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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- <body>
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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>
12
- <h1><a name="label-1" id="label-1">class methods</a></h1><!-- RDLabel: "class methods" -->
13
- <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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- <dd>
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- Set a flag (class variable) to ignore missing values.
17
- This is for data that do not have missing
18
- but is treated as potentially having missing (often
19
- by having the valid_* attributes of NetCDF.)
20
- If replace_val is specified, data missing with replaced
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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" -->
24
- <dl>
25
- <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
28
- (<a href="http://www.fftw.org">FFTW</a>) ver 3 or ver 2.
29
- A FFTW ver.2 interface is included in NArray, while
30
- to use FFTW ver.3, you have to install separately.
31
- Dimension specification by the argument dims is available
32
- only with ver.3. By default, FFT is applied to all dimensions.</p>
33
- <p>The transformation is complex. If the input data is not complex,
34
- it will be coerced to complex before transformation.</p>
35
- <p>When the FT is forward, the result is normalized
36
- (i.e., divided by the data number), unlike the default behavior of
37
- FFTW.</p>
38
- <p>Each coordinate is assumed to be equally spaced without checking.
39
- The new coordinate variables will be set equal to wavenumbers,
40
- derived as 2*PI/(length of the axis)*[0,1,2,..], where the length
41
- of the axis is derived as (coord.val.max - coord.val.min)*(n+1)/n.</p>
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- <p>REMARK</p>
43
- <ul>
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- <li>If the units of the original coordinate is degree (or its
45
- equivalent ones such as degrees_east), the wavenumber was
46
- made in integers by converting the coordinate based on
47
- radian.</li>
48
- </ul>
49
- <p>ARGUMENTS</p>
50
- <ul>
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- <li>backward (true of false) : when true, backward FT is done;
52
- otherwise forward FT is done.</li>
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- <li>dims (integers) : dimensions to apply FFT</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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- <pre>gphy.fft # forward, for all dimensions
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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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- <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>
68
- <p>ARGUMENTS</p>
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- <ul>
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- <li>dim? (Integer of String): the dimension along which you want to remove
71
- trends.</li>
72
- </ul>
73
- <p>RETURN VALUE</p>
74
- <ul>
75
- <li>a GPhys</li>
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- </ul>
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- <p>EXAMPLE</p>
78
- <ul>
79
- <li>See <a href="#label-5">detrend</a>.</li>
80
- </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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- <dd>
83
- <p>Cosine tapering along dimension(s) specified.</p>
84
- <p>Algorithm: to multiply with the half cosine curves at the both
85
- 1/10 ends of the data.</p>
86
- <pre>cos taper shape:
87
- _____________
88
- _/ \_
89
- -&gt; &lt;- -&gt; &lt;-
90
- T/10 T/10
91
- half-cosine half-cosine
92
- shaped shaped</pre>
93
- <p>The spectra of tapered data should be multiplied by 1/0.875,
94
- which is stored as GPhys::COS_TAPER_SP_FACTOR (==1/0.875).</p>
95
- <p>ARGUMENTS</p>
96
- <ul>
97
- <li>dim? (Integer of String): the dimension along which you want to remove
98
- trends.</li>
99
- </ul>
100
- <p>RETURN VALUE</p>
101
- <ul>
102
- <li>a GPhys</li>
103
- </ul>
104
- <p>EXAMPLE</p>
105
- <pre>dim = 0 # for the 1st dimension
106
- fc = gphys.detrend(dim).cos_taper(dim).fft(nil,dim)
107
- 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" -->
109
- <dd>
110
- <p>Shifts the wavenumber axis to cover from -K/2 to K/2 instead of
111
- from 0 to K-1, where the wavenumber is symbolically treated as integer,
112
- which is actually not the case, though. Since the first (-K/2) and
113
- the last (K/2) elements are duplicated, both are divided by 2.
114
- Therefore, this method is to be used for spectra (squared quantity)
115
- rather than the raw Fourier coefficients. (That is why the method name
116
- is prefixed by "spect_").</p>
117
- <p>The method is applied for a single dimension (specified by the argument
118
- dim). If you need to apply for multiple dimensions, use it for multiple
119
- times.</p>
120
- <p>ARGUMENTS</p>
121
- <ul>
122
- <li>dim (integer): the dimension you want to shift spectra elements.
123
- Count starts from zero.</li>
124
- </ul>
125
- <p>RETURN VALUE</p>
126
- <ul>
127
- <li>a GPhys</li>
128
- </ul>
129
- <p>EXAMPLE</p>
130
- <ul>
131
- <li><p>To get a spectra of a variable var along the 1st and 2nd dimensions:</p>
132
- <pre>fc = var.fft(nil, 0,1) # --&gt; Fourier coef
133
- sp = ( fc.abs**2 ).spect_zero_centering(0).spect_zero_centering(1)</pre>
134
- <p>Note that spect_zero_centering is applied after taking |fc|^2.</p></li>
135
- <li><p>Same but if you want to have the 2nd dimension one-sided:</p>
136
- <pre>fc = var.fft(nil, 0,1)
137
- sp = ( fc.abs**2 ).spect_zero_centering(0).spect_one_sided(1)</pre></li>
138
- <li><p>Similar to the first example but for cross spectra:</p>
139
- <pre>fc1 = var1.fft(nil, 0,1)
140
- fc2 = var2.fft(nil, 0,1)
141
- xsp = (fc1 * fc2.conj).spect_zero_centering(0).spect_zero_centering(1)</pre></li>
142
- </ul></dd>
143
- <dt><h4><a name="label-8" id="label-8"><code>spect_one_sided(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_one_sided" -->
144
- <dd>
145
- <p>Similar to <a href="#label-7">spect_zero_centering</a> but to make one-sided spectra.
146
- Namely, to convert from 0..K-1 to 0..K/2. To be applied for spectra;
147
- wavenumber 2..K/2-1 are multiplied by 2.</p>
148
- <p>ARGUMENTS</p>
149
- <ul>
150
- <li>dim (integer): the dimension you want to shift spectra elements.
151
- Count starts from zero.</li>
152
- </ul>
153
- <p>RETURN VALUE</p>
154
- <ul>
155
- <li>a GPhys</li>
156
- </ul>
157
- <p>EXAMPLE</p>
158
- <ul>
159
- <li>See the 2nd example of <a href="#label-7">spect_zero_centering</a>.</li>
160
- </ul></dd>
161
- <dt><h4><a name="label-9" id="label-9"><code>rawspect2powerspect(*<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "rawspect2powerspect" -->
162
- <dd>
163
- <p>Converts raw spectra obtained by gphys.fft.abs**2 into
164
- power spectra by dividing by wavenumber increments
165
- along the dimensions specified by dims.</p>
166
- <p>ARGUMENTS</p>
167
- <ul>
168
- <li>dims (integers): the dimensions corresponding to wavenumbers.</li>
169
- </ul>
170
- <p>RETURN VALUE</p>
171
- <ul>
172
- <li>a GPhys</li>
173
- </ul>
174
- <p>EXAMPLE</p>
175
- <ul>
176
- <li><p>Suppose a 2 (or more) dimensional data gphys.</p>
177
- <pre>fc = gphys.fft(nil, 0, 1)
178
- sp = fc.abs**2
179
- ps = sp.rawspect2powerspect(0,1)</pre>
180
- <p>Here, sp is the raw spectrum of gphys, and ps is the power spectrum.
181
- The Parseval relation for them are as follows:</p>
182
- <pre>(gphys**2).mean == sp.sum
183
- == pw.sum*dk*dl (== \int pw dk dl, mathematically),</pre>
184
- <p>where, dk = (pw.coord(0)[1] - pw.coord(0)[0]), and
185
- dl = (pw.coord(1)[1] - pw.coord(1)[0]).</p></li>
186
- </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" -->
188
- <dd>
189
- <p>Filtering by phase velocity (between cmin and cmax)</p>
190
- <p>REMARKS</p>
191
- <ul>
192
- <li>If the number of the grid points along x or t is an even number,
193
- the maximum wavenumber or frequency is treated as positive
194
- and negative, respectively, which results in an asymmetry of
195
- the treatment of positive and negative phase speeds.
196
- (That should be ok. -- In case its effect is significant,
197
- to do the filtering itself is not meaningful.)</li>
198
- </ul>
199
- <p>ARGUMENTS</p>
200
- <ul>
201
- <li>xdim (Integer or String): spacial dimension</li>
202
- <li>tdim (Integer or String): time dimension</li>
203
- <li>cmin (Float or nil): minimum phase velocity. nil means no specification.
204
- (at least cmin or cmax must be given by Float)</li>
205
- <li>cmax (Float or nil): maximum phase velocity. nil means no specification.
206
- (at least cmin or cmax must be given by Float)</li>
207
- <li>xconv (nil or UNumeric) : (optional) if given, xconv is multiplied
208
- with the x axis before computing the phase velocity
209
- (kconv=1/xconv is used to scale wavenumbers)</li>
210
- <li>tconv (nil or UNumeric) : (optional) if given, tconv is multiplied
211
- with the t axis before computing the phase velocity
212
- (fconv=1/tconv is used to scale frequency)</li>
213
- <li>remove_xtmean (false or true) : if false (default),
214
- components with k=0 and f=0 are counted as c=0 (stationary),
215
- (unlike <a href="#label-12">phase_velocity_binning</a>), so they are included if
216
- cmin*cmax &lt;= 0; if true, k=0 &amp; f=0 components are always removed.</li>
217
- </ul>
218
- <p>RETURN VALUE</p>
219
- <ul>
220
- <li>a GPhys</li>
221
- </ul>
222
- <p>EXAMPLE</p>
223
- <ul>
224
- <li><p>For a 4D data with [x,y,z,t] dimensions, filtering by the phase
225
- velocity in the y dimension greater than 10.0 (in the unit
226
- of y/t) can be made by</p>
227
- <pre>cmin = 10.0; cmax = nil
228
- gpfilt = gp.phase_velocity_filter(1, 3, cmin, cmax)</pre></li>
229
- <li><p>For a global data (on the Earth's surface) with
230
- [lon, lat, z, time] axes, where the units of lon is
231
- "degrees" (or "degrees_east" or "radian")
232
- and the units of time is "hours", to filter disturbances
233
- whose zonal phase speed MEASURED AT THE EQUATOR is less or
234
- equal to 30 m/s can be made by</p>
235
- <pre>cmin = -30.0; cmax = 30.0
236
- xconv = UNumeric[6.37e6, "m"] # Earth's radius (i.e., m/radian)
237
- # This is a special case since "radian" is exceptionally omitted.
238
- # See the private method __predefined_coord_units_conversion.
239
- tconv = UNumeric[3.6e3, "s/hours"]
240
- gpfilt = gp.phase_velocity_filter(1, 3, cmin, cmax, xconv, tconv)</pre></li>
241
- </ul></dd>
242
- <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" -->
243
- <dd>
244
- <p>Same as <a href="#label-12">phase_velocity_binning</a> but exclusively for
245
- equal phase velocity spacing. Also, a normalization is
246
- additionally made, to scale spectra in terms of integration
247
- along phase velocity axis --- The result of
248
- <a href="#label-12">phase_velocity_binning</a> called inside
249
- this method is divided by cint along with corresponding
250
- units conversion. Therefore, if this method is applied
251
- to spectra, a normalization is made such that an integration
252
- (not summation) along the phase velocity gives the variance
253
- (or covariance etc.) -- This normalization is suitable to
254
- quadratic quantities (such as spectra) but is not suitable to
255
- raw Fourier coefficients.</p>
256
- <p>ARGUMENTS</p>
257
- <ul>
258
- <li>kdim (Integer or String): see <a href="#label-12">phase_velocity_binning</a></li>
259
- <li>fdim (Integer or String): see <a href="#label-12">phase_velocity_binning</a></li>
260
- <li>cmin (Float) : minimum phase velocity</li>
261
- <li>cmin (Float) : maximum phase velocity</li>
262
- <li>cint (Float) : inter val with which the range [cmin and cmax]
263
- is divided.</li>
264
- <li>kconv (nil or UNumeric) : see <a href="#label-12">phase_velocity_binning</a></li>
265
- <li>fconv (nil or UNumeric) : see <a href="#label-12">phase_velocity_binning</a></li>
266
- </ul>
267
- <p>RETURN VALUE</p>
268
- <ul>
269
- <li>a GPhys</li>
270
- </ul></dd>
271
- <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" -->
272
- <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>
321
- </dl>
322
-
323
- </body>
324
- </html>
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- <title>../lib/numru/gphys/gphys_grads_io.rb</title>
8
- </head>
9
- <body>
10
- <h1><a name="label-0" id="label-0">module NumRu::GPhys::GrADS_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::GrADS_IO" -->
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" -->
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?" -->
15
- <dd>
16
- <p>test whether the file is a GrADS control file.</p>
17
- <p>ARGUMENTS</p>
18
- <ul>
19
- <li>filename (String): filename to test.</li>
20
- </ul>
21
- <p>RETURN VALUE</p>
22
- <ul>
23
- <li>true/false</li>
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" -->
26
- <dd>
27
- <p>GPhys constructor from GrADS.</p>
28
- <p>ARGUMENTS</p>
29
- <ul>
30
- <li>file (GrADS_Gridded or String): file to read. If string,
31
- it must be the name (path) of a GrADS control file. </li>
32
- <li>varname (String): name of the varible in the file, for which
33
- a GPhys object is constructed.</li>
34
- </ul>
35
- <p>RETURN VALUE</p>
36
- <ul>
37
- <li>a GPhys</li>
38
- </ul>
39
- <p>EXAMPLE</p>
40
- <ul>
41
- <li><p>Suppose that you have a file T.jan.ctl in the currentdirectly,
42
- and it contains a variable "T". The following creates a GPhys
43
- object representing the variable in the file.</p>
44
- <pre>require "numru/gphys"
45
- include GPhys
46
- temp = GPhys::GrADS_IO.open("T.jan.ctl","T")</pre></li>
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" -->
49
- <dd>
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
- <dd>
53
- <p>ARGUMENTS</p>
54
- <ul>
55
- <li>file (GrADS_Gridded or String): if string,
56
- it must be the name (path) of a GrADS control file.</li>
57
- </ul>
58
- <p>RETURN VALUE</p>
59
- <ul>
60
- <li>names of variables (Array): this return the names of variables
61
- which the file has.</li>
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" -->
64
- <dd>
65
- same as var_names</dd>
66
- </dl>
67
-
68
- </body>
69
- </html>
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- <head>
7
- <title>../lib/numru/gphys/gphys_grib_io.rb</title>
8
- </head>
9
- <body>
10
- <h1><a name="label:0" id="label:0">module NumRu::GPhys::Grib_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::Grib_IO" -->
11
- <p>helps read Grib-formatted data</p>
12
- <h2><a name="label:1" id="label:1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
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)" -->
15
- <dd>
16
- <p>test whether the file is a Grib file.</p>
17
- <p>ARGUMENTS</p>
18
- <ul>
19
- <li>filename (String): filename to test.</li>
20
- </ul>
21
- <p>RETURN VALUE</p>
22
- <ul>
23
- <li>true/false</li>
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" -->
26
- <dd>
27
- <p>GPhys constructor from Grib.</p>
28
- <p>ARGUMENTS</p>
29
- <ul>
30
- <li>file (Grib or String): file to read. If string,
31
- it must be the name (path) of a Grib file. </li>
32
- <li>varname (String): name of the varible in the file, for which
33
- a GPhys object is constructed.</li>
34
- </ul>
35
- <p>RETURN VALUE</p>
36
- <ul>
37
- <li>a GPhys</li>
38
- </ul>
39
- <p>EXAMPLE</p>
40
- <ul>
41
- <li><p>Suppose that you have a file temp in the currentdirectly,
42
- and it contains a variable "T". The following creates a GPhys
43
- object representing the variable in the file.</p>
44
- <pre>require "numru/gphys"
45
- include GPhys
46
- temp = GPhys::Grib_IO.open("temp","T")</pre></li>
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" -->
49
- <dd>
50
- <p>Write a GPhys into a Grib file. The whole data under the GPhys
51
- (such as coordinate vars) are written self-descriptively.</p>
52
- <p>ARGUMENTS</p>
53
- <ul>
54
- <li>file (Grib): the Grib file to write in. Must be writable of course.</li>
55
- <li>gphys (GPhys): the GPhys to write.</li>
56
- <li>name_dummy (nil) : Unused in this module; Just for consistency with others.</li>
57
- </ul>
58
- <p>RETURN VALUE</p>
59
- <ul>
60
- <li>nil</li>
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" -->
63
- <dd>
64
- <p>ARGUMENTS</p>
65
- <ul>
66
- <li>file (Grib or String): if string,
67
- it must be the name (path) of a Grib file.</li>
68
- </ul>
69
- <p>RETURN VALUE</p>
70
- <ul>
71
- <li>names of variables (Array): this return the names of variables
72
- which the file has.</li>
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" -->
75
- <dd>
76
- <ul>
77
- <li>same as var_names</li>
78
- </ul></dd>
79
- </dl>
80
-
81
- </body>
82
- </html>
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- <head>
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- <title>../lib/numru/gphys/gphys_io.rb</title>
8
- </head>
9
- <body>
10
- <h1><a name="label-0" id="label-0">module NumRu::GPhys::IO</a></h1><!-- RDLabel: "module NumRu::GPhys::IO" -->
11
- <p>A module to handle file IO regarding GPhys. </p>
12
- <p>Many of the functionality of this module is implemented in the modules
13
- for specific file types such as NumRu::GPhys::NetCDF_IO, to which this
14
- module directs operations.</p>
15
- <p>For example, GPhys::IO.open(file, name) simply calls
16
- GPhys::*_IO.open(file, name), where '*' is
17
- NetCDF, GrADS, or grib.</p>
18
- <h2><a name="label-1" id="label-1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
19
- <dl>
20
- <dt><h4><a name="label-2" id="label-2"><code>open(<var>files</var>, <var>varname</var>)</code></a></h4></dt><!-- 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></h4></dt><!-- 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></h4></dt><!-- 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></h4></dt><!-- RDLabel: "each_along_dims_write" -->
24
- <dt><h4><a name="label-6" id="label-6"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- 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" -->
26
- <dd>
27
- See the manual of NumRu::GPhys::NetCDF_IO for the methods listed above.</dd>
28
- <dt><h4><a name="label-8" id="label-8"><code>file2type(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2type" -->
29
- <dd>
30
- <p>Figures out the file type supported in this module.</p>
31
- <p>ARGUMENTS</p>
32
- <ul>
33
- <li>file (String, Regexp, NetCDF, Grib, or GrADS_Gridded) :
34
- What to return is of course obvious if it is
35
- NetCDF, Grib, or GrADS_Gridded. If it is a String,
36
- it is assumed to be a path of a file, and the file type
37
- is determined by its suffix when 'nc', 'ctl', or 'grib';
38
- 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>
42
- </ul>
43
- <p>RETURN VALUE</p>
44
- <ul>
45
- <li>GPhys::IO::NETCDF, GPhys::IO::GRIB, or GPhys::IO::GRADS,
46
- which are string constants.</li>
47
- </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" -->
49
- <dd>
50
- Same as <a href="#label-8">file2type</a>, but returns GPhys::NetCDF_IO,
51
- GPhys::GrADS_IO, or GPhys::Grib_IO.</dd>
52
- <dt><h4><a name="label-10" id="label-10"><code>file2file_class(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2file_class" -->
53
- <dd>
54
- Same as <a href="#label-8">file2type</a>, but returns NetCDF,
55
- GrADS_Gridded, or Grib.</dd>
56
- <dt><h4><a name="label-11" id="label-11"><code>parse_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "parse_gturl" -->
57
- <dd>
58
- <p>Parses GTOOL4-type URLs to specify path, variable name,
59
- and optionally subsets, whose format is
60
- path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</p>
61
- <p>ARGUMENTS</p>
62
- <ul>
63
- <li>gturl (String) GTOOL4 URL, whose format is
64
- path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</li>
65
- </ul>
66
- <p>RETURN VALUES</p>
67
- <ul>
68
- <li>An Array consisting of [file, var, slice, cut_slice, thinning], where
69
- <ul>
70
- <li>file (String) : path</li>
71
- <li>var (String) : variable name</li>
72
- <li>slice (Array) : subset specifier by the grid numbers
73
- to be used as GPhys#[slice].</li>
74
- <li>cut_slice (Array) : subset specifier in physical coordinate
75
- to be used as GPhys#cut[cut_slice].</li>
76
- <li>thinning (Array) : additional subset specifier for thinning
77
- with uniform intervals if needed to be used GPhys#[thinning]
78
- after appling GPhys#cut.</li>
79
- </ul></li>
80
- </ul></dd>
81
- <dt><h4><a name="label-12" id="label-12"><code>open_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "open_gturl" -->
82
- <dd>
83
- <p>a GPhys constructor from a Gtool4-type URL.
84
- See <a href="#label-11">parse_gturl</a> for its format.</p>
85
- <p>RETURN VALUE</p>
86
- <ul>
87
- <li>a GPhys</li>
88
- </ul></dd>
89
- <dt><h4><a name="label-13" id="label-13"><code>str2gphys(<var>str</var>)</code></a></h4></dt><!-- RDLabel: "str2gphys" -->
90
- <dd>
91
- <p>Open a GPhys from a slash("/")-separated String
92
- such as "U.nc/U" and "U.nc".</p>
93
- <ul>
94
- <li>Aimed to help quick jobs with interactive sessions
95
- -- This method do not handle a GPhys across multiple files.</li>
96
- <li>if the variable path is ommited such as "U.nc",
97
- try to find the variable in it -- read the file and if
98
- only one variable is found, assume that is the
99
- variable specified; otherwise, an exception is raised.</li>
100
- <li>URL is accepted, but it's only thru NetCDF assuming OPeNDAP.</li>
101
- </ul>
102
- <p>ARGUMENTS</p>
103
- <ul>
104
- <li>a String (file_path[/variable_path])
105
- e.g. "U.nc/U", "U.nc", "http://.../U.nc/U"</li>
106
- </ul>
107
- <p>RETURN VALUE</p>
108
- <ul>
109
- <li>a GPhys</li>
110
- </ul></dd>
111
- </dl>
112
- <h2><a name="label-14" id="label-14">Module constants</a></h2><!-- RDLabel: "Module constants" -->
113
- <dl>
114
- <dt><h4><a name="label-15" id="label-15"><code>GTURLfmt</code></a></h4></dt><!-- RDLabel: "GTURLfmt" -->
115
- <dd>
116
- The format of Gtool4URL.</dd>
117
- </dl>
118
-
119
- </body>
120
- </html>
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- <head>
7
- <title>../lib/numru/gphys/gphys_io_common.rb</title>
8
- </head>
9
- <body>
10
- <h1><a name="label-0" id="label-0">module NumRu::GPhys::IO_Common</a></h1><!-- RDLabel: "module NumRu::GPhys::IO_Common" -->
11
- <p>THIS MODULE IS ONLY FOR INTERNAL USAGE.
12
- (Does not work stand alone.)</p>
13
- <p>Functions independent of specific file formart.
14
- To be used by IO, NetCDF_IO, GrADS_IO etc. </p>
15
- <p>A test program is included in gphys_netcdf.rb</p>
16
-
17
- </body>
18
- </html>