copyright by Takeki Sudo and Kazushi Ahara, Meiji University, 2018
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 4 dimensional voxel data. The input data format conforms to that of DIPHA and of PERSEUS.
To make an exe file,
% make
To execute CubicalRipser,
% CR4 [option] [input_filename]
--help
print options
--format
use the specified file format for the input. Options are:
dipha (voxel data in DIPHA file format; default
perseus (voxel 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 CR4
outputs a CSV file. Otherwise, output file is DIPHA diagram file.
--print
print persistence pairs on your console.
In 2 and 3 dimensional case, we believe that CubicalRipser is much faster than DIPHA.