gphys 1.2.2.1 → 1.4.3
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- checksums.yaml +7 -0
- data/.gitignore +8 -17
- data/.rspec +2 -0
- data/.travis.yml +3 -0
- data/ChangeLog +5762 -753
- data/LICENSE.txt +30 -18
- data/Rakefile +1 -0
- data/bin/console +14 -0
- data/bin/gpcat +43 -2
- data/bin/gpcut +16 -0
- data/bin/gpvect +167 -15
- data/bin/gpview +254 -51
- data/bin/setup +7 -0
- data/dim_op.c +1220 -0
- data/doc/attribute.html +19 -0
- data/doc/attributenetcdf.html +15 -0
- data/doc/axis.html +387 -0
- data/doc/coordmapping.html +111 -0
- data/doc/coordtransform.html +36 -0
- data/doc/dclext.html +821 -0
- data/doc/derivative/gphys-derivative.html +100 -0
- data/doc/derivative/index.html +21 -0
- data/doc/derivative/index.rd +14 -0
- data/doc/derivative/math-doc/document.pdf +0 -0
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- data/doc/derivative/numru-derivative.html +158 -0
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- data/ext_init.c +1 -0
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- data/lib/numru/dclext.rb +718 -546
- data/lib/numru/derivative.rb +2 -0
- data/lib/numru/ganalysis.rb +38 -0
- data/lib/numru/ganalysis/beta_plane.rb +103 -0
- data/lib/numru/ganalysis/eof.rb +3 -2
- data/lib/numru/ganalysis/fitting.rb +559 -0
- data/lib/numru/ganalysis/histogram.rb +36 -19
- data/lib/numru/ganalysis/log_p.rb +130 -0
- data/lib/numru/ganalysis/met.rb +396 -2
- data/lib/numru/ganalysis/met_z.rb +300 -0
- data/lib/numru/ganalysis/planet.rb +17 -7
- data/lib/numru/ganalysis/qg.rb +685 -0
- data/lib/numru/ganalysis/sigma_coord.rb +90 -0
- data/lib/numru/gdir.rb +2 -1
- data/lib/numru/ggraph.rb +204 -60
- data/lib/numru/ggraph_on_merdional_section.rb +1 -1
- data/lib/numru/gphys.rb +6 -0
- data/lib/numru/gphys/assoccoords.rb +18 -3
- data/lib/numru/gphys/axis.rb +209 -8
- data/lib/numru/gphys/derivative.rb +11 -0
- data/lib/numru/gphys/gphys.rb +539 -48
- data/lib/numru/gphys/gphys_dim_op.rb +331 -0
- data/lib/numru/gphys/gphys_fft.rb +48 -2
- data/lib/numru/gphys/gphys_io.rb +241 -13
- data/lib/numru/gphys/gphys_netcdf_io.rb +77 -39
- data/lib/numru/gphys/gphys_nusdas_io.rb +3 -0
- data/lib/numru/gphys/grib.rb +133 -54
- data/lib/numru/gphys/grib_params.rb +26 -3
- data/lib/numru/gphys/grid.rb +75 -34
- data/lib/numru/gphys/interpolate.rb +24 -10
- data/lib/numru/gphys/mdstorage.rb +160 -0
- data/lib/numru/gphys/netcdf_convention.rb +4 -2
- data/lib/numru/gphys/subsetmapping.rb +0 -1
- data/lib/numru/gphys/unumeric.rb +50 -5
- data/lib/numru/gphys/varray.rb +15 -30
- data/lib/numru/gphys/varraycomposite.rb +107 -24
- data/lib/numru/gphys/varraynetcdf.rb +9 -3
- data/lib/numru/gphys/version.rb +5 -0
- data/sample/druby_cli1.rb +2 -0
- data/sample/druby_cli2.rb +0 -6
- data/sample/druby_serv2.rb +0 -13
- data/spec/gphys_spec.rb +11 -0
- data/spec/spec_helper.rb +2 -0
- data/test/test_assoccoords.rb +102 -0
- data/test/test_axis.rb +61 -0
- data/test/test_fitting.rb +116 -0
- data/test/test_gphys.rb +20 -0
- data/test/test_met_z.rb +96 -0
- data/test/test_sigma_coord.rb +50 -0
- data/{test → test_old}/eof_slp.rb +0 -0
- data/{test → test_old}/mltbit.dat +0 -0
- data/{test → test_old}/test_ep_flux.rb +0 -0
- data/{test → test_old}/test_multibitIO.rb +0 -0
- metadata +530 -191
- data/README.md +0 -29
- data/lib/gphys.rb +0 -2
- data/lib/numru/dclext_datetime_ax.rb +0 -220
- data/lib/version.rb +0 -3
data/doc/gphys_io.html
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<?xml version="1.0" ?>
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<!DOCTYPE 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_io.rb</title>
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</head>
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<body>
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<h1><a name="label-0" id="label-0">module NumRu::GPhys::IO</a></h1><!-- RDLabel: "module NumRu::GPhys::IO" -->
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<p>A module to handle file IO regarding GPhys. </p>
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<p>Many of the functionality of this module is implemented in the modules
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for specific file types such as NumRu::GPhys::NetCDF_IO, to which this
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module directs operations.</p>
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<p>For example, GPhys::IO.open(file, name) simply calls
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GPhys::*_IO.open(file, name), where '*' is
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NetCDF, GrADS, or grib.</p>
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<h2><a name="label-1" id="label-1">Module functions</a></h2><!-- RDLabel: "Module functions" -->
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<dl>
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<dt><h4><a name="label-2" id="label-2"><code>open(<var>file</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
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<dd>
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<p>Opens a GPhys in <code>file</code> having the name <code>varname</code>.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>file (String, NetCDF, GRIB,.. etc, or Array, NArray, Regexp) :
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Specifies the file. Path if String; a File pointer if NetCDF etc..
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The processing is forwarded to open_multi, if this argument is
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an Array, NArray, or Regexp. </li>
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<li>varname (String) : name of the variable</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></dd>
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<dt><h4><a name="label-3" id="label-3"><code>open_multi(<var>files</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open_multi" -->
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<dd>
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<p>Opens a GPhys by combining a variable across multiple files.
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It initializes GPhys objects over the files by calling open and
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unites them into a single GPhys object by using <code>GPhys.join</code> or
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<code>GPhys.join_md</code>.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>files (Array, NArray (NArray.object), or Regexp) : Specifies the files.
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<ul>
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<li>when Array, it must consist of paths or file pointers
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(that are accepted by open).
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All coordinates of the variable in the files are scanned,
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and a joined object is constructed properly.
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Thus, you can simply put subsets of a 2D tiling in a simple
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non-nested 1D Array. <code>GPhys.join</code> is used in this case.</li>
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<li><p>when NArray, it must consist of paths or file pointers
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(that are accepted by open).
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Each dimension with multiple elements must correspond
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to a dimension along which joining is made.
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For example, a 2D tiling can be specified as</p>
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<pre>files = NArray.to_na([['f00.nc','f10.nc'],['f01.nc','f11.nc']])
|
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gp = GPhys::IO.open_multi( files, "f" )</pre>
|
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<p><code>GPhys.join_md</code> is used in this case.</p></li>
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<li><p>When Regexp, similar to when NArray, but expresses the paths.
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The dimensions to join is specified by "captures"
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(parentheses). For example, the above 2D tiling can be specified as</p>
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<pre>files = /f(\d)(\d).nc/
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gp = GPhys::IO.open_multi( files, "f" )</pre>
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<p>The regexp can contain a directory path (e.g., /dir\/sub\/f(\d)(d).nc/),
|
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but the directory part must be unique (i.e., a simple string),
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so only a single directly can be specified. All captures must
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be in the part representing the file names (in the directory).
|
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<code>GPhys.join_md</code> is used in this case.</p></li>
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</ul></li>
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<li>varname (String) : name of the variable</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></dd>
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<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" -->
|
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<dd>
|
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<p>Writes a GPhys object in a file</p>
|
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<p>ARGUMENTS</p>
|
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<ul>
|
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<li>file (NetCDF, GRIB,.. etc) : the file. Writing must be permitted.
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To close (finalize) it after writing is left to the user.</li>
|
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<li>gphys (GPhys) : the GPhys object to write</li>
|
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<li>name (String; optional) : if specified, this name is used in the file
|
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rather than the name of gphys</li>
|
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</ul></dd>
|
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<dt><h4><a name="label-5" id="label-5"><code>write_grid(<var>file</var>, <var>grid_or_gphys</var>)</code></a></h4></dt><!-- RDLabel: "write_grid" -->
|
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<dt><h4><a name="label-6" id="label-6"><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" -->
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<dt><h4><a name="label-7" id="label-7"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
|
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<dt><h4><a name="label-8" id="label-8"><code>var_names_except_coordinates(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinates" -->
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<dd>
|
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See the manual of NumRu::GPhys::NetCDF_IO for the methods listed above.</dd>
|
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<dt><h4><a name="label-9" id="label-9"><code>file2type(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2type" -->
|
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<dd>
|
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<p>Figures out the file type supported in this module.</p>
|
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<p>ARGUMENTS</p>
|
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<ul>
|
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<li>file (String, NetCDF, Grib, or GrADS_Gridded) :
|
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What to return is of course obvious if it is
|
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NetCDF, Grib, or GrADS_Gridded. If it is a String,
|
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it is assumed to be a path of a file, and the file type
|
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is determined by its suffix when 'nc', 'ctl', or 'grib';
|
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In other cases, the type is figured out by reading in
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a few bytes from the beginning.</li>
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</ul>
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<p>RETURN VALUE</p>
|
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<ul>
|
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<li>GPhys::IO::NETCDF, GPhys::IO::GRIB, or GPhys::IO::GRADS,
|
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which are string constants.</li>
|
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</ul></dd>
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<dt><h4><a name="label-10" id="label-10"><code>file2specific_module(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2specific_module" -->
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<dd>
|
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Same as <a href="#label-9">file2type</a>, but returns GPhys::NetCDF_IO,
|
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GPhys::GrADS_IO, or GPhys::Grib_IO.</dd>
|
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<dt><h4><a name="label-11" id="label-11"><code>file2file_class(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "file2file_class" -->
|
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<dd>
|
|
117
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Same as <a href="#label-9">file2type</a>, but returns NetCDF,
|
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GrADS_Gridded, or Grib.</dd>
|
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<dt><h4><a name="label-12" id="label-12"><code>parse_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "parse_gturl" -->
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<dd>
|
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121
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<p>Parses GTOOL4-type URLs to specify path, variable name,
|
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and optionally subsets, whose format is
|
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path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</p>
|
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<p>ARGUMENTS</p>
|
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125
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<ul>
|
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126
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<li>gturl (String) GTOOL4 URL, whose format is
|
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path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]</li>
|
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</ul>
|
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<p>RETURN VALUES</p>
|
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<ul>
|
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131
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<li>An Array consisting of [file, var, slice, cut_slice, thinning], where
|
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<ul>
|
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<li>file (String) : path</li>
|
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<li>var (String) : variable name</li>
|
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<li>slice (Array) : subset specifier by the grid numbers
|
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to be used as GPhys#[slice].</li>
|
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<li>cut_slice (Array) : subset specifier in physical coordinate
|
|
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to be used as GPhys#cut[cut_slice].</li>
|
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<li>thinning (Array) : additional subset specifier for thinning
|
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with uniform intervals if needed to be used GPhys#[thinning]
|
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after appling GPhys#cut.</li>
|
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</ul></li>
|
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</ul></dd>
|
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<dt><h4><a name="label-13" id="label-13"><code>open_gturl(<var>gturl</var>)</code></a></h4></dt><!-- RDLabel: "open_gturl" -->
|
|
145
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<dd>
|
|
146
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<p>a GPhys constructor from a Gtool4-type URL.
|
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See <a href="#label-12">parse_gturl</a> for its format.</p>
|
|
148
|
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<p>RETURN VALUE</p>
|
|
149
|
+
<ul>
|
|
150
|
+
<li>a GPhys</li>
|
|
151
|
+
</ul></dd>
|
|
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<dt><h4><a name="label-14" id="label-14"><code>str2gphys(<var>str</var>)</code></a></h4></dt><!-- RDLabel: "str2gphys" -->
|
|
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|
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<dd>
|
|
154
|
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<p>Open a GPhys from a slash("/")-separated String
|
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such as "U.nc/U" and "U.nc".</p>
|
|
156
|
+
<ul>
|
|
157
|
+
<li>Aimed to help quick jobs with interactive sessions
|
|
158
|
+
-- This method do not handle a GPhys across multiple files.</li>
|
|
159
|
+
<li>if the variable path is ommited such as "U.nc",
|
|
160
|
+
try to find the variable in it -- read the file and if
|
|
161
|
+
only one variable is found, assume that is the
|
|
162
|
+
variable specified; otherwise, an exception is raised.</li>
|
|
163
|
+
<li>URL is accepted, but it's only thru NetCDF assuming OPeNDAP.</li>
|
|
164
|
+
</ul>
|
|
165
|
+
<p>ARGUMENTS</p>
|
|
166
|
+
<ul>
|
|
167
|
+
<li>a String (file_path[/variable_path])
|
|
168
|
+
e.g. "U.nc/U", "U.nc", "http://.../U.nc/U"</li>
|
|
169
|
+
</ul>
|
|
170
|
+
<p>RETURN VALUE</p>
|
|
171
|
+
<ul>
|
|
172
|
+
<li>a GPhys</li>
|
|
173
|
+
</ul></dd>
|
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174
|
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</dl>
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175
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+
<h2><a name="label-15" id="label-15">Module constants</a></h2><!-- RDLabel: "Module constants" -->
|
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<dl>
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177
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+
<dt><h4><a name="label-16" id="label-16"><code>GTURLfmt</code></a></h4></dt><!-- RDLabel: "GTURLfmt" -->
|
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178
|
+
<dd>
|
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179
|
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The format of Gtool4URL.</dd>
|
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</dl>
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</body>
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</html>
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<head>
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<title>../lib/numru/gphys/gphys_io_common.rb</title>
|
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</head>
|
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9
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<body>
|
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10
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<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>
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</body>
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</html>
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<head>
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<title>../lib/numru/gphys/gphys_netcdf_io.rb</title>
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</head>
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<body>
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<h1><a name="label-0" id="label-0">module NumRu::GPhys::NetCDF_Convention_Users_Guide</a></h1><!-- RDLabel: "module NumRu::GPhys::NetCDF_Convention_Users_Guide" -->
|
|
11
|
+
<p>(To be written.)</p>
|
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12
|
+
<h1><a name="label-1" id="label-1">module NumRu::GPhys::NetCDF_IO</a></h1><!-- RDLabel: "module NumRu::GPhys::NetCDF_IO" -->
|
|
13
|
+
<p>a NetCDF read/write helper by automatically interpreting conventions</p>
|
|
14
|
+
<h2><a name="label-2" id="label-2">Module functions</a></h2><!-- RDLabel: "Module functions" -->
|
|
15
|
+
<dl>
|
|
16
|
+
<dt><h4><a name="label-3" id="label-3"><code>is_a_NetCDF?(<var>filename</var>)</code></a></h4></dt><!-- RDLabel: "is_a_NetCDF?" -->
|
|
17
|
+
<dd>
|
|
18
|
+
<p>test whether the file is a NetCDF file.</p>
|
|
19
|
+
<p>ARGUMENTS</p>
|
|
20
|
+
<ul>
|
|
21
|
+
<li>filename (String): filename to test.</li>
|
|
22
|
+
</ul>
|
|
23
|
+
<p>RETURN VALUE</p>
|
|
24
|
+
<ul>
|
|
25
|
+
<li>true/false</li>
|
|
26
|
+
</ul></dd>
|
|
27
|
+
<dt><h4><a name="label-4" id="label-4"><code>open(<var>files</var>, <var>varname</var>)</code></a></h4></dt><!-- RDLabel: "open" -->
|
|
28
|
+
<dd>
|
|
29
|
+
<p>a GPhys constructor from a NetCDF file (or multiple NetCDF files).</p>
|
|
30
|
+
<p>ARGUMENTS</p>
|
|
31
|
+
<ul>
|
|
32
|
+
<li>files (String, NetCDF, NArray, or Regexp): file specifier.
|
|
33
|
+
A single file is specified by a String (containing the path),
|
|
34
|
+
of a NetCDF. Multiple files can be specified by a NArray of
|
|
35
|
+
String or NetCDF or by a Regexp to match paths. In that case,
|
|
36
|
+
data and axes are represented by VArrayComposite.</li>
|
|
37
|
+
<li>varname (String): name of the variable.</li>
|
|
38
|
+
</ul>
|
|
39
|
+
<p>RETURN VALUE</p>
|
|
40
|
+
<ul>
|
|
41
|
+
<li>a GPhys</li>
|
|
42
|
+
</ul>
|
|
43
|
+
<p>EXAMPLES</p>
|
|
44
|
+
<ul>
|
|
45
|
+
<li><p>From a single file:</p>
|
|
46
|
+
<pre>file = NetCDF.open('hogehoge.nc')
|
|
47
|
+
gphys = GPhys::NetCDF_IO(file, 'temp')
|
|
48
|
+
|
|
49
|
+
file = NetCDF.open('hogehoge.nc', 'a') # writable
|
|
50
|
+
gphys = GPhys::NetCDF_IO(file, 'temp')</pre></li>
|
|
51
|
+
<li><p>From a single file:</p>
|
|
52
|
+
<pre>gphys = GPhys::NetCDF_IO('hogehoge.nc', 'temp')
|
|
53
|
+
|
|
54
|
+
gphys = GPhys::NetCDF_IO('/data/netcdf/hogehoge.nc', 'temp')</pre>
|
|
55
|
+
<p>If you use a String to specify a file path, the file is opened as
|
|
56
|
+
read-only.</p></li>
|
|
57
|
+
<li><p>To use data separated into multiple files. Suppose that you have
|
|
58
|
+
hoge_yr2000.nc, hoge_yr2001.nc, and hoge_yr2002.nc in the current
|
|
59
|
+
directory. You can open it by using a regular expression as follows:</p>
|
|
60
|
+
<pre>gphys = GPhys::NetCDF_IO(/hoge_yr(\d\d\d\d).nc/, 'temp')</pre>
|
|
61
|
+
<p>Here, the parentheses to enclose \d\d\d\d is NEEDED. </p>
|
|
62
|
+
<p>The same thing can be done as follows by using Array or NArray:</p>
|
|
63
|
+
<pre>files = ['hoge_yr2000.nc', 'hoge_yr2001.nc', 'hoge_yr2002.nc']
|
|
64
|
+
gphys = GPhys::NetCDF_IO(files, 'temp')
|
|
65
|
+
|
|
66
|
+
files = NArray['hoge_yr2000.nc', 'hoge_yr2001.nc', 'hoge_yr2002.nc']
|
|
67
|
+
gphys = GPhys::NetCDF_IO(files, 'temp')</pre></li>
|
|
68
|
+
<li><p>Same as above but to use the full path:</p>
|
|
69
|
+
<pre>gphys = GPhys::NetCDF_IO(/\/data\/nc\/hoge_yr(\d\d\d\d).nc/, 'temp')</pre>
|
|
70
|
+
<p>Here, the directory separator '/' is escaped as '\/'.</p></li>
|
|
71
|
+
<li><p>To use data separated into multiple files. Suppose that you have
|
|
72
|
+
hoge_x0y0.nc, hoge_x1y0.nc, hoge_x0y1.nc, hoge_x1y1.nc, where
|
|
73
|
+
the data is separated 2 dimensionally into 2*2 = 4 files.</p>
|
|
74
|
+
<pre>gphys = GPhys::NetCDF_IO(/hoge_x(\d)y(\d).nc/, 'temp')</pre>
|
|
75
|
+
<p>Note that 2 pairs of parentheses are needed here. Alternatively,
|
|
76
|
+
you can also do it like this:</p>
|
|
77
|
+
<pre>files = NArray[ ['hoge_x0y0.nc', 'hoge_x1y0.nc'],
|
|
78
|
+
['hoge_x0y1.nc', 'hoge_x1y1.nc'] ]
|
|
79
|
+
gphys = GPhys::NetCDF_IO(files, 'temp')</pre></li>
|
|
80
|
+
</ul></dd>
|
|
81
|
+
<dt><h4><a name="label-5" id="label-5"><code>write(<var>file</var>, <var>gphys</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "write" -->
|
|
82
|
+
<dd>
|
|
83
|
+
<p>Write a GPhys into a NetCDF file. The whole data under the GPhys
|
|
84
|
+
(such as coordinate vars) are written self-descriptively.</p>
|
|
85
|
+
<p>ARGUMENTS</p>
|
|
86
|
+
<ul>
|
|
87
|
+
<li>file (NetCDF): the NetCDF file to write in. Must be writable of course.</li>
|
|
88
|
+
<li>gphys (GPhys): the GPhys to write.</li>
|
|
89
|
+
<li>name (String): (optional) name in the new file -- if you want to save
|
|
90
|
+
with a different variable name than that of gphys.</li>
|
|
91
|
+
</ul>
|
|
92
|
+
<p>RETURN VALUE</p>
|
|
93
|
+
<ul>
|
|
94
|
+
<li>nil</li>
|
|
95
|
+
</ul></dd>
|
|
96
|
+
<dt><h4><a name="label-6" id="label-6"><code>write_grid(<var>file</var>, <var>grid_or_gphys</var>)</code></a></h4></dt><!-- RDLabel: "write_grid" -->
|
|
97
|
+
<dd>
|
|
98
|
+
<p>Same as <a href="#label-5">write</a> but for writing only the contents of the grid.
|
|
99
|
+
(Used in <a href="#label-5">write</a>.)</p>
|
|
100
|
+
<p>ARGUMENTS</p>
|
|
101
|
+
<ul>
|
|
102
|
+
<li>file (NetCDF): the NetCDF file to write in. Must be writable of course.</li>
|
|
103
|
+
<li>grid_or_gphys (Grid or GPhys):</li>
|
|
104
|
+
</ul>
|
|
105
|
+
<p>RETURN VALUE</p>
|
|
106
|
+
<ul>
|
|
107
|
+
<li>a Grid, in which all VArrays in the original grid are replaced
|
|
108
|
+
with the new ones in the file.</li>
|
|
109
|
+
</ul></dd>
|
|
110
|
+
<dt><h4><a name="label-7" id="label-7"><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" -->
|
|
111
|
+
<dd>
|
|
112
|
+
<p>Iterator to process GPhys objects too big to read on memory at once.
|
|
113
|
+
Makes a loop (loops) by dividing the GPhys object(s) (<var>gphyses</var>)
|
|
114
|
+
with the dimension(s) specified by <var>loopdims</var>, and the results
|
|
115
|
+
(which is the return value of the block) are written in <var>files</var>.</p>
|
|
116
|
+
<p>ARGUMENTS</p>
|
|
117
|
+
<ul>
|
|
118
|
+
<li>gphyses (GPhys or Array of GPhys): GPhys object(s) to be processed.
|
|
119
|
+
All of them must have dimensions spcified with <var>loopdims</var>,
|
|
120
|
+
and their lengths must not vary among files. Other dimensions
|
|
121
|
+
are aribtary, so, for example, <var>gphyses</var> could be
|
|
122
|
+
[a(lon,lat,time), b(lat,time)] as long as loopdims==["time"].</li>
|
|
123
|
+
<li>files (NetCDF or Array of NetCDF): the file in which the results are
|
|
124
|
+
written. The number of the file must be smaller than or equalt to
|
|
125
|
+
the number of resultant GPhys objects (following the multiple assignment
|
|
126
|
+
rule of Ruby).</li>
|
|
127
|
+
<li>loopdims (Array of String or Integer) : name (when String) or
|
|
128
|
+
count starting from zero (when Integer) </li>
|
|
129
|
+
<li>expected block : Number of arguments == number of GPhys objects in
|
|
130
|
+
<var>gphyses</var>. Expected return value is an Array of GPhys objects
|
|
131
|
+
to be written <var>files</var>.</li>
|
|
132
|
+
</ul>
|
|
133
|
+
<p>RETURN VALUE</p>
|
|
134
|
+
<ul>
|
|
135
|
+
<li>GPhys objects in which the results are written</li>
|
|
136
|
+
</ul>
|
|
137
|
+
<p>ERRORS</p>
|
|
138
|
+
<p>The following raise exceptions (in adition to errors in arguments).</p>
|
|
139
|
+
<ul>
|
|
140
|
+
<li>Dimensions specified by <var>loopdims</var> are not shared among
|
|
141
|
+
GPhys objects in <var>gphyses</var>.</li>
|
|
142
|
+
<li>Return value of the block is not an Array of GPhys.</li>
|
|
143
|
+
<li>Dimension(s) used for looping (<var>loopdims</var>) is(are) eliminated
|
|
144
|
+
from the retunred GPhys objects.</li>
|
|
145
|
+
</ul>
|
|
146
|
+
<p>USAGE</p>
|
|
147
|
+
<ul>
|
|
148
|
+
<li><p>EXAMPLE 1</p>
|
|
149
|
+
<p>Suppose that you want to do the following:</p>
|
|
150
|
+
<pre>in = GPhys::NetCDF_IO.open(infile, varname)
|
|
151
|
+
ofile = NetCDF.create(ofilename)
|
|
152
|
+
out = in.mean(0)
|
|
153
|
+
GPhys::NetCDF_IO.write( ofile, out )
|
|
154
|
+
ofile.close</pre>
|
|
155
|
+
<p>The data object (<var>in</var>) is read on memory and an averagin is made.
|
|
156
|
+
If the size of the data is too big to read on memory at once, you can
|
|
157
|
+
divid this process by using this iterator. The following gives the
|
|
158
|
+
same result as above, but the processing is made for each subset
|
|
159
|
+
divided at the last dimension (represented by -1, as in the negative
|
|
160
|
+
indexing of Array).</p>
|
|
161
|
+
<pre>in = GPhys::NetCDF_IO.open(infile, varname)
|
|
162
|
+
ofile = NetCDF.create(ofilename)
|
|
163
|
+
out = GPhys::NetCDF_IO.each_along_dims_write(in, ofile, -1){|in_sub|
|
|
164
|
+
[ in_sub.mean(0) ]
|
|
165
|
+
}
|
|
166
|
+
ofile.close</pre>
|
|
167
|
+
<p>In this case, each_along_dims_write makes a loop by substituting
|
|
168
|
+
<var>in[false,0..0]</var>, <var>in[false,1..1]</var>, <var>in[false,2..2]</var>,..
|
|
169
|
+
into the argument of the block (<var>in_sub</var>). Thus, the return
|
|
170
|
+
value of the block (here, <var>[ in_sub.mean(0) ]</var>) consists of
|
|
171
|
+
<var>in[false,0..0].mean(0)</var>, <var>in[false,1..1].mean(0)</var>,.. .
|
|
172
|
+
This iterator creates a GPhys object in <var>out</var> that
|
|
173
|
+
represents the whole part of the results (here, <var>in.mean(0)</var>), and
|
|
174
|
+
write the resultant subsets in it one by one. Therefore, the output file
|
|
175
|
+
is filled correctly when exiting the iterator.</p>
|
|
176
|
+
<p>Note that the subset (<var>in_sub</var>) retains the last dimension
|
|
177
|
+
but the length is 1 becasue of the slicing by Range (0..0, 1..1,..).
|
|
178
|
+
Therefore, the subset has the same rank as the original.
|
|
179
|
+
The output GPhys objects, as given by the return value of the block,
|
|
180
|
+
must have the dimension retained, since the dimension (whose length
|
|
181
|
+
is one) is replaced by the original one when written in the file.
|
|
182
|
+
Therefore, THE FOLLOWING CAUSE AN ERROR (an exception is raised):</p>
|
|
183
|
+
<pre>out = GPhys::NetCDF_IO.each_along_dims_write(in, ofile, 0){|in_sub|
|
|
184
|
+
[ in_sub.mean(0) ]
|
|
185
|
+
}</pre>
|
|
186
|
+
<p>Here, looping is made by the first dimension (0), but it is eliminated
|
|
187
|
+
from the result by averaging with the same dimension. (Also, note
|
|
188
|
+
that this averaging is non-sense, since the length of the first
|
|
189
|
+
dimension of the subset is 1).</p></li>
|
|
190
|
+
<li><p>EXAMPLE 2</p>
|
|
191
|
+
<p>You can specify mutiple dimensions for looping to further
|
|
192
|
+
decrease the size of data to read on memory:</p>
|
|
193
|
+
<pre>GPhys::NetCDF_IO.each_along_dims_write(in, ofile, -2, -1){|in_sub|
|
|
194
|
+
...
|
|
195
|
+
}</pre>
|
|
196
|
+
<p>Also, you can specify the loop dimension(s) by name(s):</p>
|
|
197
|
+
<pre>GPhys::NetCDF_IO.each_along_dims_write(in, ofile, "y"){|in_sub|
|
|
198
|
+
...
|
|
199
|
+
}
|
|
200
|
+
|
|
201
|
+
GPhys::NetCDF_IO.each_along_dims_write(in, ofile, "y", "z"){|in_sub|
|
|
202
|
+
...
|
|
203
|
+
}</pre></li>
|
|
204
|
+
<li><p>EXAMPLE 3</p>
|
|
205
|
+
<p>You can give multiple objects in the iterotor if they
|
|
206
|
+
have the same shape (in future, this restriction may been loosened),
|
|
207
|
+
as follows:</p>
|
|
208
|
+
<pre>in1 = GPhys::NetCDF_IO.open(infile1, varname1)
|
|
209
|
+
in2 = GPhys::NetCDF_IO.open(infile2, varname2)
|
|
210
|
+
in3 = GPhys::NetCDF_IO.open(infile3, varname3)
|
|
211
|
+
ofile = NetCDF.create(ofilename)
|
|
212
|
+
outA, outB = \
|
|
213
|
+
GPhys::NetCDF_IO.each_along_dims_write([in1,in2,in3], ofile, -1){
|
|
214
|
+
|isub1,isub2,isub3|
|
|
215
|
+
osubA = (isub1*isub2).mean(0)
|
|
216
|
+
osubB = (isub2*isub3).mean(1)
|
|
217
|
+
[ osubA, osubB ]
|
|
218
|
+
}
|
|
219
|
+
ofile.close</pre>
|
|
220
|
+
<p>In this case, two output objects (outA and outB) are made
|
|
221
|
+
from the three input objects (in1,in2,in3) and written in a
|
|
222
|
+
single file (ofile). If you want to separate into two files,
|
|
223
|
+
you can do it like this: </p>
|
|
224
|
+
<pre>in1 = GPhys::NetCDF_IO.open(infile1, varname1)
|
|
225
|
+
in2 = GPhys::NetCDF_IO.open(infile2, varname2)
|
|
226
|
+
in3 = GPhys::NetCDF_IO.open(infile3, varname3)
|
|
227
|
+
ofile1 = NetCDF.create(ofilename1)
|
|
228
|
+
ofile2 = NetCDF.create(ofilename2)
|
|
229
|
+
outA, outB = \
|
|
230
|
+
GPhys::NetCDF_IO.each_along_dims_write([in1,in2,in3], [ofile1,ofile2], -1){
|
|
231
|
+
|isub1,isub2,isub3|
|
|
232
|
+
osubA = (isub1*isub2).mean(0)
|
|
233
|
+
osubB = (isub2*isub3).mean(1)
|
|
234
|
+
[ osubA, osubB ]
|
|
235
|
+
}
|
|
236
|
+
ofile.close</pre></li>
|
|
237
|
+
</ul></dd>
|
|
238
|
+
<dt><h4><a name="label-8" id="label-8"><code>set_convention(<var>convention</var>)</code></a></h4></dt><!-- RDLabel: "set_convention" -->
|
|
239
|
+
<dd>
|
|
240
|
+
<p>Set a NetCDF convention to be interpreted.</p>
|
|
241
|
+
<p>ARGUMENTS</p>
|
|
242
|
+
<ul>
|
|
243
|
+
<li>convention (Module): the convention</li>
|
|
244
|
+
</ul>
|
|
245
|
+
<p>RETURN VALUE</p>
|
|
246
|
+
<ul>
|
|
247
|
+
<li>convention (Module)</li>
|
|
248
|
+
</ul></dd>
|
|
249
|
+
<dt><h4><a name="label-9" id="label-9"><code>convention</code></a></h4></dt><!-- RDLabel: "convention" -->
|
|
250
|
+
<dd>
|
|
251
|
+
<p>Returns the current NetCDF convention to be interpreted.</p>
|
|
252
|
+
<p>RETURN VALUE</p>
|
|
253
|
+
<ul>
|
|
254
|
+
<li>convention (Module)</li>
|
|
255
|
+
</ul></dd>
|
|
256
|
+
<dt><h4><a name="label-10" id="label-10"><code>var_names(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names" -->
|
|
257
|
+
<dd>
|
|
258
|
+
<p>ARGUMENTS</p>
|
|
259
|
+
<ul>
|
|
260
|
+
<li>file (NetCDF or String): if string,
|
|
261
|
+
it must be the name (path) of a NetCDF file.</li>
|
|
262
|
+
</ul>
|
|
263
|
+
<p>RETURN VALUE</p>
|
|
264
|
+
<ul>
|
|
265
|
+
<li>names of variables (Array): this return the names of variables
|
|
266
|
+
which the file has.</li>
|
|
267
|
+
</ul></dd>
|
|
268
|
+
<dt><h4><a name="label-11" id="label-11"><code>var_names_except_coordinate(<var>file</var>)</code></a></h4></dt><!-- RDLabel: "var_names_except_coordinate" -->
|
|
269
|
+
<dd>
|
|
270
|
+
<p>ARGUMENTS</p>
|
|
271
|
+
<ul>
|
|
272
|
+
<li>file (NetCDF or String): if string,
|
|
273
|
+
it must be the name (path) of a NetCDF file.</li>
|
|
274
|
+
</ul>
|
|
275
|
+
<p>RETURN VALUE</p>
|
|
276
|
+
<ul>
|
|
277
|
+
<li>names of variables (Array): this return the names of variables
|
|
278
|
+
which the file has, except variables for coordinate.</li>
|
|
279
|
+
</ul></dd>
|
|
280
|
+
</dl>
|
|
281
|
+
|
|
282
|
+
</body>
|
|
283
|
+
</html>
|