mdarray 0.5.5.1-java → 0.5.5.2-java

checksums.yaml

@@ -1,7 +1,7 @@
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data/config.rb

@@ -11,7 +11,7 @@ require 'rbconfig'
 # $ENV = 'cygwin'
 
 # Dependencies that are not yet installed (still in development)
-# $DEPEND = Array.new
+$DEPEND = Array.new
 
 ##########################################################################################
 
@@ -161,4 +161,3 @@ if ($DVLP == true)
   end
 
 end
-

data/lib/mdarray/creation.rb

@@ -72,18 +72,33 @@ class MDArray
       storage = parameters[2]
     end
 
-    dtype = DataType.valueOf(type.upcase)
+    # Java-NetCDF creates an ArrayObject when given type string.  It should create an
+    # ArrayString instead.  Some string methods in Java-NetCDF expect an ArrayObject
+    # instead of an ArrayString, however, other libraries actually expect an ArrayString,
+    # so we know have two type: "string" stores internally the data as an ArrayObject, 
+    # "rstring" stores data internally as an ArrayString
+    rtype = (type == "rstring")? "string" : type
+    dtype = DataType.valueOf(rtype.upcase)
+
     jshape = shape.to_java :int
 
     if (storage)
-      jstorage = storage.to_java type.downcase.to_sym
-      nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
+      jstorage = storage.to_java rtype.downcase.to_sym
+      if (type == "rstring")
+        # circunvent bug in Java-NetCDF.  Type rstring is actually type string but should
+        # and should build and ArrayString and not an ObjectString which is currently being
+        # build.
+        index = Java::UcarMa2.Index.factory(jshape)
+        nc_array = Java::UcarMa2.ArrayString.factory(index, jstorage)
+      else
+        nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
+      end
     else
       nc_array = Java::UcarMa2.Array.factory(dtype, jshape)
     end
 
-    klass = Object.const_get("#{type.capitalize}MDArray")
-    return klass.new(type, nc_array)
+    klass = Object.const_get("#{rtype.capitalize}MDArray")
+    return klass.new(rtype, nc_array)
 
   end
 
@@ -200,7 +215,9 @@ class MDArray
   end
 
   #------------------------------------------------------------------------------------
-  # Builds a string mdarray
+  # Builds a string mdarray. Java-NetCDF does not actuallly build a string array when
+  # type string is passed, it builds an object array.  This is an open issue with 
+  # Java-NetCDF.
   # @param shape [Array] the shape of the mdarray as a ruby array
   # @param storage [Array] a ruby array with the initialization data
   #------------------------------------------------------------------------------------
@@ -209,6 +226,17 @@ class MDArray
     self.build("string", shape, storage, layout)
   end
 
+  #------------------------------------------------------------------------------------
+  # Builds a string mdarray.  Really builds an string array.  Only exists to fix the
+  # Java-NetCDF issue described above.
+  # @param shape [Array] the shape of the mdarray as a ruby array
+  # @param storage [Array] a ruby array with the initialization data
+  #------------------------------------------------------------------------------------
+
+  def self.rstring(shape, storage = nil, layout = :row)
+    self.build("rstring", shape, storage, layout)
+  end
+
   #------------------------------------------------------------------------------------
   # Builds a structure mdarray
   # @param shape [Array] the shape of the mdarray as a ruby array

data/lib/mdarray/hierarchy.rb

@@ -108,6 +108,14 @@ end
 #
 ##########################################################################################
 
+class CharMDArray < NonNumericalMDArray
+    
+end
+
+##########################################################################################
+#
+##########################################################################################
+
 class StringMDArray < NonNumericalMDArray
     
 end

data/lib/mdarray/views.rb

@@ -56,13 +56,20 @@ class MDArray
 
   end
 
-  #------------------------------------------------------------------------------------
-  #
-  #------------------------------------------------------------------------------------
+  #----------------------------------------------------------------------------------------
+  # This method fixes a bug in netcdf-java!!! 
+  #----------------------------------------------------------------------------------------
 
   def reshape!(shape)
     new_shape = shape.to_java :int
-    @nc_array = @nc_array.reshapeNoCopy(new_shape)
+    # Netcdf-Java bug... reshape of ArrayString becomes an ArrayObject.  In principle
+    # should not require comparison with ArrayString here
+    if (@nc_array.is_a? ArrayString)
+      @nc_array = Java::UcarMa2.ArrayString.factory(@nc_array.getIndex(), 
+        @nc_array.getStorage())
+    else
+      @nc_array = @nc_array.reshapeNoCopy(new_shape)
+    end
     # when we reshape an array we need to re-initialize its index and local_iterator
     @local_index = Counter.new(self)
     @local_iterator = nil

data/test/mdarray/test_non_numeric.rb

@@ -23,6 +23,7 @@ require 'rubygems'
 require "test/unit"
 require 'shoulda'
 
+require_relative '../env'
 require 'mdarray'
 
 class MDArrayTest < Test::Unit::TestCase

data/test/netcdf/netcdfwriter.rb

@@ -1,3 +1,29 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+if !(defined? $ENVIR)
+  $ENVIR = true
+  require_relative '../env.rb'
+end
+
 require 'mdarray'
 
 class NetCDF

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "mdarray"
-$version="0.5.5.1"
+$version="0.5.5.2"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mdarray
 version: !ruby/object:Gem::Version
-  version: 0.5.5.1
+  version: 0.5.5.2
 platform: java
 authors:
 - Rodrigo Botafogo
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2014-11-16 00:00:00.000000000 Z
+date: 2014-12-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: map
@@ -104,31 +104,26 @@ files:
 - config.rb
 - lib/env.rb
 - lib/mdarray.rb
+- lib/colt/colt_mdarray.rb
+- lib/colt/double_descriptive.rb
+- lib/colt/probability.rb
+- lib/colt/stat_list.rb
 - lib/colt/cern_double_functions.rb
 - lib/colt/cern_float_functions.rb
 - lib/colt/cern_int_functions.rb
 - lib/colt/cern_long_functions.rb
 - lib/colt/colt.rb
-- lib/colt/colt_mdarray.rb
-- lib/colt/double_descriptive.rb
-- lib/colt/probability.rb
-- lib/colt/stat_list.rb
 - lib/colt/matrix/algebra.rb
 - lib/colt/matrix/colt_matrix.rb
 - lib/colt/matrix/creation.rb
 - lib/colt/matrix/hierarchy.rb
 - lib/colt/matrix/property.rb
 - lib/mdarray/access.rb
-- lib/mdarray/counter.rb
 - lib/mdarray/csv.rb
 - lib/mdarray/fast_operators.rb
-- lib/mdarray/function_creation.rb
 - lib/mdarray/function_map.rb
 - lib/mdarray/hierarchy.rb
-- lib/mdarray/lazy_mdarray.rb
 - lib/mdarray/lazy_operators.rb
-- lib/mdarray/operators.rb
-- lib/mdarray/printing.rb
 - lib/mdarray/proc_util.rb
 - lib/mdarray/ruby_boolean_functions.rb
 - lib/mdarray/ruby_functions.rb
@@ -139,7 +134,12 @@ files:
 - lib/mdarray/ruby_stats.rb
 - lib/mdarray/section.rb
 - lib/mdarray/views.rb
+- lib/mdarray/counter.rb
 - lib/mdarray/creation.rb
+- lib/mdarray/function_creation.rb
+- lib/mdarray/lazy_mdarray.rb
+- lib/mdarray/operators.rb
+- lib/mdarray/printing.rb
 - lib/netcdf/attribute.rb
 - lib/netcdf/cdm_node.rb
 - lib/netcdf/dimension.rb
@@ -158,16 +158,14 @@ files:
 - test/colt/matrix/test_creation.rb
 - test/colt/matrix/test_matrix1d_floatingalgebra.rb
 - test/colt/matrix/test_matrix2d_fixpointalgebra.rb
-- test/colt/matrix/test_matrix2d_floatingalgebra.rb
 - test/colt/matrix/test_operations.rb
 - test/colt/matrix/test_properties.rb
-- test/mdarray/arithmetic_casting.rb
+- test/colt/matrix/test_matrix2d_floatingalgebra.rb
 - test/mdarray/test_access.rb
 - test/mdarray/test_boolean.rb
 - test/mdarray/test_comparison.rb
 - test/mdarray/test_complete.rb
 - test/mdarray/test_counter.rb
-- test/mdarray/test_creation.rb
 - test/mdarray/test_error.rb
 - test/mdarray/test_lazy.rb
 - test/mdarray/test_non_numeric.rb
@@ -178,6 +176,8 @@ files:
 - test/mdarray/test_shape.rb
 - test/mdarray/test_trigonometry.rb
 - test/mdarray/test_views.rb
+- test/mdarray/arithmetic_casting.rb
+- test/mdarray/test_creation.rb
 - test/netcdf/netcdfwriter.rb
 - test/netcdf/test_complete.rb
 - test/netcdf/test_netcdf.rb