gphys 1.1.1 → 1.2.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (369) hide show
  1. data/.gitignore +17 -0
  2. data/ChangeLog +221 -0
  3. data/Gemfile +4 -0
  4. data/LICENSE.txt +18 -30
  5. data/README +23 -26
  6. data/README.md +29 -0
  7. data/Rakefile +1 -56
  8. data/bin/gpaop +2 -1
  9. data/bin/gpcut +3 -2
  10. data/bin/gpedit +6 -2
  11. data/bin/gpmath +3 -2
  12. data/bin/gpmaxmin +3 -2
  13. data/bin/gpprint +2 -1
  14. data/bin/gpvect +28 -5
  15. data/bin/gpview +43 -5
  16. data/extconf.rb +5 -6
  17. data/gphys.gemspec +34 -0
  18. data/interpo.c +63 -24
  19. data/lib/gphys.rb +2 -0
  20. data/lib/numru/dclext.rb +2636 -0
  21. data/lib/numru/derivative.rb +53 -12
  22. data/lib/numru/ganalysis/eof.rb +4 -0
  23. data/lib/numru/ganalysis/histogram.rb +73 -5
  24. data/lib/numru/ganalysis/met.rb +163 -2
  25. data/lib/numru/ganalysis/planet.rb +230 -20
  26. data/lib/numru/ggraph.rb +147 -2247
  27. data/lib/numru/gphys/assoccoords.rb +19 -3
  28. data/lib/numru/gphys/axis.rb +1 -1
  29. data/lib/numru/gphys/coordmapping.rb +2 -2
  30. data/lib/numru/gphys/derivative.rb +56 -13
  31. data/lib/numru/gphys/gphys.rb +17 -1
  32. data/lib/numru/gphys/gphys_grads_io.rb +6 -5
  33. data/lib/numru/gphys/gphys_grib_io.rb +6 -6
  34. data/lib/numru/gphys/gphys_io.rb +25 -6
  35. data/lib/numru/gphys/grads_gridded.rb +31 -29
  36. data/lib/numru/gphys/grib.rb +13 -9
  37. data/lib/numru/gphys/interpolate.rb +153 -29
  38. data/lib/numru/gphys/unumeric.rb +29 -6
  39. data/lib/numru/gphys/varray.rb +9 -0
  40. data/lib/numru/gphys/varraygrib.rb +70 -8
  41. data/lib/version.rb +3 -0
  42. metadata +247 -531
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  44. data/doc/attributenetcdf.html +0 -15
  45. data/doc/axis.html +0 -376
  46. data/doc/coordmapping.html +0 -111
  47. data/doc/coordtransform.html +0 -36
  48. data/doc/derivative/gphys-derivative.html +0 -80
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- <head>
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- <title>../lib/numru/gphys/varray.rb</title>
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- </head>
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- <body>
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- <h1><a name="label-0" id="label-0">class NumRu::VArray</a></h1><!-- RDLabel: "class NumRu::VArray" -->
11
- <p>VArray is a Virtual Array class, in which a multi-dimensional array data is
12
- stored on memory (NArray, NArrayMiss) or in file (NetCDFVar etc).
13
- The in-file data handling is left to subclasses such as VArrayNetCDF,
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- and this base class handles the following two cases:</p>
15
- <ol>
16
- <li>Data are stored on memory using NArray</li>
17
- <li>Subset of another VArray (possibly a subclass such as VArrayNetCDF).</li>
18
- </ol>
19
- <p>Perhaps the latter case needs more explanation. Here, a VArray is defined
20
- as a subset of another VArray, so the current VArray has only the link
21
- and info on how the subset is mapped to the other VArray.</p>
22
- <p>A VArray behaves just like a NArray, i.e., a numeric multi-dimensional
23
- array. The important difference is that a VArray has a name and can
24
- have "attributes" like a NetCDF variable. Therefore, VArray can perfectly
25
- represent a NetCDFVar, which is realized by a sub-class VArrayNetCDF.</p>
26
- <p>NOMENCLATURE</p>
27
- <ul>
28
- <li>value(s): The multi-dimensional numeric array contained in the VArray,
29
- or its contents</li>
30
- <li>attribute(s): A combination of name and data that describes a VArray.
31
- Often realized by NumRu::Attribute class (or it is a NetCDFAttr in
32
- VArrayNetCDF). The name must be a string, and the type of attribute
33
- values is restricted to a few classes for compatibility with
34
- NetCDFAttr (See NumRu::Attribute)</li>
35
- </ul>
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- <h2><a name="label-1" id="label-1">Class Methods</a></h2><!-- RDLabel: "Class Methods" -->
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- <dl>
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- <dt><h4><a name="label-2" id="label-2"><code>VArray.new(<var>narray</var>=<var>nil</var>, <var>attr</var>=<var>nil</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "VArray.new" -->
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- <dd>
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- <p>A constructor</p>
41
- <p>ARGUMENTS</p>
42
- <ul>
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- <li>narray (NArray or NArrayMiss; default:nil) The array to be held.
44
- (nil is used to initialize a mapping to another VArray by a protected
45
- method).</li>
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- <li>attr (NumRu::Attribute; default:nil) Attributes. If nil, an empty </li>
47
- </ul>
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- <pre>attribute object is created and stored.</pre>
49
- <ul>
50
- <li>name (String; default nil) Name of the VArray. If nil, it is named "noname".</li>
51
- </ul>
52
- <p>RETURN VALUE</p>
53
- <ul>
54
- <li>a VArray</li>
55
- </ul>
56
- <p>EXAMPLE</p>
57
- <pre>na = NArray.int(6,3).indgen!
58
- va1 = VArray.new( na, nil, "test" )</pre></dd>
59
- <dt><h4><a name="label-3" id="label-3"><code>VArray.new2(<var>ntype</var>, <var>shape</var>, <var>attr</var>=<var>nil</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "VArray.new2" -->
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- <dd>
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- <p>Another constructor. Uses parameters to initialize a NArray to hold.</p>
62
- <p>ARGUMENTS</p>
63
- <ul>
64
- <li>ntype (String or NArray constants): Numeric type of the NArray to be
65
- held (e.g., "sfloat", "float", NArray::SFLOAT, NArray::FLOAT)</li>
66
- <li>shape (Array of Integers): shape of the NArray</li>
67
- <li>attr (Attribute; default:nil) Attributes. If nil, an empty attribute
68
- object is created and stored.</li>
69
- <li>name (String; default nil) Name of the VArray.</li>
70
- </ul>
71
- <p>RETURN VALUE</p>
72
- <ul>
73
- <li>a VArray</li>
74
- </ul></dd>
75
- </dl>
76
- <h2><a name="label-4" id="label-4">Instance Methods</a></h2><!-- RDLabel: "Instance Methods" -->
77
- <dl>
78
- <dt><h4><a name="label-5" id="label-5"><code>val</code></a></h4></dt><!-- RDLabel: "val" -->
79
- <dd>
80
- <p>Returns the values as a NArray (or NArrayMiss).</p>
81
- <p>This is the case even when the VArray is a mapping to another. Also,
82
- this method is to be redefined in subclasses to do the same thing.</p>
83
- <p>ARGUMENTS -- none</p>
84
- <p>RETURN VALUE</p>
85
- <ul>
86
- <li>a NArray (or NArrayMiss)</li>
87
- </ul></dd>
88
- <dt><h4><a name="label-6" id="label-6"><code>val=(<var>narray</var>)</code></a></h4></dt><!-- RDLabel: "val=" -->
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- <dd>
90
- <p>Set values.</p>
91
- <p>The whole values are set. If you want to set partly, use <a href="#label-9">[]=</a>.
92
- In this method, values are read from narray and set into the internal
93
- value holder. Thus, for exampled, the numeric type is not changed
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- regardress the numeric type of narray. Use <a href="#label-7">replace_val</a> to
95
- replace entirely with narray.</p>
96
- <p>ARGUMENTS</p>
97
- <ul>
98
- <li>narray (NArray or NArrayMiss or Numeric): If Numeric, the whole
99
- values are set to be equal to it. If NArray (or NArrayMiss), its
100
- shape must agree with the shape of the VArray.</li>
101
- </ul></dd>
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- <dt><h4><a name="label-7" id="label-7"><code>replace_val(<var>narray</var>)</code></a></h4></dt><!-- RDLabel: "replace_val" -->
103
- <dd>
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- <p>Replace the internal array data with the object narray.
105
- Use <a href="#label-6">val=</a> if you want to copy the values of narray.</p>
106
- <p>ARGUMENTS</p>
107
- <ul>
108
- <li>narray (NArray or NArrayMiss): as pxlained above.
109
- Its shape must agree with the shape of the VArray (self).</li>
110
- </ul>
111
- <p>RETURN VALUE</p>
112
- <ul>
113
- <li>if (self.class == VArray), self;
114
- otherwise (if self.class is a subclass of VArray), a new VArray.</li>
115
- </ul></dd>
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- <dt><h4><a name="label-8" id="label-8"><code>[]</code></a></h4></dt><!-- RDLabel: "[]" -->
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- <dd>
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- Get a subset. Its usage is the same as NArray#[]</dd>
119
- <dt><h4><a name="label-9" id="label-9"><code>[] = </code></a></h4></dt><!-- RDLabel: "[]=" -->
120
- <dd>
121
- Set a subset. Its usage is the same as NArray#[]=</dd>
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- <dt><h4><a name="label-10" id="label-10"><code>attr</code></a></h4></dt><!-- RDLabel: "attr" -->
123
- <dd>
124
- To be undefined.</dd>
125
- <dt><h4><a name="label-11" id="label-11"><code>ntype</code></a></h4></dt><!-- RDLabel: "ntype" -->
126
- <dd>
127
- <p>Returns the numeric type.</p>
128
- <p>ARGUMENTS -- none</p>
129
- <p>RETURN VALUE</p>
130
- <ul>
131
- <li>a String ("byte", "sint", "int", "sfloat", "float", "scomplex"
132
- "complex", or "obj"). It can be used in NArray.new to initialize
133
- another NArray.</li>
134
- </ul></dd>
135
- <dt><h4><a name="label-12" id="label-12"><code>rank</code></a></h4></dt><!-- RDLabel: "rank" -->
136
- <dd>
137
- Returns the rank (number of dimensions)</dd>
138
- <dt><h4><a name="label-13" id="label-13"><code>shape</code></a></h4></dt><!-- RDLabel: "shape" -->
139
- <dd>
140
- Returns the shape</dd>
141
- <dt><h4><a name="label-14" id="label-14"><code>shape_current</code></a></h4></dt><!-- RDLabel: "shape_current" -->
142
- <dd>
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- aliased to <a href="#label-13">shape</a>.</dd>
144
- <dt><h4><a name="label-15" id="label-15"><code>length</code></a></h4></dt><!-- RDLabel: "length" -->
145
- <dd>
146
- Returns the length of the VArray</dd>
147
- <dt><h4><a name="label-16" id="label-16"><code>typecode</code></a></h4></dt><!-- RDLabel: "typecode" -->
148
- <dd>
149
- Returns the NArray typecode</dd>
150
- <dt><h4><a name="label-17" id="label-17"><code>name</code></a></h4></dt><!-- RDLabel: "name" -->
151
- <dd>
152
- <p>Returns the name</p>
153
- <p>RETURN VALUE</p>
154
- <ul>
155
- <li>(String) name of the VArray</li>
156
- </ul></dd>
157
- <dt><h4><a name="label-18" id="label-18"><code>name=(<var>nm</var>)</code></a></h4></dt><!-- RDLabel: "name=" -->
158
- <dd>
159
- <p>Changes the name.</p>
160
- <p>ARGUMENTS</p>
161
- <ul>
162
- <li>nm(String): the new name.</li>
163
- </ul>
164
- <p>RETURN VALUE</p>
165
- <ul>
166
- <li>nm</li>
167
- </ul></dd>
168
- <dt><h4><a name="label-19" id="label-19"><code>rename!(<var>nm</var>)</code></a></h4></dt><!-- RDLabel: "rename!" -->
169
- <dd>
170
- <p>Changes the name (Same as <a href="#label-18">name=</a>, but returns self)</p>
171
- <p>ARGUMENTS</p>
172
- <ul>
173
- <li>nm(String): the new name.</li>
174
- </ul>
175
- <p>RETURN VALUE</p>
176
- <ul>
177
- <li>self</li>
178
- </ul></dd>
179
- <dt><h4><a name="label-20" id="label-20"><code>rename(<var>nm</var>)</code></a></h4></dt><!-- RDLabel: "rename" -->
180
- <dd>
181
- <p>Same as rename! but duplicate the VArray object and set its name.</p>
182
- <p>This method may not be supported in sub-classes, since it is sometimes
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- problematic not to change the original.</p></dd>
184
- <dt><h4><a name="label-21" id="label-21"><code>copy(<var>to</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "copy" -->
185
- <dd>
186
- <p>Copy a VArray. If to is nil, works as the deep cloning (duplication of the entire object).</p>
187
- <p>Both the values and the attributes are copied.</p>
188
- <p>ARGUMENTS</p>
189
- <ul>
190
- <li>to (VArray (possibly a subclass) or nil): The VArray to which the
191
- copying is made.</li>
192
- </ul></dd>
193
- <dt><h4><a name="label-22" id="label-22"><code>reshape!( *<var>shape</var> )</code></a></h4></dt><!-- RDLabel: "reshape!" -->
194
- <dd>
195
- <p>Changes the shape without changing the total size. May not be available in subclasses.</p>
196
- <p>ARGUMENTS</p>
197
- <ul>
198
- <li>shape (Array of Integer): new shape</li>
199
- </ul>
200
- <p>RETURN VALUE</p>
201
- <ul>
202
- <li>self</li>
203
- </ul>
204
- <p>EXAMPLE</p>
205
- <pre>vary = VArray.new2( "float", [10,2])
206
- vary.reshape!(5,4) # changes the vary
207
- vary.copy.reshape!(2,2,5) # make a deep clone and change it
208
- # This always works with a VArray subclass, since vary.copy
209
- # makes a deep clone to VArray with NArray.</pre></dd>
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- <dt><h4><a name="label-23" id="label-23"><code>file</code></a></h4></dt><!-- RDLabel: "file" -->
211
- <dd>
212
- <p>Returns a file object if the data of the VArray is in a file, nil if it is on memory</p>
213
- <p>ARGUMENTS</p>
214
- <ul>
215
- <li>none</li>
216
- </ul>
217
- <p>RETURN VALUE</p>
218
- <ul>
219
- <li>an object representing the file in which data are stored. Its class
220
- depends on the file type. nil is returned if the data is not in a file.</li>
221
- </ul></dd>
222
- <dt><h4><a name="label-24" id="label-24"><code>transpose(*<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "transpose" -->
223
- <dd>
224
- Transpose. Argument specification is as in NArray.</dd>
225
- <dt><h4><a name="label-25" id="label-25"><code>reshape(*<var>shape</var>)</code></a></h4></dt><!-- RDLabel: "reshape" -->
226
- <dd>
227
- Reshape. Argument specification is as in NArray.</dd>
228
- <dt><h4><a name="label-26" id="label-26"><code>axis_draw_positive</code></a></h4></dt><!-- RDLabel: "axis_draw_positive" -->
229
- <dd>
230
- <p>Returns the direction to plot the axis (meaningful only if self is a
231
- coordinate variable.) </p>
232
- <p>The current implementation is based on NetCDF conventions,
233
- so REDEFINE IT IN SUBCLASSES if it is not appropriate.</p>
234
- <p>RETURN VALUE</p>
235
- <ul>
236
- <li>one of the following:
237
- <ul>
238
- <li>true: axis should be drawn in the increasing order (to right/upward)</li>
239
- <li>false: axis should be drawn in the decreasing order</li>
240
- <li>nil: not specified</li>
241
- </ul></li>
242
- </ul></dd>
243
- <dt><h4><a name="label-27" id="label-27"><code>axis_cyclic?</code></a></h4></dt><!-- RDLabel: "axis_cyclic?" -->
244
- <dd>
245
- <p>Returns whether the axis is cyclic (meaningful only if self is a
246
- coordinate variable.) </p>
247
- <p>The current implementation is based on NetCDF conventions,
248
- so REDEFINE IT IN SUBCLASSES if it is not appropriate.</p>
249
- <p>RETURN VALUE</p>
250
- <ul>
251
- <li>one of the following:
252
- <ul>
253
- <li>true: cyclic</li>
254
- <li>false: not cyclic</li>
255
- <li>nil: not specified</li>
256
- </ul></li>
257
- </ul></dd>
258
- <dt><h4><a name="label-28" id="label-28"><code>axis_modulo</code></a></h4></dt><!-- RDLabel: "axis_modulo" -->
259
- <dd>
260
- <p>Returns the modulo of a cyclic axis (meaningful only if self is a
261
- coordinate variable and it is cyclic.) </p>
262
- <p>The current implementation is based on NetCDF conventions,
263
- so REDEFINE IT IN SUBCLASSES if it is not appropriate.</p>
264
- <p>RETURN VALUE</p>
265
- <ul>
266
- <li>one of the following:
267
- <ul>
268
- <li>Float if the modulo is defined</li>
269
- <li>nil if modulo is not found</li>
270
- </ul></li>
271
- </ul></dd>
272
- <dt><h4><a name="label-29" id="label-29"><code>axis_cyclic_extendible?</code></a></h4></dt><!-- RDLabel: "axis_cyclic_extendible?" -->
273
- <dd>
274
- (meaningful only if self is a coordinate variable.)
275
- Returns true if self is cyclic and it is suitable to exend
276
- cyclically (having the distance between both ends
277
- equal to (modulo - dx), where dx is the mean increment).</dd>
278
- <dt><h4><a name="label-30" id="label-30"><code>coerce(<var>other</var>)</code></a></h4></dt><!-- RDLabel: "coerce" -->
279
- <dd>
280
- For Numeric operators. (If you do not know it, see a manual or book of Ruby)</dd>
281
- </dl>
282
- <h2><a name="label-31" id="label-31">Methods compatible with NArray</a></h2><!-- RDLabel: "Methods compatible with NArray" -->
283
- <p>VArray is a numeric multi-dimensional array, so it supports most of the
284
- methods and operators in NArray. Here, the name of those methods are just
285
- quoted. See the documentation of NArray for their usage.</p>
286
- <h3><a name="label-32" id="label-32">Math functions</a></h3><!-- RDLabel: "Math functions" -->
287
- <h4><a name="label-33" id="label-33">sqrt, exp, log, log10, log2, sin, cos, tan, sinh, cosh, tanh, asin, acos, atan, asinh, acosh, atanh, csc, sec, cot, csch, sech, coth, acsc, asec, acot, acsch, asech, acoth</a></h4><!-- RDLabel: "sqrt, exp, log, log10, log2, sin, cos, tan, sinh, cosh, tanh, asin, acos, atan, asinh, acosh, atanh, csc, sec, cot, csch, sech, coth, acsc, asec, acot, acsch, asech, acoth" -->
288
- <h3><a name="label-34" id="label-34">Binary operators</a></h3><!-- RDLabel: "Binary operators" -->
289
- <h4><a name="label-35" id="label-35">-, +, *, /, %, **, .add!, .sub!, .mul!, .div!, mod!, &gt;, &gt;=, &lt;, &lt;=, &amp;, |, ^, .eq, .ne, .gt, .ge, .lt, .le, .and, .or, .xor, .not</a></h4><!-- RDLabel: "-, +, *, /, %, **, .add!, .sub!, .mul!, .div!, mod!, >, >=, <, <=, &, |, ^, .eq, .ne, .gt, .ge, .lt, .le, .and, .or, .xor, .not" -->
290
- <h3><a name="label-36" id="label-36">Unary operators</a></h3><!-- RDLabel: "Unary operators" -->
291
- <h4><a name="label-37" id="label-37">~ - +</a></h4><!-- RDLabel: "~ - +" -->
292
- <h3><a name="label-38" id="label-38">Mean etc</a></h3><!-- RDLabel: "Mean etc" -->
293
- <h4><a name="label-39" id="label-39">mean, sum, stddev, min, max, median</a></h4><!-- RDLabel: "mean, sum, stddev, min, max, median" -->
294
- <h3><a name="label-40" id="label-40">Other methods</a></h3><!-- RDLabel: "Other methods" -->
295
- <p>These methods returns a NArray (not a VArray).</p>
296
- <h4><a name="label-41" id="label-41">all?, any?, none?, where, where2, floor, ceil, round, to_f, to_i, to_a</a></h4><!-- RDLabel: "all?, any?, none?, where, where2, floor, ceil, round, to_f, to_i, to_a" -->
297
-
298
- </body>
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- <h1><a name="label-0" id="label-0">class NumRu::VArrayComposite &lt; NumRu::VArray</a></h1><!-- RDLabel: "class NumRu::VArrayComposite < NumRu::VArray" -->
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- <p>a VArray that consists of multiple VArrays tiled regularly
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- (possibly in multi-dimension). Except for the constructer
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- "new" and <!-- Reference, RDLabel "attr_update" doesn't exist --><em class="label-not-found">attr_update</em><!-- Reference end -->, the usage of this class is the same as VArray.</p>
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- <p>Note that the name and the attributes of a VArrayComposite is
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- borrowed form one of the VArrays contained (actually, the first one
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- is used). Currently, no check is made
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- regarding whether the names and attributes are the same among the
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- VArrays contained. If you rename a VArrayComposite, the change will
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- be made with all the VArrays contained. However, currently,
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- change of the attributes are only reflected only in the first
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- VArray. You have to call <!-- Reference, RDLabel "attr_update" doesn't exist --><em class="label-not-found">attr_update</em><!-- Reference end --> separately.</p>
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- <h2><a name="label-1" id="label-1">Class methods</a></h2><!-- RDLabel: "Class methods" -->
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- <dl>
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- <dt><h4><a name="label-2" id="label-2"><code>VArrayComposite.new(<var>varrays</var>)</code></a></h4></dt><!-- RDLabel: "VArrayComposite.new" -->
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- <dd>
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- <p>Constructor</p>
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- <p>ARGUMENTS</p>
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- <ul>
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- <li>varrays (NArray of VArray) : VArrays to be included, gridded
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- regularly in a NArray.</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 VArrayComposite</li>
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- </ul>
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- <p>EXAMPLES</p>
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- <ul>
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- <li><p>Suppose that you have VArrays va00, va01, va10, va00,
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- with va00 and va10 having a same 0th dimension length,
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- va01 and va11 having a same 0th dimension length,
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- and va00 and va01 having a same 1st dimention length.</p>
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- <pre>varrays = NArray[ [ va00, va01 ],
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- [ va10, va11 ] ]
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- vac = VArrayComposite.new(varrays)</pre>
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- <p>This will create a composite VArray tiled two-dimensionally.</p></li>
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- <li><p>You can create a VArray that lacks one or more VArrays as
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- long as the shape is unambiguous:</p>
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- <pre>vac = VArrayComposite.new( NArray[ [ va00, va01 ],
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- [ va10, nil ] ] )</pre>
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- <p>is allowed, but </p>
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- <pre>vac = VArrayComposite.new( NArray[ [ va00, nil ],
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- [ va10, nil ] ] )</pre>
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- <p>is prohibited.</p>
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- <p>NOTICE: At this moment, handling of such nil-contianing
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- VArrayComposite is very limited, and many methods do not work.</p></li>
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- <li><p>Suppose that you have 3D VArrays va0, va1, va2, va3,
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- and you want to concatenate them with the 3rd dimension.</p>
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- <pre>varrays = NArray[ va0,va1,va2,va3 ].newdim(0,0)</pre>
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- <p>This will create a 3D NArray with a shape of [1,1,4].
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- Then you can make the composite as follows:</p>
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- <pre>vac = VArrayComposite.new(varrays)</pre></li>
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- </ul></dd>
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- </dl>
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- <p>Usage of all the other class methods are the same as in VArray.</p>
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-
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