homology.dim1

This Cython module contains the core algorithms for 1-dimensional topological algorithms. In particular, RCA1 and Ripser for 1-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

• (currently none)

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

intersect_links
rca1	Perform Rips Collapse Algorithm for one-dimensional
reduce_matrix	Reduce the matrix of distances