gentooboontoo-gphys 0.6.1.3 → 1.3.1.1

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  1. checksums.yaml +4 -4
  2. data/ChangeLog +5631 -464
  3. data/LICENSE.txt +34 -0
  4. data/README +23 -25
  5. data/bin/gdir_client +25 -7
  6. data/bin/gdir_server +19 -13
  7. data/bin/gpaop +41 -28
  8. data/bin/gpcat +19 -11
  9. data/bin/gpcut +20 -11
  10. data/bin/gpedit +37 -1
  11. data/bin/gplist +5 -4
  12. data/bin/gpmath +21 -14
  13. data/bin/gpmaxmin +9 -7
  14. data/bin/gpprint +15 -11
  15. data/bin/gpvect +217 -96
  16. data/bin/gpview +278 -123
  17. data/bin/grads2nc_with_gphys +11 -6
  18. data/doc/attribute.html +1 -1
  19. data/doc/axis.html +85 -66
  20. data/doc/coordmapping.html +22 -22
  21. data/doc/dclext.html +709 -0
  22. data/doc/derivative/gphys-derivative.html +33 -13
  23. data/doc/derivative/numru-derivative.html +60 -31
  24. data/doc/gdir.html +76 -76
  25. data/doc/gdir_server.html +28 -16
  26. data/doc/ggraph.html +493 -706
  27. data/doc/gpcat.html +28 -11
  28. data/doc/gpcut.html +26 -11
  29. data/doc/gphys.html +195 -71
  30. data/doc/gphys_fft.html +162 -21
  31. data/doc/gphys_grads_io.html +9 -9
  32. data/doc/gphys_grib_io.html +7 -7
  33. data/doc/gphys_io.html +118 -31
  34. data/doc/gphys_io_common.html +1 -1
  35. data/doc/gphys_netcdf_io.html +14 -14
  36. data/doc/gplist.html +6 -5
  37. data/doc/gpmath.html +32 -14
  38. data/doc/gpmaxmin.html +9 -7
  39. data/doc/gpprint.html +14 -11
  40. data/doc/gpview.html +254 -146
  41. data/doc/grads2nc_with_gphys.html +6 -8
  42. data/doc/grads_gridded.html +77 -77
  43. data/doc/grib.html +102 -59
  44. data/doc/grid.html +45 -61
  45. data/doc/index.html +51 -41
  46. data/doc/index.rd +47 -36
  47. data/doc/netcdf_convention.html +39 -39
  48. data/doc/unumeric.html +79 -30
  49. data/doc/update +2 -1
  50. data/doc/varray.html +62 -56
  51. data/doc/varraycomposite.html +3 -3
  52. data/ext/ext_coord.c +209 -0
  53. data/ext/ext_init.c +7 -0
  54. data/ext/extconf.rb +41 -0
  55. data/ext/interpo.c +536 -0
  56. data/ext/multibitIO.c +567 -0
  57. data/lib/numru/dcl_mouse.rb +71 -0
  58. data/lib/numru/dclext.rb +2749 -0
  59. data/lib/numru/derivative.rb +124 -31
  60. data/lib/numru/ganalysis.rb +7 -0
  61. data/lib/numru/ganalysis/covariance.rb +154 -0
  62. data/lib/numru/ganalysis/eof.rb +302 -0
  63. data/lib/numru/ganalysis/histogram.rb +337 -0
  64. data/lib/numru/ganalysis/met.rb +872 -0
  65. data/lib/numru/ganalysis/planet.rb +392 -0
  66. data/lib/numru/ggraph.rb +1709 -2498
  67. data/lib/numru/gphys.rb +7 -1
  68. data/lib/numru/gphys/assoccoords.rb +384 -0
  69. data/lib/numru/gphys/attribute.rb +10 -11
  70. data/lib/numru/gphys/axis.rb +97 -25
  71. data/lib/numru/gphys/coordmapping.rb +2 -2
  72. data/lib/numru/gphys/derivative.rb +117 -46
  73. data/lib/numru/gphys/gphys.rb +595 -31
  74. data/lib/numru/gphys/gphys_fft.rb +365 -13
  75. data/lib/numru/gphys/gphys_grads_io.rb +6 -5
  76. data/lib/numru/gphys/gphys_grib_io.rb +6 -6
  77. data/lib/numru/gphys/gphys_gtool3_io.rb +162 -0
  78. data/lib/numru/gphys/gphys_hdfeos5_io.rb +672 -0
  79. data/lib/numru/gphys/gphys_io.rb +260 -20
  80. data/lib/numru/gphys/gphys_io_common.rb +1 -1
  81. data/lib/numru/gphys/gphys_netcdf_io.rb +111 -40
  82. data/lib/numru/gphys/gphys_nusdas_io.rb +64 -7
  83. data/lib/numru/gphys/grads_gridded.rb +158 -57
  84. data/lib/numru/gphys/grib.rb +205 -157
  85. data/lib/numru/gphys/grib_params.rb +196 -1
  86. data/lib/numru/gphys/grid.rb +214 -83
  87. data/lib/numru/gphys/gtool3.rb +771 -0
  88. data/lib/numru/gphys/interpolate.rb +992 -0
  89. data/lib/numru/gphys/mdstorage.rb +145 -0
  90. data/lib/numru/gphys/narray_ext.rb +34 -0
  91. data/lib/numru/gphys/netcdf_convention.rb +44 -2
  92. data/lib/numru/gphys/subsetmapping.rb +1 -1
  93. data/lib/numru/gphys/unumeric.rb +101 -8
  94. data/lib/numru/gphys/varray.rb +66 -20
  95. data/lib/numru/gphys/varraycomposite.rb +107 -29
  96. data/lib/numru/gphys/varraygrib.rb +70 -8
  97. data/lib/numru/gphys/varraygtool3.rb +226 -0
  98. data/lib/numru/gphys/varrayhdfeos5.rb +451 -0
  99. data/lib/numru/gphys/varraynetcdf.rb +13 -5
  100. data/lib/numru/gphys/version.rb +3 -0
  101. data/sample/druby_cli1.rb +2 -0
  102. data/sample/druby_cli2.rb +0 -6
  103. data/sample/druby_serv2.rb +0 -13
  104. data/sample/ncep_theta_coord.rb +79 -0
  105. data/test/eof_slp.rb +28 -0
  106. data/test/mltbit.dat +0 -0
  107. data/test/test_multibitIO.rb +19 -0
  108. data/testdata/assoc_crds.nc +0 -0
  109. metadata +79 -8
  110. data/lib/numru/dclext_datetime_ax.rb +0 -220
  111. data/lib/numru/vizshot.rb +0 -697
data/doc/gphys_fft.html CHANGED
@@ -7,22 +7,22 @@
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  <title>../lib/numru/gphys/gphys_fft.rb</title>
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  </head>
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  <body>
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- <h1><a name="label:0" id="label:0">extention of class NumRu::GPhys -- Fast Fourier transformation and its applications</a></h1><!-- RDLabel: "extention of class NumRu::GPhys &shy;&shy; Fast Fourier transformation and its applications" -->
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+ <h1><a name="label-0" id="label-0">extension of class NumRu::GPhys -- Fast Fourier transformation and its applications</a></h1><!-- RDLabel: "extension of class NumRu::GPhys &shy;&shy; Fast Fourier transformation and its applications" -->
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  <p>This manual documents the methods of NumRu::GPhys defined in gphys_fft.rb</p>
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- <h1><a name="label:1" id="label:1">class methods</a></h1><!-- RDLabel: "class methods" -->
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+ <h1><a name="label-1" id="label-1">class methods</a></h1><!-- RDLabel: "class methods" -->
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  <dl>
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- <dt><h4><a name="label:2" id="label:2"><code>GPhys::fft_ignore_missing( <var>ignore</var>=<var>true</var>, <var>replace_val</var>=<var>nil</var> )</code></a></h4></dt><!-- RDLabel: "GPhys::fft_ignore_missing" -->
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+ <dt><h4><a name="label-2" id="label-2"><code>GPhys::fft_ignore_missing( <var>ignore</var>=<var>true</var>, <var>replace_val</var>=<var>nil</var> )</code></a></h4></dt><!-- RDLabel: "GPhys::fft_ignore_missing" -->
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  <dd>
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- <p>Set a flag (class variable) to ignore missing values.
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+ Set a flag (class variable) to ignore missing values.
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  This is for data that do not have missing
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  but is treated as potentially having missing (often
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  by having the valid_* attributes of NetCDF.)
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  If replace_val is specified, data missing with replaced
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- with that value.</p></dd>
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+ with that value.</dd>
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  </dl>
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- <h1><a name="label:3" id="label:3">methods</a></h1><!-- RDLabel: "methods" -->
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+ <h1><a name="label-3" id="label-3">methods</a></h1><!-- RDLabel: "methods" -->
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  <dl>
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- <dt><h4><a name="label:4" id="label:4"><code>fft(<var>backward</var>=<var>false</var>, *<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "fft" -->
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+ <dt><h4><a name="label-4" id="label-4"><code>fft(<var>backward</var>=<var>false</var>, *<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "fft" -->
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  <dd>
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  <p>Fast Fourier Transformation (FFT) by using
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  (<a href="http://www.fftw.org">FFTW</a>) ver 3 or ver 2.
@@ -38,7 +38,14 @@ FFTW.</p>
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  <p>Each coordinate is assumed to be equally spaced without checking.
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  The new coordinate variables will be set equal to wavenumbers,
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  derived as 2*PI/(length of the axis)*[0,1,2,..], where the length
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- of the axis is derieved as (coord.val.max - coord.val.min)*(n+1)/n.</p>
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+ of the axis is derived as (coord.val.max - coord.val.min)*(n+1)/n.</p>
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+ <p>REMARK</p>
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+ <ul>
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+ <li>If the units of the original coordinate is degree (or its
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+ equivalent ones such as degrees_east), the wavenumber was
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+ made in integers by converting the coordinate based on
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+ radian.</li>
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+ </ul>
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  <p>ARGUMENTS</p>
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  <ul>
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  <li>backward (true of false) : when true, backward FT is done;
@@ -54,7 +61,7 @@ of the axis is derieved as (coord.val.max - coord.val.min)*(n+1)/n.</p>
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  gphy.fft(true) # backward, for all dimensions
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  gphy.fft(nil, 0,1) # forward, for the first and second dimensions.
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  gphy.fft(true, -1) # backward, for the last dimension.</pre></dd>
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- <dt><h4><a name="label:5" id="label:5"><code>detrend(<var>dim1</var>[,<var>dim2</var>[,...]])</code></a></h4></dt><!-- RDLabel: "detrend" -->
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+ <dt><h4><a name="label-5" id="label-5"><code>detrend(<var>dim1</var>[,<var>dim2</var>[,...]])</code></a></h4></dt><!-- RDLabel: "detrend" -->
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  <dd>
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  <p>Remove means and linear trends along dimension(s) specified.
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  Algorithm: 1st order polynomial fitting.</p>
@@ -69,9 +76,9 @@ Algorithm: 1st order polynomial fitting.</p>
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  </ul>
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  <p>EXAMPLE</p>
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  <ul>
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- <li>See <a href="#label:5">detrend</a>.</li>
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+ <li>See <a href="#label-5">detrend</a>.</li>
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  </ul></dd>
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- <dt><h4><a name="label:6" id="label:6"><code>cos_taper(<var>dim1</var>[,<var>dim2</var>[,...]])</code></a></h4></dt><!-- RDLabel: "cos_taper" -->
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+ <dt><h4><a name="label-6" id="label-6"><code>cos_taper(<var>dim1</var>[,<var>dim2</var>[,...]])</code></a></h4></dt><!-- RDLabel: "cos_taper" -->
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  <dd>
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  <p>Cosine tapering along dimension(s) specified.</p>
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  <p>Algorithm: to multiply with the half cosine curves at the both
@@ -83,7 +90,7 @@ Algorithm: 1st order polynomial fitting.</p>
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  T/10 T/10
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  half-cosine half-cosine
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  shaped shaped</pre>
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- <p>The spectra of tapered data should be multilied by 1/0.875,
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+ <p>The spectra of tapered data should be multiplied by 1/0.875,
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  which is stored as GPhys::COS_TAPER_SP_FACTOR (==1/0.875).</p>
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  <p>ARGUMENTS</p>
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  <ul>
@@ -98,10 +105,10 @@ which is stored as GPhys::COS_TAPER_SP_FACTOR (==1/0.875).</p>
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  <pre>dim = 0 # for the 1st dimension
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  fc = gphys.detrend(dim).cos_taper(dim).fft(nil,dim)
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  sp = fc.abs**2 * GPhys::COS_TAPER_SP_FACTOR</pre></dd>
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- <dt><h4><a name="label:7" id="label:7"><code>spect_zero_centering(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_zero_centering" -->
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+ <dt><h4><a name="label-7" id="label-7"><code>spect_zero_centering(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_zero_centering" -->
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  <dd>
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- <p>Shifts the waveneumber axis to cover from -K/2 to K/2 instead of
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- from 0 to K-1, where the wavenumber is simbolically treated as integer,
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+ <p>Shifts the wavenumber axis to cover from -K/2 to K/2 instead of
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+ from 0 to K-1, where the wavenumber is symbolically treated as integer,
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  which is actually not the case, though. Since the first (-K/2) and
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  the last (K/2) elements are duplicated, both are divided by 2.
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  Therefore, this method is to be used for spectra (squared quantity)
@@ -133,9 +140,9 @@ sp = ( fc.abs**2 ).spect_zero_centering(0).spect_one_sided(1)</pre></li>
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  fc2 = var2.fft(nil, 0,1)
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  xsp = (fc1 * fc2.conj).spect_zero_centering(0).spect_zero_centering(1)</pre></li>
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  </ul></dd>
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- <dt><h4><a name="label:8" id="label:8"><code>spect_one_sided(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_one_sided" -->
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+ <dt><h4><a name="label-8" id="label-8"><code>spect_one_sided(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_one_sided" -->
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  <dd>
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- <p>Similar to <a href="#label:7">spect_zero_centering</a> but to make one-sided spectra.
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+ <p>Similar to <a href="#label-7">spect_zero_centering</a> but to make one-sided spectra.
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  Namely, to convert from 0..K-1 to 0..K/2. To be applied for spectra;
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  wavenumber 2..K/2-1 are multiplied by 2.</p>
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  <p>ARGUMENTS</p>
@@ -149,13 +156,13 @@ wavenumber 2..K/2-1 are multiplied by 2.</p>
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  </ul>
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  <p>EXAMPLE</p>
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  <ul>
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- <li>See the 2nd example of <a href="#label:7">spect_zero_centering</a>.</li>
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+ <li>See the 2nd example of <a href="#label-7">spect_zero_centering</a>.</li>
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  </ul></dd>
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- <dt><h4><a name="label:9" id="label:9"><code>rawspect2powerspect(*<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "rawspect2powerspect" -->
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+ <dt><h4><a name="label-9" id="label-9"><code>rawspect2powerspect(*<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "rawspect2powerspect" -->
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  <dd>
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  <p>Converts raw spectra obtained by gphys.fft.abs**2 into
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  power spectra by dividing by wavenumber increments
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- along the dimensions spcified by dims.</p>
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+ along the dimensions specified by dims.</p>
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  <p>ARGUMENTS</p>
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  <ul>
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  <li>dims (integers): the dimensions corresponding to wavenumbers.</li>
@@ -170,13 +177,147 @@ along the dimensions spcified by dims.</p>
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  <pre>fc = gphys.fft(nil, 0, 1)
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  sp = fc.abs**2
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  ps = sp.rawspect2powerspect(0,1)</pre>
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- <p>Here, sp is the raw spectum of gphys, and ps is the power spectrum.
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+ <p>Here, sp is the raw spectrum of gphys, and ps is the power spectrum.
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  The Parseval relation for them are as follows:</p>
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  <pre>(gphys**2).mean == sp.sum
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  == pw.sum*dk*dl (== \int pw dk dl, mathematically),</pre>
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  <p>where, dk = (pw.coord(0)[1] - pw.coord(0)[0]), and
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  dl = (pw.coord(1)[1] - pw.coord(1)[0]).</p></li>
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  </ul></dd>
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+ <dt><h4><a name="label-10" id="label-10"><code>phase_velocity_filter(<var>xdim</var>, <var>tdim</var>, <var>cmin</var>=<var>nil</var>, <var>cmax</var>=<var>nil</var>, <var>xconv</var>=<var>nil</var>, <var>tconv</var>=<var>nil</var>, <var>remove_xtmean</var>=<var>false</var>)</code></a></h4></dt><!-- RDLabel: "phase_velocity_filter" -->
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+ <dd>
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+ <p>Filtering by phase velocity (between cmin and cmax)</p>
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+ <p>REMARKS</p>
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+ <ul>
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+ <li>If the number of the grid points along x or t is an even number,
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+ the maximum wavenumber or frequency is treated as positive
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+ and negative, respectively, which results in an asymmetry of
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+ the treatment of positive and negative phase speeds.
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+ (That should be ok. -- In case its effect is significant,
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+ to do the filtering itself is not meaningful.)</li>
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+ </ul>
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+ <p>ARGUMENTS</p>
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+ <ul>
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+ <li>xdim (Integer or String): spacial dimension</li>
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+ <li>tdim (Integer or String): time dimension</li>
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+ <li>cmin (Float or nil): minimum phase velocity. nil means no specification.
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+ (at least cmin or cmax must be given by Float)</li>
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+ <li>cmax (Float or nil): maximum phase velocity. nil means no specification.
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+ (at least cmin or cmax must be given by Float)</li>
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+ <li>xconv (nil or UNumeric) : (optional) if given, xconv is multiplied
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+ with the x axis before computing the phase velocity
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+ (kconv=1/xconv is used to scale wavenumbers)</li>
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+ <li>tconv (nil or UNumeric) : (optional) if given, tconv is multiplied
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+ with the t axis before computing the phase velocity
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+ (fconv=1/tconv is used to scale frequency)</li>
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+ <li>remove_xtmean (false or true) : if false (default),
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+ components with k=0 and f=0 are counted as c=0 (stationary),
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+ (unlike <a href="#label-12">phase_velocity_binning</a>), so they are included if
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+ cmin*cmax &lt;= 0; if true, k=0 &amp; f=0 components are always removed.</li>
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+ </ul>
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+ <p>RETURN VALUE</p>
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+ <ul>
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+ <li>a GPhys</li>
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+ </ul>
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+ <p>EXAMPLE</p>
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+ <ul>
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+ <li><p>For a 4D data with [x,y,z,t] dimensions, filtering by the phase
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+ velocity in the y dimension greater than 10.0 (in the unit
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+ of y/t) can be made by</p>
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+ <pre>cmin = 10.0; cmax = nil
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+ gpfilt = gp.phase_velocity_filter(1, 3, cmin, cmax)</pre></li>
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+ <li><p>For a global data (on the Earth's surface) with
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+ [lon, lat, z, time] axes, where the units of lon is
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+ "degrees" (or "degrees_east" or "radian")
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+ and the units of time is "hours", to filter disturbances
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+ whose zonal phase speed MEASURED AT THE EQUATOR is less or
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+ equal to 30 m/s can be made by</p>
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+ <pre>cmin = -30.0; cmax = 30.0
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+ xconv = UNumeric[6.37e6, "m"] # Earth's radius (i.e., m/radian)
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+ # This is a special case since "radian" is exceptionally omitted.
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+ # See the private method __predefined_coord_units_conversion.
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+ tconv = UNumeric[3.6e3, "s/hours"]
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+ gpfilt = gp.phase_velocity_filter(1, 3, cmin, cmax, xconv, tconv)</pre></li>
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+ </ul></dd>
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+ <dt><h4><a name="label-11" id="label-11"><code>phase_velocity_binning_iso_norml(<var>kdim</var>, <var>fdim</var>, <var>cmin</var>, <var>cmax</var>, <var>cint</var>, <var>kconv</var>=<var>nil</var>, <var>fconv</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "phase_velocity_binning_iso_norml" -->
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+ <dd>
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+ <p>Same as <a href="#label-12">phase_velocity_binning</a> but exclusively for
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+ equal phase velocity spacing. Also, a normalization is
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+ additionally made, to scale spectra in terms of integration
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+ along phase velocity axis --- The result of
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+ <a href="#label-12">phase_velocity_binning</a> called inside
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+ this method is divided by cint along with corresponding
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+ units conversion. Therefore, if this method is applied
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+ to spectra, a normalization is made such that an integration
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+ (not summation) along the phase velocity gives the variance
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+ (or covariance etc.) -- This normalization is suitable to
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+ quadratic quantities (such as spectra) but is not suitable to
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+ raw Fourier coefficients.</p>
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+ <p>ARGUMENTS</p>
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+ <ul>
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+ <li>kdim (Integer or String): see <a href="#label-12">phase_velocity_binning</a></li>
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+ <li>fdim (Integer or String): see <a href="#label-12">phase_velocity_binning</a></li>
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+ <li>cmin (Float) : minimum phase velocity</li>
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+ <li>cmin (Float) : maximum phase velocity</li>
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+ <li>cint (Float) : inter val with which the range [cmin and cmax]
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+ is divided.</li>
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+ <li>kconv (nil or UNumeric) : see <a href="#label-12">phase_velocity_binning</a></li>
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+ <li>fconv (nil or UNumeric) : see <a href="#label-12">phase_velocity_binning</a></li>
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+ </ul>
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+ <p>RETURN VALUE</p>
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+ <ul>
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+ <li>a GPhys</li>
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+ </ul></dd>
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+ <dt><h4><a name="label-12" id="label-12"><code>phase_velocity_binning(<var>kdim</var>, <var>fdim</var>, <var>cbins</var>, <var>kconv</var>=<var>nil</var>, <var>fconv</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "phase_velocity_binning" -->
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+ <dd>
273
+ <p>Bin a 2D spectrum in space and time based on phase velocity.
274
+ The operand (self) must be Fourier coefficients or spectra,
275
+ whose grid has not been altered since the call of the method
276
+ fft (i.e., those that have not applied with zero centering
277
+ etc, since it is done in this method).</p>
278
+ <p>Binning by this method is based on summation, leaving
279
+ the units unchanged.</p>
280
+ <p>REMARKS</p>
281
+ <ul>
282
+ <li>Components whose phase velocities are exactly equal to one
283
+ of the boundaries are divided into the two bins half by half</li>
284
+ <li>components with k=0 and f=0 are excluded -- the spatio-temporal
285
+ mean do not reflect in the result </li>
286
+ </ul>
287
+ <p>ARGUMENTS</p>
288
+ <ul>
289
+ <li>kdim (Integer or String): wavenumber dimension (from spacial dimension)</li>
290
+ <li>fdim (Integer or String): frequency dimension (from time dimension)</li>
291
+ <li>cbins : an Array of bin bounds or a Hash of max, min, int
292
+ e.g., [-10,-1,-0.1,0.1,11,10], {"min"=&gt;-30,"max"=&gt;30,"int"=&gt;5}</li>
293
+ <li>kconv (nil or UNumeric) : (optional) if given, kconv is multiplied
294
+ with the wavenumber axis before computing the phase velocity</li>
295
+ <li>fconv (nil or UNumeric) : (optional) if given, fconv is multiplied
296
+ with the frequency axis before computing the phase velocity</li>
297
+ </ul>
298
+ <p>RETURN VALUE</p>
299
+ <ul>
300
+ <li>a GPhys</li>
301
+ </ul>
302
+ <p>EXAMPLES</p>
303
+ <ul>
304
+ <li><p>Example A</p>
305
+ <pre>fu = u.fft(nil, 0, 2)
306
+ cfu = fu.phase_velocity_binning(0, 2, {"min"=&gt;-1,"max"=&gt;1,"int"=&gt;0.1})</pre></li>
307
+ <li><p>Example B</p>
308
+ <pre>fu = u.fft(nil, 0, 2)
309
+ pw = fu.abs**2rawspect2powerspect(0,2) # power spectrum
310
+ cbins = [-100.0, -10.0, -1.0, 1.0, 10.0, 100.0] # logarithmic spacing
311
+ cpw = pw.phase_velocity_binning(0, 2, cbins)</pre></li>
312
+ <li><p>Example C</p>
313
+ <pre>fu = u.fft(nil, 0, 3)
314
+ fv = v.fft(nil, 0, 3)
315
+ kconv = UNumeric[1/6.37e6, "m-1"]
316
+ fconv = UNumeric[1/3.6e3, "hours/s"]
317
+ fuv = (fu * fv.conj) # cross spectra
318
+ cfuv = fuv.phase_velocity_binning(0, 3, {"min"=&gt;-50,"max"=&gt;50,"int"=&gt;5},
319
+ kconv, fconv)</pre></li>
320
+ </ul></dd>
180
321
  </dl>
181
322
 
182
323
  </body>
data/doc/gphys_grads_io.html CHANGED
@@ -7,11 +7,11 @@
7
7
  <title>../lib/numru/gphys/gphys_grads_io.rb</title>
8
8
  </head>
9
9
  <body>
10
- <h1><a name="label:0" id="label:0">module NumRu::GPhys::GrADS_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::GrADS_IO" -->
10
+ <h1><a name="label-0" id="label-0">module NumRu::GPhys::GrADS_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::GrADS_IO" -->
11
11
  <p>helps read/write GrADS-formatted data</p>
12
- <h2><a name="label:1" id="label:1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
12
+ <h2><a name="label-1" id="label-1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
13
13
  <dl>
14
- <dt><h4><a name="label:2" id="label:2"><code>is_a_GrADS?(<var>filename</var>)</code></a></h4></dt><!-- RDLabel: "is_a_GrADS?" -->
14
+ <dt><h4><a name="label-2" id="label-2"><code>is_a_GrADS?(<var>filename</var>)</code></a></h4></dt><!-- RDLabel: "is_a_GrADS?" -->
15
15
  <dd>
16
16
  <p>test whether the file is a GrADS control file.</p>
17
17
  <p>ARGUMENTS</p>
@@ -22,7 +22,7 @@
22
22
  <ul>
23
23
  <li>true/false</li>
24
24
  </ul></dd>
25
- <dt><h4><a name="label:3" id="label:3"><code>open(<var>file</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
25
+ <dt><h4><a name="label-3" id="label-3"><code>open(<var>file</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
26
26
  <dd>
27
27
  <p>GPhys constructor from GrADS.</p>
28
28
  <p>ARGUMENTS</p>
@@ -45,10 +45,10 @@
45
45
  include GPhys
46
46
  temp = GPhys::GrADS_IO.open("T.jan.ctl","T")</pre></li>
47
47
  </ul></dd>
48
- <dt><h4><a name="label:4" id="label:4"><code>write(<var>file</var>, <var>gphys</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "write" -->
48
+ <dt><h4><a name="label-4" id="label-4"><code>write(<var>file</var>, <var>gphys</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "write" -->
49
49
  <dd>
50
- <p>writes a GPhys object into a GrADS file. -- !!only 4D data is supported!!</p></dd>
51
- <dt><h4><a name="label:5" id="label:5"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
50
+ writes a GPhys object into a GrADS file. -- !!only 4D data is supported!!</dd>
51
+ <dt><h4><a name="label-5" id="label-5"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
52
52
  <dd>
53
53
  <p>ARGUMENTS</p>
54
54
  <ul>
@@ -60,9 +60,9 @@ temp = GPhys::GrADS_IO.open("T.jan.ctl","T")</pre></li>
60
60
  <li>names of variables (Array): this return the names of variables
61
61
  which the file has.</li>
62
62
  </ul></dd>
63
- <dt><h4><a name="label:6" id="label:6"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
63
+ <dt><h4><a name="label-6" id="label-6"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
64
64
  <dd>
65
- <p>same as var_names</p></dd>
65
+ same as var_names</dd>
66
66
  </dl>
67
67
 
68
68
  </body>
data/doc/gphys_grib_io.html CHANGED
@@ -7,11 +7,11 @@
7
7
  <title>../lib/numru/gphys/gphys_grib_io.rb</title>
8
8
  </head>
9
9
  <body>
10
- <h1><a name="label:0" id="label:0">module NumRu::GPhys::Grib_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::Grib_IO" -->
10
+ <h1><a name="label-0" id="label-0">module NumRu::GPhys::Grib_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::Grib_IO" -->
11
11
  <p>helps read Grib-formatted data</p>
12
- <h2><a name="label:1" id="label:1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
12
+ <h2><a name="label-1" id="label-1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
13
13
  <dl>
14
- <dt><h4><a name="label:2" id="label:2"><code>is_a_Grib? <var>filename</var>)</code></a></h4></dt><!-- RDLabel: "is_a_Grib? filename)" -->
14
+ <dt><h4><a name="label-2" id="label-2"><code>is_a_Grib? <var>filename</var>)</code></a></h4></dt><!-- RDLabel: "is_a_Grib? filename)" -->
15
15
  <dd>
16
16
  <p>test whether the file is a Grib file.</p>
17
17
  <p>ARGUMENTS</p>
@@ -22,7 +22,7 @@
22
22
  <ul>
23
23
  <li>true/false</li>
24
24
  </ul></dd>
25
- <dt><h4><a name="label:3" id="label:3"><code>open(<var>file</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
25
+ <dt><h4><a name="label-3" id="label-3"><code>open(<var>file</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
26
26
  <dd>
27
27
  <p>GPhys constructor from Grib.</p>
28
28
  <p>ARGUMENTS</p>
@@ -45,7 +45,7 @@
45
45
  include GPhys
46
46
  temp = GPhys::Grib_IO.open("temp","T")</pre></li>
47
47
  </ul></dd>
48
- <dt><h4><a name="label:4" id="label:4"><code>write(<var>file</var>, <var>gphys</var>, <var>name_dummy</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "write" -->
48
+ <dt><h4><a name="label-4" id="label-4"><code>write(<var>file</var>, <var>gphys</var>, <var>name_dummy</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "write" -->
49
49
  <dd>
50
50
  <p>Write a GPhys into a Grib file. The whole data under the GPhys
51
51
  (such as coordinate vars) are written self-descriptively.</p>
@@ -59,7 +59,7 @@ temp = GPhys::Grib_IO.open("temp","T")</pre></li>
59
59
  <ul>
60
60
  <li>nil</li>
61
61
  </ul></dd>
62
- <dt><h4><a name="label:5" id="label:5"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
62
+ <dt><h4><a name="label-5" id="label-5"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
63
63
  <dd>
64
64
  <p>ARGUMENTS</p>
65
65
  <ul>
@@ -71,7 +71,7 @@ temp = GPhys::Grib_IO.open("temp","T")</pre></li>
71
71
  <li>names of variables (Array): this return the names of variables
72
72
  which the file has.</li>
73
73
  </ul></dd>
74
- <dt><h4><a name="label:6" id="label:6"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
74
+ <dt><h4><a name="label-6" id="label-6"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
75
75
  <dd>
76
76
  <ul>
77
77
  <li>same as var_names</li>
data/doc/gphys_io.html CHANGED
@@ -7,7 +7,7 @@
7
7
  <title>../lib/numru/gphys/gphys_io.rb</title>
8
8
  </head>
9
9
  <body>
10
- <h1><a name="label:0" id="label:0">module NumRu::GPhys::IO</a></h1><!-- RDLabel: "module NumRu::GPhys::IO" -->
10
+ <h1><a name="label-0" id="label-0">module NumRu::GPhys::IO</a></h1><!-- RDLabel: "module NumRu::GPhys::IO" -->
11
11
  <p>A module to handle file IO regarding GPhys. </p>
12
12
  <p>Many of the functionality of this module is implemented in the modules
13
13
  for specific file types such as NumRu::GPhys::NetCDF_IO, to which this
@@ -15,81 +15,168 @@ module directs operations.</p>
15
15
  <p>For example, GPhys::IO.open(file, name) simply calls
16
16
  GPhys::*_IO.open(file, name), where '*' is
17
17
  NetCDF, GrADS, or grib.</p>
18
- <h2><a name="label:1" id="label:1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
18
+ <h2><a name="label-1" id="label-1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
19
19
  <dl>
20
- <dt><h4><a name="label:2" id="label:2"><code>open(<var>files</var>, <var>varname</var>)</code></a><!-- RDLabel: "open" -->
21
- <dt><h4><a name="label:3" id="label:3"><code>write(<var>file</var>, <var>gphys</var>, <var>name</var>=<var>nil</var>)</code></a><!-- RDLabel: "write" -->
22
- <dt><h4><a name="label:4" id="label:4"><code>write_grid(<var>file</var>, <var>grid_or_gphys</var>)</code></a><!-- RDLabel: "write_grid" -->
23
- <dt><h4><a name="label:5" id="label:5"><code>each_along_dims_write(<var>gphyses</var>, <var>files</var>, *<var>loopdims</var>){...} # <var>a</var> <var>block</var> <var>is</var> <var>expected</var></code></a><!-- RDLabel: "each_along_dims_write" -->
24
- <dt><h4><a name="label:6" id="label:6"><code>var_names(<var>file</var>)</code></a><!-- RDLabel: "var_names" -->
25
- <dt><h4><a name="label:7" id="label:7"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
20
+ <dt><h4><a name="label-2" id="label-2"><code>open(<var>file</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
26
21
  <dd>
27
- <p>See the manual of NumRu::GPhys::NetCDF_IO for the methods listed above.</p></dd>
28
- <dt><h4><a name="label:8" id="label:8"><code>file2type(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2type" -->
22
+ <p>Opens a GPhys in <code>file</code> having the name <code>varname</code>.</p>
23
+ <p>ARGUMENTS</p>
24
+ <ul>
25
+ <li>file (String, NetCDF, GRIB,.. etc, or Array, NArray, Regexp) :
26
+ Specifies the file. Path if String; a File pointer if NetCDF etc..
27
+ The processing is forwarded to open_multi, if this argument is
28
+ an Array, NArray, or Regexp. </li>
29
+ <li>varname (String) : name of the variable</li>
30
+ </ul>
31
+ <p>RETURN VALUE</p>
32
+ <ul>
33
+ <li>a GPhys</li>
34
+ </ul></dd>
35
+ <dt><h4><a name="label-3" id="label-3"><code>open_multi(<var>files</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open_multi" -->
36
+ <dd>
37
+ <p>Opens a GPhys by combining a variable across multiple files.
38
+ It initializes GPhys objects over the files by calling open and
39
+ unites them into a single GPhys object by using <code>GPhys.join</code> or
40
+ <code>GPhys.join_md</code>.</p>
41
+ <p>ARGUMENTS</p>
42
+ <ul>
43
+ <li>files (Array, NArray (NArray.object), or Regexp) : Specifies the files.
44
+ <ul>
45
+ <li>when Array, it must consist of paths or file pointers
46
+ (that are accepted by open).
47
+ All coordinates of the variable in the files are scanned,
48
+ and a joined object is constructed properly.
49
+ Thus, you can simply put subsets of a 2D tiling in a simple
50
+ non-nested 1D Array. <code>GPhys.join</code> is used in this case.</li>
51
+ <li><p>when NArray, it must consist of paths or file pointers
52
+ (that are accepted by open).
53
+ Each dimension with multiple elements must correspond
54
+ to a dimension along which joining is made.
55
+ For example, a 2D tiling can be specified as</p>
56
+ <pre>files = NArray.to_na([['f00.nc','f10.nc'],['f01.nc','f11.nc']])
57
+ gp = GPhys::IO.open_multi( files, "f" )</pre>
58
+ <p><code>GPhys.join_md</code> is used in this case.</p></li>
59
+ <li><p>When Regexp, similar to when NArray, but expresses the paths.
60
+ The dimensions to join is specified by "captures"
61
+ (parentheses). For example, the above 2D tiling can be specified as</p>
62
+ <pre>files = /f(\d)(\d).nc/
63
+ gp = GPhys::IO.open_multi( files, "f" )</pre>
64
+ <p>The regexp can contain a directory path (e.g., /dir\/sub\/f(\d)(d).nc/),
65
+ but the directory part must be unique (i.e., a simple string),
66
+ so only a single directly can be specified. All captures must
67
+ be in the part representing the file names (in the directory).
68
+ <code>GPhys.join_md</code> is used in this case.</p></li>
69
+ </ul></li>
70
+ <li>varname (String) : name of the variable</li>
71
+ </ul>
72
+ <p>RETURN VALUE</p>
73
+ <ul>
74
+ <li>a GPhys</li>
75
+ </ul></dd>
76
+ <dt><h4><a name="label-4" id="label-4"><code>write(<var>file</var>, <var>gphys</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "write" -->
77
+ <dd>
78
+ <p>Writes a GPhys object in a file</p>
79
+ <p>ARGUMENTS</p>
80
+ <ul>
81
+ <li>file (NetCDF, GRIB,.. etc) : the file. Writing must be permitted.
82
+ To close (finalize) it after writing is left to the user.</li>
83
+ <li>gphys (GPhys) : the GPhys object to write</li>
84
+ <li>name (String; optional) : if specified, this name is used in the file
85
+ rather than the name of gphys</li>
86
+ </ul></dd>
87
+ <dt><h4><a name="label-5" id="label-5"><code>write_grid(<var>file</var>, <var>grid_or_gphys</var>)</code></a></h4></dt><!-- RDLabel: "write_grid" -->
88
+ <dt><h4><a name="label-6" id="label-6"><code>each_along_dims_write(<var>gphyses</var>, <var>files</var>, *<var>loopdims</var>){...} # <var>a</var> <var>block</var> <var>is</var> <var>expected</var></code></a></h4></dt><!-- RDLabel: "each_along_dims_write" -->
89
+ <dt><h4><a name="label-7" id="label-7"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
90
+ <dt><h4><a name="label-8" id="label-8"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
91
+ <dd>
92
+ See the manual of NumRu::GPhys::NetCDF_IO for the methods listed above.</dd>
93
+ <dt><h4><a name="label-9" id="label-9"><code>file2type(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2type" -->
29
94
  <dd>
30
95
  <p>Figures out the file type supported in this module.</p>
31
96
  <p>ARGUMENTS</p>
32
97
  <ul>
33
- <li>file (String, Regexp, NetCDF, Grib, or GrADS_Gridded) :
98
+ <li>file (String, NetCDF, Grib, or GrADS_Gridded) :
34
99
  What to return is of course obvious if it is
35
100
  NetCDF, Grib, or GrADS_Gridded. If it is a String,
36
101
  it is assumed to be a path of a file, and the file type
37
102
  is determined by its suffix when 'nc', 'ctl', or 'grib';
38
103
  In other cases, the type is figured out by reading in
39
- a few bytes from the beginning. If Regexp, currently,
40
- a NetCDF is assumed, since only NetCDF_IO.open supports
41
- Regexp.</li>
104
+ a few bytes from the beginning.</li>
42
105
  </ul>
43
106
  <p>RETURN VALUE</p>
44
107
  <ul>
45
108
  <li>GPhys::IO::NETCDF, GPhys::IO::GRIB, or GPhys::IO::GRADS,
46
109
  which are string constants.</li>
47
110
  </ul></dd>
48
- <dt><h4><a name="label:9" id="label:9"><code>file2specific_module(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2specific_module" -->
111
+ <dt><h4><a name="label-10" id="label-10"><code>file2specific_module(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2specific_module" -->
49
112
  <dd>
50
- <p>Same as <a href="#label:8">file2type</a>, but returns GPhys::NetCDF_IO,
51
- GPhys::GrADS_IO, or GPhys::Grib_IO.</p></dd>
52
- <dt><h4><a name="label:10" id="label:10"><code>file2file_class(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2file_class" -->
113
+ Same as <a href="#label-9">file2type</a>, but returns GPhys::NetCDF_IO,
114
+ GPhys::GrADS_IO, or GPhys::Grib_IO.</dd>
115
+ <dt><h4><a name="label-11" id="label-11"><code>file2file_class(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2file_class" -->
53
116
  <dd>
54
- <p>Same as <a href="#label:8">file2type</a>, but returns NetCDF,
55
- GrADS_Gridded, or Grib.</p></dd>
56
- <dt><h4><a name="label:11" id="label:11"><code>parse_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "parse_gturl" -->
117
+ Same as <a href="#label-9">file2type</a>, but returns NetCDF,
118
+ GrADS_Gridded, or Grib.</dd>
119
+ <dt><h4><a name="label-12" id="label-12"><code>parse_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "parse_gturl" -->
57
120
  <dd>
58
121
  <p>Parses GTOOL4-type URLs to specify path, variable name,
59
122
  and optionally subsets, whose format is
60
- path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</p>
123
+ path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</p>
61
124
  <p>ARGUMENTS</p>
62
125
  <ul>
63
126
  <li>gturl (String) GTOOL4 URL, whose format is
64
- path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</li>
127
+ path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</li>
65
128
  </ul>
66
129
  <p>RETURN VALUES</p>
67
130
  <ul>
68
- <li>An Array consisting of [file, var, slice, thinning], where
131
+ <li>An Array consisting of [file, var, slice, cut_slice, thinning], where
69
132
  <ul>
70
133
  <li>file (String) : path</li>
71
134
  <li>var (String) : variable name</li>
72
- <li>slice (Array) : subset specifier in physical coordinate
73
- to be used as GPhys#cut[slice].</li>
135
+ <li>slice (Array) : subset specifier by the grid numbers
136
+ to be used as GPhys#[slice].</li>
137
+ <li>cut_slice (Array) : subset specifier in physical coordinate
138
+ to be used as GPhys#cut[cut_slice].</li>
74
139
  <li>thinning (Array) : additional subset specifier for thinning
75
140
  with uniform intervals if needed to be used GPhys#[thinning]
76
141
  after appling GPhys#cut.</li>
77
142
  </ul></li>
78
143
  </ul></dd>
79
- <dt><h4><a name="label:12" id="label:12"><code>open_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "open_gturl" -->
144
+ <dt><h4><a name="label-13" id="label-13"><code>open_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "open_gturl" -->
80
145
  <dd>
81
146
  <p>a GPhys constructor from a Gtool4-type URL.
82
- See <a href="#label:11">parse_gturl</a> for its format.</p>
147
+ See <a href="#label-12">parse_gturl</a> for its format.</p>
148
+ <p>RETURN VALUE</p>
149
+ <ul>
150
+ <li>a GPhys</li>
151
+ </ul></dd>
152
+ <dt><h4><a name="label-14" id="label-14"><code>str2gphys(<var>str</var>)</code></a></h4></dt><!-- RDLabel: "str2gphys" -->
153
+ <dd>
154
+ <p>Open a GPhys from a slash("/")-separated String
155
+ such as "U.nc/U" and "U.nc".</p>
156
+ <ul>
157
+ <li>Aimed to help quick jobs with interactive sessions
158
+ -- This method do not handle a GPhys across multiple files.</li>
159
+ <li>if the variable path is ommited such as "U.nc",
160
+ try to find the variable in it -- read the file and if
161
+ only one variable is found, assume that is the
162
+ variable specified; otherwise, an exception is raised.</li>
163
+ <li>URL is accepted, but it's only thru NetCDF assuming OPeNDAP.</li>
164
+ </ul>
165
+ <p>ARGUMENTS</p>
166
+ <ul>
167
+ <li>a String (file_path[/variable_path])
168
+ e.g. "U.nc/U", "U.nc", "http://.../U.nc/U"</li>
169
+ </ul>
83
170
  <p>RETURN VALUE</p>
84
171
  <ul>
85
172
  <li>a GPhys</li>
86
173
  </ul></dd>
87
174
  </dl>
88
- <h2><a name="label:13" id="label:13">Module constants</a></h2><!-- RDLabel: "Module constants" -->
175
+ <h2><a name="label-15" id="label-15">Module constants</a></h2><!-- RDLabel: "Module constants" -->
89
176
  <dl>
90
- <dt><h4><a name="label:14" id="label:14"><code>GTURLfmt</code></a></h4></dt><!-- RDLabel: "GTURLfmt" -->
177
+ <dt><h4><a name="label-16" id="label-16"><code>GTURLfmt</code></a></h4></dt><!-- RDLabel: "GTURLfmt" -->
91
178
  <dd>
92
- <p>The format of Gtool4URL.</p></dd>
179
+ The format of Gtool4URL.</dd>
93
180
  </dl>
94
181
 
95
182
  </body>