hdf5 0.0.0 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 9e35636d40e1c175deb2dbe796518adb5d0ae5ab
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+  data.tar.gz: a7e1e9fdc346d66ae0b3f874b965d05938cbd34f
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+  data.tar.gz: a91d2bed998cdd3d2e3268ff3e82b8beac0b3ecea98e69e14257a5da73cd165f5a9c02d3307409245cd1fd718480e5d51816887dc346620bd03486d8f324c98a

data/Gemfile

@@ -1,5 +1,6 @@
 source "http://rubygems.org"
   gem "ffi"
+  gem "narray"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/Rakefile

@@ -21,6 +21,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{A ruby wrapper to the HDF5 data library. Currently read only.}
   gem.email = "edmundhighcock@users.sourceforge.net"
   gem.authors = ["Edmund Highcock"]
+	gem.files.exclude 'test/**/*'
   # dependencies defined in Gemfile
 end
 Jeweler::RubygemsDotOrgTasks.new
@@ -40,6 +41,8 @@ end
 
 require "rake/extensiontask"
 
+NAME = 'hdf5'
+
 Rake::ExtensionTask.new "hdf5" do |ext|
 	  ext.lib_dir = "lib/hdf5"
 end

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.1.0

data/ext/hdf5/extconf.rb

@@ -0,0 +1,20 @@
+require 'mkmf'
+
+#Need to link with C GSL libraries to use in C extensions
+#gsl_inc = `gsl-config --cflags`
+
+#$CFLAGS = " -Wall -I../include #{gsl_inc}"
+
+#srcs = Dir.glob("*.c")
+
+#p ['srcs', srcs]
+                                                                                                         
+#$objs = srcs.collect { |f| f.sub(".c", ".o") }                                                           
+nagemspec=Gem::Specification.find_by_name('narray')
+naconfig = nagemspec.full_gem_path
+$CPPFLAGS = " -I#{File.join(naconfig, '')} "+$CPPFLAGS
+p ['CPPFLAGS', $CPPFLAGS]
+
+have_header("narray.h")
+
+create_makefile("hdf5/hdf5")  

data/ext/hdf5/hdf5.c

@@ -0,0 +1,77 @@
+#include <math.h>
+#include <string.h>
+#include <ruby.h>
+#include <narray.h>
+/*#include "code_runner_ext.h"*/
+/*#include <mpi.h>*/
+#include <stdbool.h>
+
+/* Taken from the ruby-mpi gem*/
+/*struct _Comm {*/
+/*MPI_Comm Comm;*/
+/*bool free;*/
+/*};*/
+
+static VALUE narray_data_address(VALUE class, VALUE narray_obj){
+
+	struct NARRAY *narray;
+  int addrs;
+  VALUE address;
+
+  /*printf("RUNNING TRINITY!!!\n\n");*/
+	Data_Get_Struct(narray_obj, struct NARRAY, narray);
+  addrs = (int)narray->ptr;
+  address = INT2FIX(addrs);
+
+
+	/*printf("input file name was %s\n", input_file_name_c);*/
+	/**/
+	/*free(input_file_name_c);*/
+
+	
+
+	return address;
+
+}
+
+void Init_hdf5()
+{
+  VALUE ch5_simple_reader;
+  VALUE ch5_simple_reader_dataset;
+  
+  ch5_simple_reader = rb_const_get(rb_cObject, rb_intern("H5SimpleReader"));
+  ch5_simple_reader_dataset = rb_const_get(ch5_simple_reader, rb_intern("H5Dataset")); 
+  rb_define_method(ch5_simple_reader_dataset, "narray_data_address", narray_data_address, 1);
+  /*VALUE ctrinity;*/
+  /**/
+  /**//**//*cgraph_kit = Qnil;*/
+  /*ccode_runner_gs2 = Qnil;*/
+  /*ccode_runner_ext = Qnil;*/
+  /*printf("HERE!!!\n\n");*/
+  /**//*ccode_runner =  RGET_CLASS_TOP("CodeRunner");*/
+	/*VALUE ctrinity =  RGET_CLASS_TOP("CodeRunner");*/
+  /*ctrinity	= RGET_CLASS(ccode_runner, "Trinity");*/
+		/*rb_define_class_under(ccode_runner, "Trinity",*/
+		/*RGET_CLASS(*/
+		/*RGET_CLASS(ccode_runner, "Run"), */
+		/*"FortranNamelist"*/
+		/*)*/
+		/*);*/
+
+	/*ccode_runner_gs2_gsl_tensor_complexes = rb_define_module_under(ccode_runner_gs2, "GSLComplexTensors");*/
+	/*rb_include_module(ccode_runner_gs2, ccode_runner_gs2_gsl_tensor_complexes);*/
+
+	/*ccode_runner_gs2_gsl_tensors = rb_define_module_under(ccode_runner_gs2, "GSLTensors"); */
+	/*rb_include_module(ccode_runner_gs2, ccode_runner_gs2_gsl_tensors);*/
+
+	/*cgsl = RGET_CLASS_TOP("GSL");*/
+	/*cgsl_vector = RGET_CLASS(cgsl, "Vector");*/
+	/*cgsl_vector_complex = RGET_CLASS(cgsl_vector, "Complex");*/
+
+	/*rb_define_method(ccode_runner_gs2_gsl_tensor_complexes, "field_gsl_tensor_complex_2", gs2crmod_tensor_complexes_field_gsl_tensor_complex_2, 1);*/
+	/*rb_define_method(ccode_runner_gs2_gsl_tensors, "field_real_space_gsl_tensor", gs2crmod_tensor_field_gsl_tensor, 1);*/
+	/*rb_define_method(ccode_runner_gs2_gsl_tensors, "field_correlation_gsl_tensor", gs2crmod_tensor_field_correlation_gsl_tensor, 1);*/
+
+	/*rb_define_method(ccode_runner_ext, "hello_world", code_runner_ext_hello_world, 0);*/
+}
+

data/hdf5.gemspec

@@ -0,0 +1,76 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: hdf5 0.1.0 ruby lib
+# stub: ext/hdf5/extconf.rb
+
+Gem::Specification.new do |s|
+  s.name = "hdf5"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
+  s.authors = ["Edmund Highcock"]
+  s.date = "2014-07-22"
+  s.description = "A ruby wrapper to the HDF5 data library. Currently read only."
+  s.email = "edmundhighcock@users.sourceforge.net"
+  s.extensions = ["ext/hdf5/extconf.rb"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "ext/hdf5/extconf.rb",
+    "ext/hdf5/hdf5.c",
+    "hdf5.gemspec",
+    "lib/hdf5.rb"
+  ]
+  s.homepage = "http://github.com/edmundhighcock/hdf5"
+  s.licenses = ["GPLv3"]
+  s.rubygems_version = "2.2.2"
+  s.summary = "A ruby wrapper to the HDF5 data library. Currently read only."
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<ffi>, [">= 0"])
+      s.add_runtime_dependency(%q<narray>, [">= 0"])
+      s.add_development_dependency(%q<shoulda>, ["= 3.0.1"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, [">= 2.0.1"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<minitest>, ["~> 4"])
+      s.add_development_dependency(%q<rake-compiler>, [">= 0"])
+    else
+      s.add_dependency(%q<ffi>, [">= 0"])
+      s.add_dependency(%q<narray>, [">= 0"])
+      s.add_dependency(%q<shoulda>, ["= 3.0.1"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["> 1.0.0"])
+      s.add_dependency(%q<jeweler>, [">= 2.0.1"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<minitest>, ["~> 4"])
+      s.add_dependency(%q<rake-compiler>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<ffi>, [">= 0"])
+    s.add_dependency(%q<narray>, [">= 0"])
+    s.add_dependency(%q<shoulda>, ["= 3.0.1"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["> 1.0.0"])
+    s.add_dependency(%q<jeweler>, [">= 2.0.1"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<minitest>, ["~> 4"])
+    s.add_dependency(%q<rake-compiler>, [">= 0"])
+  end
+end
+

data/lib/hdf5.rb

@@ -0,0 +1,222 @@
+require 'ffi'
+module H5SimpleReader
+  module H5Types
+    extend FFI::Library
+    class << self
+      def herr_t
+        :int
+      end
+      def hid_t
+        :int
+      end
+      def hbool_t
+        :uint
+      end
+      def htri_t
+        :int
+      end
+      def hsize_t
+        :size_t
+      end
+      def h5t_class_t
+        enum [
+          :h5t_no_class         , -1,  #*error                                      */
+          :h5t_integer          , 0,   #*integer types                              */
+          :h5t_float            , 1,   #*floating-point types                       */
+          :h5t_time             , 2,   #*date and time types                        */
+          :h5t_string           , 3,   #*character string types                     */
+          :h5t_bitfield         , 4,   #*bit field types                            */
+          :h5t_opaque           , 5,   #*opaque types                               */
+          :h5t_compound         , 6,   #*compound types                             */
+          :h5t_reference        , 7,   #*reference types                            */
+          :h5t_enum    , 8, #*enumeration types                          */
+          :h5t_vlen    , 9, #*variable-length types                      */
+          :h5t_array           , 10,  #*array types                                */
+
+          :h5t_nclasses                #*this must be last                          */
+        ]
+      end
+    end
+  end
+
+  extend  FFI::Library
+  ffi_lib 'hdf5'
+  attach_function :group_open, :H5Gopen2, [H5Types.hid_t, :string, H5Types.hid_t], H5Types.hid_t
+  attach_function :get_type, :H5Iget_type, [H5Types.hid_t], H5Types.hid_t
+  #
+  # Object for wrapping an HDF file
+  class H5File
+    extend  FFI::Library
+    ffi_lib 'hdf5'
+    attach_function :basic_is_hdf5, :H5Fis_hdf5, [:string], H5Types.htri_t
+    attach_function :basic_open, :H5Fopen, [:string, :uint, H5Types.hid_t], H5Types.hid_t
+    attach_function :basic_close, :H5Fclose, [H5Types.hid_t], H5Types.herr_t
+    attr_reader :id
+    # Open the file with the given filename. Currently read only
+    def initialize(filename)
+      @filename = filename
+      @id = basic_open(filename, 0x0000, 0)
+    end
+    # Is the file a valid hdf5 file
+    def is_hdf5?
+      basic_is_hdf5(@filename) > 0
+    end
+    # Close the file
+    def close
+      basic_close(@id)
+    end
+    # Return a group object with the given name 
+    # (relative to the root of the file)
+    def group(name)
+      return H5Group.open(@id, name)
+    end
+    # Return a dataset object with the given name 
+    # (relative to the root of the file)
+    def dataset(name)
+      return H5Dataset.open(@id, name)
+    end
+  end
+  # Object wrapping an HDF5 Dataset, which contains
+  # a set of data, and information about the type of
+  # the data elements and the size and shape of the 
+  # data array.
+  class H5Dataset
+    extend  FFI::Library
+    ffi_lib 'hdf5'
+    attach_function :basic_open, :H5Dopen2, [H5Types.hid_t, :string, H5Types.hid_t], H5Types.hid_t
+    attach_function :basic_get_type, :H5Dget_type, [H5Types.hid_t], H5Types.hid_t
+    attach_function :basic_get_space, :H5Dget_space, [H5Types.hid_t], H5Types.hid_t
+    attach_function :basic_read, :H5Dread, [H5Types.hid_t, H5Types.hid_t, H5Types.hid_t, H5Types.hid_t, H5Types.hid_t, :pointer], H5Types.herr_t
+    attach_variable :h5t_native_float_g, :H5T_NATIVE_FLOAT_g, :int
+    # Open the dataset. location_id is the id of the parent
+    # file or group. Returns and H5Dataset object
+    def self.open(location_id, name)
+      return new(basic_open(location_id, name, 0))
+    end
+    # Create a new object. id is the id of the HDF5 dataset this wraps.
+    # Use H5Dataset.open to open a dataset 
+    def initialize(id)
+      @id = id
+    end
+    # Return an H5Datatype object containing information about the type
+    # of an individual member of the dataset
+    def datatype
+      H5Datatype.new(basic_get_type(@id))
+    end
+    def dataspace
+      H5Dataspace.new(basic_get_space(@id))
+    end
+    def narray_type
+      #cls = H5Types.h5t_class_t
+      #p 'datatype', datatype.h5_class
+      case datatype.h5_class
+      when :h5t_float
+        :float
+      when :h5t_compound
+        if datatype.is_complex?
+          :complex
+        else
+          :compound
+        end
+      else 
+        raise "unknown datatype"
+      end
+    end
+      #inline :C do |builder|
+        #builder.c <<EOF
+        #long asfdsf(){
+        #long b;
+        #b = 24;
+        #return b;}
+        
+#EOF
+      #end
+    def get_narray_pointer(narray)
+      p 'p address', narray_data_address(narray) 
+        #void * narray_pointer(VALUE
+      narray_data_address(narray)
+    end
+    def narray_all
+      p ['ddims', dataspace.dims]
+      narr = NArray.send(narray_type, *dataspace.dims)
+      #get_narray_pointer(narr)
+      ptr = FFI::Pointer.new(get_narray_pointer(narr))
+
+      #basic_read(@id, self.class.h5t_native_float_g, 0, 0, 0, ptr)
+      basic_read(@id, datatype.id, 0, 0, 0, ptr)
+      #p ptr.get_array_of_float64(0, 6)
+      p narr.shape
+      narr
+    end
+    #def array
+    #end
+  end
+  # Object for wrapping an HD5 dataspace, which contains
+  # information about the dimensions and size of the dataset
+  class H5Dataspace
+    extend  FFI::Library
+    ffi_lib 'hdf5'
+    attach_function :basic_get_simple_extent_ndims, :H5Sget_simple_extent_ndims, [H5Types.hid_t], :int
+    attach_function :basic_get_simple_extent_dims, :H5Sget_simple_extent_dims, [H5Types.hid_t, :pointer, :pointer], :int
+    def initialize(id)
+      @id = id
+    end
+    # Number of dimensions in the dataspace
+    def ndims
+      basic_get_simple_extent_ndims(@id)
+    end
+    def dims
+      basic_dims = FFI::MemoryPointer.new(H5Types.hsize_t, ndims)
+      basic_maxdims = FFI::MemoryPointer.new(H5Types.hsize_t, 1)
+      basic_get_simple_extent_dims(@id, basic_dims, basic_maxdims)
+      basic_dims.get_array_of_int64(0, ndims)
+    end
+  end
+  # Object for wrapping an HD5 datatype, which contains
+  # information about the type and makeup of an individual element
+  # of the dataset, which may be a float or integer, or may be 
+  # a vast compound type
+  class H5Datatype
+    extend  FFI::Library
+    ffi_lib 'hdf5'
+    attach_function :basic_get_class, :H5Tget_class, [H5Types.hid_t], H5Types.h5t_class_t
+    attach_function :basic_get_nmembers, :H5Tget_nmembers, [H5Types.hid_t], :int
+    attach_function :basic_get_member_type, :H5Tget_member_type, [H5Types.hid_t, :uint], H5Types.hid_t
+    attr_reader :id
+    def initialize(id)
+      @id = id
+    end
+    def h5_class
+      basic_get_class(@id)
+    end
+    # The number of members in a compound datatype
+    def nmembers
+      basic_get_nmembers(@id)
+    end
+    # We assume that a compound datatype with two floating point members
+    # is a complex number. This may want to be revisisted...
+    def is_complex?
+      nmembers == 2 and member_types.map{|t| t.h5_class} == [:h5t_float, :h5t_float]
+    end
+    # An array of datatypes of the members of a compound datatype
+    def member_types
+      nmembers.times.map{|i| self.class.new(basic_get_member_type(@id, i))}
+    end
+  end
+
+  # Object representing an HDF5 group
+  class H5Group
+    # Open the group. location_id is the id of the parent
+    # file or group
+    def self.open(location_id, name)
+      return new(H5SimpleReader.basic_group_open(location_id, name, 0))
+    end
+    def initialize(id)
+      @id = id
+    end
+    def open_group(name)
+      return H5Group.open(@id, name)
+    end
+  end
+end
+require 'hdf5/hdf5'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: hdf5
 version: !ruby/object:Gem::Version
-  version: 0.0.0
+  version: 0.1.0
 platform: ruby
 authors:
 - Edmund Highcock
@@ -24,6 +24,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: narray
+  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: shoulda
   requirement: !ruby/object:Gem::Requirement
@@ -125,7 +139,8 @@ dependencies:
 description: A ruby wrapper to the HDF5 data library. Currently read only.
 email: edmundhighcock@users.sourceforge.net
 executables: []
-extensions: []
+extensions:
+- ext/hdf5/extconf.rb
 extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
@@ -136,9 +151,10 @@ files:
 - README.rdoc
 - Rakefile
 - VERSION
+- ext/hdf5/extconf.rb
+- ext/hdf5/hdf5.c
+- hdf5.gemspec
 - lib/hdf5.rb
-- test/helper.rb
-- test/test_hdf5.rb
 homepage: http://github.com/edmundhighcock/hdf5
 licenses:
 - GPLv3

data/test/helper.rb

@@ -1,34 +0,0 @@
-require 'simplecov'
-
-module SimpleCov::Configuration
-  def clean_filters
-    @filters = []
-  end
-end
-
-SimpleCov.configure do
-  clean_filters
-  load_adapter 'test_frameworks'
-end
-
-ENV["COVERAGE"] && SimpleCov.start do
-  add_filter "/.rvm/"
-end
-require 'rubygems'
-require 'bundler'
-begin
-  Bundler.setup(:default, :development)
-rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
-end
-require 'test/unit'
-require 'shoulda'
-
-$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
-$LOAD_PATH.unshift(File.dirname(__FILE__))
-require 'hdf5'
-
-class Test::Unit::TestCase
-end

data/test/test_hdf5.rb

@@ -1,7 +0,0 @@
-require 'helper'
-
-class TestHdf5 < Test::Unit::TestCase
-  should "probably rename this file and start testing for real" do
-    flunk "hey buddy, you should probably rename this file and start testing for real"
-  end
-end