read in Dataset

Author: kojix2

lib/hdf5/dataset.rb

@@ -32,21 +32,39 @@ def shape
       HDF5::FFI.H5Sclose(dataspace_id) if dataspace_id && dataspace_id >= 0
     end
 
-    # def read
-    #   dtype = dtype()
-    #   shape = shape()
-
-    #   total_elements = shape.inject(:*)
-    #   case dtype
-    #   when :H5T_INTEGER
-    #     read_integer_data(total_elements)
-    #   when :H5T_FLOAT
-    #     read_float_data(total_elements)
-    #   when :H5T_STRING
-    #     read_string_data(total_elements)
-    #   else
-    #     raise 'Unsupported datatype'
-    #   end
-    # end
+    def read
+      dtype = dtype()
+      shape = shape()
+
+      total_elements = shape.inject(:*)
+      case dtype
+      when :H5T_INTEGER
+        read_integer_data(total_elements)
+      when :H5T_FLOAT
+        read_float_data(total_elements)
+      when :H5T_STRING
+        read_string_data(total_elements)
+      else
+        raise 'Unsupported datatype'
+      end
+    end
+
+    def read_integer_data(total_elements)
+      buffer = ::FFI::MemoryPointer.new(:int, total_elements)
+      mem_type_id = HDF5::FFI.H5T_NATIVE_INT
+      HDF5::FFI.H5Dread(@dataset_id, mem_type_id, 0, 0, 0, buffer)
+      buffer.read_array_of_int(total_elements)
+    end
+
+    def read_float_data(total_elements)
+      buffer = ::FFI::MemoryPointer.new(:float, total_elements)
+      mem_type_id = HDF5::FFI.H5T_NATIVE_FLOAT
+      HDF5::FFI.H5Dread(@dataset_id, mem_type_id, 0, 0, 0, buffer)
+      buffer.read_array_of_float(total_elements)
+    end
+
+    def read_string_data(total_elements)
+      raise NotImplementedError
+    end
   end
 end

lib/hdf5/ffi3.rb

@@ -231,29 +231,29 @@ class Anon_Type_1 < ::FFI::Struct
 
     typedef :int, :register_t
 
-    attach_function '__bswap_16', [
-      :__uint16_t
-    ], :__uint16_t
+    # attach_function '__bswap_16', [
+    #   :__uint16_t
+    # ], :__uint16_t
 
-    attach_function '__bswap_32', [
-      :__uint32_t
-    ], :__uint32_t
+    # attach_function '__bswap_32', [
+    #   :__uint32_t
+    # ], :__uint32_t
 
-    attach_function '__bswap_64', [
-      :__uint64_t
-    ], :__uint64_t
+    # attach_function '__bswap_64', [
+    #   :__uint64_t
+    # ], :__uint64_t
 
-    attach_function '__uint16_identity', [
-      :__uint16_t
-    ], :__uint16_t
+    # attach_function '__uint16_identity', [
+    #   :__uint16_t
+    # ], :__uint16_t
 
-    attach_function '__uint32_identity', [
-      :__uint32_t
-    ], :__uint32_t
+    # attach_function '__uint32_identity', [
+    #   :__uint32_t
+    # ], :__uint32_t
 
-    attach_function '__uint64_identity', [
-      :__uint64_t
-    ], :__uint64_t
+    # attach_function '__uint64_identity', [
+    #   :__uint64_t
+    # ], :__uint64_t
 
     class Anon_Type_2 < ::FFI::Struct
       layout \
@@ -6348,5 +6348,30 @@ class H5FDSplitterVfdConfigT < ::FFI::Struct
     attach_function 'H5Pset_fapl_stdio', [
       :hid_t
     ], :herr_t
+
+    # These variables are defined manually because c2ffi can't parse them
+
+    attach_variable :H5T_NATIVE_SCHAR, :H5T_NATIVE_SCHAR_g, :hid_t
+    attach_variable :H5T_NATIVE_UCHAR, :H5T_NATIVE_UCHAR_g, :hid_t
+    attach_variable :H5T_NATIVE_SHORT, :H5T_NATIVE_SHORT_g, :hid_t
+    attach_variable :H5T_NATIVE_USHORT, :H5T_NATIVE_USHORT_g, :hid_t
+    attach_variable :H5T_NATIVE_INT, :H5T_NATIVE_INT_g, :hid_t
+    attach_variable :H5T_NATIVE_UINT, :H5T_NATIVE_UINT_g, :hid_t
+    attach_variable :H5T_NATIVE_LONG, :H5T_NATIVE_LONG_g, :hid_t
+    attach_variable :H5T_NATIVE_ULONG, :H5T_NATIVE_ULONG_g, :hid_t
+    attach_variable :H5T_NATIVE_LLONG, :H5T_NATIVE_LLONG_g, :hid_t
+    attach_variable :H5T_NATIVE_ULLONG, :H5T_NATIVE_ULLONG_g, :hid_t
+    attach_variable :H5T_NATIVE_FLOAT, :H5T_NATIVE_FLOAT_g, :hid_t
+    attach_variable :H5T_NATIVE_DOUBLE, :H5T_NATIVE_DOUBLE_g, :hid_t
+    attach_variable :H5T_NATIVE_LDOUBLE, :H5T_NATIVE_LDOUBLE_g, :hid_t
+    attach_variable :H5T_NATIVE_HADDR, :H5T_NATIVE_HADDR_g, :hid_t
+    attach_variable :H5T_NATIVE_HSIZE, :H5T_NATIVE_HSIZE_g, :hid_t
+    attach_variable :H5T_NATIVE_HSSIZE, :H5T_NATIVE_HSSIZE_g, :hid_t
+    attach_variable :H5T_NATIVE_HERR, :H5T_NATIVE_HERR_g, :hid_t
+    attach_variable :H5T_NATIVE_HBOOL, :H5T_NATIVE_HBOOL_g, :hid_t
+    attach_variable :H5T_C_S1, :H5T_C_S1_g, :hid_t
+
+    SIZE_MAX = (1 << (::FFI::MemoryPointer.new(:size_t).size * 8)) - 1
+    H5T_VARIABLE = SIZE_MAX
   end
 end