homology.dim0

This Cython module contains the core algorithms for 0-dimension topological algorithms. In particular, MergeTree for 0-dimensional persistence.

If a function requires its own explicit iterator in a loop, probably it should go here. Anything that is just a vectorized operation in NumPy or Pandas can go in plain python elsewhere.

See http://docs.cython.org/src/tutorial/np.html for ideas on writing efficient code in Cython.

This module is compiled by either of these commands

• python setup.py install (as called by pip for standard installation and use)
• python setup.py build_ext --inplace (as run by developers for code testing)

Notes

Automatically-generated online documentation will never see the C-only functions that are defined with cdef in Cython, as shown in http://cython.readthedocs.io/en/latest/src/reference/extension_types.html Because of the limitations of Sphinx, you’ll have to simply view the sourcecode for further information. For this module, these C-only functions include

• homology.dim0.root()
• homology.dim0.connected()
• homology.dim0.merge()

Copyright

• This file is part of https://github.com/geomdata/gda-public/
• 2015, 2016, 2017 by Geometric Data Analytics, Inc. (http://geomdata.com)
• AGPL license. See LICENSE or https://github.com/geomdata/gda-public/blob/master/LICENSE

Functions

all_roots	Reference each vertex directly to its representative root, from MergeTree.
mkforestDBL	Make inclusion tree and parentage linked lists by walking across This method is for np.float64 arrays (for indexing speed).
unionfind	Apply the UnionFind algorithm to compute zero-dimensional persistence diagram.