe that CubicalRipser is much faster than DIPHA.

cubicalripser_2dim's Issues

Python Bindings

Hello,

I have created Python bindings for your CubicalRipser_2dim algorithm. I only had to make small changes to the main file, but if you would like to add this to your current code, I can fork the repository, add my changes and then issue a PR.