Merge branch 'master' into alpha_complex_3d_python

4 files changed, 64 insertions, 2 deletions

diff --git a/src/python/gudhi/bottleneck.cc b/src/python/gudhi/bottleneck.cc
index 838bf9eb..8a3d669a 100644
--- a/src/python/gudhi/bottleneck.cc
+++ b/src/python/gudhi/bottleneck.cc
@@ -33,7 +33,8 @@ PYBIND11_MODULE(bottleneck, m) {
           py::arg("diagram_1"), py::arg("diagram_2"),
           py::arg("e") = py::none(),
           R"pbdoc(
-    This function returns the point corresponding to a given vertex.
+    Compute the Bottleneck distance between two diagrams.
+    Points at infinity and on the diagonal are supported.
 
     :param diagram_1: The first diagram.
     :type diagram_1: numpy array of shape (m,2)
diff --git a/src/python/gudhi/hera/__init__.py b/src/python/gudhi/hera/__init__.py
new file mode 100644
index 00000000..f70b92b9
--- /dev/null
+++ b/src/python/gudhi/hera/__init__.py
@@ -0,0 +1,7 @@
+from .wasserstein import wasserstein_distance
+from .bottleneck import bottleneck_distance
+
+
+__author__ = "Marc Glisse"
+__copyright__ = "Copyright (C) 2020 Inria"
+__license__ = "MIT"
diff --git a/src/python/gudhi/hera/bottleneck.cc b/src/python/gudhi/hera/bottleneck.cc
new file mode 100644
index 00000000..0cb562ce
--- /dev/null
+++ b/src/python/gudhi/hera/bottleneck.cc
@@ -0,0 +1,54 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Marc Glisse
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#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 <bottleneck.h> // Hera
+
+double bottleneck_distance(Dgm d1, Dgm d2, double delta)
+{
+  // I *think* the call to request() has to be before releasing the GIL.
+  auto diag1 = numpy_to_range_of_pairs(d1);
+  auto diag2 = numpy_to_range_of_pairs(d2);
+
+  py::gil_scoped_release release;
+
+  if (delta == 0)
+    return hera::bottleneckDistExact(diag1, diag2);
+  else
+    return hera::bottleneckDistApprox(diag1, diag2, delta);
+}
+
+PYBIND11_MODULE(bottleneck, m) {
+      m.def("bottleneck_distance", &bottleneck_distance,
+          py::arg("X"), py::arg("Y"),
+          py::arg("delta") = .01,
+          R"pbdoc(
+        Compute the Bottleneck distance between two diagrams.
+        Points at infinity are supported.
+
+        .. note::
+           Points on the diagonal are not supported and must be filtered out before calling this function.
+
+        Parameters:
+            X (n x 2 numpy array): First diagram
+            Y (n x 2 numpy array): Second diagram
+            delta (float): Relative error 1+delta
+
+        Returns:
+            float: (approximate) bottleneck distance d_B(X,Y)
+    )pbdoc");
+}
diff --git a/src/python/gudhi/hera.cc b/src/python/gudhi/hera/wasserstein.cc
index ea80a9a8..1a21f02f 100644
--- a/src/python/gudhi/hera.cc
+++ b/src/python/gudhi/hera/wasserstein.cc
@@ -33,7 +33,7 @@ double wasserstein_distance(
   return hera::wasserstein_dist(diag1, diag2, params);
 }
 
-PYBIND11_MODULE(hera, m) {
+PYBIND11_MODULE(wasserstein, m) {
       m.def("wasserstein_distance", &wasserstein_distance,
           py::arg("X"), py::arg("Y"),
           py::arg("order") = 1,