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authorcjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-06-01 08:42:39 +0000
committercjamin <cjamin@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2017-06-01 08:42:39 +0000
commit0a66874247cb6ab10a2d96e22ecd5009113291d2 (patch)
tree76fc9d178c6da723b130ff8f704a1ee7ad404010 /src/Persistent_cohomology/utilities
parent3f6290ba33cedec91ca69866d1be33bb4887e31f (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
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+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