Prepare for HighFive v3.

src/readers/morphologyHDF5.cpp

@@ -194,11 +194,7 @@ void MorphologyHDF5::_readPoints(int firstSectionOffset) {
                            "': incorrect number of columns for points");
     }
 
-    std::vector<std::array<floatType, pointColumns>> hdf5Data(numberPoints);
-
-    if (!hdf5Data.empty()) {
-        pointsDataSet.read(hdf5Data.front().data());
-    }
+    auto hdf5Data = pointsDataSet.read<std::vector<std::array<floatType, pointColumns>>>();
 
     const bool hasSoma = firstSectionOffset != 0;
     const bool hasNeurites = static_cast<size_t>(firstSectionOffset) < numberPoints;
@@ -252,11 +248,7 @@ int MorphologyHDF5::_readSections() {
                            " bad number of dimensions in 'structure' dataspace"));
     }
 
-    std::vector<std::array<int, structureV1Columns>> vec(dims[0]);
-    if (dims[0] > 0) {
-        structure.read(vec.front().data());
-    }
-
+    auto vec = structure.read<std::vector<std::array<int, structureV1Columns>>>();
     assert(!vec.empty());
 
     bool hasSoma = true;

src/readers/vasculatureHDF5.cpp

@@ -81,9 +81,7 @@ void VasculatureHDF5::_readSections() {
     auto& sections = _properties.get_mut<vasculature::property::VascSection>();
     auto selection = _sections->select({0, 0}, {_sectionsDims[0], 1});
 
-    std::vector<unsigned int> vec;
-    vec.resize(_sectionsDims[0]);
-    selection.read(vec);
+    auto vec = selection.squeezeMemSpace({1}).read<std::vector<unsigned int>>();
 
     for (auto p : vec) {
         sections.push_back(p);
@@ -94,8 +92,7 @@ void VasculatureHDF5::_readSectionTypes() {
     auto& types = _properties.get_mut<vasculature::property::SectionType>();
 
     auto selection = _sections->select({0, 1}, {_sectionsDims[0], 1});
-    types.resize(_sectionsDims[0]);
-    selection.read(types);
+    selection.squeezeMemSpace({1}).read(types);
     for (int type : types) {
         if (type > SECTION_CUSTOM || type < 0) {
             const auto err = details::ErrorMessages(_uri);

tests/test_vasculature_morphology.cpp

@@ -59,9 +59,7 @@ TEST_CASE("vasculature_section_connectivity", "[vasculature]") {
 
     REQUIRE(section_connectivity.size() == n_connections);
 
-    std::vector<std::array<unsigned int, 2>> expected_connectivity(n_connections);
-
-    dset.read(expected_connectivity.front().data());
+    auto expected_connectivity = dset.read<std::vector<std::array<unsigned int, 2>>>();
 
     REQUIRE(section_connectivity == expected_connectivity);
 }