scicom 0.2.0-java

data/README.md

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+Announcement
+============
+
+SciCom (Scientific Computing) for Ruby brings the power of R to the Ruby community. SciCom 
+is based on Renjin, a JVM-based interpreter for the R language for statistical computing.
+
+R on the JVM
+------------
+
+Over the past two decades, the R language for statistical computing has emerged as the de 
+facto standard for analysts, statisticians, and scientists. Today, a wide range of 
+enterprises – from pharmaceuticals to insurance – depend on R for key business uses. Renjin 
+is a new implementation of the R language and environment for the Java Virtual Machine (JVM),
+whose goal is to enable transparent analysis of big data sets and seamless integration with 
+other enterprise systems such as databases and application servers.
+
+Renjin is still under development, but it is already being used in production for a number 
+of client projects, and supports most CRAN packages, including some with C/Fortran 
+dependencies.
+
+SciCom and Renjin
+-----------------
+
+SciCom integrates with Renjin and allows the use of R inside a Ruby script. In a sense, 
+SciCom is similar to other solutions such as RinRuby, Rpy2, PipeR, etc. However, since 
+SciCom and Renjin both target the JVM there is no need to integrate both solutions and 
+there is no need to send data between Ruby and R, as it all resides in the same JVM. 
+Further, installation of SciCom does not require the installation of GNU R; Renjin is the 
+interpreter and comes with SciCom. Finally, although SciCom provides a basic interface to 
+Renjin similar to RinRuby, a much tighter integration is also possible.
+
+SciCom and Renjin Limitations
+------------------------------
+
+Renjin is in development and still has some limitations
+
+  + Renjin does not allow dynamic loading of libaries.  My understanding is that Renjin 
+  developers are actually working on a new version on which loading of libraries will be
+  possible.
+  + Renjin does not implement any of the graphical libaries such as plot or ggplot. We
+  hope that this limitation will be solved not by implementing those libraries but by the
+  use of Ruby libraries from SciRuby such as NyaPlot (https://github.com/domitry/nyaplot) 
+  or daru (https://github.com/v0dro/daru).
+  
+
+SciCom installation and download:
+==================================
+
+  + Install Jruby
+  + jruby –S gem install scicom
+
+SciCom Homepages:
+==================
+
+  + http://rubygems.org/gems/scicom
+  + https://github.com/rbotafogo/scicom/wiki
+
+Contributors:
+=============
+Contributors are welcome.
+
+SciCom History:
+================
+
+  + 17/11//2014: Version 0.2.0 - Most R functionality available to SciCom	
+  + 21/06/2014: Version 0.0.1 - Initial release

data/README.md~

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+Announcement
+============
+
+MDArray version 0.5.5 has Just been released. MDArray is a multi dimensional array implemented 
+for JRuby inspired by NumPy (www.numpy.org) and Masahiro Tanaka´s Narray (narray.rubyforge.org).  
+MDArray stands on the shoulders of Java-NetCDF and Parallel Colt.  At this point MDArray has 
+libraries for linear algebra, mathematical, trigonometric and descriptive statistics methods.
+
+NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of 
+scientific data formats.  It is developed and distributed by Unidata (http://www.unidata.ucar.edu).
+ 
+Parallel Colt (https://sites.google.com/site/piotrwendykier/software/parallelcolt is a
+ multithreaded version of Colt (http://acs.lbl.gov/software/colt/).  Colt provides a set of 
+Open Source Libraries for High Performance Scientific and Technical Computing in Java. 
+Scientific and technical computing is characterized by demanding problem sizes and a need for 
+high performance at reasonably small memory footprint.
+
+
+What´s new:
+===========
+
+Class MDMatrix and Linear Algebra Methods
+-----------------------------------------
+
+This version of MDArray introduces class MDMatrix.  MDMatrix is a matrix class wrapping many 
+linear algebra methods from Parallel Colt (see below).  MDMatrix support only the following 
+types: i) int; ii) long; iii) float and iv) double.
+
+Differently from other libraries, in which matrix is a subclass of array, MDMatrix is a 
+twin class of MDArray.  MDMatrix is a twin class of MDArray as every time an MDMatrix is 
+instantiated, an MDArray class is also instantiated.  In reality, there is only one backing 
+store that can be viewed by either MDMatrix or MDArray. 
+ 
+Creation of MDMatrix follows the same API as MDArray API.  For instance, creating a double 
+square matrix of size 5 x 5 can be done by:
+ 
+    matrix = MDMatrix.double([5, 5], [2.0, 0.0, 8.0, 6.0, 0.0,\
+                                      1.0, 6.0, 0.0, 1.0, 7.0,\
+                                      5.0, 0.0, 7.0, 4.0, 0.0,\
+                                      7.0, 0.0, 8.0, 5.0, 0.0,\
+                                      0.0, 10.0, 0.0, 0.0, 7.0])
+
+Creating an int matrix filled with zero can be done by:
+
+    matrix = MDMatrix.int([4, 3])
+
+MDMatrix also supports creation based on methods such as fromfunction, linspace, init_with, 
+arange, typed_arange and ones:
+
+
+    array = MDArray.typed_arange("double", 0, 15)
+    array = MDMatrix.fromfunction("double", [4, 4]) { |x, y| x + y }
+
+An MDMatrix can also be created from an MDArray as follows:
+
+    d2 = MDArray.typed_arange("double", 0, 15)
+    double_matrix = MDMatrix.from_mdarray(d2)
+
+An MDMatrix can only be created from MDArrays of one, two or three dimensions.  However, 
+one can take a view from an MDArray to create an MDMatrix, as long as the view is at most 
+three dimensional:
+
+    # Instantiate an MDArray and shape it with 4 dimensions
+    > d1 = MDArray.typed_arange("double", 0, 420)
+    > d1.reshape!([5, 4, 3, 7])
+    # slice the array, getting a three dimensional array and from that, make a matrix
+    > matrix = MDMatrix.from_mdarray(d1.slice(0, 0))
+    # get a region from the array, with the first two dimensions of size 0, reduce it to a
+    # size two array and then build a two dimensional matrix
+    > matrix = MDMatrix.from_mdarray(d1.region(:spec => "0:0, 0:0, 0:2, 0:6").reduce)
+
+printing the above two dimensional matrix gives us:
+
+    > matrix.print
+    3 x 7 matrix
+    0,00000 1,00000 2,00000 3,00000 4,00000 5,00000 6,00000
+    7,00000 8,00000 9,00000 10,0000 11,0000 12,0000 13,0000
+    14,0000 15,0000 16,0000 17,0000 18,0000 19,0000 20,0000
+
+Every MDMatrix instance has a twin MDArray instance that uses the same backing store.  This 
+allows the user to treat the data as either a matrix or an array and use methods either from 
+matrix or array.  The above matrix can be printed as an array:
+
+
+    > matrix.mdarray.print
+    [[0.00 1.00 2.00 3.00 4.00 5.00 6.00]
+     [7.00 8.00 9.00 10.00 11.00 12.00 13.00]
+     [14.00 15.00 16.00 17.00 18.00 19.00 20.00]]
+
+With an MDMatrix, many linear algebra methods can be easily calculated:
+
+    # basic operations on matrix can be done, such as, ‘+’, ‘-‘, ´*’, ‘/’
+    # make a 4 x 4 matrix and fill it with ´double´ 2.5
+    > a = MDMatrix.double([4, 4])
+    > a.fill(2.5)
+    > make a 4 x 4 matrix ´b´ from a given function (block)
+    > b = MDMatrix.fromfunction("double", [4, 4]) { |x, y| x + y }
+    # add both matrices
+    > c = a + b
+    # multiply by scalar
+    > c = a * 2
+    # divide two matrices.  Matrix ´b´ has to be non-singular, otherwise an exception is
+    # raised.
+    # generate a non-singular matrix from a given matrix
+    > b.generate_non_singular!
+    > c = a / b
+
+Linear algebra methods:
+
+    # create a matrix with the given data
+    > pos = MDArray.double([3, 3], [4, 12, -16, 12, 37, -43, -16, -43, 98])
+    > matrix = MDMatrix.from_mdarray(pos)
+    # Cholesky decomposition from wikipedia example
+    > chol = matrix.chol
+    > assert_equal(2, chol[0, 0])
+    > assert_equal(6, chol[1, 0])
+    > assert_equal(-8, chol[2, 0])
+    > assert_equal(5, chol[2, 1])
+    > assert_equal(3, chol[2, 2])
+
+All other linear algebra methods are called the same way.
+
+
+MDArray and SciRuby:
+====================
+
+MDArray subscribes fully to the SciRuby Manifesto (http://sciruby.com/). 
+
+“Ruby has for some time had no equivalent to the beautifully constructed NumPy, SciPy, and 
+matplotlib libraries for Python. 
+
+We believe that the time for a Ruby science and visualization package has come. Sometimes 
+when a solution of sugar and water becomes super-saturated, from it precipitates a pure, 
+delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap of a 
+finger. So is occurring now, we believe, with numeric and visualization libraries for Ruby.”
+
+MDArray main properties are:
+============================
+
+ + Homogeneous multidimensional array, a table of elements (usually numbers), all of the 
+     same type, indexed by a tuple of positive integers;
+ + Support for many linear algebra methods (see bellow);
+ + Easy calculation for large numerical multi dimensional arrays;
+ + Basic types are: boolean, byte, short, int, long, float, double, string, structure;
+ + Based on JRuby, which allows importing Java libraries;
+ + Operator: +,-,*,/,%,**, >, >=, etc.;
+ + Functions: abs, ceil, floor, truncate, is_zero, square, cube, fourth;
+ + Binary Operators: &, |, ^, ~ (binary_ones_complement), <<, >>;
+ + Ruby Math functions: acos, acosh, asin, asinh, atan, atan2, atanh, cbrt, cos, erf, exp, 
+     gamma, hypot, ldexp, log, log10, log2, sin, sinh, sqrt, tan, tanh, neg;
+ + Boolean operations on boolean arrays: and, or, not;
+ + Fast descriptive statistics from Parallel Colt (complete list found bellow);
+ + Easy manipulation of arrays: reshape, reduce dimension, permute, section, slice, etc.;
+ + Support for reading and writing NetCDF-3 files;
+ + Reading of two dimensional arrays from CSV files (mainly for debugging and simple testing 
+     purposes);
+ + StatList: a list that can grow/shrink and that can compute Parallel Colt descriptive 
+     statistics;
+ + Experimental lazy evaluation (still slower than eager evaluation).
+
+Supported linear algebra methods:
+=================================
+
+  + backwardSolve:  Solves the upper triangular system U*x=b;
+  + chol: Constructs and returns the cholesky-decomposition of the given matrix.
+  + cond: Returns the condition of matrix A, which is the ratio of largest to smallest singular value.
+  + det: Returns the determinant of matrix A.
+  + eig: Constructs and returns the Eigenvalue-decomposition of the given matrix.
+  + forwardSolve:  Solves the lower triangular system L*x=b;
+  + inverse: Returns the inverse or pseudo-inverse of matrix A.
+  + kron: Computes the Kronecker product of two real matrices.
+  + lu: Constructs and returns the LU-decomposition of the given matrix.
+  + mult: Inner product of two vectors; Sum(x[i] * y[i]).
+  + mult: Linear algebraic matrix-vector multiplication; z = A * y.
+  + mult: Linear algebraic matrix-matrix multiplication; C = A x B.
+  + multOuter: Outer product of two vectors; Sets A[i,j] = x[i] * y[j].
+  + norm1: Returns the one-norm of vector x, which is Sum(abs(x[i])).
+  + norm1: Returns the one-norm of matrix A, which is the maximum absolute column sum.
+  + norm2: Returns the two-norm (aka euclidean norm) of vector x; equivalent to Sqrt(mult(x,x)).
+  + norm2: Returns the two-norm of matrix A, which is the maximum singular value; obtained from SVD.
+  + normF: Returns the Frobenius norm of matrix A, which is Sqrt(Sum(A[i]2)).
+  + normF: Returns the Frobenius norm of matrix A, which is Sqrt(Sum(A[i,j]2)).
+  + normInfinity: Returns the infinity norm of vector x, which is Max(abs(x[i])).
+  + normInfinity: Returns the infinity norm of matrix A, which is the maximum absolute row sum.
+  + pow: Linear algebraic matrix power; B = Ak <==> B = A*A*...*A.
+  + qr: Constructs and returns the QR-decomposition of the given matrix.
+  + rank: Returns the effective numerical rank of matrix A, obtained from Singular Value Decomposition.
+  + solve: Solves A*x = b.
+  + solve: Solves A*X = B.
+  + solveTranspose: Solves X*A = B, which is also A'*X' = B'.
+  + svd: Constructs and returns the SingularValue-decomposition of the given matrix.
+  + trace: Returns the sum of the diagonal elements of matrix A; Sum(A[i,i]).
+  + trapezoidalLower: Modifies the matrix to be a lower trapezoidal matrix.
+  + vectorNorm2: Returns the two-norm (aka euclidean norm) of vector X.vectorize();
+  + xmultOuter: Outer product of two vectors; Returns a matrix with A[i,j] = x[i] * y[j].
+  + xpowSlow: Linear algebraic matrix power; B = Ak <==> B = A*A*...*A.
+
+Properties´ methods tested on matrices:
+=======================================
+
+  + density: Returns the matrix's fraction of non-zero cells; A.cardinality() / A.size().
+  + generate_non_singular!: Modifies the given square matrix A such that it is diagonally dominant by row and column, hence non-singular, hence invertible.
+  + diagonal?: A matrix A is diagonal if A[i,j] == 0 whenever i != j.
+  + diagonally_dominant_by_column?: A matrix A is diagonally dominant by column if the absolute value of each diagonal element is larger than the sum of the absolute values of the off-diagonal elements in the corresponding column.
+  + diagonally_dominant_by_row?: A matrix A is diagonally dominant by row if the absolute value of each diagonal element is larger than the sum of the absolute values of the off-diagonal elements in the corresponding row.
+  + identity?: A matrix A is an identity matrix if A[i,i] == 1 and all other cells are zero.
+  + lower_bidiagonal?: A matrix A is lower bidiagonal if A[i,j]==0 unless i==j || i==j+1.
+  + lower_triangular?: A matrix A is lower triangular if A[i,j]==0 whenever i < j.
+  + nonnegative?: A matrix A is non-negative if A[i,j] >= 0 holds for all cells.
+  + orthogonal?: A square matrix A is orthogonal if A*transpose(A) = I.
+  + positive?: A matrix A is positive if A[i,j] > 0 holds for all cells.
+  + singular?: A matrix A is singular if it has no inverse, that is, iff det(A)==0.
+  + skew_symmetric?: A square matrix A is skew-symmetric if A = -transpose(A), that is A[i,j] == -A[j,i].
+  + square?: A matrix A is square if it has the same number of rows and columns.
+  + strictly_lower_triangular?: A matrix A is strictly lower triangular if A[i,j]==0 whenever i <= j.
+  + strictly_triangular?: A matrix A is strictly triangular if it is triangular and its diagonal elements all equal 0.
+  + strictly_upper_triangular?: A matrix A is strictly upper triangular if A[i,j]==0 whenever i >= j.
+  + symmetric?: A matrix A is symmetric if A = tranpose(A), that is A[i,j] == A[j,i].
+  + triangular?: A matrix A is triangular iff it is either upper or lower triangular.
+  + tridiagonal?: A matrix A is tridiagonal if A[i,j]==0 whenever Math.abs(i-j) > 1.
+  + unit_triangular?: A matrix A is unit triangular if it is triangular and its diagonal elements all equal 1.
+  + upper_bidiagonal?: A matrix A is upper bidiagonal if A[i,j]==0 unless i==j || i==j-1.
+  + upper_triangular?: A matrix A is upper triangular if A[i,j]==0 whenever i > j.
+  + zero?: A matrix A is zero if all its cells are zero.
+  + lower_bandwidth: The lower bandwidth of a square matrix A is the maximum i-j for which A[i,j] is nonzero and i > j.
+  + semi_bandwidth: Returns the semi-bandwidth of the given square matrix A.
+  + upper_bandwidth: The upper bandwidth of a square matrix A is the maximum j-i for which A[i,j] is nonzero and j > i.
+
+Descriptive statistics methods imported from Parallel Colt:
+===========================================================
+
+  + auto_correlation, correlation, covariance, durbin_watson, frequencies, geometric_mean, 
+  + harmonic_mean, kurtosis, lag1, max, mean, mean_deviation, median, min, moment, moment3, 
+  + moment4, pooled_mean, pooled_variance, product, quantile, quantile_inverse, 
+  + rank_interpolated, rms, sample_covariance, sample_kurtosis, sample_kurtosis_standard_error, 
+  + sample_skew, sample_skew_standard_error, sample_standard_deviation, sample_variance, 
+  + sample_weighted_variance, skew, split,  standard_deviation, standard_error, sum, 
+  + sum_of_inversions, sum_of_logarithms, sum_of_powers, sum_of_power_deviations, 
+  + sum_of_squares, sum_of_squared_deviations, trimmed_mean, variance, weighted_mean, 
+  + weighted_rms, weighted_sums, winsorized_mean.
+
+Double and Float methods from Parallel Colt:
+============================================
+
+  + acos, asin, atan, atan2, ceil, cos, exp, floor, greater, IEEEremainder, inv, less, lg, 
+  + log, log2, rint, sin, sqrt, tan.
+
+Double, Float, Long and Int methods from Parallel Colt:
+=======================================================
+
+  + abs, compare, div, divNeg, equals, isEqual (is_equal), isGreater (is_greater), 
+  + isles (is_less), max, min, minus, mod, mult, multNeg (mult_neg), multSquare (mult_square), 
+  + neg, plus (add), plusAbs (plus_abs), pow (power), sign, square.
+
+Long and Int methods from Parallel Colt
+=======================================
+
+  + and, dec, factorial, inc, not, or, shiftLeft (shift_left), shiftRightSigned 
+      (shift_right_signed), shiftRightUnsigned (shift_right_unsigned), xor.
+
+MDArray installation and download:
+==================================
+
+  + Install Jruby
+  + jruby –S gem install mdarray
+
+MDArray Homepages:
+==================
+
+  + http://rubygems.org/gems/mdarray
+  + https://github.com/rbotafogo/mdarray/wiki
+
+Contributors:
+=============
+Contributors are welcome.
+
+MDArray History:
+================
+
+  + 14/11/2013: Version 0.5.5 - Support for linear algebra methods
+  + 07/08/2013: Version 0.5.4 - Support for reading and writing NetCDF-3 files
+  + 24/06/2013: Version 0.5.3 – Over 90% Performance improvements for methods imported 
+      from Parallel Colt and over 40% performance improvements for all other methods 
+      (implemented in Ruby); 
+  + 16/05/2013: Version 0.5.0 - All loops transferred to Java with over 50% performance 
+      improvements.  Descriptive statistics from Parallel Colt;
+  + 19/04/2013: Version 0.4.3 - Fixes a simple, but fatal bug in 0.4.2.  No new features;
+  + 17/04/2013: Version 0.4.2 - Adds simple statistics and boolean operators;
+  + 05/04/2013: Version 0.4.0 – Initial release.
+

data/Rakefile

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+require 'rake/testtask'
+require_relative 'version'
+
+name = "#{$gem_name}-#{$version}.gem"
+
+rule '.class' => '.java' do |t|
+  sh "javac #{t.source}"
+end
+
+desc 'default task'
+task :default => [:install_gem]
+
+desc 'Makes a Gem'
+task :make_gem do
+  sh "gem build #{$gem_name}.gemspec"
+end
+
+desc 'Install the gem in the standard location'
+task :install_gem => [:make_gem] do
+  sh "gem install #{$gem_name}-#{$version}-java.gem"
+end
+
+desc 'Make documentation'
+task :make_doc do
+  sh "yard doc lib/*.rb lib/**/*.rb"
+end
+
+desc 'Push project to github'
+task :push do
+  sh "git push origin master"
+end
+
+desc 'Push gem to rubygem'
+task :push_gem do
+  sh "push #{name} -p $http_proxy"
+end
+
+desc 'Counts the number of lines of ruby code'
+task :count do
+  sh "find . -name '*.rb' | xargs wc -l"
+end
+
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/complete.rb']
+  t.ruby_opts = ["--server", "-Xinvokedynamic.constants=true", "-J-Xmn512m", 
+                 "-J-Xms1024m", "-J-Xmx1024m"]
+  t.verbose = true
+  t.warning = true
+end
+

data/config.rb

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+require 'rbconfig'
+
+##########################################################################################
+# Configuration. Remove setting before publishing Gem.
+##########################################################################################
+
+# set to true if development environment
+# $DVLP = true
+
+# Set to 'cygwin' when in cygwin
+# $ENV = 'cygwin'
+
+# Set development dependency: those are gems that are also in development and thus not
+# installed in the gem directory.  Need a way of accessing them
+# $DEPEND=["MDArray"]
+
+##########################################################################################
+
+# the platform
+@platform = 
+  case RUBY_PLATFORM
+  when /mswin/ then 'windows'
+  when /mingw/ then 'windows'
+  when /bccwin/ then 'windows'
+  when /cygwin/ then 'windows-cygwin'
+  when /java/
+    require 'java' #:nodoc:
+    if java.lang.System.getProperty("os.name") =~ /[Ww]indows/
+      'windows-java'
+    else
+      'default-java'
+    end
+  else 'default'
+  end
+
+#---------------------------------------------------------------------------------------
+# Add path to load path
+#---------------------------------------------------------------------------------------
+
+def mklib(path, home_path = true)
+  
+  if (home_path)
+    lib = path + "/lib"
+  else
+    lib = path
+  end
+  
+  $LOAD_PATH << lib
+  
+end
+
+##########################################################################################
+# Prepare environment to work inside Cygwin
+##########################################################################################
+
+if $ENV == 'cygwin'
+  
+  #---------------------------------------------------------------------------------------
+  # Return the cygpath of a path
+  #---------------------------------------------------------------------------------------
+  
+  def set_path(path)
+    `cygpath -a -p -m #{path}`.tr("\n", "")
+  end
+  
+else
+  
+  #---------------------------------------------------------------------------------------
+  # Return  the path
+  #---------------------------------------------------------------------------------------
+  
+  def set_path(path)
+    path
+  end
+  
+end
+
+#---------------------------------------------------------------------------------------
+# Set the project directories
+#---------------------------------------------------------------------------------------
+
+class SciCom
+
+  @home_dir = File.expand_path File.dirname(__FILE__)
+
+  class << self
+    attr_reader :home_dir
+  end
+
+  @project_dir = SciCom.home_dir + "/.."
+  @doc_dir = SciCom.home_dir + "/doc"
+  @lib_dir = SciCom.home_dir + "/lib"
+  @src_dir = SciCom.home_dir + "/src"
+  @target_dir = SciCom.home_dir + "/target"
+  @test_dir = SciCom.home_dir + "/test"
+  @vendor_dir = SciCom.home_dir + "/vendor"
+  
+  class << self
+    attr_reader :project_dir
+    attr_reader :doc_dir
+    attr_reader :lib_dir
+    attr_reader :src_dir
+    attr_reader :target_dir
+    attr_reader :test_dir
+    attr_reader :vendor_dir
+  end
+
+  @build_dir = SciCom.src_dir + "/build"
+
+  class << self
+    attr_reader :build_dir
+  end
+
+  @classes_dir = SciCom.build_dir + "/classes"
+
+  class << self
+    attr_reader :classes_dir
+  end
+
+end
+
+#---------------------------------------------------------------------------------------
+# Set dependencies
+#---------------------------------------------------------------------------------------
+
+def depend(name)
+  
+  dependency_dir = SciCom.project_dir + "/" + name
+  mklib(dependency_dir)
+  
+end
+
+##########################################################################################
+# If development
+##########################################################################################
+
+if ($DVLP == true)
+
+  mklib(SciCom.home_dir)
+  
+  # Add dependencies here
+  # depend(<other_gems>)
+  $DEPEND.each do |dep|
+    depend(dep)
+  end if $DEPEND
+
+  #----------------------------------------------------------------------------------------
+  # If we need to test for coverage
+  #----------------------------------------------------------------------------------------
+  
+  if $COVERAGE == 'true'
+  
+    require 'simplecov'
+    
+    SimpleCov.start do
+      @filters = []
+      add_group "SciCom", "lib/scicom"
+    end
+    
+  end
+
+end
+