Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 10 Jul 2013 14:39:29 -0700] rev 276
lscubes.py output infinite pairs + small bugfix
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 10 Jun 2013 17:25:57 +0200] rev 275
Fixed non-POD array problem in homology-zigzags
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 10 Jun 2013 16:58:01 +0200] rev 274
Added homology zigzags by Steve Oudot and Don Sheehy
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 26 Apr 2013 22:31:58 -0700] rev 273
Added standalone bottleneck-distance.cpp
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
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 26 Oct 2012 11:45:58 -0700] rev 271
Added CGAL_USE_FILE + added option use_cgal
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 10 Jun 2012 18:54:26 -0700] rev 270
Bug in show_diagram() with empty diagrams
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 10 Jun 2012 11:26:38 -0700] rev 269
subcomplex in show_complex() + pan/zoom in ComplexViewer2D
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 09 Jun 2012 12:56:36 -0700] rev 268
DiagramViewer can show multiple diagrams at once
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
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 08 Jun 2012 15:40:09 -0700] rev 266
Display lists in ComplexViewer3D + circular.smooth() raises exceptions
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 21:36:53 -0700] rev 265
Set center and radius in ComplexViewer3D
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 21:21:11 -0700] rev 264
Points at infinity in DiagramViewer
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 21:16:06 -0700] rev 263
Fixed scale points in the diagram + noise filtering
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 10:52:15 -0700] rev 261
Straightened out QApplication problems (made it global)
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jun 2012 10:11:01 -0700] rev 260
Started show_complex_3D()
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
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
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
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 03 Jun 2012 16:39:18 -0700] rev 254
Merged upstream
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 03 Jun 2012 16:17:27 -0700] rev 253
Added adaptor for StaticCohomologyPersistence and ImagePersistence
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
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 11 May 2012 17:06:55 -0700] rev 251
Merge
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 11 May 2012 10:25:57 -0700] rev 250
Added store_negative argument to StaticPersistence.pair_simpices()
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()
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 10 May 2012 15:42:21 -0700] rev 247
Added wasserstein_distance()
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 10 May 2012 14:24:40 -0700] rev 246
Exposed init_diagrams() to Python
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 08 May 2012 13:07:28 -0700] rev 245
Minor changes to compile with GCC 4.7
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
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 06 May 2011 10:38:06 -0700] rev 243
Minor fixes in tools/draw-diagram
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 28 Jan 2011 08:01:37 -0800] rev 241
Fixed combinations in closure() for older versions of Python
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 07 Jan 2011 23:11:46 -0800] rev 240
closure() in Python can handle simplex data
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 20 Dec 2010 11:21:57 -0800] rev 239
Fixed a typo in b/p/persistence-diagram.cpp
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 08 Dec 2010 10:29:26 -0800] rev 238
Added a note about GPL to the documentation
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 03 Dec 2010 11:26:12 -0800] rev 237
Cleaned up CMake files to play nice with CGAL
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 09 Oct 2010 13:56:26 -0700] rev 236
Cleaned up PersistenceDiagram bindings
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 04 Oct 2010 18:03:35 -0700] rev 235
Fixed a link to SYNAPS
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 15:36:13 -0700] rev 234
Merged in Python bindings for DynamicPersistenceChains
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 15:00:34 -0700] rev 233
Added documentation for DynamicPersistenceChains
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 12 Sep 2010 09:55:44 -0700] rev 232
Added Python bindings for DynamicPersistenceChains
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 11:34:11 -0700] rev 231
Added the ability to pickle Simplex class in Python
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 14 Sep 2010 11:12:33 -0700] rev 230
Added ability to iterate over ZigzagPersistence cycles in Python
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 10 Sep 2010 21:21:27 -0700] rev 229
Fixed a typo in the documentation of SPNode.cycle
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 02 Sep 2010 09:13:42 -0700] rev 227
Removed the unnecessary typename in filtration-homology.cpp
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
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Aug 2010 14:36:11 -0700] rev 225
Minor touches in documentation
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Aug 2010 14:31:36 -0700] rev 224
Merged docs with upstream
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 15 Jul 2010 10:25:08 -0700] rev 223
CGAL is unncessary for vineyards (update in the documentation)
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 25 Aug 2010 14:29:54 -0700] rev 222
Merged in Aravind's changes
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.
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.
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.
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.
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 ).
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.
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.
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 15 Jul 2010 10:20:06 -0700] rev 214
Merged docs with upstream
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 12 Jul 2010 09:53:30 -0700] rev 212
Fixed path for lsfiltration.py
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 05 Jul 2010 23:51:26 -0700] rev 211
Bug in the tutorial: simplices = [] -> simplices = Filtration()
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 13 Apr 2010 09:09:04 -0700] rev 210
More typos in the docs
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 12 Apr 2010 19:01:01 -0700] rev 209
Fixed a link: dionysis -> dionysus
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>
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()
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()
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 05 Mar 2010 09:26:54 -0800] rev 205
Count cocycles in CohomologyPersistence
Mikael Vejdemo Johansson <mik@math.stanford.edu> [Tue, 23 Feb 2010 17:39:15 -0800] rev 204
Andrew Yarmola's compilation fix for MacOSX.
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 22 Feb 2010 17:24:02 -0800] rev 203
Removed unused instrumentation of cohomology and unnecessary includes
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 09 Feb 2010 11:05:48 -0800] rev 202
Removed reference to reference in ThreeOutcomeComparison
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)
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
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 06 Feb 2010 23:22:43 -0800] rev 199
Switched to internal KineticSort
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 05 Feb 2010 11:49:52 -0800] rev 198
Added linear kernel for my own KineticSort
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 04 Feb 2010 23:43:36 -0800] rev 196
Fixed non-copyable temporary bug
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
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)
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 26 Jan 2010 11:14:50 -0800] rev 192
Added rips-explicit-cohomology
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)
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
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 11 Jan 2010 10:21:37 -0800] rev 189
vertex_coface -> vertex_cofaces in Rips documentation (in Python)
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 Jan 2010 10:27:18 -0800] rev 187
CohomologyPersistence::add returns the dying cocycle
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 31 Dec 2009 11:28:49 -0800] rev 185
Added pl-vineyard documentation
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)
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
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 20 Dec 2009 08:27:01 -0800] rev 182
Merged Vineyards code changes with the main development line
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 20 Dec 2009 07:45:29 -0800] rev 181
Python bindings work again
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
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 02 Dec 2009 14:03:54 -0800] rev 177
StaticPersistence operates on chains consisting of only positive simplices
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 01 Dec 2009 20:34:31 -0800] rev 176
alphashapes3d.cpp measures persistence time
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
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 28 Oct 2009 14:38:36 -0700] rev 172
Added image persistence functionality to CohomologyPersistence
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 23 Oct 2009 11:51:23 -0700] rev 171
Added draw.py under tools/draw-diagram
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
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
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.
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
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 21 Aug 2009 14:26:56 -0700] rev 166
Exposed store argument to CohomologyPersistence.add() in Python
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 13 Aug 2009 13:16:15 -0700] rev 164
Consistency zigzag outputs intervals supported over a single complex
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
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
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
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 04 Aug 2009 17:12:47 -0700] rev 158
Merged in Chris' changes
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.
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.
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
Christos Mantoulidis <cmad@stanford.edu> [Tue, 28 Jul 2009 11:42:03 -0700] rev 154
Merged upstream
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())
Christos Mantoulidis <cmad@stanford.edu> [Mon, 27 Jul 2009 21:42:51 -0700] rev 152
added logging to WeightedRips (still needs debugging)
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.
Christos Mantoulidis <cmad@stanford.edu> [Thu, 02 Jul 2009 15:42:44 -0700] rev 150
Added weighted rips code and libraries
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)
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 30 Jul 2009 10:35:49 -0700] rev 147
Switched PairwiseDistances in Python bindings to C++
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 30 Jul 2009 10:23:31 -0700] rev 146
Added Python bindings for CohomologyPersistence (+ example + documentation)
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
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 17 Jun 2009 16:02:52 -0700] rev 144
Disable alphashapes in Python bindings if no CGAL
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 07:47:22 -0700] rev 141
Fixed plot.py in tools/plot-values
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 14 May 2009 17:43:19 -0700] rev 140
In documentation put contents into sidebar
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 02:46:53 -0700] rev 139
Documentation for parametrization using persistent cohomology
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
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Jul 2009 00:59:32 -0700] rev 137
Added field arithmetic to CohomologyPersistence (Zp + Q)
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 14 May 2009 14:04:43 -0700] rev 136
Moved PairwiseDistances and ExplicitDistances into include/geometry/distances.h
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 '#'
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 11 May 2009 12:45:49 -0700] rev 134
Added documentation; for now mostly for the Python bindings
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 07 May 2009 14:53:13 -0700] rev 133
Touch up to compile with GCC 4.4
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 15 Apr 2009 14:17:21 -0700] rev 130
Placed all Python bindings code into dionysus::python namespace
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
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 11 Apr 2009 10:29:53 -0700] rev 126
Added Python bindings for the Rips complex + an example
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
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 01 May 2009 15:36:25 -0700] rev 124
Added tools/extract-diagram + minor fixes
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 10 Apr 2009 14:35:43 -0700] rev 123
Added intrusive containers issue and issue filters
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Apr 2009 14:43:37 -0700] rev 122
Moved l2distance.h into include/geometry
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 09 Apr 2009 14:39:12 -0700] rev 121
Added categories to some of the issues
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
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
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 24 Mar 2009 15:17:39 -0700] rev 118
Added consistency zigzag
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 23 Mar 2009 11:40:29 -0700] rev 117
Merged in cohomology branch
Dmitriy Morozov <dmitriy@mrzv.org> [Fri, 27 Feb 2009 10:14:26 -0800] rev 116
Added CohomologyPersistence and Rips pairwise distances computation
Dmitriy Morozov <dmitriy@mrzv.org> [Sun, 22 Mar 2009 11:18:07 -0700] rev 115
Added DynamicPersistenceChains (no dynamic part yet)
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 31 Jan 2009 23:02:22 -0800] rev 113
Switched Rips complex computation to Bron-Kerbosch algorithm
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 29 Jan 2009 10:16:56 -0800] rev 112
Added python bindings for ZigzagPersistence (as well as ImageZigzagPersistence)
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
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
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)
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 31 Dec 2008 11:54:34 -0800] rev 107
Added DequeChains (for ZigzagPersistence)
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 31 Dec 2008 11:51:14 -0800] rev 106
Added ZigzagPersistence
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 27 Dec 2008 14:51:38 -0800] rev 105
Merged in Python branch
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 25 Dec 2008 13:09:00 -0800] rev 104
Initial commit of Python bindings
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
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 23 Dec 2008 15:10:15 -0800] rev 102
Removed boundary() from AlphaSimplex3D
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())
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)
Dmitriy Morozov <dmitriy@mrzv.org> [Thu, 25 Dec 2008 14:24:02 -0800] rev 99
Initial addition of tools/diagram-viewer
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 23 Dec 2008 11:02:08 -0800] rev 98
Closed #8a1 and #96b, added #de6 and #f64
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
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:53:25 -0700] rev 96
Switching README to PanDoc
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:53:16 -0700] rev 95
Added Rips complex-based distance computation to fitness
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:49:22 -0700] rev 94
Added ExplicitDistance + Evaluator to Rips complexes
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:41:18 -0700] rev 93
Merged in Rips complexes
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:40:03 -0700] rev 92
Added initial code for Rips complexes
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:38:54 -0700] rev 91
Added join() operation for a Simplex
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
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
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
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 04 Apr 2008 21:14:44 -0400] rev 87
Merge in AR branch
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 19 Mar 2008 13:50:51 -0400] rev 86
Fixed #c42 for ar-vineyard
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 19 Mar 2008 12:50:35 -0400] rev 85
Merged in upstream changes and reopened #c42
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 02 Mar 2008 16:42:33 -0500] rev 84
KineticEvaluator takes the maximum time between the two simulators
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 02 Mar 2008 16:11:05 -0500] rev 83
Small logging additions + maintain_lazy = false + eventqueue
- Filtration::transpose( ..., maintain_lazy = false )
- EventQueue inserts a new event after all the ones equal to it, not before
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 01 Mar 2008 04:48:49 -0500] rev 82
Marked #c66 and #d2a as fixed (fixes in f236c7d659d0 and abba2950aced, respectively)
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 29 Feb 2008 19:43:11 -0500] rev 81
Fixed Vineyard to preserve the vine addresses after we add a new dimension vine (was a major bug)
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 29 Feb 2008 15:46:12 -0500] rev 80
Using two simulators in ARVineyard (one for simplices and one for trajectories)
- Fixes #c66
- Simulator::reached_infinity() examines the queue instead of
keeping state in a variable
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 29 Feb 2008 14:39:48 -0500] rev 79
ConeSimplex and ARConeSimplex3D adjusted to work correctly with operator<(), operator==(), and boundary()
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 27 Feb 2008 17:44:46 -0500] rev 78
ConeSimplex correctly reports dimension()
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 27 Feb 2008 16:32:12 -0500] rev 77
program_options + trajectory knees
- added boost::program_options
- recording knees when trajectories change