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author | glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-02-01 18:21:07 +0000 |
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committer | glisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2018-02-01 18:21:07 +0000 |
commit | 7100f2e782d21bfbbb3947ba66fe235b424e2902 (patch) | |
tree | 0066eacaf521040e42d058eb3be6e10ecbd47be1 /src/Rips_complex/utilities | |
parent | 24386d494ba4b8bb19b4559f6d2b3e4ecc980571 (diff) |
Really remove README, merge didn't dare.
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-glisse@3202 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 7b05c5e75821d6a1b0759db13d326a6e142cc01b
Diffstat (limited to 'src/Rips_complex/utilities')
-rw-r--r-- | src/Rips_complex/utilities/README | 110 |
1 files changed, 0 insertions, 110 deletions
diff --git a/src/Rips_complex/utilities/README b/src/Rips_complex/utilities/README deleted file mode 100644 index 390e31f8..00000000 --- a/src/Rips_complex/utilities/README +++ /dev/null @@ -1,110 +0,0 @@ -# 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. 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` - -outputs: -``` -2 0 0 inf -2 1 0.0983494 inf -2 1 0.104347 inf -2 2 0.138335 inf -``` - -**Example 2 with Z/3Z coefficients** - -rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 3 - -outputs: -``` -3 0 0 inf -3 1 0.0983494 inf -3 1 0.104347 inf -3 2 0.138335 inf -``` - - - - -## `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` - -outputs: -``` -The complex contains 46 simplices - and has dimension 3 -3 0 0 inf -3 0 0 8.94427 -3 0 0 7.28011 -3 0 0 6.08276 -3 0 0 5.83095 -3 0 0 5.38516 -3 0 0 5 -3 1 11 12.0416 -3 1 6.32456 6.7082 -``` - - - - -## `rips_persistence` ## -This program computes the persistent homology with coefficient field *Z/pZ* -of a sparse (1+epsilon)-approximation of the Rips complex defined on a set of input points. 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** -`sparse_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. -* `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex. -* `-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. - -**Example with Z/2Z coefficients** -`rips_persistence ../../data/points/tore3D_1307.off -e .5 -m .2 -d 3 -p 2` - -may output (there is randomness involved): -``` -The complex contains 17002096 simplices - and has dimension 3 -2 0 0 inf -2 1 0.104347 1.29343 -2 2 0.138335 0.577743 -2 1 0.0983494 0.529708 -``` |