mdarray 0.4.3.pre-java → 0.5.0-java

data/README.md

@@ -1,22 +1,90 @@
 MDArray
 =======
 
-MDArray is a multi dimensional array implemented for JRuby with similar functionalities 
-(but still less) to numpy and narray by Masahiro Tanaka. MDArray targets specifically JRuby 
-as it uses Java-NetCDF library from Unidata (http://www.unidata.ucar.edu).
+MDArray is a multi dimensional array implemented for JRuby inspired by NumPy (www.numpy.org) 
+and Narray (narray.rubyforge.org) by Masahiro Tanaka.  MDArray stands on the shoulders of 
+Java-NetCDF and Parallel Colt.
+ 
+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). 
 
-Copying from numpy documentation but also valid for MDArray:
+Parallel Colt (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.
 
-MDArray main object is the homogeneous multidimensional array. It is a table of elements 
-(usually numbers), all of the same type, indexed by a tuple of positive integers. In 
-MDArray dimensions are called axes. The number of axes is rank.
+MDArray and SciRuby
+===================
 
-For example, the coordinates of a point in 3D space [1, 2, 1] is an array of rank 1, 
-because it has one axis. That axis has a length of 3. In example pictured below, the array 
-has rank 2 (it is 2-dimensional). The first dimension (axis) has a length of 2, the 
-second dimension has a length of 3.
+MDArray subscribes fully to the SciRuby Manifesto (http://sciruby.com/).  
 
-[[ 1., 0., 0.],
- [ 0., 1., 2.]]
+“Ruby has for some time had no equivalent to the beautifully constructed NumPy, SciPy, 
+and matplotlib libraries for Python. 
 
-MDArray wiki can be found at: https://github.com/rbotafogo/mdarray/wiki
+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.”
+
+Main properties
+===============
+
+  + Homogeneous multidimensional array, a table of elements (usually numbers), all of the 
+      same type, indexed by a tuple of positive integers;
+  + 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.  Version 0.4.0 only imports
+      Java-NetCDF;
+  + 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.
+  + 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. 
+
+Descriptive statistics methods
+==============================
+
+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.
+
+Installation and download
+=========================
+
+  + Install Jruby
+  + jruby –S gem install mdarray
+
+Contributors
+============
+
+  + Contributors are welcome.
+
+Homepages
+=========
+
+  + http://rubygems.org/gems/mdarray
+  + https://github.com/rbotafogo/mdarray/wiki
+
+
+HISTORY
+=======
+
+  + 16/05/2013: Version 0.5.0: All loops transfered to Java with over 50% performance 
+      improvement.  Descriptive statistics from Parallel Colt.
+  + 19/04/2013: Version 0.4.3: Fixes a simple (but fatal bug).  No new features
+  + 17/04/2013: Version 0.4.2: Adds simple statistics and boolean operators
+  + 05/05/2013: Version 0.4.0: Initial release

data/Rakefile

@@ -30,11 +30,17 @@ task :push do
   sh "git push origin master"
 end
 
-=begin
+desc 'Push gem to rubygem'
+task :push_gem do
+  sh "push #{name} -p $http_proxy"
+end
+
 Rake::TestTask.new do |t|
   t.libs << "test"
   t.test_files = FileList['test/test_complete.rb']
+  t.ruby_opts = ["--server", "-Xinvokedynamic.constants=true", "-J-Xmn512m", 
+                 "-J-Xms1024m", "-J-Xmx1024m"]
   t.verbose = true
   t.warning = true
 end
-=end
+

data/doc/BinaryOperator.html

@@ -0,0 +1,227 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>
+  Class: BinaryOperator
+  
+    &mdash; Documentation by YARD 0.8.5.2
+  
+</title>
+
+  <link rel="stylesheet" href="css/style.css" type="text/css" media="screen" charset="utf-8" />
+
+  <link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
+
+<script type="text/javascript" charset="utf-8">
+  hasFrames = window.top.frames.main ? true : false;
+  relpath = '';
+  framesUrl = "frames.html#!" + escape(window.location.href);
+</script>
+
+
+  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
+
+  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
+
+
+  </head>
+  <body>
+    <div id="header">
+      <div id="menu">
+  
+    <a href="_index.html">Index (B)</a> &raquo;
+    
+    
+    <span class="title">BinaryOperator</span>
+  
+
+  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
+</div>
+
+      <div id="search">
+  
+    <a class="full_list_link" id="class_list_link"
+        href="class_list.html">
+      Class List
+    </a>
+  
+    <a class="full_list_link" id="method_list_link"
+        href="method_list.html">
+      Method List
+    </a>
+  
+    <a class="full_list_link" id="file_list_link"
+        href="file_list.html">
+      File List
+    </a>
+  
+</div>
+      <div class="clear"></div>
+    </div>
+
+    <iframe id="search_frame"></iframe>
+
+    <div id="content"><h1>Class: BinaryOperator
+  
+  
+  
+</h1>
+
+<dl class="box">
+  
+    <dt class="r1">Inherits:</dt>
+    <dd class="r1">
+      <span class="inheritName"><span class='object_link'><a href="Operator.html" title="Operator (class)">Operator</a></span></span>
+      
+        <ul class="fullTree">
+          <li>Object</li>
+          
+            <li class="next"><span class='object_link'><a href="Operator.html" title="Operator (class)">Operator</a></span></li>
+          
+            <li class="next">BinaryOperator</li>
+          
+        </ul>
+        <a href="#" class="inheritanceTree">show all</a>
+      
+      </dd>
+    
+  
+  
+    
+  
+    
+  
+  
+  
+    <dt class="r2 last">Defined in:</dt>
+    <dd class="r2 last">lib/mdarray/operators.rb</dd>
+  
+</dl>
+<div class="clear"></div>
+
+<div id="subclasses">
+  <h2>Direct Known Subclasses</h2>
+  <p class="children"><span class='object_link'><a href="FastBinaryOperator.html" title="FastBinaryOperator (class)">FastBinaryOperator</a></span>, <span class='object_link'><a href="RubyBinaryOperator.html" title="RubyBinaryOperator (class)">RubyBinaryOperator</a></span></p>
+</div>
+
+
+
+
+
+
+  <h2>Instance Attribute Summary</h2>
+  
+  <h3 class="inherited">Attributes inherited from <span class='object_link'><a href="Operator.html" title="Operator (class)">Operator</a></span></h3>
+  <p class="inherited"><span class='object_link'><a href="Operator.html#arity-instance_method" title="Operator#arity (method)">#arity</a></span>, <span class='object_link'><a href="Operator.html#exec_type-instance_method" title="Operator#exec_type (method)">#exec_type</a></span>, <span class='object_link'><a href="Operator.html#force_type-instance_method" title="Operator#force_type (method)">#force_type</a></span>, <span class='object_link'><a href="Operator.html#name-instance_method" title="Operator#name (method)">#name</a></span>, <span class='object_link'><a href="Operator.html#post_condition-instance_method" title="Operator#post_condition (method)">#post_condition</a></span>, <span class='object_link'><a href="Operator.html#pre_condition-instance_method" title="Operator#pre_condition (method)">#pre_condition</a></span>, <span class='object_link'><a href="Operator.html#type-instance_method" title="Operator#type (method)">#type</a></span></p>
+
+
+  
+    <h2>
+      Instance Method Summary
+      <small>(<a href="#" class="summary_toggle">collapse</a>)</small>
+    </h2>
+
+    <ul class="summary">
+      
+        <li class="public ">
+  <span class="summary_signature">
+    
+      <a href="#initialize-instance_method" title="#initialize (instance method)">- (BinaryOperator) <strong>initialize</strong>(name, exec_type, force_type = nil, pre_condition = nil, post_condition = nil) </a>
+    
+
+    
+  </span>
+  
+  
+    <span class="note title constructor">constructor</span>
+  
+  
+  
+  
+  
+  
+
+  
+    <span class="summary_desc"><div class='inline'>
+<p>?????????????????????????????.</p>
+</div></span>
+  
+</li>
+
+      
+    </ul>
+  
+
+
+  
+  
+  
+  
+  
+  
+  
+  
+  <h3 class="inherited">Methods inherited from <span class='object_link'><a href="Operator.html" title="Operator (class)">Operator</a></span></h3>
+  <p class="inherited"><span class='object_link'><a href="Operator.html#exec-instance_method" title="Operator#exec (method)">#exec</a></span></p>
+<div id="constructor_details" class="method_details_list">
+  <h2>Constructor Details</h2>
+  
+    <div class="method_details first">
+  <h3 class="signature first" id="initialize-instance_method">
+  
+    - (<tt><span class='object_link'><a href="" title="BinaryOperator (class)">BinaryOperator</a></span></tt>) <strong>initialize</strong>(name, exec_type, force_type = nil, pre_condition = nil, post_condition = nil) 
+  
+
+  
+
+  
+</h3><div class="docstring">
+  <div class="discussion">
+    <hr style="height: 10px">
+<hr style="height: 10px">
+
+
+  </div>
+</div>
+<div class="tags">
+  
+
+</div><table class="source_code">
+  <tr>
+    <td>
+      <pre class="lines">
+
+
+124
+125
+126
+127</pre>
+    </td>
+    <td>
+      <pre class="code"><span class="info file"># File 'lib/mdarray/operators.rb', line 124</span>
+
+<span class='rubyid_def def kw'>def</span> <span class='rubyid_initialize identifier id'>initialize</span><span class='lparen token'>(</span><span class='rubyid_name identifier id'>name</span><span class='comma token'>,</span> <span class='rubyid_exec_type identifier id'>exec_type</span><span class='comma token'>,</span> <span class='rubyid_force_type identifier id'>force_type</span> <span class='assign token'>=</span> <span class='rubyid_nil nil kw'>nil</span><span class='comma token'>,</span> <span class='rubyid_pre_condition identifier id'>pre_condition</span> <span class='assign token'>=</span> <span class='rubyid_nil nil kw'>nil</span><span class='comma token'>,</span> 
+               <span class='rubyid_post_condition identifier id'>post_condition</span> <span class='assign token'>=</span> <span class='rubyid_nil nil kw'>nil</span><span class='rparen token'>)</span>
+  <span class='rubyid_super super kw'>super</span><span class='lparen token'>(</span><span class='rubyid_name identifier id'>name</span><span class='comma token'>,</span> <span class='integer val'>2</span><span class='comma token'>,</span> <span class='rubyid_exec_type identifier id'>exec_type</span><span class='comma token'>,</span> <span class='rubyid_force_type identifier id'>force_type</span><span class='comma token'>,</span> <span class='rubyid_pre_condition identifier id'>pre_condition</span><span class='comma token'>,</span> <span class='rubyid_post_condition identifier id'>post_condition</span><span class='rparen token'>)</span>
+<span class='rubyid_end end kw'>end</span>
+</pre>
+    </td>
+  </tr>
+</table>
+</div>
+  
+</div>
+
+
+</div>
+
+    <div id="footer">
+  Generated on Thu May 16 12:48:41 2013 by
+  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
+  0.8.5.2 (ruby-1.9.3).
+</div>
+
+  </body>
+</html>

data/doc/BitwiseOperators.html

@@ -0,0 +1,135 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>
+  Module: BitwiseOperators
+  
+    &mdash; Documentation by YARD 0.8.5.2
+  
+</title>
+
+  <link rel="stylesheet" href="css/style.css" type="text/css" media="screen" charset="utf-8" />
+
+  <link rel="stylesheet" href="css/common.css" type="text/css" media="screen" charset="utf-8" />
+
+<script type="text/javascript" charset="utf-8">
+  hasFrames = window.top.frames.main ? true : false;
+  relpath = '';
+  framesUrl = "frames.html#!" + escape(window.location.href);
+</script>
+
+
+  <script type="text/javascript" charset="utf-8" src="js/jquery.js"></script>
+
+  <script type="text/javascript" charset="utf-8" src="js/app.js"></script>
+
+
+  </head>
+  <body>
+    <div id="header">
+      <div id="menu">
+  
+    <a href="_index.html">Index (B)</a> &raquo;
+    
+    
+    <span class="title">BitwiseOperators</span>
+  
+
+  <div class="noframes"><span class="title">(</span><a href="." target="_top">no frames</a><span class="title">)</span></div>
+</div>
+
+      <div id="search">
+  
+    <a class="full_list_link" id="class_list_link"
+        href="class_list.html">
+      Class List
+    </a>
+  
+    <a class="full_list_link" id="method_list_link"
+        href="method_list.html">
+      Method List
+    </a>
+  
+    <a class="full_list_link" id="file_list_link"
+        href="file_list.html">
+      File List
+    </a>
+  
+</div>
+      <div class="clear"></div>
+    </div>
+
+    <iframe id="search_frame"></iframe>
+
+    <div id="content"><h1>Module: BitwiseOperators
+  
+  
+  
+</h1>
+
+<dl class="box">
+  
+  
+    
+      <dt class="r1">Extended by:</dt>
+      <dd class="r1"><span class='object_link'><a href="FunctionCreation.html" title="FunctionCreation (module)">FunctionCreation</a></span>, <span class='object_link'><a href="RubyFunctions.html" title="RubyFunctions (module)">RubyFunctions</a></span></dd>
+      
+    
+  
+    
+  
+  
+    <dt class="r2">Included in:</dt>
+    <dd class="r2"><span class='object_link'><a href="LongMDArray.html" title="LongMDArray (class)">LongMDArray</a></span></dd>
+    
+  
+  
+    <dt class="r1 last">Defined in:</dt>
+    <dd class="r1 last">lib/mdarray/ruby_numeric_functions.rb</dd>
+  
+</dl>
+<div class="clear"></div>
+
+
+
+
+
+
+
+
+
+  
+  
+  
+  
+  
+  
+  <h2>Method Summary</h2>
+  
+  <h3 class="inherited">Methods included from <span class='object_link'><a href="RubyFunctions.html" title="RubyFunctions (module)">RubyFunctions</a></span></h3>
+  <p class="inherited"><span class='object_link'><a href="RubyFunctions.html#ruby_binary_function-instance_method" title="RubyFunctions#ruby_binary_function (method)">ruby_binary_function</a></span>, <span class='object_link'><a href="RubyFunctions.html#ruby_unary_function-instance_method" title="RubyFunctions#ruby_unary_function (method)">ruby_unary_function</a></span></p>
+
+  
+  
+  
+  
+  
+  
+  
+  
+  <h3 class="inherited">Methods included from <span class='object_link'><a href="FunctionCreation.html" title="FunctionCreation (module)">FunctionCreation</a></span></h3>
+  <p class="inherited"><span class='object_link'><a href="FunctionCreation.html#make_binary_op-instance_method" title="FunctionCreation#make_binary_op (method)">make_binary_op</a></span>, <span class='object_link'><a href="FunctionCreation.html#make_binary_operators-instance_method" title="FunctionCreation#make_binary_operators (method)">make_binary_operators</a></span>, <span class='object_link'><a href="FunctionCreation.html#make_comparison_op-instance_method" title="FunctionCreation#make_comparison_op (method)">make_comparison_op</a></span>, <span class='object_link'><a href="FunctionCreation.html#make_unary_op-instance_method" title="FunctionCreation#make_unary_op (method)">make_unary_op</a></span>, <span class='object_link'><a href="FunctionCreation.html#make_unary_operators-instance_method" title="FunctionCreation#make_unary_operators (method)">make_unary_operators</a></span></p>
+
+
+</div>
+
+    <div id="footer">
+  Generated on Thu May 16 12:48:35 2013 by
+  <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
+  0.8.5.2 (ruby-1.9.3).
+</div>
+
+  </body>
+</html>