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-rw-r--r--src/python/CMakeLists.txt52
-rw-r--r--src/python/doc/wasserstein_distance_user.rst15
-rw-r--r--src/python/gudhi/hera.cc62
-rw-r--r--src/python/setup.py.in32
4 files changed, 132 insertions, 29 deletions
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index b558d4c4..edb1ba02 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -86,6 +86,7 @@ if(PYTHONINTERP_FOUND)
endif(MSVC)
if(CMAKE_COMPILER_IS_GNUCXX)
set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-frounding-math', ")
+ set(GUDHI_PYBIND11_EXTRA_COMPILE_ARGS "${GUDHI_PYBIND11_EXTRA_COMPILE_ARGS}'-fvisibility=hidden', ")
endif(CMAKE_COMPILER_IS_GNUCXX)
if (CMAKE_CXX_COMPILER_ID MATCHES Intel)
set(GUDHI_PYTHON_EXTRA_COMPILE_ARGS "${GUDHI_PYTHON_EXTRA_COMPILE_ARGS}'-fp-model strict', ")
@@ -406,32 +407,37 @@ endif(CGAL_FOUND)
if(SCIPY_FOUND)
if(SKLEARN_FOUND)
if(OT_FOUND)
- if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
- set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
- # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
- # Images and biblio warnings because not found on developper version
- if (GUDHI_PYTHON_PATH STREQUAL "src/python")
- set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
- endif()
- # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
- add_custom_target(sphinx
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
- DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
- COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
+ if(PYBIND11_FOUND)
+ if(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+ set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
+ # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
+ # Images and biblio warnings because not found on developper version
+ if (GUDHI_PYTHON_PATH STREQUAL "src/python")
+ set (GUDHI_SPHINX_MESSAGE "${GUDHI_SPHINX_MESSAGE} \n WARNING : Sphinx is configured for user version, you run it on developper version. Images and biblio will miss")
+ endif()
+ # sphinx target requires gudhi.so, because conf.py reads gudhi version from it
+ add_custom_target(sphinx
+ WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
+ DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
+ COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
- add_test(NAME sphinx_py_test
- WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
- ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
+ add_test(NAME sphinx_py_test
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
- # Set missing or not modules
- set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
- else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
- message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0")
+ # Set missing or not modules
+ set(GUDHI_MODULES ${GUDHI_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MODULES")
+ else(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+ message("++ Python documentation module will not be compiled because it requires a Eigen3 and CGAL version >= 4.11.0")
+ set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
+ endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+ else(PYBIND11_FOUND)
+ message("++ Python documentation module will not be compiled because pybind11 was not found")
set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
- endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+ endif(PYBIND11_FOUND)
else(OT_FOUND)
message("++ Python documentation module will not be compiled because POT was not found")
set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python-documentation" CACHE INTERNAL "GUDHI_MISSING_MODULES")
diff --git a/src/python/doc/wasserstein_distance_user.rst b/src/python/doc/wasserstein_distance_user.rst
index 32999a0c..648cc568 100644
--- a/src/python/doc/wasserstein_distance_user.rst
+++ b/src/python/doc/wasserstein_distance_user.rst
@@ -9,12 +9,21 @@ Definition
.. include:: wasserstein_distance_sum.inc
-This implementation is based on ideas from "Large Scale Computation of Means and Cluster for Persistence Diagrams via Optimal Transport".
+Functions
+---------
+This implementation uses the Python Optimal Transport library and is based on
+ideas from "Large Scale Computation of Means and Cluster for Persistence
+Diagrams via Optimal Transport".
-Function
---------
.. autofunction:: gudhi.wasserstein.wasserstein_distance
+This other implementation comes from `Hera
+<https://bitbucket.org/grey_narn/hera/src/master/>`_ (BSD-3-Clause) and is
+based on `"Geometry Helps to Compare Persistence Diagrams."
+<http://dx.doi.org/10.1137/1.9781611974317.9>`_ by Michael Kerber, Dmitriy
+Morozov, and Arnur Nigmetov, at ALENEX 2016.
+
+.. autofunction:: gudhi.hera.wasserstein_distance
Basic example
-------------
diff --git a/src/python/gudhi/hera.cc b/src/python/gudhi/hera.cc
new file mode 100644
index 00000000..61f0da10
--- /dev/null
+++ b/src/python/gudhi/hera.cc
@@ -0,0 +1,62 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+
+#include <boost/range/iterator_range.hpp>
+
+#include <wasserstein.h>
+
+#include <array>
+
+namespace py = pybind11;
+typedef py::array_t<double, py::array::c_style | py::array::forcecast> Dgm;
+
+double wasserstein_distance(
+ Dgm d1, Dgm d2,
+ double wasserstein_power, double internal_p,
+ double delta)
+{
+ py::buffer_info buf1 = d1.request();
+ py::buffer_info buf2 = d2.request();
+ // shape (n,2) or (0) for empty
+ if((buf1.ndim!=2 || buf1.shape[1]!=2) && (buf1.ndim!=1 || buf1.shape[0]!=0))
+ throw std::runtime_error("Diagram 1 must be an array of size n x 2");
+ if((buf2.ndim!=2 || buf2.shape[1]!=2) && (buf2.ndim!=1 || buf2.shape[0]!=0))
+ throw std::runtime_error("Diagram 2 must be an array of size n x 2");
+ typedef std::array<double, 2> Point;
+ auto p1 = (Point*)buf1.ptr;
+ auto p2 = (Point*)buf2.ptr;
+ auto diag1 = boost::make_iterator_range(p1, p1+buf1.shape[0]);
+ auto diag2 = boost::make_iterator_range(p2, p2+buf2.shape[0]);
+
+ hera::AuctionParams<double> params;
+ params.wasserstein_power = wasserstein_power;
+ // hera encodes infinity as -1...
+ if(std::isinf(internal_p)) internal_p = hera::get_infinity<double>();
+ params.internal_p = internal_p;
+ params.delta = delta;
+ // The extra parameters are purposedly not exposed for now.
+ return hera::wasserstein_dist(diag1, diag2, params);
+}
+
+PYBIND11_MODULE(hera, m) {
+ m.def("wasserstein_distance", &wasserstein_distance,
+ py::arg("X"), py::arg("Y"),
+ // Should we name those q, p and d instead?
+ py::arg("order") = 1,
+ py::arg("internal_p") = std::numeric_limits<double>::infinity(),
+ py::arg("delta") = .01,
+ R"pbdoc(
+ Compute the Wasserstein distance between two diagrams.
+ Points at infinity are supported.
+
+ Parameters:
+ X (n x 2 numpy array): First diagram
+ Y (n x 2 numpy array): Second diagram
+ order (float): Wasserstein exponent W_q
+ internal_p (float): Internal Minkowski norm L^p in R^2
+ delta (float): Relative error 1+delta
+
+ Returns:
+ float: Approximate Wasserstein distance W_q(X,Y)
+ )pbdoc");
+}
diff --git a/src/python/setup.py.in b/src/python/setup.py.in
index 9c2124f4..08c46ced 100644
--- a/src/python/setup.py.in
+++ b/src/python/setup.py.in
@@ -27,6 +27,20 @@ library_dirs=[@GUDHI_PYTHON_LIBRARY_DIRS@]
include_dirs = [numpy_get_include(), '@CMAKE_CURRENT_SOURCE_DIR@/gudhi/', @GUDHI_PYTHON_INCLUDE_DIRS@]
runtime_library_dirs=[@GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS@]
+# Copied from https://github.com/pybind/python_example/blob/master/setup.py
+class get_pybind_include(object):
+ """Helper class to determine the pybind11 include path
+ The purpose of this class is to postpone importing pybind11
+ until it is actually installed, so that the ``get_include()``
+ method can be invoked. """
+
+ def __init__(self, user=False):
+ self.user = user
+
+ def __str__(self):
+ import pybind11
+ return pybind11.get_include(self.user)
+
# Create ext_modules list from module list
ext_modules = []
for module in modules:
@@ -42,6 +56,18 @@ for module in modules:
runtime_library_dirs=runtime_library_dirs,
cython_directives = {'language_level': str(sys.version_info[0])},))
+ext_modules = cythonize(ext_modules)
+
+ext_modules.append(Extension(
+ 'gudhi.hera',
+ sources = [source_dir + 'hera.cc'],
+ language = 'c++',
+ include_dirs = include_dirs +
+ ['@CMAKE_SOURCE_DIR@/ext/hera/geom_matching/wasserstein/include',
+ get_pybind_include(False), get_pybind_include(True)],
+ extra_compile_args=extra_compile_args + [@GUDHI_PYBIND11_EXTRA_COMPILE_ARGS@],
+ ))
+
setup(
name = 'gudhi',
packages=["gudhi",],
@@ -49,7 +75,7 @@ setup(
author_email='gudhi-contact@lists.gforge.inria.fr',
version='@GUDHI_VERSION@',
url='http://gudhi.gforge.inria.fr/',
- ext_modules = cythonize(ext_modules),
- install_requires = ['cython','numpy >= 1.9',],
- setup_requires = ['numpy >= 1.9',],
+ ext_modules = ext_modules,
+ install_requires = ['cython','numpy >= 1.9','pybind11',],
+ setup_requires = ['numpy >= 1.9','pybind11',],
)
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-11 04:00:22 +0000