Merge pull request #302 from mglisse/hera-gil

Fewer copies and no GIL for hera

1 files changed, 30 insertions, 15 deletions

diff --git a/src/python/gudhi/hera.cc b/src/python/gudhi/hera.cc
index 0d562b4c..5aec1806 100644
--- a/src/python/gudhi/hera.cc
+++ b/src/python/gudhi/hera.cc
@@ -11,32 +11,47 @@
 #include <pybind11/pybind11.h>
 #include <pybind11/numpy.h>
 
-#include <boost/range/iterator_range.hpp>
+#include <boost/range/counting_range.hpp>
+#include <boost/range/adaptor/transformed.hpp>
 
 #include <wasserstein.h> // Hera
 
-#include <array>
+#include <utility>
 
 namespace py = pybind11;
-typedef py::array_t<double, py::array::c_style | py::array::forcecast> Dgm;
+typedef py::array_t<double> Dgm;
+
+// Get m[i,0] and m[i,1] as a pair
+static auto pairify(void* p, ssize_t h, ssize_t w) {
+  return [=](ssize_t i){
+    char* birth = (char*)p + i * h;
+    char* death = birth + w;
+    return std::make_pair(*(double*)birth, *(double*)death);
+  };
+}
+
+inline auto numpy_to_range_of_pairs(py::array_t<double> dgm) {
+  py::buffer_info buf = dgm.request();
+  // shape (n,2) or (0) for empty
+  if((buf.ndim!=2 || buf.shape[1]!=2) && (buf.ndim!=1 || buf.shape[0]!=0))
+    throw std::runtime_error("Diagram must be an array of size n x 2");
+  // In the case of shape (0), avoid reading non-existing strides[1] even if we won't use it.
+  ssize_t stride1 = buf.ndim == 2 ? buf.strides[1] : 0;
+  auto cnt = boost::counting_range<ssize_t>(0, buf.shape[0]);
+  return boost::adaptors::transform(cnt, pairify(buf.ptr, buf.strides[0], stride1));
+  // Be careful that the returned range cannot contain references to dead temporaries.
+}
 
 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]);
+  // 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;
 
   hera::AuctionParams<double> params;
   params.wasserstein_power = wasserstein_power;