hdf5 0.2.2 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: f87349d9ad32fe5bf91ee2b354e422a33d58c6dd
-  data.tar.gz: 123edc76244a070d15879c517833db299541840a
+  metadata.gz: 0ff1af6e7836f2531fbadc9744c5d35825c7b9ae
+  data.tar.gz: df8346f1e5fce5df73518e961e7a5aa45ef41327
 SHA512:
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-  data.tar.gz: 352c2115bd2e5e6383a050a12ab6bca2db9a4a1c9b9fa70aeb54f057f6ecbcbe1dbb599a53297a2d027079fd64f1e4ab5845528d43869a597a43bcfb6936f64e
+  metadata.gz: f388ab35ef657c5912817f79f3731b47db30ff7b2042562c5369a767653c4b756bad53aa738270e8ae152093026233e876dac11d9709c1ad6a406de53be8cc4c
+  data.tar.gz: 0fec9ef227844f49831910167ae9c2773468d71ea9c273717f3a05a45183c023d56ecbd091afd873dcfe05eda4fb4633b8371ae88b13cbb4d5e631e6ce767955

data/Rakefile

@@ -17,8 +17,8 @@ Jeweler::Tasks.new do |gem|
   gem.name = "hdf5"
   gem.homepage = "http://github.com/edmundhighcock/hdf5"
   gem.license = "GPLv3"
-  gem.summary = %Q{A ruby wrapper to the HDF5 data library. Currently read only.}
-  gem.description = %Q{A ruby wrapper to the HDF5 data library. Currently read only.}
+  gem.summary = %Q{A ruby wrapper to the HDF5 data library. Currently can only read existing HDF5 files.}
+  gem.description = %Q{A ruby wrapper to the HDF5 data library. Currently can only read HDF5 files.}
   gem.email = "edmundhighcock@users.sourceforge.net"
   gem.authors = ["Edmund Highcock"]
 	gem.files.exclude 'test/**/*'

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.3.0

data/hdf5.gemspec

@@ -2,18 +2,18 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: hdf5 0.2.2 ruby lib
+# stub: hdf5 0.3.0 ruby lib
 # stub: ext/hdf5/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "hdf5"
-  s.version = "0.2.2"
+  s.version = "0.3.0"
 
   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 = "2014-07-23"
-  s.description = "A ruby wrapper to the HDF5 data library. Currently read only."
+  s.description = "A ruby wrapper to the HDF5 data library. Currently can only read HDF5 files."
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extensions = ["ext/hdf5/extconf.rb"]
   s.extra_rdoc_files = [
@@ -35,7 +35,7 @@ Gem::Specification.new do |s|
   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."
+  s.summary = "A ruby wrapper to the HDF5 data library. Currently can only read existing HDF5 files."
 
   if s.respond_to? :specification_version then
     s.specification_version = 4

data/lib/hdf5.rb

@@ -1,4 +1,5 @@
 require 'ffi'
+require 'narray'
 class NArray
   # Returns an FFI::Pointer which points to the location
   # of the actual data array in memory.
@@ -195,21 +196,51 @@ module Hdf5
     # scope in the future for writing custom closures for reading in more
     # complex datatypes.
     def narray_all
-      narr = NArray.send(narray_type, *dataspace.dims)
+      narr = NArray.send(narray_type, *dataspace.dims.reverse) # Note narray is fortran-style column major
       basic_read(@id, datatype.id, 0, 0, 0, narr.ffi_pointer)
       narr
     end
+    # Create an NArray of the appropriate type and size and a subsection of
+    # the dataset into it. start_indexes and end_indexes should be arrays 
+    # of size ndims. start_indexes should contain the (zero-based) offset
+    # of the start of the read, and end_indexes should contain the offset of 
+    # the end of the read. Each element of end_indexes can either be a zero
+    # based positive offset, or a negative offset where -1 corresponds to the
+    # end of the dataset dimension. This function 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.
+    # As an example, consider a two-dimensional 6x10 dataset. 
+    #   dataset.narray_read([0,0], [-1,-1]) # would read the whole of the dataset
+    #   dataset.narray_read([0,0], [5,9]) # would read the whole of the dataset
+    #   dataset.narray_read([0,0], [2,-1]) # would read half the dataset
+    #   dataset.narray_read([0,0], [-4,-1]) # would read the same half of the dataset
+    #   dataset.narray_read([2,4], [2,4]) # would read one element of the dataset
+    def narray_simple_read(start_indexes, end_indexes)
+      nd = dataspace.ndims
+      raise ArgumentError.new("start_indexes and end_indexes must be of size ndims") unless start_indexes.size == nd and end_indexes.size == nd
+      szs = dataspace.dims
+      counts = end_indexes.zip(start_indexes.zip(szs)).map{|ei, (si, sz)| ei < 0 ? ei + sz - si + 1 : ei - si + 1}
+      dtspce = H5Dataspace.create_simple(counts)
+      dtspce.offset_simple(start_indexes)
+      narr = NArray.send(narray_type, *dtspce.dims.reverse) # Note narray is fortran-style column major
+      basic_read(@id, datatype.id, 0, dtspce.id, 0, narr.ffi_pointer)
+      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
+    attr_reader :id
     extend  FFI::Library
     ffi_lib H5Library.library_path
     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
+    attach_function :basic_offset_simple, :H5Soffset_simple, [H5Types.hid_t, :pointer], H5Types.herr_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
@@ -240,12 +271,20 @@ module Hdf5
       return [basic_dims, basic_maxdims]
     end
     private :basic_dims_maxdims
+    # Get the size of the dataspace
     def dims      
       basic_dims_maxdims[0].get_array_of_int64(0, ndims)
     end
+    # Get the maximum size of the dataspace
     def maxdims      
       basic_dims_maxdims[1].get_array_of_int64(0, ndims)
     end
+    # Set the offset of the dataspace. offsets should be an ndims-sized array
+    # of zero-based integer offsets. 
+    def offset_simple(offsets)
+      raise ArgumentError.new("offsets should have ndims elements") unless offsets.size == ndims
+      basic_offset_simple(@id, offsets.ffi_mem_pointer_hsize_t)
+    end
   end
   # Object for wrapping an HD5 datatype, which contains
   # information about the type and makeup of an individual element

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: hdf5
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.3.0
 platform: ruby
 authors:
 - Edmund Highcock
@@ -136,7 +136,8 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-description: A ruby wrapper to the HDF5 data library. Currently read only.
+description: A ruby wrapper to the HDF5 data library. Currently can only read HDF5
+  files.
 email: edmundhighcock@users.sourceforge.net
 executables: []
 extensions:
@@ -178,5 +179,6 @@ rubyforge_project:
 rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
-summary: A ruby wrapper to the HDF5 data library. Currently read only.
+summary: A ruby wrapper to the HDF5 data library. Currently can only read existing
+  HDF5 files.
 test_files: []