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-rw-r--r--src/Alpha_complex/utilities/CMakeLists.txt2
-rw-r--r--src/Alpha_complex/utilities/alpha_complex_3d_helper.h8
-rw-r--r--src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp59
-rw-r--r--src/Alpha_complex/utilities/alphacomplex.md (renamed from src/Alpha_complex/utilities/README)173
-rw-r--r--src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp43
-rw-r--r--src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp54
-rw-r--r--src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp51
-rw-r--r--src/Alpha_complex/utilities/weighted_periodic_alpha_complex_3d_persistence.cpp95
8 files changed, 206 insertions, 279 deletions
diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 79d9e7dd..a2dfac20 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -54,7 +54,7 @@ if(CGAL_FOUND)
target_link_libraries(weighted_periodic_alpha_complex_3d_persistence ${TBB_LIBRARIES})
endif(TBB_FOUND)
- add_test(NAME Persistent_cohomology_example_weigted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_periodic_alpha_complex_3d_persistence>
+ add_test(NAME Alpha_complex_utilities_weigted_periodic_alpha_complex_3d COMMAND $<TARGET_FILE:weighted_periodic_alpha_complex_3d_persistence>
"${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.off" "${CMAKE_SOURCE_DIR}/data/points/grid_10_10_10_in_0_1.weights"
"${CMAKE_SOURCE_DIR}/data/points/iso_cuboid_3_in_0_1.txt" "3" "1.0")
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
index 6b3b7d5d..a59f0654 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_helper.h
@@ -52,13 +52,11 @@ 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 = 0; i < 4; i++) {
- if ((edg.second == i) || (edg.third == i)) {
+ for (auto i : {edg.second, edg.third}) {
#ifdef DEBUG_TRACES
- std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
+ std::cout << "from edge[" << i << "]=" << edg.first->vertex(i)->point() << std::endl;
#endif // DEBUG_TRACES
- the_list.push_back(edg.first->vertex(i));
- }
+ the_list.push_back(edg.first->vertex(i));
}
return the_list;
}
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 0a021a0f..8ef5ffb2 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -20,9 +20,14 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
+#include <boost/version.hpp>
#include <boost/program_options.hpp>
#include <boost/variant.hpp>
+#if BOOST_VERSION >= 105400
+#include <boost/container/static_vector.hpp>
+#endif
+
#include <gudhi/Simplex_tree.h>
#include <gudhi/Persistent_cohomology.h>
#include <gudhi/Points_3D_off_io.h>
@@ -38,7 +43,6 @@
#include <tuple>
#include <map>
#include <utility>
-#include <list>
#include <vector>
#include <cstdlib>
@@ -66,14 +70,18 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+
+#if BOOST_VERSION >= 105400
+using Vertex_list = boost::container::static_vector<Alpha_shape_3::Vertex_handle, 4>;
+#else
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
+#endif
// gudhi type definition
using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -97,7 +105,7 @@ int main(int argc, char **argv) {
exit(-1);
}
- // Retrieve the triangulation
+ // Retrieve the points
std::vector<Point_3> lp = off_reader.get_point_cloud();
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
@@ -128,37 +136,23 @@ int main(int argc, char **argv) {
ST simplex_tree;
Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
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++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } 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++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } 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++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } 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);
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
+ Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -167,30 +161,25 @@ int main(int argc, char **argv) {
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+ the_simplex.push_back(vertex);
+ map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
+ the_simplex.push_back(vertex);
}
}
// 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
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
- if (the_alpha_value_iterator != the_alpha_values.end())
- ++the_alpha_value_iterator;
- else
- std::cout << "This shall not happen" << std::endl;
+ simplex_tree.insert_simplex(the_simplex, filtr);
+ GUDHI_CHECK(the_alpha_value_iterator != the_alpha_values.end(), "CGAL provided more simplices than values");
+ ++the_alpha_value_iterator;
}
#ifdef DEBUG_TRACES
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 9a266418..cceac46e 100644
--- a/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/exact_alpha_complex_3d_persistence.cpp
@@ -38,7 +38,6 @@
#include <tuple>
#include <map>
#include <utility>
-#include <list>
#include <vector>
#include <cstdlib>
@@ -67,14 +66,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Vertex_handle>;
+using Vertex_list = std::vector<Vertex_handle>;
// gudhi type definition
using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -98,7 +96,7 @@ int main(int argc, char **argv) {
exit(-1);
}
- // Retrieve the triangulation
+ // Retrieve the points
std::vector<Point_3> lp = off_reader.get_point_cloud();
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode.
@@ -129,37 +127,23 @@ int main(int argc, char **argv) {
ST simplex_tree;
Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
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++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } 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++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } 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++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } 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);
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
+ Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -168,27 +152,24 @@ int main(int argc, char **argv) {
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+ the_simplex.push_back(vertex);
+ map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
+ the_simplex.push_back(vertex);
}
}
// 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
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
+ simplex_tree.insert_simplex(the_simplex, filtr);
if (the_alpha_value_iterator != the_alpha_values.end())
++the_alpha_value_iterator;
else
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 186a58f8..188cf604 100644
--- a/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/periodic_alpha_complex_3d_persistence.cpp
@@ -3,6 +3,7 @@
* library for computational topology.
*
* Author(s): Vincent Rouvreau
+ * Pawel Dlotko - 2017 - Swansea University, UK
*
* Copyright (C) 2014 INRIA
*
@@ -39,7 +40,6 @@
#include <tuple>
#include <map>
#include <utility>
-#include <list>
#include <vector>
#include <cstdlib>
@@ -72,14 +72,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
// gudhi type definition
using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -114,8 +113,13 @@ 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)) {
+ std::cerr << "The size of the cuboid in every directions is not the same." << std::endl;
+ exit(-1);
+ }
- // Retrieve the triangulation
+ // Retrieve the points
std::vector<Point_3> lp = off_reader.get_point_cloud();
// Define the periodic cube
@@ -123,7 +127,12 @@ int main(int argc, char **argv) {
// Heuristic for inserting large point sets (if pts is reasonably large)
pdt.insert(lp.begin(), lp.end(), true);
// As pdt won't be modified anymore switch to 1-sheeted cover if possible
- if (pdt.is_triangulation_in_1_sheet()) pdt.convert_to_1_sheeted_covering();
+ if (pdt.is_triangulation_in_1_sheet()) {
+ pdt.convert_to_1_sheeted_covering();
+ } else {
+ std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
+ exit(-1);
+ }
std::cout << "Periodic Delaunay computed." << std::endl;
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
@@ -152,37 +161,23 @@ int main(int argc, char **argv) {
ST simplex_tree;
Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
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++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } 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++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } 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++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } 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);
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
+ Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -191,15 +186,15 @@ int main(int argc, char **argv) {
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+ the_simplex.push_back(vertex);
+ map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
+ the_simplex.push_back(vertex);
}
}
// Construction of the simplex_tree
@@ -207,10 +202,7 @@ int main(int argc, char **argv) {
#ifdef DEBUG_TRACES
std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
+ simplex_tree.insert_simplex(the_simplex, filtr);
if (the_alpha_value_iterator != the_alpha_values.end())
++the_alpha_value_iterator;
else
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 0e73a99b..93be8a05 100644
--- a/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/weighted_alpha_complex_3d_persistence.cpp
@@ -44,7 +44,6 @@
#include <tuple>
#include <map>
#include <utility>
-#include <list>
#include <vector>
#include <cstdlib>
@@ -66,13 +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;
@@ -92,14 +91,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
// gudhi type definition
using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -125,7 +123,7 @@ int main(int argc, char **argv) {
exit(-1);
}
- // Retrieve the triangulation
+ // Retrieve the points
std::vector<Point_3> lp = off_reader.get_point_cloud();
// Read weights information from file
@@ -177,37 +175,23 @@ int main(int argc, char **argv) {
ST simplex_tree;
Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
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++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
- } 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++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
- } 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++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
- } 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);
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
+ Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -216,15 +200,15 @@ int main(int argc, char **argv) {
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+ the_simplex.push_back(vertex);
+ map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
+ the_simplex.push_back(vertex);
}
}
// Construction of the simplex_tree
@@ -232,10 +216,7 @@ int main(int argc, char **argv) {
#ifdef DEBUG_TRACES
std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
+ simplex_tree.insert_simplex(the_simplex, filtr);
if (the_alpha_value_iterator != the_alpha_values.end())
++the_alpha_value_iterator;
else
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 13634ff7..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
@@ -3,6 +3,7 @@
* library for computational topology.
*
* Author(s): Vincent Rouvreau
+ * Pawel Dlotko - 2017 - Swansea University, UK
*
* Copyright (C) 2014 INRIA
*
@@ -38,7 +39,6 @@
#include <tuple>
#include <map>
#include <utility>
-#include <list>
#include <vector>
#include <cstdlib>
@@ -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;
@@ -74,14 +74,13 @@ using Cell_handle = Alpha_shape_3::Cell_handle;
using Facet = Alpha_shape_3::Facet;
using Edge_3 = Alpha_shape_3::Edge;
using Vertex_handle = Alpha_shape_3::Vertex_handle;
-using Vertex_list = std::list<Alpha_shape_3::Vertex_handle>;
+using Vertex_list = std::vector<Alpha_shape_3::Vertex_handle>;
// gudhi type definition
using ST = Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence>;
using Filtration_value = ST::Filtration_value;
using Simplex_tree_vertex = ST::Vertex_handle;
using Alpha_shape_simplex_tree_map = std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
-using Alpha_shape_simplex_tree_pair = std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex>;
using Simplex_tree_vector_vertex = std::vector<Simplex_tree_vertex>;
using Persistent_cohomology =
Gudhi::persistent_cohomology::Persistent_cohomology<ST, Gudhi::persistent_cohomology::Field_Zp>;
@@ -112,18 +111,46 @@ int main(int argc, char* const argv[]) {
usage(argv[0]);
}
- // Retrieve the triangulation
+ // Retrieve the points
std::vector<Point_3> lp = off_reader.get_point_cloud();
+ // Read iso_cuboid_3 information from file
+ std::ifstream iso_cuboid_str(argv[3]);
+ double x_min, y_min, z_min, x_max, y_max, z_max;
+ if (iso_cuboid_str.is_open()) {
+ if (!(iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max)) {
+ std::cerr << argv[3] << " - Bad file format." << std::endl;
+ usage(argv[0]);
+ }
+
+ } else {
+ 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)) {
+ 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);
+
// Read weights information from file
std::ifstream weights_ifstr(argv[2]);
std::vector<Weighted_point_3> wp;
- if (weights_ifstr.good()) {
+ if (weights_ifstr.is_open()) {
double weight = 0.0;
std::size_t index = 0;
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)) {
+ 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;
+ exit(-1);
+ }
+
wp.push_back(Weighted_point_3(lp[index], weight));
index++;
}
@@ -136,23 +163,18 @@ int main(int argc, char* const argv[]) {
usage(argv[0]);
}
- // Read iso_cuboid_3 information from file
- std::ifstream iso_cuboid_str(argv[3]);
- double x_min, y_min, z_min, x_max, y_max, z_max;
- if (iso_cuboid_str.good()) {
- iso_cuboid_str >> x_min >> y_min >> z_min >> x_max >> y_max >> z_max;
- } else {
- std::cerr << "Unable to read file " << argv[3] << std::endl;
- usage(argv[0]);
- }
-
// Define the periodic cube
P3RT3 prt(PK::Iso_cuboid_3(x_min, y_min, z_min, x_max, y_max, z_max));
// Heuristic for inserting large point sets (if pts is reasonably large)
prt.insert(wp.begin(), wp.end(), true);
// As prt won't be modified anymore switch to 1-sheeted cover if possible
- if (prt.is_triangulation_in_1_sheet()) prt.convert_to_1_sheeted_covering();
- std::cout << "Periodic Delaunay computed." << std::endl;
+ if (prt.is_triangulation_in_1_sheet()) {
+ prt.convert_to_1_sheeted_covering();
+ } else {
+ std::cerr << "ERROR: we were not able to construct a triangulation within a single periodic domain." << std::endl;
+ exit(-1);
+ }
+ std::cout << "Weighted Periodic Delaunay computed." << std::endl;
// alpha shape construction from points. CGAL has a strange behavior in REGULARIZED mode. This is the default mode
// Maybe need to set it to GENERAL mode
@@ -180,37 +202,23 @@ int main(int argc, char* const argv[]) {
ST simplex_tree;
Alpha_shape_simplex_tree_map map_cgal_simplex_tree;
std::vector<Alpha_value_type>::iterator the_alpha_value_iterator = the_alpha_values.begin();
- int dim_max = 0;
- Filtration_value filtration_max = 0.0;
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)) {
vertex_list = from_cell<Vertex_list, Cell_handle>(*cell);
count_cells++;
- if (dim_max < 3) {
- // Cell is of dim 3
- dim_max = 3;
- }
} else if (const Facet* facet = CGAL::object_cast<Facet>(&object_iterator)) {
vertex_list = from_facet<Vertex_list, Facet>(*facet);
count_facets++;
- if (dim_max < 2) {
- // Facet is of dim 2
- dim_max = 2;
- }
} else if (const Edge_3* edge = CGAL::object_cast<Edge_3>(&object_iterator)) {
vertex_list = from_edge<Vertex_list, Edge_3>(*edge);
count_edges++;
- if (dim_max < 1) {
- // Edge_3 is of dim 1
- dim_max = 1;
- }
} else if (const Vertex_handle* vertex = CGAL::object_cast<Vertex_handle>(&object_iterator)) {
count_vertices++;
vertex_list = from_vertex<Vertex_list, Vertex_handle>(*vertex);
}
// Construction of the vector of simplex_tree vertex from list of alpha_shapes vertex
- Simplex_tree_vector_vertex the_simplex_tree;
+ Simplex_tree_vector_vertex the_simplex;
for (auto the_alpha_shape_vertex : vertex_list) {
Alpha_shape_simplex_tree_map::iterator the_map_iterator = map_cgal_simplex_tree.find(the_alpha_shape_vertex);
if (the_map_iterator == map_cgal_simplex_tree.end()) {
@@ -219,15 +227,15 @@ int main(int argc, char* const argv[]) {
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] not found - insert " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
- map_cgal_simplex_tree.insert(Alpha_shape_simplex_tree_pair(the_alpha_shape_vertex, vertex));
+ the_simplex.push_back(vertex);
+ map_cgal_simplex_tree.emplace(the_alpha_shape_vertex, vertex);
} else {
// alpha shape found
Simplex_tree_vertex vertex = the_map_iterator->second;
#ifdef DEBUG_TRACES
std::cout << "vertex [" << the_alpha_shape_vertex->point() << "] found in " << vertex << std::endl;
#endif // DEBUG_TRACES
- the_simplex_tree.push_back(vertex);
+ the_simplex.push_back(vertex);
}
}
// Construction of the simplex_tree
@@ -235,10 +243,7 @@ int main(int argc, char* const argv[]) {
#ifdef DEBUG_TRACES
std::cout << "filtration = " << filtr << std::endl;
#endif // DEBUG_TRACES
- if (filtr > filtration_max) {
- filtration_max = filtr;
- }
- simplex_tree.insert_simplex(the_simplex_tree, filtr);
+ simplex_tree.insert_simplex(the_simplex, filtr);
if (the_alpha_value_iterator != the_alpha_values.end())
++the_alpha_value_iterator;
else
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-07 07:47:01 +0000