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author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-02-02 15:45:06 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-02-02 15:45:06 +0000 |
commit | 5ae31a73253f6b29f5cbf1e04af17acf62741d9e (patch) | |
tree | 512041b9bf0835f2520e5b6b2fde0f972998efc4 /src/Rips_complex/utilities/ripscomplex.md | |
parent | 4a5332dfb88ec27157c82f77df87f588f7016736 (diff) | |
parent | 265484997185f3bf900744406206a2d64ca0a20d (diff) |
Merge last trunk modificat
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@3212 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: ea6296547b67ad82f5983d4309493e9131da7dd0
Diffstat (limited to 'src/Rips_complex/utilities/ripscomplex.md')
-rw-r--r-- | src/Rips_complex/utilities/ripscomplex.md | 49 |
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diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md new file mode 100644 index 00000000..4291fae7 --- /dev/null +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -0,0 +1,49 @@ + + +# Rips complex # + +## rips_persistence ## +This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention: + +`p dim birth death` + +where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number). + +**Usage** + +`rips_persistence [options] <OFF input file>` + +**Allowed options** + +* `-h [ --help ]` Produce help message +* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output. +* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Rips complex construction. +* `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute. +* `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology. +* `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals. + +Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value. + +**Example 1 with Z/2Z coefficients** + +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2` + +**Example 2 with Z/3Z coefficients** + +`rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3` + + +## rips_distance_matrix_persistence ## + +Same as `rips_persistence` but taking a distance matrix as input. + +**Usage** + +`rips_persistence [options] <CSV input file>` + +where +`<CSV input file>` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'. + +**Example** + +`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0` |