mdarray 0.4.3.pre-java → 0.5.0-java

data/lib/colt/probability.rb

@@ -0,0 +1,12 @@
+Returns the area from zero to x under the beta density function.
+                          x
+            -             -
+           | (a+b)       | |  a-1      b-1
+ P(x)  =  ----------     |   t    (1-t)    dt
+           -     -     | |
+          | (a) | (b)   -
+                         0
+ 
+This function is identical to the incomplete beta integral function 
+Gamma.incompleteBeta(a, b, x). The complemented function is 1 - P(1-x) = 
+Gamma.incompleteBeta( b, a, x );

data/lib/colt/stat_list.rb

@@ -0,0 +1,192 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation for educational, research, and 
+# not-for-profit purposes, 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. Contact Rodrigo
+# Botafogo - rodrigo.a.botafogo@gmail.com for commercial licensing opportunities.
+#
+# 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 'double_descriptive'
+
+##########################################################################################
+#
+##########################################################################################
+
+class StatList
+
+  attr_reader :array_list
+
+  #------------------------------------------------------------------------------------
+  # Appends the specified element to the end of this list.
+  #------------------------------------------------------------------------------------
+
+  def add(element)
+    @array_list.add(element)
+  end
+
+  #------------------------------------------------------------------------------------
+  # Inserts the specified element before the specified position into the receiver.
+  #------------------------------------------------------------------------------------
+
+  def before_insert(index, element)
+    @array_list.beforeInsert(index, element)
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def binary_search(key, from = 0, to = @array_list.size() - 1)
+    sorted_data.binarySearchFromTo(key, from, to)
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def copy
+    DoubleStatList.new(@array_list.copy)
+  end
+
+  #------------------------------------------------------------------------------------
+  # Returns the elements currently stored.  Trims the list to the maximum size.
+  #------------------------------------------------------------------------------------
+
+  def elements
+    @array_list.trimToSize
+    @array_list.elements().to_a
+  end
+
+  #------------------------------------------------------------------------------------
+  # Returns the element at the specified position in the receiver.
+  #------------------------------------------------------------------------------------
+
+  def get(index)
+    @array_list.get(index)
+  end
+
+  alias :[] :get
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def index_of(element, from = 0, to = @array_list.size() - 1)
+    @array_list.indexOfFromTo(element, from, to)
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def last_index_of(element, from = 0, to = @array_list.size() - 1)
+    @array_list.lastIndexOfFromTo(element, from, to)
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def reverse
+    @array_list.reverse()
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def set(index, element)
+    @array_list.set(index, element)
+  end
+
+  alias :[]= :set
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def shuffle(from = 0, to = @array_list.size() - 1)
+    @array_list.shuffleFromTo(from, to)
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def trim_to_size
+    @array_list.trimToSize()
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def print
+    puts @array_list.toString()
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def to_s
+    print
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  private
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def initialize(value = nil)
+    reset_statistics
+  end
+
+end
+
+
+##########################################################################################
+#
+##########################################################################################
+
+class DoubleStatList < StatList
+  include DDescriptive
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def initialize(value = nil)
+
+    super(value)
+
+    if (value == nil)
+      @array_list = Java::CernColtListTdouble::DoubleArrayList.new()
+    elsif (value.is_a? Integer)
+      @array_list = Java::CernColtListTdouble::DoubleArrayList.new(value)
+    else # Receiving a DoubleArrayList
+      @array_list = value
+    end
+
+  end
+
+end # StatList

data/lib/env.rb

@@ -3,5 +3,9 @@ require 'java'
 $CLASSPATH << "#{File.dirname(__FILE__)}/../vendor/"
 
 Dir["#{File.dirname(__FILE__)}/../vendor/*.jar"].each do |jar|
-   require jar
+  require jar
+end
+
+Dir["#{File.dirname(__FILE__)}/../target/*.jar"].each do |jar|
+  require jar
 end

data/lib/mdarray.rb

@@ -108,6 +108,8 @@ class MDArray
     @local_iterator = nil
     @section = section
     @coerced = false            # should never be set by the user! For internal use only!
+    @binary_operator = nil
+    @unary_operator = nil
 
     # initialize printing defaults
     printing_defaults
@@ -377,8 +379,11 @@ require_relative 'mdarray/function_creation'
 require_relative 'mdarray/ruby_functions'
 require_relative 'mdarray/operators'
 require_relative 'mdarray/ruby_operators'
+require_relative 'mdarray/fast_operators'
 require_relative 'mdarray/access'
 require_relative 'mdarray/views'
 require_relative 'mdarray/printing'
 require_relative 'mdarray/counter'
 require_relative 'mdarray/ruby_stats'
+require_relative 'mdarray/csv'
+require_relative 'colt/colt'

data/lib/mdarray/access.rb

@@ -103,8 +103,8 @@ class MDArray
   #---------------------------------------------------------------------------------------
   # When set is used to assign to an element, it is assumed that the index does not need
   # correction, for instance, no negative index is allowed.  If one wants to use 
-  # negative indexes, then method set should be used.  So mat[-1, 0, 0] = 10, raises an
-  # exection while mat.set([-1, 0, 0], 10) sets the last value for the first dimension.
+  # negative indexes, then method [] should be used.  So mat.set([-1, 0, 0], 10), raises 
+  # an exection while mat[-1, 0, 0] = 10 sets the last value for the first dimension.
   # *<tt>index</tt>: array with the index position
   # *<tt>value</tt>: value to be set
   #---------------------------------------------------------------------------------------

data/lib/mdarray/creation.rb

@@ -25,6 +25,13 @@
 
 class MDArray
 
+  class << self
+    
+    attr_accessor :binary_operator
+    attr_accessor :unary_operator
+
+  end
+
   #------------------------------------------------------------------------------------
   # Given two types returns the upcasted one
   #------------------------------------------------------------------------------------
@@ -42,28 +49,12 @@ class MDArray
   #
   #------------------------------------------------------------------------------------
 
-  def self.binary_operator=(operator)
-    @@binary_operator = operator
-  end
-
-  def self.binary_operator
-    @@binary_operator
-  end
-
-  def self.unary_operator=(operator)
-    @@unary_operator = operator
-  end
-
-  def self.unary_operator
-    @@unary_operator
-  end
-
   def get_binary_op
-    (@binary_operator)? @binary_operator : @@binary_operator
+    (@binary_operator)? @binary_operator : MDArray.binary_operator
   end
 
   def get_unary_op
-    (@unary_operator)? @unary_operator : @@unary_operator
+    (@unary_operator)? @unary_operator : MDArray.unary_operator
   end
 
   # Factory Methods
@@ -77,7 +68,17 @@ class MDArray
   #------------------------------------------------------------------------------------
 
   def self.build(type, shape, storage = nil)
-    
+
+    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
+
     dtype = DataType.valueOf(type.upcase)
     jshape = shape.to_java :int
 
@@ -93,6 +94,20 @@ class MDArray
 
   end
 
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def self.build_from_nc_array(type, nc_array, section = false)
+    klass = Object.const_get("#{type.capitalize}MDArray")
+    return klass.new(type, nc_array, section)
+  end
+
   #------------------------------------------------------------------------------------
   # Builds a boolean mdarray
   # @param shape [Array] the shape of the mdarray as a ruby array

data/lib/mdarray/csv.rb

@@ -0,0 +1,61 @@
+require 'csv'
+require 'date'
+
+class Csv
+
+  attr_reader :col_sep
+  attr_reader :row_sep
+  attr_reader :quote_char
+
+  @epoch = Date.new(1970, 1, 1)
+
+  class << self
+    attr_reader :epoch
+  end
+
+  #------------------------------------------------------------------------------------
+  #
+  #------------------------------------------------------------------------------------
+
+  def self.read_numeric(filename, headers = false)
+
+    buffer = Array.new
+    lines = 0
+    columns = nil
+
+    CSV.foreach(filename,  
+                {return_headers: false, 
+                  # headers: true,
+                  converters: [:numeric, :date]} ) do |row|
+
+      if (headers)
+        headers = false
+        next
+      end
+
+      columns ||= row.size
+      lines += 1
+
+      row.each do |data|
+
+        if (row.size != columns)
+          raise "Data does not have the same number of columns for all lines"
+        end
+
+        # if it is a Date, then convert it to seconds since epoch
+        if (data.is_a? Date)
+          buffer << data.to_time.to_i
+        end
+
+        if (data.is_a? Numeric)
+          buffer << data
+        end
+      end
+
+    end
+
+    [lines, columns, buffer]
+
+  end
+
+end # Csv

data/lib/mdarray/fast_operators.rb

@@ -0,0 +1,241 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation for educational, research, and 
+# not-for-profit purposes, 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. Contact Rodrigo
+# Botafogo - rodrigo.a.botafogo@gmail.com for commercial licensing opportunities.
+#
+# 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 FastBinaryOperator < BinaryOperator
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def get_args(*args)
+
+    parse_args(*args)
+
+    if (@op1.is_a? NumericalMDArray)
+      if (@op2.is_a? Numeric)
+        arg2 = @op2
+      elsif (@op2.is_a? NumericalMDArray)
+        if (!@op1.compatible(@op2))
+          raise "Invalid operation - arrays are incompatible"
+        end
+        arg2 = @op2.nc_array
+      else # Operation with another user defined type
+        false
+        # *TODO: make it more general using coerce if other_val type is not recognized
+        # if (arg is not recognized)
+        #  self_equiv, arg_equiv = arg.coerce(self)
+        #  self_equiv * arg_equiv
+        # end
+      end
+      
+    else  # NonNumericalMDArray
+      if (!@op1.compatible(@op2))
+        raise "Invalid operation - arrays are incompatible"
+      end
+
+      # Will not work if we have subclasses!!!!
+      if (@op1.class != @op2.class)
+        raise "Invalid operation - array are not of compatible types"
+      end
+
+      arg2 = @op2.nc_array
+    end
+
+    yield @op1.nc_array, arg2, @op1.shape, *args
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def default(*args)
+
+    calc = nil
+    get_args(*args) do |op1, op2, shape, *other_args|
+      calc = MDArray.build(@type, shape)
+      if (@coerced)
+        helper = Java::RbMdarrayLoopsBinops::CoerceBinaryOperator
+        helper.send("apply", calc.nc_array, op1, op2, @do_func)
+      elsif (@op1.is_a? NumericalMDArray)
+        helper = Java::RbMdarrayLoopsBinops::DefaultBinaryOperator
+        helper.send("apply", calc.nc_array, op1, op2, @do_func)
+      else
+        helper = Java::RbMdarrayLoopsBinops::DefaultBinaryOperator
+        helper.send("apply#{@op1.class}", calc.nc_array, op1, op2, @do_func)
+      end
+    end
+    return calc
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def fill(*args)
+
+    get_args(*args) do |op1, op2, shape, *other_args|
+      helper = Java::RbMdarrayLoopsBinops::FillBinaryOperator
+      helper.send("apply", op1, op2)
+    end
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def in_place(*args)
+
+    get_args(*args) do |op1, op2, shape, *other_args|
+      helper = Java::RbMdarrayLoopsBinops::InplaceBinaryOperator
+      helper.send("apply", op1, op2, @do_func)
+    end
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def reduce(*args)
+
+    calc = nil
+
+    get_args(*args) do |op1, op2, shape, *other_args|
+      helper = Java::RbMdarrayLoopsBinops::ReduceBinaryOperator
+      calc = @pre_condition_result
+      calc = helper.send("apply", calc, op1, op2, @do_func)
+    end
+
+    return calc
+
+  end
+  
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def complex_reduce(*args)
+
+    calc = nil
+
+    get_args(*args) do |op1, op2, shape, *other_args|
+      helper = Java::RbMdarrayLoopsBinops::ComplexReduceBinaryOperator
+      calc = @pre_condition_result
+      calc = helper.send("apply", calc, op1, op2, @do_func)
+    end
+
+    return calc
+
+  end
+
+end # FastBinaryOperator
+
+##########################################################################################
+#
+##########################################################################################
+
+class FastUnaryOperator < UnaryOperator
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def get_args(*args)
+
+    parse_args(*args)
+    yield @op.nc_array, @op.shape, *@other_args
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def set_block(*args)
+
+    get_args(*args) do |op1, shape, *other_args|
+      block = other_args[0]
+      helper = Java::RbMdarrayLoopsUnops::SetAll
+      func = (shape.size <= 7)? "apply#{shape.size}" : "apply"
+      helper.send(func, op1, &block) if block
+    end
+    
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def default(*args)
+    
+    calc = nil
+    get_args(*args) do |op1, shape, *other_args|
+      calc = MDArray.build(@type, shape)
+      helper = Java::RbMdarrayLoopsUnops::DefaultUnaryOperator
+      helper.send("apply", calc.nc_array, op1, @do_func)
+    end
+    return calc
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def in_place(*args)
+
+    get_args(*args) do |op1, shape, *other_args|
+      helper = Java::RbMdarrayLoopsUnops::InplaceUnaryOperator
+      helper.send("apply", op1, @do_func)
+    end
+
+  end
+
+  #---------------------------------------------------------------------------------------
+  #
+  #---------------------------------------------------------------------------------------
+
+  def reduce(*args)
+
+    calc = nil
+
+    get_args(*args) do |op1, shape, *other_args|
+      helper = Java::RbMdarrayLoopsUnops::ReduceUnaryOperator
+      calc = @pre_condition_result
+      calc = helper.send("apply", calc, op1, @do_func)
+    end
+
+    return calc
+
+  end
+  
+end # UnaryOperator
+
+MDArray.binary_operator = FastBinaryOperator
+MDArray.unary_operator = FastUnaryOperator