mdarray 0.4.3.pre-java → 0.5.0-java

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Files changed (111) hide show
  1. data/README.md +82 -14
  2. data/Rakefile +8 -2
  3. data/doc/BinaryOperator.html +227 -0
  4. data/doc/BitwiseOperators.html +135 -0
  5. data/doc/BooleanFunctions.html +135 -0
  6. data/doc/BooleanMDArray.html +193 -0
  7. data/doc/ByteMDArray.html +271 -0
  8. data/doc/Colt.html +269 -0
  9. data/doc/ComparisonOperators.html +135 -0
  10. data/doc/Const.html +490 -0
  11. data/doc/Csv.html +589 -0
  12. data/doc/DDescriptive.html +4373 -0
  13. data/doc/DoubleMDArray.html +555 -0
  14. data/doc/DoubleStatList.html +256 -0
  15. data/doc/FastBinaryOperator.html +743 -0
  16. data/doc/FastBoolean.html +512 -0
  17. data/doc/FastUnaryOperator.html +583 -0
  18. data/doc/FloatMDArray.html +237 -0
  19. data/doc/FunctionCreation.html +520 -0
  20. data/doc/FunctionMap.html +813 -0
  21. data/doc/GenericFunctions.html +135 -0
  22. data/doc/IntMDArray.html +259 -0
  23. data/doc/LongMDArray.html +257 -0
  24. data/doc/MDArray.html +9639 -0
  25. data/doc/MDArray/Counter.html +2767 -0
  26. data/doc/MDArray/IteratorFast.html +872 -0
  27. data/doc/MDArray/IteratorFastBoolean.html +384 -0
  28. data/doc/MDArray/IteratorFastByte.html +373 -0
  29. data/doc/MDArray/IteratorFastChar.html +384 -0
  30. data/doc/MDArray/IteratorFastDouble.html +384 -0
  31. data/doc/MDArray/IteratorFastFloat.html +384 -0
  32. data/doc/MDArray/IteratorFastInt.html +384 -0
  33. data/doc/MDArray/IteratorFastLong.html +384 -0
  34. data/doc/MDArray/IteratorFastShort.html +384 -0
  35. data/doc/MDArrayTest.html +125 -0
  36. data/doc/NonNumericalMDArray.html +177 -0
  37. data/doc/NumericFunctions.html +297 -0
  38. data/doc/NumericalMDArray.html +278 -0
  39. data/doc/Operator.html +826 -0
  40. data/doc/Proc.html +1097 -0
  41. data/doc/RubyBinaryOperator.html +526 -0
  42. data/doc/RubyFunctions.html +232 -0
  43. data/doc/RubyMath.html +135 -0
  44. data/doc/RubyStats.html +135 -0
  45. data/doc/RubyUnaryOperator.html +510 -0
  46. data/doc/ShortMDArray.html +267 -0
  47. data/doc/StatList.html +1176 -0
  48. data/doc/StringMDArray.html +181 -0
  49. data/doc/StructureMDArray.html +181 -0
  50. data/doc/UnaryOperator.html +227 -0
  51. data/doc/UserFunction.html +297 -0
  52. data/doc/_index.html +467 -0
  53. data/doc/class_list.html +53 -0
  54. data/doc/css/common.css +1 -0
  55. data/doc/css/full_list.css +57 -0
  56. data/doc/css/style.css +338 -0
  57. data/doc/file.README.html +173 -0
  58. data/doc/file_list.html +55 -0
  59. data/doc/frames.html +28 -0
  60. data/doc/index.html +173 -0
  61. data/doc/js/app.js +214 -0
  62. data/doc/js/full_list.js +173 -0
  63. data/doc/js/jquery.js +4 -0
  64. data/doc/method_list.html +2524 -0
  65. data/doc/top-level-namespace.html +114 -0
  66. data/lib/colt/colt.rb +56 -0
  67. data/lib/colt/colt_mdarray.rb +95 -0
  68. data/lib/colt/double_descriptive.rb +636 -0
  69. data/lib/colt/probability.rb +12 -0
  70. data/lib/colt/stat_list.rb +192 -0
  71. data/lib/env.rb +5 -1
  72. data/lib/mdarray.rb +5 -0
  73. data/lib/mdarray/access.rb +2 -2
  74. data/lib/mdarray/creation.rb +34 -19
  75. data/lib/mdarray/csv.rb +61 -0
  76. data/lib/mdarray/fast_operators.rb +241 -0
  77. data/lib/mdarray/operators.rb +18 -0
  78. data/lib/mdarray/ruby_operators.rb +2 -18
  79. data/lib/mdarray/ruby_stats.rb +1 -1
  80. data/lib/mdarray/views.rb +8 -8
  81. data/target/helper.jar +0 -0
  82. data/test/colt/VALE3.csv +3437 -0
  83. data/test/colt/VALE3.xlsx +0 -0
  84. data/test/colt/VALE3_short-err.csv +20 -0
  85. data/test/colt/VALE3_short.csv +20 -0
  86. data/test/colt/VALE3_short.xlsx +0 -0
  87. data/test/colt/test_complete.rb +25 -0
  88. data/test/colt/test_stat_list.rb +128 -0
  89. data/test/colt/test_statistics.rb +114 -0
  90. data/test/complete.rb +25 -0
  91. data/test/env.rb +54 -30
  92. data/test/{arithmetic_casting.rb → mdarray/arithmetic_casting.rb} +0 -0
  93. data/test/{test_access.rb → mdarray/test_access.rb} +0 -0
  94. data/test/{test_boolean.rb → mdarray/test_boolean.rb} +0 -2
  95. data/test/{test_comparison.rb → mdarray/test_comparison.rb} +0 -0
  96. data/test/{test_complete.rb → mdarray/test_complete.rb} +3 -14
  97. data/test/{test_counter.rb → mdarray/test_counter.rb} +0 -0
  98. data/test/{test_creation.rb → mdarray/test_creation.rb} +0 -0
  99. data/test/{test_error.rb → mdarray/test_error.rb} +8 -5
  100. data/test/{test_operator.rb → mdarray/test_operator.rb} +6 -2
  101. data/test/{test_speed.rb → mdarray/test_performance.rb} +74 -39
  102. data/test/{test_printing.rb → mdarray/test_printing.rb} +0 -1
  103. data/test/{test_shape.rb → mdarray/test_shape.rb} +0 -0
  104. data/test/mdarray/test_statistics.rb +80 -0
  105. data/test/{test_trigonometry.rb → mdarray/test_trigonometry.rb} +0 -0
  106. data/test/{test_views.rb → mdarray/test_views.rb} +0 -0
  107. data/vendor/parallelcolt-0.10.0.jar +0 -0
  108. data/version.rb +1 -1
  109. metadata +122 -39
  110. data/test/test_lazy.rb +0 -52
  111. data/test/test_statistics.rb +0 -38
data/doc/file.README.html ADDED
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+ &mdash; Documentation by YARD 0.8.5.2
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+ </div>
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+ <iframe id="search_frame"></iframe>
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+
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+ <div id="content"><div id='filecontents'><h1 id="mdarray">MDArray</h1>
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+
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+ <p>MDArray is a multi dimensional array implemented for JRuby inspired by NumPy (www.numpy.org)
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+ and Narray (narray.rubyforge.org) by Masahiro Tanaka. MDArray stands on the shoulders of
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+ Java-NetCDF and Parallel Colt.</p>
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+
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+ <p>NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of
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+ scientific data formats. It is developed and distributed by Unidata (http://www.unidata.ucar.edu). </p>
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+
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+ <p>Parallel Colt (sites.google.com/site/piotrwendykier/software/parallelcolt) is a multithreaded
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+ version of Colt (http://acs.lbl.gov/software/colt/). Colt provides a set of Open Source
75
+ Libraries for High Performance Scientific and Technical Computing in Java. Scientific
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+ and technical computing is characterized by demanding problem sizes and a need for high
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+ performance at reasonably small memory footprint.</p>
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+
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+ <h1 id="mdarray-and-sciruby">MDArray and SciRuby</h1>
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+
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+ <p>MDArray subscribes fully to the SciRuby Manifesto (http://sciruby.com/). </p>
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+
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+ <p>“Ruby has for some time had no equivalent to the beautifully constructed NumPy, SciPy,
84
+ and matplotlib libraries for Python. </p>
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+
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+ <p>We believe that the time for a Ruby science and visualization package has come. Sometimes
87
+ when a solution of sugar and water becomes super-saturated, from it precipitates a pure,
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+ delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap
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+ of a finger. So is occurring now, we believe, with numeric and visualization libraries for Ruby.”</p>
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+
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+ <h1 id="main-properties">Main properties</h1>
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+
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+ <ul>
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+ <li>Homogeneous multidimensional array, a table of elements (usually numbers), all of the
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+ same type, indexed by a tuple of positive integers;</li>
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+ <li>Easy calculation for large numerical multi dimensional arrays;</li>
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+ <li>Basic types are: boolean, byte, short, int, long, float, double, string, structure;</li>
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+ <li>Based on JRuby, which allows importing Java libraries. Version 0.4.0 only imports
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+ Java-NetCDF;</li>
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+ <li>Operator: +,-,*,/,%,**, &gt;, &gt;=, etc.</li>
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+ <li>Functions: abs, ceil, floor, truncate, is_zero, square, cube, fourth;</li>
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+ <li>
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+ <table>
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+ <tbody>
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+ <tr>
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+ <td>Binary Operators: &amp;,</td>
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+ <td>, ^, ~ (binary_ones_complement), «, »;</td>
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+ </tr>
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+ </tbody>
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+ </table>
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+ </li>
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+ <li>Ruby Math functions: acos, acosh, asin, asinh, atan, atan2, atanh, cbrt, cos, erf, exp,
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+ gamma, hypot, ldexp, log, log10, log2, sin, sinh, sqrt, tan, tanh, neg;</li>
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+ <li>Boolean operations on boolean arrays: and, or, not;</li>
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+ <li>Fast descriptive statistics from Parallel Colt (complete list found bellow);</li>
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+ <li>Easy manipulation of arrays: reshape, reduce dimension, permute, section, slice, etc.</li>
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+ <li>Reading of two dimensional arrays from CSV files (mainly for debugging and simple
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+ testing purposes);</li>
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+ <li>StatList: a list that can grow/shrink and that can compute Parallel Colt descriptive
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+ statistics. </li>
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+ </ul>
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+
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+ <h1 id="descriptive-statistics-methods">Descriptive statistics methods</h1>
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+
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+ <p>auto_correlation, correlation, covariance, durbin_watson, frequencies, geometric_mean,
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+ harmonic_mean, kurtosis, lag1, max, mean, mean_deviation, median, min, moment, moment3,
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+ moment4, pooled_mean, pooled_variance, product, quantile, quantile_inverse,
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+ rank_interpolated, rms, sample_covariance, sample_kurtosis,
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+ sample_kurtosis_standard_error, sample_skew, sample_skew_standard_error,
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+ sample_standard_deviation, sample_variance, sample_weighted_variance, skew, split,<br />
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+ standard_deviation, standard_error, sum, sum_of_inversions, sum_of_logarithms,
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+ sum_of_powers, sum_of_power_deviations, sum_of_squares, sum_of_squared_deviations,
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+ trimmed_mean, variance, weighted_mean, weighted_rms, weighted_sums, winsorized_mean.</p>
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+
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+ <h1 id="installation-and-download">Installation and download</h1>
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+
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+ <ul>
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+ <li>Install Jruby</li>
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+ <li>jruby –S gem install mdarray</li>
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+ </ul>
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+
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+ <h1 id="contributors">Contributors</h1>
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+
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+ <ul>
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+ <li>Contributors are welcome.</li>
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+ </ul>
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+
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+ <h1 id="homepages">Homepages</h1>
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+
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+ <ul>
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+ <li>http://rubygems.org/gems/mdarray</li>
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+ <li>https://github.com/rbotafogo/mdarray/wiki</li>
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+ </ul>
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+
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+ <h1 id="history">HISTORY</h1>
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+
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+ <ul>
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+ <li>16/05/2013: Version 0.5.0: All loops transfered to Java with over 50% performance
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+ improvement. Descriptive statistics from Parallel Colt.</li>
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+ <li>19/04/2013: Version 0.4.3: Fixes a simple (but fatal bug). No new features</li>
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+ <li>17/04/2013: Version 0.4.2: Adds simple statistics and boolean operators</li>
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+ <li>05/05/2013: Version 0.4.0: Initial release</li>
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+ </ul>
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+ </div></div>
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+
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+ <div id="footer">
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+ Generated on Thu May 16 12:48:34 2013 by
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+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
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+ 0.8.5.2 (ruby-1.9.3).
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+ </div>
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+
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+ </body>
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+ </html>
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+ <div id="content"><div id='filecontents'><h1 id="mdarray">MDArray</h1>
65
+
66
+ <p>MDArray is a multi dimensional array implemented for JRuby inspired by NumPy (www.numpy.org)
67
+ and Narray (narray.rubyforge.org) by Masahiro Tanaka. MDArray stands on the shoulders of
68
+ Java-NetCDF and Parallel Colt.</p>
69
+
70
+ <p>NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of
71
+ scientific data formats. It is developed and distributed by Unidata (http://www.unidata.ucar.edu). </p>
72
+
73
+ <p>Parallel Colt (sites.google.com/site/piotrwendykier/software/parallelcolt) is a multithreaded
74
+ version of Colt (http://acs.lbl.gov/software/colt/). Colt provides a set of Open Source
75
+ Libraries for High Performance Scientific and Technical Computing in Java. Scientific
76
+ and technical computing is characterized by demanding problem sizes and a need for high
77
+ performance at reasonably small memory footprint.</p>
78
+
79
+ <h1 id="mdarray-and-sciruby">MDArray and SciRuby</h1>
80
+
81
+ <p>MDArray subscribes fully to the SciRuby Manifesto (http://sciruby.com/). </p>
82
+
83
+ <p>“Ruby has for some time had no equivalent to the beautifully constructed NumPy, SciPy,
84
+ and matplotlib libraries for Python. </p>
85
+
86
+ <p>We believe that the time for a Ruby science and visualization package has come. Sometimes
87
+ when a solution of sugar and water becomes super-saturated, from it precipitates a pure,
88
+ delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap
89
+ of a finger. So is occurring now, we believe, with numeric and visualization libraries for Ruby.”</p>
90
+
91
+ <h1 id="main-properties">Main properties</h1>
92
+
93
+ <ul>
94
+ <li>Homogeneous multidimensional array, a table of elements (usually numbers), all of the
95
+ same type, indexed by a tuple of positive integers;</li>
96
+ <li>Easy calculation for large numerical multi dimensional arrays;</li>
97
+ <li>Basic types are: boolean, byte, short, int, long, float, double, string, structure;</li>
98
+ <li>Based on JRuby, which allows importing Java libraries. Version 0.4.0 only imports
99
+ Java-NetCDF;</li>
100
+ <li>Operator: +,-,*,/,%,**, &gt;, &gt;=, etc.</li>
101
+ <li>Functions: abs, ceil, floor, truncate, is_zero, square, cube, fourth;</li>
102
+ <li>
103
+ <table>
104
+ <tbody>
105
+ <tr>
106
+ <td>Binary Operators: &amp;,</td>
107
+ <td>, ^, ~ (binary_ones_complement), «, »;</td>
108
+ </tr>
109
+ </tbody>
110
+ </table>
111
+ </li>
112
+ <li>Ruby Math functions: acos, acosh, asin, asinh, atan, atan2, atanh, cbrt, cos, erf, exp,
113
+ gamma, hypot, ldexp, log, log10, log2, sin, sinh, sqrt, tan, tanh, neg;</li>
114
+ <li>Boolean operations on boolean arrays: and, or, not;</li>
115
+ <li>Fast descriptive statistics from Parallel Colt (complete list found bellow);</li>
116
+ <li>Easy manipulation of arrays: reshape, reduce dimension, permute, section, slice, etc.</li>
117
+ <li>Reading of two dimensional arrays from CSV files (mainly for debugging and simple
118
+ testing purposes);</li>
119
+ <li>StatList: a list that can grow/shrink and that can compute Parallel Colt descriptive
120
+ statistics. </li>
121
+ </ul>
122
+
123
+ <h1 id="descriptive-statistics-methods">Descriptive statistics methods</h1>
124
+
125
+ <p>auto_correlation, correlation, covariance, durbin_watson, frequencies, geometric_mean,
126
+ harmonic_mean, kurtosis, lag1, max, mean, mean_deviation, median, min, moment, moment3,
127
+ moment4, pooled_mean, pooled_variance, product, quantile, quantile_inverse,
128
+ rank_interpolated, rms, sample_covariance, sample_kurtosis,
129
+ sample_kurtosis_standard_error, sample_skew, sample_skew_standard_error,
130
+ sample_standard_deviation, sample_variance, sample_weighted_variance, skew, split,<br />
131
+ standard_deviation, standard_error, sum, sum_of_inversions, sum_of_logarithms,
132
+ sum_of_powers, sum_of_power_deviations, sum_of_squares, sum_of_squared_deviations,
133
+ trimmed_mean, variance, weighted_mean, weighted_rms, weighted_sums, winsorized_mean.</p>
134
+
135
+ <h1 id="installation-and-download">Installation and download</h1>
136
+
137
+ <ul>
138
+ <li>Install Jruby</li>
139
+ <li>jruby –S gem install mdarray</li>
140
+ </ul>
141
+
142
+ <h1 id="contributors">Contributors</h1>
143
+
144
+ <ul>
145
+ <li>Contributors are welcome.</li>
146
+ </ul>
147
+
148
+ <h1 id="homepages">Homepages</h1>
149
+
150
+ <ul>
151
+ <li>http://rubygems.org/gems/mdarray</li>
152
+ <li>https://github.com/rbotafogo/mdarray/wiki</li>
153
+ </ul>
154
+
155
+ <h1 id="history">HISTORY</h1>
156
+
157
+ <ul>
158
+ <li>16/05/2013: Version 0.5.0: All loops transfered to Java with over 50% performance
159
+ improvement. Descriptive statistics from Parallel Colt.</li>
160
+ <li>19/04/2013: Version 0.4.3: Fixes a simple (but fatal bug). No new features</li>
161
+ <li>17/04/2013: Version 0.4.2: Adds simple statistics and boolean operators</li>
162
+ <li>05/05/2013: Version 0.4.0: Initial release</li>
163
+ </ul>
164
+ </div></div>
165
+
166
+ <div id="footer">
167
+ Generated on Thu May 16 12:48:34 2013 by
168
+ <a href="http://yardoc.org" title="Yay! A Ruby Documentation Tool" target="_parent">yard</a>
169
+ 0.8.5.2 (ruby-1.9.3).
170
+ </div>
171
+
172
+ </body>
173
+ </html>
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183
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184
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185
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186
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