--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LEGAL Fri Jul 14 14:04:13 2017 -0700
@@ -0,0 +1,15 @@
+Copyright (C) 2006-2017 Dmitriy Morozov <dmitriy@mrzv.org>
+
+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 2 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, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/LICENSE Fri Jul 14 14:04:13 2017 -0700
@@ -0,0 +1,280 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
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+
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+Foundation.
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+ 10. If you wish to incorporate parts of the Program into other free
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+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
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+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
--- a/bindings/python/persistence-diagram.cpp Sun Apr 27 13:49:14 2014 -0700
+++ b/bindings/python/persistence-diagram.cpp Fri Jul 14 14:04:13 2017 -0700
@@ -13,6 +13,7 @@
#include<boost/shared_ptr.hpp>
#include<boost/python/stl_iterator.hpp>
#include<boost/python/def.hpp>
+#include<boost/python/register_ptr_to_python.hpp>
namespace bp = boost::python;
@@ -210,6 +211,7 @@
.def("__iter__", bp::range(&dp::PersistenceDiagramD::begin, &dp::PersistenceDiagramD::end))
.def("__len__", &dp::PersistenceDiagramD::size)
;
+ bp::register_ptr_to_python<dp::PDgmPtr>();
bp::def("init_diagrams", &InitDiagrams<dp::SPersistence>::init,
(bp::arg("persistence"),
--- a/doc/get-build-install.rst Sun Apr 27 13:49:14 2014 -0700
+++ b/doc/get-build-install.rst Fri Jul 14 14:04:13 2017 -0700
@@ -11,7 +11,6 @@
hg clone |dionysus-url|
cd Dionysus
- hg up tip
If you don't have time or desire to deal with Mercurial, you can download the
`tarball of the entire repository`_. The advantage of using Mercurial is that it
--- a/examples/bottleneck-distance.cpp Sun Apr 27 13:49:14 2014 -0700
+++ b/examples/bottleneck-distance.cpp Fri Jul 14 14:04:13 2017 -0700
@@ -60,8 +60,9 @@
PDgm dgm1, dgm2;
read_diagram(dgm1, filename1);
read_diagram(dgm2, filename2);
- std::cout << "Size dgm1: " << dgm1.size() << std::endl;
- std::cout << "Size dgm2: " << dgm2.size() << std::endl;
+ //std::cout << "Size dgm1: " << dgm1.size() << std::endl;
+ //std::cout << "Size dgm2: " << dgm2.size() << std::endl;
- std::cout << "Distance: " << bottleneck_distance(dgm1, dgm2) << std::endl;
+ //std::cout << "Distance: " << bottleneck_distance(dgm1, dgm2) << std::endl;
+ std::cout << "L2-Distance: " << wasserstein_distance(dgm1, dgm2, 2) << std::endl;
}
--- a/include/topology/simplex.hpp Sun Apr 27 13:49:14 2014 -0700
+++ b/include/topology/simplex.hpp Fri Jul 14 14:04:13 2017 -0700
@@ -1,3 +1,4 @@
+#include <boost/serialization/serialization.hpp>
#include <boost/serialization/base_object.hpp>
#include <boost/serialization/set.hpp>
#include <boost/serialization/nvp.hpp>
--- a/tools/matching/CMakeLists.txt Sun Apr 27 13:49:14 2014 -0700
+++ b/tools/matching/CMakeLists.txt Fri Jul 14 14:04:13 2017 -0700
@@ -4,3 +4,6 @@
# Build compare-diagrams
add_executable (bottleneck bottleneck.cpp)
target_link_libraries (bottleneck ${libraries})
+
+add_executable (wasserstein wasserstein.cpp)
+target_link_libraries (wasserstein ${libraries})
--- a/tools/matching/bottleneck.cpp Sun Apr 27 13:49:14 2014 -0700
+++ b/tools/matching/bottleneck.cpp Fri Jul 14 14:04:13 2017 -0700
@@ -23,7 +23,7 @@
read_diagram(filename1, dgm1);
read_diagram(filename2, dgm2);
- std::cout << "Distance: " << bottleneck_distance(dgm1, dgm2) << std::endl;
+ std::cout << bottleneck_distance(dgm1, dgm2) << std::endl;
}
@@ -34,6 +34,7 @@
while(in)
{
in >> birth >> death;
+ //std::cout << "birth: " << birth << ", death: " << death << std::endl;
if (in)
dgm.push_back(Point(birth, death));
}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/matching/wasserstein.cpp Fri Jul 14 14:04:13 2017 -0700
@@ -0,0 +1,74 @@
+#include <iostream>
+#include <fstream>
+
+#include <topology/persistence-diagram.h>
+
+#include <boost/program_options.hpp>
+namespace po = boost::program_options;
+
+typedef PersistenceDiagram<> PDgm;
+typedef PDgm::Point Point;
+
+
+void read_diagram(const std::string& filename, PDgm& dgm);
+void process_program_options(int argc, char* argv[], std::string& filename1, std::string& filename2, double& wasserPower);
+
+
+int main(int argc, char* argv[])
+{
+ std::string filename1, filename2;
+ double wasserPower;
+ process_program_options(argc, argv, filename1, filename2, wasserPower);
+
+ PDgm dgm1, dgm2;
+ read_diagram(filename1, dgm1);
+ read_diagram(filename2, dgm2);
+
+ std::cout << pow(wasserstein_distance(dgm1, dgm2, wasserPower), 1.0 / wasserPower) << std::endl;
+}
+
+
+void read_diagram(const std::string& filename, PDgm& dgm)
+{
+ std::ifstream in(filename.c_str());
+ double birth, death;
+ while(in)
+ {
+ in >> birth >> death;
+ //std::cout << "birth: " << birth << ", death: " << death << std::endl;
+ if (in)
+ dgm.push_back(Point(birth, death));
+ }
+}
+
+void process_program_options(int argc, char* argv[], std::string& filename1, std::string& filename2, double& wasserPower)
+{
+ po::options_description hidden("Hidden options");
+ hidden.add_options()
+ ("input-file1", po::value<std::string>(&filename1), "The first collection of persistence diagrams")
+ ("input-file2", po::value<std::string>(&filename2), "The second collection of persistence diagrams")
+ ("wasser-power", po::value<double>(&wasserPower), "The power of Wasserstein distance");
+
+ po::positional_options_description p;
+ p.add("input-file1", 1);
+ p.add("input-file2", 1);
+ p.add("wasser-power", 1);
+
+ po::options_description all; all.add(hidden);
+
+ po::variables_map vm;
+ po::store(po::command_line_parser(argc, argv).
+ options(all).positional(p).run(), vm);
+ po::notify(vm);
+
+ if (!vm.count("input-file1") || !vm.count("input-file2"))
+ {
+ std::cout << "Usage: " << argv[0] << " input-file1 input-file2" << std::endl;
+ std::abort();
+ }
+ if (!vm.count("wasser-power"))
+ {
+ // use L2 by default
+ wasserPower = 2;
+ }
+}