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authorglisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2018-02-01 18:21:07 +0000
committerglisse <glisse@636b058d-ea47-450e-bf9e-a15bfbe3eedb>2018-02-01 18:21:07 +0000
commit7100f2e782d21bfbbb3947ba66fe235b424e2902 (patch)
tree0066eacaf521040e42d058eb3be6e10ecbd47be1 /src/Rips_complex
parent24386d494ba4b8bb19b4559f6d2b3e4ecc980571 (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
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-# 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
-```