Allow Buffers to depend on the file datatype.

The upcoming `StringBuffer` will need to know the file datatype, because in HDF5 the expect datalayout, and therefore the way the buffer is populated, is different for fixed and variable length strings.
BlueBrain · Jul 12, 2023 · 51ea857 · 51ea857
1 parent 8423365
commit 51ea857
Show file tree

Hide file tree

Showing 3 changed files with 27 additions and 17 deletions.
diff --git a/include/highfive/bits/H5Attribute_misc.hpp b/include/highfive/bits/H5Attribute_misc.hpp
@@ -61,8 +61,9 @@ inline T Attribute::read() const {
 template <typename T>
 inline void Attribute::read(T& array) const {
     const DataSpace& mem_space = getMemSpace();
+    auto file_datatype = getDataType();
     const details::BufferInfo<T> buffer_info(
-        getDataType(),
+        file_datatype,
         [this]() -> std::string { return this->getName(); },
         details::BufferInfo<T>::read);
 
@@ -82,7 +83,7 @@ inline void Attribute::read(T& array) const {
         return;
     }
 
-    auto r = details::data_converter::get_reader<T>(dims, array);
+    auto r = details::data_converter::get_reader<T>(dims, array, file_datatype);
     read(r.get_pointer(), buffer_info.data_type);
     // re-arrange results
     r.unserialize(array);
@@ -125,8 +126,10 @@ inline void Attribute::write(const T& buffer) {
         return;
     }
 
+    auto file_datatype = getDataType();
+
     const details::BufferInfo<T> buffer_info(
-        getDataType(),
+        file_datatype,
         [this]() -> std::string { return this->getName(); },
         details::BufferInfo<T>::write);
 
@@ -136,7 +139,7 @@ inline void Attribute::write(const T& buffer) {
            << " into dataset of dimensions " << mem_space.getNumberDimensions();
         throw DataSpaceException(ss.str());
     }
-    auto w = details::data_converter::serialize<T>(buffer);
+    auto w = details::data_converter::serialize<T>(buffer, file_datatype);
     write_raw(w.get_pointer(), buffer_info.data_type);
 }
 

diff --git a/include/highfive/bits/H5Converter_misc.hpp b/include/highfive/bits/H5Converter_misc.hpp
@@ -22,6 +22,7 @@ struct enable_shallow_copy: public std::enable_if<inspector<T>::is_trivially_cop
 template <class T, class V = void>
 struct enable_deep_copy: public std::enable_if<!inspector<T>::is_trivially_copyable, V> {};
 
+
 template <typename T, bool IsReadOnly>
 struct ShallowCopyBuffer {
     using type = unqualified_t<T>;
@@ -83,19 +84,18 @@ struct Writer<T, typename enable_shallow_copy<T>::type>: public ShallowCopyBuffe
     using super = ShallowCopyBuffer<T, true>;
 
   public:
-    explicit Writer(const T& val)
+    explicit Writer(const T& val, const DataType& file_datatype)
         : super(val){};
 };
 
 template <typename T>
 struct Writer<T, typename enable_deep_copy<T>::type>: public DeepCopyBuffer<T> {
-    explicit Writer(const T& val)
+    explicit Writer(const T& val, const DataType& file_datatype)
         : DeepCopyBuffer<T>(inspector<T>::getDimensions(val)) {
         inspector<T>::serialize(val, this->get_pointer());
     }
 };
 
-
 template <typename T, typename Enable = void>
 struct Reader;
 
@@ -106,7 +106,7 @@ struct Reader<T, typename enable_shallow_copy<T>::type>: public ShallowCopyBuffe
     using type = typename super::type;
 
   public:
-    Reader(const std::vector<size_t>&, type& val)
+    Reader(const std::vector<size_t>&, type& val, const DataType&)
         : super(val) {}
 };
 
@@ -117,23 +117,26 @@ struct Reader<T, typename enable_deep_copy<T>::type>: public DeepCopyBuffer<T> {
     using type = typename super::type;
 
   public:
-    Reader(const std::vector<size_t>& _dims, type&)
+    Reader(const std::vector<size_t>& _dims, type&, const DataType&)
         : super(_dims) {}
 };
 
 
 struct data_converter {
     template <typename T>
-    static Writer<T> serialize(const typename inspector<T>::type& val) {
-        return Writer<T>(val);
+    static Writer<T> serialize(const typename inspector<T>::type& val,
+                               const DataType& file_datatype) {
+        return Writer<T>(val, file_datatype);
     }
 
     template <typename T>
-    static Reader<T> get_reader(const std::vector<size_t>& dims, T& val) {
+    static Reader<T> get_reader(const std::vector<size_t>& dims,
+                                T& val,
+                                const DataType& file_datatype) {
         // TODO Use bufferinfo for recursive_ndim
         auto effective_dims = details::squeezeDimensions(dims, inspector<T>::recursive_ndim);
         inspector<T>::prepare(val, effective_dims);
-        return Reader<T>(effective_dims, val);
+        return Reader<T>(effective_dims, val, file_datatype);
     }
 };
 

diff --git a/include/highfive/bits/H5Slice_traits_misc.hpp b/include/highfive/bits/H5Slice_traits_misc.hpp
@@ -172,8 +172,10 @@ inline void SliceTraits<Derivate>::read(T& array, const DataTransferProps& xfer_
     const auto& slice = static_cast<const Derivate&>(*this);
     const DataSpace& mem_space = slice.getMemSpace();
 
+    auto file_datatype = slice.getDataType();
+
     const details::BufferInfo<T> buffer_info(
-        slice.getDataType(),
+        file_datatype,
         [&slice]() -> std::string { return details::get_dataset(slice).getPath(); },
         details::BufferInfo<T>::Operation::read);
 
@@ -193,7 +195,7 @@ inline void SliceTraits<Derivate>::read(T& array, const DataTransferProps& xfer_
         return;
     }
 
-    auto r = details::data_converter::get_reader<T>(dims, array);
+    auto r = details::data_converter::get_reader<T>(dims, array, file_datatype);
     read(r.get_pointer(), buffer_info.data_type, xfer_props);
     // re-arrange results
     r.unserialize(array);
@@ -251,8 +253,10 @@ inline void SliceTraits<Derivate>::write(const T& buffer, const DataTransferProp
         return;
     }
 
+    auto file_datatype = slice.getDataType();
+
     const details::BufferInfo<T> buffer_info(
-        slice.getDataType(),
+        file_datatype,
         [&slice]() -> std::string { return details::get_dataset(slice).getPath(); },
         details::BufferInfo<T>::Operation::write);
 
@@ -263,7 +267,7 @@ inline void SliceTraits<Derivate>::write(const T& buffer, const DataTransferProp
            << " into dataset with n = " << buffer_info.n_dimensions << " dimensions.";
         throw DataSpaceException(ss.str());
     }
-    auto w = details::data_converter::serialize<T>(buffer);
+    auto w = details::data_converter::serialize<T>(buffer, file_datatype);
     write_raw(w.get_pointer(), buffer_info.data_type, xfer_props);
 }