Class: HDF5::AttributeManager

Inherits:
Object
  • Object
show all
Defined in:
lib/hdf5/attribute.rb

Instance Method Summary collapse

Constructor Details

#initialize(dataset_id, context = nil) ⇒ AttributeManager

Returns a new instance of AttributeManager.



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# File 'lib/hdf5/attribute.rb', line 92

def initialize(dataset_id, context = nil)
  @dataset_id = dataset_id
  @context = context
end

Instance Method Details

#[](attr_name) ⇒ Object 



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# File 'lib/hdf5/attribute.rb', line 97

def [](attr_name)
  @context&.ensure_open!(@dataset_id)
  attr = Attribute.new(@dataset_id, attr_name, @context)
  attr.read
ensure
  Native.close_object(attr)
end

#[]=(attr_name, value) ⇒ Object 



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# File 'lib/hdf5/attribute.rb', line 105

def []=(attr_name, value)
  write(attr_name, value)
end

#create(attr_name, value, dtype: nil, casting: :safe) ⇒ Object

Raises:



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# File 'lib/hdf5/attribute.rb', line 140

def create(attr_name, value, dtype: nil, casting: :safe)
  raise HDF5::Error, "Attribute already exists: #{attr_name}" if key?(attr_name)

  write(attr_name, value, dtype:, casting:)
end

#delete(attr_name) ⇒ Object

Raises:



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# File 'lib/hdf5/attribute.rb', line 132

def delete(attr_name)
  @context&.ensure_open!(@dataset_id)
  status = HDF5::FFI.H5Adelete(@dataset_id, attr_name)
  raise NativeError, "Failed to delete attribute: #{attr_name}" if status < 0

  self
end

#key?(attr_name) ⇒ Boolean

Returns:

  • (Boolean)

Raises:



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# File 'lib/hdf5/attribute.rb', line 124

def key?(attr_name)
  @context&.ensure_open!(@dataset_id)
  exists = HDF5::FFI.H5Aexists(@dataset_id, attr_name)
  raise NativeError, "Failed to check attribute existence: #{attr_name}" if exists.negative?

  exists.positive?
end

#keys ⇒ Object

Raises:



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# File 'lib/hdf5/attribute.rb', line 109

def keys
  @context&.ensure_open!(@dataset_id)
  names = []
  index = ::FFI::MemoryPointer.new(:ulong_long)
  index.write_ulong_long(0)
  callback = ::FFI::Function.new(:int, %i[int64_t string pointer pointer]) do |_, name, _, _|
    names << name
    0
  end
  status = HDF5::FFI.H5Aiterate2(@dataset_id, :H5_INDEX_NAME, :H5_ITER_NATIVE, index, callback, nil)
  raise NativeError, 'Failed to iterate over attributes' if status < 0

  names
end

#modify(attr_name, value, casting: :safe) ⇒ Object 



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# File 'lib/hdf5/attribute.rb', line 146

def modify(attr_name, value, casting: :safe)
  @context&.ensure_open!(@dataset_id)
  DataHelpers.validate_casting!(casting)
  raise HDF5::Error, "Attribute not found: #{attr_name}" unless key?(attr_name)

  attr_id = HDF5::FFI.H5Aopen(@dataset_id, attr_name, HDF5::DEFAULT_PROPERTY_LIST)
  raise NativeError, "Failed to open attribute: #{attr_name}" if attr_id < 0

  type_id = HDF5::FFI.H5Aget_type(attr_id)
  space_id = HDF5::FFI.H5Aget_space(attr_id)
  raise NativeError, "Failed to inspect attribute: #{attr_name}" if type_id < 0 || space_id < 0

  if Native.extent_type(space_id) == :H5S_NULL
    unless value.is_a?(HDF5::Empty) && value.dtype.to_sym == DType.for_hdf5(type_id).to_sym
      raise ShapeError, 'Cannot assign a value to a Null attribute'
    end
    return value
  end

  if Native.datatype_class(type_id) == :H5T_STRING
    unless HDF5::StringCodec.variable?(type_id)
      raise UnsupportedTypeError, 'Fixed-length string attributes are not yet supported'
    end

    encoding = HDF5::StringCodec.encoding_for(type_id)
    string_values, string_shape = HDF5::StringCodec.normalize_data(value, encoding:)
    unless string_shape == attribute_shape(space_id)
      raise ShapeError,
            'Attribute shape must not change when modifying'
    end

    buffer, _string_pointers = HDF5::StringCodec.buffer_for_values(string_values, encoding:)
    status = HDF5::FFI.H5Awrite(attr_id, type_id, buffer)
  else
    dtype_object = DType.for_hdf5(type_id)
    values = HDF5::DataHelpers.normalize_data(value, label: 'Attribute data', dtype: dtype_object, casting:, convert: false)
    expected_shape = attribute_shape(space_id)
    raise ShapeError, 'Attribute shape must not change when modifying' unless values.shape == expected_shape

    status = HDF5::FFI.H5Awrite(attr_id, DType.for_numo(values).memory_type_id, HDF5::DataHelpers.buffer_for(values))
  end
  raise NativeError, "Failed to modify attribute: #{attr_name}" if status < 0

  value
ensure
  Native.close([:H5Sclose, space_id], [:H5Tclose, type_id], [:H5Aclose, attr_id])
end

#write(attr_name, value, dtype: nil, casting: :safe) ⇒ Object 



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# File 'lib/hdf5/attribute.rb', line 194

def write(attr_name, value, dtype: nil, casting: :safe)
  @context&.ensure_open!(@dataset_id)
  DataHelpers.validate_casting!(casting)

  empty_data = value.is_a?(HDF5::Empty)
  explicit_dtype = DType.for_symbol(dtype) if dtype
  if empty_data && explicit_dtype && explicit_dtype.to_sym != value.dtype.to_sym
    raise ConversionError, 'dtype must match the Null attribute dtype'
  end
  inferred_string = HDF5::StringCodec.string_data?(value)
  if inferred_string && explicit_dtype && explicit_dtype.kind != :string
    raise ConversionError, 'Cannot create a numeric attribute from string data'
  end
  string_type = inferred_string || explicit_dtype&.kind == :string || empty_data && value.dtype.kind == :string
  string_data = string_type && !empty_data
  string_values, string_shape = HDF5::StringCodec.normalize_data(value) if string_data
  values = HDF5::DataHelpers.normalize_data(value, label: 'Attribute data', dtype: explicit_dtype, casting:) unless string_type || empty_data
  dtype_object = empty_data ? value.dtype : (explicit_dtype || DType.for_numo(values)) unless string_type
  type_id = string_type ? HDF5::StringCodec.datatype_id : dtype_object.storage_type_id

  exists = HDF5::FFI.H5Aexists(@dataset_id, attr_name)
  raise NativeError, "Failed to check attribute existence: #{attr_name}" if exists.negative?

  # Write a replacement completely before changing the existing attribute.
  written_name = exists.positive? ? temporary_attribute_name : attr_name

  dataspace_id = create_dataspace(empty_data ? nil : (string_data ? string_shape : values.shape))
  raise NativeError, 'Failed to create attribute dataspace' if dataspace_id < 0

  attr_id = HDF5::FFI.H5Acreate2(
    @dataset_id,
    written_name,
    type_id,
    dataspace_id,
    HDF5::DEFAULT_PROPERTY_LIST,
    HDF5::DEFAULT_PROPERTY_LIST
  )
  raise NativeError, "Failed to create attribute: #{attr_name}" if attr_id < 0

  created = true

  unless empty_data || string_data && string_values.empty?
    buffer, _string_pointers = if string_data
                                 HDF5::StringCodec.buffer_for_values(string_values)
                               else
                                 [HDF5::DataHelpers.buffer_for(values), nil]
                               end
    memory_type_id = string_data ? type_id : dtype_object.memory_type_id
    status = HDF5::FFI.H5Awrite(attr_id, memory_type_id, buffer)
    raise NativeError, "Failed to write attribute: #{attr_name}" if status < 0
  end

  replace_attribute(attr_name, written_name) if exists.positive?
  initialized = true

  value
ensure
  begin
    if created && !initialized && HDF5::FFI.H5Aexists(@dataset_id, written_name).positive?
      HDF5::FFI.H5Adelete(@dataset_id, written_name)
    end
  ensure
    Native.close([:H5Aclose, attr_id], [:H5Sclose, dataspace_id], [:H5Tclose, string_type ? type_id : nil])
  end
end