descriptionPersistent homology C++ library; documentation
ownerDmitriy Morozov <>
last changeMon, 27 Nov 2017 10:26:59 -0800
15 months ago Dmitriy Morozov Add CGAL pre-4.11 support back to e/a/alphashapes3d-periodic default tip
15 months ago Dmitriy Morozov Vanessa's fix for e/a/alphashapes3d-periodic for CGAL 4.11
15 months ago Dmitriy Morozov Add Vanessa Robins' periodic alpha shapes 2D code
17 months ago Dmitriy Morozov Add Vanessa Robins' periodic alpha shapes code
19 months ago Dmitriy Morozov Add a note about Dionysus 2 to the docs
19 months ago Dmitriy Morozov Merge
2014-04-27 Dmitriy Morozov Added a practical guide slides and examples to the docs dev
20 months ago Dmitriy Morozov Remove 'hg up tip' from doc/get-build-install.rst
20 months ago Dmitriy Morozov Merge dev into default, to avoid the need for 'hg up tip' after clone
22 months ago Dmitriy Morozov Add LICENSE + LEGAL dev
2016-08-22 Dmitriy Morozov Add register_ptr_to_python to PersistenceDiagram bindings to match changes in Boost.Python dev
2015-10-05 Dmitriy Morozov Fix compilation with Boost 1.58 (load_construct_data_adl error) dev
2015-03-02 Arnur Nigmetov Added executable to compute Wasserstein distance. dev
2013-12-06 Dmitriy Morozov Disabled glibcxx specific concept checks dev
2013-12-06 Dmitriy Morozov Dave Millman's fix for and rlog problem dev
2013-10-16 Dmitriy Morozov Increase template depth to fix a bug with XCode 5 dev
2013-08-09 Dmitriy Morozov Brit Fasy's fix to compile with logging=on dev
2013-07-10 Dmitriy Morozov output infinite pairs + small bugfix dev
2013-06-10 Dmitriy Morozov Fixed non-POD array problem in homology-zigzags dev
2013-06-10 Dmitriy Morozov Added homology zigzags by Steve Oudot and Don Sheehy dev
2013-04-26 Dmitriy Morozov Added standalone bottleneck-distance.cpp dev
2013-02-28 Dmitriy Morozov Dave Millman's fixes to compile with LLVM-based compilers dev
2012-10-26 Dmitriy Morozov Added CGAL_USE_FILE + added option use_cgal dev
2012-06-10 Dmitriy Morozov Bug in show_diagram() with empty diagrams dev
2012-06-10 Dmitriy Morozov subcomplex in show_complex() + pan/zoom in ComplexViewer2D dev
2012-06-09 Dmitriy Morozov DiagramViewer can show multiple diagrams at once dev
2012-06-09 Dmitriy Morozov CohomologyPersistence returns dying cocycles + StaticCohomologyPersistence records them and normalizes coefficients + minor changes dev
2012-06-08 Dmitriy Morozov Display lists in ComplexViewer3D + circular.smooth() raises exceptions dev
2012-06-07 Dmitriy Morozov Set center and radius in ComplexViewer3D dev
2012-06-07 Dmitriy Morozov Points at infinity in DiagramViewer dev
2012-06-07 Dmitriy Morozov Fixed scale points in the diagram + noise filtering dev
2012-06-07 Dmitriy Morozov Added pan + zoom to diagram viewer; show_diagram() didn't return; added PyQt, PyOpenGL, NumPy as dependencies in the docs dev
2012-06-07 Dmitriy Morozov Straightened out QApplication problems (made it global) dev
2012-06-07 Dmitriy Morozov Started show_complex_3D() dev
2012-06-06 Dmitriy Morozov Fixed bugs in and + added coloring of points in show_complex_2D(); Filtration can be initialized from iterator without comparison dev
2012-06-05 Dmitriy Morozov Added viewer.show_complex_2D + center points in the persistence diagram dev
2012-06-05 Dmitriy Morozov Moved dionysus.circular into its own subdirectory + added dionysus.viewer dev
2012-06-05 Dmitriy Morozov Added docs for StaticCohomologyPersistence + ImagePersistence + circular.smooth + minor fixes in dev
2012-06-04 Dmitriy Morozov Added smooth() to Python binding + fixed a bug in dev
2012-06-03 Dmitriy Morozov Merged upstream dev
2012-06-03 Dmitriy Morozov Added adaptor for StaticCohomologyPersistence and ImagePersistence dev
2012-05-14 Dmitriy Morozov Added a note about reducing matrix Z in i/t/zigzag-persistence.hpp dev
2012-05-11 Dmitriy Morozov Merge dev
2012-05-11 Dmitriy Morozov Added store_negative argument to StaticPersistence.pair_simpices() dev
2012-05-10 Dmitriy Morozov Added a note about wasserstein_distance() to documentation + cleaned up docs for init_diagrams() dev
2012-05-10 Dmitriy Morozov Inlcuded munkres.cpp from munkres.h + matrix.cpp -> matrix.hpp dev
2012-05-10 Dmitriy Morozov Added wasserstein_distance() dev
2012-05-10 Dmitriy Morozov Exposed init_diagrams() to Python dev
2012-05-08 Dmitriy Morozov Minor changes to compile with GCC 4.7 dev
2011-07-25 Dmitriy Morozov Added cohomology/candidates counter to i/t/cohomology-persistence.hpp dev
2011-05-06 Dmitriy Morozov Minor fixes in tools/draw-diagram dev
2011-04-05 Dmitriy Morozov alphashapes2d can handle degenerate inputs (thanks to Taras Galkovskyi for the bug report and the fix) dev
2011-01-28 Dmitriy Morozov Fixed combinations in closure() for older versions of Python dev
2011-01-07 Dmitriy Morozov closure() in Python can handle simplex data dev
2010-12-20 Dmitriy Morozov Fixed a typo in b/p/persistence-diagram.cpp dev
2010-12-08 Dmitriy Morozov Added a note about GPL to the documentation dev
2010-12-03 Dmitriy Morozov Cleaned up CMake files to play nice with CGAL dev
2010-10-09 Dmitriy Morozov Cleaned up PersistenceDiagram bindings dev
2010-10-04 Dmitriy Morozov Fixed a link to SYNAPS dev
2010-09-14 Dmitriy Morozov Merged in Python bindings for DynamicPersistenceChains dev
2010-09-14 Dmitriy Morozov Added documentation for DynamicPersistenceChains dev
2010-09-12 Dmitriy Morozov Added Python bindings for DynamicPersistenceChains dev
2010-09-14 Dmitriy Morozov Added the ability to pickle Simplex class in Python dev
2010-09-14 Dmitriy Morozov Added ability to iterate over ZigzagPersistence cycles in Python dev
2010-09-10 Dmitriy Morozov Fixed a typo in the documentation of SPNode.cycle dev
2010-09-07 Dmitriy Morozov Added Python closure function (for computing a k-skeleton of a closure of a list of simplices) dev
2010-09-02 Dmitriy Morozov Removed the unnecessary typename in filtration-homology.cpp dev
2010-08-30 Dmitriy Morozov Added output of essential cycles for any given input filtration dev
2010-08-25 Dmitriy Morozov Minor touches in documentation dev
2010-08-25 Dmitriy Morozov Merged docs with upstream dev
2010-07-15 Dmitriy Morozov CGAL is unncessary for vineyards (update in the documentation) dev
2010-08-25 Dmitriy Morozov Merged in Aravind's changes dev
2010-08-18 Aravindakshan Babu Changed the first iterator of PersistenceDiagram to accept dimension as well. Modified documentation. dev
2010-08-18 Aravindakshan Babu Removed the points iterator in PersistenceDaigram; replaced it with a __iter__ method. dev
2010-08-17 Aravindakshan Babu Added documentation for the python classes Point and PersistenceDiagram. Removed the __sub__ method for PersistenceDiagram. Minor renaming. dev
2010-08-11 Aravindakshan Babu Added a __iter__ method to the PersistenceDiagram class in python. Renamed the points iterator to the intervals iterator. dev
2010-07-08 Aravindakshan Babu Added extra functionality to Point class( an iterator ) and PersistenceDiagram( dimension property and __len__ func ). dev
2010-07-02 Aravindakshan Babu Made the data argument in Point's __init__method to be an optional argument by making it a boost::python::optional. dev
2010-07-02 Aravindakshan Babu Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python. dev
2010-07-15 Dmitriy Morozov Merged docs with upstream dev
2010-07-15 Dmitriy Morozov Removed the warning about compiler versions (seems unnecessary after Andrew's fixes) dev
2010-07-12 Dmitriy Morozov Fixed path for dev
2010-07-05 Dmitriy Morozov Bug in the tutorial: simplices = [] -> simplices = Filtration() dev
2010-04-13 Dmitriy Morozov More typos in the docs dev
2010-04-12 Dmitriy Morozov Fixed a link: dionysis -> dionysus dev
2010-04-20 Dmitriy Morozov Andrew Yarmola's fix to the in-class intialization syntax in OrderList<T> dev
2010-03-09 Dmitriy Morozov Added Persistence::initialize(f) + fixed minor bug LinearKernel::sign_at_negative_infinity() dev
2010-03-06 Dmitriy Morozov Added insert-at-the-end optimization for CohomologyPersistence::add_cocycle() dev
2010-03-05 Dmitriy Morozov Count cocycles in CohomologyPersistence dev
2010-02-23 Mikael Vejdemo Johansson Andrew Yarmola's compilation fix for MacOSX. dev
2010-02-22 Dmitriy Morozov Removed unused instrumentation of cohomology and unnecessary includes dev
2010-02-09 Dmitriy Morozov Removed reference to reference in ThreeOutcomeComparison dev
2010-02-07 Dmitriy Morozov Made EventQueue into a binary heap (for efficiency and sanity) dev
2010-02-07 Dmitriy Morozov Replaced list with multi_index representation in EventQueue making it more efficient dev
2010-02-06 Dmitriy Morozov Switched to internal KineticSort dev
2010-02-05 Dmitriy Morozov Added linear kernel for my own KineticSort dev
2010-02-05 Dmitriy Morozov Commented out QField to get rid of the artifical dependence on GMP dev
2010-02-04 Dmitriy Morozov Fixed non-copyable temporary bug dev
2010-02-03 Dmitriy Morozov Fixed the duplicates (degeneracy) and another assertion problem in LSVineyard dev
2010-02-03 Dmitriy Morozov Removed a buggy assertion in LSVineard::transpose_vertices() (j points at the end() when moving the last simplex of the filtration) dev
2010-02-02 Dmitriy Morozov StaticPersistence::pair_simplices() has an option to not display progress (LSVineyard uses it during consistency checking) dev
2010-01-26 Dmitriy Morozov Added rips-explicit-cohomology dev
2010-01-26 Dmitriy Morozov Moved into examples/pl-functions + added example (cubical lower-star filtration) dev
2010-01-12 Dmitriy Morozov Fixed Python constructor of CohomologyPersistence + minor changes to dev
2010-01-11 Dmitriy Morozov vertex_coface -> vertex_cofaces in Rips documentation (in Python) dev
2010-01-09 Dmitriy Morozov Henry Adams' fixes to python/dionysus/ + added CohomologyPersistence.show_cocycles method dev
2010-01-07 Dmitriy Morozov CohomologyPersistence::add returns the dying cocycle dev
2010-01-05 Dmitriy Morozov Check Boost version in include/utilities/property-maps.h + minor changes to dev
2009-12-31 Dmitriy Morozov Added pl-vineyard documentation dev
2009-12-25 Dmitriy Morozov Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea: dev
2009-12-20 Dmitriy Morozov Moved files around: lsvineyard.h -> include/topology, examples/grid -> examples/pl-functions dev
2009-12-20 Dmitriy Morozov Merged Vineyards code changes with the main development line dev
2009-12-20 Dmitriy Morozov Python bindings work again dev
2009-12-16 Dmitriy Morozov Created pl-vineyard.cpp to compute vineyards given a complex and a sequence of values at each vertex dev
2009-12-16 Dmitriy Morozov Resurrected vineyard code: dev
2009-12-03 Dmitriy Morozov Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again dev
2009-12-02 Dmitriy Morozov StaticPersistence operates on chains consisting of only positive simplices dev
2009-12-01 Dmitriy Morozov alphashapes3d.cpp measures persistence time dev
2009-11-28 Dmitriy Morozov Fixed DynamicPersistenceTrails::PairingTrailsVisitor to match the changes in StaticPersistence::PairVisitor dev
2009-11-28 Dmitriy Morozov Instrumented code for counting: dev
2009-11-06 Dmitriy Morozov Added arbitrary coefficients in boundaries (to C++ and Python) + cleaned up CohomologyPersistence.add overloading in Python dev
2009-10-28 Dmitriy Morozov Added image persistence functionality to CohomologyPersistence dev
2009-10-23 Dmitriy Morozov Added under tools/draw-diagram dev
2009-10-23 Dmitriy Morozov Added link to CVXOPT in get-build-install documentation + progress bar to rips-pairwise-cohomology dev
2009-10-20 Dmitriy Morozov Fixed a typo in documentation + added a warning and a tip about GCC 4.2 on a Mac dev
2009-08-31 mridul The if-else cases in were not exhaustive. They become exhaustive by changing ab > aa to ab >= aa. dev
2009-08-31 Dmitriy Morozov Removed Qt4 requirement + added link to download and tutorial to the front page of the documentation dev
2009-08-21 Dmitriy Morozov Exposed store argument to CohomologyPersistence.add() in Python dev
2009-08-19 Dmitriy Morozov uses vertex list, and does not make any assumptions about the vertex-simplex order dev
2009-08-13 Dmitriy Morozov Consistency zigzag outputs intervals supported over a single complex dev
2009-08-12 Camille Wormser explicitely converts a Dimension (short int) into a size_t, for removing a warning dev
2009-08-12 Camille Wormser Removing unused parameter names in order to avoid warnings dev
2009-08-12 Dmitriy Morozov doesn't output the union, rips-consistency-zigzag.cpp fixed show_progress dev
2009-08-10 Dmitriy Morozov Fixed bugs in introduced when was originally added dev
2009-08-10 Dmitriy Morozov Fixed bugs in whose origin is unclear to me dev
2009-08-04 Dmitriy Morozov Merged in Chris' changes dev
2009-08-04 Christos Mantoulidis Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage. dev
2009-08-04 Christos Mantoulidis Changed implementation of WeightedRips to store simplex values (max distance between simplices' vertices) as an invisible layer on top of each simplex object, so that the data() field of WeightedRips has been freed for use by the users again. dev
2009-07-28 Christos Mantoulidis Added rips-weighted-cohomology, and channeled WeightedRips logging to the same channel as Rips dev
2009-07-28 Christos Mantoulidis Merged upstream dev
2009-07-28 Christos Mantoulidis Modified WeightedRips::generate() to incorporate the simplex-appearance-value computation (before it would have to be done explicitly by the user by a for-loop after the call to generate()) dev
2009-07-27 Christos Mantoulidis added logging to WeightedRips (still needs debugging) dev
2009-07-13 Christos Mantoulidis Updated weighted rips libraries to make use of OOP--now WeightedRips inherits from Rips. It is possible that logging for WeightedRips does not work. dev
2009-07-02 Christos Mantoulidis Added weighted rips code and libraries dev
2009-08-04 Dmitriy Morozov Simplices are deleted from the complex after removal in + touched up documentation (to mention CohomologyPersistence better) dev
2009-07-28 Dmitriy Morozov Consistency zigzag outputs intervals for dimensions less than the skeleton dimension only dev
2009-07-30 Dmitriy Morozov Switched PairwiseDistances in Python bindings to C++ dev
2009-07-30 Dmitriy Morozov Added Python bindings for CohomologyPersistence (+ example + documentation) dev
2009-07-24 Dmitriy Morozov Minor changes in + wrapped into a main() function dev
2009-06-17 Dmitriy Morozov Disable alphashapes in Python bindings if no CGAL dev
2009-05-17 Dmitriy Morozov Made ListRandomAccessIterator generic with respect to value, and moved it to utils.h dev
2009-07-24 Dmitriy Morozov Cleaner output in rips-pairwise.cpp + added + added dev
2009-07-09 Dmitriy Morozov Fixed in tools/plot-values dev
2009-05-14 Dmitriy Morozov In documentation put contents into sidebar dev
2009-07-09 Dmitriy Morozov Documentation for parametrization using persistent cohomology dev
2009-07-09 Dmitriy Morozov Rips pairwise cohomology produces output necessary for 1-cocycle parametrization dev
2009-07-09 Dmitriy Morozov Added field arithmetic to CohomologyPersistence (Zp + Q) dev
2009-05-14 Dmitriy Morozov Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h dev
2009-05-14 Dmitriy Morozov read_points() does not need ambient dimension and ignores lines starting with '#' dev
2009-05-11 Dmitriy Morozov Added documentation; for now mostly for the Python bindings dev
2009-05-07 Dmitriy Morozov Touch up to compile with GCC 4.4 dev
2009-04-29 Dmitriy Morozov Cleaned up simplex comparison functions, outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags dev
2009-04-16 Dmitriy Morozov Alphashapes and Python bindings dev
2009-04-15 Dmitriy Morozov Placed all Python bindings code into dionysus::python namespace dev
2009-04-14 Dmitriy Morozov Cleaned up Python bindings to restore functionality: dev
2009-04-13 Dmitriy Morozov Renamed header files in bindings/python to get rid of the "python-" prefix dev
2009-04-13 Dmitriy Morozov Changes in Python Bindings: dev
2009-04-11 Dmitriy Morozov Added Python bindings for the Rips complex + an example dev
2009-05-01 Dmitriy Morozov Cleaned up traits (chain and container) for static- and dynamic-persistence dev
2009-05-01 Dmitriy Morozov Added tools/extract-diagram + minor fixes dev
2009-04-10 Dmitriy Morozov Added intrusive containers issue and issue filters dev
2009-04-09 Dmitriy Morozov Moved l2distance.h into include/geometry dev
2009-04-09 Dmitriy Morozov Added categories to some of the issues dev
2009-04-09 Dmitriy Morozov Fixed distance to diagonal calculation + added stand-alone bottleneck distance tool dev
2009-03-25 Dmitriy Morozov Added ZigzagPersistence::is_alive() + consistency zigzag outputs betti 1 at each stage dev
2009-03-24 Dmitriy Morozov Added consistency zigzag dev
2009-03-23 Dmitriy Morozov Merged in cohomology branch dev
2009-02-27 Dmitriy Morozov Added CohomologyPersistence and Rips pairwise distances computation dev
2009-03-22 Dmitriy Morozov Added DynamicPersistenceChains (no dynamic part yet) dev
2009-02-03 Dmitriy Morozov Updated Rips zigzags dev
2009-01-31 Dmitriy Morozov Switched Rips complex computation to Bron-Kerbosch algorithm dev
2009-01-29 Dmitriy Morozov Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence) dev
2009-01-28 Dmitriy Morozov Switched to CGAL 3.4 (native CMake configuration): for now only alphashapes dev
2009-01-20 Dmitriy Morozov Implemented ImageZigzagPersistence dev
2009-01-12 Dmitriy Morozov Debugged ZigzagPersistence (having added heavier consistency checking) dev
2009-01-02 Dmitriy Morozov Added rips-zigzag; in the process caught a number of bugs in ZigzagPersistence (added check_consistency() to it) dev
2008-12-31 Dmitriy Morozov Added DequeChains (for ZigzagPersistence) dev
2008-12-31 Dmitriy Morozov Added ZigzagPersistence dev
2008-12-27 Dmitriy Morozov Merged in Python branch dev
2008-12-25 Dmitriy Morozov Initial commit of Python bindings dev
2008-12-25 Dmitriy Morozov Empty is now a template, replaced RecursiveIterator with boost::counting_iterator dev
2008-12-23 Dmitriy Morozov Removed boundary() from AlphaSimplex3D dev
2008-12-23 Dmitriy Morozov Changed Simplex::boundary() to be iterator-based (replaced it with boundary_begin() and boundary_end()) dev
2008-12-27 Dmitriy Morozov Commit before merging in Python branch: dev
2008-12-25 Dmitriy Morozov Initial addition of tools/diagram-viewer dev
2008-12-23 Dmitriy Morozov Closed #8a1 and #96b, added #de6 and #f64 dev
2008-12-18 Dmitriy Morozov Intermediate commit while converting to the new architecture dev
2008-09-22 Dmitriy Morozov Switching README to PanDoc dev
2008-09-22 Dmitriy Morozov Added Rips complex-based distance computation to fitness dev
2008-09-22 Dmitriy Morozov Added ExplicitDistance + Evaluator to Rips complexes dev
15 months ago bc7bd0ac9af6 default
2014-04-27 d3a10e66c6ab dev
2008-03-19 73a54447b54a ar
2008-03-14 7558e122ba4f fitness