1 files changed, 56 insertions, 33 deletions
diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/README
index 6e7d16b7..c3dd170b 100644
--- a/src/Alpha_complex/utilities/README
+++ b/src/Alpha_complex/utilities/README
@@ -8,22 +8,24 @@ This program computes the persistent homology with coefficient field Z/pZ of the
 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` must be a prime number).
 
 **Usage**
-`alpha_complex_3d_persistence <input OFF file> <p> <min_persistence>` 
-where
-`<input OFF file>` is the path to the input point cloud in OFF format.
-`<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer.
-`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+`alpha_complex_3d_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.
+* `-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**
-`alpha_complex_3d_persistence ../../data/points/tore3D_300.off 2 0.45`
+`alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45`
 
 outputs:
 ```
 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 
+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:
@@ -48,21 +50,34 @@ Same as `alpha_complex_3d_persistence`, but using exact computation. It is slowe
 Same as `alpha_complex_3d_persistence`, but using weighted points.
 
 **Usage**
-`weighted_alpha_complex_3d_persistence <input OFF file> <input weights file> <p> <min_persistence>` 
-where
-`<input OFF file>` is the path to the input point cloud in OFF format.
-`<input weights file>` is the path to the file containing the weights of the points (one value per line).
-`<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer.
-`<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
+`weighted_alpha_complex_3d_persistence [options] <OFF input file> <weights 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.
+* `-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**
+`weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -p 2 -m 0.45`
 
-## `periodic_alpha_complex_3d_persistence` ##
-This program computes the persistent homology with coefficient field Z/pZ of the 3D periodic alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:
+outputs:
+```
+Simplex_tree dim: 3
+2  0 -1 inf
+2  1 -0.931784 0.000103311
+2  1 -0.906588 2.60165e-05
+2  2 -0.43556 0.0393798
+```
 
-`p dim b d`
+N.B.:
+* Weights values are explained on CGAL [Alpha shape](https://doc.cgal.org/latest/Alpha_shapes_3/index.html#title0)
+and [Regular triangulation](https://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation3secclassRegulartriangulation) documentation.
+* Filtration values are alpha square values.
 
-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` must be a prime number).
+
+## `periodic_alpha_complex_3d_persistence` ##
+Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d.
 
 **Usage**
 `periodic_alpha_complex_3d_persistence <input OFF file> <cuboid file> <p> <min_persistence>`
@@ -72,21 +87,31 @@ where
 `<p>` is the characteristic p of the coefficient field *Z/pZ* for computing homology. It must be a stricly positive integer.
 `<min_persistence>` is the minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
 
+**Usage**
+`./periodic_alpha_complex_3d_persistence [options] input-file cuboid-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.
+* `-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**
-`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`
+`periodic_alpha_complex_3d_persistence ../../data/points/grid_10_10_10_in_0_1.off ../../data/points/iso_cuboid_3_in_0_1.txt -p 3 -m 1.0`
 
 outputs:
 ```
 Periodic Delaunay computed.
 Simplex_tree dim: 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 
+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 an 3D iso-oriented cuboids:
@@ -98,14 +123,12 @@ Betti numbers[3] = 1
 ```
 
 N.B.: 
-* `periodic_alpha_complex_3d_persistence` only accepts OFF files in dimension 3.
-* In this example, the periodic cube is hard coded to { x = [0,1]; y = [0,1]; z = [0,1] }
+* Cuboid file must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).
 * Filtration values are alpha square values.
 
 
 
 
-
 ## `alpha_complex_persistence` ##
 This program computes the persistent homology with coefficient field Z/pZ of the dD alpha complex built from a dD point cloud. The output diagram contains one bar per line, written with the convention:
 
@@ -119,7 +142,7 @@ where `dim` is the dimension of the homological feature, `b` and `d` are respect
 **Allowed options**
 
 * `-h [ --help ]` Produce help message
-* `-o [ --output-file ]` Name of file in which the persistence diagram is written. By default, print in std::cout.
+* `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
 * `-r [ --max-alpha-square-value ]` (default = inf) Maximal alpha square value for the Alpha complex construction.
 * `-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.