gphys 1.1.1a
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- data/ChangeLog +1777 -0
- data/LICENSE.txt +34 -0
- data/README +33 -0
- data/Rakefile +57 -0
- data/TODO_ep_flux +6 -0
- data/bin/gdir_client +27 -0
- data/bin/gdir_server +129 -0
- data/bin/gpaop +146 -0
- data/bin/gpcat +148 -0
- data/bin/gpcut +102 -0
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- data/bin/gpmath +120 -0
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- data/lib/numru/ganalysis/covariance.rb +154 -0
- data/lib/numru/ganalysis/eof.rb +298 -0
- data/lib/numru/ganalysis/histogram.rb +252 -0
- data/lib/numru/ganalysis/met.rb +317 -0
- data/lib/numru/ganalysis/planet.rb +182 -0
- data/lib/numru/ganalysis.rb +7 -0
- data/lib/numru/gdir.rb +1038 -0
- data/lib/numru/gdir_connect_ftp-like.rb +149 -0
- data/lib/numru/ggraph.rb +5838 -0
- data/lib/numru/ggraph_on_merdional_section.rb +178 -0
- data/lib/numru/gphys/assoccoords.rb +359 -0
- data/lib/numru/gphys/attribute.rb +129 -0
- data/lib/numru/gphys/attributenetcdf.rb +80 -0
- data/lib/numru/gphys/axis.rb +963 -0
- data/lib/numru/gphys/coordmapping.rb +286 -0
- data/lib/numru/gphys/coordtransform.rb +209 -0
- data/lib/numru/gphys/derivative.rb +314 -0
- data/lib/numru/gphys/ep_flux.rb +868 -0
- data/lib/numru/gphys/gpcommon.rb +52 -0
- data/lib/numru/gphys/gphys.rb +1207 -0
- data/lib/numru/gphys/gphys_fft.rb +886 -0
- data/lib/numru/gphys/gphys_grads_io.rb +212 -0
- data/lib/numru/gphys/gphys_grib_io.rb +214 -0
- data/lib/numru/gphys/gphys_gtool3_io.rb +162 -0
- data/lib/numru/gphys/gphys_hdfeos5_io.rb +672 -0
- data/lib/numru/gphys/gphys_io.rb +452 -0
- data/lib/numru/gphys/gphys_io_common.rb +126 -0
- data/lib/numru/gphys/gphys_netcdf_io.rb +800 -0
- data/lib/numru/gphys/gphys_nusdas_io.rb +132 -0
- data/lib/numru/gphys/grads_gridded.rb +1638 -0
- data/lib/numru/gphys/grib.rb +2049 -0
- data/lib/numru/gphys/grib_params.rb +1465 -0
- data/lib/numru/gphys/grid.rb +723 -0
- data/lib/numru/gphys/gtool3.rb +771 -0
- data/lib/numru/gphys/interpolate.rb +854 -0
- data/lib/numru/gphys/narray_ext.rb +34 -0
- data/lib/numru/gphys/netcdf_convention.rb +406 -0
- data/lib/numru/gphys/subsetmapping.rb +332 -0
- data/lib/numru/gphys/unumeric.rb +522 -0
- data/lib/numru/gphys/varray.rb +1109 -0
- data/lib/numru/gphys/varraycomposite.rb +415 -0
- data/lib/numru/gphys/varraygrads.rb +225 -0
- data/lib/numru/gphys/varraygrib.rb +177 -0
- data/lib/numru/gphys/varraygtool3.rb +226 -0
- data/lib/numru/gphys/varrayhdfeos5.rb +451 -0
- data/lib/numru/gphys/varraynetcdf.rb +350 -0
- data/lib/numru/gphys/varraynusdas.rb +59 -0
- data/lib/numru/gphys.rb +9 -0
- data/lib/numru/htdir.rb +170 -0
- data/multibitIO.c +567 -0
- data/sample/cira86_to_nc.rb +122 -0
- data/sample/druby_cli1.rb +21 -0
- data/sample/druby_cli2.rb +34 -0
- data/sample/druby_serv1.rb +30 -0
- data/sample/druby_serv2.rb +64 -0
- data/sample/ep_flux/demo_NCEP_1.rb +48 -0
- data/sample/ep_flux/demo_NCEP_2.rb +57 -0
- data/sample/ep_flux/demo_NCEP_3.rb +81 -0
- data/sample/ggraph_latlon_labelling_dr002690.rb +159 -0
- data/sample/ggraph_mapfit-axes_dr002687.rb +131 -0
- data/sample/map_projection.rb +121 -0
- data/sample/ncep_theta_coord.rb +79 -0
- data/test/eof_slp.rb +28 -0
- data/test/mltbit.dat +0 -0
- data/test/test_ep_flux.rb +533 -0
- data/test/test_multibitIO.rb +19 -0
- data/testdata/T.jan.ctl +12 -0
- data/testdata/T.jan.dat +0 -0
- data/testdata/T.jan.grib +0 -0
- data/testdata/T.jan.nc +0 -0
- data/testdata/T.jan.packed.withmiss.nc +0 -0
- data/testdata/UV.jan.nc +0 -0
- data/testdata/assoc_crds.nc +0 -0
- data/testdata/cira86.dat +1332 -0
- metadata +621 -0
data/doc/gphys_fft.html
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<title>../lib/numru/gphys/gphys_fft.rb</title>
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</head>
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<body>
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<h1><a name="label-0" id="label-0">extension of class NumRu::GPhys -- Fast Fourier transformation and its applications</a></h1><!-- RDLabel: "extension of class NumRu::GPhys ­­ Fast Fourier transformation and its applications" -->
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<p>This manual documents the methods of NumRu::GPhys defined in gphys_fft.rb</p>
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<h1><a name="label-1" id="label-1">class methods</a></h1><!-- RDLabel: "class methods" -->
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<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.
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This is for data that do not have missing
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but is treated as potentially having missing (often
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by having the valid_* attributes of NetCDF.)
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If replace_val is specified, data missing with replaced
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with that value.</dd>
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</dl>
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<h1><a name="label-3" id="label-3">methods</a></h1><!-- RDLabel: "methods" -->
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<dl>
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<dt><h4><a name="label-4" id="label-4"><code>fft(<var>backward</var>=<var>false</var>, *<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "fft" -->
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<dd>
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<p>Fast Fourier Transformation (FFT) by using
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(<a href="http://www.fftw.org">FFTW</a>) ver 3 or ver 2.
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A FFTW ver.2 interface is included in NArray, while
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to use FFTW ver.3, you have to install separately.
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Dimension specification by the argument dims is available
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only with ver.3. By default, FFT is applied to all dimensions.</p>
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<p>The transformation is complex. If the input data is not complex,
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it will be coerced to complex before transformation.</p>
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<p>When the FT is forward, the result is normalized
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(i.e., divided by the data number), unlike the default behavior of
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FFTW.</p>
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<p>Each coordinate is assumed to be equally spaced without checking.
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The new coordinate variables will be set equal to wavenumbers,
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derived as 2*PI/(length of the axis)*[0,1,2,..], where the length
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of the axis is derived as (coord.val.max - coord.val.min)*(n+1)/n.</p>
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<p>REMARK</p>
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<ul>
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<li>If the units of the original coordinate is degree (or its
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equivalent ones such as degrees_east), the wavenumber was
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made in integers by converting the coordinate based on
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radian.</li>
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</ul>
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<p>ARGUMENTS</p>
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<ul>
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<li>backward (true of false) : when true, backward FT is done;
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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>
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<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
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trends.</li>
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</ul>
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<p>RETURN VALUE</p>
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<ul>
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<li>a GPhys</li>
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</ul>
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<p>EXAMPLE</p>
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<ul>
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<li>See <a href="#label-5">detrend</a>.</li>
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</ul></dd>
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<dt><h4><a name="label-6" id="label-6"><code>cos_taper(<var>dim1</var>[,<var>dim2</var>[,...]])</code></a></h4></dt><!-- RDLabel: "cos_taper" -->
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<dd>
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<p>Cosine tapering along dimension(s) specified.</p>
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<p>Algorithm: to multiply with the half cosine curves at the both
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1/10 ends of the data.</p>
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<pre>cos taper shape:
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_____________
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_/ \_
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-> <- -> <-
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T/10 T/10
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half-cosine half-cosine
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shaped shaped</pre>
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<p>The spectra of tapered data should be multiplied by 1/0.875,
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which is stored as GPhys::COS_TAPER_SP_FACTOR (==1/0.875).</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>dim? (Integer of String): the dimension along which you want to remove
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trends.</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>dim = 0 # for the 1st dimension
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fc = gphys.detrend(dim).cos_taper(dim).fft(nil,dim)
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sp = fc.abs**2 * GPhys::COS_TAPER_SP_FACTOR</pre></dd>
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<dt><h4><a name="label-7" id="label-7"><code>spect_zero_centering(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_zero_centering" -->
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<dd>
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<p>Shifts the wavenumber axis to cover from -K/2 to K/2 instead of
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from 0 to K-1, where the wavenumber is symbolically treated as integer,
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which is actually not the case, though. Since the first (-K/2) and
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the last (K/2) elements are duplicated, both are divided by 2.
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Therefore, this method is to be used for spectra (squared quantity)
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rather than the raw Fourier coefficients. (That is why the method name
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is prefixed by "spect_").</p>
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<p>The method is applied for a single dimension (specified by the argument
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dim). If you need to apply for multiple dimensions, use it for multiple
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times.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>dim (integer): the dimension you want to shift spectra elements.
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Count starts from zero.</li>
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</ul>
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<p>RETURN VALUE</p>
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<ul>
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<li>a GPhys</li>
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</ul>
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<p>EXAMPLE</p>
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<ul>
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<li><p>To get a spectra of a variable var along the 1st and 2nd dimensions:</p>
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<pre>fc = var.fft(nil, 0,1) # --> Fourier coef
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sp = ( fc.abs**2 ).spect_zero_centering(0).spect_zero_centering(1)</pre>
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<p>Note that spect_zero_centering is applied after taking |fc|^2.</p></li>
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<li><p>Same but if you want to have the 2nd dimension one-sided:</p>
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<pre>fc = var.fft(nil, 0,1)
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sp = ( fc.abs**2 ).spect_zero_centering(0).spect_one_sided(1)</pre></li>
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<li><p>Similar to the first example but for cross spectra:</p>
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<pre>fc1 = var1.fft(nil, 0,1)
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fc2 = var2.fft(nil, 0,1)
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xsp = (fc1 * fc2.conj).spect_zero_centering(0).spect_zero_centering(1)</pre></li>
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</ul></dd>
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<dt><h4><a name="label-8" id="label-8"><code>spect_one_sided(<var>dim</var>)</code></a></h4></dt><!-- RDLabel: "spect_one_sided" -->
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<dd>
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<p>Similar to <a href="#label-7">spect_zero_centering</a> but to make one-sided spectra.
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Namely, to convert from 0..K-1 to 0..K/2. To be applied for spectra;
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wavenumber 2..K/2-1 are multiplied by 2.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>dim (integer): the dimension you want to shift spectra elements.
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Count starts from zero.</li>
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</ul>
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<p>RETURN VALUE</p>
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<ul>
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<li>a GPhys</li>
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</ul>
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<p>EXAMPLE</p>
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<ul>
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<li>See the 2nd example of <a href="#label-7">spect_zero_centering</a>.</li>
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</ul></dd>
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<dt><h4><a name="label-9" id="label-9"><code>rawspect2powerspect(*<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "rawspect2powerspect" -->
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<dd>
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<p>Converts raw spectra obtained by gphys.fft.abs**2 into
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power spectra by dividing by wavenumber increments
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along the dimensions specified by dims.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>dims (integers): the dimensions corresponding to wavenumbers.</li>
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</ul>
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<p>RETURN VALUE</p>
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<ul>
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<li>a GPhys</li>
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</ul>
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<p>EXAMPLE</p>
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<ul>
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<li><p>Suppose a 2 (or more) dimensional data gphys.</p>
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<pre>fc = gphys.fft(nil, 0, 1)
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sp = fc.abs**2
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ps = sp.rawspect2powerspect(0,1)</pre>
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<p>Here, sp is the raw spectrum of gphys, and ps is the power spectrum.
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The Parseval relation for them are as follows:</p>
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<pre>(gphys**2).mean == sp.sum
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== pw.sum*dk*dl (== \int pw dk dl, mathematically),</pre>
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<p>where, dk = (pw.coord(0)[1] - pw.coord(0)[0]), and
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dl = (pw.coord(1)[1] - pw.coord(1)[0]).</p></li>
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</ul></dd>
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<dt><h4><a name="label-10" id="label-10"><code>phase_velocity_filter(<var>xdim</var>, <var>tdim</var>, <var>cmin</var>=<var>nil</var>, <var>cmax</var>=<var>nil</var>, <var>xconv</var>=<var>nil</var>, <var>tconv</var>=<var>nil</var>, <var>remove_xtmean</var>=<var>false</var>)</code></a></h4></dt><!-- RDLabel: "phase_velocity_filter" -->
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<dd>
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<p>Filtering by phase velocity (between cmin and cmax)</p>
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<p>REMARKS</p>
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<ul>
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<li>If the number of the grid points along x or t is an even number,
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the maximum wavenumber or frequency is treated as positive
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and negative, respectively, which results in an asymmetry of
|
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the treatment of positive and negative phase speeds.
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(That should be ok. -- In case its effect is significant,
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to do the filtering itself is not meaningful.)</li>
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</ul>
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<p>ARGUMENTS</p>
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<ul>
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<li>xdim (Integer or String): spacial dimension</li>
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<li>tdim (Integer or String): time dimension</li>
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<li>cmin (Float or nil): minimum phase velocity. nil means no specification.
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(at least cmin or cmax must be given by Float)</li>
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<li>cmax (Float or nil): maximum phase velocity. nil means no specification.
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(at least cmin or cmax must be given by Float)</li>
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<li>xconv (nil or UNumeric) : (optional) if given, xconv is multiplied
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|
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with the x axis before computing the phase velocity
|
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|
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(kconv=1/xconv is used to scale wavenumbers)</li>
|
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|
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<li>tconv (nil or UNumeric) : (optional) if given, tconv is multiplied
|
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|
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with the t axis before computing the phase velocity
|
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|
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(fconv=1/tconv is used to scale frequency)</li>
|
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<li>remove_xtmean (false or true) : if false (default),
|
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components with k=0 and f=0 are counted as c=0 (stationary),
|
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(unlike <a href="#label-12">phase_velocity_binning</a>), so they are included if
|
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cmin*cmax <= 0; if true, k=0 & f=0 components are always removed.</li>
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|
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</ul>
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|
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<p>RETURN VALUE</p>
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<ul>
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|
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<li>a GPhys</li>
|
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</ul>
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<p>EXAMPLE</p>
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<ul>
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<li><p>For a 4D data with [x,y,z,t] dimensions, filtering by the phase
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velocity in the y dimension greater than 10.0 (in the unit
|
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of y/t) can be made by</p>
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<pre>cmin = 10.0; cmax = nil
|
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|
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gpfilt = gp.phase_velocity_filter(1, 3, cmin, cmax)</pre></li>
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<li><p>For a global data (on the Earth's surface) with
|
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[lon, lat, z, time] axes, where the units of lon is
|
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"degrees" (or "degrees_east" or "radian")
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and the units of time is "hours", to filter disturbances
|
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whose zonal phase speed MEASURED AT THE EQUATOR is less or
|
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equal to 30 m/s can be made by</p>
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<pre>cmin = -30.0; cmax = 30.0
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xconv = UNumeric[6.37e6, "m"] # Earth's radius (i.e., m/radian)
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# This is a special case since "radian" is exceptionally omitted.
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# See the private method __predefined_coord_units_conversion.
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tconv = UNumeric[3.6e3, "s/hours"]
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gpfilt = gp.phase_velocity_filter(1, 3, cmin, cmax, xconv, tconv)</pre></li>
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</ul></dd>
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<dt><h4><a name="label-11" id="label-11"><code>phase_velocity_binning_iso_norml(<var>kdim</var>, <var>fdim</var>, <var>cmin</var>, <var>cmax</var>, <var>cint</var>, <var>kconv</var>=<var>nil</var>, <var>fconv</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "phase_velocity_binning_iso_norml" -->
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<dd>
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<p>Same as <a href="#label-12">phase_velocity_binning</a> but exclusively for
|
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equal phase velocity spacing. Also, a normalization is
|
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|
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additionally made, to scale spectra in terms of integration
|
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|
+
along phase velocity axis --- The result of
|
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|
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<a href="#label-12">phase_velocity_binning</a> called inside
|
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|
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this method is divided by cint along with corresponding
|
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|
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units conversion. Therefore, if this method is applied
|
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|
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to spectra, a normalization is made such that an integration
|
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|
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(not summation) along the phase velocity gives the variance
|
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|
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(or covariance etc.) -- This normalization is suitable to
|
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|
+
quadratic quantities (such as spectra) but is not suitable to
|
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|
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raw Fourier coefficients.</p>
|
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|
+
<p>ARGUMENTS</p>
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|
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<ul>
|
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|
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<li>kdim (Integer or String): see <a href="#label-12">phase_velocity_binning</a></li>
|
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|
+
<li>fdim (Integer or String): see <a href="#label-12">phase_velocity_binning</a></li>
|
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<li>cmin (Float) : minimum phase velocity</li>
|
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|
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<li>cmin (Float) : maximum phase velocity</li>
|
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|
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<li>cint (Float) : inter val with which the range [cmin and cmax]
|
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|
+
is divided.</li>
|
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|
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<li>kconv (nil or UNumeric) : see <a href="#label-12">phase_velocity_binning</a></li>
|
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|
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<li>fconv (nil or UNumeric) : see <a href="#label-12">phase_velocity_binning</a></li>
|
|
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|
+
</ul>
|
|
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|
+
<p>RETURN VALUE</p>
|
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|
+
<ul>
|
|
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|
+
<li>a GPhys</li>
|
|
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|
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</ul></dd>
|
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|
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<dt><h4><a name="label-12" id="label-12"><code>phase_velocity_binning(<var>kdim</var>, <var>fdim</var>, <var>cbins</var>, <var>kconv</var>=<var>nil</var>, <var>fconv</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "phase_velocity_binning" -->
|
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|
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<dd>
|
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|
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<p>Bin a 2D spectrum in space and time based on phase velocity.
|
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|
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The operand (self) must be Fourier coefficients or spectra,
|
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|
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whose grid has not been altered since the call of the method
|
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|
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fft (i.e., those that have not applied with zero centering
|
|
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|
+
etc, since it is done in this method).</p>
|
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|
+
<p>Binning by this method is based on summation, leaving
|
|
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|
+
the units unchanged.</p>
|
|
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|
+
<p>REMARKS</p>
|
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|
+
<ul>
|
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|
+
<li>Components whose phase velocities are exactly equal to one
|
|
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|
+
of the boundaries are divided into the two bins half by half</li>
|
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|
+
<li>components with k=0 and f=0 are excluded -- the spatio-temporal
|
|
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|
+
mean do not reflect in the result </li>
|
|
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|
+
</ul>
|
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|
+
<p>ARGUMENTS</p>
|
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|
+
<ul>
|
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289
|
+
<li>kdim (Integer or String): wavenumber dimension (from spacial dimension)</li>
|
|
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|
+
<li>fdim (Integer or String): frequency dimension (from time dimension)</li>
|
|
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|
+
<li>cbins : an Array of bin bounds or a Hash of max, min, int
|
|
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|
+
e.g., [-10,-1,-0.1,0.1,11,10], {"min"=>-30,"max"=>30,"int"=>5}</li>
|
|
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|
+
<li>kconv (nil or UNumeric) : (optional) if given, kconv is multiplied
|
|
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|
+
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"=>-1,"max"=>1,"int"=>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"=>-50,"max"=>50,"int"=>5},
|
|
319
|
+
kconv, fconv)</pre></li>
|
|
320
|
+
</ul></dd>
|
|
321
|
+
</dl>
|
|
322
|
+
|
|
323
|
+
</body>
|
|
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|
+
</html>
|
|
@@ -0,0 +1,69 @@
|
|
|
1
|
+
<?xml version="1.0" ?>
|
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2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
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|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
6
|
+
<head>
|
|
7
|
+
<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>
|
|
@@ -0,0 +1,82 @@
|
|
|
1
|
+
<?xml version="1.0" ?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
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
ADDED
|
@@ -0,0 +1,120 @@
|
|
|
1
|
+
<?xml version="1.0" ?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
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>
|
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
<?xml version="1.0" ?>
|
|
2
|
+
<!DOCTYPE html
|
|
3
|
+
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
+
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
|
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>
|