gphys 1.5.0 → 1.5.1
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- checksums.yaml +7 -0
- data/ChangeLog +7414 -0
- data/LICENSE.txt +1 -1
- data/Rakefile +0 -2
- data/doc/derivative/math-doc/document/images.log +385 -0
- data/doc/ep_flux/math-doc/document/images.log +1375 -0
- data/doc/ganalysis/doc/NumRu.html +203 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis.html +931 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/BetaPlane.html +574 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/Fitting.html +576 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/LogP.html +425 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/Met.html +2021 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/MetZ.html +524 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/Planet.html +1047 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/QG.html +794 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/QG/Uninitialized.html +215 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/QG_common.html +603 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/QG_sphere.html +760 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/QG_sphere_common.html +251 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/QG_sphere_div.html +424 -0
- data/doc/ganalysis/doc/NumRu/GAnalysis/SigmaCoord.html +321 -0
- data/doc/ganalysis/doc/NumRu/GGraph.html +334 -0
- data/doc/ganalysis/doc/NumRu/GPhys.html +579 -0
- data/doc/ganalysis/doc/Object.html +210 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/beta_plane_rb.html +60 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/covariance_rb.html +56 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/eof_rb.html +64 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/fitting_rb.html +54 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/histogram_rb.html +58 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/log_p_rb.html +60 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/met_rb.html +60 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/met_z_rb.html +58 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/planet_rb.html +58 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/qg_rb.html +64 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis/sigma_coord_rb.html +56 -0
- data/doc/ganalysis/doc/__/__/lib/numru/ganalysis_rb.html +98 -0
- data/doc/ganalysis/doc/created.rid +13 -0
- data/doc/ganalysis/doc/images/brick.png +0 -0
- data/doc/ganalysis/doc/images/brick_link.png +0 -0
- data/doc/ganalysis/doc/images/bug.png +0 -0
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- data/doc/ganalysis/doc/images/date.png +0 -0
- data/doc/ganalysis/doc/images/find.png +0 -0
- data/doc/ganalysis/doc/images/loadingAnimation.gif +0 -0
- data/doc/ganalysis/doc/images/macFFBgHack.png +0 -0
- data/doc/ganalysis/doc/images/package.png +0 -0
- data/doc/ganalysis/doc/images/page_green.png +0 -0
- data/doc/ganalysis/doc/images/page_white_text.png +0 -0
- data/doc/ganalysis/doc/images/page_white_width.png +0 -0
- data/doc/ganalysis/doc/images/plugin.png +0 -0
- data/doc/ganalysis/doc/images/ruby.png +0 -0
- data/doc/ganalysis/doc/images/tag_green.png +0 -0
- data/doc/ganalysis/doc/images/wrench.png +0 -0
- data/doc/ganalysis/doc/images/wrench_orange.png +0 -0
- data/doc/ganalysis/doc/images/zoom.png +0 -0
- data/doc/ganalysis/doc/index.html +383 -0
- data/doc/ganalysis/doc/js/darkfish.js +118 -0
- data/doc/ganalysis/doc/js/jquery.js +32 -0
- data/doc/ganalysis/doc/js/quicksearch.js +114 -0
- data/doc/ganalysis/doc/js/thickbox-compressed.js +10 -0
- data/doc/ganalysis/doc/rdoc.css +763 -0
- data/ext/numru/gphys/ext_init.c +1 -0
- data/ext/numru/gphys/quad_mesh_sample.c +478 -0
- data/gphys.gemspec +2 -2
- data/lib/numru/dclext.rb +394 -14
- data/lib/numru/derivative.rb +6 -0
- data/lib/numru/ganalysis/qg.rb +6 -4
- data/lib/numru/ggraph.rb +41 -8
- data/lib/numru/gphys/gphys.rb +62 -14
- data/lib/numru/gphys/gphys_io.rb +4 -4
- data/lib/numru/gphys/version.rb +2 -2
- metadata +84 -79
- data/.gitignore +0 -14
- data/TODO_ep_flux +0 -6
- data/gphys-bigmem.gemspec +0 -44
- data/install.rb +0 -130
- data/sample/cira86_to_nc.rb +0 -122
- data/sample/druby_cli1.rb +0 -23
- data/sample/druby_cli2.rb +0 -28
- data/sample/druby_serv1.rb +0 -30
- data/sample/druby_serv2.rb +0 -51
- data/sample/ep_flux/demo_NCEP_1.rb +0 -48
- data/sample/ep_flux/demo_NCEP_2.rb +0 -57
- data/sample/ep_flux/demo_NCEP_3.rb +0 -81
- data/sample/ggraph_latlon_labelling_dr002690.rb +0 -159
- data/sample/ggraph_mapfit-axes_dr002687.rb +0 -131
- data/sample/map_projection.rb +0 -121
- data/sample/ncep_theta_coord.rb +0 -79
- data/test_old/eof_slp.rb +0 -28
- data/test_old/mltbit.dat +0 -0
- data/test_old/test_ep_flux.rb +0 -533
- data/test_old/test_multibitIO.rb +0 -19
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<p>Library for function fitting</p>
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<dt><a name="X">X</a></dt>
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<dd class="description"><p>predefined Proc for fitting: Polynomial x (function of the 1st dim)</p></dd>
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<dd class="description"><p>predefined Proc for fitting: Polynomial x**2 (function of the 1st dim)</p></dd>
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<dd class="description"><p>predefined Proc for fitting: Polynomial x*y (function of the 1st&2nd
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<dd class="description"><p>predefined Proc for fitting: Polynomial y (function of the 2nd dim)</p></dd>
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<dd class="description"><p>predefined Proc for fitting: Polynomial y**2 (function of the 2nd dim)</p></dd>
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<!-- Methods -->
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<div id="least_square_fit-method" class="method-detail ">
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<a name="method-i-least_square_fit"></a>
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<span class="method-name">least_square_fit</span><span
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class="method-args">(data, grid_locs, functions, ensemble_dims=nil, indep_dims=nil)</span>
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<p>Least square fit of a linear combination of any functions (basic NArray
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<p><tt>functions</tt> [Array of Procs] Proc objects to represent the
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ensemble averaging</p>
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<p>Note that the sum of the lengths of <tt>grid_locs</tt>,
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<tt>ensemble_dims</tt> and <tt>indep_dims</tt> must be equal to the rank (#
|
|
234
|
+
of dims) of <tt>data</tt>.</p>
|
|
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|
+
|
|
236
|
+
<h3>RETURN VALUES</h3>
|
|
237
|
+
|
|
238
|
+
<pre>[ c, bf, diff ]</pre>
|
|
239
|
+
|
|
240
|
+
<p>where</p>
|
|
241
|
+
<ul><li>
|
|
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|
+
<p><tt>c</tt> is a NArray containing the coefficients of the functions and the
|
|
243
|
+
constant offset; its length is one greater than the number of
|
|
244
|
+
<tt>functions</tt> because of the offset. It is 1D unless the
|
|
245
|
+
<tt>indep_dims</tt> argument is used (see the examples below).</p>
|
|
246
|
+
</li><li>
|
|
247
|
+
<p><tt>bf</tt> is a NArray having the best fit grid point values. Its rank is
|
|
248
|
+
equal to data.rank, but the lengths along <tt>ensemble_dims</tt> are
|
|
249
|
+
simply 1.</p>
|
|
250
|
+
</li><li>
|
|
251
|
+
<p>rms of the difference between the data and best fit</p>
|
|
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|
+
</li></ul>
|
|
253
|
+
|
|
254
|
+
<h3>EXAMPLES</h3>
|
|
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|
+
<ul><li>
|
|
256
|
+
<p>Simple 1D case</p>
|
|
257
|
+
|
|
258
|
+
<p>Line fitting:</p>
|
|
259
|
+
|
|
260
|
+
<pre>nx = 5
|
|
261
|
+
x = NArray.float(nx).indgen! - nx/2
|
|
262
|
+
data = x + x*x*0.1
|
|
263
|
+
c, bf = GAnalysis::Fitting.least_square_fit(data, [x],
|
|
264
|
+
[GAnalysis::Fitting::X])
|
|
265
|
+
p "data:", data, "c:", c, "bf:", bf</pre>
|
|
266
|
+
|
|
267
|
+
<p>Here, +GAnalysis::Fitting::X+ is a predefined Proc to represent the first
|
|
268
|
+
order polynomial x. The data values given as above follow f(x) = x +
|
|
269
|
+
x**2/10. Then the result printed by the last line is</p>
|
|
270
|
+
|
|
271
|
+
<pre>"data:"
|
|
272
|
+
NArray.float(5):
|
|
273
|
+
[ -1.6, -0.9, 0.0, 1.1, 2.4 ]
|
|
274
|
+
"c:"
|
|
275
|
+
NArray.float(2):
|
|
276
|
+
[ 1.0, 0.2 ]
|
|
277
|
+
"bf:"
|
|
278
|
+
NArray.float(5):
|
|
279
|
+
[ -1.8, -0.8, 0.2, 1.2, 2.2 ]</pre>
|
|
280
|
+
|
|
281
|
+
<p>The <tt>c</tt> values indicate that the fitting result is f(x) = 1.0*x +
|
|
282
|
+
0.2, and the <tt>bf</tt> values are its grid point values.</p>
|
|
283
|
+
|
|
284
|
+
<p>Parabolic fitting:</p>
|
|
285
|
+
|
|
286
|
+
<p>You can also fit the data by 2nd order polynomial as</p>
|
|
287
|
+
|
|
288
|
+
<pre>c, bf = GAnalysis::Fitting.least_square_fit(data, [x],
|
|
289
|
+
[GAnalysis::Fitting::XX,GAnalysis::Fitting::X])</pre>
|
|
290
|
+
|
|
291
|
+
<p>Then the result will be</p>
|
|
292
|
+
|
|
293
|
+
<pre>p c #--> [0.1, 1.0, 0.0]</pre>
|
|
294
|
+
|
|
295
|
+
<p>which indicates the original 2nd order polynomial 0.1 x**2 + x, so it
|
|
296
|
+
follows <tt>data == bf</tt> (except for round-off error if any).</p>
|
|
297
|
+
</li><li>
|
|
298
|
+
<p>1D fitting of multi-D data (ensemble case)</p>
|
|
299
|
+
|
|
300
|
+
<p>Suppose you have a 2D NArray (or NArrayMiss) data, in which the 1st dim
|
|
301
|
+
represents x and the 2nd dim represents something else (such as time
|
|
302
|
+
sequence, or just a simple ensemble). If you want to use the entire data to
|
|
303
|
+
get a single fit, use the <tt>ensemble_dims</tt> argument to specify the
|
|
304
|
+
non-x dimension(s). You can fit the data, for example, by p*sin(x) +
|
|
305
|
+
q*cos(x) + r as follows:</p>
|
|
306
|
+
|
|
307
|
+
<pre>sin = proc{|x| NMath.sin(x)}
|
|
308
|
+
cos = proc{|x| NMath.cos(x)}
|
|
309
|
+
c, bf = GAnalysis::Fitting.least_square_fit(data, [x],
|
|
310
|
+
[sin, cos], [1])</pre>
|
|
311
|
+
|
|
312
|
+
<p>Here, the last parameter [1] is given as the arguemnt
|
|
313
|
+
<tt>ensemble_dims</tt> to express that the dimension 1 (2nd dimension) of
|
|
314
|
+
<tt>data</tt> is the ensemble dimension, so the x coordinate is the
|
|
315
|
+
remaining dimension 0 (1st dimension). The coefficients of the functions
|
|
316
|
+
are returned by the 1st return value as a NArray, so</p>
|
|
317
|
+
|
|
318
|
+
<pre>p = c[0]
|
|
319
|
+
q = c[1]
|
|
320
|
+
r = c[2]</pre>
|
|
321
|
+
</li><li>
|
|
322
|
+
<p>1D fitting of multi-D data (individual fitting)</p>
|
|
323
|
+
|
|
324
|
+
<p>Suppose you have the same data as above, but you want to fit it for each of
|
|
325
|
+
the 2nd dim elements. You can do it as follows:</p>
|
|
326
|
+
|
|
327
|
+
<pre>c, bf = GAnalysis::Fitting.least_square_fit(data, [x],
|
|
328
|
+
[sin, cos], nil, [1])</pre>
|
|
329
|
+
|
|
330
|
+
<p>Here, <tt>nil</tt> is given as the 4th argument (<tt>ensemble_dims</tt>)
|
|
331
|
+
and [1] is given as the fifth (<tt>indep_dims</tt>). In this case, the
|
|
332
|
+
return value <tt>c</tt> is 2-dimensional; the first being the coefficients
|
|
333
|
+
as above and the second representing the non-x (i.e., the second) dim of
|
|
334
|
+
<tt>data</tt>.</p>
|
|
335
|
+
</li><li>
|
|
336
|
+
<p>2D fitting</p>
|
|
337
|
+
|
|
338
|
+
<p>It can be done like</p>
|
|
339
|
+
|
|
340
|
+
<pre>cosx = proc {|x,y| NMath.cos(x).newdim!(-1)}
|
|
341
|
+
sinx = proc {|x,y| NMath.sin(x).newdim!(-1)}
|
|
342
|
+
cosy = proc {|x,y| NMath.cos(y).newdim!(0)}
|
|
343
|
+
siny = proc {|x,y| NMath.sin(y).newdim!(0)}
|
|
344
|
+
c, bf = GAnalysis::Fitting.least_square_fit(data4D, [x,y],
|
|
345
|
+
[cosx, sinx, cosy, siny], [2,3])</pre>
|
|
346
|
+
|
|
347
|
+
<p>where <tt>data4D</tt> is a 4D NArray, whose first and second dimensions
|
|
348
|
+
(dimensions 0 and 1) represent x and y axis, respectively, and the 1D
|
|
349
|
+
NArrays <tt>x</tt> and <tt>y</tt> are the grid points. Note that the
|
|
350
|
+
functions (<tt>cosx</tt> etc) accept 2 arguments (x and y), and they use
|
|
351
|
+
NArray’s <tt>newdim</tt> method to return 2D NArray (newdim!(-1) inserts a
|
|
352
|
+
1-element dim to the end, and newdim(0) inserts a 1-element dim to the
|
|
353
|
+
beginning).</p>
|
|
354
|
+
</li></ul>
|
|
355
|
+
|
|
356
|
+
<p>TYPICAL ERRORS</p>
|
|
357
|
+
<ul><li>
|
|
358
|
+
<p>Error is raised (from the LU decomposition), if the problem cannot be
|
|
359
|
+
solved. That happens if you specify a same function twice (redundantly) in
|
|
360
|
+
the <tt>functions</tt> argument, as a matter of course.</p>
|
|
361
|
+
</li><li>
|
|
362
|
+
<p>Error is raised if the number of data is insuffcient for the number of
|
|
363
|
+
functions (also unsolvable).</p>
|
|
364
|
+
</li></ul>
|
|
365
|
+
|
|
366
|
+
|
|
367
|
+
|
|
368
|
+
<div class="method-source-code" id="least_square_fit-source">
|
|
369
|
+
<pre>
|
|
370
|
+
<span class="ruby-comment"># File ../../lib/numru/ganalysis/fitting.rb, line 217</span>
|
|
371
|
+
<span class="ruby-keyword">def</span> <span class="ruby-identifier">least_square_fit</span>(<span class="ruby-identifier">data</span>, <span class="ruby-identifier">grid_locs</span>, <span class="ruby-identifier">functions</span>, <span class="ruby-identifier">ensemble_dims</span>=<span class="ruby-keyword">nil</span>,
|
|
372
|
+
<span class="ruby-identifier">indep_dims</span>=<span class="ruby-keyword">nil</span>)
|
|
373
|
+
|
|
374
|
+
<span class="ruby-comment">#< argument check ></span>
|
|
375
|
+
|
|
376
|
+
<span class="ruby-identifier">grid_locs</span>.<span class="ruby-identifier">each_with_index</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">x</span>,<span class="ruby-identifier">i</span><span class="ruby-operator">|</span> <span class="ruby-keyword">self</span>.<span class="ruby-identifier">ensure_1D_NArray</span>(<span class="ruby-identifier">x</span>, <span class="ruby-identifier">i</span>)}
|
|
377
|
+
<span class="ruby-identifier">functions</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-identifier">raise</span>(<span class="ruby-string">"Found non-Proc arg"</span>) <span class="ruby-keyword">if</span> <span class="ruby-operator">!</span><span class="ruby-identifier">f</span>.<span class="ruby-identifier">is_a?</span>(<span class="ruby-constant">Proc</span>)}
|
|
378
|
+
|
|
379
|
+
<span class="ruby-identifier">functions</span> = <span class="ruby-identifier">functions</span> <span class="ruby-operator">+</span> [<span class="ruby-identifier">@@unity</span>] <span class="ruby-comment"># constanf offset</span>
|
|
380
|
+
|
|
381
|
+
<span class="ruby-identifier">ng</span> = <span class="ruby-identifier">grid_locs</span>.<span class="ruby-identifier">length</span>
|
|
382
|
+
<span class="ruby-identifier">rank</span> = <span class="ruby-identifier">data</span>.<span class="ruby-identifier">rank</span>
|
|
383
|
+
<span class="ruby-identifier">ensemble_dims</span> = [ <span class="ruby-identifier">ensemble_dims</span> ] <span class="ruby-keyword">if</span> <span class="ruby-identifier">ensemble_dims</span>.<span class="ruby-identifier">is_a?</span>(<span class="ruby-constant">Integer</span>)
|
|
384
|
+
<span class="ruby-identifier">indep_dims</span> = [ <span class="ruby-identifier">indep_dims</span> ] <span class="ruby-keyword">if</span> <span class="ruby-identifier">indep_dims</span>.<span class="ruby-identifier">is_a?</span>(<span class="ruby-constant">Integer</span>)
|
|
385
|
+
|
|
386
|
+
<span class="ruby-identifier">ensemble_dims</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">ensemble_dims</span>.<span class="ruby-identifier">nil?</span> <span class="ruby-comment"># --> always an Array</span>
|
|
387
|
+
<span class="ruby-identifier">n_indep</span> = ( <span class="ruby-identifier">indep_dims</span> <span class="ruby-operator">?</span> <span class="ruby-identifier">indep_dims</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">:</span> <span class="ruby-value">0</span> )
|
|
388
|
+
|
|
389
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">ng</span> <span class="ruby-operator"><</span> <span class="ruby-identifier">rank</span>
|
|
390
|
+
<span class="ruby-identifier">ensemble_dims</span> = <span class="ruby-identifier">ensemble_dims</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span>
|
|
391
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">d</span><span class="ruby-operator"><</span><span class="ruby-operator">-</span><span class="ruby-identifier">rank</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">d</span><span class="ruby-operator">>=</span><span class="ruby-identifier">rank</span>
|
|
392
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-node">"Invalid ensemble_dims value (#{d}) for rank #{rank} NArray"</span>
|
|
393
|
+
<span class="ruby-keyword">end</span>
|
|
394
|
+
<span class="ruby-identifier">d</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">rank</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">d</span><span class="ruby-operator"><</span><span class="ruby-value">0</span>
|
|
395
|
+
<span class="ruby-identifier">d</span>
|
|
396
|
+
}
|
|
397
|
+
<span class="ruby-identifier">ensemble_dims</span>.<span class="ruby-identifier">sort!</span>
|
|
398
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">indep_dims</span>
|
|
399
|
+
<span class="ruby-identifier">indep_dims</span> = <span class="ruby-identifier">indep_dims</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span>
|
|
400
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">d</span><span class="ruby-operator"><</span><span class="ruby-operator">-</span><span class="ruby-identifier">rank</span> <span class="ruby-operator">||</span> <span class="ruby-identifier">d</span><span class="ruby-operator">>=</span><span class="ruby-identifier">rank</span>
|
|
401
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-node">"Invalid indep_dims value (#{d}) for rank #{rank} NArray"</span>
|
|
402
|
+
<span class="ruby-keyword">end</span>
|
|
403
|
+
<span class="ruby-identifier">d</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">rank</span> <span class="ruby-keyword">if</span> <span class="ruby-identifier">d</span><span class="ruby-operator"><</span><span class="ruby-value">0</span>
|
|
404
|
+
<span class="ruby-identifier">d</span>
|
|
405
|
+
}
|
|
406
|
+
<span class="ruby-identifier">indep_dims</span>.<span class="ruby-identifier">sort!</span>
|
|
407
|
+
<span class="ruby-keyword">end</span>
|
|
408
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">ng</span> <span class="ruby-operator">></span> <span class="ruby-identifier">rank</span>
|
|
409
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-node">"# of grid_locs (#{ng}) > data.rank (#{rank})"</span>
|
|
410
|
+
<span class="ruby-keyword">end</span>
|
|
411
|
+
|
|
412
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">data</span>.<span class="ruby-identifier">rank</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ng</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">ensemble_dims</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">n_indep</span>
|
|
413
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>,
|
|
414
|
+
<span class="ruby-string">"lengths of grid_locs, ensemble_dims and indep_dims != data.rank"</span>
|
|
415
|
+
<span class="ruby-keyword">end</span>
|
|
416
|
+
|
|
417
|
+
<span class="ruby-identifier">otherdims</span> = <span class="ruby-identifier">ensemble_dims</span>
|
|
418
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">indep_dims</span>
|
|
419
|
+
<span class="ruby-identifier">otherdims</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">indep_dims</span>
|
|
420
|
+
<span class="ruby-identifier">otherdims</span>.<span class="ruby-identifier">sort!</span>.<span class="ruby-identifier">uniq!</span>
|
|
421
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">otherdims</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">!=</span> <span class="ruby-identifier">ensemble_dims</span>.<span class="ruby-identifier">length</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">n_indep</span>
|
|
422
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-constant">ArgumentError</span>, <span class="ruby-string">"Overlap in ensemble_dims and indep_dims"</span>
|
|
423
|
+
<span class="ruby-keyword">end</span>
|
|
424
|
+
<span class="ruby-keyword">end</span>
|
|
425
|
+
|
|
426
|
+
<span class="ruby-comment">#< pre-process data ></span>
|
|
427
|
+
|
|
428
|
+
<span class="ruby-identifier">d0</span> = <span class="ruby-identifier">data</span>.<span class="ruby-identifier">mean</span>
|
|
429
|
+
<span class="ruby-identifier">data</span> = <span class="ruby-identifier">data</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">d0</span> <span class="ruby-comment"># constant offset for numerical stability</span>
|
|
430
|
+
|
|
431
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">data</span>.<span class="ruby-identifier">is_a?</span>(<span class="ruby-constant">NArrayMiss</span>)
|
|
432
|
+
<span class="ruby-identifier">mask</span> = <span class="ruby-identifier">data</span>.<span class="ruby-identifier">get_mask</span>
|
|
433
|
+
<span class="ruby-keyword">elsif</span> <span class="ruby-identifier">data</span>.<span class="ruby-identifier">is_a?</span>(<span class="ruby-constant">NArray</span>)
|
|
434
|
+
<span class="ruby-identifier">mask</span> = <span class="ruby-keyword">nil</span> <span class="ruby-comment"># NArray.byte(*data.shape).fill!(1)</span>
|
|
435
|
+
<span class="ruby-keyword">else</span>
|
|
436
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-node">"Data type (#{data.class}) is not NArray or NArrayMiss"</span>
|
|
437
|
+
<span class="ruby-keyword">end</span>
|
|
438
|
+
|
|
439
|
+
<span class="ruby-comment">#< derive the matrix ></span>
|
|
440
|
+
|
|
441
|
+
<span class="ruby-identifier">fv</span> = <span class="ruby-identifier">functions</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span>
|
|
442
|
+
<span class="ruby-identifier">f</span> = <span class="ruby-identifier">f</span>[*<span class="ruby-identifier">grid_locs</span>]
|
|
443
|
+
<span class="ruby-identifier">otherdims</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span> <span class="ruby-identifier">f</span>.<span class="ruby-identifier">newdim!</span>(<span class="ruby-identifier">d</span>)}
|
|
444
|
+
<span class="ruby-identifier">f</span>
|
|
445
|
+
}
|
|
446
|
+
|
|
447
|
+
<span class="ruby-identifier">ms</span> = <span class="ruby-identifier">fv</span>.<span class="ruby-identifier">length</span> <span class="ruby-comment"># matrix size</span>
|
|
448
|
+
|
|
449
|
+
<span class="ruby-keyword">if</span> ( (<span class="ruby-identifier">len</span>=<span class="ruby-identifier">data</span>.<span class="ruby-identifier">length</span>) <span class="ruby-operator"><</span> <span class="ruby-identifier">ms</span> )
|
|
450
|
+
<span class="ruby-identifier">raise</span> <span class="ruby-node">"Insufficient data length (#{len}) for the # of funcs+1 (#{ms})"</span>
|
|
451
|
+
<span class="ruby-keyword">end</span>
|
|
452
|
+
|
|
453
|
+
<span class="ruby-identifier">mat</span> = <span class="ruby-constant">NMatrix</span>.<span class="ruby-identifier">float</span>(<span class="ruby-identifier">ms</span>,<span class="ruby-identifier">ms</span>) <span class="ruby-comment"># wil be symmetric</span>
|
|
454
|
+
|
|
455
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">i</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span>
|
|
456
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-identifier">i</span>
|
|
457
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">mask</span>
|
|
458
|
+
<span class="ruby-identifier">fvij</span> = <span class="ruby-constant">NArrayMiss</span>.<span class="ruby-identifier">to_nam</span>( <span class="ruby-identifier">fv</span>[<span class="ruby-identifier">i</span>] * <span class="ruby-identifier">fv</span>[<span class="ruby-identifier">j</span>] * <span class="ruby-identifier">mask</span>, <span class="ruby-identifier">mask</span> )
|
|
459
|
+
<span class="ruby-identifier">mat</span>[<span class="ruby-identifier">i</span>,<span class="ruby-identifier">j</span>] = (<span class="ruby-identifier">fvij</span>).<span class="ruby-identifier">mean</span>
|
|
460
|
+
<span class="ruby-keyword">else</span>
|
|
461
|
+
<span class="ruby-identifier">mat</span>[<span class="ruby-identifier">i</span>,<span class="ruby-identifier">j</span>] = (<span class="ruby-identifier">fv</span>[<span class="ruby-identifier">i</span>] * <span class="ruby-identifier">fv</span>[<span class="ruby-identifier">j</span>]).<span class="ruby-identifier">mean</span>
|
|
462
|
+
<span class="ruby-keyword">end</span>
|
|
463
|
+
<span class="ruby-keyword">end</span>
|
|
464
|
+
<span class="ruby-keyword">end</span>
|
|
465
|
+
|
|
466
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">i</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span>
|
|
467
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">j</span> <span class="ruby-keyword">in</span> <span class="ruby-identifier">i</span><span class="ruby-operator">+</span><span class="ruby-value">1</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span>
|
|
468
|
+
<span class="ruby-identifier">mat</span>[<span class="ruby-identifier">i</span>,<span class="ruby-identifier">j</span>] = <span class="ruby-identifier">mat</span>[<span class="ruby-identifier">j</span>,<span class="ruby-identifier">i</span>] <span class="ruby-comment"># symmetric</span>
|
|
469
|
+
<span class="ruby-keyword">end</span>
|
|
470
|
+
<span class="ruby-keyword">end</span>
|
|
471
|
+
<span class="ruby-comment">#p "*** mat ***",mat</span>
|
|
472
|
+
<span class="ruby-identifier">lu</span> = <span class="ruby-identifier">mat</span>.<span class="ruby-identifier">lu</span>
|
|
473
|
+
|
|
474
|
+
<span class="ruby-comment">#< derive the vector, solve, and best fit ></span>
|
|
475
|
+
|
|
476
|
+
<span class="ruby-keyword">unless</span> <span class="ruby-identifier">indep_dims</span> <span class="ruby-comment"># fitting only once</span>
|
|
477
|
+
<span class="ruby-comment"># derive the vector</span>
|
|
478
|
+
<span class="ruby-identifier">b</span> = <span class="ruby-constant">NVector</span>.<span class="ruby-identifier">float</span>(<span class="ruby-identifier">ms</span>)
|
|
479
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">i</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span>
|
|
480
|
+
<span class="ruby-identifier">b</span>[<span class="ruby-identifier">i</span>] = (<span class="ruby-identifier">data</span> * <span class="ruby-identifier">fv</span>[<span class="ruby-identifier">i</span>]).<span class="ruby-identifier">mean</span>
|
|
481
|
+
<span class="ruby-keyword">end</span>
|
|
482
|
+
|
|
483
|
+
<span class="ruby-comment"># solve</span>
|
|
484
|
+
<span class="ruby-identifier">c</span> = <span class="ruby-identifier">lu</span>.<span class="ruby-identifier">solve</span>(<span class="ruby-identifier">b</span>)
|
|
485
|
+
<span class="ruby-identifier">c</span>[<span class="ruby-value">-1</span>] <span class="ruby-operator">+=</span> <span class="ruby-identifier">d0</span> <span class="ruby-comment"># add the mean subtracted</span>
|
|
486
|
+
|
|
487
|
+
<span class="ruby-comment"># convert c from NVector to NArray (just for cleanliness)</span>
|
|
488
|
+
<span class="ruby-identifier">na</span> = <span class="ruby-constant">NArray</span>.<span class="ruby-identifier">float</span>(<span class="ruby-identifier">ms</span>)
|
|
489
|
+
<span class="ruby-identifier">na</span>[<span class="ruby-keyword">true</span>] = <span class="ruby-identifier">c</span>[<span class="ruby-keyword">true</span>]
|
|
490
|
+
<span class="ruby-identifier">c</span> = <span class="ruby-identifier">na</span>
|
|
491
|
+
|
|
492
|
+
<span class="ruby-comment"># best fit</span>
|
|
493
|
+
<span class="ruby-identifier">bf</span> = <span class="ruby-identifier">c</span>[<span class="ruby-value">-1</span>] <span class="ruby-comment"># the constant offset</span>
|
|
494
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">i</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>
|
|
495
|
+
<span class="ruby-identifier">bf</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">c</span>[<span class="ruby-identifier">i</span>]*<span class="ruby-identifier">fv</span>[<span class="ruby-identifier">i</span>]
|
|
496
|
+
<span class="ruby-keyword">end</span>
|
|
497
|
+
|
|
498
|
+
<span class="ruby-keyword">else</span> <span class="ruby-comment"># fitting multiple times</span>
|
|
499
|
+
|
|
500
|
+
<span class="ruby-comment"># derive vectors</span>
|
|
501
|
+
<span class="ruby-identifier">idshp</span> = <span class="ruby-identifier">indep_dims</span>.<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span> <span class="ruby-identifier">data</span>.<span class="ruby-identifier">shape</span>[<span class="ruby-identifier">d</span>]}
|
|
502
|
+
<span class="ruby-identifier">bs</span> = <span class="ruby-constant">NArray</span>.<span class="ruby-identifier">float</span>(<span class="ruby-identifier">ms</span>,*<span class="ruby-identifier">idshp</span>)
|
|
503
|
+
<span class="ruby-identifier">meandims</span> = (<span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">rank</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">d</span><span class="ruby-operator">|</span> <span class="ruby-identifier">d</span>} <span class="ruby-operator">-</span> <span class="ruby-identifier">indep_dims</span>
|
|
504
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">i</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span>
|
|
505
|
+
<span class="ruby-identifier">bsi</span> = (<span class="ruby-identifier">data</span> * <span class="ruby-identifier">fv</span>[<span class="ruby-identifier">i</span>]).<span class="ruby-identifier">mean</span>(*<span class="ruby-identifier">meandims</span>)
|
|
506
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">bsi</span>.<span class="ruby-identifier">is_a?</span>(<span class="ruby-constant">NArrayMiss</span>)
|
|
507
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">bsi</span>.<span class="ruby-identifier">count_invalid</span> <span class="ruby-operator">></span> <span class="ruby-value">0</span>
|
|
508
|
+
<span class="ruby-identifier">raise</span>(<span class="ruby-string">"Found invalid data everywhere along indep_dims. Trim data in advance and try again."</span>)
|
|
509
|
+
<span class="ruby-keyword">end</span>
|
|
510
|
+
<span class="ruby-identifier">bsi</span> = <span class="ruby-identifier">bsi</span>.<span class="ruby-identifier">to_na</span>
|
|
511
|
+
<span class="ruby-keyword">end</span>
|
|
512
|
+
<span class="ruby-identifier">bs</span>[<span class="ruby-identifier">i</span>,<span class="ruby-keyword">false</span>] = <span class="ruby-identifier">bsi</span>
|
|
513
|
+
<span class="ruby-keyword">end</span>
|
|
514
|
+
<span class="ruby-identifier">idlen</span> = <span class="ruby-value">1</span>
|
|
515
|
+
<span class="ruby-identifier">idshp</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">l</span><span class="ruby-operator">|</span> <span class="ruby-identifier">idlen</span> <span class="ruby-operator">*=</span> <span class="ruby-identifier">l</span>}
|
|
516
|
+
|
|
517
|
+
<span class="ruby-comment"># solve</span>
|
|
518
|
+
<span class="ruby-identifier">bs</span> = <span class="ruby-identifier">bs</span>.<span class="ruby-identifier">reshape</span>(<span class="ruby-identifier">ms</span>, <span class="ruby-identifier">idlen</span>)
|
|
519
|
+
<span class="ruby-identifier">c</span> = <span class="ruby-constant">NArray</span>.<span class="ruby-identifier">float</span>(<span class="ruby-identifier">ms</span>,<span class="ruby-identifier">idlen</span>)
|
|
520
|
+
<span class="ruby-identifier">b</span> = <span class="ruby-constant">NVector</span>.<span class="ruby-identifier">float</span>(<span class="ruby-identifier">ms</span>)
|
|
521
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">id</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">idlen</span>
|
|
522
|
+
<span class="ruby-identifier">b</span>[<span class="ruby-keyword">true</span>] = <span class="ruby-identifier">bs</span>[<span class="ruby-keyword">true</span>,<span class="ruby-identifier">id</span>]
|
|
523
|
+
<span class="ruby-identifier">c</span>[<span class="ruby-keyword">true</span>,<span class="ruby-identifier">id</span>] = <span class="ruby-identifier">lu</span>.<span class="ruby-identifier">solve</span>(<span class="ruby-identifier">b</span>)
|
|
524
|
+
<span class="ruby-keyword">end</span>
|
|
525
|
+
<span class="ruby-identifier">c</span>[<span class="ruby-value">-1</span>,<span class="ruby-keyword">true</span>] <span class="ruby-operator">+=</span> <span class="ruby-identifier">d0</span>
|
|
526
|
+
<span class="ruby-identifier">c</span> = <span class="ruby-identifier">c</span>.<span class="ruby-identifier">reshape</span>(<span class="ruby-identifier">ms</span>, *<span class="ruby-identifier">idshp</span>)
|
|
527
|
+
|
|
528
|
+
<span class="ruby-comment"># best fit</span>
|
|
529
|
+
<span class="ruby-identifier">idshp_full</span> = <span class="ruby-constant">Array</span>.<span class="ruby-identifier">new</span>
|
|
530
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">d</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">rank</span>
|
|
531
|
+
<span class="ruby-keyword">if</span> <span class="ruby-identifier">indep_dims</span>.<span class="ruby-identifier">include?</span>(<span class="ruby-identifier">d</span>)
|
|
532
|
+
<span class="ruby-identifier">idshp_full</span>[<span class="ruby-identifier">d</span>] = <span class="ruby-identifier">data</span>.<span class="ruby-identifier">shape</span>[<span class="ruby-identifier">d</span>]
|
|
533
|
+
<span class="ruby-keyword">else</span>
|
|
534
|
+
<span class="ruby-identifier">idshp_full</span>[<span class="ruby-identifier">d</span>] = <span class="ruby-value">1</span>
|
|
535
|
+
<span class="ruby-keyword">end</span>
|
|
536
|
+
<span class="ruby-keyword">end</span>
|
|
537
|
+
<span class="ruby-identifier">cs</span> = <span class="ruby-identifier">c</span>.<span class="ruby-identifier">reshape</span>(<span class="ruby-identifier">ms</span>, *<span class="ruby-identifier">idshp_full</span>)
|
|
538
|
+
<span class="ruby-identifier">bf</span> = <span class="ruby-identifier">cs</span>[<span class="ruby-value">-1</span>,<span class="ruby-keyword">false</span>]
|
|
539
|
+
<span class="ruby-keyword">for</span> <span class="ruby-identifier">i</span> <span class="ruby-keyword">in</span> <span class="ruby-value">0</span><span class="ruby-operator">...</span><span class="ruby-identifier">ms</span><span class="ruby-operator">-</span><span class="ruby-value">1</span>
|
|
540
|
+
<span class="ruby-identifier">bf</span> <span class="ruby-operator">+=</span> <span class="ruby-identifier">cs</span>[<span class="ruby-identifier">i</span>,<span class="ruby-keyword">false</span>]*<span class="ruby-identifier">fv</span>[<span class="ruby-identifier">i</span>]
|
|
541
|
+
<span class="ruby-keyword">end</span>
|
|
542
|
+
|
|
543
|
+
<span class="ruby-keyword">end</span>
|
|
544
|
+
|
|
545
|
+
<span class="ruby-identifier">diff</span> = <span class="ruby-constant">Math</span>.<span class="ruby-identifier">sqrt</span>( ( (<span class="ruby-identifier">data</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">d0</span> <span class="ruby-operator">-</span> <span class="ruby-identifier">bf</span>)<span class="ruby-operator">**</span><span class="ruby-value">2</span> ).<span class="ruby-identifier">mean</span> )
|
|
546
|
+
|
|
547
|
+
<span class="ruby-comment">#< return ></span>
|
|
548
|
+
|
|
549
|
+
[ <span class="ruby-identifier">c</span>, <span class="ruby-identifier">bf</span>, <span class="ruby-identifier">diff</span> ]
|
|
550
|
+
<span class="ruby-keyword">end</span></pre>
|
|
551
|
+
</div><!-- least_square_fit-source -->
|
|
552
|
+
|
|
553
|
+
</div>
|
|
554
|
+
|
|
555
|
+
|
|
556
|
+
|
|
557
|
+
|
|
558
|
+
</div><!-- least_square_fit-method -->
|
|
559
|
+
|
|
560
|
+
|
|
561
|
+
</div><!-- public-instance-method-details -->
|
|
562
|
+
|
|
563
|
+
</div><!-- 5Buntitled-5D -->
|
|
564
|
+
|
|
565
|
+
|
|
566
|
+
</div><!-- documentation -->
|
|
567
|
+
|
|
568
|
+
<div id="validator-badges">
|
|
569
|
+
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
570
|
+
<p><small>Generated with the <a href="http://deveiate.org/projects/Darkfish-Rdoc/">Darkfish
|
|
571
|
+
Rdoc Generator</a> 2</small>.</p>
|
|
572
|
+
</div>
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573
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+
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574
|
+
</body>
|
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575
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+
</html>
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576
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+
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