Refactor HDF5 File and Group classes

Drop 1.0

Author: kojix2

README.md

@@ -4,6 +4,64 @@
 
 experimental Ruby bindings for the HDF5 library
 
+## Supported HDF5 Versions
+
+- HDF5 1.14
+- HDF5 2.x
+
+HDF5 1.10 and older are not supported.
+
+## Basic I/O
+
+Current high-level API supports these operations:
+
+- open an existing HDF5 file
+- create a new HDF5 file
+- create groups
+- create, write, and read one-dimensional numeric datasets
+
+Not supported yet:
+
+- string datasets
+- attribute writes
+- multidimensional array writes
+
+### Read an existing file
+
+```ruby
+require 'hdf5'
+
+file = HDF5::File.open('example.h5')
+group = file['foo']
+dataset = group['bar_int']
+
+p dataset.shape
+p dataset.dtype
+p dataset.read
+
+dataset.close
+group.close
+file.close
+```
+
+### Create and write a file
+
+```ruby
+require 'hdf5'
+
+file = HDF5::File.create('numbers.h5')
+group = file.create_group('values')
+dataset = group.create_dataset('ints', [1, 2, 3, 4])
+
+dataset.close
+group.close
+file.close
+
+reopened = HDF5::File.open('numbers.h5')
+p reopened['values']['ints'].read
+reopened.close
+```
+
 ## Development
 
 - [c2ffi](https://github.com/rpav/c2ffi)

lib/hdf5/dataset.rb

@@ -1,15 +1,84 @@
 module HDF5
   class Dataset
+    H5P_DEFAULT = 0
+
+    class << self
+      def create(parent_id, name, data)
+        values = normalize_data(data)
+        dims = ::FFI::MemoryPointer.new(:ulong_long, 1)
+        dims.write_array_of_ulong_long([values.length])
+        datatype_id = datatype_id_for(values)
+        dataspace_id = HDF5::FFI.H5Screate_simple(1, dims, nil)
+        raise "Failed to create dataspace for dataset: #{name}" if dataspace_id < 0
+
+        dataset_id = HDF5::FFI.H5Dcreate2(parent_id, name, datatype_id, dataspace_id, H5P_DEFAULT, H5P_DEFAULT,
+                                          H5P_DEFAULT)
+        dataset = from_id(dataset_id, name)
+        dataset.write(values)
+        dataset
+      ensure
+        HDF5::FFI.H5Sclose(dataspace_id) if dataspace_id && dataspace_id >= 0
+      end
+
+      def open(parent_id, name)
+        from_id(HDF5::FFI.H5Dopen2(parent_id, name, H5P_DEFAULT), name)
+      end
+
+      def normalize_data(data)
+        values = data.is_a?(Array) ? data : [data]
+        raise 'Dataset data must not be empty' if values.empty?
+        raise 'Nested arrays are not supported' if values.any? { |value| value.is_a?(Array) }
+
+        values
+      end
+
+      def datatype_id_for(data)
+        if data.all? { |value| value.is_a?(Integer) }
+          HDF5::FFI.H5T_NATIVE_INT
+        elsif data.all? { |value| value.is_a?(Numeric) }
+          HDF5::FFI.H5T_NATIVE_DOUBLE
+        else
+          raise 'Only numeric dataset data is supported'
+        end
+      end
+
+      def buffer_for(data)
+        if data.all? { |value| value.is_a?(Integer) }
+          buffer = ::FFI::MemoryPointer.new(:int, data.length)
+          buffer.write_array_of_int(data)
+        else
+          buffer = ::FFI::MemoryPointer.new(:double, data.length)
+          buffer.write_array_of_double(data.map(&:to_f))
+        end
+
+        buffer
+      end
+
+      private
+
+      def from_id(dataset_id, name)
+        dataset = allocate
+        dataset.send(:initialize_from_id, dataset_id, name)
+        dataset
+      end
+    end
+
     def initialize(parent_id, name)
-      @dataset_id = HDF5::FFI.H5Dopen1(parent_id, name)
+      initialize_from_id(HDF5::FFI.H5Dopen2(parent_id, name, H5P_DEFAULT), name)
     end
 
     def attrs
       @attrs ||= AttributeManager.new(@dataset_id)
     end
 
     def write(data)
-      HDF5::FFI.H5Dwrite(@dataset_id, data)
+      values = self.class.normalize_data(data)
+      buffer = self.class.buffer_for(values)
+      mem_type_id = self.class.datatype_id_for(values)
+      status = HDF5::FFI.H5Dwrite(@dataset_id, mem_type_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT, buffer)
+      raise 'Failed to write dataset' if status < 0
+
+      data
     end
 
     def close
@@ -18,7 +87,11 @@ def close
 
     def dtype
       datatype_id = HDF5::FFI.H5Dget_type(@dataset_id)
+      raise 'Failed to get datatype' if datatype_id < 0
+
       HDF5::FFI.H5Tget_class(datatype_id)
+    ensure
+      HDF5::FFI.H5Tclose(datatype_id) if datatype_id && datatype_id >= 0
     end
 
     def shape
@@ -55,20 +128,32 @@ def read
 
     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)
+      status = HDF5::FFI.H5Dread(@dataset_id, HDF5::FFI.H5T_NATIVE_INT, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT, buffer)
+      raise 'Failed to read integer dataset' if status < 0
+
       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)
+      buffer = ::FFI::MemoryPointer.new(:double, total_elements)
+      status = HDF5::FFI.H5Dread(@dataset_id, HDF5::FFI.H5T_NATIVE_DOUBLE, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT,
+                                 buffer)
+      raise 'Failed to read float dataset' if status < 0
+
+      buffer.read_array_of_double(total_elements)
     end
 
     def read_string_data(total_elements)
       raise NotImplementedError
     end
+
+    private
+
+    def initialize_from_id(dataset_id, name)
+      raise "Failed to open dataset: #{name}" if dataset_id < 0
+
+      @dataset_id = dataset_id
+      @name = name
+    end
   end
 end

lib/hdf5/ffi.rb

@@ -2,6 +2,10 @@ module HDF5
   module FFI
     extend ::FFI::Library
 
+    class << self
+      attr_reader :backend
+    end
+
     begin
       ffi_lib HDF5.lib_path
     rescue LoadError => e
@@ -39,13 +43,15 @@ def self.attach_variable(*)
     minor = minor_ptr.read_uint
     release = release_ptr.read_uint
 
-    case [major, minor]
-    in [1, 10]
-      require_relative 'ffi_10'
-    in [1, 14..] | [2.., _]
-      require_relative 'ffi_14'
-    else
-      raise "Unsupported HDF5 version #{major}.#{minor}.#{release}"
-    end
+    @backend = case [major, minor]
+               in [1, 14..]
+                 'ffi_14'
+               in [2.., _]
+                 'ffi_14'
+               else
+                 raise "Unsupported HDF5 version #{major}.#{minor}.#{release}"
+               end
+
+    require_relative @backend
   end
 end