Merge from trunk.

hand-merge README that moved to *.md.


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/sparserips-glisse@3201 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f1922a265c79937e507bbb963875d21fae88069e

7 files changed, 114 insertions, 137 deletions

diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
index 3747923f..a59f0654 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
@@ -52,7 +52,7 @@ Vertex_list from_facet(const Facet& fct) {
 template <class Vertex_list, class Edge_3>
 Vertex_list from_edge(const Edge_3& edg) {
   Vertex_list the_list;
-  for (auto i : { edg.second, edg.third }) {
+  for (auto i : {edg.second, edg.third}) {
 #ifdef DEBUG_TRACES
     std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
 #endif  // DEBUG_TRACES
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 1070d17b..8ef5ffb2 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -138,16 +138,16 @@ int main(int argc, char **argv) {
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
-    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
-    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
-    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
@@ -173,13 +173,12 @@ int main(int argc, char **argv) {
       }
     }
     // Construction of the simplex_tree
-    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
+    Filtration_value filtr = /*std::sqrt*/ (*the_alpha_value_iterator);
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
     simplex_tree.insert_simplex(the_simplex, filtr);
-    GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(),
-        "CGAL provided more simplices than values");
+    GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values");
     ++the_alpha_value_iterator;
   }
 
diff --git a/src/Alpha_complex/utilities/README b/src/Alpha_complex/utilities/alphacomplex.md
index 1cd2ca95..aace85d3 100644
--- a/src/Alpha_complex/utilities/README
+++ b/src/Alpha_complex/utilities/alphacomplex.md
@@ -1,14 +1,26 @@
-# Alpha_complex #

 

-## `alpha_complex_3d_persistence` ##

-This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:

 

-`p dim birth death`

+# Alpha complex #

 

-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).

+

+## 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:

+

+```

+   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**

-`alpha_complex_3d_persistence [options] <input OFF file>`

+

+```

+   alpha_complex_persistence [options] <input OFF file>

+```

+

 where

 `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

 

@@ -16,47 +28,37 @@ where
 

 * `-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.

+* `-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.

 

 **Example**

-`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

+   alpha_complex_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off

 ```

 

-Here we retrieve expected Betti numbers on a tore 3D:

-```

-Betti numbers[0] = 1

-Betti numbers[1] = 2

-Betti numbers[2] = 1

-```

+N.B.:

 

-N.B.: 

-* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3.

 * Filtration values are alpha square values.

 

 

+## alpha_complex_3d_persistence ##

+This program computes the persistent homology with coefficient field Z/pZ of the 3D alpha complex built from a 3D point cloud. The output diagram contains one bar per line, written with the convention:

 

-## `exact_alpha_complex_3d_persistence` ##

-Same as `alpha_complex_3d_persistence`, but using exact computation. It is slower, but it is necessary when points are on a grid for instance.

+```

+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**

 

-## `weighted_alpha_complex_3d_persistence` ##

-Same as `alpha_complex_3d_persistence`, but using weighted points.

+```

+   alpha_complex_3d_persistence [options] <input OFF file>

+```

 

-**Usage**

-`weighted_alpha_complex_3d_persistence [options] <input OFF file> <weights input file>`

-where

-`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

-`<input weights file>` is the path to the file containing the weights of the points (one value per line).

+where `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

 

 **Allowed options**

 

@@ -66,112 +68,91 @@ where
 * `-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`

 

-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

+alpha_complex_3d_persistence ../../data/points/tore3D_300.off -p 2 -m 0.45

 ```

 

 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.

+

+* `alpha_complex_3d_persistence` only accepts OFF files in dimension 3.

 * Filtration values are alpha square values.

 

 

-## `periodic_alpha_complex_3d_persistence` ##

-Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d.

-Refer to the [CGAL's 3D Periodic Triangulations User Manual](https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) for more details.

+## exact_alpha_complex_3d_persistence ##

+

+Same as `alpha_complex_3d_persistence`, but using exact computation.

+It is slower, but it is necessary when points are on a grid for instance.

+

+

+

+## weighted_alpha_complex_3d_persistence ##

+

+Same as `alpha_complex_3d_persistence`, but using weighted points.

 

 **Usage**

-`periodic_alpha_complex_3d_persistence [options] <input OFF file> <cuboid file>`

+

+```

+   weighted_alpha_complex_3d_persistence [options] <input OFF file> <weights input file>

+```

+

 where

-`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

-`<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described [here](http://gudhi.gforge.inria.fr/doc/latest/fileformats.html#FileFormatsIsoCuboid).

+

+* `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+* `<input weights file>` is the path to the file containing the weights of the points (one value per line).

 

 **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

-

+* `-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 -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

-```

 

-Here we retrieve expected Betti numbers on an 3D iso-oriented cuboids:

 ```

-Betti numbers[0] = 1

-Betti numbers[1] = 3

-Betti numbers[2] = 3

-Betti numbers[3] = 1

+   weighted_alpha_complex_3d_persistence ../../data/points/tore3D_300.off ../../data/points/tore3D_300.weights -p 2 -m 0.45

 ```

 

-N.B.: 

-* 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.

 

+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.

 

 

-## `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:

+## periodic_alpha_complex_3d_persistence ##

+Same as `alpha_complex_3d_persistence`, but using periodic alpha shape 3d.

+Refer to the [CGAL's 3D Periodic Triangulations User Manual](https://doc.cgal.org/latest/Periodic_3_triangulation_3/index.html) for more details.

 

-`p dim birth death`

+**Usage**

 

-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).

+```

+   periodic_alpha_complex_3d_persistence [options] <input OFF file> <cuboid file>

+```

 

-**Usage**

-`alpha_complex_persistence [options] <input OFF file>`

 where

-`<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+

+* `<input OFF file>` is the path to the input point cloud in [nOFF ASCII format](http://www.geomview.org/docs/html/OFF.html).

+* `<cuboid file>` is the path to the file describing the periodic domain. It must be in the format described

+[here](/doc/latest/fileformats.html#FileFormatsIsoCuboid).

 

 **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-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.

+* `-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_persistence -r 32 -p 2 -m 0.45 ../../data/points/tore3D_300.off`

 

-outputs:

-```

-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 

-```

+**Example**

 

-Here we retrieve expected Betti numbers on a tore 3D:

 ```

-Betti numbers[0] = 1

-Betti numbers[1] = 2

-Betti numbers[2] = 1

+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

 ```

 

 N.B.:

+

+* Cuboid file must be in the format described [here](/doc/latest/fileformats.html#FileFormatsIsoCuboid).

 * Filtration values are alpha square values.

diff --git a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
index 3b9a2ae0..cceac46e 100644
--- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
@@ -129,16 +129,16 @@ int main(int argc, char **argv) {
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
-    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
-    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
-    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
@@ -165,7 +165,7 @@ int main(int argc, char **argv) {
     }
     // Construction of the simplex_tree
     // you can also use the_alpha_value_iterator->exact()
-    Filtration_value filtr = /*std::sqrt*/CGAL::to_double(the_alpha_value_iterator->exact());
+    Filtration_value filtr = /*std::sqrt*/ CGAL::to_double(the_alpha_value_iterator->exact());
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
diff --git a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
index ac72dcc4..188cf604 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -113,9 +113,8 @@ int main(int argc, char **argv) {
     std::cerr << "Unable to read file " << cuboid_file << std::endl;
     exit(-1);
   }
-  //Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
-  if ((x_max-x_min != y_max-y_min) || (x_max-x_min != z_max-z_min) || (z_max-z_min != y_max-y_min))
-  {
+  // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
+  if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) {
     std::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
     exit(-1);
   }
@@ -164,16 +163,16 @@ int main(int argc, char **argv) {
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
-    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
-    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
-    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
diff --git a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
index f46f1a58..93be8a05 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -65,13 +65,13 @@ using Point_3 = Gt::Bare_point;
 using Weighted_point_3 = Gt::Weighted_point;
 
 // For CGAL >= 4.11
-#else  // CGAL_VERSION_NR < 1041100000
+#else   // CGAL_VERSION_NR < 1041100000
 using Rvb = CGAL::Regular_triangulation_vertex_base_3<Kernel>;
-using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel,Rvb>;
+using Vb = CGAL::Alpha_shape_vertex_base_3<Kernel, Rvb>;
 using Rcb = CGAL::Regular_triangulation_cell_base_3<Kernel>;
-using Cb = CGAL::Alpha_shape_cell_base_3<Kernel,Rcb>;
-using Tds = CGAL::Triangulation_data_structure_3<Vb,Cb>;
-using Triangulation_3 = CGAL::Regular_triangulation_3<Kernel,Tds>;
+using Cb = CGAL::Alpha_shape_cell_base_3<Kernel, Rcb>;
+using Tds = CGAL::Triangulation_data_structure_3<Vb, Cb>;
+using Triangulation_3 = CGAL::Regular_triangulation_3<Kernel, Tds>;
 
 // From file type definition
 using Point_3 = Triangulation_3::Bare_point;
@@ -177,16 +177,16 @@ int main(int argc, char **argv) {
   std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
   for (auto object_iterator : the_objects) {
     // Retrieve Alpha shape vertex list from object
-    if (const Cell_handle* cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
+    if (const Cell_handle *cell = CGAL::object_cast<Cell_handle>(&object_iterator)) {
       vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
       count_cells++;
-    } else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
+    } else if (const Facet *facet = CGAL::object_cast<Facet>(&object_iterator)) {
       vertex_list = from_facet<Vertex_list, Facet>(*facet);
       count_facets++;
-    } else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
+    } else if (const Edge_3 *edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
       vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
       count_edges++;
-    } else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
+    } else if (const Vertex_handle *vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
       count_vertices++;
       vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
     }
diff --git a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
index 0fe8931f..5321bb0a 100644
--- a/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp
@@ -50,14 +50,14 @@ using PK = CGAL::Periodic_3_regular_triangulation_traits_3<Kernel>;
 
 // Vertex type
 using DsVb = CGAL::Periodic_3_triangulation_ds_vertex_base_3<>;
-using Vb = CGAL::Regular_triangulation_vertex_base_3<PK,DsVb>;
-using AsVb = CGAL::Alpha_shape_vertex_base_3<PK,Vb>;
+using Vb = CGAL::Regular_triangulation_vertex_base_3<PK, DsVb>;
+using AsVb = CGAL::Alpha_shape_vertex_base_3<PK, Vb>;
 // Cell type
 using DsCb = CGAL::Periodic_3_triangulation_ds_cell_base_3<>;
-using Cb = CGAL::Regular_triangulation_cell_base_3<PK,DsCb>;
-using AsCb = CGAL::Alpha_shape_cell_base_3<PK,Cb>;
-using Tds = CGAL::Triangulation_data_structure_3<AsVb,AsCb>;
-using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK,Tds>;
+using Cb = CGAL::Regular_triangulation_cell_base_3<PK, DsCb>;
+using AsCb = CGAL::Alpha_shape_cell_base_3<PK, Cb>;
+using Tds = CGAL::Triangulation_data_structure_3<AsVb, AsCb>;
+using P3RT3 = CGAL::Periodic_3_regular_triangulation_3<PK, Tds>;
 using Alpha_shape_3 = CGAL::Alpha_shape_3<P3RT3>;
 
 using Point_3 = P3RT3::Bare_point;
@@ -127,14 +127,13 @@ int main(int argc, char* const argv[]) {
     std::cerr << "Unable to read file " << argv[3] << std::endl;
     usage(argv[0]);
   }
-  //Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
-  if ((x_max-x_min != y_max-y_min) || (x_max-x_min != z_max-z_min) || (z_max-z_min != y_max-y_min))
-  {
+  // Checking if the cuboid is the same in x,y and z direction. If not, CGAL will not process it.
+  if ((x_max - x_min != y_max - y_min) || (x_max - x_min != z_max - z_min) || (z_max - z_min != y_max - y_min)) {
     std::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
     exit(-1);
   }
 
-  double maximal_possible_weight = 0.015625 * (x_max-x_min) * (x_max-x_min);
+  double maximal_possible_weight = 0.015625 * (x_max - x_min) * (x_max - x_min);
 
   // Read weights information from file
   std::ifstream weights_ifstr(argv[2]);
@@ -145,8 +144,7 @@ int main(int argc, char* const argv[]) {
     wp.reserve(lp.size());
     // Attempt read the weight in a double format, return false if it fails
     while ((weights_ifstr >> weight) && (index < lp.size())) {
-      if ((weight >= maximal_possible_weight) || (weight < 0))
-      {
+      if ((weight >= maximal_possible_weight) || (weight < 0)) {
         std::cerr << "At line " << (index + 1) << ", the weight (" << weight
                   << ") is negative or more than or equal to maximal possible weight (" << maximal_possible_weight
                   << ") = 1/64*cuboid length squared, which is not an acceptable input." << std::endl;