From 6819bc56a4b7975b172cd7e086e04ed9626cfccb Mon Sep 17 00:00:00 2001
From: Carl Johnsen <carl-johannes@di.ku.dk>
Date: Tue, 14 May 2024 08:23:51 +0200
Subject: [PATCH] #24 Added (missing) namespaces to the morphology C++
 implementations

---
 src/lib/cpp/cpu/morphology.cc     |  5 ++++-
 src/lib/cpp/cpu_seq/morphology.cc |  6 +++++-
 src/lib/cpp/gpu/morphology.cc     |  6 +++++-
 src/lib/cpp/include/morphology.hh |  4 ++++
 src/pybind/morphology-pybind.cc   | 32 +++++++++++++++++++++++++++----
 5 files changed, 46 insertions(+), 7 deletions(-)

diff --git a/src/lib/cpp/cpu/morphology.cc b/src/lib/cpp/cpu/morphology.cc
index a180aa5..4fe79b8 100644
--- a/src/lib/cpp/cpu/morphology.cc
+++ b/src/lib/cpp/cpu/morphology.cc
@@ -1,6 +1,8 @@
 #include "morphology.hh"
 #include "datatypes.hh"
 
+namespace cpu_par {
+
 template <typename Op, bool neutral>
 void morphology_3d_sphere(
         const mask_type *voxels,
@@ -43,4 +45,5 @@ void morphology_3d_sphere(
             }
         }
     }
-}
\ No newline at end of file
+}
+} // namespace cpu_par
\ No newline at end of file
diff --git a/src/lib/cpp/cpu_seq/morphology.cc b/src/lib/cpp/cpu_seq/morphology.cc
index 50c16bf..3744689 100644
--- a/src/lib/cpp/cpu_seq/morphology.cc
+++ b/src/lib/cpp/cpu_seq/morphology.cc
@@ -1,6 +1,8 @@
 #include "morphology.hh"
 #include "datatypes.hh"
 
+namespace cpu_seq {
+
 template <typename Op, bool neutral>
 void morphology_3d_sphere(
         const mask_type *voxels,
@@ -41,4 +43,6 @@ void morphology_3d_sphere(
             }
         }
     }
-}
\ No newline at end of file
+}
+
+} // namespace cpu_seq
\ No newline at end of file
diff --git a/src/lib/cpp/gpu/morphology.cc b/src/lib/cpp/gpu/morphology.cc
index 5125354..b8e1945 100644
--- a/src/lib/cpp/gpu/morphology.cc
+++ b/src/lib/cpp/gpu/morphology.cc
@@ -1,6 +1,8 @@
 #include "morphology.hh"
 #include "datatypes.hh"
 
+namespace gpu {
+
 template <typename Op, bool neutral>
 void morphology_3d_sphere(
         const mask_type *voxels,
@@ -107,4 +109,6 @@ void morphology_3d_sphere_r16(
 #else
     throw runtime_error("Library wasn't compiled with OpenACC.");
 #endif
-}
\ No newline at end of file
+}
+
+} // namespace gpu
\ No newline at end of file
diff --git a/src/lib/cpp/include/morphology.hh b/src/lib/cpp/include/morphology.hh
index 66a28e4..e33cadc 100644
--- a/src/lib/cpp/include/morphology.hh
+++ b/src/lib/cpp/include/morphology.hh
@@ -3,6 +3,8 @@
 
 #include "datatypes.hh"
 
+namespace NS {
+
 template <typename Op, bool neutral>
 void morphology_3d_sphere(
         const mask_type *voxels,
@@ -11,4 +13,6 @@ void morphology_3d_sphere(
         const int64_t strides[3],
         mask_type *result);
 
+
+} // namespace NS
 #endif
\ No newline at end of file
diff --git a/src/pybind/morphology-pybind.cc b/src/pybind/morphology-pybind.cc
index f208e89..78d4af5 100644
--- a/src/pybind/morphology-pybind.cc
+++ b/src/pybind/morphology-pybind.cc
@@ -7,6 +7,8 @@ namespace py = pybind11;
 #include "morphology.cc"
 #include "datatypes.hh"
 
+namespace python_api {
+
 template <typename Op, bool neutral>
 void morphology_3d_sphere_wrapper(
         const py::array_t<mask_type> &np_voxels,
@@ -24,15 +26,37 @@ void morphology_3d_sphere_wrapper(
     mask_type *result = static_cast<mask_type*>(result_info.ptr);
 
     if (radius == (int64_t) 16) {
-        morphology_3d_sphere_r16<Op, neutral>(voxels, N, strides, result);
+        NS::morphology_3d_sphere_r16<Op, neutral>(voxels, N, strides, result);
     } else {
-    morphology_3d_sphere<Op, neutral>(voxels, radius, N, strides, result);
+        NS::morphology_3d_sphere<Op, neutral>(voxels, radius, N, strides, result);
     }
 }
+
+template <typename Op, bool neutral>
+void morphology_3d_sphere_wrapper_alt(
+        const py::array_t<mask_type> &np_voxels,
+        const int64_t radius,
+        py::array_t<mask_type> np_result) {
+    auto
+        voxels_info = np_voxels.request(),
+        result_info = np_result.request();
+
+    int64_t Nz = voxels_info.shape[0], Ny = voxels_info.shape[1], Nx = voxels_info.shape[2];
+    int64_t N[3] = {Nz, Ny, Nx};
+    int64_t strides[3] = {Ny*Nx, Nx, 1};
+
+    const mask_type *voxels = static_cast<const mask_type*>(voxels_info.ptr);
+    mask_type *result = static_cast<mask_type*>(result_info.ptr);
+
+    NS::morphology_3d_sphere_alt(voxels, radius, N, strides, result);
 }
 
+} // namespace python_api
+
 PYBIND11_MODULE(morphology, m) {
     m.doc() = "Morphology operations."; // optional module docstring
-    m.def("dilate_3d_sphere", &morphology_3d_sphere_wrapper<std::bit_or<mask_type>, false>, py::arg("np_voxels"), py::arg("radius"), py::arg("np_result").noconvert());
-    m.def("erode_3d_sphere", &morphology_3d_sphere_wrapper<std::bit_and<mask_type>, true>, py::arg("np_voxels"), py::arg("radius"), py::arg("np_result").noconvert());
+    m.def("dilate_3d_sphere", &python_api::morphology_3d_sphere_wrapper<std::bit_or<mask_type>, false>, py::arg("np_voxels"), py::arg("radius"), py::arg("np_result").noconvert());
+    m.def("dilate_3d_sphere_alt", &python_api::morphology_3d_sphere_wrapper_alt<std::bit_or<mask_type>, false>, py::arg("np_voxels"), py::arg("radius"), py::arg("np_result").noconvert());
+    m.def("erode_3d_sphere", &python_api::morphology_3d_sphere_wrapper<std::bit_and<mask_type>, true>, py::arg("np_voxels"), py::arg("radius"), py::arg("np_result").noconvert());
+    m.def("erode_3d_sphere_alt", &python_api::morphology_3d_sphere_wrapper_alt<std::bit_and<mask_type>, true>, py::arg("np_voxels"), py::arg("radius"), py::arg("np_result").noconvert());
 }
\ No newline at end of file