mdarray 0.5.4-java → 0.5.5-java

data/lib/colt/matrix/creation.rb

@@ -0,0 +1,374 @@
+# -*- 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 'java'
+
+class MDMatrix
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.build(type, shape, storage = nil)
+    if (shape.size > 3)
+      raise "Cannot create MDMatrix of size greater than 3"
+    end
+    self.from_mdarray(MDArray.build(type, shape, storage))
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.double(shape, storage = nil)
+    self.build("double", shape, storage)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.float(shape, storage = nil)
+    self.build("float", shape, storage)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.long(shape, storage = nil)
+    self.build("long", shape, storage)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.int(shape, storage = nil)
+    self.build("int", shape, storage)
+  end
+
+  #------------------------------------------------------------------------------------
+  # Creates a MDMatrix from an MDArray.
+  # (int rows, int columns, double[] elements, int rowZero, int columnZero, 
+  # int rowStride, int columnStride, boolean isView)
+  #------------------------------------------------------------------------------------
+
+  def self.from_mdarray(mdarray)
+
+    case mdarray.rank
+
+    when 1
+      dense1D(mdarray)
+    when 2
+      dense2D(mdarray)
+    when 3
+      dense3D(mdarray)
+    else
+      raise "Cannot create MDMatrix of rank greater than 3"
+    end
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # Creates a new MDMatrix from a given colt_matrix
+  #------------------------------------------------------------------------------------
+
+  def self.from_colt_matrix(colt_matrix)
+
+    if (colt_matrix.is_a? DenseDoubleMatrix3D)
+      mdarray = MDArray.from_jstorage("double", 
+                                      [colt_matrix.slices, colt_matrix.rows, 
+                                       colt_matrix.columns], colt_matrix.elements)
+      return DoubleMDMatrix3D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseFloatMatrix3D)
+      mdarray = MDArray.from_jstorage("float", 
+                                      [colt_matrix.slices, colt_matrix.rows, 
+                                       colt_matrix.columns], colt_matrix.elements)
+      return FloatMDMatrix3D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseLongMatrix3D)
+      mdarray = MDArray.from_jstorage("long", 
+                                      [colt_matrix.slices, colt_matrix.rows, 
+                                       colt_matrix.columns], colt_matrix.elements)
+      return LongMDMatrix3D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseIntMatrix3D)
+      mdarray = MDArray.from_jstorage("int", 
+                                      [colt_matrix.slices, colt_matrix.rows, 
+                                       colt_matrix.columns], colt_matrix.elements)
+      return IntMDMatrix3D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseDoubleMatrix2D)
+      mdarray = MDArray.from_jstorage("double", [colt_matrix.rows, colt_matrix.columns], 
+                                      colt_matrix.elements)
+      return DoubleMDMatrix2D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseFloatMatrix2D)
+      mdarray = MDArray.from_jstorage("float", [colt_matrix.rows, colt_matrix.columns], 
+                                      colt_matrix.elements)
+      return FloatMDMatrix2D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseLongMatrix2D)
+      mdarray = MDArray.from_jstorage("long", [colt_matrix.rows, colt_matrix.columns], 
+                                      colt_matrix.elements)
+      return LongMDMatrix2D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseIntMatrix2D)
+      mdarray = MDArray.from_jstorage("int", [colt_matrix.rows, colt_matrix.columns], 
+                                      colt_matrix.elements)
+      return IntMDMatrix2D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseDoubleMatrix1D)
+      mdarray = MDArray.from_jstorage("double", [colt_matrix.size], colt_matrix.elements)
+      return DoubleMDMatrix1D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseFloatMatrix1D)
+      mdarray = MDArray.from_jstorage("float", [colt_matrix.size], colt_matrix.elements)
+      return FloatMDMatrix1D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseLongMatrix1D)
+      mdarray = MDArray.from_jstorage("long", [colt_matrix.size], colt_matrix.elements)
+      return LongMDMatrix1D.from_mdarray(mdarray)
+    elsif (colt_matrix.is_a? DenseIntMatrix1D)
+      mdarray = MDArray.from_jstorage("int", [colt_matrix.size], colt_matrix.elements)
+      return IntMDMatrix1D.from_mdarray(mdarray)
+    end
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.fromfunction(type, shape, &block)
+
+    mdarray = MDArray.fromfunction(type, shape, &block)
+    MDMatrix.from_mdarray(mdarray)
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.init_with(type, shape, value)
+    mdarray = MDArray.init_with(type, shape, value)
+    MDMatrix.from_mdarray(mdarray)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.arange(*args)
+    mdarray = MDArray.arange(*args)
+    MDMatrix.from_mdarray(mdarray)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.typed_arange(type, *args)
+    mdarray = MDArray.typed_arange(type, *args)
+    MDMatrix.from_mdarray(mdarray)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.linspace(type, start, stop, number)
+    mdarray = MDArray.linspace(type, start, stop, number)
+    MDMatrix.from_mdarray(mdarray)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.ones(type, shape)
+    mdarray = MDArray.ones(type, shape)
+    MDMatrix.from_mdarray(mdarray)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def copy
+    MDMatrix.from_mdarray(self.mdarray.copy)
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  private
+
+  #------------------------------------------------------------------------------------
+  # Only Floating Matrices have algebra.  Long and Int matrices do not have algebra.
+  #------------------------------------------------------------------------------------
+  
+  def initialize(mdarray, colt_matrix, colt_property, colt_algebra = nil)
+    @mdarray = mdarray
+    @colt_matrix = colt_matrix
+    @colt_property = colt_property
+    @colt_algebra = colt_algebra
+    @rank = @mdarray.rank
+    @coerced = false                # should never be changed by any client
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.dense1D(mdarray)
+
+    storage = mdarray.nc_array.getStorage()
+    index = mdarray.nc_array.getIndex()
+    size = index.size
+
+    klass = index.getClass
+    field = klass.getDeclaredField("stride0")
+    field.setAccessible true
+    stride0 = field.get(index)
+    # p stride0
+
+    klass = klass.getSuperclass()
+    field = klass.getDeclaredField("offset")
+    field.setAccessible true
+    offset = field.get(index)
+    # p offset
+
+    case mdarray.type
+    when "double"
+      colt_matrix = DenseDoubleMatrix1D.new(size, storage, offset, stride0, false)
+      DoubleMDMatrix1D.new(mdarray, colt_matrix)
+    when "float"
+      colt_matrix = DenseFloatMatrix1D.new(size, storage, offset, stride0, false)
+      FloatMDMatrix1D.new(mdarray, colt_matrix)
+    when "long"
+      colt_matrix = DenseLongMatrix1D.new(size, storage, offset, stride0, false)
+      LongMDMatrix1D.new(mdarray, colt_matrix)
+    when "int"
+      colt_matrix = DenseIntMatrix1D.new(size, storage, offset, stride0, false)
+      IntMDMatrix1D.new(mdarray, colt_matrix)
+    end
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.dense2D(mdarray)
+
+    storage = mdarray.nc_array.getStorage()
+    index = mdarray.nc_array.getIndex()
+    shape = index.getShape()
+
+    klass = index.getClass
+    field = klass.getDeclaredField("stride0")
+    field.setAccessible true
+    stride0 = field.get(index)
+    # p stride0
+
+    field = klass.getDeclaredField("stride1")
+    field.setAccessible true
+    stride1 = field.get(index)
+    # p stride1
+
+    klass = klass.getSuperclass()
+    field = klass.getDeclaredField("offset")
+    field.setAccessible true
+    offset = field.get(index)
+    # p offset
+
+    case mdarray.type
+    when "double"
+      colt_matrix = DenseDoubleMatrix2D.new(shape[0], shape[1], storage, offset, 0, 
+                                            stride0, stride1, false)
+      DoubleMDMatrix2D.new(mdarray, colt_matrix)
+    when "float"
+      colt_matrix = DenseFloatMatrix2D.new(shape[0], shape[1], storage, offset, 0, 
+                                           stride0, stride1, false)
+      FloatMDMatrix2D.new(mdarray, colt_matrix)
+    when "long"
+      colt_matrix = DenseLongMatrix2D.new(shape[0], shape[1], storage, offset, 0, 
+                                          stride0, stride1, false)
+      LongMDMatrix2D.new(mdarray, colt_matrix)
+    when "int"
+      colt_matrix = DenseIntMatrix2D.new(shape[0], shape[1], storage, offset, 0, 
+                                         stride0, stride1, false)
+      IntMDMatrix2D.new(mdarray, colt_matrix)
+    end
+
+  end
+
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
+
+  def self.dense3D(mdarray)
+
+    storage = mdarray.nc_array.getStorage()
+    index = mdarray.nc_array.getIndex()
+    shape = index.getShape()
+
+    klass = index.getClass
+    field = klass.getDeclaredField("stride0")
+    field.setAccessible true
+    stride0 = field.get(index)
+    # p stride0
+
+    field = klass.getDeclaredField("stride1")
+    field.setAccessible true
+    stride1 = field.get(index)
+    # p stride1
+
+    field = klass.getDeclaredField("stride2")
+    field.setAccessible true
+    stride2 = field.get(index)
+    # p stride2
+
+    klass = klass.getSuperclass()
+    field = klass.getDeclaredField("offset")
+    field.setAccessible true
+    offset = field.get(index)
+    # p offset
+
+    case mdarray.type
+    when "double"
+      colt_matrix = DenseDoubleMatrix3D.new(shape[0], shape[1], shape[2], storage, 
+                                            offset, 0, 0, stride0, stride1, stride2, false)
+      DoubleMDMatrix3D.new(mdarray, colt_matrix)
+    when "float"
+      colt_matrix = DenseFloatMatrix3D.new(shape[0], shape[1], shape[2], storage, 
+                                           offset, 0, 0, stride0, stride1, stride2, false)
+      FloatMDMatrix3D.new(mdarray, colt_matrix)
+    when "long"
+      colt_matrix = DenseLongMatrix3D.new(shape[0], shape[1], shape[2], storage, 
+                                          offset, 0, 0, stride0, stride1, stride2, false)
+      LongMDMatrix3D.new(mdarray, colt_matrix)
+    when "int"
+      colt_matrix = DenseIntMatrix3D.new(shape[0], shape[1], shape[2], storage, 
+                                         offset, 0, 0, stride0, stride1, stride2, false)
+      IntMDMatrix3D.new(mdarray, colt_matrix)
+    end
+
+  end
+
+end # MDMatrix
+

data/lib/colt/matrix/{matrix_hierarchy.rb → hierarchy.rb}

@@ -20,146 +20,144 @@
 # OR MODIFICATIONS.
 ##########################################################################################
 
-
 ##########################################################################################
-# Floating point 1D Matrices
+# Floating point Matrices
 ##########################################################################################
 
-class FloatingMDMatrix1D < MDMatrix
-
-end # FloatingMDMatrix1D
+class FloatingMDMatrix < MDMatrix
 
-##########################################################################################
-#
-##########################################################################################
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
 
-class DoubleMDMatrix1D < FloatingMDMatrix1D
-  include_package "cern.colt.matrix.tdouble.algo"
+  private
 
   #------------------------------------------------------------------------------------
   # 
   #------------------------------------------------------------------------------------
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-    @algebra = DenseDoubleAlgebra.new
+  def initialize(mdarray, colt_matrix, algebra)
+    super(mdarray, colt_matrix, algebra.property(), algebra)
   end
 
-end # DoubleMDMatrix1D
+end
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class FloatMDMatrix1D < FloatingMDMatrix1D
-  include_package "cern.colt.matrix.tfloat.algo"
+class DoubleMDMatrix < FloatingMDMatrix
+  include_package "cern.colt.matrix.tdouble.algo"
 
   #------------------------------------------------------------------------------------
   # 
   #------------------------------------------------------------------------------------
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-    @algebra = DenseFloatAlgebra.new
+  def initialize(mdarray, colt_matrix, tolerance = nil)
+    super(mdarray, colt_matrix, DenseDoubleAlgebra.new)
   end
 
-end # FloatMDMatrix1D
+end # DoubleMDMatrix
+
+##########################################################################################
+#
+##########################################################################################
 
+class DoubleMDMatrix1D < DoubleMDMatrix
 
+end # DoubleMDMatrix1D
 
 ##########################################################################################
-# Floating point 2D Matrices
+#
 ##########################################################################################
 
-class FloatingMDMatrix2D < MDMatrix
+class DoubleMDMatrix2D < DoubleMDMatrix
 
-end # FloatingMDMatrix2D
+end # DoubleMDMatrix2D
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class DoubleMDMatrix2D < FloatingMDMatrix2D
-  include_package "cern.colt.matrix.tdouble.algo"
+class DoubleMDMatrix3D < DoubleMDMatrix
 
-  #------------------------------------------------------------------------------------
-  # 
-  #------------------------------------------------------------------------------------
+end # DoubleMDMatrix3D
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-    @algebra = DenseDoubleAlgebra.new
-  end
 
-end # DoubleMDMatrix
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class FloatMDMatrix2D < FloatingMDMatrix2D
+class FloatMDMatrix < FloatingMDMatrix
   include_package "cern.colt.matrix.tfloat.algo"
 
   #------------------------------------------------------------------------------------
   # 
   #------------------------------------------------------------------------------------
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-    @algebra = DenseFloatAlgebra.new
+  def initialize(mdarray, colt_matrix, tolerance = nil)
+    super(mdarray, colt_matrix, DenseFloatAlgebra.new)
   end
 
 end # FloatMDMatrix
 
+##########################################################################################
+#
+##########################################################################################
 
+class FloatMDMatrix1D < FloatMDMatrix
 
+end # FloatMDMatrix1D
 
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class DoubleMDMatrix3D < MDMatrix
-  include_package "cern.colt.matrix.tdouble.algo"
-
-  #------------------------------------------------------------------------------------
-  # 
-  #------------------------------------------------------------------------------------
+class FloatMDMatrix2D < FloatMDMatrix
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-    @algebra = DenseDoubleAlgebra.new
-  end
+end # FloatMDMatrix2D
 
-end # DoubleMDMatrix
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class FloatMDMatrix3D < MDMatrix
-  include_package "cern.colt.matrix.tfloat.algo"
+class FloatMDMatrix3D < FloatMDMatrix
+
+end # FloatMDMatrix3D
+
+
+
+##########################################################################################
+# Floating point Matrices
+##########################################################################################
+
+class FixPointMDMatrix < MDMatrix
 
   #------------------------------------------------------------------------------------
   # 
   #------------------------------------------------------------------------------------
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-    @algebra = DenseFloatAlgebra.new
-  end
-
-end # FloatMDMatrix
+  private
 
+  #------------------------------------------------------------------------------------
+  # 
+  #------------------------------------------------------------------------------------
 
+  def initialize(mdarray, colt_matrix, property)
+    super(mdarray, colt_matrix, property)
+  end
 
+end # FixPointMDMatrix
 
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class LongMDMatrix1D < MDMatrix
+class LongMDMatrix < FixPointMDMatrix
   include_package "cern.colt.matrix.tlong.algo"
 
   #------------------------------------------------------------------------------------
@@ -167,7 +165,7 @@ class LongMDMatrix1D < MDMatrix
   #------------------------------------------------------------------------------------
 
   def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
+    super(mdarray, colt_matrix, LongProperty.new)
   end
 
 end # LongMDMatrix
@@ -176,41 +174,32 @@ end # LongMDMatrix
 #
 ##########################################################################################
 
-class LongMDMatrix2D < MDMatrix
-  include_package "cern.colt.matrix.tlong.algo"
+class LongMDMatrix1D < LongMDMatrix
 
-  #------------------------------------------------------------------------------------
-  # 
-  #------------------------------------------------------------------------------------
+end # LongMDMatrix1D
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-  end
+##########################################################################################
+#
+##########################################################################################
 
-end # LongMDMatrix
+class LongMDMatrix2D < LongMDMatrix
+
+end # LongMDMatrix2D
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class LongMDMatrix3D < MDMatrix
-  include_package "cern.colt.matrix.tlong.algo"
-
-  #------------------------------------------------------------------------------------
-  # 
-  #------------------------------------------------------------------------------------
+class LongMDMatrix3D < LongMDMatrix
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-  end
+end # LongMDMatrix3D
 
-end # LongMDMatrix
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class IntMDMatrix1D < MDMatrix
+class IntMDMatrix < FixPointMDMatrix
   include_package "cern.colt.matrix.tint.algo"
 
   #------------------------------------------------------------------------------------
@@ -218,7 +207,7 @@ class IntMDMatrix1D < MDMatrix
   #------------------------------------------------------------------------------------
 
   def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
+    super(mdarray, colt_matrix, IntProperty.new)
   end
 
 end # IntMDMatrix
@@ -227,32 +216,22 @@ end # IntMDMatrix
 #
 ##########################################################################################
 
-class IntMDMatrix2D < MDMatrix
-  include_package "cern.colt.matrix.tint.algo"
-
-  #------------------------------------------------------------------------------------
-  # 
-  #------------------------------------------------------------------------------------
-
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-  end
+class IntMDMatrix1D < IntMDMatrix
 
-end # IntMDMatrix
+end # IntMDMatrix1D
 
 ##########################################################################################
 #
 ##########################################################################################
 
-class IntMDMatrix3D < MDMatrix
-  include_package "cern.colt.matrix.tint.algo"
+class IntMDMatrix2D < IntMDMatrix
 
-  #------------------------------------------------------------------------------------
-  # 
-  #------------------------------------------------------------------------------------
+end # IntMDMatrix2D
 
-  def initialize(mdarray, colt_matrix)
-    super(mdarray, colt_matrix)
-  end
+##########################################################################################
+#
+##########################################################################################
 
-end # IntMDMatrix
+class IntMDMatrix3D < IntMDMatrix
+
+end # IntMDMatrix3D