scicom 0.2.0-java

data/lib/JRubyR/as_mdarray.rb

@@ -0,0 +1,60 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# 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.
+##########################################################################################
+
+
+###########################################################################################
+#
+###########################################################################################
+
+class MDArray
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def z
+    self[0]
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def pp
+    print
+  end
+
+end
+
+###########################################################################################
+#
+###########################################################################################
+
+class Renjin
+
+  class Vector
+
+    
+  end
+  
+end

data/lib/JRubyR/attributes.rb

@@ -0,0 +1,74 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# 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.
+##########################################################################################
+
+#==========================================================================================
+#
+#==========================================================================================
+
+class Renjin
+
+  class Attributes
+
+    attr_reader :rbsexp
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def initialize(rbsexp)
+      @rbsexp = rbsexp
+    end
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def method_missing(symbol, *args)
+      
+      name = symbol.id2name
+      name.sub!(/__/,".")
+      # Method 'rclass' is a substitute for R method 'class'.  Needed, as 'class' is also
+      # a Ruby method on an object
+      name.gsub!("rclass", "class")
+      
+      if name =~ /(.*)=$/
+        super if args.length != 1
+        args = R.parse(*args)
+        ret = R.eval("attr(#{@rbsexp.r}, \"#{name.delete!('=')}\") = #{args}")
+      else
+        if (args.length == 0)
+          # p "retrieving attribute: #{name}"
+          ret = R.eval("attr(#{@rbsexp.r}, \"#{name}\")")
+          ret.scope = ["attr", @rbsexp, name]
+        else
+          raise "An attribute cannot have parameters"
+        end
+      end
+
+      ret
+      
+    end
+    
+  end
+  
+end

data/lib/JRubyR/dataframe.rb

@@ -0,0 +1,35 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# 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.
+##########################################################################################
+
+class Renjin
+
+  class DataFrame < Renjin::List
+
+  def colnames(names)
+    R.eval("colnames(#{r}) = c(#{names})") 
+  end
+
+  end
+
+end
+

data/lib/JRubyR/environment.rb

@@ -0,0 +1,60 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# 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.
+##########################################################################################
+
+
+class Renjin
+
+  class Environment < Renjin::RubySexp
+
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+
+    def method_missing(symbol, *args)
+      
+      name = symbol.id2name
+      if name =~ /(.*)=$/
+        # should never reach this point.  Parse error... but check
+        raise ArgumentError, "You shouldn't assign nil" if args==[nil]
+        super if args.length != 1
+        ret = R.assign($1,args[0])
+      else
+        name.gsub!(/__/,".")
+        # super if args.length != 0
+        if (args.length == 0)
+          # treat the argument as a named item of the list
+          ret = Renjin::RubySexp.build(@sexp.getVariable(name))
+        else
+          params = parse(*args)
+          ret = eval("#{name}(#{params})")
+        end
+      end
+      
+      ret
+      
+    end
+
+  end
+
+end
+

data/lib/JRubyR/function.rb

@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# 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_relative "attributes"
+
+#==========================================================================================
+#
+#==========================================================================================
+
+class Renjin
+
+  #========================================================================================
+  #
+  #========================================================================================
+
+  class Function < Renjin::RubySexp
+
+    def call(*args)
+      args = R.parse(*args)
+      R.eval("#{r}(#{args})")
+    end
+
+  end
+
+  #========================================================================================
+  #
+  #========================================================================================
+
+  class Closure < Function
+
+  end
+
+  #========================================================================================
+  #
+  #========================================================================================
+
+  class Primitive < Function
+
+  end
+
+end

data/lib/JRubyR/index.rb

@@ -0,0 +1,278 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# 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 'java'
+require 'set'
+
+class Java::UcarMa2::Index
+  field_accessor :stride
+
+  def currentElement
+    getCurrentCounter()
+    super
+  end
+
+end
+
+#------------------------------------------------------------------------------------------
+#
+#------------------------------------------------------------------------------------------
+
+class MDArray
+
+  @LAYOUT = Set.new [:row, :column, :r]
+
+  #------------------------------------------------------------------------------------
+  # Builds a new MDArray
+  # @param type the type of the new mdarray to build, could be boolean, byte, short,
+  #  int, long, float, double, string, structure
+  # @param shape [Array] the shape of the mdarray as a ruby array
+  # @param storage [Array] a ruby array with the initialization data
+  #------------------------------------------------------------------------------------
+
+  def self.build(type, shape, storage = nil, layout = :row)
+
+    if !@LAYOUT.include?(layout)
+      raise "Unknown layout #{layout}"
+    end
+
+    if (shape.is_a? String)
+      # building from csv
+      # using shape as filename
+      # using storage as flag for headers
+      storage = (storage)? storage : false
+      parameters = Csv.read_numeric(shape, storage)
+      shape=[parameters[0], parameters[1]]
+      storage = parameters[2]
+    end
+
+    if (storage)
+      # nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
+      nc_array = make_nc_array(type, shape, storage, layout)
+    else
+      nc_array = Java::UcarMa2.Array
+        .factory(DataType.valueOf(type.upcase), shape.to_java(:int))
+    end
+
+    klass = Object.const_get("#{type.capitalize}MDArray")
+    return klass.new(type, nc_array)
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # Creates new index with the given shape and column-major layout
+  #------------------------------------------------------------------------------------
+
+  def self.index_factory(shape)
+
+    stride = comp_stride(shape)
+    index = Java::UcarMa2.Index.factory(shape.to_java(:int))
+    index.stride = stride.to_java(:int)
+    index.precalc
+    index
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  private
+
+  #------------------------------------------------------------------------------------
+  # Computes the stride for the given shape and column-major layout
+  #------------------------------------------------------------------------------------
+
+  def self.comp_stride(shape)
+
+    stride = Array.new(shape.size)
+    stride[-1], stride[-2] = shape[-2], 1
+    product = shape[-1] * shape[-2]
+
+    if (shape.size > 2)
+      (shape.length - 3).downto(0).each do |i|
+        stride[i] = product
+        product *= shape[i]
+      end
+    end
+
+    stride
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # Makes a NetCDF Array with the given storage and layout.
+  #------------------------------------------------------------------------------------
+
+  def self.make_nc_array(type, shape, storage, layout)
+
+    dtype = DataType.valueOf(type.upcase)
+    jshape = shape.to_java :int
+    jstorage = storage.to_java type.downcase.to_sym
+
+    if (layout == :row || shape.size == 1)
+      nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
+    else
+      jclass = Java::UcarMa2::Array.java_class
+      nc_array = Java::RbScicom::PrivateCall
+        .factoryInvoke(jclass, type.capitalize, index_factory(shape), jstorage)
+    end
+
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def self.from_jstorage(type, shape, jstorage, section = false, layout = :row)
+
+    if !@LAYOUT.include?(layout)
+      raise "Unknown layout #{layout}"
+    end
+
+    if (shape.size == 1 && shape[0] == 0)
+      return nil
+    end
+
+    dtype = DataType.valueOf(type.upcase)
+    jshape = shape.to_java :int
+
+    case layout
+    when :row
+      nc_array = Java::UcarMa2.Array.factory(dtype, jshape, jstorage)
+      klass = Object.const_get("#{type.capitalize}MDArray")
+      return klass.new(type, nc_array, section)
+    else
+      jclass = Java::UcarMa2::Array.java_class
+      jstorage = storage.to_java(type)
+      nc_array = Java::RbScicom::PrivateCall
+        .factoryInvoke(jclass, type.capitalize, index_factory(shape), jstorage)
+      MDArray.build_from_nc_array(type, nc_array)
+    end
+
+  end
+
+end
+
+
+
+
+
+
+=begin
+
+#------------------------------------------------------------------------------------------
+# Derived class from Index does not work as we need to create Index1D, Index2D, etc.
+# classes, and this will only create the Index class
+#------------------------------------------------------------------------------------------
+
+class ColumnIndex < Java::UcarMa2::Index
+
+  field_reader :stride
+  field_reader :offset
+  field_reader :current
+
+  def initialize(shape)
+
+    stride = comp_stride(shape)
+    stride = stride.to_java(:int)
+    # index = Java::UcarMa2.Index.factory(shape.to_java(:int))
+    super(shape.to_java(:int), stride)
+
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  private
+
+  #------------------------------------------------------------------------------------
+  # Computes the stride for the given shape and a column-major layout
+  #------------------------------------------------------------------------------------
+
+  def comp_stride(shape)
+
+    stride = Array.new(shape.size)
+    stride[-1], stride[-2] = shape[-2], 1
+    product = shape[-1] * shape[-2]
+
+    if (shape.size > 2)
+      (shape.length - 3).downto(0).each do |i|
+        stride[i] = product
+        product *= shape[i]
+      end
+    end
+
+    stride
+
+  end
+
+end
+
+
+
+
+    # jclass is a java class
+    jclass = Java::UcarMa2::Array.java_class
+    # p jclass.private_methods
+    # p jclass.methods
+    # p jclass.declared_method_smart(:factory)
+
+    new = Java::UcarMa2::ArrayDouble.java_class
+    
+    # p jclass.declared_class_methods
+    # method = jclass.declared_class_methods[2]
+    # p method.inspect
+
+    method = jclass.declared_class_methods.each do |method|
+      p method if method.name == "factory" && method.arity == 3
+    end
+
+    p method
+    method.accessible = true
+    arr = method.invoke(self, new, index, jstorage.to_java)
+    p arr
+    p arr[0, 0, 0, 0, 0, 0, 0, 0, 0]
+
+    # p jclass.methods
+    # p jclass.java_class_methods
+
+    # jclass.declared_method (Java::UcarMa2::Array.factory, [java.lang.Class, Java::UcarMa2.Index])
+    # java_class = Java::UcarMa2.Array
+    # p java_class
+    # p java_class.methods
+    # p java_class.java_class_methods
+    # const = Java::UcarMa2::ArrayDouble.java_method :factory, [Java::UcarMa2.Index]
+    # const = Java::UcarMa2::Array.java_method :factory, [java.lang.Class, Java::int[]]
+      # p const
+    # constructor = java_class.declared_method (Java::UcarMa2.Array.factory)
+  end
+
+    # java_class = Java::JavaClass.for_name("ucar.ma2.Array")
+    # java_class.getCanonicalName()
+
+    # get a bound Method based on the add(int, Object) method from ArrayList
+    # add = list.java_method :add, [Java::int, java.lang.Object]
+    # add.call(0, 'foo')
+=end