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-rw-r--r--src/CMakeLists.txt2
-rw-r--r--src/Contraction/include/gudhi/Edge_contraction.h4
-rw-r--r--src/Doxyfile11
-rw-r--r--src/Persistent_cohomology/example/CMakeLists.txt4
-rw-r--r--src/Persistent_cohomology/example/performance_rips_persistence.cpp81
-rw-r--r--src/Persistent_cohomology/example/plain_homology.cpp84
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h32
-rw-r--r--src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h3
-rw-r--r--src/Simplex_tree/concept/SimplexTreeOptions.h6
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree.h23
-rw-r--r--src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h2
-rw-r--r--src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h4
-rw-r--r--src/common/doc/main_page.h182
13 files changed, 314 insertions, 124 deletions
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index a84090e9..68eca65e 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -75,7 +75,7 @@ else()
# Install the GUDHIConfig.cmake and GUDHIConfigVersion.cmake
install(FILES
- "${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/GUDHIConfig.cmake"
+ "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake"
"${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake"
DESTINATION share/gudhi)
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index b996d9fb..ee3e3de1 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -37,7 +37,7 @@ namespace Gudhi {
namespace contraction {
-/** \defgroup contr Contraction
+/** \defgroup contr Edge contraction
\author David Salinas
@@ -226,7 +226,7 @@ Time to simplify and enumerate simplices:
\copyright GNU General Public License v3.
-\verbatim Contact: David Salinas, david.salinas@inria.fr \endverbatim
+\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
*/
/** @} */ // end defgroup
} // namespace contraction
diff --git a/src/Doxyfile b/src/Doxyfile
index 85c496a8..faa0d3fe 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -38,7 +38,7 @@ PROJECT_NAME = "Gudhi"
# could be handy for archiving the generated documentation or if some version
# control system is used.
-PROJECT_NUMBER = "1.1.0"
+PROJECT_NUMBER = "1.2.0"
# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
@@ -672,7 +672,8 @@ LAYOUT_FILE =
# search path. Do not use file names with spaces, bibtex cannot handle them. See
# also \cite for info how to create references.
-CITE_BIB_FILES = biblio/bibliography.bib
+CITE_BIB_FILES = biblio/bibliography.bib \
+ biblio/how_to_cite_gudhi.bib
#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
@@ -811,7 +812,7 @@ EXCLUDE_SYMBOLS =
# that contain example code fragments that are included (see the \include
# command).
-EXAMPLE_PATH =
+EXAMPLE_PATH = biblio/
# If the value of the EXAMPLE_PATH tag contains directories, you can use the
# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and
@@ -1338,7 +1339,7 @@ ECLIPSE_DOC_ID = org.doxygen.Project
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
-DISABLE_INDEX = NO
+DISABLE_INDEX = YES
# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
# structure should be generated to display hierarchical information. If the tag
@@ -1355,7 +1356,7 @@ DISABLE_INDEX = NO
# The default value is: NO.
# This tag requires that the tag GENERATE_HTML is set to YES.
-GENERATE_TREEVIEW = NO
+GENERATE_TREEVIEW = YES
# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that
# doxygen will group on one line in the generated HTML documentation.
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index ea69352e..50d10025 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -5,6 +5,10 @@ project(GUDHIExPersCohom)
add_definitions( -DBOOST_ALL_NO_LIB )
add_definitions( -DBOOST_ALL_DYN_LINK )
+add_executable(plain_homology plain_homology.cpp)
+target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
+add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
+
add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
diff --git a/src/Persistent_cohomology/example/performance_rips_persistence.cpp b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
index 0e912d57..fc48d6b1 100644
--- a/src/Persistent_cohomology/example/performance_rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/performance_rips_persistence.cpp
@@ -63,10 +63,11 @@ void timing_persistence(FilteredComplex & cpx
*/
int main(int argc, char * argv[]) {
std::chrono::time_point<std::chrono::system_clock> start, end;
- int enlapsed_sec;
+ int elapsed_sec;
+ {
- std::string filepoints = "../examples/Kl.txt";
- Filtration_value threshold = 0.3;
+ std::string filepoints = "../../../data/points/Kl.txt";
+ Filtration_value threshold = 0.27;
int dim_max = 3;
int p = 2;
int q = 1223;
@@ -81,8 +82,8 @@ int main(int argc, char * argv[]) {
Graph_t prox_graph = compute_proximity_graph(points, threshold
, euclidean_distance<Point_t>);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
- std::cout << "Compute Rips graph in " << enlapsed_sec << " sec.\n";
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << "Compute Rips graph in " << elapsed_sec << " ms.\n";
// Construct the Rips complex in a Simplex Tree
Simplex_tree<> st;
@@ -94,8 +95,8 @@ int main(int argc, char * argv[]) {
st.expansion(dim_max);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
- std::cout << "Compute Rips complex in " << enlapsed_sec << " sec.\n";
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << "Compute Rips complex in " << elapsed_sec << " ms.\n";
std::cout << " - dimension = " << st.dimension() << std::endl;
std::cout << " - number of simplices = " << st.num_simplices() << std::endl;
@@ -103,15 +104,26 @@ int main(int argc, char * argv[]) {
start = std::chrono::system_clock::now();
st.initialize_filtration();
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
- std::cout << "Order the simplices of the filtration in " << enlapsed_sec << " sec.\n";
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << "Order the simplices of the filtration in " << elapsed_sec << " ms.\n";
+
+ // Copy the keys inside the simplices
+ start = std::chrono::system_clock::now();
+ {
+ int count = 0;
+ for (auto sh : st.filtration_simplex_range())
+ st.assign_key(sh, count++);
+ }
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << "Copied the keys inside the simplices in " << elapsed_sec << " ms.\n";
// Convert the simplex tree into a hasse diagram
start = std::chrono::system_clock::now();
Hasse_complex<> hcpx(st);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
- std::cout << "Convert the simplex tree into a Hasse diagram in " << enlapsed_sec << " sec.\n";
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << "Convert the simplex tree into a Hasse diagram in " << elapsed_sec << " ms.\n";
std::cout << "Timings when using a simplex tree: \n";
@@ -124,6 +136,11 @@ int main(int argc, char * argv[]) {
timing_persistence(hcpx, q);
timing_persistence(hcpx, p, q);
+ start = std::chrono::system_clock::now();
+ }
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << "Running the complex destructors in " << elapsed_sec << " ms.\n";
return 0;
}
@@ -132,19 +149,32 @@ void
timing_persistence(FilteredComplex & cpx
, int p) {
std::chrono::time_point<std::chrono::system_clock> start, end;
- int enlapsed_sec;
-
+ int elapsed_sec;
+ {
+ start = std::chrono::system_clock::now();
Persistent_cohomology< FilteredComplex, Field_Zp > pcoh(cpx);
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n";
// initializes the coefficient field for homology
+ start = std::chrono::system_clock::now();
pcoh.init_coefficients(p);
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n";
start = std::chrono::system_clock::now();
pcoh.compute_persistent_cohomology(INFINITY);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
- std::cout << " Compute persistent homology in Z/" << p << "Z in " << enlapsed_sec << " sec.\n";
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Compute persistent homology in Z/" << p << "Z in " << elapsed_sec << " ms.\n";
+ start = std::chrono::system_clock::now();
+ }
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n";
}
template< typename FilteredComplex>
@@ -153,11 +183,19 @@ timing_persistence(FilteredComplex & cpx
, int p
, int q) {
std::chrono::time_point<std::chrono::system_clock> start, end;
- int enlapsed_sec;
-
+ int elapsed_sec;
+ {
+ start = std::chrono::system_clock::now();
Persistent_cohomology< FilteredComplex, Multi_field > pcoh(cpx);
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Initialize pcoh in " << elapsed_sec << " ms.\n";
// initializes the coefficient field for homology
+ start = std::chrono::system_clock::now();
pcoh.init_coefficients(p, q);
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Initialize the coefficient field in " << elapsed_sec << " ms.\n";
// compute persistent homology, disgarding persistent features of life shorter than min_persistence
start = std::chrono::system_clock::now();
@@ -165,7 +203,12 @@ timing_persistence(FilteredComplex & cpx
pcoh.compute_persistent_cohomology(INFINITY);
end = std::chrono::system_clock::now();
- enlapsed_sec = std::chrono::duration_cast<std::chrono::seconds>(end - start).count();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
std::cout << " Compute multi-field persistent homology in all coefficient fields Z/pZ "
- << "with p in [" << p << ";" << q << "] in " << enlapsed_sec << " sec.\n";
+ << "with p in [" << p << ";" << q << "] in " << elapsed_sec << " ms.\n";
+ start = std::chrono::system_clock::now();
+ }
+ end = std::chrono::system_clock::now();
+ elapsed_sec = std::chrono::duration_cast<std::chrono::milliseconds>(end - start).count();
+ std::cout << " Run the persistence destructors in " << elapsed_sec << " ms.\n";
}
diff --git a/src/Persistent_cohomology/example/plain_homology.cpp b/src/Persistent_cohomology/example/plain_homology.cpp
new file mode 100644
index 00000000..0a692717
--- /dev/null
+++ b/src/Persistent_cohomology/example/plain_homology.cpp
@@ -0,0 +1,84 @@
+/* This file is part of the Gudhi Library. The Gudhi library
+ * (Geometric Understanding in Higher Dimensions) is a generic C++
+ * library for computational topology.
+ *
+ * Author(s): Marc Glisse
+ *
+ * Copyright (C) 2015 INRIA Saclay - Ile-de-France (France)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <iostream>
+
+using namespace Gudhi;
+
+/* We could perfectly well use the default Simplex_tree<> (which uses
+ * Simplex_tree_options_full_featured), the following simply demonstrates
+ * how to save on storage by not storing a filtration value. */
+
+struct MyOptions : Simplex_tree_options_full_featured {
+ // Implicitly use 0 as filtration value for all simplices
+ static const bool store_filtration = false;
+ // The persistence algorithm needs this
+ static const bool store_key = true;
+ // I have few vertices
+ typedef short Vertex_handle;
+};
+typedef Simplex_tree<MyOptions> ST;
+
+int main() {
+ ST st;
+
+ /* Complex to build. */
+ /* 1 3 */
+ /* o---o */
+ /* /X\ / */
+ /* o---o o */
+ /* 2 0 4 */
+
+ const short triangle012[] = {0, 1, 2};
+ const short edge03[] = {0, 3};
+ const short edge13[] = {1, 3};
+ const short vertex4[] = {4};
+ st.insert_simplex_and_subfaces(triangle012);
+ st.insert_simplex_and_subfaces(edge03);
+ st.insert_simplex(edge13);
+ st.insert_simplex(vertex4);
+ // FIXME: Remove this line
+ st.set_dimension(2);
+
+ // Sort the simplices in the order of the filtration
+ st.initialize_filtration();
+
+ // Class for homology computation
+ persistent_cohomology::Persistent_cohomology<ST, persistent_cohomology::Field_Zp> pcoh(st);
+
+ // Initialize the coefficient field Z/2Z for homology
+ pcoh.init_coefficients(2);
+
+ // Compute the persistence diagram of the complex
+ pcoh.compute_persistent_cohomology();
+
+ // Print the result. The format is, on each line: 2 dim 0 inf
+ // where 2 represents the field, dim the dimension of the feature.
+ // 2 0 0 inf
+ // 2 0 0 inf
+ // 2 1 0 inf
+ // means that in Z/2Z-homology, the Betti numbers are b0=2 and b1=1.
+ pcoh.output_diagram();
+}
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index d096792f..2a405830 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -431,9 +431,12 @@ class Persistent_cohomology {
std::map<Simplex_key, Arith_element> & map_a_ds, Simplex_handle sigma,
int dim_sigma) {
// traverses the boundary of sigma, keeps track of the annotation vectors,
- // with multiplicity, in a map.
- std::map<Column *, int> annotations_in_boundary;
- std::pair<typename std::map<Column *, int>::iterator, bool> result_insert_bound;
+ // with multiplicity. We used to sum the coefficients directly in
+ // annotations_in_boundary by using a map, we now do it later.
+ typedef std::pair<Column *, int> annotation_t;
+ // Danger: not thread-safe!
+ static std::vector<annotation_t> annotations_in_boundary;
+ annotations_in_boundary.clear();
int sign = 1 - 2 * (dim_sigma % 2); // \in {-1,1} provides the sign in the
// alternate sum in the boundary.
Simplex_key key;
@@ -445,22 +448,29 @@ class Persistent_cohomology {
// Find its annotation vector
curr_col = ds_repr_[dsets_.find_set(key)];
if (curr_col != NULL) { // and insert it in annotations_in_boundary with multyiplicative factor "sign".
- result_insert_bound = annotations_in_boundary.insert(std::pair<Column *, int>(curr_col, sign));
- if (!(result_insert_bound.second)) {
- result_insert_bound.first->second += sign;
- }
+ annotations_in_boundary.emplace_back(curr_col, sign);
}
}
sign = -sign;
}
+ // Place identical annotations consecutively so we can easily sum their multiplicities.
+ std::sort(annotations_in_boundary.begin(), annotations_in_boundary.end(),
+ [](annotation_t const& a, annotation_t const& b) { return a.first < b.first; });
+
// Sum the annotations with multiplicity, using a map<key,coeff>
// to represent a sparse vector.
std::pair<typename std::map<Simplex_key, Arith_element>::iterator, bool> result_insert_a_ds;
- for (auto ann_ref : annotations_in_boundary) {
- if (ann_ref.second != coeff_field_.additive_identity()) { // For all columns in the boundary,
- for (auto cell_ref : ann_ref.first->col_) { // insert every cell in map_a_ds with multiplicity
- Arith_element w_y = coeff_field_.times(cell_ref.coefficient_, ann_ref.second); // coefficient * multiplicity
+ for (auto ann_it = annotations_in_boundary.begin(); ann_it != annotations_in_boundary.end(); /**/) {
+ Column* col = ann_it->first;
+ int mult = ann_it->second;
+ while (++ann_it != annotations_in_boundary.end() && ann_it->first == col) {
+ mult += ann_it->second;
+ }
+ // The following test is just a heuristic, it is not required, and it is fine that is misses p == 0.
+ if (mult != coeff_field_.additive_identity()) { // For all columns in the boundary,
+ for (auto cell_ref : col->col_) { // insert every cell in map_a_ds with multiplicity
+ Arith_element w_y = coeff_field_.times(cell_ref.coefficient_, mult); // coefficient * multiplicity
if (w_y != coeff_field_.additive_identity()) { // if != 0
result_insert_a_ds = map_a_ds.insert(std::pair<Simplex_key, Arith_element>(cell_ref.key_, w_y));
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
index 0591fc95..38bc08d1 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology/Multi_field.h
@@ -81,8 +81,7 @@ class Multi_field {
// set m to primorial(bound_prime)
prod_characteristics_ = 1;
for (auto p : primes_) {
- mpz_mul_ui(prod_characteristics_.get_mpz_t(),
- prod_characteristics_.get_mpz_t(), p);
+ prod_characteristics_ *= p;
}
// Uvect_
diff --git a/src/Simplex_tree/concept/SimplexTreeOptions.h b/src/Simplex_tree/concept/SimplexTreeOptions.h
index a50a2bf1..add3ebdd 100644
--- a/src/Simplex_tree/concept/SimplexTreeOptions.h
+++ b/src/Simplex_tree/concept/SimplexTreeOptions.h
@@ -34,8 +34,8 @@ struct SimplexTreeOptions {
/// Must be a signed integer type.
typedef SimplexKey Simplex_key;
/// If true, each simplex has extra storage for one `Simplex_key`. Necessary for `Persistent_cohomology`.
- static constexpr bool store_key;
- /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree<SimplexTreeOptions>::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology.
- static constexpr bool store_filtration;
+ static const bool store_key;
+ /// If true, each simplex has extra storage for one `Filtration_value`, and this value is propagated by operations like `Gudhi::Simplex_tree::expansion`. Without it, `Persistent_cohomology` degenerates to computing usual (non-persistent) cohomology.
+ static const bool store_filtration;
};
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index 6e51d107..ea61fa2e 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -39,6 +39,7 @@
#include <utility>
#include <vector>
#include <functional> // for greater<>
+#include <initializer_list>
namespace Gudhi {
@@ -531,7 +532,7 @@ class Simplex_tree {
* The type InputVertexRange must be a range of <CODE>Vertex_handle</CODE>
* on which we can call std::begin() function
*/
- template<class InputVertexRange>
+ template<class InputVertexRange=std::initializer_list<Vertex_handle>>
Simplex_handle find(const InputVertexRange & s) {
auto first = std::begin(s);
auto last = std::end(s);
@@ -625,7 +626,7 @@ class Simplex_tree {
*
* The type InputVertexRange must be a range for which .begin() and
* .end() return input iterators, with 'value_type' Vertex_handle. */
- template<class InputVertexRange>
+ template<class InputVertexRange=std::initializer_list<Vertex_handle>>
std::pair<Simplex_handle, bool> insert_simplex(const InputVertexRange & simplex,
Filtration_value filtration = 0) {
auto first = std::begin(simplex);
@@ -654,7 +655,7 @@ class Simplex_tree {
* output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
* null_simplex.
*/
- template<class InputVertexRange>
+ template<class InputVertexRange=std::initializer_list<Vertex_handle>>
std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const InputVertexRange& Nsimplex,
Filtration_value filtration = 0) {
auto first = std::begin(Nsimplex);
@@ -771,12 +772,6 @@ class Simplex_tree {
* assigned a Simplex_key corresponding to its order in the filtration (from 0 to m-1 for a
* simplicial complex with m simplices).
*
- * The use of a depth-first traversal of the simplex tree, provided by
- * complex_simplex_range(), combined with
- * a stable sort is meant to optimize the order of simplices with same
- * filtration value. The heuristic consists in inserting the cofaces of a
- * simplex as soon as possible.
- *
* Will be automatically called when calling filtration_simplex_range()
* if the filtration has never been initialized yet. */
void initialize_filtration() {
@@ -785,7 +780,15 @@ class Simplex_tree {
for (Simplex_handle sh : complex_simplex_range())
filtration_vect_.push_back(sh);
- // the stable sort ensures the ordering heuristic
+ /* We use stable_sort here because with libstdc++ it is faster than sort.
+ * is_before_in_filtration is now a total order, but we used to call
+ * stable_sort for the following heuristic:
+ * The use of a depth-first traversal of the simplex tree, provided by
+ * complex_simplex_range(), combined with a stable sort is meant to
+ * optimize the order of simplices with same filtration value. The
+ * heuristic consists in inserting the cofaces of a simplex as soon as
+ * possible.
+ */
std::stable_sort(filtration_vect_.begin(), filtration_vect_.end(),
is_before_in_filtration(this));
}
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index e1f53f48..615b3a81 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -240,7 +240,7 @@ their collaboration to write the two initial papers
\copyright GNU General Public License v3.
-\verbatim Contact: David Salinas, david.salinas@inria.fr \endverbatim
+\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
*/
/** @} */ // end defgroup
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 6612722e..5b774f25 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -1068,7 +1068,7 @@ class Skeleton_blocker_complex {
}
//@}
- /** @Simplification operations
+ /** @name Simplification operations
*/
//@{
@@ -1183,7 +1183,7 @@ class Skeleton_blocker_complex {
}
//@}
- /** @Edge contraction operations
+ /** @name Edge contraction operations
*/
//@{
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 315aa0ac..689e7a4d 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -1,72 +1,118 @@
-/**
-\mainpage
-
-\image html "Gudhi_banner.jpg" "" width=20cm
-
-The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for
-topological analysis of high-dimensional data whose goal is to provide robust, efficient, flexible and easy to use
-implementations of
-state-of-the-art algorithms and data structures for computational topology.
-This library is part of the <a href="https://project.inria.fr/gudhi/">Gudhi project</a>.
-
-The current release of the library allows to use several data-structures for simplicial complexes :
-simplex tree, Hasse diagram or skeleton-blocker. Several operations can then be done on top of these
-representations such as persistent homology computation or simplification.
-All data-structures are generic and several of their aspects (such as stored elements, policies)
-can be parameterized via template classes.
-We refer to
-\cite gudhilibrary_ICMS14
-for a detailed description of the design of the library.
-
-\section installation Gudhi installation
-
-As Gudhi is a header only library, there is no need to install the library.
-
-Examples of Gudhi headers inclusion can be found in \ref demos.
-
-
-\section compiling Compiling
-
-The library uses c++11 and requires <a href="http://www.boost.org/">Boost</a> with version 1.48.0 or more recent.
-It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
-
-
-\subsection gmp GMP:
-The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
-arithmetic, operating on signed integers, rational numbers, and floating point numbers.
-
-The following examples require the <a href="http://gmplib.org/">GNU Multiple Precision Arithmetic Library</a> (GMP)
-and will not be built if GMP is not installed:
- - Persistent_cohomology/rips_multifield_persistence
- - Simplex_tree/simplex_tree_from_alpha_shapes_3
-
-Having GMP version 4.2 or higher installed is recommended.
-
-\subsection cgal CGAL:
-CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
-
-The following example requires the <a href="http://www.cgal.org/">Computational Geometry Algorithms Library</a> (CGAL)
-and will not be built if CGAL is not installed:
- - Simplex_tree/simplex_tree_from_alpha_shapes_3
-
-Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
-your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
-
-\subsection demos Demos and examples
-
-To build the demos and libraries, run the following commands in a terminal:
-
-\verbatim
-cd /path-to-gudhi/
-mkdir build
-cd build/
-cmake ..
-make
-\endverbatim
+/*! \mainpage
+ * \image html "Gudhi_banner.jpg" "" width=20cm
+ *
+ * \section Introduction Introduction
+ * The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic open source C++ library for
+ * Computational Topology and Topological Data Analysis
+ * (<a class="el" target="_blank" href="https://en.wikipedia.org/wiki/Topological_data_analysis">TDA</a>).
+ * The GUDHI library is developed as part of the
+ * <a class="el" target="_blank" href="https://project.inria.fr/gudhi/">GUDHI project</a> supported by the European
+ * Research Council. The GUDHI library intends to help the development of new algorithmic solutions in TDA and their
+ * transfer to applications. It provides robust, efficient, flexible and easy to use implementations of
+ * state-of-the-art algorithms and data structures.
+ *
+ * The current release of the GUDHI library includes:
+ *
+ * \li Data structures to represent, construct and manipulate simplicial complexes.
+ * \li Algorithms to compute persistent homology and multi-field persistent homology.
+ * \li Simplication of simplicial complexes by edge contraction.
+ *
+ * All data-structures are generic and several of their aspects can be parameterized via template classes.
+ * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
+ *
+ * The library is available <a class="el" target="_blank" href="https://gforge.inria.fr/frs/?group_id=3865">here</a>
+ * and the documentation is available at this <a class="el" href="http://gudhi.gforge.inria.fr/doc/latest/">
+ * webpage</a>.
+ *
+ * The library comes with data sets, \ref demos and \ref testsuites.
+ *
+ * Gudhi is also accessible though the
+ * <a class="el" target="_blank" href="https://cran.r-project.org/web/packages/TDA/index.html">R package TDA</a>
+ * (Statistical Tools for Topological Data Analysis).
+ *
+ * The development of the GUDHI library is steered by an Editorial Board composed of:
+ *
+ * \li <a class="el" target="_blank" href="http://www-sop.inria.fr/members/Jean-Daniel.Boissonnat/">
+ * Jean-Daniel Boissonnat</a> | INRIA Sophia Antipolis - Méditerranée
+ * \li <a class="el" target="_blank" href="http://geometrica.saclay.inria.fr/team/Marc.Glisse/">Marc Glisse</a> | INRIA Saclay - Ile de France
+ * \li Clément Jamin | INRIA Sophia Antipolis - Méditerranée
+ * \li Vincent Rouvreau | INRIA Saclay - Ile de France
+ *
+*/
-\details
+/*! \page installation Gudhi installation
+ * As Gudhi is a header only library, there is no need to install the library.
+ *
+ * Examples of Gudhi headers inclusion can be found in \ref demos.
+ *
+ * \section compiling Compiling
+ * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a> with version 1.48.0 or
+ * more recent. It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2013.
+ *
+ * \subsection gmp GMP:
+ * The multi-field persistent homology algorithm requires GMP which is a free library for arbitrary-precision
+ * arithmetic, operating on signed integers, rational numbers, and floating point numbers.
+ *
+ * The following example requires the <a target="_blank" href="http://gmplib.org/">GNU Multiple Precision Arithmetic
+ * Library</a> (GMP) and will not be built if GMP is not installed:
+ * \li Persistent_cohomology/rips_multifield_persistence
+ * Having GMP version 4.2 or higher installed is recommended.
+ *
+ * \subsection cgal CGAL:
+ * CGAL is a C++ library which provides easy access to efficient and reliable geometric algorithms.
+ *
+ * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
+ * Library</a> (CGAL) and will not be built if CGAL is not installed:
+ * \li GudhUI
+ * \li Persistent_cohomology/alpha_shapes_persistence
+ * \li Simplex_tree/simplex_tree_from_alpha_shapes_3
+ *
+ * Having CGAL version 4.4 or higher installed is recommended. The procedure to install this library according to
+ * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
+ *
+ * \subsection demos Demos and examples
+ * To build the demos and libraries, run the following commands in a terminal:
+ * \verbatim
+ * cd /path-to-gudhi/
+ * mkdir build
+ * cd build/
+ * cmake ..
+ * make
+ * \endverbatim
+ *
+ * \subsection testsuites Test suites
+ * To test your build, run the following command in a terminal:
+ * \verbatim
+ * make test
+ * \endverbatim
+ *
+ * \section Contributions Bug reports and contributions
+ * Please help us improving the quality of the GUDHI library. You may report bugs or suggestions to:
+ * \verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ *
+ * Gudhi is open to external contributions. If you want to join our development team, please contact us.
+ *
+*/
-\copyright GNU General Public License v3.
-\verbatim Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+/*! \page Upcoming Upcoming
+ *
+ * The library is under active development. New packages to be released next include:
+ * \li Alpha complex.
+ * \li Bottleneck distance.
+ * \li Zig zag persistence.
+ * \li Witness complex.
+ * \li Tangential complex.
+ * \li Clustering.
+*/
+/*! \page Citation Acknowledging the GUDHI library
+ * We kindly ask users to cite the GUDHI library as appropriately as possible in their papers, and to mention the use
+ * of the GUDHI library on the web pages of their projects using GUDHI and provide us with links to these web pages.
+ * Feel free to contact us in case you have any question or remark on this topic.
+ *
+ * We provide \ref GudhiBibtex entries for the modules of the User and Reference Manual, as well as for publications
+ * directly related to the GUDHI library.
+ * \section GudhiBibtex GUDHI bibtex
+ * \verbinclude biblio/how_to_cite_gudhi.bib
*/
+
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