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author | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-06-01 08:42:39 +0000 |
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committer | cjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2017-06-01 08:42:39 +0000 |
commit | 0a66874247cb6ab10a2d96e22ecd5009113291d2 (patch) | |
tree | 76fc9d178c6da723b130ff8f704a1ee7ad404010 /src/Persistent_cohomology/utilities/README | |
parent | 3f6290ba33cedec91ca69866d1be33bb4887e31f (diff) |
Split and fix README file
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2496 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 0eecb1e37fd208522de15369ac8cf4c960c214c5
Diffstat (limited to 'src/Persistent_cohomology/utilities/README')
-rw-r--r-- | src/Persistent_cohomology/utilities/README | 114 |
1 files changed, 114 insertions, 0 deletions
diff --git a/src/Persistent_cohomology/utilities/README b/src/Persistent_cohomology/utilities/README new file mode 100644 index 00000000..76e960da --- /dev/null +++ b/src/Persistent_cohomology/utilities/README @@ -0,0 +1,114 @@ +To build the utilities, run in a Terminal: + +cd /path-to-utilities/ +cmake . +make + +*********************************************************************************************************************** +Example of use of RIPS: + +Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points +sampling a 3D torus: + +./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2 + +output: +2 0 0 inf +2 1 0.0983494 inf +2 1 0.104347 inf +2 2 0.138335 inf + + +Every line is of this format: p1*...*pr dim b d +where + p1*...*pr is the product of prime numbers pi such that the homology feature exists in homology with Z/piZ coefficients. + dim is the dimension of the homological feature, + b and d are respectively the birth and death of the feature and + + + +with Z/3Z coefficients: + +./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 + +output: +3 0 0 inf +3 1 0.0983494 inf +3 1 0.104347 inf +3 2 0.138335 inf + +*********************************************************************************************************************** +Example of use of ALPHA: + +For a more verbose mode, please run cmake with option "DEBUG_TRACES=TRUE" and recompile the programs. + +1) 3D special case +------------------ +Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points +sampling a torus 3D: + +./alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45 + +output: +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 + +N.B.: - alpha_complex_3d_persistence accepts only OFF files in 3D dimension. + - filtration values are alpha square values + +2) d-Dimension case +------------------- +Computation of the persistent homology with Z/2Z coefficients of the alpha complex on points +sampling a torus 3D: + +./alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off + +output: +Alpha complex is of dimension 3 - 9273 simplices - 300 vertices. +Simplex_tree dim: 3 +2 0 0 inf +2 1 0.0682162 1.0001 +2 1 0.0934117 1.00003 +2 2 0.56444 1.03938 + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 2 +Betti numbers[2] = 1 + +N.B.: - alpha_complex_persistence accepts OFF files in d-Dimension. + - filtration values are alpha square values + +3) 3D periodic special case +--------------------------- +./periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt 3 1.0 + +output: +Periodic Delaunay computed. +Simplex_tree dim: 3 +3 0 0 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 1 0.0025 inf +3 2 0.005 inf +3 2 0.005 inf +3 2 0.005 inf +3 3 0.0075 inf + +Here we retrieve expected Betti numbers on a tore 3D: +Betti numbers[0] = 1 +Betti numbers[1] = 3 +Betti numbers[2] = 3 +Betti numbers[3] = 1 + +N.B.: - periodic_alpha_complex_3d_persistence accepts only OFF files in 3D dimension. In this example, the periodic cube +is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] } + - filtration values are alpha square values |