ruby-hdf5 0.0.1

data/lib/hdf5/file.rb

@@ -0,0 +1,126 @@
+module HDF5
+  class File
+    H5F_ACC_RDONLY = 0x0000
+    H5F_ACC_RDWR = 0x0001
+    H5F_ACC_TRUNC = 0x0002
+
+    class << self
+      def create(filename, flags = H5F_ACC_TRUNC)
+        file = from_id(HDF5::FFI.H5Fcreate(filename, flags, HDF5::DEFAULT_PROPERTY_LIST, HDF5::DEFAULT_PROPERTY_LIST),
+                       filename, flags)
+        return file unless block_given?
+
+        begin
+          yield file
+        ensure
+          file.close
+        end
+      end
+
+      def open(filename, mode = H5F_ACC_RDONLY)
+        file = from_id(HDF5::FFI.H5Fopen(filename, mode, HDF5::DEFAULT_PROPERTY_LIST), filename, mode)
+        return file unless block_given?
+
+        begin
+          yield file
+        ensure
+          file.close
+        end
+      end
+
+      private
+
+      def from_id(file_id, filename, mode)
+        file = allocate
+        file.send(:initialize_from_id, file_id, filename, mode)
+        file
+      end
+    end
+
+    def initialize(filename, mode = H5F_ACC_RDONLY)
+      initialize_from_id(HDF5::FFI.H5Fopen(filename, mode, HDF5::DEFAULT_PROPERTY_LIST), filename, mode)
+    end
+
+    def close
+      return if @file_id.nil?
+
+      HDF5::FFI.H5Fclose(@file_id)
+      @file_id = nil
+    end
+
+    def create_group(name, &block)
+      Group.create(@file_id, name, &block)
+    end
+
+    def create_dataset(name, data, &block)
+      Dataset.create(@file_id, name, data, &block)
+    end
+
+    def list_entries
+      list = []
+      callback = ::FFI::Function.new(:int, %i[int64_t string pointer pointer]) do |_, name, _, _|
+        list << name
+        0 # continue
+      end
+
+      case HDF5::FFI::MiV
+      when 10
+        HDF5::FFI.H5Literate(@file_id, :H5_INDEX_NAME, :H5_ITER_NATIVE, nil, callback, nil)
+      else
+        HDF5::FFI.H5Literate2(@file_id, :H5_INDEX_NAME, :H5_ITER_NATIVE, nil, callback, nil)
+      end.negative? && raise(HDF5::Error, 'Failed to iterate over file entries')
+
+      list
+    end
+
+    def [](name)
+      if group?(name)
+        Group.open(@file_id, name)
+      elsif dataset?(name)
+        Dataset.open(@file_id, name)
+      else
+        raise HDF5::Error, 'Unknown object type'
+      end
+    end
+
+    def attrs
+      @attrs ||= AttributeManager.new(@file_id)
+    end
+
+    private
+
+    def initialize_from_id(file_id, filename, mode)
+      raise HDF5::Error, "Failed to open file: #{filename}" if file_id < 0
+
+      @filename = filename
+      @mode = mode
+      @file_id = file_id
+    end
+
+    def group?(name)
+      info = if HDF5::FFI::MiV == 10
+               HDF5::FFI::H5OInfoT.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name(@file_id, name, i, 0)
+               end
+             else
+               HDF5::FFI::H5OInfo1T.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name1(@file_id, name, i, 0)
+               end
+             end
+      info[:type] == :H5O_TYPE_GROUP
+    end
+
+    def dataset?(name)
+      info = if HDF5::FFI::MiV == 10
+               HDF5::FFI::H5OInfoT.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name(@file_id, name, i, 0)
+               end
+             else
+               HDF5::FFI::H5OInfo1T.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name1(@file_id, name, i, 0)
+               end
+             end
+      info[:type] == :H5O_TYPE_DATASET
+    end
+  end
+end

data/lib/hdf5/group.rb

@@ -0,0 +1,123 @@
+module HDF5
+  class Group
+    class << self
+      def create(parent_id, name)
+        group = from_id(
+          HDF5::FFI.H5Gcreate2(parent_id, name, HDF5::DEFAULT_PROPERTY_LIST, HDF5::DEFAULT_PROPERTY_LIST,
+                               HDF5::DEFAULT_PROPERTY_LIST), name
+        )
+        return group unless block_given?
+
+        begin
+          yield group
+        ensure
+          group.close
+        end
+      end
+
+      def open(parent_id, name)
+        group = from_id(HDF5::FFI.H5Gopen2(parent_id, name, HDF5::DEFAULT_PROPERTY_LIST), name)
+        return group unless block_given?
+
+        begin
+          yield group
+        ensure
+          group.close
+        end
+      end
+
+      private
+
+      def from_id(group_id, name)
+        group = allocate
+        group.send(:initialize_from_id, group_id, name)
+        group
+      end
+    end
+
+    def initialize(file_id, name)
+      initialize_from_id(HDF5::FFI.H5Gopen2(file_id, name, HDF5::DEFAULT_PROPERTY_LIST), name)
+    end
+
+    def close
+      return if @group_id.nil?
+
+      HDF5::FFI.H5Gclose(@group_id)
+      @group_id = nil
+    end
+
+    def create_group(name, &block)
+      self.class.create(@group_id, name, &block)
+    end
+
+    def create_dataset(name, data, &block)
+      Dataset.create(@group_id, name, data, &block)
+    end
+
+    def list_datasets
+      datasets = []
+      callback = ::FFI::Function.new(:int, %i[int64_t string pointer pointer]) do |_, name, _, _|
+        datasets << name
+        0 # continue
+      end
+
+      (if HDF5::FFI::MiV == 10
+         HDF5::FFI.H5Literate(@group_id, :H5_INDEX_NAME, :H5_ITER_NATIVE, nil, callback, nil)
+       else
+         HDF5::FFI.H5Literate2(@group_id, :H5_INDEX_NAME, :H5_ITER_NATIVE, nil, callback, nil)
+       end).negative? &&
+        raise('Failed to list datasets')
+
+      datasets
+    end
+
+    def [](name)
+      if group?(name)
+        self.class.open(@group_id, name)
+      elsif dataset?(name)
+        Dataset.open(@group_id, name)
+      else
+        raise HDF5::Error, 'Group or Dataset not found'
+      end
+    end
+
+    def attrs
+      @attrs ||= AttributeManager.new(@group_id)
+    end
+
+    private
+
+    def initialize_from_id(group_id, name)
+      raise HDF5::Error, "Failed to open group: #{name}" if group_id < 0
+
+      @group_id = group_id
+      @name = name
+    end
+
+    def group?(name)
+      info = if HDF5::FFI::MiV == 10
+               HDF5::FFI::H5OInfoT.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name(@group_id, name, i, 0)
+               end
+             else
+               HDF5::FFI::H5OInfo1T.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name1(@group_id, name, i, 0)
+               end
+             end
+      info[:type] == :H5O_TYPE_GROUP
+    end
+
+    def dataset?(name)
+      info = if HDF5::FFI::MiV == 10
+               HDF5::FFI::H5OInfoT.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name(@group_id, name, i, 0)
+               end
+             else
+               HDF5::FFI::H5OInfo1T.new.tap do |i|
+                 HDF5::FFI.H5Oget_info_by_name1(@group_id, name, i, 0)
+               end
+             end
+      info[:type] == :H5O_TYPE_DATASET
+    end
+  end
+end

data/lib/hdf5/version.rb

@@ -0,0 +1,5 @@
+# frozen_string_literal: true
+
+module HDF5
+  VERSION = '0.0.1'
+end

data/lib/hdf5.rb

@@ -0,0 +1,43 @@
+# frozen_string_literal: true
+
+require 'ffi'
+require_relative 'hdf5/version'
+
+module HDF5
+  class Error < StandardError; end
+  DEFAULT_PROPERTY_LIST = 0
+
+  class << self
+    attr_accessor :lib_path
+
+    def search_hdf5lib
+      name = "libhdf5.#{FFI::Platform::LIBSUFFIX}"
+      env_path = ENV['HDF5_LIB_PATH']
+      return env_path if env_path && File.file?(env_path)
+      return File.expand_path(name, env_path) if env_path && File.directory?(env_path)
+
+      begin
+        require 'pkg-config'
+        libs = PKGConfig.libs('hdf5')
+        pattern = %r{(?<=-L)/[^ ]+}
+        libs.scan(pattern).each do |lib_dir|
+          lib_path = File.expand_path(name, lib_dir)
+          return lib_path if File.exist?(lib_path)
+        end
+      rescue PackageConfig::NotFoundError
+        warn 'hdf5.pc not found.'
+      end
+
+      name
+    end
+  end
+
+  self.lib_path = search_hdf5lib
+end
+
+require_relative 'hdf5/ffi'
+
+require_relative 'hdf5/file'
+require_relative 'hdf5/group'
+require_relative 'hdf5/dataset'
+require_relative 'hdf5/attribute'

metadata

@@ -0,0 +1,79 @@
+--- !ruby/object:Gem::Specification
+name: ruby-hdf5
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- kojix2
+bindir: bin
+cert_chain: []
+date: 1980-01-02 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pkg-config
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: hdf5
+email:
+- 2xijok@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- LICENSE.txt
+- README.md
+- lib/hdf5.rb
+- lib/hdf5/attribute.rb
+- lib/hdf5/dataset.rb
+- lib/hdf5/ffi.rb
+- lib/hdf5/ffi_10.rb
+- lib/hdf5/ffi_14.rb
+- lib/hdf5/file.rb
+- lib/hdf5/group.rb
+- lib/hdf5/version.rb
+licenses:
+- MIT
+metadata:
+  msys2_mingw_dependencies: hdf5
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: 3.2.0
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 4.0.6
+specification_version: 4
+summary: hdf5
+test_files: []