nmatrix-atlas 0.2.0

data/spec/01_enum_spec.rb

@@ -0,0 +1,190 @@
+# = 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
+#
+# == 01_enum_spec.rb
+#
+# Enumerator tests for NMatrix. These should load early, as they
+# test functionality essential to matrix printing.
+#
+require 'spec_helper'
+
+describe "NMatrix enumeration for" do
+  [:dense, :yale, :list].each do |stype|
+    context stype do
+      let(:n) { create_rectangular_matrix(stype) }
+      let(:m) { n[1..4,1..3] }
+
+      if stype == :yale
+        it "should iterate properly along each row of a slice" do
+          vv = []
+          ii = []
+          jj = []
+          m.extend NMatrix::YaleFunctions
+          m.each_row do |row|
+            row.each_with_indices do |v,i,j|
+              vv << v
+              ii << i
+              jj << j
+            end
+          end
+
+          expect(vv).to eq([7,8,9, 12,13,0, 0,0,0, 0,17,18])
+          expect(ii).to eq([0]*12)
+          expect(jj).to eq([0,1,2]*4)
+        end
+
+        it "should iterate along diagonal portion of A array" do
+          vv = []
+          ii = []
+          jj = []
+          n.send :__yale_stored_diagonal_each_with_indices__ do |v,i,j|
+            vv << v
+            ii << i
+            jj << j
+          end
+          expect(vv).to eq([1,7,13,0,19])
+          expect(ii).to eq([0,1,2,3,4])
+          expect(jj).to eq(ii)
+        end
+
+        it "should iterate along non-diagonal portion of A array" do
+          vv = []
+          ii = []
+          jj = []
+          n.send :__yale_stored_nondiagonal_each_with_indices__ do |v,i,j|
+            vv << v
+            ii << i
+            jj << j
+          end
+
+          expect(vv).to eq([2,3,4,5,  6,8,9,10,  11,12,14,15,  16,17,18,20])
+          expect(ii).to eq([[0]*4, [1]*4, [2]*4, [4]*4].flatten)
+          expect(jj).to eq([1,2,3,4,  0,2,3,5,   0,1,4,5,      0,2,3,5])
+        end
+
+        it "should iterate along a sliced diagonal portion of an A array" do
+          m = n[0..3,1..3]
+          vv = []
+          ii = []
+          jj = []
+          m.send :__yale_stored_diagonal_each_with_indices__ do |v,i,j|
+            vv << v
+            ii << i
+            jj << j
+          end
+          expect(vv).to eq([7,13,0])
+          expect(ii).to eq([1,2,3])
+          expect(jj).to eq([0,1,2])
+        end
+
+        it "should iterate along a sliced non-diagonal portion of a sliced A array" do
+          vv = []
+          ii = []
+          jj = []
+          n.extend NMatrix::YaleFunctions
+          m.extend NMatrix::YaleFunctions
+          m.send :__yale_stored_nondiagonal_each_with_indices__ do |v,i,j|
+            vv << v
+            ii << i
+            jj << j
+          end
+
+          expect(ii).to eq([0,0, 1,   3,3 ])
+          expect(jj).to eq([1,2, 0,   1,2 ])
+          expect(vv).to eq([8,9, 12, 17,18])
+        end
+
+        it "should visit each stored element of the matrix in order by indices" do
+          vv = []
+          ii = []
+          jj = []
+          n.each_ordered_stored_with_indices do |v,i,j|
+            vv << v
+            ii << i
+            jj << j
+          end
+
+          expect(vv).to eq([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 0, 16, 17, 18, 19, 20])
+          expect(ii).to eq([[0]*5, [1]*5, [2]*5, [3]*1, [4]*5].flatten)
+          expect(jj).to eq([0,1,2,3,4,  0,1,2,3,5,  0,1,2,4,5,  3,  0,2,3,4,5])
+        end
+
+        it "should visit each stored element of the slice in order by indices" do
+
+          vv = []
+          ii = []
+          jj = []
+          m.each_ordered_stored_with_indices do |v,i,j|
+            vv << v
+            ii << i
+            jj << j
+          end
+          expect(ii).to eq([0,0,0, 1,1,   2,  3,3  ])
+          expect(jj).to eq([0,1,2, 0,1,   2,  1,2  ])
+          expect(vv).to eq([7,8,9, 12,13, 0, 17,18 ])
+        end
+      end
+
+      it "should visit each cell in the matrix as if dense, making indices available" do
+        vv = []
+        ii = []
+        jj = []
+        n.each_with_indices do |v,i,j|
+          vv << v
+          ii << i
+          jj << j
+        end
+
+        expect(vv).to eq([1,2,3,4,5,0,6,7,8,9,0,10,11,12,13,0,14,15,0,0,0,0,0,0,16,0,17,18,19,20])
+        expect(ii).to eq([[0]*6, [1]*6, [2]*6, [3]*6, [4]*6].flatten)
+        expect(jj).to eq([0,1,2,3,4,5]*5)
+      end
+
+      it "should visit each cell in the slice as if dense, making indices available" do
+        vv = []
+        ii = []
+        jj = []
+        m.each_with_indices do |v,i,j|
+          vv << v
+          ii << i
+          jj << j
+        end
+        expect(jj).to eq([0,1,2]*4)
+        expect(ii).to eq([[0]*3, [1]*3, [2]*3, [3]*3].flatten)
+        expect(vv).to eq([7,8,9,12,13,0,0,0,0,0,17,18])
+
+      end
+
+      if stype == :list or stype == :dense then
+        it "should correctly map to a matrix with a single element" do
+          nm = N.new([1], [2.0], stype: stype)
+          expect(nm.map { |e| e**2 }).to eq N.new([1], [4.0], stype: stype)
+        end
+
+        it "should correctly map to a matrix with multiple elements" do
+          nm = N.new([2], [2.0, 2.0], stype: stype)
+          expect(nm.map { |e| e**2 }).to eq N.new([2], [4.0, 4.0], stype: stype)
+        end
+      end
+    end
+  end
+end

data/spec/02_slice_spec.rb

@@ -0,0 +1,389 @@
+# = 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
+#
+# == 02_slice_spec.rb
+#
+# Test of slice operations. High priority tests since reference
+# slicing is needed for pretty_print.
+#
+require 'spec_helper'
+
+describe "Slice operation" do
+  include RSpec::Longrun::DSL
+
+  [:dense, :list, :yale].each do |stype|
+    context "for #{stype}" do
+        #GC.start # don't have to do this, but it helps to make sure we've cleaned up our pointers properly.
+      let(:stype_matrix) { create_matrix(stype) }
+
+      it "should correctly return a row of a reference-slice" do
+        n = create_rectangular_matrix(stype)
+        stype_matrix = n[1..4,1..3]
+        expect(stype_matrix.row(1, :copy)).to eq(stype_matrix.row(1, :reference))
+        expect(stype_matrix.row(1, :copy).to_flat_array).to eq([12,13,0])
+      end
+
+      if stype == :yale
+        it "should binary search for the left boundary of a partial row of stored indices correctly" do
+          n = NMatrix.new(10, stype: :yale, dtype: :int32)
+          n[3,0] = 1
+          #n[3,2] = 2
+          n[3,3] = 3
+          n[3,4] = 4
+          n[3,6] = 5
+          n[3,8] = 6
+          n[3,9] = 7
+          vs = []
+          is = []
+          js = []
+
+          n[3,1..9].each_stored_with_indices do |v,i,j|
+            vs << v
+            is << i
+            js << j
+          end
+
+          expect(vs).to eq([3,4,5,6,7])
+          expect(js).to eq([2,3,5,7,8])
+          expect(is).to eq([0,0,0,0,0])
+        end
+      elsif stype == :list
+        it "should iterate across a partial row of stored indices" do
+          vs = []
+          is = []
+          js = []
+
+          STDERR.puts("now") if stype == :yale
+          stype_matrix[2,1..2].each_stored_with_indices do |v,i,j|
+            vs << v
+            is << i
+            js << j
+          end
+
+          expect(vs).to eq([7,8])
+          expect(is).to eq([0,0])
+          expect(js).to eq([0,1])
+        end
+      end
+
+      unless stype == :dense
+        it "should iterate across a row of stored indices" do
+
+          vs = []
+          is = []
+          js = []
+          stype_matrix[2,0..2].each_stored_with_indices do |v,i,j|
+            vs << v
+            is << i
+            js << j
+          end
+          expect(vs).to eq(stype == :yale ? [8,6,7] : [6,7,8])
+          expect(is).to eq([0,0,0])
+          expect(js).to eq(stype == :yale ? [2,0,1] : [0,1,2])
+        end
+
+        it "should iterate across a submatrix of stored indices" do
+          vs = []
+          is = []
+          js = []
+          stype_matrix[0..1,1..2].each_stored_with_indices do |v,i,j|
+            vs << v
+            is << i
+            js << j
+          end
+
+          expect(vs).to eq(stype == :yale ? [4,1,2,5] : [1,2,4,5])
+          expect(is).to eq(stype == :yale ? [1,0,0,1] : [0,0,1,1])
+          expect(js).to eq(stype == :yale ? [0,0,1,1] : [0,1,0,1])
+        end
+      end
+
+      it "should return correct supershape" do
+        x = NMatrix.random([10,12])
+        y = x[0...8,5...12]
+        expect(y.shape).to eq([8,7])
+        expect(y.supershape).to eq([10,12])
+      end
+
+      it "should have #is_ref? method" do
+        a = stype_matrix[0..1, 0..1]
+        b = stype_matrix.slice(0..1, 0..1)
+        expect(stype_matrix.is_ref?).to be_false
+        expect(a.is_ref?).to be_true
+        expect(b.is_ref?).to be_false
+      end
+
+      it "reference should compare with non-reference" do
+        expect(stype_matrix.slice(1..2,0..1)).to eq(stype_matrix[1..2, 0..1])
+        expect(stype_matrix[1..2,0..1]).to eq(stype_matrix.slice(1..2, 0..1))
+        expect(stype_matrix[1..2,0..1]).to eq(stype_matrix[1..2, 0..1])
+      end
+
+      context "with copying" do
+        it 'should return an NMatrix' do
+          n = stype_matrix.slice(0..1,0..1)
+          expect(nm_eql(n, NMatrix.new([2,2], [0,1,3,4], dtype: :int32))).to be_true
+        end
+
+        it 'should return a copy of 2x2 matrix to self elements' do
+          n = stype_matrix.slice(1..2,0..1)
+          expect(n.shape).to eql([2,2])
+
+          expect(n[1,1]).to eq(stype_matrix[2,1])
+          n[1,1] = -9
+          expect(stype_matrix[2,1]).to eql(7)
+        end
+
+        it 'should return a 1x2 matrix without refs to self elements' do
+          n = stype_matrix.slice(0,1..2)
+          expect(n.shape).to eql([1,2])
+
+          expect(n[0]).to eq(stype_matrix[0,1])
+          expect(n[1]).to eq(stype_matrix[0,2])
+          n[0] = -9
+          expect(stype_matrix[0,1]).to eql(1)
+          expect(stype_matrix[0,2]).to eql(2)
+        end
+
+        it 'should return a 2x1 matrix without refs to self elements' do
+          stype_matrix.extend NMatrix::YaleFunctions
+
+          n = stype_matrix.slice(0..1,1)
+          expect(n.shape).to eql([2,1])
+
+          expect(n[0]).to eq(stype_matrix[0,1])
+          expect(n[1]).to eq(stype_matrix[1,1])
+          n[0] = -9
+          expect(stype_matrix[0,1]).to eql(1)
+          expect(stype_matrix[1,1]).to eql(4)
+        end
+
+        it 'should be correct slice for range 0..2 and 0...3' do
+          expect(stype_matrix.slice(0..2,0..2)).to eq(stype_matrix.slice(0...3,0...3))
+        end
+
+        [:dense, :list, :yale].each do |cast_type|
+          it "should cast copied slice from #{stype.upcase} to #{cast_type.upcase}" do
+            expect(nm_eql(stype_matrix.slice(1..2, 1..2).cast(cast_type, :int32), stype_matrix.slice(1..2,1..2))).to be_true
+            expect(nm_eql(stype_matrix.slice(0..1, 1..2).cast(cast_type, :int32), stype_matrix.slice(0..1,1..2))).to be_true
+            expect(nm_eql(stype_matrix.slice(1..2, 0..1).cast(cast_type, :int32), stype_matrix.slice(1..2,0..1))).to be_true
+            expect(nm_eql(stype_matrix.slice(0..1, 0..1).cast(cast_type, :int32), stype_matrix.slice(0..1,0..1))).to be_true
+
+            # Non square
+            expect(nm_eql(stype_matrix.slice(0..2, 1..2).cast(cast_type, :int32), stype_matrix.slice(0..2,1..2))).to be_true
+            #require 'pry'
+            #binding.pry if cast_type == :yale
+            expect(nm_eql(stype_matrix.slice(1..2, 0..2).cast(cast_type, :int32), stype_matrix.slice(1..2,0..2))).to be_true
+
+            # Full
+            expect(nm_eql(stype_matrix.slice(0..2, 0..2).cast(cast_type, :int32), stype_matrix)).to be_true
+          end
+        end
+      end
+
+      # Yale:
+      #context "by copy" do
+        #it "should correctly preserve zeros" do
+        #  stype_matrix = NMatrix.new(:yale, 3, :int64)
+        #  column_slice = stype_matrix.column(2, :copy)
+        #  column_slice[0].should == 0
+        #  column_slice[1].should == 0
+        #  column_slice[2].should == 0
+        #end
+      #end
+
+      context "by reference" do
+        it 'should return an NMatrix' do
+          n = stype_matrix[0..1,0..1]
+          expect(nm_eql(n, NMatrix.new([2,2], [0,1,3,4], dtype: :int32))).to be_true
+        end
+
+        it 'should return a 2x2 matrix with refs to self elements' do
+          n = stype_matrix[1..2,0..1]
+          expect(n.shape).to eql([2,2])
+
+          expect(n[0,0]).to eq(stype_matrix[1,0])
+          n[0,0] = -9
+          expect(stype_matrix[1,0]).to eql(-9)
+        end
+
+        it 'should return a 1x2 vector with refs to self elements' do
+          n = stype_matrix[0,1..2]
+          expect(n.shape).to eql([1,2])
+
+          expect(n[0]).to eq(stype_matrix[0,1])
+          n[0] = -9
+          expect(stype_matrix[0,1]).to eql(-9)
+        end
+
+        it 'should return a 2x1 vector with refs to self elements' do
+          n = stype_matrix[0..1,1]
+          expect(n.shape).to eql([2,1])
+
+          expect(n[0]).to eq(stype_matrix[0,1])
+          n[0] = -9
+          expect(stype_matrix[0,1]).to eql(-9)
+        end
+
+        it 'should slice again' do
+          n = stype_matrix[1..2, 1..2]
+          expect(nm_eql(n[1,0..1], NVector.new(2, [7,8], dtype: :int32).transpose)).to be_true
+        end
+
+        it 'should be correct slice for range 0..2 and 0...3' do
+          expect(stype_matrix[0..2,0..2]).to eq(stype_matrix[0...3,0...3])
+        end
+
+        it 'should correctly handle :* slice notation' do
+          expect(stype_matrix[:*,0]).to eq stype_matrix[0...stype_matrix.shape[0], 0]
+        end
+
+        if stype == :dense
+          [:byte,:int8,:int16,:int32,:int64,:float32,:float64].each do |left_dtype|
+            [:byte,:int8,:int16,:int32,:int64,:float32,:float64].each do |right_dtype|
+
+              # Won't work if they're both 1-byte, due to overflow.
+              next if [:byte,:int8].include?(left_dtype) && [:byte,:int8].include?(right_dtype)
+
+              # For now, don't bother testing int-int mult.
+              #next if [:int8,:int16,:int32,:int64].include?(left_dtype) && [:int8,:int16,:int32,:int64].include?(right_dtype)
+              it "handles #{left_dtype.to_s} dot #{right_dtype.to_s} matrix multiplication" do
+                #STDERR.puts "dtype=#{dtype.to_s}"
+                #STDERR.puts "2"
+
+                nary = if left_dtype.to_s =~ /complex/
+                         COMPLEX_MATRIX43A_ARRAY
+                       else
+                         MATRIX43A_ARRAY
+                       end
+
+                mary = if right_dtype.to_s =~ /complex/
+                         COMPLEX_MATRIX32A_ARRAY
+                       else
+                         MATRIX32A_ARRAY
+                       end
+
+                n = NMatrix.new([4,3], nary, dtype: left_dtype)[1..3,1..2]
+                m = NMatrix.new([3,2], mary, dtype: right_dtype)[1..2,0..1]
+
+                r = n.dot m
+                expect(r.shape).to eql([3,2])
+
+                expect(r[0,0]).to eq(219.0)
+                expect(r[0,1]).to eq(185.0)
+                expect(r[1,0]).to eq(244.0)
+                expect(r[1,1]).to eq(205.0)
+                expect(r[2,0]).to eq(42.0)
+                expect(r[2,1]).to eq(35.0)
+
+              end
+            end
+          end
+
+          context "operations" do
+
+            it "correctly transposes slices" do
+              expect(stype_matrix[0...3,0].transpose).to eq NMatrix[[0, 3, 6]]
+              expect(stype_matrix[0...3,1].transpose).to eq NMatrix[[1, 4, 7]]
+              expect(stype_matrix[0...3,2].transpose).to eq NMatrix[[2, 5, 8]]
+              expect(stype_matrix[0,0...3].transpose).to eq NMatrix[[0], [1], [2]]
+              expect(stype_matrix[1,0...3].transpose).to eq NMatrix[[3], [4], [5]]
+              expect(stype_matrix[2,0...3].transpose).to eq NMatrix[[6], [7], [8]]
+              expect(stype_matrix[1..2,1..2].transpose).to eq NMatrix[[4, 7], [5, 8]]
+            end
+
+            it "adds slices" do
+              expect(NMatrix[[0,0,0]] + stype_matrix[1,0..2]).to eq NMatrix[[3, 4, 5]]
+            end
+
+            it "scalar adds to slices" do
+              expect(stype_matrix[1,0..2]+1).to eq NMatrix[[4, 5, 6]]
+            end
+
+            it "compares slices to scalars" do
+              (stype_matrix[1, 0..2] > 2).each { |e| expect(e != 0).to be_true }
+            end
+
+            it "iterates only over elements in the slice" do
+              els = []
+              stype_matrix[1, 0..2].each { |e| els << e }
+              expect(els.size).to eq 3
+              expect(els[0]).to eq 3
+              expect(els[1]).to eq 4
+              expect(els[2]).to eq 5
+            end
+
+            it "iterates with index only over elements in the slice" do
+              els = []
+              stype_matrix[1, 0..2].each_stored_with_indices { |a| els << a }
+              expect(els.size).to eq 3
+              expect(els[0]).to eq [3, 0, 0]
+              expect(els[1]).to eq [4, 0, 1]
+              expect(els[2]).to eq [5, 0, 2]
+            end
+
+          end
+
+        end
+
+        example 'should be cleaned up by garbage collector without errors'  do
+          step "reference slice" do
+            1.times do
+              n = stype_matrix[1..2,0..1]
+            end
+            GC.start
+          end
+
+          step "reference slice of casted-copy" do
+            expect(stype_matrix).to eq(NMatrix.new([3,3], (0..9).to_a, dtype: :int32).cast(stype, :int32))
+            n = nil
+            1.times do
+              m = NMatrix.new([2,2], [1,2,3,4]).cast(stype, :int32)
+              n = m[0..1,0..1]
+            end
+            GC.start
+            expect(n).to eq(NMatrix.new([2,2], [1,2,3,4]).cast(stype, :int32))
+          end
+        end
+
+        [:dense, :list, :yale].each do |cast_type|
+          it "should cast a square reference-slice from #{stype.upcase} to #{cast_type.upcase}" do
+            expect(nm_eql(stype_matrix[1..2, 1..2].cast(cast_type), stype_matrix[1..2,1..2])).to be_true
+            expect(nm_eql(stype_matrix[0..1, 1..2].cast(cast_type), stype_matrix[0..1,1..2])).to be_true
+            expect(nm_eql(stype_matrix[1..2, 0..1].cast(cast_type), stype_matrix[1..2,0..1])).to be_true
+            expect(nm_eql(stype_matrix[0..1, 0..1].cast(cast_type), stype_matrix[0..1,0..1])).to be_true
+          end
+
+          it "should cast a rectangular reference-slice from #{stype.upcase} to #{cast_type.upcase}" do
+            # Non square
+            expect(nm_eql(stype_matrix[0..2, 1..2].cast(cast_type), stype_matrix[0..2,1..2])).to be_true # FIXME: memory problem.
+            expect(nm_eql(stype_matrix[1..2, 0..2].cast(cast_type), stype_matrix[1..2,0..2])).to be_true # this one is fine
+          end
+
+          it "should cast a square full-matrix reference-slice from #{stype.upcase} to #{cast_type.upcase}" do
+            expect(nm_eql(stype_matrix[0..2, 0..2].cast(cast_type), stype_matrix)).to be_true
+          end
+        end
+      end
+    end
+  end
+end