2014-04-27Added a practical guide slides and examples to the docs dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 27 Apr 2014 13:49:14 -0700] rev 287
Added a practical guide slides and examples to the docs

17 months agoRemove 'hg up tip' from doc/get-build-install.rst
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 27 Jun 2017 09:38:20 -0700] rev 286
Remove 'hg up tip' from doc/get-build-install.rst

17 months agoMerge dev into default, to avoid the need for 'hg up tip' after clone
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 27 Jun 2017 09:37:05 -0700] rev 285
Merge dev into default, to avoid the need for 'hg up tip' after clone

20 months agoAdd LICENSE + LEGAL dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 16 Apr 2017 13:35:24 -0700] rev 284
Add LICENSE + LEGAL

2016-08-22Add register_ptr_to_python to PersistenceDiagram bindings to match changes in Boost.Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 22 Aug 2016 11:17:45 -0700] rev 283
Add register_ptr_to_python to PersistenceDiagram bindings to match changes in Boost.Python

2015-10-05Fix compilation with Boost 1.58 (load_construct_data_adl error) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 05 Oct 2015 09:02:38 -0700] rev 282
Fix compilation with Boost 1.58 (load_construct_data_adl error)

2015-03-02Added executable to compute Wasserstein distance. dev
"Arnur Nigmetov <a.nigmetov@gmail.com>" [Mon, 02 Mar 2015 13:20:51 +0100] rev 281
Added executable to compute Wasserstein distance.

Powering to 1/q is done in output. Maybe, should be changed in the
function itself?

2013-12-06Disabled glibcxx specific concept checks dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 06 Dec 2013 19:09:12 -0800] rev 280
Disabled glibcxx specific concept checks

2013-12-06Dave Millman's fix for and rlog problem dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 06 Dec 2013 19:02:42 -0800] rev 279
Dave Millman's fix for and rlog problem

2013-10-16Increase template depth to fix a bug with XCode 5 dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 16 Oct 2013 09:58:02 -0700] rev 278
Increase template depth to fix a bug with XCode 5

2013-08-09Brit Fasy's fix to compile with logging=on dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 09 Aug 2013 15:08:23 -0700] rev 277
Brit Fasy's fix to compile with logging=on

2013-07-10lscubes.py output infinite pairs + small bugfix dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 10 Jul 2013 14:39:29 -0700] rev 276
lscubes.py output infinite pairs + small bugfix

2013-06-10Fixed non-POD array problem in homology-zigzags dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 10 Jun 2013 17:25:57 +0200] rev 275
Fixed non-POD array problem in homology-zigzags

2013-06-10Added homology zigzags by Steve Oudot and Don Sheehy dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 10 Jun 2013 16:58:01 +0200] rev 274
Added homology zigzags by Steve Oudot and Don Sheehy

2013-04-26Added standalone bottleneck-distance.cpp dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 26 Apr 2013 22:31:58 -0700] rev 273
Added standalone bottleneck-distance.cpp

2013-02-28Dave Millman's fixes to compile with LLVM-based compilers dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 28 Feb 2013 11:12:02 +0800] rev 272
Dave Millman's fixes to compile with LLVM-based compilers

2012-10-26Added CGAL_USE_FILE + added option use_cgal dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 26 Oct 2012 11:45:58 -0700] rev 271
Added CGAL_USE_FILE + added option use_cgal

2012-06-10Bug in show_diagram() with empty diagrams dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 10 Jun 2012 18:54:26 -0700] rev 270
Bug in show_diagram() with empty diagrams

2012-06-10subcomplex in show_complex() + pan/zoom in ComplexViewer2D dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 10 Jun 2012 11:26:38 -0700] rev 269
subcomplex in show_complex() + pan/zoom in ComplexViewer2D

2012-06-09DiagramViewer can show multiple diagrams at once dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 09 Jun 2012 12:56:36 -0700] rev 268
DiagramViewer can show multiple diagrams at once

2012-06-09CohomologyPersistence returns dying cocycles + StaticCohomologyPersistence records them and normalizes coefficients + minor changes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 09 Jun 2012 12:17:17 -0700] rev 267
CohomologyPersistence returns dying cocycles + StaticCohomologyPersistence records them and normalizes coefficients + minor changes

2012-06-08Display lists in ComplexViewer3D + circular.smooth() raises exceptions dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 08 Jun 2012 15:40:09 -0700] rev 266
Display lists in ComplexViewer3D + circular.smooth() raises exceptions

2012-06-07Set center and radius in ComplexViewer3D dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 21:36:53 -0700] rev 265
Set center and radius in ComplexViewer3D

2012-06-07Points at infinity in DiagramViewer dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 21:21:11 -0700] rev 264
Points at infinity in DiagramViewer

2012-06-07Fixed scale points in the diagram + noise filtering dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 21:16:06 -0700] rev 263
Fixed scale points in the diagram + noise filtering

2012-06-07Added pan + zoom to diagram viewer; show_diagram() didn't return; added PyQt, PyOpenGL, NumPy as dependencies in the docs dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 11:57:33 -0700] rev 262
Added pan + zoom to diagram viewer; show_diagram() didn't return; added PyQt, PyOpenGL, NumPy as dependencies in the docs

2012-06-07Straightened out QApplication problems (made it global) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 10:52:15 -0700] rev 261
Straightened out QApplication problems (made it global)

2012-06-07Started show_complex_3D() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 10:11:01 -0700] rev 260
Started show_complex_3D()

2012-06-06Fixed bugs in diagram.py and adaptor.py + added coloring of points in show_complex_2D(); Filtration can be initialized from iterator without comparison dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 06 Jun 2012 23:15:57 -0700] rev 259
Fixed bugs in diagram.py and adaptor.py + added coloring of points in show_complex_2D(); Filtration can be initialized from iterator without comparison

2012-06-05Added viewer.show_complex_2D + center points in the persistence diagram dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 05 Jun 2012 17:53:08 -0700] rev 258
Added viewer.show_complex_2D + center points in the persistence diagram

2012-06-05Moved dionysus.circular into its own subdirectory + added dionysus.viewer dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 05 Jun 2012 17:04:10 -0700] rev 257
Moved dionysus.circular into its own subdirectory + added dionysus.viewer

2012-06-05Added docs for StaticCohomologyPersistence + ImagePersistence + circular.smooth + minor fixes in adaptor.py dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 05 Jun 2012 14:50:58 -0700] rev 256
Added docs for StaticCohomologyPersistence + ImagePersistence + circular.smooth + minor fixes in adaptor.py

2012-06-04Added smooth() to Python binding + fixed a bug in adaptor.py dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 04 Jun 2012 09:05:45 -0700] rev 255
Added smooth() to Python binding + fixed a bug in adaptor.py

2012-06-03Merged upstream dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 03 Jun 2012 16:39:18 -0700] rev 254
Merged upstream

2012-06-03Added adaptor for StaticCohomologyPersistence and ImagePersistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 03 Jun 2012 16:17:27 -0700] rev 253
Added adaptor for StaticCohomologyPersistence and ImagePersistence

2012-05-14Added a note about reducing matrix Z in i/t/zigzag-persistence.hpp dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 14 May 2012 10:47:46 -0700] rev 252
Added a note about reducing matrix Z in i/t/zigzag-persistence.hpp

2012-05-11Merge dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 11 May 2012 17:06:55 -0700] rev 251
Merge

2012-05-11Added store_negative argument to StaticPersistence.pair_simpices() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 11 May 2012 10:25:57 -0700] rev 250
Added store_negative argument to StaticPersistence.pair_simpices()

2012-05-10Added a note about wasserstein_distance() to documentation + cleaned up docs for init_diagrams() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 10 May 2012 15:52:53 -0700] rev 249
Added a note about wasserstein_distance() to documentation + cleaned up docs for init_diagrams()

2012-05-10Inlcuded munkres.cpp from munkres.h + matrix.cpp -> matrix.hpp dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 10 May 2012 15:46:52 -0700] rev 248
Inlcuded munkres.cpp from munkres.h + matrix.cpp -> matrix.hpp

2012-05-10Added wasserstein_distance() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 10 May 2012 15:42:21 -0700] rev 247
Added wasserstein_distance()

2012-05-10Exposed init_diagrams() to Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 10 May 2012 14:24:40 -0700] rev 246
Exposed init_diagrams() to Python

2012-05-08Minor changes to compile with GCC 4.7 dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 08 May 2012 13:07:28 -0700] rev 245
Minor changes to compile with GCC 4.7

2011-07-25Added cohomology/candidates counter to i/t/cohomology-persistence.hpp dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 25 Jul 2011 23:21:29 -0700] rev 244
Added cohomology/candidates counter to i/t/cohomology-persistence.hpp

2011-05-06Minor fixes in tools/draw-diagram dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 06 May 2011 10:38:06 -0700] rev 243
Minor fixes in tools/draw-diagram

2011-04-05alphashapes2d can handle degenerate inputs (thanks to Taras Galkovskyi for the bug report and the fix) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 05 Apr 2011 18:29:50 -0700] rev 242
alphashapes2d can handle degenerate inputs (thanks to Taras Galkovskyi for the bug report and the fix)

2011-01-28Fixed combinations in closure() for older versions of Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 28 Jan 2011 08:01:37 -0800] rev 241
Fixed combinations in closure() for older versions of Python

2011-01-07closure() in Python can handle simplex data dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 07 Jan 2011 23:11:46 -0800] rev 240
closure() in Python can handle simplex data

2010-12-20Fixed a typo in b/p/persistence-diagram.cpp dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 20 Dec 2010 11:21:57 -0800] rev 239
Fixed a typo in b/p/persistence-diagram.cpp

2010-12-08Added a note about GPL to the documentation dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 08 Dec 2010 10:29:26 -0800] rev 238
Added a note about GPL to the documentation

2010-12-03Cleaned up CMake files to play nice with CGAL dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 03 Dec 2010 11:26:12 -0800] rev 237
Cleaned up CMake files to play nice with CGAL

2010-10-09Cleaned up PersistenceDiagram bindings dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 09 Oct 2010 13:56:26 -0700] rev 236
Cleaned up PersistenceDiagram bindings

2010-10-04Fixed a link to SYNAPS dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 04 Oct 2010 18:03:35 -0700] rev 235
Fixed a link to SYNAPS

2010-09-14Merged in Python bindings for DynamicPersistenceChains dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 15:36:13 -0700] rev 234
Merged in Python bindings for DynamicPersistenceChains

2010-09-14Added documentation for DynamicPersistenceChains dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 15:00:34 -0700] rev 233
Added documentation for DynamicPersistenceChains

2010-09-12Added Python bindings for DynamicPersistenceChains dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 12 Sep 2010 09:55:44 -0700] rev 232
Added Python bindings for DynamicPersistenceChains

2010-09-14Added the ability to pickle Simplex class in Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 11:34:11 -0700] rev 231
Added the ability to pickle Simplex class in Python

2010-09-14Added ability to iterate over ZigzagPersistence cycles in Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 11:12:33 -0700] rev 230
Added ability to iterate over ZigzagPersistence cycles in Python

2010-09-10Fixed a typo in the documentation of SPNode.cycle dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 10 Sep 2010 21:21:27 -0700] rev 229
Fixed a typo in the documentation of SPNode.cycle

2010-09-07Added Python closure function (for computing a k-skeleton of a closure of a list of simplices) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 07 Sep 2010 13:54:53 -0700] rev 228
Added Python closure function (for computing a k-skeleton of a closure of a list of simplices)

2010-09-02Removed the unnecessary typename in filtration-homology.cpp dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 02 Sep 2010 09:13:42 -0700] rev 227
Removed the unnecessary typename in filtration-homology.cpp

2010-08-30Added output of essential cycles for any given input filtration dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 30 Aug 2010 12:28:58 -0700] rev 226
Added output of essential cycles for any given input filtration

2010-08-25Minor touches in documentation dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Aug 2010 14:36:11 -0700] rev 225
Minor touches in documentation

2010-08-25Merged docs with upstream dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Aug 2010 14:31:36 -0700] rev 224
Merged docs with upstream

2010-07-15CGAL is unncessary for vineyards (update in the documentation) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 15 Jul 2010 10:25:08 -0700] rev 223
CGAL is unncessary for vineyards (update in the documentation)

2010-08-25Merged in Aravind's changes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Aug 2010 14:29:54 -0700] rev 222
Merged in Aravind's changes

2010-08-18Changed the first iterator of PersistenceDiagram to accept dimension as well. Modified documentation. dev
Aravindakshan Babu <akshan@stanford.edu> [Wed, 18 Aug 2010 15:35:48 -0700] rev 221
Changed the first iterator of PersistenceDiagram to accept dimension as well. Modified documentation.

2010-08-18Removed the points iterator in PersistenceDaigram; replaced it with a __iter__ method. dev
Aravindakshan Babu <akshan@stanford.edu> [Wed, 18 Aug 2010 12:05:18 -0700] rev 220
Removed the points iterator in PersistenceDaigram; replaced it with a __iter__ method.

Got rid of some python code in __init__.py, since it was not needed with the above change.
Changed the docs to reflect this.

2010-08-17Added documentation for the python classes Point and PersistenceDiagram. Removed the __sub__ method for PersistenceDiagram. Minor renaming. dev
Aravindakshan Babu <akshan@stanford.edu> [Tue, 17 Aug 2010 22:19:19 -0700] rev 219
Added documentation for the python classes Point and PersistenceDiagram. Removed the __sub__ method for PersistenceDiagram. Minor renaming.

Renamed BottleneckDistance to bottleneck_distance.
Renamed intervals iterator for PersistenceDiagram to points. Seems in better conformance with usage.

2010-08-11Added a __iter__ method to the PersistenceDiagram class in python. Renamed the points iterator to the intervals iterator. dev
Aravindakshan Babu <akshan@stanford.edu> [Wed, 11 Aug 2010 17:07:09 -0700] rev 218
Added a __iter__ method to the PersistenceDiagram class in python. Renamed the points iterator to the intervals iterator.

2010-07-08Added extra functionality to Point class( an iterator ) and PersistenceDiagram( dimension property and __len__ func ). dev
Aravindakshan Babu <akshan@stanford.edu> [Thu, 08 Jul 2010 23:50:39 -0700] rev 217
Added extra functionality to Point class( an iterator ) and PersistenceDiagram( dimension property and __len__ func ).

persistence-diagram.h:

Added a new read-only dimension member and member function to access it.
With a new constructor that that takes in an int type to initialize dimension.


persistence-diagram.cpp:

Added new bp::init constructor. Takes in an integer type to initialize the dimension. Exposed the dimension property. Exposed the size property via a __len__ method.


__init__.py:

Added an iterator for Point objects. This iterates over the coords and then the data( if present ).

2010-07-02Made the data argument in Point's __init__method to be an optional argument by making it a boost::python::optional. dev
Aravindakshan Babu <akshan@stanford.edu> [Fri, 02 Jul 2010 17:08:02 -0700] rev 216
Made the data argument in Point's __init__method to be an optional argument by making it a boost::python::optional.

2010-07-02Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python. dev
Aravindakshan Babu <akshan@stanford.edu> [Fri, 02 Jul 2010 04:19:29 -0700] rev 215
Added code to expose the persistence_diagram class, the bottleneck_distance function and the point class to python.

Most of the commonly used methods for each class have been exported.
The constructor for point now requires that a data argument be provided along with x and y coord. This needs to be made optional.
The constructor for persistence_diagram could possibly be rewritten as well.

2010-07-15Merged docs with upstream dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 15 Jul 2010 10:20:06 -0700] rev 214
Merged docs with upstream

2010-07-15Removed the warning about compiler versions (seems unnecessary after Andrew's fixes) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 15 Jul 2010 10:19:18 -0700] rev 213
Removed the warning about compiler versions (seems unnecessary after Andrew's fixes)

2010-07-12Fixed path for lsfiltration.py dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 12 Jul 2010 09:53:30 -0700] rev 212
Fixed path for lsfiltration.py

2010-07-05Bug in the tutorial: simplices = [] -> simplices = Filtration() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 05 Jul 2010 23:51:26 -0700] rev 211
Bug in the tutorial: simplices = [] -> simplices = Filtration()

2010-04-13More typos in the docs dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 13 Apr 2010 09:09:04 -0700] rev 210
More typos in the docs

2010-04-12Fixed a link: dionysis -> dionysus dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 12 Apr 2010 19:01:01 -0700] rev 209
Fixed a link: dionysis -> dionysus

2010-04-20Andrew Yarmola's fix to the in-class intialization syntax in OrderList<T> dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 20 Apr 2010 13:58:23 -0700] rev 208
Andrew Yarmola's fix to the in-class intialization syntax in OrderList<T>

2010-03-09Added Persistence::initialize(f) + fixed minor bug LinearKernel::sign_at_negative_infinity() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 09 Mar 2010 15:22:57 -0800] rev 207
Added Persistence::initialize(f) + fixed minor bug LinearKernel::sign_at_negative_infinity()

2010-03-06Added insert-at-the-end optimization for CohomologyPersistence::add_cocycle() dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 06 Mar 2010 14:39:15 -0800] rev 206
Added insert-at-the-end optimization for CohomologyPersistence::add_cocycle()

2010-03-05Count cocycles in CohomologyPersistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 05 Mar 2010 09:26:54 -0800] rev 205
Count cocycles in CohomologyPersistence

2010-02-23Andrew Yarmola's compilation fix for MacOSX. dev
Mikael Vejdemo Johansson <mik@math.stanford.edu> [Tue, 23 Feb 2010 17:39:15 -0800] rev 204
Andrew Yarmola's compilation fix for MacOSX.

2010-02-22Removed unused instrumentation of cohomology and unnecessary includes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 22 Feb 2010 17:24:02 -0800] rev 203
Removed unused instrumentation of cohomology and unnecessary includes

2010-02-09Removed reference to reference in ThreeOutcomeComparison dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 09 Feb 2010 11:05:48 -0800] rev 202
Removed reference to reference in ThreeOutcomeComparison

2010-02-07Made EventQueue into a binary heap (for efficiency and sanity) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 07 Feb 2010 21:10:54 -0800] rev 201
Made EventQueue into a binary heap (for efficiency and sanity)

2010-02-07Replaced list with multi_index representation in EventQueue making it more efficient dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 07 Feb 2010 10:46:23 -0800] rev 200
Replaced list with multi_index representation in EventQueue making it more efficient

2010-02-06Switched to internal KineticSort dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 06 Feb 2010 23:22:43 -0800] rev 199
Switched to internal KineticSort

2010-02-05Added linear kernel for my own KineticSort dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 05 Feb 2010 11:49:52 -0800] rev 198
Added linear kernel for my own KineticSort

2010-02-05Commented out QField to get rid of the artifical dependence on GMP dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 05 Feb 2010 11:07:42 -0800] rev 197
Commented out QField to get rid of the artifical dependence on GMP

2010-02-04Fixed non-copyable temporary bug dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 04 Feb 2010 23:43:36 -0800] rev 196
Fixed non-copyable temporary bug

2010-02-03Fixed the duplicates (degeneracy) and another assertion problem in LSVineyard dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 03 Feb 2010 14:51:38 -0800] rev 195
Fixed the duplicates (degeneracy) and another assertion problem in LSVineyard

2010-02-03Removed a buggy assertion in LSVineard::transpose_vertices() (j points at the end() when moving the last simplex of the filtration) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 03 Feb 2010 11:20:40 -0800] rev 194
Removed a buggy assertion in LSVineard::transpose_vertices() (j points at the end() when moving the last simplex of the filtration)

2010-02-02StaticPersistence::pair_simplices() has an option to not display progress (LSVineyard uses it during consistency checking) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 02 Feb 2010 23:43:46 -0800] rev 193
StaticPersistence::pair_simplices() has an option to not display progress (LSVineyard uses it during consistency checking)

2010-01-26Added rips-explicit-cohomology dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 26 Jan 2010 11:14:50 -0800] rev 192
Added rips-explicit-cohomology

2010-01-26Moved lsfiltration.py into examples/pl-functions + added lscubes.py example (cubical lower-star filtration) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 26 Jan 2010 11:00:51 -0800] rev 191
Moved lsfiltration.py into examples/pl-functions + added lscubes.py example (cubical lower-star filtration)

2010-01-12Fixed Python constructor of CohomologyPersistence + minor changes to cocycle.py dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 12 Jan 2010 14:36:38 -0800] rev 190
Fixed Python constructor of CohomologyPersistence + minor changes to cocycle.py

2010-01-11vertex_coface -> vertex_cofaces in Rips documentation (in Python) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 11 Jan 2010 10:21:37 -0800] rev 189
vertex_coface -> vertex_cofaces in Rips documentation (in Python)

2010-01-09Henry Adams' fixes to python/dionysus/zigzag.py + added CohomologyPersistence.show_cocycles method dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 09 Jan 2010 15:03:52 -0800] rev 188
Henry Adams' fixes to python/dionysus/zigzag.py + added CohomologyPersistence.show_cocycles method

2010-01-07CohomologyPersistence::add returns the dying cocycle dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jan 2010 10:27:18 -0800] rev 187
CohomologyPersistence::add returns the dying cocycle

2010-01-05Check Boost version in include/utilities/property-maps.h + minor changes to cocycle.py dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 05 Jan 2010 11:02:07 -0800] rev 186
Check Boost version in include/utilities/property-maps.h + minor changes to cocycle.py

2009-12-31Added pl-vineyard documentation dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 31 Dec 2009 11:28:49 -0800] rev 185
Added pl-vineyard documentation

2009-12-25Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea: dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 25 Dec 2009 06:56:27 -0800] rev 184
Fixed a serious bug in DynamicPersistenceTrails + LSVineyard sorts filtration by attachment + miscellanea:
* added program options to pdbdistance-vineyard
* pdbdistance-vineyard takes frame list in a file
* more logging
* verification of pairing after vertex transpositions (commented out)

2009-12-20Moved files around: lsvineyard.h -> include/topology, examples/grid -> examples/pl-functions dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 20 Dec 2009 10:43:00 -0800] rev 183
Moved files around: lsvineyard.h -> include/topology, examples/grid -> examples/pl-functions

2009-12-20Merged Vineyards code changes with the main development line dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 20 Dec 2009 08:27:01 -0800] rev 182
Merged Vineyards code changes with the main development line

2009-12-20Python bindings work again dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 20 Dec 2009 07:45:29 -0800] rev 181
Python bindings work again

2009-12-16Created pl-vineyard.cpp to compute vineyards given a complex and a sequence of values at each vertex dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 16 Dec 2009 15:39:38 -0800] rev 180
Created pl-vineyard.cpp to compute vineyards given a complex and a sequence of values at each vertex

2009-12-16Resurrected vineyard code: dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 16 Dec 2009 15:39:06 -0800] rev 179
Resurrected vineyard code:
* Switched StaticPersistence + (serializable) Filtration to Boost.MultiIndex
* Updated DynamicPersistenceTrails to work with the new MultiIndex way
* Created LSVineyard class, and fixed the grid examples

2009-12-03Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 03 Dec 2009 13:21:23 -0800] rev 178
Made storing negative simplices in StaticPersistence parameter-based, so that DynamicPersistence works again

2009-12-02StaticPersistence operates on chains consisting of only positive simplices dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 02 Dec 2009 14:03:54 -0800] rev 177
StaticPersistence operates on chains consisting of only positive simplices

2009-12-01alphashapes3d.cpp measures persistence time dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 01 Dec 2009 20:34:31 -0800] rev 176
alphashapes3d.cpp measures persistence time

2009-11-28Fixed DynamicPersistenceTrails::PairingTrailsVisitor to match the changes in StaticPersistence::PairVisitor dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 28 Nov 2009 17:01:52 -0800] rev 175
Fixed DynamicPersistenceTrails::PairingTrailsVisitor to match the changes in StaticPersistence::PairVisitor

2009-11-28Instrumented code for counting: dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 28 Nov 2009 16:45:42 -0800] rev 174
Instrumented code for counting:
* added counters to addition in cohomology and ChainWrapper
* rips-pairwise-cohomology counts the maximum elements stored in the cycles
* added alphashapes3d-cohomology
* moved progress_display from DynamicPersistence to StaticPersistence

2009-11-06Added arbitrary coefficients in boundaries (to C++ and Python) + cleaned up CohomologyPersistence.add overloading in Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 06 Nov 2009 14:19:08 -0800] rev 173
Added arbitrary coefficients in boundaries (to C++ and Python) + cleaned up CohomologyPersistence.add overloading in Python

2009-10-28Added image persistence functionality to CohomologyPersistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 28 Oct 2009 14:38:36 -0700] rev 172
Added image persistence functionality to CohomologyPersistence

2009-10-23Added draw.py under tools/draw-diagram dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 23 Oct 2009 11:51:23 -0700] rev 171
Added draw.py under tools/draw-diagram

2009-10-23Added link to CVXOPT in get-build-install documentation + progress bar to rips-pairwise-cohomology dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 23 Oct 2009 09:36:55 -0700] rev 170
Added link to CVXOPT in get-build-install documentation + progress bar to rips-pairwise-cohomology

2009-10-20Fixed a typo in documentation + added a warning and a tip about GCC 4.2 on a Mac dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 20 Oct 2009 22:05:23 -0700] rev 169
Fixed a typo in documentation + added a warning and a tip about GCC 4.2 on a Mac

2009-08-31The if-else cases in lsqr.py were not exhaustive. They become exhaustive by changing ab > aa to ab >= aa. dev
mridul@ramrod.Stanford.EDU [Mon, 31 Aug 2009 13:45:28 -0700] rev 168
The if-else cases in lsqr.py were not exhaustive. They become exhaustive by changing ab > aa to ab >= aa.

2009-08-31Removed Qt4 requirement + added link to download and tutorial to the front page of the documentation dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 31 Aug 2009 10:51:56 -0700] rev 167
Removed Qt4 requirement + added link to download and tutorial to the front page of the documentation

2009-08-21Exposed store argument to CohomologyPersistence.add() in Python dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 21 Aug 2009 14:26:56 -0700] rev 166
Exposed store argument to CohomologyPersistence.add() in Python

2009-08-19cocycle.py uses vertex list, and does not make any assumptions about the vertex-simplex order dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 19 Aug 2009 12:01:47 -0700] rev 165
cocycle.py uses vertex list, and does not make any assumptions about the vertex-simplex order

2009-08-13Consistency zigzag outputs intervals supported over a single complex dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 13 Aug 2009 13:16:15 -0700] rev 164
Consistency zigzag outputs intervals supported over a single complex

2009-08-12explicitely converts a Dimension (short int) into a size_t, for removing a warning dev
Camille Wormser <camille.wormser@normalesup.org> [Wed, 12 Aug 2009 21:32:38 -0700] rev 163
explicitely converts a Dimension (short int) into a size_t, for removing a warning

2009-08-12Removing unused parameter names in order to avoid warnings dev
Camille Wormser <camille.wormser@normalesup.org> [Wed, 12 Aug 2009 07:16:35 -0700] rev 162
Removing unused parameter names in order to avoid warnings
-> no warning anymore in zigzag-persistence

2009-08-12make-zigzag-subsamples.py doesn't output the union, rips-consistency-zigzag.cpp fixed show_progress dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 12 Aug 2009 11:32:42 -0700] rev 161
make-zigzag-subsamples.py doesn't output the union, rips-consistency-zigzag.cpp fixed show_progress

2009-08-10Fixed bugs in cocycle.py introduced when rips-pairwise-cohomology.py was originally added dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 10 Aug 2009 16:48:13 -0700] rev 160
Fixed bugs in cocycle.py introduced when rips-pairwise-cohomology.py was originally added

2009-08-10Fixed bugs in rips-pairwise-cohomology.py whose origin is unclear to me dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 10 Aug 2009 15:22:32 -0700] rev 159
Fixed bugs in rips-pairwise-cohomology.py whose origin is unclear to me

2009-08-04Merged in Chris' changes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 04 Aug 2009 17:12:47 -0700] rev 158
Merged in Chris' changes

2009-08-04Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage. dev
Christos Mantoulidis <cmad@stanford.edu> [Tue, 04 Aug 2009 16:58:44 -0700] rev 157
Modified cohomology code (unweighted and weighted) so that it doesn't use std::map for boundary computations, which should optimize memory usage.

2009-08-04Changed 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
Christos Mantoulidis <cmad@stanford.edu> [Tue, 04 Aug 2009 13:23:16 -0700] rev 156
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.

2009-07-28Added rips-weighted-cohomology, and channeled WeightedRips logging to the same channel as Rips dev
Christos Mantoulidis <cmad@stanford.edu> [Tue, 28 Jul 2009 15:04:06 -0700] rev 155
Added rips-weighted-cohomology, and channeled WeightedRips logging to the same channel as Rips

2009-07-28Merged upstream dev
Christos Mantoulidis <cmad@stanford.edu> [Tue, 28 Jul 2009 11:42:03 -0700] rev 154
Merged upstream

2009-07-28Modified 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
Christos Mantoulidis <cmad@stanford.edu> [Tue, 28 Jul 2009 10:58:53 -0700] rev 153
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())

2009-07-27added logging to WeightedRips (still needs debugging) dev
Christos Mantoulidis <cmad@stanford.edu> [Mon, 27 Jul 2009 21:42:51 -0700] rev 152
added logging to WeightedRips (still needs debugging)

2009-07-13Updated weighted rips libraries to make use of OOP--now WeightedRips inherits from Rips. It is possible that logging for WeightedRips does not work. dev
Christos Mantoulidis <cmad@stanford.edu> [Mon, 13 Jul 2009 19:44:04 -0700] rev 151
Updated weighted rips libraries to make use of OOP--now WeightedRips inherits from Rips. It is possible that logging for WeightedRips does not work.

2009-07-02Added weighted rips code and libraries dev
Christos Mantoulidis <cmad@stanford.edu> [Thu, 02 Jul 2009 15:42:44 -0700] rev 150
Added weighted rips code and libraries

2009-08-04Simplices are deleted from the complex after removal in triangle-zigzag.py + touched up documentation (to mention CohomologyPersistence better) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 04 Aug 2009 14:28:17 -0700] rev 149
Simplices are deleted from the complex after removal in triangle-zigzag.py + touched up documentation (to mention CohomologyPersistence better)

2009-07-28Consistency zigzag outputs intervals for dimensions less than the skeleton dimension only dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 28 Jul 2009 13:27:13 -0700] rev 148
Consistency zigzag outputs intervals for dimensions less than the skeleton dimension only

2009-07-30Switched PairwiseDistances in Python bindings to C++ dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 30 Jul 2009 10:35:49 -0700] rev 147
Switched PairwiseDistances in Python bindings to C++

2009-07-30Added Python bindings for CohomologyPersistence (+ example + documentation) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 30 Jul 2009 10:23:31 -0700] rev 146
Added Python bindings for CohomologyPersistence (+ example + documentation)

2009-07-24Minor changes in distances.py + rips-pairwise.py wrapped into a main() function dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 24 Jul 2009 14:18:16 -0700] rev 145
Minor changes in distances.py + rips-pairwise.py wrapped into a main() function

2009-06-17Disable alphashapes in Python bindings if no CGAL dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 17 Jun 2009 16:02:52 -0700] rev 144
Disable alphashapes in Python bindings if no CGAL

2009-05-17Made ListRandomAccessIterator generic with respect to value, and moved it to utils.h dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 17 May 2009 20:05:26 -0700] rev 143
Made ListRandomAccessIterator generic with respect to value, and moved it to utils.h

2009-07-24Cleaner output in rips-pairwise.cpp + added make-zigzag-subsamples.py + added lsfiltration.py dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 24 Jul 2009 11:08:48 -0700] rev 142
Cleaner output in rips-pairwise.cpp + added make-zigzag-subsamples.py + added lsfiltration.py

2009-07-09Fixed plot.py in tools/plot-values dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 07:47:22 -0700] rev 141
Fixed plot.py in tools/plot-values

2009-05-14In documentation put contents into sidebar dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 14 May 2009 17:43:19 -0700] rev 140
In documentation put contents into sidebar

2009-07-09Documentation for parametrization using persistent cohomology dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 02:46:53 -0700] rev 139
Documentation for parametrization using persistent cohomology

2009-07-09Rips pairwise cohomology produces output necessary for 1-cocycle parametrization dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 02:42:47 -0700] rev 138
Rips pairwise cohomology produces output necessary for 1-cocycle parametrization

2009-07-09Added field arithmetic to CohomologyPersistence (Zp + Q) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 00:59:32 -0700] rev 137
Added field arithmetic to CohomologyPersistence (Zp + Q)

2009-05-14Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 14 May 2009 14:04:43 -0700] rev 136
Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h

2009-05-14read_points() does not need ambient dimension and ignores lines starting with '#' dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 14 May 2009 13:09:06 -0700] rev 135
read_points() does not need ambient dimension and ignores lines starting with '#'

2009-05-11Added documentation; for now mostly for the Python bindings dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 11 May 2009 12:45:49 -0700] rev 134
Added documentation; for now mostly for the Python bindings

2009-05-07Touch up to compile with GCC 4.4 dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 May 2009 14:53:13 -0700] rev 133
Touch up to compile with GCC 4.4

2009-04-29Cleaned up simplex comparison functions, rip-pairwise.py outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 29 Apr 2009 10:16:03 -0700] rev 132
Cleaned up simplex comparison functions, rip-pairwise.py outputs a diagram, auxilliary add_simplices() + remove_simplices() for zigzags

2009-04-16Alphashapes and Python bindings dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 16 Apr 2009 00:23:01 -0700] rev 131
Alphashapes and Python bindings
* converted alphashapes2d to the new format
* added Python bindings for alphashapes
* added sample alphashapes.py that dynamically distinguishes between 2D and 3D

2009-04-15Placed all Python bindings code into dionysus::python namespace dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 15 Apr 2009 14:17:21 -0700] rev 130
Placed all Python bindings code into dionysus::python namespace

2009-04-14Cleaned up Python bindings to restore functionality: dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Apr 2009 14:38:08 -0700] rev 129
Cleaned up Python bindings to restore functionality:
* StaticPersistence is iterable, its nodes are usable (sign, pair, cycle)
* StaticPersistence knows how to map its nodes into Filtration indices
* moved PythonCmp into utils.h
* minor cosmetic changes

2009-04-13Renamed header files in bindings/python to get rid of the "python-" prefix dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 13 Apr 2009 20:44:31 -0700] rev 128
Renamed header files in bindings/python to get rid of the "python-" prefix

2009-04-13Changes in Python Bindings: dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 13 Apr 2009 20:38:46 -0700] rev 127
Changes in Python Bindings:
* the exposed C++ simplex has Empty data
* Python Simplex constructor with data as well as data-based
comparison functions are implemented in pure Python

2009-04-11Added Python bindings for the Rips complex + an example dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 11 Apr 2009 10:29:53 -0700] rev 126
Added Python bindings for the Rips complex + an example

2009-05-01Cleaned up traits (chain and container) for static- and dynamic-persistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 01 May 2009 15:09:38 -0700] rev 125
Cleaned up traits (chain and container) for static- and dynamic-persistence

2009-05-01Added tools/extract-diagram + minor fixes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 01 May 2009 15:36:25 -0700] rev 124
Added tools/extract-diagram + minor fixes

2009-04-10Added intrusive containers issue and issue filters dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 10 Apr 2009 14:35:43 -0700] rev 123
Added intrusive containers issue and issue filters

2009-04-09Moved l2distance.h into include/geometry dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Apr 2009 14:43:37 -0700] rev 122
Moved l2distance.h into include/geometry

2009-04-09Added categories to some of the issues dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Apr 2009 14:39:12 -0700] rev 121
Added categories to some of the issues

2009-04-09Fixed distance to diagonal calculation + added stand-alone bottleneck distance tool dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Apr 2009 12:58:10 -0700] rev 120
Fixed distance to diagonal calculation + added stand-alone bottleneck distance tool

2009-03-25Added ZigzagPersistence::is_alive() + consistency zigzag outputs betti 1 at each stage dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Mar 2009 09:56:52 -0700] rev 119
Added ZigzagPersistence::is_alive() + consistency zigzag outputs betti 1 at each stage

2009-03-24Added consistency zigzag dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 24 Mar 2009 15:17:39 -0700] rev 118
Added consistency zigzag

2009-03-23Merged in cohomology branch dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 23 Mar 2009 11:40:29 -0700] rev 117
Merged in cohomology branch

2009-02-27Added CohomologyPersistence and Rips pairwise distances computation dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 27 Feb 2009 10:14:26 -0800] rev 116
Added CohomologyPersistence and Rips pairwise distances computation

2009-03-22Added DynamicPersistenceChains (no dynamic part yet) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 22 Mar 2009 11:18:07 -0700] rev 115
Added DynamicPersistenceChains (no dynamic part yet)

2009-02-03Updated Rips zigzags dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 03 Feb 2009 11:31:10 -0800] rev 114
Updated Rips zigzags
* Updated to use Bron-Kerbosch
* Compute in the order of increasing epsilon, and decreasing point sizes
* Split into plain zigzag (rips-zigzag) and image zigzag (rips-image-zigzag)
* Added minor enhancements (show_progress and timers)

2009-01-31Switched Rips complex computation to Bron-Kerbosch algorithm dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 31 Jan 2009 23:02:22 -0800] rev 113
Switched Rips complex computation to Bron-Kerbosch algorithm

2009-01-29Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 29 Jan 2009 10:16:56 -0800] rev 112
Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence)

2009-01-28Switched to CGAL 3.4 (native CMake configuration): for now only alphashapes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 28 Jan 2009 14:57:17 -0800] rev 111
Switched to CGAL 3.4 (native CMake configuration): for now only alphashapes

2009-01-20Implemented ImageZigzagPersistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 20 Jan 2009 10:53:35 -0800] rev 110
Implemented ImageZigzagPersistence
* Changed ZigzagPersistence to support a visitor, and implemented
ImageZigzagPersistence
* examples/rips/rips-zigzag now computes using ImageZigzagPersistence
* PersistenceDiagram no longer records zero persistence pairs
* Added utilities/memory.h with report_memory() function

2009-01-12Debugged ZigzagPersistence (having added heavier consistency checking) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 12 Jan 2009 15:33:04 -0800] rev 109
Debugged ZigzagPersistence (having added heavier consistency checking)
* Added DEBUG_CONTAINERS option (uses std::__debug::* containers for chains
and in ZigzagPersistence)
* Added SizeStorage specialization for std::deque<T>
* ZigzagPersistence got a lot more consistency checking (in debug mode only,
which now crawls); as a result it's been debugged (running on non-trivial examples)
* examples/rips/rips-zigzag takes command-line options
* added ChainWrapper::clear()
* added Simplex::VertexDimensionComparison
* added PairwiseDistances class (for computing distances between points in a
container according to a distance functor)

2009-01-02Added rips-zigzag; in the process caught a number of bugs in ZigzagPersistence (added check_consistency() to it) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 02 Jan 2009 14:54:15 -0800] rev 108
Added rips-zigzag; in the process caught a number of bugs in ZigzagPersistence (added check_consistency() to it)

2008-12-31Added DequeChains (for ZigzagPersistence) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 31 Dec 2008 11:54:34 -0800] rev 107
Added DequeChains (for ZigzagPersistence)

2008-12-31Added ZigzagPersistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 31 Dec 2008 11:51:14 -0800] rev 106
Added ZigzagPersistence

2008-12-27Merged in Python branch dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 27 Dec 2008 14:51:38 -0800] rev 105
Merged in Python branch

2008-12-25Initial commit of Python bindings dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 25 Dec 2008 13:09:00 -0800] rev 104
Initial commit of Python bindings

2008-12-25Empty is now a template, replaced RecursiveIterator with boost::counting_iterator dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 25 Dec 2008 13:08:41 -0800] rev 103
Empty is now a template, replaced RecursiveIterator with boost::counting_iterator

2008-12-23Removed boundary() from AlphaSimplex3D dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 23 Dec 2008 15:10:15 -0800] rev 102
Removed boundary() from AlphaSimplex3D

2008-12-23Changed Simplex::boundary() to be iterator-based (replaced it with boundary_begin() and boundary_end()) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 23 Dec 2008 11:40:38 -0800] rev 101
Changed Simplex::boundary() to be iterator-based (replaced it with boundary_begin() and boundary_end())

2008-12-27Commit before merging in Python branch: dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 27 Dec 2008 14:33:25 -0800] rev 100
Commit before merging in Python branch:
* converted more examples: poincare, rips, some fitness
* two generators for Rips complexes
* ChainWrapper uses stl algorithms for everything,
added CountingBackInserter and switched SizeStorage to use operators
* retabbing files along the way
* added #957a (namespace dionysus)

2008-12-25Initial addition of tools/diagram-viewer dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 25 Dec 2008 14:24:02 -0800] rev 99
Initial addition of tools/diagram-viewer

2008-12-23Closed #8a1 and #96b, added #de6 and #f64 dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 23 Dec 2008 11:02:08 -0800] rev 98
Closed #8a1 and #96b, added #de6 and #f64

2008-12-18Intermediate commit while converting to the new architecture dev
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 18 Dec 2008 16:43:42 -0800] rev 97
Intermediate commit while converting to the new architecture
* Converted Filtration into StaticPersistence and DynamicPersistenceTrails
(both right now work with the underlying std::vector rather than std::list order)
* Filtration is now just an auxilliary glue (a map between Complex and Persistence)
* Whether chains are vectors or lists can be interchanged
* Added PersistenceDiagram with a simple bottleneck_distance() function
* Converted triangle, alphashapes3d, and cech-complex examples
* Lots of organizational changes
(factoring utilities out into containers.h, indirect.h, property-maps.h)
* Trying to document along the way with NaturalDocs-type comments

2008-09-22Switching README to PanDoc dev
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:53:25 -0700] rev 96
Switching README to PanDoc

2008-09-22Added Rips complex-based distance computation to fitness dev
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:53:16 -0700] rev 95
Added Rips complex-based distance computation to fitness

2008-09-22Added ExplicitDistance + Evaluator to Rips complexes dev
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:49:22 -0700] rev 94
Added ExplicitDistance + Evaluator to Rips complexes

2008-09-15Merged in Rips complexes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:41:18 -0700] rev 93
Merged in Rips complexes

2008-09-15Added initial code for Rips complexes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:40:03 -0700] rev 92
Added initial code for Rips complexes

2008-09-15Added join() operation for a Simplex dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:38:54 -0700] rev 91
Added join() operation for a Simplex

2008-09-15Removed inclusion of seemingly unnecessary boost/serialization/is_abstract.hpp header dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:33:34 -0700] rev 90
Removed inclusion of seemingly unnecessary boost/serialization/is_abstract.hpp header

2008-09-09Converted issues to Maildir format, added Boost 1.36 issue dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 09 Sep 2008 18:04:04 -0700] rev 89
Converted issues to Maildir format, added Boost 1.36 issue

2008-09-03Added cmake_minimum_required for compatibility with CMake 2.6 dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 03 Sep 2008 10:59:35 -0700] rev 88
Added cmake_minimum_required for compatibility with CMake 2.6