summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--biblio/how_to_cite_gudhi.bib.in362
m---------ext/hera0
-rw-r--r--src/Simplex_tree/include/gudhi/Simplex_tree.h32
-rw-r--r--src/Simplex_tree/test/simplex_tree_unit_test.cpp14
-rw-r--r--src/Tangential_complex/include/gudhi/Tangential_complex.h5
-rw-r--r--src/cmake/modules/GUDHI_submodules.cmake6
-rw-r--r--src/cmake/modules/GUDHI_user_version_target.cmake5
-rw-r--r--src/python/gudhi/hera/bottleneck.cc2
-rw-r--r--src/python/gudhi/hera/wasserstein.cc10
-rw-r--r--src/python/gudhi/representations/vector_methods.py7
-rw-r--r--src/python/gudhi/simplex_tree.pyx8
-rw-r--r--src/python/include/Alpha_complex_factory.h4
-rw-r--r--src/python/setup.py.in6
-rwxr-xr-xsrc/python/test/test_wasserstein_distance.py9
14 files changed, 252 insertions, 218 deletions
diff --git a/biblio/how_to_cite_gudhi.bib.in b/biblio/how_to_cite_gudhi.bib.in
index a1a971fc..02c09dea 100644
--- a/biblio/how_to_cite_gudhi.bib.in
+++ b/biblio/how_to_cite_gudhi.bib.in
@@ -1,190 +1,190 @@
@book{gudhi:urm
-, title = "{GUDHI} User and Reference Manual"
-, author = "{The GUDHI Project}"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, year = @GUDHI_VERSION_YEAR@
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/"
+, title = {GUDHI User and Reference Manual}
+, author = {The GUDHI Project}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, year = {@GUDHI_VERSION_YEAR@}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/}
}
@incollection{gudhi:CubicalComplex
-, author = "Pawel Dlotko"
-, title = "Cubical complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cubical__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Pawel Dlotko}
+, title = {Cubical complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cubical__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:FilteredComplexes
-, author = "Cl\'ement Maria"
-, title = "Filtered Complexes"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__simplex__tree.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Cl{\'{e}}ment Maria}
+, title = {Filtered Complexes}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__simplex__tree.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:ToplexMap
-, author = "Fran{{\c{c}}ois Godi"
-, title = "Toplex map"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__toplex__map.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Fran{\c{c}}ois Godi}
+, title = {Toplex map}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__toplex__map.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:SkeletonBlocker
-, author = "David Salinas"
-, title = "Skeleton-Blocker"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__skbl.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {David Salinas}
+, title = {Skeleton-Blocker}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__skbl.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:Contraction
-, author = "David Salinas"
-, title = "Contraction"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__contr.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {David Salinas}
+, title = {Contraction}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__contr.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:AlphaComplex
-, author = "Vincent Rouvreau"
-, title = "Alpha complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__alpha__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Vincent Rouvreau}
+, title = {Alpha complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__alpha__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:CechComplex
-, author = "Vincent Rouvreau, Hind Montassif"
-, title = "\v{C}ech complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cech__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Vincent Rouvreau and Hind Montassif}
+, title = {{\v{C}}ech complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cech__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:RipsComplex
-, author = "Cl\'ement Maria, Pawel Dlotko, Vincent Rouvreau, Marc Glisse"
-, title = "Rips complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__rips__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Cl{\'{e}}ment Maria and Pawel Dlotko and Vincent Rouvreau and Marc Glisse}
+, title = {Rips complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__rips__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:Collapse
-, author = "Siddharth Pritam, Marc Glisse"
-, title = "Edge collapse"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__edge__collapse.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Siddharth Pritam and Marc Glisse}
+, title = {Edge collapse}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__edge__collapse.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:WitnessComplex
-, author = "Siargey Kachanovich"
-, title = "Witness complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__witness__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Siargey Kachanovich}
+, title = {Witness complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__witness__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:CoverComplex
-, author = "Mathieu Carri\`ere"
-, title = "Cover complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Mathieu Carri{\`{e}}re}
+, title = {Cover complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:CoxeterTriangulation
-, author = "Siargey Kachanovich"
-, title = "Coxeter triangulation"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Siargey Kachanovich}
+, title = {Coxeter triangulation}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__cover__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:TangentialComplex
-, author = "Cl\'ement Jamin"
-, title = "Tangential complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__tangential__complex.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Cl{\'{e}}ment Jamin}
+, title = {Tangential complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__tangential__complex.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:PersistentCohomology
-, author = "Cl\'ement Maria"
-, title = "Persistent Cohomology"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__persistent__cohomology.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Cl{\'{e}}ment Maria}
+, title = {Persistent Cohomology}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__persistent__cohomology.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:BottleneckDistance
-, author = "Fran{{\c{c}}ois Godi"
-, title = "Bottleneck distance"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__bottleneck__distance.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Fran{\c{c}}ois Godi}
+, title = {Bottleneck distance}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__bottleneck__distance.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:PersistenceRepresentations
-, author = "Pawel Dlotko"
-, title = "Persistence representations"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group___persistence__representations.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Pawel Dlotko}
+, title = {Persistence representations}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group___persistence__representations.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:SubSampling
-, author = "Cl\'ement Jamin, Siargey Kachanovich"
-, title = "Subsampling"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__subsampling.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Cl{\'{e}}ment Jamin and Siargey Kachanovich}
+, title = {Subsampling}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__subsampling.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:SpatialSearching
-, author = "Cl\'ement Jamin"
-, title = "Spatial searching"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__spatial__searching.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Cl{\'{e}}ment Jamin}
+, title = {Spatial searching}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/doc/@GUDHI_VERSION@/group__spatial__searching.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -192,71 +192,71 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@incollection{gudhi:WeightedRipsComplex
-, author = "Rapha\"el Tinarrage, Yuichi Ike, Masatoshi Takenouchi"
-, title = "Weighted Rips Complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/rips_complex_user.html#weighted-rips-complex"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Rapha{\"{e}}l Tinarrage and Yuichi Ike and Masatoshi Takenouchi}
+, title = {Weighted Rips Complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/rips_complex_user.html#weighted-rips-complex}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:DTMRipsComplex
-, author = "Yuichi Ike"
-, title = "DTM Rips Complex"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/rips_complex_user.html#dtm-rips-complex"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Yuichi Ike}
+, title = {DTM Rips Complex}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/rips_complex_user.html#dtm-rips-complex}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:WassersteinDistance
-, author = "Theo Lacombe, Marc Glisse"
-, title = "Wasserstein distance"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/wasserstein_distance_user.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Th{\'{e}}o Lacombe and Marc Glisse}
+, title = {Wasserstein distance}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/wasserstein_distance_user.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:PersistenceRepresentationsScikitlearnInterface
-, author = "Mathieu Carri\`ere, Gard Spreemann, Wojciech Reise"
-, title = "Persistence representations scikit-learn like interface"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/representations.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Mathieu Carri{\`{e}}re and Gard Spreemann and Wojciech Reise}
+, title = {Persistence representations scikit-learn like interface}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/representations.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:Atol
-, author = "Martin Royer"
-, title = "Measure Vectorization for Automatic Topologically-Oriented Learning"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/representations.html#gudhi.representations.vector_methods.Atol"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Martin Royer}
+, title = {Measure Vectorization for Automatic Topologically-Oriented Learning}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/representations.html#gudhi.representations.vector_methods.Atol}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:DistanceToMeasure
-, author = "Marc Glisse"
-, title = "Distance to measure"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/point_cloud.html#module-gudhi.point_cloud.knn"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Marc Glisse}
+, title = {Distance to measure}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/point_cloud.html#module-gudhi.point_cloud.knn}
+, year = {@GUDHI_VERSION_YEAR@}
}
@incollection{gudhi:PersistenceBasedClustering
-, author = "Marc Glisse"
-, title = "persistence-based clustering"
-, publisher = "{GUDHI Editorial Board}"
-, edition = "{@GUDHI_VERSION@}"
-, booktitle = "{GUDHI} User and Reference Manual"
-, url = "https://gudhi.inria.fr/python/@GUDHI_VERSION@/clustering.html"
-, year = @GUDHI_VERSION_YEAR@
+, author = {Marc Glisse}
+, title = {persistence-based clustering}
+, publisher = {GUDHI Editorial Board}
+, edition = {@GUDHI_VERSION@}
+, booktitle = {GUDHI User and Reference Manual}
+, url = {https://gudhi.inria.fr/python/@GUDHI_VERSION@/clustering.html}
+, year = {@GUDHI_VERSION_YEAR@}
}
diff --git a/ext/hera b/ext/hera
-Subproject b528c4067a8aac346eb307d3c23b82d5953cfe2
+Subproject 8bfdd4bd32f005c18b5c75c502b987de552d6e4
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index ef9f8428..4177a0b8 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -24,6 +24,7 @@
#include <boost/iterator/transform_iterator.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/range/adaptor/reversed.hpp>
+#include <boost/range/adaptor/transformed.hpp>
#include <boost/range/size.hpp>
#include <boost/container/static_vector.hpp>
@@ -1122,16 +1123,12 @@ class Simplex_tree {
dimension_ = 1;
}
- root_.members_.reserve(num_vertices(skel_graph));
+ root_.members_.reserve(num_vertices(skel_graph)); // probably useless in most cases
+ auto verts = vertices(skel_graph) | boost::adaptors::transformed([&](auto v){
+ return Dit_value_t(v, Node(&root_, get(vertex_filtration_t(), skel_graph, v))); });
+ root_.members_.insert(boost::begin(verts), boost::end(verts));
+ // This automatically sorts the vertices, the graph concept doesn't guarantee the order in which we iterate.
- typename boost::graph_traits<OneSkeletonGraph>::vertex_iterator v_it,
- v_it_end;
- for (std::tie(v_it, v_it_end) = vertices(skel_graph); v_it != v_it_end;
- ++v_it) {
- root_.members_.emplace_hint(
- root_.members_.end(), *v_it,
- Node(&root_, get(vertex_filtration_t(), skel_graph, *v_it)));
- }
std::pair<typename boost::graph_traits<OneSkeletonGraph>::edge_iterator,
typename boost::graph_traits<OneSkeletonGraph>::edge_iterator> boost_edges = edges(skel_graph);
// boost_edges.first is the equivalent to boost_edges.begin()
@@ -1140,7 +1137,7 @@ class Simplex_tree {
auto edge = *(boost_edges.first);
auto u = source(edge, skel_graph);
auto v = target(edge, skel_graph);
- if (u == v) throw "Self-loops are not simplicial";
+ if (u == v) throw std::invalid_argument("Self-loops are not simplicial");
// We cannot skip edges with the wrong orientation and expect them to
// come a second time with the right orientation, that does not always
// happen in practice. emplace() should be a NOP when an element with the
@@ -1159,6 +1156,21 @@ class Simplex_tree {
}
}
+ /** \brief Inserts several vertices.
+ * @param[in] vertices A range of Vertex_handle
+ * @param[in] filt filtration value of the new vertices (the same for all)
+ *
+ * This may be faster than inserting the vertices one by one, especially in a random order.
+ * The complex does not need to be empty before calling this function. However, if a vertex is
+ * already present, its filtration value is not modified, unlike with other insertion functions. */
+ template <class VertexRange>
+ void insert_batch_vertices(VertexRange const& vertices, Filtration_value filt = 0) {
+ auto verts = vertices | boost::adaptors::transformed([&](auto v){
+ return Dit_value_t(v, Node(&root_, filt)); });
+ root_.members_.insert(boost::begin(verts), boost::end(verts));
+ if (dimension_ < 0 && !root_.members_.empty()) dimension_ = 0;
+ }
+
/** \brief Expands the Simplex_tree containing only its one skeleton
* until dimension max_dim.
*
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 79bb5a93..ebcc406c 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -1038,3 +1038,17 @@ BOOST_AUTO_TEST_CASE_TEMPLATE(simplex_tree_boundaries_and_opposite_vertex_iterat
BOOST_CHECK(opposite_vertices.size() == 0);
}
}
+
+BOOST_AUTO_TEST_CASE(batch_vertices) {
+ typedef Simplex_tree<> typeST;
+ std::clog << "********************************************************************" << std::endl;
+ std::clog << "TEST BATCH VERTEX INSERTION" << std::endl;
+ typeST st;
+ st.insert_simplex_and_subfaces({3}, 1.5);
+ std::vector verts { 2, 3, 5, 6 };
+ st.insert_batch_vertices(verts);
+ BOOST_CHECK(st.num_vertices() == 4);
+ BOOST_CHECK(st.num_simplices() == 4);
+ BOOST_CHECK(st.filtration(st.find({2})) == 0.);
+ BOOST_CHECK(st.filtration(st.find({3})) == 1.5);
+}
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h
index 56a24af0..b448db2d 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h
@@ -345,10 +345,11 @@ class Tangential_complex {
m_stars.resize(m_points.size());
m_squared_star_spheres_radii_incl_margin.resize(m_points.size(), FT(-1));
#ifdef GUDHI_TC_PERTURB_POSITION
- if (m_points.empty())
+ if (m_points.empty()) {
m_translations.clear();
- else
+ } else {
m_translations.resize(m_points.size(), m_k.construct_vector_d_object()(m_ambient_dim));
+ }
#if defined(GUDHI_USE_TBB)
delete[] m_p_perturb_mutexes;
m_p_perturb_mutexes = new Mutex_for_perturb[m_points.size()];
diff --git a/src/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake
index 78b045bd..c844386d 100644
--- a/src/cmake/modules/GUDHI_submodules.cmake
+++ b/src/cmake/modules/GUDHI_submodules.cmake
@@ -1,5 +1,3 @@
# For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera.
-set(HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/wasserstein/include)
-set(HERA_WASSERSTEIN_INCLUDE_DIR ${HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's wasserstein.h")
-set(HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/bottleneck/include)
-set(HERA_BOTTLENECK_INCLUDE_DIR ${HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find Hera's bottleneck.h") \ No newline at end of file
+set(HERA_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/include)
+set(HERA_INCLUDE_DIR ${HERA_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find hera/{wasserstein.h,bottleneck.h}")
diff --git a/src/cmake/modules/GUDHI_user_version_target.cmake b/src/cmake/modules/GUDHI_user_version_target.cmake
index 4487ad86..2144ff6f 100644
--- a/src/cmake/modules/GUDHI_user_version_target.cmake
+++ b/src/cmake/modules/GUDHI_user_version_target.cmake
@@ -60,10 +60,9 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
copy_directory ${CMAKE_SOURCE_DIR}/src/GudhUI ${GUDHI_USER_VERSION_DIR}/GudhUI)
-if(HERA_WASSERSTEIN_INCLUDE_DIR STREQUAL HERA_WASSERSTEIN_INTERNAL_INCLUDE_DIR OR
- HERA_BOTTLENECK_INCLUDE_DIR STREQUAL HERA_BOTTLENECK_INTERNAL_INCLUDE_DIR)
+if(HERA_INCLUDE_DIR STREQUAL HERA_INTERNAL_INCLUDE_DIR)
add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
- copy_directory ${CMAKE_SOURCE_DIR}/ext/hera ${GUDHI_USER_VERSION_DIR}/ext/hera)
+ copy_directory ${CMAKE_SOURCE_DIR}/ext/hera/include ${GUDHI_USER_VERSION_DIR}/ext/hera/include)
endif()
set(GUDHI_DIRECTORIES "doc;example;concept;utilities")
diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
index 0cb562ce..ec461f7c 100644
--- a/src/python/gudhi/hera/bottleneck.cc
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -16,7 +16,7 @@
using py::ssize_t;
#endif
-#include <bottleneck.h> // Hera
+#include <hera/bottleneck.h> // Hera
double bottleneck_distance(Dgm d1, Dgm d2, double delta)
{
diff --git a/src/python/gudhi/hera/wasserstein.cc b/src/python/gudhi/hera/wasserstein.cc
index fa0cf8aa..3516352e 100644
--- a/src/python/gudhi/hera/wasserstein.cc
+++ b/src/python/gudhi/hera/wasserstein.cc
@@ -8,10 +8,16 @@
* - YYYY/MM Author: Description of the modification
*/
-#include <wasserstein.h> // Hera
-
#include <pybind11_diagram_utils.h>
+#ifdef _MSC_VER
+// https://github.com/grey-narn/hera/issues/3
+// ssize_t is a non-standard type (well, posix)
+using py::ssize_t;
+#endif
+
+#include <hera/wasserstein.h> // Hera
+
double wasserstein_distance(
Dgm d1, Dgm d2,
double wasserstein_power, double internal_p,
diff --git a/src/python/gudhi/representations/vector_methods.py b/src/python/gudhi/representations/vector_methods.py
index a169aee8..d52185ef 100644
--- a/src/python/gudhi/representations/vector_methods.py
+++ b/src/python/gudhi/representations/vector_methods.py
@@ -13,8 +13,13 @@ import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.exceptions import NotFittedError
from sklearn.preprocessing import MinMaxScaler, MaxAbsScaler
-from sklearn.neighbors import DistanceMetric
from sklearn.metrics import pairwise
+try:
+ # New location since 1.0
+ from sklearn.metrics import DistanceMetric
+except ImportError:
+ # Will be removed in 1.3
+ from sklearn.neighbors import DistanceMetric
from .preprocessing import DiagramScaler, BirthPersistenceTransform
diff --git a/src/python/gudhi/simplex_tree.pyx b/src/python/gudhi/simplex_tree.pyx
index 24b970c4..18215d2f 100644
--- a/src/python/gudhi/simplex_tree.pyx
+++ b/src/python/gudhi/simplex_tree.pyx
@@ -466,7 +466,7 @@ cdef class SimplexTree:
"""
return self.get_ptr().prune_above_filtration(filtration)
- def expansion(self, max_dim):
+ def expansion(self, max_dimension):
"""Expands the simplex tree containing only its one skeleton
until dimension max_dim.
@@ -480,10 +480,10 @@ cdef class SimplexTree:
The simplex tree must contain no simplex of dimension bigger than
1 when calling the method.
- :param max_dim: The maximal dimension.
- :type max_dim: int
+ :param max_dimension: The maximal dimension.
+ :type max_dimension: int
"""
- cdef int maxdim = max_dim
+ cdef int maxdim = max_dimension
with nogil:
self.get_ptr().expansion(maxdim)
diff --git a/src/python/include/Alpha_complex_factory.h b/src/python/include/Alpha_complex_factory.h
index 3d20aa8f..41eb72c1 100644
--- a/src/python/include/Alpha_complex_factory.h
+++ b/src/python/include/Alpha_complex_factory.h
@@ -106,7 +106,7 @@ class Exact_alpha_complex_dD final : public Abstract_alpha_complex {
return alpha_complex_.create_complex(*simplex_tree, max_alpha_square, exact_version_, default_filtration_value);
}
- virtual std::size_t num_vertices() const {
+ virtual std::size_t num_vertices() const override {
return alpha_complex_.num_vertices();
}
@@ -141,7 +141,7 @@ class Inexact_alpha_complex_dD final : public Abstract_alpha_complex {
return alpha_complex_.create_complex(*simplex_tree, max_alpha_square, false, default_filtration_value);
}
- virtual std::size_t num_vertices() const {
+ virtual std::size_t num_vertices() const override {
return alpha_complex_.num_vertices();
}
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 2c67c2c5..1ecbe985 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -48,10 +48,8 @@ ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'}
for module in pybind11_modules:
my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)]
- if module == 'hera/wasserstein':
- my_include_dirs = ['@HERA_WASSERSTEIN_INCLUDE_DIR@'] + my_include_dirs
- elif module == 'hera/bottleneck':
- my_include_dirs = ['@HERA_BOTTLENECK_INCLUDE_DIR@'] + my_include_dirs
+ if module.startswith('hera/'):
+ my_include_dirs = ['@HERA_INCLUDE_DIR@'] + my_include_dirs
ext_modules.append(Extension(
'gudhi.' + module.replace('/', '.'),
sources = [source_dir + module + '.cc'],
diff --git a/src/python/test/test_wasserstein_distance.py b/src/python/test/test_wasserstein_distance.py
index 3a004d77..a76b6ce7 100755
--- a/src/python/test/test_wasserstein_distance.py
+++ b/src/python/test/test_wasserstein_distance.py
@@ -90,10 +90,11 @@ def test_get_essential_parts():
def test_warn_infty():
- assert _warn_infty(matching=False)==np.inf
- c, m = _warn_infty(matching=True)
- assert (c == np.inf)
- assert (m is None)
+ with pytest.warns(UserWarning):
+ assert _warn_infty(matching=False)==np.inf
+ c, m = _warn_infty(matching=True)
+ assert (c == np.inf)
+ assert (m is None)
def _basic_wasserstein(wasserstein_distance, delta, test_infinity=True, test_matching=True):
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-14 09:17:59 +0000