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2016-02-19Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1032 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0e5b89e0ea0d69ebfdb74ba3bbf29518f7ce5ce8
2016-02-04CMake strategy modificationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Win64_Boost_Xunit_fix@1003 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c917934525e020b54b2f4506b5c9d060a28c9d89
2016-02-02Make example for doc shorter. Include strategy reviewalvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@992 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 23d3e71d7d0fb4d649f73e53959626c5cbb0acd8
2016-02-02rename alpha_shapes_persistence test with alpha_complex_3d_persistencevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@991 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 455ee94450098bbcc000fb2ab2c4d39a326dea2c
2016-01-12Backmerge of last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@959 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a5c6ef0ae2ee1e18fff88b98131ff4d14a252152
2016-01-12Fix alpha complex remarks and bugsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@957 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fa837fd1a4373c2322db16353d98767907f34c79
2016-01-08cpplint and cppcheck fixesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@956 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f54c0a2a375e8818c7162aec05249e446361834b
2016-01-08tbb branch merge. Link with Intel TBB for parallel programmation.vrouvrea
Reduce persistence UT timings. Add parallel_rips_persistence compilatino and test. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@954 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4623c6a0c31d2b9574e2bb33836261fc26a89555
2016-01-07Backmerge from trunkvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tbb@953 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 06624ae4ed4031c7bae56e0b8fa305a318b934bc
2016-01-07Backmerge of trunkvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/contiguous_vertices@949 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b20b49bab38fdcbc6571c159200125148e9a1bd6
2015-12-15Don't use boost::tuple.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@946 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3988b09fafda67297cac8bd68629310cdfdc607e
2015-12-11Clarify the semantics of FilteredComplex::simplex(key).glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@941 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a2cb908a642ef53c5de25ba5113e03bb45652b9b
2015-11-27After doc reviewvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@931 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 578da0e6fff453560e666e8f00147f9e10cb6de6
2015-11-23Backmerge of trunkvrouvrea
Add alpha complex in bibtex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@929 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c8975be439b3e9e91d1fd6ad988db12c75d0395b
2015-11-15Fix for older libstdc++.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@922 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d370bbf81488ef6b07a17d63ad43ba2b813e2210
2015-11-13Reintegrate branch annotations_in_boundary.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@916 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4dc69dee0f4417a7fe6b0544bb5fe561466f54db
2015-11-13Unobfuscate a multiplication.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@915 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 771fd96e47209ceee8ffa05519134f0c8069b1cf
2015-11-13Using a static variable really helps.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/annotations_in_boundary@914 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 695a6f642399c2646e5a26fac20173fbd57fe160
2015-11-13Rename variable.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/annotations_in_boundary@913 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0afbcbee5739c1649d1c9b968d9f0748c7d1d219
2015-11-13Clean-up.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/annotations_in_boundary@912 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f5652acf2ed5eb6f11428d2907963b5d1a1359be
2015-11-11Make annotations_in_boundary a vector, sorted once after construction, with ↵glisse
entries sharing the same annotation accumulated as we go. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/annotations_in_boundary@909 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 34b2ae74dc017c18a90e08caee6f707b6b0d4cc2
2015-11-11Revert the last commit, this was supposed to go to a branch.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@908 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 66d468165b97b852fbe897bea212c85ac9fb0e14
2015-11-11Make annotations_in_boundary a vector, sorted once after construction, with ↵glisse
entries sharing the same annotation accumulated as we go. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@907 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 68351e5d61b1e3eb0b2d6c3623d7d213da9371d4
2015-11-10Update a comment in plain_homology.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@901 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9a04cd581e4b4a2ea26c474ec0928a67b990dc98
2015-11-10Merge from trunk.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/contiguous_vertices@900 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9b9e886cd54b1a91c5c794242fe099e57e6d6a19
2015-11-10Use Simplex_tree_options_fast_persistence in one more place.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/contiguous_vertices@899 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b22785182c0140dd36d1a4876c240aa4deabef75
2015-11-09New Simplex_tree_options_fast_persistence, while ↵glisse
Simplex_tree_options_full_featured switches to the safe default of allowing non-contiguous vertices. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/contiguous_vertices@896 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 60bc11a90027ed17233903d22a6494198f30eeb1
2015-11-09Backmerge from trunk.vrouvrea
Alpha complex code review. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@894 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 702c4d667de4e7191d1050e6d855d2f79117f954
2015-11-09Modification for Porquerolles Workshopvrouvrea
Bar_code_persistence and alpha_complex_persistence git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@893 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 63d2d21d5ff7c9a94a67eafc326bf8a561bf8166
2015-10-29Add an example that computes (non-persistent) homology.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@880 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 21606fab3356681780ad446e73d5da56b29ec31d
2015-10-25Example to compute persistence of a Rips filtration "in parallel". On a machineglisse
with a gazillion cores, it gains a factor >2 at the expense of some memory. At this point, construction of the Rips graph and expansion are not negligible anymore and could use some parallelism. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/tbb@875 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 53d6a74338f1346bd7d1ca018ec15dd1ee8287e8
2015-10-18Update performance_rips_persistence, which hasn't been working for a long ↵glisse
time. We might want to run it in the testsuite with a smaller parameter so it doesn't take too long. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@863 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1fd91395f855297cf4815d64e94b06a8c400c99b
2015-10-12Fix program_options issue with MSVCvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@850 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b2a90b0c494f0eae1da67e23527946733d501643
2015-10-08cpplint fixesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@845 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8b15f0805527b494f3a57625de5c69d836b287dd
2015-10-08Fix cpplint on examples.vrouvrea
Bug fix on persistence_from_simple_simplex_tree. Add persistence examples tests. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@843 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9b7b73abb4a5d6bb110376deb689247bfdae035c
2015-10-05No need for Persistent_cohomology_column to have everything private.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@828 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9eea246613f29f78d88e8f1b25cf341c05e5098c
2015-10-05cpplint fixes - simplex_tree_from_file.cpp renamed ↵vrouvrea
simplex_tree_from_cliques_of_graph.cpp - #include "" vs #include <> for skeleton blockers git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@826 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1bd1ad535e4283bce35eeb31fa8d7896b9de474b
2015-10-02Doxygen to be made from user version. Hypergenerator fix. Add definitions ↵vrouvrea
for debug traces. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@821 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5625aaab792264df86d7d442a2e6ff9886cf5d24
2015-09-28Minor optimization: no need to return memory to the dying pool.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/pool@803 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5ea7edddd00890a060d4a77302d239e9e8ef0c85
2015-09-28Merge from trunkglisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/pool@802 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4928a537016044c8263cf7f4980caabfcdd108a0
2015-09-28Release CAM cells.glisse
There are a lot of intrusive containers in there, and I believe that most could be replaced with regular containers. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@800 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7246d7db0511ac6bffee2f645c006416a986629d
2015-09-28Minor clean-ups (const, for-range, etc).glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@798 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: de10cc12d852eab34e258bbfb98ff0aef864e453
2015-09-26Replace boost::object_pool by a simpler, more scalable version.glisse
Not ready for trunk, it causes a memory leak, visible for instance with valgrind on PersistentCohomologyMultiFieldUT. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/pool@797 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 20a8296db22f253d49c10edd565557123fdc7c6f
2015-09-16Filtration_simplex_iterator's reference type does not have to be a ↵glisse
reference, and Simplex_handle has to be cheap anyway. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@789 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a3fbf340b9ab3d2186616f14f4b96d3188dafd14
2015-08-20Store num_simplices in persistent_cohomology to avoid to call the function 3 ↵vrouvrea
times. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/num_simplices@748 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 868c69508bd6307c805cfc1a0cab00631c79c000
2015-08-19num_simplices computation instead of increment/set methods.vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/num_simplices@743 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 42bad5e259ea540b5ec020f293b2dff86c83101f
2015-07-11Clean-upsglisse
Avoid duplicate search with find+insert. No need to store 0 and 1 and return them by reference. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@702 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 28403136284a9fe2044b9d51bc2f10861b3a09e7
2015-07-11Clean-upsglisse
Use vector instead of list. Use emplace more. Use std::max. Some const. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@701 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 275156e94b4c9900c0af43ed7b74c7bff40bd7fd
2015-07-08Clang boost test segmentation fault fixvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@697 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ddfc6fe41d7112fd6b6c68eadf45e468f2c8904b
2015-06-30clang requires include fstream (Persistent_cohomology.h)vrouvrea
clang build fails if include guard macro are not correctly defined + goole style fix (Skeleton_blockers_simplices_iterators.h) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/compil_fix@665 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4bbc74ac4726af768816c322bf77e104a1dcf1e6
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