hdf5 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: a7e1e9fdc346d66ae0b3f874b965d05938cbd34f
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+  data.tar.gz: d1437ce28a4b03e0f7d6566f70645805901694cc
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+  data.tar.gz: 8129fed65a5829e1f902a9f9642910e1b8c31f643ec8178ced2515ee07acb0964346dd8d50ff295bef65120a38afdb82770bdbd30bb7dc027278ef7c2a41f9d2

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/ext/hdf5/hdf5.c

@@ -37,11 +37,11 @@ static VALUE narray_data_address(VALUE class, VALUE narray_obj){
 void Init_hdf5()
 {
   VALUE ch5_simple_reader;
-  VALUE ch5_simple_reader_dataset;
+  /*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);
+  ch5_simple_reader = rb_const_get(rb_cObject, rb_intern("Hdf5"));
+  /*ch5_simple_reader_dataset = rb_const_get(ch5_simple_reader, rb_intern("H5Dataset")); */
+  rb_define_singleton_method(ch5_simple_reader, "narray_data_address", narray_data_address, 1);
   /*VALUE ctrinity;*/
   /**/
   /**//**//*cgraph_kit = Qnil;*/

data/hdf5.gemspec

@@ -2,17 +2,17 @@
 # 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: hdf5 0.2.0 ruby lib
 # stub: ext/hdf5/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "hdf5"
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   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.date = "2014-07-23"
   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"]

data/lib/hdf5.rb

@@ -1,5 +1,10 @@
 require 'ffi'
-module H5SimpleReader
+class NArray
+  def ffi_mem_pointer
+    FFI::Pointer.new(Hdf5.narray_data_address(self))
+  end
+end
+module Hdf5
   module H5Types
     extend FFI::Library
     class << self
@@ -65,12 +70,12 @@ module H5SimpleReader
     def close
       basic_close(@id)
     end
-    # Return a group object with the given name 
+    # 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 
+    # Return a dataset object with the given name
     # (relative to the root of the file)
     def dataset(name)
       return H5Dataset.open(@id, name)
@@ -78,7 +83,7 @@ module H5SimpleReader
   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 
+  # the data elements and the size and shape of the
   # data array.
   class H5Dataset
     extend  FFI::Library
@@ -94,7 +99,7 @@ module H5SimpleReader
       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 
+    # Use H5Dataset.open to open a dataset
     def initialize(id)
       @id = id
     end
@@ -106,46 +111,37 @@ module H5SimpleReader
     def dataspace
       H5Dataspace.new(basic_get_space(@id))
     end
+    # Gives the narray type corresponding to the datatype of the dataset
+    # Raises an error for unsupported datatypes.
+    # datatypes (basically only works for ints, floats and complexes, where a datatype
+    # composed of two floats is assumed to be a complex).
     def narray_type
       #cls = H5Types.h5t_class_t
       #p 'datatype', datatype.h5_class
-      case datatype.h5_class
+      case h5c = datatype.h5_class
+      when :h5t_integer
+        :integer
       when :h5t_float
         :float
       when :h5t_compound
         if datatype.is_complex?
           :complex
         else
-          :compound
+          raise "Unsupported datatype for narray: #{h5c}"
         end
-      else 
-        raise "unknown datatype"
+      else
+        raise "Unsupported datatype for narray: #{h5c}"
       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
+    # Create an NArray of the appropriate size and read the entire 
+    # content of the dataset into it. Will not work for complicated 
+    # datatypes (basically only works for ints, floats and complexes, where a datatype
+    # composed of two floats is assumed to be a complex). There is 
+    # scope in the future for writing custom closures for reading in more
+    # complex datatypes.
     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
+      basic_read(@id, datatype.id, 0, 0, 0, narr.ffi_mem_pointer)
       narr
     end
     #def array
@@ -158,6 +154,22 @@ module H5SimpleReader
     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
+    attach_function :basic_create_simple, :H5Screate_simple, [:int, :pointer, :pointer], H5Types.hid_t
+    # Create a new HDF5 dataspace with the given current and maximum 
+    # dimensions. If maximum_dims is omitted it is set to current_dims.
+    # Returns an H5Dataspace object wrapping the dataspace
+    def self.create_simple(current_dims, maximum_dims=nil)
+      maximum_dims ||= current_dims
+      raise ArgumentError.new("current_dims and maximum_dims must be the same size") unless current_dims.size == maximum_dims.size
+      n = current_dims.size
+      basic_dims = FFI::MemoryPointer.new(H5Types.hsize_t, n)
+      basic_maxdims = FFI::MemoryPointer.new(H5Types.hsize_t, n)
+      basic_dims.write_array_of_int64(current_dims)
+      basic_maxdims.write_array_of_int64(maximum_dims)
+      new(basic_create_simple(n, basic_dims, basic_maxdims))
+    end
+    # Create a new H5Dataspace object. id must be the id
+    # of a pre-existing HDF5 dataspace.
     def initialize(id)
       @id = id
     end
@@ -165,16 +177,23 @@ module H5SimpleReader
     def ndims
       basic_get_simple_extent_ndims(@id)
     end
-    def dims
+    def basic_dims_maxdims
       basic_dims = FFI::MemoryPointer.new(H5Types.hsize_t, ndims)
-      basic_maxdims = FFI::MemoryPointer.new(H5Types.hsize_t, 1)
+      basic_maxdims = FFI::MemoryPointer.new(H5Types.hsize_t, ndims)
       basic_get_simple_extent_dims(@id, basic_dims, basic_maxdims)
-      basic_dims.get_array_of_int64(0, ndims)
+      return [basic_dims, basic_maxdims]
+    end
+    private :basic_dims_maxdims
+    def dims      
+      basic_dims_maxdims[0].get_array_of_int64(0, ndims)
+    end
+    def maxdims      
+      basic_dims_maxdims[1].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 
+  # of the dataset, which may be a float or integer, or may be
   # a vast compound type
   class H5Datatype
     extend  FFI::Library
@@ -209,7 +228,7 @@ module H5SimpleReader
     # 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))
+      return new(Hdf5.basic_group_open(location_id, name, 0))
     end
     def initialize(id)
       @id = id

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: hdf5
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-22 00:00:00.000000000 Z
+date: 2014-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi