1 files changed, 51 insertions, 99 deletions
diff --git a/src/Persistent_cohomology/utilities/README b/src/Persistent_cohomology/utilities/README
index 76e960da..eecee7ee 100644
--- a/src/Persistent_cohomology/utilities/README
+++ b/src/Persistent_cohomology/utilities/README
@@ -1,114 +1,66 @@
-To build the utilities, run in a Terminal:
+# Persistent_cohomology #
 
-cd /path-to-utilities/
-cmake .
-make
+## `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:
 
-***********************************************************************************************************************
-Example of use of RIPS:
+`p dim b d`
 
-Computation of the persistent homology with Z/2Z coefficients of the Rips complex on points 
-sampling a 3D torus:
+where `dim` is the dimension of the homological feature, `b` and `d` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p = p1*...*pr` is the product of prime numbers *pi* such that the homology feature exists in homology with *Z/piZ* coefficients).
 
-./rips_persistence ../../data/points/tore3D_1307.off -r 0.25 -m 0.5 -d 3 -p 2
+**Usage**
+`rips_persistence [options] <OFF input file>`
 
-output:
-2  0 0 inf 
+**Allowed options**
+
+* `-h [ --help ]` Produce help message
+* `-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.
+
+**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**
 
-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
-   
+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
+```
 
-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
+
+## `rips_distance_matrix_persistence` ##
+Same as `rips_persistence` but taking an distance matrix as input.
+
+**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  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
+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 
+```