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/varray.html
ADDED
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<?xml version="1.0" ?>
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<!DOCTYPE html
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PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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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">
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<head>
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<title>../lib/numru/gphys/varray.rb</title>
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</head>
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<body>
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<h1><a name="label-0" id="label-0">class NumRu::VArray</a></h1><!-- RDLabel: "class NumRu::VArray" -->
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<p>VArray is a Virtual Array class, in which a multi-dimensional array data is
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stored on memory (NArray, NArrayMiss) or in file (NetCDFVar etc).
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The in-file data handling is left to subclasses such as VArrayNetCDF,
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and this base class handles the following two cases:</p>
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<ol>
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<li>Data are stored on memory using NArray</li>
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<li>Subset of another VArray (possibly a subclass such as VArrayNetCDF).</li>
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</ol>
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<p>Perhaps the latter case needs more explanation. Here, a VArray is defined
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as a subset of another VArray, so the current VArray has only the link
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and info on how the subset is mapped to the other VArray.</p>
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<p>A VArray behaves just like a NArray, i.e., a numeric multi-dimensional
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array. The important difference is that a VArray has a name and can
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have "attributes" like a NetCDF variable. Therefore, VArray can perfectly
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represent a NetCDFVar, which is realized by a sub-class VArrayNetCDF.</p>
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<p>NOMENCLATURE</p>
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<ul>
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<li>value(s): The multi-dimensional numeric array contained in the VArray,
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or its contents</li>
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<li>attribute(s): A combination of name and data that describes a VArray.
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Often realized by NumRu::Attribute class (or it is a NetCDFAttr in
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VArrayNetCDF). The name must be a string, and the type of attribute
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values is restricted to a few classes for compatibility with
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NetCDFAttr (See NumRu::Attribute)</li>
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</ul>
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<h2><a name="label-1" id="label-1">Class Methods</a></h2><!-- RDLabel: "Class Methods" -->
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<dl>
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<dt><h4><a name="label-2" id="label-2"><code>VArray.new(<var>narray</var>=<var>nil</var>, <var>attr</var>=<var>nil</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "VArray.new" -->
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<dd>
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<p>A constructor</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>narray (NArray or NArrayMiss; default:nil) The array to be held.
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(nil is used to initialize a mapping to another VArray by a protected
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method).</li>
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<li>attr (NumRu::Attribute; default:nil) Attributes. If nil, an empty </li>
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</ul>
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<pre>attribute object is created and stored.</pre>
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<ul>
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<li>name (String; default nil) Name of the VArray. If nil, it is named "noname".</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 VArray</li>
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</ul>
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<p>EXAMPLE</p>
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<pre>na = NArray.int(6,3).indgen!
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va1 = VArray.new( na, nil, "test" )</pre></dd>
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<dt><h4><a name="label-3" id="label-3"><code>VArray.new2(<var>ntype</var>, <var>shape</var>, <var>attr</var>=<var>nil</var>, <var>name</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "VArray.new2" -->
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<dd>
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<p>Another constructor. Uses parameters to initialize a NArray to hold.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>ntype (String or NArray constants): Numeric type of the NArray to be
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held (e.g., "sfloat", "float", NArray::SFLOAT, NArray::FLOAT)</li>
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<li>shape (Array of Integers): shape of the NArray</li>
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<li>attr (Attribute; default:nil) Attributes. If nil, an empty attribute
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object is created and stored.</li>
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<li>name (String; default nil) Name of the VArray.</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 VArray</li>
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</ul></dd>
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</dl>
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<h2><a name="label-4" id="label-4">Instance Methods</a></h2><!-- RDLabel: "Instance Methods" -->
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<dl>
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<dt><h4><a name="label-5" id="label-5"><code>val</code></a></h4></dt><!-- RDLabel: "val" -->
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<dd>
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<p>Returns the values as a NArray (or NArrayMiss).</p>
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<p>This is the case even when the VArray is a mapping to another. Also,
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this method is to be redefined in subclasses to do the same thing.</p>
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<p>ARGUMENTS -- none</p>
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<p>RETURN VALUE</p>
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<ul>
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<li>a NArray (or NArrayMiss)</li>
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</ul></dd>
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<dt><h4><a name="label-6" id="label-6"><code>val=(<var>narray</var>)</code></a></h4></dt><!-- RDLabel: "val=" -->
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<dd>
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<p>Set values.</p>
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<p>The whole values are set. If you want to set partly, use <a href="#label-9">[]=</a>.
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In this method, values are read from narray and set into the internal
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value holder. Thus, for exampled, the numeric type is not changed
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regardress the numeric type of narray. Use <a href="#label-7">replace_val</a> to
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replace entirely with narray.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>narray (NArray or NArrayMiss or Numeric): If Numeric, the whole
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values are set to be equal to it. If NArray (or NArrayMiss), its
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shape must agree with the shape of the VArray.</li>
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</ul></dd>
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<dt><h4><a name="label-7" id="label-7"><code>replace_val(<var>narray</var>)</code></a></h4></dt><!-- RDLabel: "replace_val" -->
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<dd>
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<p>Replace the internal array data with the object narray.
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Use <a href="#label-6">val=</a> if you want to copy the values of narray.</p>
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<p>ARGUMENTS</p>
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<ul>
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<li>narray (NArray or NArrayMiss): as pxlained above.
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Its shape must agree with the shape of the VArray (self).</li>
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</ul>
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<p>RETURN VALUE</p>
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<ul>
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<li>if (self.class == VArray), self;
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otherwise (if self.class is a subclass of VArray), a new VArray.</li>
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</ul></dd>
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<dt><h4><a name="label-8" id="label-8"><code>[]</code></a></h4></dt><!-- RDLabel: "[]" -->
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<dd>
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Get a subset. Its usage is the same as NArray#[]</dd>
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<dt><h4><a name="label-9" id="label-9"><code>[] = </code></a></h4></dt><!-- RDLabel: "[]=" -->
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<dd>
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Set a subset. Its usage is the same as NArray#[]=</dd>
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<dt><h4><a name="label-10" id="label-10"><code>attr</code></a></h4></dt><!-- RDLabel: "attr" -->
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<dd>
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To be undefined.</dd>
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<dt><h4><a name="label-11" id="label-11"><code>ntype</code></a></h4></dt><!-- RDLabel: "ntype" -->
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<dd>
|
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<p>Returns the numeric type.</p>
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<p>ARGUMENTS -- none</p>
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<p>RETURN VALUE</p>
|
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<ul>
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<li>a String ("byte", "sint", "int", "sfloat", "float", "scomplex"
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"complex", or "obj"). It can be used in NArray.new to initialize
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another NArray.</li>
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</ul></dd>
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<dt><h4><a name="label-12" id="label-12"><code>rank</code></a></h4></dt><!-- RDLabel: "rank" -->
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<dd>
|
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Returns the rank (number of dimensions)</dd>
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<dt><h4><a name="label-13" id="label-13"><code>shape</code></a></h4></dt><!-- RDLabel: "shape" -->
|
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<dd>
|
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Returns the shape</dd>
|
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<dt><h4><a name="label-14" id="label-14"><code>shape_current</code></a></h4></dt><!-- RDLabel: "shape_current" -->
|
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<dd>
|
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aliased to <a href="#label-13">shape</a>.</dd>
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<dt><h4><a name="label-15" id="label-15"><code>length</code></a></h4></dt><!-- RDLabel: "length" -->
|
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<dd>
|
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Returns the length of the VArray</dd>
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<dt><h4><a name="label-16" id="label-16"><code>typecode</code></a></h4></dt><!-- RDLabel: "typecode" -->
|
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<dd>
|
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149
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Returns the NArray typecode</dd>
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<dt><h4><a name="label-17" id="label-17"><code>name</code></a></h4></dt><!-- RDLabel: "name" -->
|
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<dd>
|
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<p>Returns the name</p>
|
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<p>RETURN VALUE</p>
|
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<ul>
|
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<li>(String) name of the VArray</li>
|
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</ul></dd>
|
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<dt><h4><a name="label-18" id="label-18"><code>name=(<var>nm</var>)</code></a></h4></dt><!-- RDLabel: "name=" -->
|
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<dd>
|
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159
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<p>Changes the name.</p>
|
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<p>ARGUMENTS</p>
|
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<ul>
|
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162
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<li>nm(String): the new name.</li>
|
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</ul>
|
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164
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<p>RETURN VALUE</p>
|
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<ul>
|
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166
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<li>nm</li>
|
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</ul></dd>
|
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<dt><h4><a name="label-19" id="label-19"><code>rename!(<var>nm</var>)</code></a></h4></dt><!-- RDLabel: "rename!" -->
|
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<dd>
|
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<p>Changes the name (Same as <a href="#label-18">name=</a>, but returns self)</p>
|
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<p>ARGUMENTS</p>
|
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<ul>
|
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173
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<li>nm(String): the new name.</li>
|
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</ul>
|
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175
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<p>RETURN VALUE</p>
|
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<ul>
|
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177
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<li>self</li>
|
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</ul></dd>
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<dt><h4><a name="label-20" id="label-20"><code>rename(<var>nm</var>)</code></a></h4></dt><!-- RDLabel: "rename" -->
|
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<dd>
|
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181
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<p>Same as rename! but duplicate the VArray object and set its name.</p>
|
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<p>This method may not be supported in sub-classes, since it is sometimes
|
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problematic not to change the original.</p></dd>
|
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<dt><h4><a name="label-21" id="label-21"><code>copy(<var>to</var>=<var>nil</var>)</code></a></h4></dt><!-- RDLabel: "copy" -->
|
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<dd>
|
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186
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<p>Copy a VArray. If to is nil, works as the deep cloning (duplication of the entire object).</p>
|
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<p>Both the values and the attributes are copied.</p>
|
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<p>ARGUMENTS</p>
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<ul>
|
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<li>to (VArray (possibly a subclass) or nil): The VArray to which the
|
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copying is made.</li>
|
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</ul></dd>
|
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<dt><h4><a name="label-22" id="label-22"><code>reshape!( *<var>shape</var> )</code></a></h4></dt><!-- RDLabel: "reshape!" -->
|
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<dd>
|
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195
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<p>Changes the shape without changing the total size. May not be available in subclasses.</p>
|
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<p>ARGUMENTS</p>
|
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<ul>
|
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198
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<li>shape (Array of Integer): new shape</li>
|
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199
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</ul>
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<p>RETURN VALUE</p>
|
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<ul>
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202
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<li>self</li>
|
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</ul>
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<p>EXAMPLE</p>
|
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205
|
+
<pre>vary = VArray.new2( "float", [10,2])
|
|
206
|
+
vary.reshape!(5,4) # changes the vary
|
|
207
|
+
vary.copy.reshape!(2,2,5) # make a deep clone and change it
|
|
208
|
+
# This always works with a VArray subclass, since vary.copy
|
|
209
|
+
# makes a deep clone to VArray with NArray.</pre></dd>
|
|
210
|
+
<dt><h4><a name="label-23" id="label-23"><code>file</code></a></h4></dt><!-- RDLabel: "file" -->
|
|
211
|
+
<dd>
|
|
212
|
+
<p>Returns a file object if the data of the VArray is in a file, nil if it is on memory</p>
|
|
213
|
+
<p>ARGUMENTS</p>
|
|
214
|
+
<ul>
|
|
215
|
+
<li>none</li>
|
|
216
|
+
</ul>
|
|
217
|
+
<p>RETURN VALUE</p>
|
|
218
|
+
<ul>
|
|
219
|
+
<li>an object representing the file in which data are stored. Its class
|
|
220
|
+
depends on the file type. nil is returned if the data is not in a file.</li>
|
|
221
|
+
</ul></dd>
|
|
222
|
+
<dt><h4><a name="label-24" id="label-24"><code>transpose(*<var>dims</var>)</code></a></h4></dt><!-- RDLabel: "transpose" -->
|
|
223
|
+
<dd>
|
|
224
|
+
Transpose. Argument specification is as in NArray.</dd>
|
|
225
|
+
<dt><h4><a name="label-25" id="label-25"><code>reshape(*<var>shape</var>)</code></a></h4></dt><!-- RDLabel: "reshape" -->
|
|
226
|
+
<dd>
|
|
227
|
+
Reshape. Argument specification is as in NArray.</dd>
|
|
228
|
+
<dt><h4><a name="label-26" id="label-26"><code>axis_draw_positive</code></a></h4></dt><!-- RDLabel: "axis_draw_positive" -->
|
|
229
|
+
<dd>
|
|
230
|
+
<p>Returns the direction to plot the axis (meaningful only if self is a
|
|
231
|
+
coordinate variable.) </p>
|
|
232
|
+
<p>The current implementation is based on NetCDF conventions,
|
|
233
|
+
so REDEFINE IT IN SUBCLASSES if it is not appropriate.</p>
|
|
234
|
+
<p>RETURN VALUE</p>
|
|
235
|
+
<ul>
|
|
236
|
+
<li>one of the following:
|
|
237
|
+
<ul>
|
|
238
|
+
<li>true: axis should be drawn in the increasing order (to right/upward)</li>
|
|
239
|
+
<li>false: axis should be drawn in the decreasing order</li>
|
|
240
|
+
<li>nil: not specified</li>
|
|
241
|
+
</ul></li>
|
|
242
|
+
</ul></dd>
|
|
243
|
+
<dt><h4><a name="label-27" id="label-27"><code>axis_cyclic?</code></a></h4></dt><!-- RDLabel: "axis_cyclic?" -->
|
|
244
|
+
<dd>
|
|
245
|
+
<p>Returns whether the axis is cyclic (meaningful only if self is a
|
|
246
|
+
coordinate variable.) </p>
|
|
247
|
+
<p>The current implementation is based on NetCDF conventions,
|
|
248
|
+
so REDEFINE IT IN SUBCLASSES if it is not appropriate.</p>
|
|
249
|
+
<p>RETURN VALUE</p>
|
|
250
|
+
<ul>
|
|
251
|
+
<li>one of the following:
|
|
252
|
+
<ul>
|
|
253
|
+
<li>true: cyclic</li>
|
|
254
|
+
<li>false: not cyclic</li>
|
|
255
|
+
<li>nil: not specified</li>
|
|
256
|
+
</ul></li>
|
|
257
|
+
</ul></dd>
|
|
258
|
+
<dt><h4><a name="label-28" id="label-28"><code>axis_modulo</code></a></h4></dt><!-- RDLabel: "axis_modulo" -->
|
|
259
|
+
<dd>
|
|
260
|
+
<p>Returns the modulo of a cyclic axis (meaningful only if self is a
|
|
261
|
+
coordinate variable and it is cyclic.) </p>
|
|
262
|
+
<p>The current implementation is based on NetCDF conventions,
|
|
263
|
+
so REDEFINE IT IN SUBCLASSES if it is not appropriate.</p>
|
|
264
|
+
<p>RETURN VALUE</p>
|
|
265
|
+
<ul>
|
|
266
|
+
<li>one of the following:
|
|
267
|
+
<ul>
|
|
268
|
+
<li>Float if the modulo is defined</li>
|
|
269
|
+
<li>nil if modulo is not found</li>
|
|
270
|
+
</ul></li>
|
|
271
|
+
</ul></dd>
|
|
272
|
+
<dt><h4><a name="label-29" id="label-29"><code>axis_cyclic_extendible?</code></a></h4></dt><!-- RDLabel: "axis_cyclic_extendible?" -->
|
|
273
|
+
<dd>
|
|
274
|
+
(meaningful only if self is a coordinate variable.)
|
|
275
|
+
Returns true if self is cyclic and it is suitable to exend
|
|
276
|
+
cyclically (having the distance between both ends
|
|
277
|
+
equal to (modulo - dx), where dx is the mean increment).</dd>
|
|
278
|
+
<dt><h4><a name="label-30" id="label-30"><code>coerce(<var>other</var>)</code></a></h4></dt><!-- RDLabel: "coerce" -->
|
|
279
|
+
<dd>
|
|
280
|
+
For Numeric operators. (If you do not know it, see a manual or book of Ruby)</dd>
|
|
281
|
+
</dl>
|
|
282
|
+
<h2><a name="label-31" id="label-31">Methods compatible with NArray</a></h2><!-- RDLabel: "Methods compatible with NArray" -->
|
|
283
|
+
<p>VArray is a numeric multi-dimensional array, so it supports most of the
|
|
284
|
+
methods and operators in NArray. Here, the name of those methods are just
|
|
285
|
+
quoted. See the documentation of NArray for their usage.</p>
|
|
286
|
+
<h3><a name="label-32" id="label-32">Math functions</a></h3><!-- RDLabel: "Math functions" -->
|
|
287
|
+
<h4><a name="label-33" id="label-33">sqrt, exp, log, log10, log2, sin, cos, tan, sinh, cosh, tanh, asin, acos, atan, asinh, acosh, atanh, csc, sec, cot, csch, sech, coth, acsc, asec, acot, acsch, asech, acoth</a></h4><!-- RDLabel: "sqrt, exp, log, log10, log2, sin, cos, tan, sinh, cosh, tanh, asin, acos, atan, asinh, acosh, atanh, csc, sec, cot, csch, sech, coth, acsc, asec, acot, acsch, asech, acoth" -->
|
|
288
|
+
<h3><a name="label-34" id="label-34">Binary operators</a></h3><!-- RDLabel: "Binary operators" -->
|
|
289
|
+
<h4><a name="label-35" id="label-35">-, +, *, /, %, **, .add!, .sub!, .mul!, .div!, mod!, >, >=, <, <=, &, |, ^, .eq, .ne, .gt, .ge, .lt, .le, .and, .or, .xor, .not</a></h4><!-- RDLabel: "-, +, *, /, %, **, .add!, .sub!, .mul!, .div!, mod!, >, >=, <, <=, &, |, ^, .eq, .ne, .gt, .ge, .lt, .le, .and, .or, .xor, .not" -->
|
|
290
|
+
<h3><a name="label-36" id="label-36">Unary operators</a></h3><!-- RDLabel: "Unary operators" -->
|
|
291
|
+
<h4><a name="label-37" id="label-37">~ - +</a></h4><!-- RDLabel: "~ - +" -->
|
|
292
|
+
<h3><a name="label-38" id="label-38">Mean etc</a></h3><!-- RDLabel: "Mean etc" -->
|
|
293
|
+
<h4><a name="label-39" id="label-39">mean, sum, stddev, min, max, median</a></h4><!-- RDLabel: "mean, sum, stddev, min, max, median" -->
|
|
294
|
+
<h3><a name="label-40" id="label-40">Other methods</a></h3><!-- RDLabel: "Other methods" -->
|
|
295
|
+
<p>These methods returns a NArray (not a VArray).</p>
|
|
296
|
+
<h4><a name="label-41" id="label-41">all?, any?, none?, where, where2, floor, ceil, round, to_f, to_i, to_a</a></h4><!-- RDLabel: "all?, any?, none?, where, where2, floor, ceil, round, to_f, to_i, to_a" -->
|
|
297
|
+
|
|
298
|
+
</body>
|
|
299
|
+
</html>
|
|
@@ -0,0 +1,67 @@
|
|
|
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/varraycomposite.rb</title>
|
|
8
|
+
</head>
|
|
9
|
+
<body>
|
|
10
|
+
<h1><a name="label-0" id="label-0">class NumRu::VArrayComposite < NumRu::VArray</a></h1><!-- RDLabel: "class NumRu::VArrayComposite < NumRu::VArray" -->
|
|
11
|
+
<p>a VArray that consists of multiple VArrays tiled regularly
|
|
12
|
+
(possibly in multi-dimension). Except for the constructer
|
|
13
|
+
"new" and <!-- Reference, RDLabel "attr_update" doesn't exist --><em class="label-not-found">attr_update</em><!-- Reference end -->, the usage of this class is the same as VArray.</p>
|
|
14
|
+
<p>Note that the name and the attributes of a VArrayComposite is
|
|
15
|
+
borrowed form one of the VArrays contained (actually, the first one
|
|
16
|
+
is used). Currently, no check is made
|
|
17
|
+
regarding whether the names and attributes are the same among the
|
|
18
|
+
VArrays contained. If you rename a VArrayComposite, the change will
|
|
19
|
+
be made with all the VArrays contained. However, currently,
|
|
20
|
+
change of the attributes are only reflected only in the first
|
|
21
|
+
VArray. You have to call <!-- Reference, RDLabel "attr_update" doesn't exist --><em class="label-not-found">attr_update</em><!-- Reference end --> separately.</p>
|
|
22
|
+
<h2><a name="label-1" id="label-1">Class methods</a></h2><!-- RDLabel: "Class methods" -->
|
|
23
|
+
<dl>
|
|
24
|
+
<dt><h4><a name="label-2" id="label-2"><code>VArrayComposite.new(<var>varrays</var>)</code></a></h4></dt><!-- RDLabel: "VArrayComposite.new" -->
|
|
25
|
+
<dd>
|
|
26
|
+
<p>Constructor</p>
|
|
27
|
+
<p>ARGUMENTS</p>
|
|
28
|
+
<ul>
|
|
29
|
+
<li>varrays (NArray of VArray) : VArrays to be included, gridded
|
|
30
|
+
regularly in a NArray.</li>
|
|
31
|
+
</ul>
|
|
32
|
+
<p>RETURN VALUE</p>
|
|
33
|
+
<ul>
|
|
34
|
+
<li>a VArrayComposite</li>
|
|
35
|
+
</ul>
|
|
36
|
+
<p>EXAMPLES</p>
|
|
37
|
+
<ul>
|
|
38
|
+
<li><p>Suppose that you have VArrays va00, va01, va10, va00,
|
|
39
|
+
with va00 and va10 having a same 0th dimension length,
|
|
40
|
+
va01 and va11 having a same 0th dimension length,
|
|
41
|
+
and va00 and va01 having a same 1st dimention length.</p>
|
|
42
|
+
<pre>varrays = NArray[ [ va00, va01 ],
|
|
43
|
+
[ va10, va11 ] ]
|
|
44
|
+
vac = VArrayComposite.new(varrays)</pre>
|
|
45
|
+
<p>This will create a composite VArray tiled two-dimensionally.</p></li>
|
|
46
|
+
<li><p>You can create a VArray that lacks one or more VArrays as
|
|
47
|
+
long as the shape is unambiguous:</p>
|
|
48
|
+
<pre>vac = VArrayComposite.new( NArray[ [ va00, va01 ],
|
|
49
|
+
[ va10, nil ] ] )</pre>
|
|
50
|
+
<p>is allowed, but </p>
|
|
51
|
+
<pre>vac = VArrayComposite.new( NArray[ [ va00, nil ],
|
|
52
|
+
[ va10, nil ] ] )</pre>
|
|
53
|
+
<p>is prohibited.</p>
|
|
54
|
+
<p>NOTICE: At this moment, handling of such nil-contianing
|
|
55
|
+
VArrayComposite is very limited, and many methods do not work.</p></li>
|
|
56
|
+
<li><p>Suppose that you have 3D VArrays va0, va1, va2, va3,
|
|
57
|
+
and you want to concatenate them with the 3rd dimension.</p>
|
|
58
|
+
<pre>varrays = NArray[ va0,va1,va2,va3 ].newdim(0,0)</pre>
|
|
59
|
+
<p>This will create a 3D NArray with a shape of [1,1,4].
|
|
60
|
+
Then you can make the composite as follows:</p>
|
|
61
|
+
<pre>vac = VArrayComposite.new(varrays)</pre></li>
|
|
62
|
+
</ul></dd>
|
|
63
|
+
</dl>
|
|
64
|
+
<p>Usage of all the other class methods are the same as in VArray.</p>
|
|
65
|
+
|
|
66
|
+
</body>
|
|
67
|
+
</html>
|
data/ext_coord.c
ADDED
|
@@ -0,0 +1,209 @@
|
|
|
1
|
+
/* ext_coord.c : Extention library related to coordinate handling in GPhys
|
|
2
|
+
*/
|
|
3
|
+
|
|
4
|
+
#include<stdio.h>
|
|
5
|
+
#include<string.h>
|
|
6
|
+
#include "ruby.h"
|
|
7
|
+
#include "narray.h"
|
|
8
|
+
|
|
9
|
+
#ifndef RARRAY_PTR
|
|
10
|
+
# define RARRAY_PTR(ary) (RARRAY(ary)->ptr)
|
|
11
|
+
#endif
|
|
12
|
+
#ifndef RARRAY_LEN
|
|
13
|
+
# define RARRAY_LEN(ary) (RARRAY(ary)->len)
|
|
14
|
+
#endif
|
|
15
|
+
|
|
16
|
+
/* cut_range : a private method for AssocCoord (used in AssocCoord#cut)
|
|
17
|
+
*/
|
|
18
|
+
static VALUE
|
|
19
|
+
assoc_coord_cut_range(self, vmins, vmaxs, crds, masks, crdaxexist, orgaxlens)
|
|
20
|
+
VALUE self, vmins, vmaxs, crds, masks, crdaxexist, orgaxlens;
|
|
21
|
+
// All input variables are supposed to be Arrays
|
|
22
|
+
{
|
|
23
|
+
VALUE wheres, whna; // return value (Array)
|
|
24
|
+
int nc, ic, na, ia, jlen, j, klen, k, ndimk, dimk;
|
|
25
|
+
int *lens, lentot, lenmax, *mod, *sub, **mlt, *jmlt, *dimk2a;
|
|
26
|
+
int last_non0, l, cidx, *natype, *nomask, included, whcount;
|
|
27
|
+
int32_t **axexist, *whptr, *whbuf;
|
|
28
|
+
double *vmax, *vmin, val, **dval;
|
|
29
|
+
float **fval;
|
|
30
|
+
int8_t **mask;
|
|
31
|
+
|
|
32
|
+
nc = RARRAY_LEN(crds); // lengths of vmins,vmaxs,crds,masks,crdaxexist
|
|
33
|
+
na = RARRAY_LEN(orgaxlens);
|
|
34
|
+
wheres = rb_ary_new();
|
|
35
|
+
|
|
36
|
+
/* input check */
|
|
37
|
+
|
|
38
|
+
if(nc==0){rb_raise(rb_eArgError,"crds empty [%s:%d]",__FILE__,__LINE__);}
|
|
39
|
+
if(na==0){rb_raise(rb_eArgError,"orgaxlens empty [%s:%d]",__FILE__,__LINE__);}
|
|
40
|
+
if ( nc!=RARRAY_LEN(vmins) || nc!=RARRAY_LEN(vmaxs) ||
|
|
41
|
+
nc!=RARRAY_LEN(masks) || nc!=RARRAY_LEN(crdaxexist) ) {
|
|
42
|
+
rb_raise(rb_eArgError,"lengths of array do not agree [%s:%d]",
|
|
43
|
+
__FILE__,__LINE__);
|
|
44
|
+
}
|
|
45
|
+
|
|
46
|
+
/* info regaring lengths of original axes */
|
|
47
|
+
|
|
48
|
+
lentot = 1;
|
|
49
|
+
lenmax = -1;
|
|
50
|
+
lens = ALLOCA_N(int,na);
|
|
51
|
+
for(ia=0; ia<na; ia++){
|
|
52
|
+
lens[ia] = NUM2INT( RARRAY_PTR(orgaxlens)[ia] );
|
|
53
|
+
lentot *= lens[ia];
|
|
54
|
+
if (lens[ia] > lenmax) { lenmax = lens[ia]; }
|
|
55
|
+
}
|
|
56
|
+
ndimk = ( (na==1) ? 1 : (na-1) ) ;
|
|
57
|
+
mod = ALLOCA_N(int,ndimk);
|
|
58
|
+
sub = ALLOCA_N(int,ndimk);
|
|
59
|
+
mlt = ALLOCA_N(int*,nc);
|
|
60
|
+
axexist = ALLOCA_N(int32_t*,nc);
|
|
61
|
+
for(ic=0; ic<nc; ic++){
|
|
62
|
+
mlt[ic] = ALLOCA_N(int,ndimk);
|
|
63
|
+
axexist[ic] = NA_PTR_TYPE( RARRAY_PTR(crdaxexist)[ic], int32_t* );
|
|
64
|
+
}
|
|
65
|
+
jmlt = ALLOCA_N(int,nc);
|
|
66
|
+
dimk2a = ALLOCA_N(int,ndimk);
|
|
67
|
+
|
|
68
|
+
/* ruby objs to C for coordinates and cut params */
|
|
69
|
+
|
|
70
|
+
vmin = ALLOCA_N(double,nc);
|
|
71
|
+
vmax = ALLOCA_N(double,nc);
|
|
72
|
+
dval = ALLOCA_N(double*,nc);
|
|
73
|
+
fval = ALLOCA_N(float*,nc);
|
|
74
|
+
mask = ALLOCA_N(int8_t*,nc);
|
|
75
|
+
nomask = ALLOCA_N(int,nc);
|
|
76
|
+
natype = ALLOCA_N(int,nc);
|
|
77
|
+
for(ic=0; ic<nc; ic++){
|
|
78
|
+
vmin[ic] = NUM2DBL( RARRAY_PTR(vmins)[ic] );
|
|
79
|
+
vmax[ic] = NUM2DBL( RARRAY_PTR(vmaxs)[ic] );
|
|
80
|
+
natype[ic] = NA_TYPE( RARRAY_PTR(crds)[ic]);
|
|
81
|
+
if ( natype[ic] == NA_DFLOAT ) {
|
|
82
|
+
dval[ic] = NA_PTR_TYPE( RARRAY_PTR(crds)[ic], double* );
|
|
83
|
+
} else if ( natype[ic] == NA_SFLOAT ) {
|
|
84
|
+
fval[ic] = NA_PTR_TYPE( RARRAY_PTR(crds)[ic], float* );
|
|
85
|
+
} else {
|
|
86
|
+
rb_raise(rb_eArgError,"Associate coordinates must be float or sfloat [%s:%d]",__FILE__,__LINE__);
|
|
87
|
+
}
|
|
88
|
+
if ( RARRAY_PTR(masks)[ic] == Qnil ){
|
|
89
|
+
mask[ic] = NULL;
|
|
90
|
+
nomask[ic] = 1;
|
|
91
|
+
} else {
|
|
92
|
+
mask[ic] = NA_PTR_TYPE( RARRAY_PTR(masks)[ic], u_int8_t* );
|
|
93
|
+
nomask[ic] = 0;
|
|
94
|
+
}
|
|
95
|
+
}
|
|
96
|
+
|
|
97
|
+
/* prepare output objs */
|
|
98
|
+
whbuf = ALLOCA_N(int32_t,lenmax);
|
|
99
|
+
|
|
100
|
+
/* main loop */
|
|
101
|
+
for(ia=0; ia<na; ia++){
|
|
102
|
+
|
|
103
|
+
/* parameters for positioning */
|
|
104
|
+
jlen = lens[ia];
|
|
105
|
+
klen = lentot / jlen;
|
|
106
|
+
|
|
107
|
+
for(dimk=0; dimk<ndimk; dimk++){
|
|
108
|
+
if (dimk<ia || na==1) {
|
|
109
|
+
dimk2a[dimk] = dimk;
|
|
110
|
+
} else {
|
|
111
|
+
dimk2a[dimk] = dimk+1;
|
|
112
|
+
}
|
|
113
|
+
}
|
|
114
|
+
for(dimk=0; dimk<ndimk; dimk++){
|
|
115
|
+
if(dimk==0){
|
|
116
|
+
mod[dimk] = lens[dimk2a[dimk]];
|
|
117
|
+
sub[dimk] = 1;
|
|
118
|
+
for(ic=0; ic<nc; ic++){
|
|
119
|
+
if( axexist[ic][dimk2a[dimk]] == 1 ){ // has the ax
|
|
120
|
+
mlt[ic][dimk] = 1;
|
|
121
|
+
} else {
|
|
122
|
+
mlt[ic][dimk] = 0;
|
|
123
|
+
}
|
|
124
|
+
}
|
|
125
|
+
} else {
|
|
126
|
+
mod[dimk] = mod[dimk-1] * lens[dimk2a[dimk]];
|
|
127
|
+
sub[dimk] = mod[dimk-1];
|
|
128
|
+
for(ic=0; ic<nc; ic++){
|
|
129
|
+
if( axexist[ic][dimk2a[dimk]] == 1 ){ // has the ax
|
|
130
|
+
last_non0 = 1;
|
|
131
|
+
for(l=dimk-1; l>=0; l--) {
|
|
132
|
+
if( mlt[ic][l] != 0){
|
|
133
|
+
last_non0 = mlt[ic][l];
|
|
134
|
+
break;
|
|
135
|
+
}
|
|
136
|
+
}
|
|
137
|
+
mlt[ic][dimk] = last_non0 * lens[dimk2a[dimk]];
|
|
138
|
+
} else {
|
|
139
|
+
mlt[ic][dimk] = 0;
|
|
140
|
+
}
|
|
141
|
+
}
|
|
142
|
+
}
|
|
143
|
+
for(ic=0; ic<nc; ic++){
|
|
144
|
+
if (dimk>=ia) { mlt[ic][dimk] *= lens[ia];}
|
|
145
|
+
}
|
|
146
|
+
//printf("## %d %d %d %d : ",ia,dimk,mod[dimk],sub[dimk]);//DEL later
|
|
147
|
+
//for(ic=0;ic<nc;ic++){printf(" %d",mlt[ic][dimk]);} //DEL later
|
|
148
|
+
//printf("\n"); //DEL later
|
|
149
|
+
}
|
|
150
|
+
for(ic=0; ic<nc; ic++){
|
|
151
|
+
jmlt[ic] = 1;
|
|
152
|
+
for(dimk=0; dimk<ia; dimk++){
|
|
153
|
+
if( axexist[ic][dimk] == 1 ){ // has the ax
|
|
154
|
+
jmlt[ic] *= lens[dimk];
|
|
155
|
+
}
|
|
156
|
+
}
|
|
157
|
+
}
|
|
158
|
+
|
|
159
|
+
/* judge in/out */
|
|
160
|
+
whcount = 0;
|
|
161
|
+
for(j=0; j<jlen; j++){
|
|
162
|
+
for(k=0; k<klen; k++){
|
|
163
|
+
included = 0; // initialization to avoid -Wall warning
|
|
164
|
+
for(ic=0; ic<nc; ic++){
|
|
165
|
+
cidx = 0;
|
|
166
|
+
for(dimk=0; dimk<ndimk; dimk++){
|
|
167
|
+
cidx += ( (k/sub[dimk]) % mod[dimk] ) * mlt[ic][dimk];
|
|
168
|
+
}
|
|
169
|
+
cidx += jmlt[ic]*j;
|
|
170
|
+
if ( natype[ic] == NA_DFLOAT ) {
|
|
171
|
+
val = dval[ic][cidx];
|
|
172
|
+
} else {
|
|
173
|
+
val = fval[ic][cidx];
|
|
174
|
+
}
|
|
175
|
+
//printf("! %d %d %d %d %f\n",j,k,ic,cidx,val); //DEL later
|
|
176
|
+
included = ( (nomask[ic] || mask[ic][cidx]) &&
|
|
177
|
+
val >= vmin[ic] &&
|
|
178
|
+
val <= vmax[ic] );
|
|
179
|
+
if (!included) {break;}
|
|
180
|
+
}
|
|
181
|
+
if(included){
|
|
182
|
+
whbuf[whcount] = j;
|
|
183
|
+
whcount++;
|
|
184
|
+
break;
|
|
185
|
+
}
|
|
186
|
+
}
|
|
187
|
+
}
|
|
188
|
+
whna = na_make_object(NA_LINT, 1, &whcount, cNArray);
|
|
189
|
+
rb_ary_push( wheres, whna );
|
|
190
|
+
whptr = NA_PTR_TYPE( whna, int32_t* );
|
|
191
|
+
for(j=0; j<whcount; j++){
|
|
192
|
+
whptr[j] = whbuf[j];
|
|
193
|
+
}
|
|
194
|
+
}
|
|
195
|
+
|
|
196
|
+
return( wheres );
|
|
197
|
+
}
|
|
198
|
+
|
|
199
|
+
void
|
|
200
|
+
init_ext_coord()
|
|
201
|
+
{
|
|
202
|
+
static VALUE mNumRu;
|
|
203
|
+
static VALUE cAssocCoords;
|
|
204
|
+
|
|
205
|
+
// rb_require("narray"); // it does not work
|
|
206
|
+
mNumRu = rb_define_module("NumRu");
|
|
207
|
+
cAssocCoords = rb_define_class_under(mNumRu, "AssocCoords", rb_cObject);
|
|
208
|
+
rb_define_private_method(cAssocCoords,"cut_range",assoc_coord_cut_range,6);
|
|
209
|
+
}
|
data/ext_init.c
ADDED
data/extconf.rb
ADDED
|
@@ -0,0 +1,42 @@
|
|
|
1
|
+
require "mkmf"
|
|
2
|
+
$extout_prefix = '/numru'
|
|
3
|
+
alias __install_dirs install_dirs
|
|
4
|
+
def install_dirs
|
|
5
|
+
dirs = __install_dirs
|
|
6
|
+
dirs.assoc("RUBYARCHDIR")[1].sub!(/target_prefix/,'extout_prefix')
|
|
7
|
+
dirs
|
|
8
|
+
end
|
|
9
|
+
|
|
10
|
+
#dir_config('narray',$sitearchdir,$sitearchdir)
|
|
11
|
+
hoge = Gem::GemPathSearcher.new.find("narray")
|
|
12
|
+
narray_fullname = hoge.full_name
|
|
13
|
+
narray_installpath = hoge.installation_path
|
|
14
|
+
narray_include = "#{narray_installpath}/gems/#{narray_fullname}/"
|
|
15
|
+
narray_lib = "#{narray_installpath}/gems/#{narray_fullname}/"
|
|
16
|
+
dir_config('narray',narray_include,narray_lib)
|
|
17
|
+
|
|
18
|
+
if ( ! ( have_header("narray.h") && have_header("narray_config.h") ) ) then
|
|
19
|
+
print <<EOS
|
|
20
|
+
** configure error **
|
|
21
|
+
Header narray.h or narray_config.h is not found. If you have these files in
|
|
22
|
+
/narraydir/include, try the following:
|
|
23
|
+
|
|
24
|
+
% ruby extconf.rb --with-narray-include=/narraydir/include
|
|
25
|
+
|
|
26
|
+
EOS
|
|
27
|
+
exit(-1)
|
|
28
|
+
end
|
|
29
|
+
|
|
30
|
+
if /cygwin|mingw/ =~ RUBY_PLATFORM
|
|
31
|
+
unless have_library("narray")
|
|
32
|
+
print <<-EOS
|
|
33
|
+
** configure error **
|
|
34
|
+
libnarray.a is not found.
|
|
35
|
+
% ruby extconf.rb --with-narray-lib=/narraydir/lib
|
|
36
|
+
|
|
37
|
+
EOS
|
|
38
|
+
exit(-1)
|
|
39
|
+
end
|
|
40
|
+
end
|
|
41
|
+
|
|
42
|
+
create_makefile("numru/gphys_ext")
|