nmatrix 0.0.9 → 0.1.0.rc1

data/lib/nmatrix/nvector.rb

@@ -9,8 +9,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
-# NMatrix is Copyright (c) 2013, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #
@@ -159,68 +159,6 @@ class NVector < NMatrix
     min_so_far
   end
 
-  #
-  # call-seq:
-  #     absolute_sum -> Numeric
-  #
-  # == Arguments
-  #   - +incx+ -> the skip size (defaults to 1, no skip)
-  #   - +n+ -> the number of elements to include
-  #
-  # Return the sum of the contents of the vector. This is the BLAS asum routine.
-  def asum incx=1, n=nil
-    NMatrix::BLAS::asum(self, incx, self.size / incx)
-  end
-  alias :absolute_sum :asum
-
-  #
-  # call-seq:
-  #     norm2 -> Numeric
-  #
-  # == Arguments
-  #   - +incx+ -> the skip size (defaults to 1, no skip)
-  #   - +n+ -> the number of elements to include
-  #
-  # Return the 2-norm of the vector. This is the BLAS nrm2 routine.
-  def nrm2 incx=1, n=nil
-    NMatrix::BLAS::nrm2(self, incx, self.size / incx)
-  end
-  alias :norm2 :nrm2
-
-
-  #
-  # call-seq:
-  #     sorted_indices -> Array
-  #
-  # Returns an array of the indices ordered by value sorted.
-  #
-  def sorted_indices
-    ary = self.to_a
-    ary.each_index.sort_by { |i| ary[i] }  # from: http://stackoverflow.com/a/17841159/170300
-  end
-
-  #
-  # call-seq:
-  #     binned_sorted_indices -> Array
-  #
-  # Returns an array of arrays of indices ordered by value sorted. Functions basically like +sorted_indices+, but
-  # groups indices together for those values that are the same.
-  #
-  def binned_sorted_indices
-    ary = self.to_a
-    ary2 = []
-    last_bin = ary.each_index.sort_by { |i| [ary[i]] }.inject([]) do |result, element|
-      if result.empty? || ary[result[-1]] == ary[element]
-        result << element
-      else
-        ary2 << result
-        [element]
-      end
-    end
-    ary2 << last_bin unless last_bin.empty?
-    ary2
-  end
-
 
   # TODO: Make this actually pretty.
   def pretty_print(q = nil) #:nodoc:

data/lib/nmatrix/rspec.rb

@@ -8,8 +8,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-# NMatrix is Copyright (c) 2012, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #

data/lib/nmatrix/shortcuts.rb

@@ -9,8 +9,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
-# NMatrix is Copyright (c) 2013, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #
@@ -295,6 +295,14 @@ class NMatrix
     # call-seq:
     #     seq(shape) -> NMatrix
     #     seq(shape, options) -> NMatrix
+    #     bindgen(shape) -> NMatrix of :byte
+    #     indgen(shape) -> NMatrix of :int64
+    #     findgen(shape) -> NMatrix of :float32
+    #     dindgen(shape) -> NMatrix of :float64
+    #     cindgen(shape) -> NMatrix of :complex64
+    #     zindgen(shape) -> NMatrix of :complex128
+    #     rindgen(shape) -> NMatrix of :rational128
+    #     rbindgen(shape) -> NMatrix of :object
     #
     # Creates a matrix filled with a sequence of integers starting at zero.
     #
@@ -322,66 +330,11 @@ class NMatrix
       NMatrix.new(shape, values, {:stype => :dense}.merge(options))
     end
 
-    #
-    # call-seq:
-    #     indgen(size) -> NMatrix
-    #
-    # Returns an integer NMatrix. Equivalent to <tt>seq(n, dtype: :int32)</tt>.
-    #
-    # * *Arguments* :
-    #   - +shape+ -> Shape of the sequence.
-    # * *Returns* :
-    #   - NMatrix with dtype +:int32+.
-    #
-    def indgen(shape)
-      NMatrix.seq(shape, dtype: :int32)
-    end
-
-    #
-    # call-seq:
-    #     findgen(shape) -> NMatrix
-    #
-    # Returns a float NMatrix. Equivalent to <tt>seq(n, dtype: :float32)</tt>.
-    #
-    # * *Arguments* :
-    #   - +shape+ -> Shape of the sequence.
-    # * *Returns* :
-    #   - NMatrix with dtype +:float32+.
-    #
-    def findgen(shape)
-      NMatrix.seq(shape, dtype: :float32)
+    {:bindgen => :byte, :indgen => :int64, :findgen => :float32, :dindgen => :float64,
+     :cindgen => :complex64, :zindgen => :complex128,
+     :rindgen => :rational128, :rbindgen => :object}.each_pair do |meth, dtype|
+      define_method(meth) { |shape| NMatrix.seq(shape, :dtype => dtype) }
     end
-
-    #
-    # call-seq:
-    #     bindgen(size) -> NMatrix
-    #
-    # Returns a byte NMatrix. Equivalent to <tt>seq(n, dtype: :byte)</tt>.
-    #
-    # * *Arguments* :
-    #   - +size+ -> Shape of the sequence.
-    # * *Returns* :
-    #   - NMatrix with dtype +:byte+.
-    #
-    def bindgen(shape)
-      NMatrix.seq(shape, dtype: :byte)
-    end
-
-    #
-    # call-seq:
-    #     cindgen(shape) -> NMatrix
-    #
-    # Returns a complex NMatrix. Equivalent to <tt>seq(n, dtype: :complex64)</tt>.
-    #
-    # * *Arguments* :
-    #   - +shape+ -> Shape of the sequence.
-    # * *Returns* :
-    #   - NMatrix with dtype +:complex64+.
-    #
-    def cindgen(shape)
-      NMatrix.seq(shape, dtype: :complex64)
-    end
-
   end
 end
 

data/lib/nmatrix/version.rb

@@ -9,8 +9,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
-# NMatrix is Copyright (c) 2013, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #
@@ -26,6 +26,14 @@ class NMatrix
   # Note that the format of the VERSION string is needed for NMatrix
   # native IO. If you change the format, please make sure that native
   # IO can still understand NMatrix::VERSION.
-  VERSION = "0.0.9"
+  #VERSION = "0.1.0"
+  module VERSION
+    MAJOR = 0
+    MINOR = 1
+    TINY = 0
+    PRE = "rc1"
+
+    STRING = [MAJOR, MINOR, TINY, PRE].compact.join(".")
+  end
 end
 

data/lib/nmatrix/yale_functions.rb

@@ -9,8 +9,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2013, Ruby Science Foundation
-# NMatrix is Copyright (c) 2013, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #
@@ -81,7 +81,7 @@ module NMatrix::YaleFunctions
   # Returns the diagonal and non-digonal column indices stored in a given row.
   def yale_ja_d_keys_at i
     ary = yale_nd_row(i, :keys)
-    return ary if i >= self.shape[1] || self[i,i].nil? || self[i,i] == 0
+    return ary if i >= self.shape[1] || self[i,i] == self.default_value
     ary << i
   end
   alias :yale_row_as_array :yale_ja_d_keys_at
@@ -112,7 +112,7 @@ module NMatrix::YaleFunctions
   # Returns the diagonal and non-diagonal column indices and entries stored in a given row.
   def yale_row_as_hash i
     h = yale_nd_row(i, :hash)
-    return h if i >= self.shape[1] || self[i,i].nil? || self[i,i] == 0
+    return h if i >= self.shape[1] || self[i,i] == self.default_value
     h[i] = self[i,i]
   end
 end

data/nmatrix.gemspec

@@ -5,22 +5,17 @@ require 'nmatrix/version'
 
 Gem::Specification.new do |gem|
   gem.name = "nmatrix"
-  gem.version = NMatrix::VERSION
+  gem.version = NMatrix::VERSION::STRING
   gem.summary = "NMatrix is an experimental linear algebra library for Ruby, written mostly in C." 
   gem.description = "NMatrix is an experimental linear algebra library for Ruby, written mostly in C." 
   gem.homepage = 'http://sciruby.com'
   gem.authors = ['John Woods', 'Chris Wailes', 'Aleksey Timin']
   gem.email =  ['john.o.woods@gmail.com']
+  gem.license = 'BSD 2-clause'
   gem.post_install_message = <<-EOF
 ***********************************************************
 Welcome to SciRuby: Tools for Scientific Computing in Ruby!
 
-                     *** WARNING ***
-Please be aware that NMatrix is in ALPHA status. If you're
-thinking of using NMatrix to write mission critical code,
-such as for driving a car or flying a space shuttle, you
-may wish to choose other software (for now).
-
 NMatrix requires a C compiler, and has been tested only
 with GCC 4.6+. We are happy to accept contributions
 which improve the portability of this project.

data/scripts/mac-brew-gcc.sh

@@ -1,5 +1,9 @@
 #!/bin/bash
-VERSION="4.7.2"
+
+# Script will not work for GCC 4.8 or 4.9. For those, please see
+# mac-mavericks-brew-gcc.sh
+
+VERSION="4.7.2" # Script should also work with GCC 4.7.1.
 PREFIX="/usr/gcc-${VERSION}"
 LANGUAGES="c,c++,fortran"
 MAKE="make -j 4"
@@ -8,11 +12,9 @@ brew-path() { brew info $1 | head -n3 | tail -n1 | cut -d' ' -f1; }
 
 # Prerequisites
 
-brew install gmp
-brew install mpfr
-brew install libmpc
+brew install gmp mpfr libmpc
 
-# Download & install the latest GCC
+# Next, download & install the latest GCC:
 
 mkdir -p $PREFIX
 mkdir temp-gcc
@@ -25,11 +27,12 @@ cd gcc-$VERSION
 mkdir build
 cd build
 
+# Older versions of brew need brew-path instead of brew --prefix.
 ../configure \
      --prefix=$PREFIX \
-     --with-gmp=$(brew-path gmp) \
-     --with-mpfr=$(brew-path mpfr) \
-     --with-mpc=$(brew-path libmpc) \
+     --with-gmp=$(brew --prefix gmp) \
+     --with-mpfr=$(brew --prefix mpfr) \
+     --with-mpc=$(brew --prefix libmpc) \
      --program-suffix=-$VERSION \
      --enable-languages=$LANGUAGES \
      --with-system-zlib \

data/scripts/mac-mavericks-brew-gcc.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+brew-path() { brew info $1 | head -n3 | tail -n1 | cut -d' ' -f1; }
+
+# Try using the following for GCC 4.9:
+#
+#   brew install gmp4 mpfr2 libmpc08 isl011 cloog018
+#
+#
+
+brew install gcc49 --enable-fortran
+# Source for this is: http://stackoverflow.com/questions/19535422/os-x-10-9-gcc-links-to-clang
+
+
+# You may wish to re-install your Ruby if you're using rbenv. To do
+# so, make sure you've installed openssl, readline, and libyaml.
+#
+# The commands for this are:
+#
+#    CC=gcc-4.8 RUBY_CONFIGURE_OPTS="--with-openssl-dir=`brew --prefix openssl` --with-readline-dir=`brew --prefix readline` --with-gcc=gcc-4.8 --enable-shared" rbenv install --keep 2.0.0-p247
+#
+#

data/spec/00_nmatrix_spec.rb

@@ -8,8 +8,8 @@
 #
 # == Copyright Information
 #
-# SciRuby is Copyright (c) 2010 - 2012, Ruby Science Foundation
-# NMatrix is Copyright (c) 2012, Ruby Science Foundation
+# SciRuby is Copyright (c) 2010 - 2014, Ruby Science Foundation
+# NMatrix is Copyright (c) 2012 - 2014, John Woods and the Ruby Science Foundation
 #
 # Please see LICENSE.txt for additional copyright notices.
 #
@@ -29,6 +29,10 @@
 require File.dirname(__FILE__) + "/spec_helper.rb"
 
 describe NMatrix do
+  #after :each do
+  #  GC.start
+  #end
+
   it "creates a matrix with the new constructor" do
     n = NMatrix.new([2,2], [0,1,2,3], dtype: :int64)
   end
@@ -40,17 +44,15 @@ describe NMatrix do
   end
 
   it "calculates exact determinants on small square matrices" do
-    a = NMatrix.new(:dense, 2, [1,2,3,4], :int64)
-    a.det_exact.should == -2
+    NMatrix.new(2, [1,2,3,4], stype: :dense, dtype: :int64).det_exact.should == -2
   end
 
   it "calculates determinants" do
-    m = NMatrix.new(3, [-2,2,3,-1,1,3,2,0,-1])
-    m.det.should == 6
+    NMatrix.new(3, [-2,2,3,-1,1,3,2,0,-1], stype: :dense, dtype: :int64).det.should == 6
   end
 
   it "allows casting to Ruby objects" do
-    m = NMatrix.new(:dense, [3,3], [0,0,1,0,2,0,3,4,5], :int64)
+    m = NMatrix.new([3,3], [0,0,1,0,2,0,3,4,5], dtype: :int64, stype: :dense)
     n = m.cast(:dense, :object)
     n.should == m
   end
@@ -367,3 +369,110 @@ describe NMatrix do
   end
 
 end
+
+
+describe "NMatrix#upper_triangle" do
+  it "should create a copy with the lower corner set to zero" do
+    n = NMatrix.seq(4)+1
+    n.upper_triangle.should == NMatrix.new(4, [1,2,3,4,0,6,7,8,0,0,11,12,0,0,0,16])
+    n.upper_triangle(2).should == NMatrix.new(4, [1,2,3,4,5,6,7,8,9,10,11,12,0,14,15,16])
+  end
+end
+
+describe "NMatrix#lower_triangle" do
+  it "should create a copy with the lower corner set to zero" do
+    n = NMatrix.seq(4)+1
+    n.lower_triangle.should == NMatrix.new(4, [1,0,0,0,5,6,0,0,9,10,11,0,13,14,15,16])
+    n.lower_triangle(2).should == NMatrix.new(4, [1,2,3,0,5,6,7,8,9,10,11,12,13,14,15,16])
+  end
+end
+
+describe "NMatrix#upper_triangle!" do
+  it "should create a copy with the lower corner set to zero" do
+    n = NMatrix.seq(4)+1
+    n.upper_triangle!.should == NMatrix.new(4, [1,2,3,4,0,6,7,8,0,0,11,12,0,0,0,16])
+    n = NMatrix.seq(4)+1
+    n.upper_triangle!(2).should == NMatrix.new(4, [1,2,3,4,5,6,7,8,9,10,11,12,0,14,15,16])
+  end
+end
+
+describe "NMatrix#lower_triangle!" do
+  it "should create a copy with the lower corner set to zero" do
+    n = NMatrix.seq(4)+1
+    n.lower_triangle!.should == NMatrix.new(4, [1,0,0,0,5,6,0,0,9,10,11,0,13,14,15,16])
+    n = NMatrix.seq(4)+1
+    n.lower_triangle!(2).should == NMatrix.new(4, [1,2,3,0,5,6,7,8,9,10,11,12,13,14,15,16])
+  end
+end
+
+describe "NMatrix#reshape" do
+  it "should change the shape of a matrix without the contents changing" do
+    n = NMatrix.seq(4)+1
+    n.reshape([8,2]).to_flat_array.should == n.to_flat_array
+  end
+
+  it "should permit a change of dimensionality" do
+    n = NMatrix.seq(4)+1
+    n.reshape([8,1,2]).to_flat_array.should == n.to_flat_array
+  end
+
+  it "should prevent a resize" do
+    n = NMatrix.seq(4)+1
+    expect { n.reshape([5,2]) }.to raise_error(ArgumentError)
+  end
+end
+
+describe "NMatrix#transpose" do
+  [:dense, :list, :yale].each do |stype|
+    context(stype) do
+      it "should transpose a #{stype} matrix (2-dimensional)" do
+        n = NMatrix.seq(4, stype: stype)
+        n.transpose.to_a.flatten.should == [0,4,8,12,1,5,9,13,2,6,10,14,3,7,11,15]
+      end
+    end
+  end
+
+  [:dense, :list].each do |stype|
+    context(stype) do
+      it "should transpose a #{stype} matrix (3-dimensional)" do
+        n = NMatrix.new([4,4,1], [0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15], stype: stype)
+        n.transpose([2,1,0]).to_flat_array.should == [0,4,8,12,1,5,9,13,2,6,10,14,3,7,11,15]
+        n.transpose([1,0,2]).to_flat_array.should == [0,4,8,12,1,5,9,13,2,6,10,14,3,7,11,15]
+        n.transpose([0,2,1]).to_flat_array.should == n.to_flat_array # for dense, make this reshape!
+      end
+    end
+  end
+
+end
+
+describe "NMatrix#==" do
+  [:dense, :list, :yale].each do |left|
+    [:dense, :list, :yale].each do |right|
+      next if left == right
+      context ("#{left}?#{right}") do
+        it "should compare two matrices of differing stypes" do
+          n = NMatrix.new([3,4], [0,0,1,2,0,0,3,4,0,0,0,0,5,6,7,0], stype: left)
+          m = NMatrix.new([3,4], [0,0,1,2,0,0,3,4,0,0,0,0,5,6,7,0], stype: right)
+          n.should == m
+        end
+      end
+    end
+  end
+end
+
+describe "NMatrix#concat" do
+  it "should default to horizontal concatenation" do
+    n = NMatrix.new([1,3], [1,2,3])
+    n.concat(n).should == NMatrix.new([1,6], [1,2,3,1,2,3])
+  end
+
+  it "should permit vertical concatenation" do
+    n = NMatrix.new([1,3], [1,2,3])
+    n.vconcat(n).should == NMatrix.new([2,3], [1,2,3])
+  end
+
+  it "should permit depth concatenation on tensors" do
+    n = NMatrix.new([1,3,1], [1,2,3])
+    n.dconcat(n).should == NMatrix.new([1,3,2], [1,1,2,2,3,3])
+  end
+end