Immutable dataset views for readonly morphology classes

binds/python/bind_immutable.cpp

@@ -80,9 +80,8 @@ void bind_immutable_module(py::module& m) {
         // Property accessors
         .def_property_readonly(
             "points",
-            [](morphio::Morphology* morpho) {
-                const auto& data = morpho->points();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            [](const morphio::Morphology& morpho) {
+                return internal_vector_as_readonly_array(morpho.points(), morpho);
             },
             "Returns a list with all points from all sections (soma points are not included)\n"
             "Note: points belonging to the n'th section are located at indices:\n"
@@ -96,17 +95,15 @@ void bind_immutable_module(py::module& m) {
         .def_property_readonly(
             "diameters",
             [](const morphio::Morphology& morpho) {
-                const auto& data = morpho.diameters();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+                return internal_vector_as_readonly_array(morpho.diameters(), morpho);
             },
             "Returns a list with all diameters from all sections (soma points are not included)\n"
             "Note: diameters belonging to the n'th section are located at indices:\n"
             "[Morphology.sectionOffsets(n), Morphology.sectionOffsets(n+1)[")
         .def_property_readonly(
             "perimeters",
-            [](const morphio::Morphology& obj) {
-                const auto& data = obj.perimeters();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            [](const morphio::Morphology& morpho) {
+                return internal_vector_as_readonly_array(morpho.perimeters(), morpho);
             },
             "Returns a list with all perimeters from all sections (soma points are not included)\n"
             "Note: perimeters belonging to the n'th section are located at indices:\n"
@@ -125,8 +122,7 @@ void bind_immutable_module(py::module& m) {
         .def_property_readonly(
             "section_types",
             [](const morphio::Morphology& morph) {
-                const auto& data = morph.sectionTypes();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+                return internal_vector_as_readonly_array(morph.sectionTypes(), morph);
             },
             "Returns a vector with the section type of every section")
         .def_property_readonly("connectivity",
@@ -268,7 +264,9 @@ void bind_immutable_module(py::module& m) {
                                "(dendrite, axon, ...)")
         .def_property_readonly(
             "points",
-            [](morphio::Section* section) { return span_array_to_ndarray(section->points()); },
+            [](const morphio::Section& self) {
+                return internal_vector_as_readonly_array(self.points(), self);
+            },
             "Returns list of section's point coordinates")
 
         .def_property_readonly(
@@ -278,11 +276,15 @@ void bind_immutable_module(py::module& m) {
 
         .def_property_readonly(
             "diameters",
-            [](morphio::Section* section) { return span_to_ndarray(section->diameters()); },
+            [](const morphio::Section& self) {
+                return internal_vector_as_readonly_array(self.diameters(), self);
+            },
             "Returns list of section's point diameters")
         .def_property_readonly(
             "perimeters",
-            [](morphio::Section* section) { return span_to_ndarray(section->perimeters()); },
+            [](const morphio::Section& self) {
+                return internal_vector_as_readonly_array(self.perimeters(), self);
+            },
             "Returns list of section's point perimeters")
 
         .def("is_heterogeneous",
@@ -411,18 +413,16 @@ void bind_immutable_module(py::module& m) {
         // Property accessors
         .def_property_readonly(
             "points",
-            [](morphio::DendriticSpine* morpho) {
-                const auto& data = morpho->points();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            [](const morphio::DendriticSpine& morph) {
+                return internal_vector_as_readonly_array(morph.points(), morph);
             },
             "Returns a list with all points from all sections\n"
             "Note: points belonging to the n'th section are located at indices:\n"
             "[DendriticSpine.sectionOffsets(n), DendriticSpine.sectionOffsets(n+1)[")
         .def_property_readonly(
             "diameters",
-            [](const morphio::DendriticSpine& morpho) {
-                const auto& data = morpho.diameters();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            [](const morphio::DendriticSpine& morph) {
+                return internal_vector_as_readonly_array(morph.diameters(), morph);
             },
             "Returns a list with all diameters from all sections\n"
             "Note: diameters belonging to the n'th section are located at indices:\n"
@@ -443,8 +443,7 @@ void bind_immutable_module(py::module& m) {
         .def_property_readonly(
             "section_types",
             [](const morphio::DendriticSpine& morph) {
-                const auto& data = morph.sectionTypes();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+                return internal_vector_as_readonly_array(morph.diameters(), morph);
             },
             "Returns a vector with the section type of every section")
         .def_property_readonly("connectivity",

binds/python/bind_vasculature.cpp

@@ -54,9 +54,8 @@ void bind_vasculature(py::module& m) {
         // Property accessors
         .def_property_readonly(
             "points",
-            [](morphio::vasculature::Vasculature* morpho) {
-                return py::array(static_cast<py::ssize_t>(morpho->points().size()),
-                                 morpho->points().data());
+            [](const morphio::vasculature::Vasculature& self) {
+                return internal_vector_as_readonly_array(self.points(), self);
             },
             "Returns a list with all points from all sections")
 
@@ -67,24 +66,21 @@ void bind_vasculature(py::module& m) {
 
         .def_property_readonly(
             "diameters",
-            [](morphio::vasculature::Vasculature* morpho) {
-                auto diameters = morpho->diameters();
-                return py::array(static_cast<py::ssize_t>(diameters.size()), diameters.data());
+            [](const morphio::vasculature::Vasculature& self) {
+                return internal_vector_as_readonly_array(self.diameters(), self);
             },
             "Returns a list with all diameters from all sections")
         .def_property_readonly(
             "section_types",
-            [](morphio::vasculature::Vasculature* obj) {
-                auto data = obj->sectionTypes();
-                return py::array(static_cast<py::ssize_t>(data.size()), data.data());
+            [](const morphio::vasculature::Vasculature& self) {
+                return internal_vector_as_readonly_array(self.sectionTypes(), self);
             },
             "Returns a vector with the section type of every section")
 
         .def_property_readonly(
             "section_connectivity",
-            [](morphio::vasculature::Vasculature* morpho) {
-                return py::array(static_cast<py::ssize_t>(morpho->sectionConnectivity().size()),
-                                 morpho->sectionConnectivity().data());
+            [](const morphio::vasculature::Vasculature& self) {
+                return internal_vector_as_readonly_array(self.sectionConnectivity(), self);
             },
             "Returns a 2D array of the section connectivity")
 
@@ -128,8 +124,8 @@ void bind_vasculature(py::module& m) {
                                "Returns the morphological type of this section")
         .def_property_readonly(
             "points",
-            [](morphio::vasculature::Section* section) {
-                return span_array_to_ndarray(section->points());
+            [](const morphio::vasculature::Section& self) {
+                return internal_vector_as_readonly_array(self.points(), self);
             },
             "Returns list of section's point coordinates")
 
@@ -140,8 +136,8 @@ void bind_vasculature(py::module& m) {
 
         .def_property_readonly(
             "diameters",
-            [](morphio::vasculature::Section* section) {
-                return span_to_ndarray(section->diameters());
+            [](const morphio::vasculature::Section& self) {
+                return internal_vector_as_readonly_array(self.points(), self);
             },
             "Returns list of section's point diameters")
 

binds/python/bindings_utils.h

@@ -48,3 +48,21 @@ inline py::array_t<typename Sequence::value_type> as_pyarray(Sequence&& seq) {
                      capsule           // numpy array references this parent
     );
 }
+
+/**
+ * @brief Exposes an internal vector (not temporary) as a non-writeable numpy array.
+ */
+template <typename Sequence, typename Parent>
+inline py::array internal_vector_as_readonly_array(const Sequence& seq, const Parent& parent) {
+    // The correct base must be used here so that refcounting is done correctly on the python
+    // sire. The parent that holds that returned data should be passed as a base. See:
+    // https://github.com/pybind/pybind11/issues/2271#issuecomment-650740842
+    auto res = py::array(static_cast<py::ssize_t>(seq.size()), seq.data(), py::cast(parent));
+
+    // pybind11 casts away const-ness in return values. Thus, we need to explicitly set the
+    // numpy array flag to not writeable to prevent mutating the unerlying data. See limitations:
+    // https://pybind11.readthedocs.io/en/stable/limitations.html
+    py::detail::array_proxy(res.ptr())->flags &= ~py::detail::npy_api::NPY_ARRAY_WRITEABLE_;
+
+    return res;
+}

tests/test_4_immut.py

@@ -46,6 +46,7 @@ def test_components():
     for cell in CELLS.values():
         assert cell.n_points == len(cell.points)
         assert cell.section(0).n_points == len(cell.section(0).points)
+        assert not cell.points.flags.writeable
 
 
 def test_is_root():