nmatrix-atlas 0.2.0

data/spec/03_nmatrix_monkeys_spec.rb

@@ -0,0 +1,78 @@
+require 'spec_helper'
+
+describe NMatrix do
+  describe "#to_a" do
+    it "creates an Array with the same dimensions" do
+      n = NMatrix.seq([3,2])
+      expect(n.to_a).to eq([[0, 1], [2, 3], [4, 5]])
+    end
+
+    it "creates an Array with the proper element type" do
+      n = NMatrix.seq([3,2], dtype: :float64)
+      expect(n.to_a).to eq([[0.0, 1.0], [2.0, 3.0], [4.0, 5.0]])
+    end
+
+    it "properly interprets list matrices" do
+      n = NMatrix.seq([3,2], stype: :list)
+      expect(n.to_a).to eq([[0, 1], [2, 3], [4, 5]])
+    end
+
+    it "properly interprets yale matrices" do
+      n = NMatrix.seq([3,2], stype: :yale)
+      expect(n.to_a).to eq([[0, 1], [2, 3], [4, 5]])
+    end
+  end
+end
+
+describe Array do
+  describe "#to_nm" do
+    # [0, 1, 2, 3, 4, 5]
+    let(:a) {(0..5).to_a}
+
+    it "uses a given shape and type" do
+      expect(a.to_nm([3,2]).dtype).to eq :int64
+      expect(a.to_nm([3,2])).to eq(NMatrix.seq([3,2]))
+    end
+
+    it "guesses dtype based on first element" do
+      a[0] = 0.0
+      expect(a.to_nm([3,2]).dtype).to eq :float64
+    end
+
+    it "defaults to dtype :object if necessary" do
+      a = %w(this is an array of strings)
+      expect(a.to_nm([3,2]).dtype).to eq :object
+      expect(a.to_nm([3,2])).to eq(NMatrix.new([3,2], a, dtype: :object))
+    end
+
+    it "attempts to intuit the shape of the Array" do
+      a = [[0, 1], [2, 3], [4, 5]]
+      expect(a.to_nm).to eq(NMatrix.new([3,2], a.flatten))
+      expect(a.to_nm.dtype).to eq :int64
+    end
+
+    it "creates an object Array for inconsistent dimensions" do
+      a = [[0, 1, 2], [3], [4, 5]]
+      expect(a.to_nm).to eq(NMatrix.new([3], a, dtype: :object))
+      expect(a.to_nm.dtype).to eq :object
+    end
+
+    it "intuits shape of Array into multiple dimensions" do
+      a = [[[0], [1]], [[2], [3]], [[4], [5]]]
+      expect(a.to_nm).to eq(NMatrix.new([3,2,1], a.flatten))
+      expect(a).to eq(a.to_nm.to_a)
+    end
+
+    it "is reflective with NMatrix#to_a" do
+      a = [[0, 1, 2], [3], [4, 5]]
+      expect(a).to eq(a.to_nm.to_a)
+    end
+
+    it "does not permanently alter the Array" do
+      a = [[0, 1], [2, 3], [4, 5]]
+      expect(a.to_nm).to eq(NMatrix.new([3,2], a.flatten))
+      expect(a).to eq([[0, 1], [2, 3], [4, 5]])
+    end
+  end
+end
+

data/spec/blas_spec.rb

@@ -0,0 +1,193 @@
+# = NMatrix
+#
+# A linear algebra library for scientific computation in Ruby.
+# NMatrix is part of SciRuby.
+#
+# NMatrix was originally inspired by and derived from NArray, by
+# Masahiro Tanaka: http://narray.rubyforge.org
+#
+# == Copyright Information
+#
+# 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.
+#
+# == Contributing
+#
+# By contributing source code to SciRuby, you agree to be bound by
+# our Contributor Agreement:
+#
+# * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
+#
+# == blas_spec.rb
+#
+# Tests for properly exposed BLAS functions.
+#
+
+require 'spec_helper'
+
+describe NMatrix::BLAS do
+  [:byte, :int8, :int16, :int32, :int64,
+   :float32, :float64, :complex64, :complex128,
+   :object
+  ].each do |dtype|
+    context dtype do
+      it "exposes cblas_scal" do
+        x = NMatrix.new([3, 1], [1, 2, 3], dtype: dtype)
+        NMatrix::BLAS.cblas_scal(3, 2, x, 1)
+        expect(x).to eq(NMatrix.new([3, 1], [2, 4, 6], dtype: dtype))
+      end
+
+      it "exposes cblas_imax" do
+        u = NMatrix.new([3,1], [1, 4, 3], dtype: dtype)
+        index = NMatrix::BLAS.cblas_imax(3, u, 1)
+        expect(index).to eq(1)
+      end
+    end
+  end
+
+  [:float32, :float64, :complex64, :complex128].each do |dtype|
+    context dtype do
+      # This is not the same as "exposes cblas trsm", which would be for a version defined in blas.rb (which
+      # would greatly simplify the calling of cblas_trsm in terms of arguments, and which would be accessible
+      # as NMatrix::BLAS::trsm)
+      it "exposes unfriendly cblas_trsm" do
+        a     = NMatrix.new(3, [4,-1.0/2, -3.0/4, -2, 2, -1.0/4, -4, -2, -1.0/2], dtype: dtype)
+        b     = NMatrix.new([3,1], [-1, 17, -9], dtype: dtype)
+        NMatrix::BLAS::cblas_trsm(:row, :right, :lower, :transpose, :nonunit, 1, 3, 1.0, a, 3, b, 3)
+
+        # These test results all come from actually running a matrix through BLAS. We use them to ensure that NMatrix's
+        # version of these functions give similar results.
+
+        expect(b[0]).to eq(-1.0/4)
+        expect(b[1]).to eq(33.0/4)
+        expect(b[2]).to eq(-13)
+
+        NMatrix::BLAS::cblas_trsm(:row, :right, :upper, :transpose, :unit, 1, 3, 1.0, a, 3, b, 3)
+
+        expect(b[0]).to eq(-15.0/2)
+        expect(b[1]).to eq(5)
+        expect(b[2]).to eq(-13)
+      end
+
+      # trmm multiplies two matrices, where one of the two is required to be
+      # triangular
+      it "exposes cblas_trmm" do
+        a = NMatrix.new([3,3], [1,1,1, 0,1,2, 0,0,-1], dtype: dtype)
+        b = NMatrix.new([3,3], [1,2,3, 4,5,6, 7,8,9], dtype: dtype)
+
+        begin
+          NMatrix::BLAS.cblas_trmm(:row, :left, :upper, false, :not_unit, 3, 3, 1, a, 3, b, 3)
+        rescue NotImplementedError => e
+          pending e.to_s
+        end
+
+        product = NMatrix.new([3,3], [12,15,18, 18,21,24, -7,-8,-9], dtype: dtype)
+        expect(b).to eq(product)
+      end
+    end
+  end
+
+  #should have a separate test for complex
+  [:float32, :float64, :complex64, :complex128, :object].each do |dtype|
+    context dtype do
+
+      it "exposes cblas rot" do
+        x = NMatrix.new([5,1], [1,2,3,4,5], dtype: dtype)
+        y = NMatrix.new([5,1], [-5,-4,-3,-2,-1], dtype: dtype)
+        x, y = NMatrix::BLAS::rot(x, y, 1.0/2, Math.sqrt(3)/2, -1)
+
+        expect(x).to be_within(1e-4).of(
+                   NMatrix.new([5,1], [-0.3660254037844386, -0.7320508075688772, -1.098076211353316, -1.4641016151377544, -1.8301270189221928], dtype: dtype)
+                 )
+
+        expect(y).to be_within(1e-4).of(
+                   NMatrix.new([5,1], [-6.830127018922193, -5.464101615137754, -4.098076211353316, -2.732050807568877, -1.3660254037844386], dtype: dtype)
+                 )
+      end
+
+    end
+  end
+
+  [:float32, :float64, :complex64, :complex128, :object].each do |dtype|
+    context dtype do
+
+      it "exposes cblas rotg" do
+        pending("broken for :object") if dtype == :object
+
+        ab = NMatrix.new([2,1], [6,-8], dtype: dtype)
+        begin
+          c,s = NMatrix::BLAS::rotg(ab)
+        rescue NotImplementedError => e
+          pending e.to_s
+        end
+
+        if [:float32, :float64].include?(dtype)
+          expect(ab[0]).to be_within(1e-6).of(-10)
+          expect(ab[1]).to be_within(1e-6).of(-5.0/3)
+          expect(c).to be_within(1e-6).of(-3.0/5)
+        else
+          pending "need correct test cases"
+          expect(ab[0]).to be_within(1e-6).of(10)
+          expect(ab[1]).to be_within(1e-6).of(5.0/3)
+          expect(c).to be_within(1e-6).of(3.0/5)
+        end
+        expect(s).to be_within(1e-6).of(4.0/5)
+      end
+
+      # Note: this exposes gemm, not cblas_gemm (which is the unfriendly CBLAS no-error-checking version)
+      it "exposes gemm" do
+        n = NMatrix.new([4,3], [14.0,9.0,3.0, 2.0,11.0,15.0, 0.0,12.0,17.0, 5.0,2.0,3.0], dtype: dtype)
+        m = NMatrix.new([3,2], [12.0,25.0, 9.0,10.0, 8.0,5.0], dtype: dtype)
+
+        #c = NMatrix.new([4,2], dtype)
+        r = NMatrix::BLAS.gemm(n, m) #, c)
+        #c.should equal(r) # check that both are same memory address
+
+        expect(r).to eq(NMatrix.new([4,2], [273,455,243,235,244,205,102,160], dtype: dtype))
+      end
+
+      it "exposes gemv" do
+        a = NMatrix.new([4,3], [1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0], dtype: dtype)
+        x = NMatrix.new([3,1], [2.0, 1.0, 0.0], dtype: dtype)
+        y = NMatrix::BLAS.gemv(a, x)
+        expect(y).to eq(NMatrix.new([4,1],[4.0,13.0,22.0,31.0],dtype: dtype))
+      end
+
+      it "exposes asum" do
+        pending("broken for :object") if dtype == :object
+
+        x = NMatrix.new([4,1], [-1,2,3,4], dtype: dtype)
+        expect(NMatrix::BLAS.asum(x)).to eq(10)
+      end
+
+      it "exposes asum for single element" do
+        if [:complex64,:complex128].include?(dtype)
+          x = NMatrix.new([1], [Complex(-3,2)], dtype: dtype)
+          expect(x.asum).to eq(5.0)
+        else
+          x = NMatrix.new([1], [-1], dtype: dtype)
+          expect(x.asum).to eq(1.0)
+        end
+      end
+
+      it "exposes nrm2" do
+        pending("broken for :object") if dtype == :object
+        pending("Temporarily disable because the internal implementation of nrm2 is broken -WL 2015-05-17") if dtype == :complex64 || dtype == :complex128
+
+        x = NMatrix.new([4,1], [2,-4,3,5], dtype: dtype)
+        err = case dtype
+                when :float32, :complex64
+                  1e-6
+                when :float64, :complex128
+                  1e-14
+                else
+                  1e-14
+              end
+        expect(NMatrix::BLAS.nrm2(x, 1, 3)).to be_within(err).of(5.385164807134504)
+      end
+
+    end
+  end
+end

data/spec/elementwise_spec.rb

@@ -0,0 +1,303 @@
+# = NMatrix
+#
+# A linear algebra library for scientific computation in Ruby.
+# NMatrix is part of SciRuby.
+#
+# NMatrix was originally inspired by and derived from NArray, by
+# Masahiro Tanaka: http://narray.rubyforge.org
+#
+# == Copyright Information
+#
+# 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.
+#
+# == Contributing
+#
+# By contributing source code to SciRuby, you agree to be bound by
+# our Contributor Agreement:
+#
+# * https://github.com/SciRuby/sciruby/wiki/Contributor-Agreement
+#
+# == nmatrix_spec.rb
+#
+# Element-wise operation tests.
+#
+
+require 'spec_helper'
+
+describe NMatrix do
+  context "yale" do
+    before :each do
+      @n = NMatrix.new(3, stype: :yale, dtype: :int64)
+      @n.extend NMatrix::YaleFunctions
+      @m = NMatrix.new(3, stype: :yale, dtype: :int64)
+      @n[0,0] = 52
+      @n[0,2] = 5
+      @n[1,1] = 40
+      @n[0,1] = 30
+      @n[2,0] = 6
+      @m[1,1] = -48
+      @m[0,2] = -5
+      @n.extend NMatrix::YaleFunctions
+    end
+
+    it "should perform scalar math" do
+      x = @n * 3
+      expect(x[0,0]).to eq(52 * 3)
+      expect(x[0,1]).to eq(30 * 3)
+      expect(x[0,2]).to eq(5 * 3)
+      expect(x[1,1]).to eq(40 * 3)
+      expect(x[2,0]).to eq(6 * 3)
+
+      r = NMatrix.new(3, stype: :yale, dtype: :int64)
+      y = r + 3
+      expect(y[0,0]).to eq(3)
+    end
+
+    it "should refuse to perform a dot operation on a yale with non-zero default" do
+      r = NMatrix.new(3, stype: :yale, dtype: :int64)
+      y = r + 3
+      expect { y.dot(r) }.to raise_error
+      expect { r.dot(y) }.to raise_error
+    end
+
+    it "should perform element-wise addition" do
+      expect(@n+@m).to eq(NMatrix.new(:dense, 3, [52,30,0,0,-8,0,6,0,0], :int64).cast(:yale, :int64))
+    end
+
+    it "should perform element-wise subtraction" do
+      expect(@n-@m).to eq(NMatrix.new(:dense, 3, [52,30,10,0,88,0,6,0,0], :int64).cast(:yale, :int64))
+    end
+
+    it "should perform element-wise multiplication" do
+      r = NMatrix.new(:dense, 3, [0,0,-25,0,-1920,0,0,0,0], :int64).cast(:yale, :int64)
+      m = NMatrix.new(2, stype: :yale, dtype: :int64)
+      expect(@n*@m).to eq(r)
+    end
+
+    it "should perform element-wise division" do
+      r = NMatrix.new(:dense, 3, [52, 30, -2, 0, -1, 0, 6, 0, 0], :int64).cast(:yale, :int64)
+      expect(@n/(@m+1)).to eq(r)
+    end
+
+    it "should perform element-wise modulo" do
+      m = NMatrix.new(3, stype: :yale, dtype: :int64, default: 0) + 5
+      expect(@n % m).to eq(NMatrix.new(:dense, 3, [2,0,0,0,0,0,1,0,0], :int64).cast(:yale, :int64))
+    end
+
+    it "should handle element-wise equality (=~)" do
+      expect(@n =~ @m).to eq(NMatrix.new(:dense, 3, [false,false,false,true,false,true,false,true,true], :object).cast(:yale, :object, false))
+    end
+
+    it "should handle element-wise inequality (!~)" do
+      expect(@n !~ @m).to eq(NMatrix.new(:dense, 3, [true,true,true,false,true,false,true,false,false], :object).cast(:yale, :object, true))
+    end
+
+    it "should handle element-wise less-than (<)" do
+      expect(@m < @n).to eq(NMatrix.new(:dense, 3, [true,true,true,false,true,false,true,false,false], :object).cast(:yale, :object, true))
+    end
+
+    it "should handle element-wise greater-than (>)" do
+      expect(@n > @m).to eq(NMatrix.new(:dense, 3, [true,true,true,false,true,false,true,false,false], :object).cast(:yale, :object, false))
+    end
+
+    it "should handle element-wise greater-than-or-equals (>=)" do
+      expect(@n >= @m).to eq(NMatrix.new(:dense, 3, true, :object).cast(:yale,:object, true))
+    end
+
+    it "should handle element-wise less-than-or-equals (<=)" do
+      r = NMatrix.new(:dense, 3, [false,false,false,true,false,true,false,true,true], :object).cast(:yale, :object, false)
+      expect(@n <= @m).to eq(r)
+    end
+  end
+
+
+  context "list" do
+    before :each do
+      @n = NMatrix.new(:list, 2, 0, :int64)
+      @m = NMatrix.new(:list, 2, 0, :int64)
+      @n[0,0] = 52
+      @m[1,1] = -48
+      @n[1,1] = 40
+    end
+
+    it "should perform scalar math" do
+      x = @n * 3
+      expect(x[0,0]).to eq(52 * 3)
+      expect(x[1,1]).to eq(40 * 3)
+      expect(x[0,1]).to eq(0)
+
+      r = NMatrix.new(3, stype: :list, default: 1)
+      y = r + 3
+      expect(y[0,0]).to eq(4)
+    end
+
+    it "should perform element-wise addition" do
+      r = NMatrix.new(2, stype: :list, dtype: :int64, default: 0)
+      r[0,0] = 52
+      r[1,1] = -8
+      q = @n + @m
+      expect(q).to eq(r)
+    end
+
+    it "should perform element-wise subtraction" do
+      r = NMatrix.new(:dense, 2, [52, 0, 0, 88], :int64).cast(:list, :int64)
+      expect(@n-@m).to eq(r)
+    end
+
+    it "should perform element-wise multiplication" do
+      r = NMatrix.new(:dense, 2, [52, 0, 0, -1920], :int64).cast(:list, :int64)
+      m = NMatrix.new(:list, 2, 1, :int64)
+      m[1,1] = -48
+      expect(@n*m).to eq(r)
+    end
+
+    it "should perform element-wise division" do
+      m = NMatrix.new(:list, 2, 1, :int64)
+      m[1,1] = 2
+      r = NMatrix.new(:dense, 2, [52, 0, 0, 20], :int64).cast(:list, :int64)
+      expect(@n/m).to eq(r)
+    end
+
+    it "should perform element-wise modulo" do
+      m = NMatrix.new(:list, 2, 1, :int64)
+      m[0,0] = 50
+      m[1,1] = 40
+      (@n % m)
+    end
+
+    it "should handle element-wise equality (=~)" do
+      r = NMatrix.new(:list, 2, false, :object)
+      r[0,1] = true
+      r[1,0] = true
+
+      expect(@n =~ @m).to eq(r)
+    end
+
+    it "should handle element-wise inequality (!~)" do
+      r = NMatrix.new(:list, 2, false, :object)
+      r[0,0] = true
+      r[1,1] = true
+
+      expect(@n !~ @m).to eq(r)
+    end
+
+    it "should handle element-wise less-than (<)" do
+      expect(@n < @m).to eq(NMatrix.new(:list, 2, false, :object))
+    end
+
+    it "should handle element-wise greater-than (>)" do
+      r = NMatrix.new(:list, 2, false, :object)
+      r[0,0] = true
+      r[1,1] = true
+      expect(@n > @m).to eq(r)
+    end
+
+    it "should handle element-wise greater-than-or-equals (>=)" do
+      expect(@n >= @m).to eq(NMatrix.new(:list, 2, true, :object))
+    end
+
+    it "should handle element-wise less-than-or-equals (<=)" do
+      r = NMatrix.new(:list, 2, false, :object)
+      r[0,1] = true
+      r[1,0] = true
+      expect(@n <= @m).to eq(r)
+    end
+  end
+
+  context "dense" do
+    context "scalar arithmetic" do
+      before :each do
+        @n = NMatrix.new(:dense, 2, [1,2,3,4], :int64)
+      end
+
+      it "works for integers" do
+        expect(@n+1).to eq(NMatrix.new(:dense, 2, [2,3,4,5], :int64))
+      end
+
+      #it "works for complex64" do
+      #  n = @n.cast(:dtype => :complex64)
+      #  (n + 10.0).to_a.should == [Complex(11.0), Complex(12.0), Complex(13.0), Complex(14.0)]
+      #end
+    end
+
+    context "elementwise arithmetic" do
+      before :each do
+        @n = NMatrix.new(:dense, 2, [1,2,3,4], :int64)
+        @m = NMatrix.new(:dense, 2, [-4,-1,0,66], :int64)
+      end
+
+      it "adds" do
+        r = @n+@m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [-3, 1, 3, 70], :int64))
+      end
+
+      it "subtracts" do
+        r = @n-@m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [5, 3, 3, -62], :int64))
+      end
+
+      it "multiplies" do
+        r = @n*@m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [-4, -2, 0, 264], :int64))
+      end
+
+      it "divides in the Ruby way" do
+        m = @m.clone
+        m[1,0] = 3
+        r = @n/m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [-1, -2, 1, 0], :int64))
+      end
+
+      it "exponentiates" do
+        r = @n ** 2
+        # TODO: We might have problems with the dtype.
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [1, 4, 9, 16], :int64))
+      end
+
+      it "modulo" do
+        expect(@n % (@m + 2)).to eq(NMatrix.new(:dense, [2,2], [-1, 0, 1, 4], :int64))
+      end
+    end
+
+    context "elementwise comparisons" do
+      before :each do
+        @n = NMatrix.new(:dense, 2, [1,2,3,4], :int64)
+        @m = NMatrix.new(:dense, 2, [-4,-1,3,2], :int64)
+      end
+
+      it "equals" do
+        r = @n =~ @m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [false, false, true, false], :object))
+      end
+
+      it "is not equal" do
+        r = @n !~ @m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [true, true, false, true], :object))
+      end
+
+      it "is less than" do
+        r = @n < @m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], false, :object))
+      end
+
+      it "is greater than" do
+        r = @n > @m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [true, true, false, true], :object))
+      end
+
+      it "is less than or equal to" do
+        r = @n <= @m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [false, false, true, false], :object))
+      end
+
+      it "is greater than or equal to" do
+        n = NMatrix.new(:dense, [2,2], [1, 2, 2, 4], :int64)
+        r = n >= @m
+        expect(r).to eq(NMatrix.new(:dense, [2,2], [true, true, false, true], :object))
+      end
+    end
+  end
+end