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---
layout: page
title: "Rips complex"
meta_title: "Rips complex"
teaser: ""
permalink: /ripscomplex/
---
{::comment}
Leave the lines above as it is required by the web site generator 'Jekyll'
{:/comment}
## 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_distance_matrix_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 ';'.
The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input.
Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file.
**Example**
`rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
## rips_correlation_matrix_persistence ##
Same as `rips_distance_matrix_persistence` but taking a correlation matrix as input.
**Usage**
`rips_correlation_matrix_persistence [options] <CSV input file>`
where
`<CSV input file>` is the path to the file containing a correlation matrix. Can be square or lower triangular matrix. Separator is ';'.
Note that no check is performed if the matrix given as the input is a correlation matrix.
It is the user responsibility to ensure that this is the case.
Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file.
**Example**
`rips_correlation_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
**Warning**
As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical tool will not work
properly, this is a known issue.
## sparse_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 Euclidean 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**
`sparse_rips_persistence ../../data/points/tore3D_1307.off -e .5 -m .2 -d 3 -p 2`
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