scicom 0.2.2-java → 0.2.3-java

data/test/test_dataframe.rb

@@ -42,7 +42,7 @@ class SciComTest < Test::Unit::TestCase
     #--------------------------------------------------------------------------------------
     # 
     #--------------------------------------------------------------------------------------
-=begin
+
     should "create data-frame from a single vector" do
 
       vec = R.seq(20)
@@ -142,7 +142,6 @@ class SciComTest < Test::Unit::TestCase
       mtcars[R.c("mpg", "hp")].pp
 
     end
-=end
 
     #--------------------------------------------------------------------------------------
     # 
@@ -195,7 +194,6 @@ class SciComTest < Test::Unit::TestCase
     #--------------------------------------------------------------------------------------
 
     should "create data-frame from multiple vectors" do
-=begin
 
       # name     age  hgt  wgt  race year   SAT 
       # Bob       21   70  180  Cauc   Jr  1080
@@ -229,7 +227,7 @@ class SciComTest < Test::Unit::TestCase
       # variable rbvec.
       rbvec.print
 
-
+=begin
       # R.colnames(df) = R.c("name", "age", "height", "weigth", "race", "SAT")
       df.print
       summ = R.summary(df.r)
@@ -240,7 +238,6 @@ class SciComTest < Test::Unit::TestCase
       col = R.colnames(:df)
       col.print
 =end
-
     end
 
   end

data/test/test_double_receive.rb

@@ -36,10 +36,6 @@ class SciComTest < Test::Unit::TestCase
 
     setup do 
 
-      # creating two distinct instances of SciCom
-      @r1 = R.new
-      @r2 = R.new
-
     end
 
     #--------------------------------------------------------------------------------------

data/test/test_linear_model.rb

@@ -48,14 +48,14 @@ class SciComTest < Test::Unit::TestCase
         baseball = R.read__csv("baseball.csv")
         # Lets look at the data available for Momeyball.
         # (baseball.Year < R.d(2002)).pp
-        moneyball = R.subset(baseball, baseball.Year < 2002)
+        moneyball = baseball.subset(baseball.Year < 2002)
 
         # Let's see if we can predict the number of wins, by looking at
         # runs allowed (RA) and runs scored (RS).  RD is the runs difference.
         # We are making a linear model for predicting wins (W) based on RD
         moneyball.RD = moneyball.RS - moneyball.RA
         wins_reg = R.lm("W ~ RD", data: moneyball)
-        R.summary(wins_reg).pp
+        wins_reg.summary.pp
 
     end
 

data/test/test_matrix.rb

@@ -96,11 +96,11 @@ class SciComTest < Test::Unit::TestCase
       # from the digits 0-9. For the purpose of this demonstration, we will set the random 
       # number seed to a memorable number so that it will yield the same answer each time.
       R.set__seed(42)
-      xij = R.matrix(R.sample(R.seq(0, 9), 40, replace: TRUE), ncol: 4)
-
-      xij.fassign(:rownames, R.paste("S", R.seq(1, xij.attr.dim[1]), sep: ""))
-      xij.fassign(:colnames, R.paste("V", R.seq(1, xij.attr.dim[2]), sep: ""))
-      xij.pp
+      xij = R.seq(0,9).sample(40, replace: TRUE).matrix(ncol: 4)
+      xij
+        .fassign(:rownames, R.paste("S", R.seq(1, xij.attr.dim[1]), sep: ""))
+        .fassign(:colnames, R.paste("V", R.seq(1, xij.attr.dim[2]), sep: ""))
+        .pp
 
       # Just as we could with vectors, we can add, subtract, muliply or divide the matrix 
       # by a scaler (a number with out a dimension)
@@ -183,17 +183,13 @@ class SciComTest < Test::Unit::TestCase
       x_cov.diag.round(2).pp
 
       sdi = (1 / x_cov.diag.sqrt).diag
-      sdi.fassign(:rownames, x_cov.rownames)
-      sdi.fassign(:colnames, x_cov.colnames)
-      sdi.round(2).pp
+        .fassign(:rownames, x_cov.rownames)
+        .fassign(:colnames, x_cov.colnames)
+        .pp
 
       x_cor = (sdi._ :*, x_cov)._ :*, sdi
-      x_cor.fassign(:rownames, x_cov.rownames)
-      x_cor.fassign(:colnames, x_cov.colnames)
-      x_cor.round(2).pp
-
-      # use the cor function to find the correlation
-      xij.cor.round(2).pp
+        .fassign(:rownames, x_cov.rownames)
+        .fassign(:colnames, x_cov.colnames)
 
       assert_equal(true, (x_cor.round(2) == xij.cor.round(2)).all.gt)
 

data/version.rb

@@ -1,2 +1,2 @@
 $gem_name = "scicom"
-$version="0.2.2"
+$version="0.2.3"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: scicom
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
 platform: java
 authors:
 - Rodrigo Botafogo
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2014-11-19 00:00:00.000000000 Z
+date: 2014-12-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -113,23 +113,20 @@ files:
 - lib/JRubyR/list.rb
 - lib/JRubyR/vector.rb
 - lib/JRubyR/attributes.rb
-- lib/JRubyR/as_mdarray.rb
 - lib/JRubyR/logical_value.rb
-- lib/JRubyR/sequence.rb
 - lib/JRubyR/environment.rb
-- lib/JRubyR/list_orig.rb
 - lib/JRubyR/ruby_classes.rb
 - lib/JRubyR/function.rb
-- lib/JRubyR/index.rb
 - lib/JRubyR/rbsexp.rb
 - lib/JRubyR/renjin.rb
 - lib/JRubyR/dataframe.rb
 - test/env.rb
 - test/test_tmp.rb
+- test/test_assign_mdarray_2d.rb
 - test/test_attributes.rb
 - test/test_complete.rb
 - test/test_column-major.rb
-- test/test_double_assign.rb
+- test/test_assign_mdarray.rb
 - test/test_double_receive.rb
 - test/test_distribution.rb
 - test/test_creation.rb
@@ -146,6 +143,8 @@ files:
 - test/test_operators.rb
 - test/test_linear_model.rb
 - test/test_matrix.rb
+- test/test_assign_mdarray_3d.rb
+- test/test_assign_mdarray_4d.rb
 - test/test_dataframe.rb
 - test/test_list.rb
 - test/baseball.csv
@@ -185,10 +184,11 @@ summary: Scientific Computing for Ruby
 test_files:
 - test/env.rb
 - test/test_tmp.rb
+- test/test_assign_mdarray_2d.rb
 - test/test_attributes.rb
 - test/test_complete.rb
 - test/test_column-major.rb
-- test/test_double_assign.rb
+- test/test_assign_mdarray.rb
 - test/test_double_receive.rb
 - test/test_distribution.rb
 - test/test_creation.rb
@@ -205,5 +205,7 @@ test_files:
 - test/test_operators.rb
 - test/test_linear_model.rb
 - test/test_matrix.rb
+- test/test_assign_mdarray_3d.rb
+- test/test_assign_mdarray_4d.rb
 - test/test_dataframe.rb
 - test/test_list.rb

data/lib/JRubyR/as_mdarray.rb

@@ -1,60 +0,0 @@
-# -*- 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/index.rb

@@ -1,278 +0,0 @@
-# -*- 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