Fewer copies and no GIL for hera

Now the input arrays are not copied as long as they use a float64 data
type, even if they are not contiguous. That's not important here, but I
wanted an example of how to do it.
More importantly, no need to hold the GIL.
I was too lazy to benchmark to see if that changed anything...

1 files changed, 20 insertions, 8 deletions

diff --git a/src/python/gudhi/hera.cc b/src/python/gudhi/hera.cc
index 0d562b4c..50d49c77 100644
--- a/src/python/gudhi/hera.cc
+++ b/src/python/gudhi/hera.cc
@@ -11,14 +11,24 @@
 #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
+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);
+  };
+}
 
 double wasserstein_distance(
     Dgm d1, Dgm d2,
@@ -27,16 +37,18 @@ double wasserstein_distance(
 {
   py::buffer_info buf1 = d1.request();
   py::buffer_info buf2 = d2.request();
+
+  py::gil_scoped_release release;
+
   // 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]);
+  auto cnt1 = boost::counting_range<ssize_t>(0, buf1.shape[0]);
+  auto diag1 = boost::adaptors::transform(cnt1, pairify(buf1.ptr, buf1.strides[0], buf1.strides[1]));
+  auto cnt2 = boost::counting_range<ssize_t>(0, buf2.shape[0]);
+  auto diag2 = boost::adaptors::transform(cnt2, pairify(buf2.ptr, buf2.strides[0], buf2.strides[1]));
 
   hera::AuctionParams<double> params;
   params.wasserstein_power = wasserstein_power;