carray-netcdf 1.0.0

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Files changed (11) hide show
  1. checksums.yaml +7 -0
  2. data/API.html +238 -0
  3. data/API.md +270 -0
  4. data/README.md +3 -0
  5. data/carray-netcdf.gemspec +23 -0
  6. data/examples/test.rb +1 -0
  7. data/extconf.rb +11 -0
  8. data/lib/carray-netcdf.rb +2 -0
  9. data/lib/io/netcdf.rb +533 -0
  10. data/rb_netcdflib.c +1914 -0
  11. metadata +52 -0
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data/API.html ADDED
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+
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+ <html>
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+ <head><title>API.md</title></head>
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+ <body>
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+ <h1>CArray/NetCDF library API document</h1>
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+
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+ <h2>1. Loading library</h2>
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+
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+ <pre><code>gem install carray-netcdf
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+
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+ require "carray-netcdf"
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+ </code></pre>
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+
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+ <h2>2. Methods </h2>
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+
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+ <p>This API provides the way of calling functions</p>
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+
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+ <pre><code>include NC
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+ nc_funcname(...)
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+
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+ NC.funcname(...)
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+ </code></pre>
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+
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+ <h3>2.1. Data types</h3>
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+
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+ <pre><code>data_type = NC.ca_type(xtype)
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+ xtype = NC.nc_type(data_type)
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+ </code></pre>
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+
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+ <h3>2.2. NetCDF File</h3>
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+
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+ <pre><code>fd = nc_create(FILENAME[, mode=NC_CLOBBER])
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+
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+ mode : NC_CLOBBER - permit overwrite
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+ NC_NOCLOBBER - inhibit overwrite
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+ NC_SHARE - no buffering
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+
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+ fd = nc_open(FILENAME[, mode=NC_NOWRITE])
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+
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+ mode : NC_NOWRITE - readonly
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+ NC_WRTIE - writable
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+ NC_SHARE - no buffering
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+
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+ nc_close(fd)
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+
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+ nc_redef(fd)
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+ nc_enddef(fd)
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+
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+ nc_sync(fd)
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+
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+ ndims = nc_inq_ndims(fd)
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+ nvars = nc_inq_nvars(fd)
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+ natts = nc_inq_natts(fd)
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+ unlimdim = nc_inq_unlimdim(fd)
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+
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+ oldmode = nc_set_fill(mode)
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+
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+ mode : NC_FILL
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+ NC_NOFILL
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+ </code></pre>
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+
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+ <h3>2.3. NetCDF Dimension</h3>
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+
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+ <pre><code>dimid = nc_def_dim(fd, dimname, len)
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+ dimid = nc_inq_dimid(fd, dimname) =&gt; Integer | nil
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+
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+ dimname = nc_inq_dimname(fd, dimid)
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+ dimlen = nc_inq_dimlen(fd, dimid)
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+
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+ nc_rename_dim(fd, dimid, newname)
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+ </code></pre>
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+
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+ <h3>2.4. NetCDF Variable</h3>
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+
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+ <pre><code>varid = nc_def_var(fd, varname, type, dim)
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+ varid = nc_inq_varid(fd, varname) =&gt; Integer | nil
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+
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+ vartype = nc_inq_vartype(fd, varid)
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+ varndims = nc_inq_varndims(fd, varid)
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+ vardimid = nc_inq_varndimid(fd, varid) =&gt; Array of dimids
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+
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+ nc_put_var1(fd, varid, [i,j,..], val)
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+ nc_put_var(fd, varid, ca)
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+ nc_put_vara(fd, varid, start, count, ca)
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+ nc_put_vars(fd, varid, start, count, stride, ca)
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+ nc_put_varm(fd, varid, start, count, stride, imap, ca)
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+
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+ + with data_type conversion
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+
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+ val = nc_get_var1(fd, varid, [i,j,..])
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+ ca = nc_get_var(fd, varid) [useful]
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+ ca = nc_get_vara(fd, varid, start, count) [useful]
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+ ca = nc_get_vars(fd, varid, start, count, stride) [useful]
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+ ca = nc_get_varm(fd, varid, start, count, stride, imap) [useful]
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+
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+ + no data_type conversion
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+
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+ nc_get_var(fd, varid, ca) [pedantic]
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+ nc_get_vara(fd, varid, start, count, ca) [pedantic]
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+ nc_get_vars(fd, varid, start, count, stride, ca) [pedantic]
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+ nc_get_varm(fd, varid, start, count, stride, imap, ca) [pedantic]
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+
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+ + with data_type conversion.
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+
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+ nc_rename_var(fd, varid, newname)
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+ </code></pre>
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+
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+ <h3>2.5. NetCDF Attribute</h3>
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+
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+ <pre><code>varnatts = nc_inq_varnatts(fd, varid)
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+ attid = nc_inq_attid(fd, varid, attname)
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+
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+ attname = nc_inq_attname(fd, varid, attid)
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+ atttype = nc_inq_atttype(fd, varid, attname)
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+ attlen = nc_inq_attlen(fd, varid, attname)
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+
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+ nc_put_att(fd, varid, attname, val)
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+
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+ varid : NC_GLOBAL for global att
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+ val : String -&gt; NC_CHAR
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+ Integer -&gt; NC_INT
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+ Float -&gt; NC_DOUBLE
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+ CArray -&gt; NC.nc_type(val.data_type)
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+
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+
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+ val = nc_get_att(fd, varid, attname) =&gt; String | Numeric | CArray | nil
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+
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+ varid : NC_GLOBAL for global att
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+
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+ nc_get_att(fd, varid, attname, ca) [pedantic]
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+
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+ nc_rename_att(fd, varid, attname, newname)
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+ nc_del_att(fd, varid, attname)
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+
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+ nc_copy_att(fd1, varid1, attname, fd2, varid2)
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+ </code></pre>
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+
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+ <h3>2.6 Constants</h3>
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+
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+ <pre><code>NC_NAT
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+ NC_BYTE
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+ NC_SHORT
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+ NC_INT
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+ NC_FLOAT
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+ NC_DOUBLE
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+
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+ NC_NOERR - status of API routines
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+
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+ NC_CLOBBER - permit overwrite [nc_create]
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+ NC_NOCLOBBER - inhibit overwrite [nc_create]
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+ NC_NOWRITE - readonly [nc_open]
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+ NC_WRITE - writable [nc_open]
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+ NC_SHARE - no buffering [nc_create, nc_open]
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+
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+ NC_GLOBAL - varid for global attributes
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+
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+ NC_NOFILL - nc_set_fill(fd, varid, NC_NOFILL)
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+ NC_FILL - nc_set_fill(fd, varid, NC_FILL)
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+
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+ NC_MAX_NAME
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+ NC_MAX_VAR_DIMS
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+ NC_MAX_DIMS
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+
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+ NC_LOCK - ???
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+ NC_SIZEHINT_DEFAULT - ???
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+ </code></pre>
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+
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+ <h2>3. NCFile interface</h2>
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+
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+ <p>NCFile interface provides the way of <em>READ-ONLY</em> access to the netcdf file.</p>
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+
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+ <h3>3.1. NCFile</h3>
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+
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+ <pre><code>nc = NCFile.open(FILENAME)
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+
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+ nc = NCFile.new(file_id)
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+ file_id: return value of nc_open in read-only mode
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+ </code></pre>
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+
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+ <h3>3.2. Dimensions</h3>
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+
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+ <pre><code>nc.has_dim?(DIMNAME)
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+ nc.dims - Array of dimension
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+
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+ dim = nc.dim(DIMNAME) - NCDim object or nil
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+ dim.to_i - size of dimension
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+ dim.to_ca
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+ </code></pre>
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+
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+ <h3>3.3. Variables</h3>
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+
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+ <pre><code>nc.has_var?(VARNAME)
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+ nc.vars - Array of variables
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+
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+ var = nc[VARNAME] - NCVar object or nil
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+ var.is_dim? - true if dimension variable
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+ var.to_ca - get array as CArray object
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+ var[...] - Cooked value array with CArray-like indexing
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+ var.get!(...) - same as [...]
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+ var.get(...) - Non-cooked value array with CArray-like indexing
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+
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+ var.get_var1(...) - interface to original get function
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+ var.get_var()
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+ var.get_vara(start, count)
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+ var.get_vars(start, count, stride)
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+ var.get_varm(start, count, stride, imap)
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+ var.get_var1!(...)
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+ var.get_var!()
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+ var.get_vara!(start, count)
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+ var.get_vars!(start, count, stride)
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+ var.get_varm!(start, count, stride, imap)
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+ </code></pre>
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+
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+ <h3>3.4. Attributes</h3>
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+
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+ <p>All attributes are already read in initializing process of NCFile object.</p>
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+
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+ <pre><code>nc.attributes - Hash
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+ dim.attributes
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+ var.attributes
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+
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+ nc.attribute(ATTNAME) - accessor
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+ dim.attribute(ATTNAME)
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+ var.attribute(ATTNAME)
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+ </code></pre>
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+
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+ <h3>3.5. Iteration</h3>
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+
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+ <p>No iteration methods is provided, but accessor methods for dims, vars, attributes can be used.</p>
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+
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+ <pre><code>ex)
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+
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+ nc.attributes.each {|key, value| ... }
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+ nc.dims.each {|dim| ... }
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+ nc.vars.each {|var| ... }
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+ </code></pre>
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+ </body>
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+ </html>
data/API.md ADDED
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+ CArray/NetCDF library API document
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+ ==================================
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+
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+ 1. Loading library
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+ ------------------
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+
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+ gem install carray-netcdf
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+
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+ require "carray-netcdf"
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+
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+ 2. Methods
12
+ ----------
13
+
14
+ This API provides the way of calling functions
15
+
16
+ include NC
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+ nc_funcname(...)
18
+
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+ NC.funcname(...)
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+
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+ ### 2.1. Data types
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+
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+ data_type = NC.ca_type(xtype)
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+ xtype = NC.nc_type(data_type)
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+
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+ ### 2.2. NetCDF File
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+
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+ fd = nc_create(FILENAME[, mode=NC_CLOBBER])
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+
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+ mode : NC_CLOBBER - permit overwrite
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+ NC_NOCLOBBER - inhibit overwrite
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+ NC_SHARE - no buffering
33
+
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+ fd = nc_open(FILENAME[, mode=NC_NOWRITE])
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+
36
+ mode : NC_NOWRITE - readonly
37
+ NC_WRTIE - writable
38
+ NC_SHARE - no buffering
39
+
40
+ nc_close(fd)
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+
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+ nc_redef(fd)
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+ nc_enddef(fd)
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+
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+ nc_sync(fd)
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+
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+ ndims = nc_inq_ndims(fd)
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+ nvars = nc_inq_nvars(fd)
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+ natts = nc_inq_natts(fd)
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+ unlimdim = nc_inq_unlimdim(fd)
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+
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+ oldmode = nc_set_fill(mode)
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+
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+ mode : NC_FILL
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+ NC_NOFILL
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+
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+ ### 2.3. NetCDF Dimension
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+
59
+ dimid = nc_def_dim(fd, dimname, len)
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+ dimid = nc_inq_dimid(fd, dimname) => Integer | nil
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+
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+ dimname = nc_inq_dimname(fd, dimid)
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+ dimlen = nc_inq_dimlen(fd, dimid)
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+
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+ nc_rename_dim(fd, dimid, newname)
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+
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+ ### 2.4. NetCDF Variable
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+
69
+ varid = nc_def_var(fd, varname, type, dim)
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+ varid = nc_inq_varid(fd, varname) => Integer | nil
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+
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+ vartype = nc_inq_vartype(fd, varid)
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+ varndims = nc_inq_varndims(fd, varid)
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+ vardimid = nc_inq_varndimid(fd, varid) => Array of dimids
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+
76
+ nc_put_var1(fd, varid, [i,j,..], val)
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+ nc_put_var(fd, varid, ca)
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+ nc_put_vara(fd, varid, start, count, ca)
79
+ nc_put_vars(fd, varid, start, count, stride, ca)
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+ nc_put_varm(fd, varid, start, count, stride, imap, ca)
81
+
82
+ + with data_type conversion
83
+
84
+ val = nc_get_var1(fd, varid, [i,j,..])
85
+ ca = nc_get_var(fd, varid) [useful]
86
+ ca = nc_get_vara(fd, varid, start, count) [useful]
87
+ ca = nc_get_vars(fd, varid, start, count, stride) [useful]
88
+ ca = nc_get_varm(fd, varid, start, count, stride, imap) [useful]
89
+
90
+ + no data_type conversion
91
+
92
+ nc_get_var(fd, varid, ca) [pedantic]
93
+ nc_get_vara(fd, varid, start, count, ca) [pedantic]
94
+ nc_get_vars(fd, varid, start, count, stride, ca) [pedantic]
95
+ nc_get_varm(fd, varid, start, count, stride, imap, ca) [pedantic]
96
+
97
+ + with data_type conversion.
98
+
99
+ nc_rename_var(fd, varid, newname)
100
+
101
+ ### 2.5. NetCDF Attribute
102
+
103
+ varnatts = nc_inq_varnatts(fd, varid)
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+ attid = nc_inq_attid(fd, varid, attname)
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+
106
+ attname = nc_inq_attname(fd, varid, attid)
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+ atttype = nc_inq_atttype(fd, varid, attname)
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+ attlen = nc_inq_attlen(fd, varid, attname)
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+
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+ nc_put_att(fd, varid, attname, val)
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+
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+ varid : NC_GLOBAL for global att
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+ val : String -> NC_CHAR
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+ Integer -> NC_INT
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+ Float -> NC_DOUBLE
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+ CArray -> NC.nc_type(val.data_type)
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+
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+
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+ val = nc_get_att(fd, varid, attname) => String | Numeric | CArray | nil
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+
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+ varid : NC_GLOBAL for global att
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+
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+ nc_get_att(fd, varid, attname, ca) [pedantic]
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+
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+ nc_rename_att(fd, varid, attname, newname)
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+ nc_del_att(fd, varid, attname)
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+
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+ nc_copy_att(fd1, varid1, attname, fd2, varid2)
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+
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+ ### 2.6 Constants
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+
132
+ NC_NAT
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+ NC_BYTE
134
+ NC_SHORT
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+ NC_INT
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+ NC_FLOAT
137
+ NC_DOUBLE
138
+
139
+ NC_NOERR - status of API routines
140
+
141
+ NC_CLOBBER - permit overwrite [nc_create]
142
+ NC_NOCLOBBER - inhibit overwrite [nc_create]
143
+ NC_NOWRITE - readonly [nc_open]
144
+ NC_WRITE - writable [nc_open]
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+ NC_SHARE - no buffering [nc_create, nc_open]
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+
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+ NC_GLOBAL - varid for global attributes
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+
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+ NC_NOFILL - nc_set_fill(fd, varid, NC_NOFILL)
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+ NC_FILL - nc_set_fill(fd, varid, NC_FILL)
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+
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+ NC_MAX_NAME
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+ NC_MAX_VAR_DIMS
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+ NC_MAX_DIMS
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+
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+ NC_LOCK - ???
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+ NC_SIZEHINT_DEFAULT - ???
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+
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+ 3. NCFile interface
160
+ -------------------
161
+
162
+ NCFile interface provides the way of *READ-ONLY* access to the netcdf file.
163
+
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+ ### 3.1. NCFile
165
+
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+ nc = NCFile.open(FILENAME)
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+
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+ nc = NCFile.new(file_id)
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+ file_id: return value of nc_open in read-only mode
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+
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+ ### 3.2. Dimensions
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+
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+ nc.has_dim?(DIMNAME)
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+ nc.dims - Array of dimension
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+
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+ dim = nc.dim(DIMNAME) - NCDim object or nil
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+ dim.to_i - size of dimension
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+ dim.to_ca
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+
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+ ### 3.3. Variables
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+
182
+ nc.has_var?(VARNAME)
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+ nc.vars - Array of variables
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+
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+ var = nc.var(VARNAME) - NCVar object or nil
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+ var.is_dim? - true if dimension variable
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+ var.to_ca - get array as CArray object
188
+ var[...] - Cooked value array with CArray-like indexing
189
+ var.get!(...) - same as [...]
190
+ var.get(...) - Non-cooked value array with CArray-like indexing
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+
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+ var.get_var1(...) - interface to original get function
193
+ var.get_var()
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+ var.get_vara(start, count)
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+ var.get_vars(start, count, stride)
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+ var.get_varm(start, count, stride, imap)
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+ var.get_var1!(...)
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+ var.get_var!()
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+ var.get_vara!(start, count)
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+ var.get_vars!(start, count, stride)
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+ var.get_varm!(start, count, stride, imap)
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+
203
+ ### 3.4. Attributes
204
+
205
+ All attributes are already read in initializing process of NCFile object.
206
+
207
+ nc.attributes - Hash
208
+ dim.attributes
209
+ var.attributes
210
+
211
+ nc.attribute(ATTNAME) - accessor
212
+ dim.attribute(ATTNAME)
213
+ var.attribute(ATTNAME)
214
+
215
+
216
+ ### 3.5. Iteration
217
+
218
+ No iteration methods is provided, but accessor methods for dims, vars, attributes can be used.
219
+
220
+ ex)
221
+
222
+ nc.attributes.each {|key, value| ... }
223
+ nc.dims.each {|dim| ... }
224
+ nc.vars.each {|var| ... }
225
+
226
+ 4. NCFileWriter interface
227
+ -------------------------
228
+
229
+ It provides simple interface to create netcdf file.
230
+ If you want the detailed controling to create netcdf, use nc_function API.
231
+
232
+ out = NCFileWrite.new("test.nc")
233
+
234
+ out.define(
235
+ dims: { ### dimension
236
+ lon: 230, name: Integer
237
+ lat: 120,
238
+ time: 24
239
+ },
240
+ vars: { ### variables
241
+ temp: { name: definition
242
+ type: NC::NC_FLOAT, type: Integer
243
+ dims: ["time", "lat", "lon"], dims: Array of dim names
244
+ attributes: { attributes: Hash
245
+ long_name: "air temperature",
246
+ units: "degC"
247
+ }
248
+ }
249
+ },
250
+ attributes: { ### global attributes (Hash)
251
+ creator: "foobar"
252
+ }
253
+ )
254
+
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+ out["lon"] = lon
256
+ out["lat"] = lat
257
+ out["time"] = time
258
+ out["temp"][nil] = temp ### CArray index can be used
259
+ out.write ### call nc_close
260
+
261
+
262
+ nc = NCFile.open("test.nc")
263
+ nc.definition ### return definition Hash
264
+
265
+
266
+
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+
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+
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+
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+
data/README.md ADDED
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+ This directory contains the plugin library used as the interface to NetCDF
2
+ from Ruby/CArray.
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+
data/carray-netcdf.gemspec ADDED
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+
2
+ Gem::Specification::new do |s|
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+ version = "1.0.0"
4
+
5
+ files = Dir.glob("**/*") - [
6
+ Dir.glob("carray-*.gem"),
7
+ ].flatten
8
+
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+ s.platform = Gem::Platform::RUBY
10
+ s.name = "carray-netcdf"
11
+ s.summary = "Extension for manipulating NetCDF3 file with CArray"
12
+ s.description = <<-HERE
13
+ Extension for manipulating NetCDF3 file with CArray
14
+ HERE
15
+ s.version = version
16
+ s.author = "Hiroki Motoyoshi"
17
+ s.email = ""
18
+ s.homepage = 'https://github.com/himotoyoshi/carray-netcdf'
19
+ s.files = files
20
+ s.extensions = [ "extconf.rb" ]
21
+ s.has_rdoc = false
22
+ s.required_ruby_version = ">= 1.8.1"
23
+ end
data/examples/test.rb ADDED
@@ -0,0 +1 @@
1
+ require "carray-netcdf"
data/extconf.rb ADDED
@@ -0,0 +1,11 @@
1
+ require "mkmf"
2
+ require "carray/mkmf"
3
+
4
+ $CFLAGS += " -Wall"
5
+
6
+ dir_config("netcdf", possible_includes("netcdf","netcdf3","netcdf-3"), possible_libs)
7
+
8
+ if have_carray() and have_header("netcdf.h") and have_library("netcdf")
9
+ create_makefile("carray/netcdflib")
10
+ end
11
+
data/lib/carray-netcdf.rb ADDED
@@ -0,0 +1,2 @@
1
+ require "carray"
2
+ require "carray/io/netcdf"