gphys 1.1.1 → 1.2.2

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  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
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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>
14
- <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" -->
15
- <dd>
16
- 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
21
- 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" -->
26
- <dd>
27
- <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>
42
- <p>REMARK</p>
43
- <ul>
44
- <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>
51
- <li>backward (true of false) : when true, backward FT is done;
52
- otherwise forward FT is done.</li>
53
- <li>dims (integers) : dimensions to apply FFT</li>
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- </ul>
55
- <p>RETURN VALUE</p>
56
- <ul>
57
- <li>a GPhys</li>
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- </ul>
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- <p>EXAMPLE</p>
60
- <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.
67
- Algorithm: 1st order polynomial fitting.</p>
68
- <p>ARGUMENTS</p>
69
- <ul>
70
- <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>
76
- </ul>
77
- <p>EXAMPLE</p>
78
- <ul>
79
- <li>See <a href="#label-5">detrend</a>.</li>
80
- </ul></dd>
81
- <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>
108
- <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>
187
- <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
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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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6
- <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>
data/doc/gphys_io.html DELETED
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6
- <head>
7
- <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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6
- <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>