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2017-11-09Answer to Vincent's comments.pdlotko
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2859 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1a049ce98ccf893fc6af6c2631e508d3a9dc6c09
2017-11-09Merge last trunk modificationsvrouvrea
Comment some bad code Try to cythonize rips from correlation matrix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2858 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3b9bcdfdeae247ed5486e20cb62f2812fdd14b0d
2017-11-07Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake.3.9.fix@2847 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 02939a55292a81e9fed3387f8d3e6726283d964b
2017-11-07Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cgal_4.11.fix@2839 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 22158e5d4aae2b6c0e5502c585cb6c513c08ac63
2017-11-06Add Alpha complex 3d fix for cgal 4.11vrouvrea
Add weighted_periodic_alpha_complex_3d_persistence example git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cgal_4.11.fix@2837 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 07d016f7879220064b53ccfe19b169f06e79c86f
2017-11-06Fix typedefcjamin
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cgal_4.11.fix@2833 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1f970c56378222a29d03724d4ebd2e3c3084ba57
2017-11-06Rollback commented linesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2831 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 052a8f264877e7ffa87f8c81abf0f0c83cb60d54
2017-11-06Doc review : dimension() method documentation can not mention ↵vrouvrea
lower_upper_bound_dimension as it is a private method. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2830 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fec09d2a0b0f896c848a13c54d21625d08efc997
2017-11-06doc review : upper_bond_dimension to be replaced with upper_bound_dimensionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2829 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ca70d79176d406f63c3372dd7e062f108365b99f
2017-11-03a few more changespdlotko
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2823 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d12b2413620003883e82b3022f8d933aa05e2856
2017-10-26Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2811 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2a37c02ca51d0df28a981207db6ecc1bd0991ffa
2017-10-26Code review: downgrade_dimension renamed lower_upper_bound_dimension and ↵vrouvrea
make it private. Automatically when dimension_to_be_lowered_ is set (on removal) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2810 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c764433bcc5357acc6454683d4f4182c7c960d6d
2017-10-20Use simplices iterator instead of skeleton iteratorvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2798 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 856d2655901b01dd3e75f428f364ab7ac4f07aee
2017-10-20Code review : rename automatic_dimension_set with downgrade_dimensionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2796 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3b094bc579367d40790c3791f2c4a3700a3d93ae
2017-10-20Doc review: remove_maximal_simplex about automatic_dimension_set mechanism ↵vrouvrea
was too strict. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2795 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0226b3ee6a082b109185c9eff8c1601b61d4f667
2017-10-19Code review : remove template specification for std::maxvrouvrea
Fix cython tests accordingly to the other modifications git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2794 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e1009a3304455fa26fbd368c4cce4451bc3d7784
2017-10-10Fix tests and homogenize codevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2775 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bdcc278981e2683a5b49f241f07704f3d5c7ca4e
2017-10-10Fix CGAL 4.11 bug and remove old_interface file. Better done with #ifvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2774 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9a905b04cfa2718f9d5abc80e14ab1ee26d16279
2017-10-05Doc review : automatic_dimension_set return documentation was not clearvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2761 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 04b4dee9d228923f36062001529476251eac4ef0
2017-10-05Doc review : prune_above_filtration about automatic_dimension_set mechanism ↵vrouvrea
was too strict. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2760 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bccef80ba3f70f87dff28cfa3a85c50f072f695e
2017-10-05Merge the branch graph_expansion_with_blocker_oracle for the Simplex_treevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2759 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fa4cf79042f8e9b162617a5a571e06a3feb4c191
2017-10-05Doc review : fix find_child explanationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/graph_expansion_with_blocker_oracle@2758 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 30759214110b29a525cbbf2d97ff84b92b4eace2
2017-10-02Fix weighted periodic alpa complex 3d example testvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2748 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ddf754a1f8046c7b17db89668cf8d4dd95f69dac
2017-10-02remove test_cgalvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2747 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9b036eb3ccef79e012eacb045a0dda37db1de994
2017-10-02Fix weighted periodicvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2746 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: bf90bfffbc00efe5f391e45ac8ece6ff6e9d57ea
2017-10-02Fix weighted_alpha_complex_3d_persistence to work with CGAL 4.11 (2 cpp and ↵vrouvrea
cmake compiles the correct one) Homogeneize alpha_complex_3d* codes Fix weighted_periodic_alpha_complex_3d_persistence with CGAL doc help Add grid off file with weights to test weighted_periodic_alpha_complex_3d_persistence git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2744 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ecc4f3629e75bd986ffd22ec348f0412163e4dbd
2017-10-01Euclidean Witness examples requires CGAL >= 4.8.1 because it is using ↵vrouvrea
subsampling (CMake and install doc) Bad link to Gudhi bibtex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2741 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8c1b84a4030029ec7d1470c49662e15836cf02de
2017-09-29Build doc issuevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2736 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 438179e355d47083f9db2c237d7ceb132c7b0168
2017-09-29Gudhi version 2.0.1vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2734 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3ce829b94a61b9649b663ee85bc68b74f75eb59e
2017-09-29Doc issue fixvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2733 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ea0323fed1ca42ecee50d6fbf9db9fbfb3e64cc9
2017-09-29Rename a few functions in Kd_tree_searchcjamin
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2730 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f009977d25c76cc0f6116093a448fab258c8626b
2017-09-28Fix some doc issuevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2728 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9a9745d18a37b53618aa3054114f26a8bdbc0009
2017-09-28Remove python rips_complex construction from files as it can lead to errors ↵vrouvrea
with correlation matrix Add examples for doxygen Cythonization of rips correlation matrix git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2727 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8aae33839fa27f9d26897e625904671b2c05e0e7
2017-09-28Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2725 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 78f35b92214c207f00b26ea87ca88d20abeea53d
2017-09-27Fix some cpplintsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2721 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 76b127e54d9511b70294ab48336ca6dbd6fdb1d6
2017-09-27Merge last trunk modificationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2720 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 37cec1ea1e06c9e9656962614fcddc0fa022c5d0
2017-09-27Replace INFINITY with std::numeric_limits<Filtration_value>::infinity()vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2719 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b24d3381da60cd634142e3024d5f5ed53294f8e8
2017-09-26adding a version of periodic weighted alpha shape (that unfortunatelly do ↵pdlotko
not work yet...) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2718 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 611967b7fc8257fb2ae27ecc42f0e303c183755a
2017-09-26Doc review : Simplex tree remove maximal simplex is an implementatino detail ↵vrouvrea
that is not needed by the developper git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/graph_expansion_with_blocker_oracle@2717 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d096485bf30e50c804cf349f040f57764770136f
2017-09-26Merge weighted alpha complex fix branchvrouvrea
Add some text to 3d alpha complexes in the usage function git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2716 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6f2ee1897438a6bf75b484c2c625c43f2571ab41
2017-09-26Gudhi 2.0.1-rc2 versionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2715 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 76499766ca670017df0c963c3b5a49c343eb1a47
2017-09-25a missing file...pdlotko
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2713 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ecdf0da96de01e37758e157d84aee13c8825dc0e
2017-09-25Adding all that is needed for Rips complex construction from correlation ↵pdlotko
matrix. Moduo the fact that I cannot see the doc (althoug make doxygen do not create any errors), this is ready for review. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2712 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e8e7acceaf2be6f17baa3d77c85e207a74a4fb33
2017-09-25Do not advertise nor use the exact bottleneck distance versionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2711 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e441b042d15bfbe727789803ca17b17711a48d9c
2017-09-25Fix weighted alpha complex 3dvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2709 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3e7d1f73038d193b566e790a3095b6f802c48b48
2017-09-22Remove global filtration attribute of te simplex tree (including getter and ↵vrouvrea
setter) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2705 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a6c179ae47e61d1ca12d1f54c4ae1fc0e3c1fde2
2017-09-22Remove automatic_dimension_set call from remove and prune functionsvrouvrea
Make it public to be available Modify tests accordingly git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2703 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2ff42d5327ae76b121390a913c4e548d6f59ea99
2017-09-21Remove set_dimension from examplesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2698 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cde0919e6bb53ad8ace21f1c6894708468449276
2017-09-21Add some comments for readabilityvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2697 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 986cc3b862ceca993a6fdd8cdee6da2c1ed4cc14
2017-09-20Roll back simplex tree set_filtration modification (assign_filtration ↵vrouvrea
asserts in debug) and modify test git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_automatic_dimension_set@2694 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d08cc4b4f310784975b81d10b7ebd78063c42378
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