Fri, 01 May 2009 15:36:25 -0700 Added 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
Fri, 10 Apr 2009 14:35:43 -0700 Added 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
Thu, 09 Apr 2009 14:43:37 -0700 Moved 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
Thu, 09 Apr 2009 14:39:12 -0700 Added 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
Thu, 09 Apr 2009 12:58:10 -0700 Fixed 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
Wed, 25 Mar 2009 09:56:52 -0700 Added 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
Tue, 24 Mar 2009 15:17:39 -0700 Added consistency zigzag dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 24 Mar 2009 15:17:39 -0700] rev 118
Added consistency zigzag
Mon, 23 Mar 2009 11:40:29 -0700 Merged in cohomology branch dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 23 Mar 2009 11:40:29 -0700] rev 117
Merged in cohomology branch
Fri, 27 Feb 2009 10:14:26 -0800 Added 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
Sun, 22 Mar 2009 11:18:07 -0700 Added 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)
Tue, 03 Feb 2009 11:31:10 -0800 Updated 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)
Sat, 31 Jan 2009 23:02:22 -0800 Switched 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
Thu, 29 Jan 2009 10:16:56 -0800 Added 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)
Wed, 28 Jan 2009 14:57:17 -0800 Switched 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
Tue, 20 Jan 2009 10:53:35 -0800 Implemented 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
Mon, 12 Jan 2009 15:33:04 -0800 Debugged 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)
Fri, 02 Jan 2009 14:54:15 -0800 Added 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)
Wed, 31 Dec 2008 11:54:34 -0800 Added DequeChains (for ZigzagPersistence) dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 31 Dec 2008 11:54:34 -0800] rev 107
Added DequeChains (for ZigzagPersistence)
Wed, 31 Dec 2008 11:51:14 -0800 Added ZigzagPersistence dev
Dmitriy Morozov <dmitriy@mrzv.org> [Wed, 31 Dec 2008 11:51:14 -0800] rev 106
Added ZigzagPersistence
Sat, 27 Dec 2008 14:51:38 -0800 Merged in Python branch dev
Dmitriy Morozov <dmitriy@mrzv.org> [Sat, 27 Dec 2008 14:51:38 -0800] rev 105
Merged in Python branch
Thu, 25 Dec 2008 13:09:00 -0800 Initial 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
Thu, 25 Dec 2008 13:08:41 -0800 Empty 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
Tue, 23 Dec 2008 15:10:15 -0800 Removed boundary() from AlphaSimplex3D dev
Dmitriy Morozov <dmitriy@mrzv.org> [Tue, 23 Dec 2008 15:10:15 -0800] rev 102
Removed boundary() from AlphaSimplex3D
Tue, 23 Dec 2008 11:40:38 -0800 Changed 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())
Sat, 27 Dec 2008 14:33:25 -0800 Commit 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)
Thu, 25 Dec 2008 14:24:02 -0800 Initial 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
Tue, 23 Dec 2008 11:02:08 -0800 Closed #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
Thu, 18 Dec 2008 16:43:42 -0800 Intermediate 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
Mon, 22 Sep 2008 21:53:25 -0700 Switching README to PanDoc dev
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 22 Sep 2008 21:53:25 -0700] rev 96
Switching README to PanDoc
Mon, 22 Sep 2008 21:53:16 -0700 Added 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
Mon, 22 Sep 2008 21:49:22 -0700 Added 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
Mon, 15 Sep 2008 16:41:18 -0700 Merged in Rips complexes dev
Dmitriy Morozov <dmitriy@mrzv.org> [Mon, 15 Sep 2008 16:41:18 -0700] rev 93
Merged in Rips complexes
Mon, 15 Sep 2008 16:40:03 -0700 Added 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
Mon, 15 Sep 2008 16:38:54 -0700 Added 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
Mon, 15 Sep 2008 16:33:34 -0700 Removed 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
Tue, 09 Sep 2008 18:04:04 -0700 Converted 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
Wed, 03 Sep 2008 10:59:35 -0700 Added 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
Fri, 04 Apr 2008 21:14:44 -0400 Merge in AR branch dev
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 04 Apr 2008 21:14:44 -0400] rev 87
Merge in AR branch
Wed, 19 Mar 2008 13:50:51 -0400 Fixed #c42 for ar-vineyard ar
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 19 Mar 2008 13:50:51 -0400] rev 86
Fixed #c42 for ar-vineyard
Wed, 19 Mar 2008 12:50:35 -0400 Merged in upstream changes and reopened #c42 ar
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 19 Mar 2008 12:50:35 -0400] rev 85
Merged in upstream changes and reopened #c42
Sun, 02 Mar 2008 16:42:33 -0500 KineticEvaluator takes the maximum time between the two simulators ar
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
Sun, 02 Mar 2008 16:11:05 -0500 Small logging additions + maintain_lazy = false + eventqueue ar
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
Sat, 01 Mar 2008 04:48:49 -0500 Marked #c66 and #d2a as fixed (fixes in f236c7d659d0 and abba2950aced, respectively) ar
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)
Fri, 29 Feb 2008 19:43:11 -0500 Fixed Vineyard to preserve the vine addresses after we add a new dimension vine (was a major bug) ar
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)
Fri, 29 Feb 2008 15:46:12 -0500 Using two simulators in ARVineyard (one for simplices and one for trajectories) ar
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
Fri, 29 Feb 2008 14:39:48 -0500 ConeSimplex and ARConeSimplex3D adjusted to work correctly with operator<(), operator==(), and boundary() ar
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()
Wed, 27 Feb 2008 17:44:46 -0500 ConeSimplex correctly reports dimension() ar
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 27 Feb 2008 17:44:46 -0500] rev 78
ConeSimplex correctly reports dimension()
Wed, 27 Feb 2008 16:32:12 -0500 program_options + trajectory knees ar
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
Wed, 27 Feb 2008 07:57:45 -0500 Merged upstream changes (to get boost::program_options setup in CMake) ar
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 27 Feb 2008 07:57:45 -0500] rev 76
Merged upstream changes (to get boost::program_options setup in CMake)
Mon, 25 Feb 2008 16:54:34 -0500 Merged in fitness branch dev
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 16:54:34 -0500] rev 75
Merged in fitness branch
Wed, 27 Feb 2008 07:56:26 -0500 ar-vinyeard compiles and runs: ar
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 27 Feb 2008 07:56:26 -0500] rev 74
ar-vinyeard compiles and runs: - ar-function-kernel uses int for sign rather than bool in sign_at - switched to dealing with a single functions themselves in value_at - order of thresholds is handled correctly in ar-vineyard (max is the last one)
Tue, 26 Feb 2008 18:25:27 -0500 Added intostring() issue (#89a) ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 26 Feb 2008 18:25:27 -0500] rev 73
Added intostring() issue (#89a)
Tue, 26 Feb 2008 16:45:25 -0500 KineticSort can deal with equal trajectories: ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 26 Feb 2008 16:45:25 -0500] rev 72
KineticSort can deal with equal trajectories: UPolynomial::sign_at_negative_infinity() can handle 0 and so can Simulator::add()
Tue, 26 Feb 2008 16:15:12 -0500 Fixed UPolynomial<T>::sign_at_negative_infinity() + Simulator::add() ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 26 Feb 2008 16:15:12 -0500] rev 71
Fixed UPolynomial<T>::sign_at_negative_infinity() + Simulator::add() Bug in the former and resulting logic problems in the latter.
Tue, 26 Feb 2008 08:02:56 -0500 Added and fixed CGAL debugging problem (issue #c42) ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 26 Feb 2008 08:02:56 -0500] rev 70
Added and fixed CGAL debugging problem (issue #c42)
Mon, 25 Feb 2008 11:43:33 -0500 Added EventQueue efficiency issue (#ebd) ar
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 11:43:33 -0500] rev 69
Added EventQueue efficiency issue (#ebd)
Mon, 25 Feb 2008 04:37:49 -0500 Initial commit of KineticSort-based ARVineyard ar
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 04:37:49 -0500] rev 68
Initial commit of KineticSort-based ARVineyard Compiles, but needs to be runtime debugged.
Mon, 25 Feb 2008 04:33:13 -0500 Issue #cd7: incorrect UPolynomial<double>::sign_at() ar
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 04:33:13 -0500] rev 67
Issue #cd7: incorrect UPolynomial<double>::sign_at()
Fri, 22 Feb 2008 18:29:43 -0500 Fixed Simulator not processing events correctly ar
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 22 Feb 2008 18:29:43 -0500] rev 66
Fixed Simulator not processing events correctly Event that is being processed needed to be removed from the queue while its own process() method ran.
Fri, 22 Feb 2008 13:06:40 -0500 Fixed segfault in test-kinetic-sort (#b5d) ar
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 22 Feb 2008 13:06:40 -0500] rev 65
Fixed segfault in test-kinetic-sort (#b5d)
Thu, 21 Feb 2008 06:49:06 -0500 Added segfault in test-kinetic-sort issue ar
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 21 Feb 2008 06:49:06 -0500] rev 64
Added segfault in test-kinetic-sort issue
Thu, 21 Feb 2008 04:50:09 -0500 Changed PolynomialKernel to FunctionKernel ar
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 21 Feb 2008 04:50:09 -0500] rev 63
Changed PolynomialKernel to FunctionKernel
Tue, 19 Feb 2008 09:10:51 -0500 Changed geometry to RLog-based logging and counters ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 19 Feb 2008 09:10:51 -0500] rev 62
Changed geometry to RLog-based logging and counters
Tue, 19 Feb 2008 07:26:01 -0500 Added class groups to Doxygen documentation ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 19 Feb 2008 07:26:01 -0500] rev 61
Added class groups to Doxygen documentation
Tue, 19 Feb 2008 06:56:49 -0500 Merged in changes from master ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 19 Feb 2008 06:56:49 -0500] rev 60
Merged in changes from master
Tue, 19 Feb 2008 06:51:23 -0500 Commit to merge in changes from master. ar
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 19 Feb 2008 06:51:23 -0500] rev 59
Commit to merge in changes from master.
Fri, 24 Aug 2007 16:58:25 -0400 Fixed handling of degeneracies in KineticSort, Simulator is aware of the sign of the RationalFunction
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 24 Aug 2007 16:58:25 -0400] rev 58
Fixed handling of degeneracies in KineticSort, Simulator is aware of the sign of the RationalFunction
Fri, 17 Aug 2007 15:08:27 -0400 Merged CGAL 3.3 changes with the work on ARVineyard
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 17 Aug 2007 15:08:27 -0400] rev 57
Merged CGAL 3.3 changes with the work on ARVineyard
Fri, 17 Aug 2007 15:04:28 -0400 Work in progress on ARVineyard and KineticSort. Commit to merge in CGAL 3.3 changes.
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 17 Aug 2007 15:04:28 -0400] rev 56
Work in progress on ARVineyard and KineticSort. Commit to merge in CGAL 3.3 changes.
Wed, 15 Aug 2007 11:52:17 -0400 tests/geometry now match the include/ breakup and are switched to CMake
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 15 Aug 2007 11:52:17 -0400] rev 55
tests/geometry now match the include/ breakup and are switched to CMake
Fri, 04 Apr 2008 16:17:28 -0400 Fixed the mislabeled Case 1.2 dev
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 04 Apr 2008 16:17:28 -0400] rev 54
Fixed the mislabeled Case 1.2
Wed, 26 Mar 2008 05:53:03 -0400 Added Poincare sphere example dev
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 26 Mar 2008 05:53:03 -0400] rev 53
Added Poincare sphere example
Wed, 26 Mar 2008 05:52:39 -0400 Fixed to compile with GCC 4.3 dev
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 26 Mar 2008 05:52:39 -0400] rev 52
Fixed to compile with GCC 4.3
Wed, 19 Mar 2008 12:43:33 -0400 Fixed CGAL assertion failures in alphashapes (explicitly checking for infinite simplices) dev
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 19 Mar 2008 12:43:33 -0400] rev 51
Fixed CGAL assertion failures in alphashapes (explicitly checking for infinite simplices)
Fri, 14 Mar 2008 20:21:15 -0400 Added ability to disable the use of DSR-PDB (disabled by default) dev
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Mar 2008 20:21:15 -0400] rev 50
Added ability to disable the use of DSR-PDB (disabled by default)
Fri, 14 Mar 2008 18:35:41 -0400 Normalized persistence (#cff) + unpaired simplices output pairs with 0 fitness
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Mar 2008 18:35:41 -0400] rev 49
Normalized persistence (#cff) + unpaired simplices output pairs with 0
Mon, 25 Feb 2008 16:24:29 -0500 avida-landscape: added MST (fixing #919) + switched to boost::program_options fitness
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 16:24:29 -0500] rev 48
avida-landscape: added MST (fixing #919) + switched to boost::program_options
Mon, 25 Feb 2008 04:39:27 -0500 avida-landscape pairs maxima of fitness rather than minima fitness
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Feb 2008 04:39:27 -0500] rev 47
avida-landscape pairs maxima of fitness rather than minima
Sun, 17 Feb 2008 16:32:33 -0500 avida-landscape computes 0-dimensional persistence of the fitness landscape
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 16:32:33 -0500] rev 46
avida-landscape computes 0-dimensional persistence of the fitness landscape
Sun, 17 Feb 2008 09:16:30 -0500 Merged the branch resulting from the upstream pull
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 09:16:30 -0500] rev 45
Merged the branch resulting from the upstream pull
Sun, 17 Feb 2008 09:16:00 -0500 Started examples/fitness/avida-landscape
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 09:16:00 -0500] rev 44
Started examples/fitness/avida-landscape
Thu, 27 Dec 2007 00:00:00 -0500 Added initial Avida code (computes 0-dimensional persistence of the hamming distance function)
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 27 Dec 2007 00:00:00 -0500] rev 43
Added initial Avida code (computes 0-dimensional persistence of the hamming distance function)
Sun, 17 Feb 2008 08:47:20 -0500 LowerStarFiltration provides a base class for VertexType
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 08:47:20 -0500] rev 42
LowerStarFiltration provides a base class for VertexType
Sun, 17 Feb 2008 08:23:55 -0500 Added issues
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 17 Feb 2008 08:23:55 -0500] rev 41
Added issues
Sun, 25 Nov 2007 09:12:36 -0500 Don't print a line if counters unused; in example/alphashapes converted cout to rInfo
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 25 Nov 2007 09:12:36 -0500] rev 40
Don't print a line if counters unused; in example/alphashapes converted cout to rInfo
Thu, 11 Oct 2007 11:46:00 -0400 Added 2D alpha shape filtration example
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 11 Oct 2007 11:46:00 -0400] rev 39
Added 2D alpha shape filtration example
Thu, 20 Sep 2007 08:02:49 -0400 Added ability to not store trails in pair_simplices() computation
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 20 Sep 2007 08:02:49 -0400] rev 38
Added ability to not store trails in pair_simplices() computation
Thu, 20 Sep 2007 07:31:40 -0400 Added counter of total trail and cycle lengths. Added CountBy.
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 20 Sep 2007 07:31:40 -0400] rev 37
Added counter of total trail and cycle lengths. Added CountBy.
Tue, 18 Sep 2007 05:45:19 -0400 Minor fixed to CMake (fixed include directory for rlog)
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 18 Sep 2007 05:45:19 -0400] rev 36
Minor fixed to CMake (fixed include directory for rlog)
Tue, 18 Sep 2007 05:45:04 -0400 Removed sz from Cycle (size is kept track of in the parent)
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 18 Sep 2007 05:45:04 -0400] rev 35
Removed sz from Cycle (size is kept track of in the parent)
Sat, 15 Sep 2007 14:31:36 -0400 Counter omits color codes only if connected to a TTY
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 15 Sep 2007 14:31:36 -0400] rev 34
Counter omits color codes only if connected to a TTY
Sat, 15 Sep 2007 04:42:15 -0400 Updated README to reflect changes to the logging
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 15 Sep 2007 04:42:15 -0400] rev 33
Updated README to reflect changes to the logging
Fri, 14 Sep 2007 17:32:11 -0400 Changes to CMakeLists:
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Sep 2007 17:32:11 -0400] rev 32
Changes to CMakeLists: * Optimize and debug options derive flags from CMKAE_CXX_FLAGS* * Moved CGAL CXX flags from the top level to the specific locations where they are required
Fri, 14 Sep 2007 06:34:43 -0400 Added counters to Cycle, added timestamp to Counter output
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Sep 2007 06:34:43 -0400] rev 31
Added counters to Cycle, added timestamp to Counter output
Fri, 14 Sep 2007 05:51:51 -0400 Fixed logging and counters
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 14 Sep 2007 05:51:51 -0400] rev 30
Fixed logging and counters
Thu, 13 Sep 2007 10:31:39 -0400 Counters straightened out (at least the code compiles)
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 13 Sep 2007 10:31:39 -0400] rev 29
Counters straightened out (at least the code compiles)
Thu, 13 Sep 2007 04:43:33 -0400 Merged in changes from master
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 13 Sep 2007 04:43:33 -0400] rev 28
Merged in changes from master
Thu, 13 Sep 2007 04:42:39 -0400 Changed counters and added setup for new logging. Everything but tests is broken.
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 13 Sep 2007 04:42:39 -0400] rev 27
Changed counters and added setup for new logging. Everything but tests is broken.
Wed, 12 Sep 2007 09:40:23 -0400 Merged in README changes from master
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 12 Sep 2007 09:40:23 -0400] rev 26
Merged in README changes from master
Wed, 12 Sep 2007 09:39:34 -0400 Changed SimplexWithVertices<V>::VertexContainer to std::vector<V> from std::set<V>
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 12 Sep 2007 09:39:34 -0400] rev 25
Changed SimplexWithVertices<V>::VertexContainer to std::vector<V> from std::set<V>
Wed, 12 Sep 2007 08:28:33 -0400 Fixed typos in README
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 12 Sep 2007 08:28:33 -0400] rev 24
Fixed typos in README
Thu, 16 Aug 2007 17:12:52 -0400 Fixed to compile with CGAL 3.3
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 16 Aug 2007 17:12:52 -0400] rev 23
Fixed to compile with CGAL 3.3
Wed, 15 Aug 2007 11:39:34 -0400 Merged geometry and include breakup with AR vineyard
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 15 Aug 2007 11:39:34 -0400] rev 22
Merged geometry and include breakup with AR vineyard
Wed, 15 Aug 2007 11:25:35 -0400 Initial AR vineyard commit (CGAL based, and not working)
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 15 Aug 2007 11:25:35 -0400] rev 21
Initial AR vineyard commit (CGAL based, and not working)
Tue, 14 Aug 2007 17:15:08 -0400 Broke include/ into separate topology/ and utilities/ subdirectories
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 14 Aug 2007 17:15:08 -0400] rev 20
Broke include/ into separate topology/ and utilities/ subdirectories
Sun, 01 Jul 2007 00:00:00 -0400 Initial geometry commit
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 01 Jul 2007 00:00:00 -0400] rev 19
Initial geometry commit
Wed, 23 May 2007 10:48:04 -0400 Added Cech complex example
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 23 May 2007 10:48:04 -0400] rev 18
Added Cech complex example
Wed, 07 Feb 2007 14:00:39 -0500 Switched counters to macros
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 07 Feb 2007 14:00:39 -0500] rev 17
Switched counters to macros
Wed, 31 Jan 2007 16:53:35 -0500 Alpha shapes examples compile with debugging enabled (Added AlphaSimplex3D::boundary())
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 31 Jan 2007 16:53:35 -0500] rev 16
Alpha shapes examples compile with debugging enabled (Added AlphaSimplex3D::boundary())
Tue, 30 Jan 2007 13:51:04 -0500 Switched to CMake
Dmitriy Morozov <morozov@cs.duke.edu> [Tue, 30 Jan 2007 13:51:04 -0500] rev 15
Switched to CMake
Wed, 24 Jan 2007 17:50:45 -0500 Added computation of PDBDistanceGrid for all atoms of the backbone (not just alpha-carbons)
Dmitriy Morozov <morozov@cs.duke.edu> [Wed, 24 Jan 2007 17:50:45 -0500] rev 14
Added computation of PDBDistanceGrid for all atoms of the backbone (not just alpha-carbons)
Sat, 20 Jan 2007 13:39:51 -0500 Removed config/ directory
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 20 Jan 2007 13:39:51 -0500] rev 13
Removed config/ directory
Fri, 12 Jan 2007 12:49:29 -0500 Options read from home or config directories; documentation built by default
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 12 Jan 2007 12:49:29 -0500] rev 12
Options read from home or config directories; documentation built by default
Mon, 01 Jan 2007 11:45:28 -0500 Added option to maintain lazy RU-decomposition during transpositions. Plus minor fixes.
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 01 Jan 2007 11:45:28 -0500] rev 11
Added option to maintain lazy RU-decomposition during transpositions. Plus minor fixes.
Fri, 29 Dec 2006 18:20:50 -0500 Added operator() to OrderList<T>::OrderComparison
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 29 Dec 2006 18:20:50 -0500] rev 10
Added operator() to OrderList<T>::OrderComparison
Mon, 25 Dec 2006 12:28:13 -0500 Added pair_simplices() to Filtration (without arguments)
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 25 Dec 2006 12:28:13 -0500] rev 9
Added pair_simplices() to Filtration (without arguments)
Fri, 22 Dec 2006 12:52:35 -0500 Added examples/alphashapes
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 22 Dec 2006 12:52:35 -0500] rev 8
Added examples/alphashapes
Fri, 22 Dec 2006 10:25:26 -0500 Added combustion-vineyard, Grid2DVineyard records diagram after adding a grid
Dmitriy Morozov <morozov@cs.duke.edu> [Fri, 22 Dec 2006 10:25:26 -0500] rev 7
Added combustion-vineyard, Grid2DVineyard records diagram after adding a grid
Thu, 21 Dec 2006 13:37:23 -0500 Removed missing tests/test-realtype from tests/SConscript
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 21 Dec 2006 13:37:23 -0500] rev 6
Removed missing tests/test-realtype from tests/SConscript
Thu, 21 Dec 2006 13:32:34 -0500 Switched to a new architecture (Vineyard is a visitor for Filtration),
Dmitriy Morozov <morozov@cs.duke.edu> [Thu, 21 Dec 2006 13:32:34 -0500] rev 5
Switched to a new architecture (Vineyard is a visitor for Filtration), added LowerStarFilation, examples/grid (pdbdistance-vineyard in particular)
Sat, 16 Dec 2006 15:34:46 -0500 Split OrderList into OrderList and ConsistencyList. Made efficient insertions possible.
Dmitriy Morozov <morozov@cs.duke.edu> [Sat, 16 Dec 2006 15:34:46 -0500] rev 4
Split OrderList into OrderList and ConsistencyList. Made efficient insertions possible.
Mon, 04 Dec 2006 22:39:35 -0500 Moved config to a separate directory
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 04 Dec 2006 22:39:35 -0500] rev 3
Moved config to a separate directory
Sun, 03 Dec 2006 22:38:34 -0500 Cleaned up AssertMsg in debug.h, and adjusted assertions in filtration.hpp
Dmitriy Morozov <morozov@cs.duke.edu> [Sun, 03 Dec 2006 22:38:34 -0500] rev 2
Cleaned up AssertMsg in debug.h, and adjusted assertions in filtration.hpp
Mon, 30 Oct 2006 14:40:34 -0500 Disabled missing qt4 tool, and added missing src/Sconcript
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 30 Oct 2006 14:40:34 -0500] rev 1
Disabled missing qt4 tool, and added missing src/Sconcript
Mon, 30 Oct 2006 14:20:45 -0500 Initial conversion to Dionysus architecture
Dmitriy Morozov <morozov@cs.duke.edu> [Mon, 30 Oct 2006 14:20:45 -0500] rev 0
Initial conversion to Dionysus architecture
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