appliedtopology / tda4j

TDA library for the JVM

TDA4j

Persistent Homology and Topological Data Analysis Library

The TDA4j library implements persistent homology and related techniques from computational and applied topology, in a library designed for ease of use, ease of access from Matlab and java-based systems, and ease of extensions for further research projects and approaches.

The library is based on previous libraries from the Computational Topology workgroup at Stanford University.

For persistent homology and its capabilities, we recommend the survey article Topology and Data by Gunnar Carlsson.

tda4j's Issues

Create PH Algorithms Class and Functions

Creation of Chain.kts

refer to Edelsbrunner and INTRODUCTION TO SIMPLICIAL COMPLEXES

Note: Full implementation is done when SortedMaps is done.

Create A Sorted Map Class

Leverage Kotlin's stdlib kotlin.collections.Map. to create SortedMap. We will also use TDA4j kotlin branch's Sets.kts SortedSet implementation.

Error message: PH of ExplicitSimplexStream before finalizeStream() has been called

When one builds an ExplicitSimplexStream but forgets to call finalizeStream() before computing persistent homology, then sometimes the results are nonsense but no error message is thrown. It'd be nice the the user instead received an error that they can't compute homology before calling finalizeStream()

Remove `Plex4`

We still have the masterclass api.Plex4 containing interface functions built with Matlab in mind. This class should probably be renamed -- but doing so means updating ALL the Matlab files.

Finish and sanity-check namechange

I have done search/replace to change out of a edu.stanford namespace into an org.appliedtopology namespace. Nevertheless, I have not checked everything.

Create Matlab-friendly classes

It would be nice to have a collection of classes that basically just inherit good default choices of things from basically all classes in circulation, so that we might have, say, tda4j.matlab.BarcodeCollection and tda4j.matlab.VietorisRipsStream that do not actually require parametrizations and thus should work out of the box from Matlab.

Error in adding vertices to an `AbstractSimplex`

The current implementation of the Simplex functionality has an error, whereby the following code fails to behave as expected:

val s = Simplex(1,2,3)
(s + 4).contains(4)

This is documented in the test suite, which now fails two different tests based on this: both

tda4j/src/test/scala/org/appliedtopology/tda4j/SimplexSpec.scala

Line 37 in b8f2a02

sAdd4.contains(4) must beTrue

and

tda4j/src/test/scala/org/appliedtopology/tda4j/SimplexSpec.scala

Line 34 in b8f2a02

s.boundary() must contain(Simplex(1, 2), Simplex(1, 3), Simplex(2, 3))

fail currently.

The boundary test fails because the construction of simplices includes using the AbstractSimplex.incl method to add elements to the simplex object.

kotlinOptions.jvmTarget should be set to 19 in kotlin branch

Causing problems creating build of project & merging with other branches

Port HomologySpec.kts to Scala