mdarray 0.5.3-java → 0.5.4-java

data/test/netcdf/test_complete.rb

@@ -0,0 +1,27 @@
+# -*- 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.
+##########################################################################################
+
+Dir.mkdir($TMP_TEST_DIR) unless File.exists?($TMP_TEST_DIR)
+
+#=begin
+require_relative 'test_netcdf'
+require_relative 'netcdfwriter'
+#=end

data/test/netcdf/test_netcdf.rb

@@ -0,0 +1,331 @@
+# -*- 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.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'mdarray'
+
+class MDArrayTest < Test::Unit::TestCase
+
+  context "NetCDF implementation" do
+
+    setup do
+
+      @directory = $TMP_TEST_DIR
+
+    end
+
+    #-------------------------------------------------------------------------------------
+    #
+    #-------------------------------------------------------------------------------------
+
+    should "Allow definition of a NetCDF-3 file" do
+
+      # Opens a file for definition, passing the directory and file name.
+      # Creates a new scope for defining the NetCDF file.  In order to access the 
+      # ouside scope, that is, "here", we pass self as the third argument to define.
+      # When self is passed as argument, @outside_scope is available inside the block.
+      # NetCDF.define block is in define mode, so it is not possible to write data in
+      # this block.  We need to open a new block with NetCDF.write for writing.  The
+      # cost of doing this is that we close the file at the end of the define block and
+      # need to reopen the file for writing.  However, since we probably only define the
+      # file once and write many times, this is not much of a problem.  If one prefers, 
+      # one could not use the define block and use the normal APIs.
+      
+      NetCDF.define(cygpath(@directory), "nc_output", "netcdf3", self) do
+        
+        #=================================================================================
+        # Add global attributes by adding a single valued attribute or an array of 
+        # attributes.  When adding an array of attributes all elements of the array must
+        # be of the same type, i.e, fixnum, floats or strings. Attributes with long numbers
+        # are not allowed. This seems to be a restriction of Java-NetCDF.
+        # 
+        # Note that the attribute name can be used to make access to the attribute, for
+        # instance, on the first example "Values" can be accessed as @value later on.
+        #=================================================================================
+
+        global_att "Fixnum", 3
+        @outside_scope.assert_equal(3, @ga_fixnum.numeric_value)
+
+        global_att "Float", 3.45, "float"
+        @outside_scope.assert_equal("float", @ga_float.data_type)
+
+        global_att "Double", 3.45, "double"
+        @outside_scope.assert_equal("double", @ga_double.data_type)
+
+        global_att "Int", 3.45
+        @outside_scope.assert_equal("int", @ga_int.data_type)
+
+        global_att "Byte", 3, "byte"
+        @outside_scope.assert_equal("byte", @ga_byte.data_type)
+
+        global_att "Short", 3, "short"
+        @outside_scope.assert_equal("short", @ga_short.data_type)
+        
+        global_att "String", "this is a string"
+        global_att "Description", "This is a test file created by MDArray"
+        @outside_scope.assert_equal("String", @ga_description.data_type)
+        @outside_scope.assert_equal("Description", @ga_description.name)
+        @outside_scope.assert_equal("This is a test file created by MDArray", 
+                                    @ga_description.string_value)
+        @outside_scope.assert_equal(true, @ga_description.string?)
+        @outside_scope.assert_equal(false, @ga_description.unsigned?)
+
+        global_att "Values", [1, 2, 3, 4], "double"
+        @outside_scope.assert_equal(true, @ga_values.array?)
+        @outside_scope.assert_equal("Values", @ga_values.name)
+        @outside_scope.assert_equal(2.0, @ga_values.numeric_value(1))
+
+        global_att "Strings", ["abc", "efg"]
+        @outside_scope.assert_equal("abc", @ga_strings.string_value(0))
+
+        global_att "Floats", [1.34, 2.45], "float"
+
+        att = find_global_attribute("Fixnum")
+        @outside_scope.assert_equal("Fixnum", att.name)
+
+        att = find_global_attribute("doesnotexists")
+        @outside_scope.assert_equal(nil, att)
+
+        # print all global attributes
+        global_attributes.each do |att|
+          p att.name
+        end
+
+        #=================================================================================
+        # Adding dimensions
+        #=================================================================================
+
+        dimension "dim1", 5
+        @outside_scope.assert_equal(5, @dim_dim1.length)
+        @outside_scope.assert_equal("dim1", @dim_dim1.name)
+        @outside_scope.assert_equal(true, @dim_dim1.shared?)
+        @outside_scope.assert_equal(false, @dim_dim1.unlimited?)
+        @outside_scope.assert_equal(false, @dim_dim1.variable_length?)
+
+        dimension "dim2", 10
+        @outside_scope.assert_equal(true, @dim_dim2.shared?)
+
+        # create an unlimited dimension by setting the size to 0
+        dimension "dim3", 0
+        @outside_scope.assert_equal(true, @dim_dim3.shared?)
+        @outside_scope.assert_equal(true, @dim_dim3.unlimited?)
+        @outside_scope.assert_equal(false, @dim_dim3.variable_length?)
+
+        # Cannot create a variable_length dimension in NetCDF-3 file.  Might
+        # work on NetCDF-4.  Not tested.
+        # dimension "dim4", -1
+        # @outside_scope.assert_equal(true, @dim_dim4.variable_length?)
+
+        # Create a dimension that is not shared. Don't know exactly what happens
+        # in NetCDF-3 files.  It does not give any bugs but the dimension does
+        # not appear on a write_cdl call.
+        dimension "dim5", 5, false
+        @outside_scope.assert_equal("dim5", @dim_dim5.name)
+        @outside_scope.assert_equal(false, @dim_dim5.shared?)
+
+        #=================================================================================
+        # Adding variables
+        #=================================================================================
+
+        # One dimensional variable
+        variable "arr1", "int", [@dim_dim1]
+        variable_att @var_arr1, "description", "this is a variable"
+        variable_att @var_arr1, "size", 5
+        variable_att @var_arr1, "date", 10
+        variable_att @var_arr1, "String List", ["abc", "def"]
+        variable_att @var_arr1, "Float list", [1.37, 5.18]
+
+        # two dimensional variable string variable is actually a three dimensional
+        # variable.  NetCDF-3 does not support string variable, so this variable
+        # is transformed to a "char" variable with one extra dimension, the string
+        # size
+        variable "var3", "int", [@dim_dim3]
+        variable "var4", "string", [@dim_dim3, @dim_dim2]
+        variable "var5", "double", [@dim_dim3, @dim_dim2]
+
+        # controlling the size of the string variable
+        variable "Short", "string", [@dim_dim2], {:max_strlen => 20}
+        @outside_scope.assert_equal("Short", @var_short.name)
+
+        # double variable with fixed size dimensions
+        variable "Double", "double", [@dim_dim1, @dim_dim2]
+
+        # double variable with an unlimited dimension.  Unlimited dimension must be the
+        # first dimension in NetCDF-3 files.
+        variable "Double3", "double", [@dim_dim3, @dim_dim1, @dim_dim2]
+        variable_att @var_double3, "_FillValue", -1
+
+        variable "Scalar", "double", []
+
+        #=================================================================================
+        # Add additional flags
+        #=================================================================================
+
+        # set fill to true... all elements should be filled with the fill_value
+        fill = true
+        large_file = true
+
+      end
+
+    end
+
+#=begin
+    #-------------------------------------------------------------------------------------
+    # Opens a NetCDF file for writing data
+    #-------------------------------------------------------------------------------------
+  
+    should "open a file for writing data" do
+      
+      NetCDF.write(cygpath(@directory), "nc_output", self) do
+
+        # create some data to add to variable
+        array = MDArray.typed_arange("double", 0, 50)
+        array2 = MDArray.typed_arange("double", 0, 10)
+        array3 = MDArray.typed_arange("double", 0, 6)
+        string_array = MDArray.string([5], ["this", "is", "a", "string", "array"])
+
+        var = find_variable("Double")
+        @outside_scope.assert_equal("Double", var.name)
+        # reshape the first array to fit the variable shape
+        array.reshape!([5, 10])
+        # Fill variable Double with data.  The whole variable gets data
+        write(var, array)
+
+        # writing data only to the last dimension
+        array2.reshape!([1, 10])
+        write(var, array2, [4, 0])
+
+        # writing data to a variable with unlimited dimension.  Writing on the third
+        # index of the unlimited dimension.  Array needs to be reshaped to the same
+        # shape as the variable
+        var3 = find_variable("Double3")
+        @outside_scope.assert_equal("Double3", var3.name)
+        array.reshape!([1, 5, 10])
+        write(var3, array, [2, 0, 0])
+
+        # adding data to a subsection of the variable
+        array3.reshape!([1, 1, 6])
+        write(var3, array3, [1, 1, 1])
+
+        # reshaping the data in another way
+        array3.reshape!([1, 3, 2])
+        write(var3, array3, [0, 2, 3])
+
+        # writing string data
+        short = find_variable("Short") 
+        @outside_scope.assert_equal("Short", short.name)
+        write_string(short, string_array)
+
+        var4 = find_variable("var4")
+        string_array.reshape!([1, 5])
+        @outside_scope.assert_equal("var4", var4.name)
+        write_string(var4, string_array)
+
+        scalar = find_variable("Scalar")
+        @outside_scope.assert_equal("Scalar", scalar.name)
+        write(scalar, 5.34)
+
+      end
+      
+    end
+#=end
+    #-------------------------------------------------------------------------------------
+    # Opens a NetCDF file for reading only
+    #-------------------------------------------------------------------------------------
+#=begin
+    should "open a file just for reading" do
+
+      # Opens a file for definition, passing the directory and file name.
+      # Creates a new scope for defining the NetCDF file.  In order to access the 
+      # ouside scope, that is, "here", we pass self as the third argument to define.
+      # When self is passed as argument, @outside_scope is available inside the block.
+      
+      NetCDF.read(cygpath(@directory), "nc_output", self) do
+
+        # print all global attributes
+        global_attributes.each do |att|
+          p att.name
+        end
+
+        att = find_global_attribute("Fixnum")
+        @outside_scope.assert_equal("Fixnum", att.name)
+
+        # att 
+
+        dim1 = find_dimension("dim1")
+        @outside_scope.assert_equal(5, dim1.length)
+        @outside_scope.assert_equal("dim1", dim1.name)
+        @outside_scope.assert_equal(true, dim1.shared?)
+        @outside_scope.assert_equal(false, dim1.unlimited?)
+        @outside_scope.assert_equal(false, dim1.variable_length?)
+
+        unlimited = find_unlimited_dimension
+        @outside_scope.assert_equal("dim3", unlimited.name)
+
+        # Although adding an unshared dimension seemed to work on NetCDF-3 file, 
+        # trying to retrieve this dimension does not work.
+        # unshared = find_dimension("dim5")
+        # @outside_scope.assert_equal("dim5", unshared.name)
+
+        # reading the whole Double variable
+        var = find_variable("Double")
+        var.read
+
+        # reading a section of Double using origin and shape
+        var.read(:origin => [1, 1], :shape => [2, 3])
+
+        # reading a section of Double using a section specification
+        var.read(:spec => "0:4:2, 4:9:3")
+
+        # reading the whole Double3 variable
+        var2 = find_variable("Double3")
+        var2.read
+
+        # makes a new variable as a subsection of Double3
+        var3 = var2.section(:origin => [0, 1, 1], :shape => [1, 4, 9])
+
+        # reading a section of Double3 using origin and shape
+        var2.read(:origin => [0, 1, 1], :shape => [1, 4, 9])
+
+        write_cdl
+
+        p detail_info
+        p file_type_description
+        p file_type_id
+        p id
+        p last_modified
+        p location
+        p title
+        p unlimited_dimension?
+
+      end
+      
+    end
+#=end    
+    
+  end
+  
+end
+  
+# require_relative 'test_redefine'

data/test/netcdf/test_redefine.rb

@@ -0,0 +1,120 @@
+# -*- 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.
+##########################################################################################
+
+require 'rubygems'
+require "test/unit"
+require 'shoulda'
+
+require 'mdarray'
+
+class MDArrayTest < Test::Unit::TestCase
+
+  context "NetCDF implementation" do
+
+    setup do
+
+      @directory = "/home/zxb3/tmp"
+
+    end
+
+
+    #-------------------------------------------------------------------------------------
+    #
+    #-------------------------------------------------------------------------------------
+
+    should "Open a file for redefinition" do
+
+      NetCDF.redefine(cygpath(@directory), "nc_output", self) do
+        
+        # rename_global_att("Values", "New_values")
+        # delete_global_att("Values")
+        rename_dimension("dim1", "new_dim1")
+        # rename_variable("arr1", "new_arr1")
+
+        var1 = find_variable("arr1")
+        @outside_scope.assert_equal("arr1", var1.name)
+        delete_variable_att(var1, "description")
+        rename_variable_att(var1, "size", "new_size")
+
+        p var1.extra_info
+        att = var1.find_attribute("date")
+        @outside_scope.assert_equal("date", att.name)
+        @outside_scope.assert_equal(0, var1.find_dimension_index("new_dim1"))
+        atts = var1.find_attributes
+        atts.each do |att|
+          p att.name
+        end
+        @outside_scope.assert_equal("int", var1.get_data_type)
+        p var1.get_description
+        dim = var1.get_dimension(0)
+        p dim.name
+        p var1.find_dimensions
+        p var1.get_dimensions_string
+        p var1.get_element_size
+        p var1.get_name_and_dimensions
+        p var1.rank
+        p var1.shape
+        p var1.size
+        p var1.get_units_string
+
+      end
+
+    end
+
+    #-------------------------------------------------------------------------------------
+    # Opens a NetCDF file for reading only
+    #-------------------------------------------------------------------------------------
+
+    should "open a file just for reading" do
+
+      # Opens a file for definition, passing the directory and file name.
+      # Creates a new scope for defining the NetCDF file.  In order to access the 
+      # ouside scope, that is, "here", we pass self as the third argument to define.
+      # When self is passed as argument, @outside_scope is available inside the block.
+      
+      reader = NetCDF.read(cygpath(@directory), "nc_output", self) do
+=begin      
+        # print all global attributes
+        global_attributes.each do |att|
+          p att.name
+        end
+=end
+        write_cdl
+
+=begin
+        p detail_info
+        p file_type_description
+        p file_type_id
+        p id
+        p last_modified
+        p location
+        p title
+        p unlimited_dimension?
+=end
+
+      end
+      
+    end
+
+    
+  end
+  
+end