gphys 1.1.1a

data/LICENSE.txt

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+GPhys is copyrighted free software by Takeshi Horinouchi and
+GFD Dennou Club (http://www.gfd-dennou.org/).
+
+Copyright 2011 (C) Takeshi Horinouchi and GFD Dennou Club
+(http://www.gfd-dennou.org/) All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the
+      distribution.
+
+THIS SOFTWARE IS PROVIDED BY GFD DENNOU CLUB AND CONTRIBUTORS ``AS IS'' 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GFD DENNOU CLUB OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation
+are those of the authors and should not be interpreted as representing
+official policies, either expressed or implied, of Takeshi Horinouchi
+and GFD Dennou Club.

data/README

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+
+GPhys -- a class of multi-dimensional Gridded Physical quantities
+
+by T Horinouchi
+2003/05/14
+
+* DESCRIPTION
+
+To be written. 
+See http://ruby.gfd-dennou.org/workshop200303/horinout/ (in Japanese).
+
+* INSTALL
+
+# ruby extconf.rb && make && make install
+# ruby ./install.rb
+
+* SAMPLE PROGRAMS
+
+Each library file has a sample program part, which is invoked by
+directly feeding the file to Ruby. For example
+
+% cd lib/numru/
+% ruby ggraph.rb
+
+% cd lib/numru/gphys
+% ruby gphys.rb
+% ruby gphys_netcdf_io.rb
+
+Sample programs are also found in the
+
+   ./sample
+
+diredtory.

data/Rakefile

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+require 'rake/gempackagetask'
+
+NAME = 'gphys'
+VER = '1.1.1a'
+
+PKG_FILES = FileList[
+  '**',
+  'bin/**/*',
+  'doc/**/*',
+  'lib/**/*',
+  'sample/**/*',
+  'test/**/*',
+  'testdata/**/*'
+]
+
+spec = Gem::Specification.new do |s|
+  s.name             = NAME
+  s.version          = VER
+  s.authors           = ["Takeshi Horinouchi", "Ryo Mizuta",\
+    "Daisuke Tsukahara", "Seiya Nishizawa", "Shin-ichi Takehiro"]
+  s.email            = ['eriko@gfd-dennou.org']
+  s.homepage         = 'http://www.gfd-dennou.org/arch/ruby/products/gphys/'
+  s.licenses         = ["GFD Dennou Club"]
+  s.platform         = Gem::Platform::RUBY
+  s.summary          = %q{a multi-purpose class to handle Gridded Physical quantities}
+  s.description      = %q{comprehensive library for self-descriptive gridded physical data (in NetCDF, GrADS, or on memory) with graphicsgraphicsgraphicsgraphics.}
+
+  s.files            = PKG_FILES.to_a
+  s.require_paths    = ['lib']
+  s.test_files = Dir.glob("test/*")
+  s.bindir    = 'bin'
+  s.executables = ['gdir_client','gpaop','gpcut','gplist'\
+    ,'gpmaxmin','gpvect','grads2nc_with_gphys','gdir_server'\
+    ,'gpcat','gpedit','gpmath','gpprint','gpview']
+
+  s.has_rdoc         = false
+  #s.extra_rdoc_files = ['README']
+
+  s.required_ruby_version = Gem::Requirement.new(">= 1.6")
+
+  s.add_runtime_dependency(%q<narray>, [">= 0"])
+  s.add_runtime_dependency(%q<numru-misc>, [">= 0.0.4"])
+  s.add_runtime_dependency(%q<numru-units>, [">= 1.5"])
+  s.add_runtime_dependency(%q<narray_miss>, [">= 0"])
+  s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.5.2"])
+  s.add_runtime_dependency(%q<ruby-dcl>, [">= 1.2.1"])
+  s.add_runtime_dependency(%q<ruby-fftw3>, [">= 0.3"])
+
+  s.extensions << "extconf.rb"
+  #s.extensions << "extconf.rb --enable-shared"
+end
+
+Rake::GemPackageTask.new(spec) do |pkg|
+  pkg.gem_spec = spec
+  pkg.need_tar = true
+end
+

data/TODO_ep_flux

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+* mathmatical documents
+  * add method reference
+* write tutrial
+  * for user
+    * about precision
+  * for devloper

data/bin/gdir_client

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+#!/usr/bin/env ruby
+irb -r numru/gdir_connect_ftp-like
+
+=begin
+= NAME
+
+gdir_client - A client of gdir_server using irb.
+
+= SYNOPSIS
+
+  % gdir_client top_dir [[host:]port] [-a allowed_address] ...
+
+= DESCRIPTION
+
+((*gdir_client*)) command is just equal to
+
+   irb -r numru/gdir_connect_ftp-like
+
+= OPTIONS
+
+same as gdir_server
+
+= SEE ALSO
+
+((*gdir_server(1)*))
+
+=end

data/bin/gdir_server

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+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gdir_server - A stand-alone server program to provide a directory service of GPhys
+
+= SYNOPSIS
+
+   % gdir_server top_dir [[host:]port] [-a allowed_address]..
+
+= DESCRIPTION
+
+A stand-alone server program to provide a directory service of GPhys
+objects by using GDir.
+
+= OPTION
+
+:top_dir: 
+  can be ".", "/", or whatever directory in your files system.
+:host: 
+  host address (name or ip) -- use it if you want to specify
+  explicitly, such as "localhost", which is useful for ssh port forwarding.
+:port: 
+  the port number you want to assign (internally determined
+  if not specified). A complete URI is printed if the server is started.
+:-a: 
+  limits accesses from remote hosts only to the ones specified.
+  Can be repeated multiple times. (Need the space between '-a' and the rest)
+
+    % gdir_server . 12345
+    % gdir_server . localhost:12345 -a all
+    % gdir_server . -a hoge.hero.org -a localhost
+    % gdir_server . 12345 -a '192.168.1.*' -a localhost
+
+=end
+
+require "drb/drb"
+require "drb/timeridconv"
+require "drb/acl"
+require "numru/gdir"
+
+DRb.install_id_conv(DRb::TimerIdConv.new(1200))
+
+module NumRu
+  class GDir
+    include DRbUndumped
+  end
+end
+
+class NArray
+  def self._load(o) to_na(*Marshal::load(o)).ntoh end
+  def _dump(limit) 
+    Marshal::dump([hton.to_s, typecode, *shape]) 
+  end
+end
+
+include NumRu
+
+usage = <<EOS
+
+
+USAGE: % #{$0} top_dir [[host:]port] [-a allowed_address]..
+
+where
+* top_dir: can be ".", "/", or whatever directory in your files system.
+* host: host address (name or ip) -- use it if you want to specify
+  explicitly, such as "localhost", which is useful for ssh port forwarding.
+* port: the port number you want to assign (internally determined
+  if not specified). A complete URI is printed if the server is started.
+* -a: Allows accesses from those hosts specified with this option.
+  Can be repeated multiple times. (Need the space between '-a' and the rest)
+  By default, only connections from the localhost is allowed.
+  If you use this option, you need to specify localhost explicitly
+  if connection from the localhost is needed.
+
+EXAMPLES:
+    % #{$0} . 12345
+    % #{$0} . localhost:12345 -a all
+    % #{$0} . -a hoge.hero.org -a localhost
+    % #{$0} . 12345 -a '192.168.1.*' -a localhost
+EOS
+
+# <interpret comman-line arguments>
+
+if ARGV.include?('-a')
+  # Access control
+  list = ['deny', 'all']
+  while(idx=ARGV.index('-a'))
+    ARGV.delete_at(idx) 
+    begin
+      list.push( 'allow', ARGV.delete_at(idx) )
+    rescue
+      raise usage
+    end
+  end
+  acl = ACL.new(list)
+  DRb.install_acl(acl)
+else
+  list = %W!deny all allow localhost allow 127.0.0.1 allow #{Socket.gethostname}!
+  acl = ACL.new(list)
+  DRb.install_acl(acl)
+end
+
+top = ARGV.shift || raise(usage)
+host_port = ARGV.shift
+
+# <set the top & direcotry>
+begin
+  GDir.top = top
+  rootdir = GDir.new('/')
+rescue
+  print "\n",usage,"\n"
+  raise
+end
+
+# <start the server>
+if !host_port
+  uri_seed = nil
+elsif /:/ =~ host_port
+  uri_seed = 'druby://'+host_port
+else
+  port = host_port     # port number only
+  print usage if port && port.to_i.to_s != port   # make sure it is an integer
+  uri_seed = 'druby://:'+port
+end
+DRb.start_service(uri_seed, rootdir)
+puts 'URI: '+DRb.uri
+puts '[return] to exit'
+gets

data/bin/gpaop

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+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gpaop - Carrying out an arithmetric operation multiple GPhys variables.
+
+= USAGE
+
+   % gpaop -f func [options] gturl1 gturl2 ...
+
+= DESCRIPTION
+
+Carrying out an arithmetric operation (addition, subtraction, 
+multiplication and division) multiple GPhys variables. 
+
+= SYNOPSYS 
+
+Operation, gphys1 (+-*/) gphys2 (+-*/) gphys3 (+-*/) ... is performed 
+by the following  command formats. 
+
+  % gpaop -f func [options] gturl1 gturl2 ...
+
+Format of 'gturl*' is 'path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'
+
+  % gpaop -f func --var varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]] [options] gtfile1 gtfile2 ...
+
+Commands which compute arithmetric operation on gphys variables are 
+successively installed by linking this sciript as a 
+"gp+(add|sub|multi|div)". You can omit '--func' option by using 
+these commands.  
+
+= OPTIONS
+
+:-f func, --func func
+  kind of operation (add|sub|multi|div|)
+:-v url, --var url
+  set the variable name and slicing parameters.
+:-h, --help
+  print this message. 
+:-o file, --output file
+  output filename (optional). 
+  Default output filename is 'gphys.nc'.
+
+Usage Examples
+
+ % gpaop -f add gtool.nc@temp gtool.nc@temp
+ % gpaop -f sub gtool.nc@temp,t=1 gtool.nc@temp,t=2
+
+ % gpaop -f multi --var temp gtool*.nc
+ % gpaop -f div --var temp,t=1 gtool*.nc
+ % gpaop -o temp.nc --var temp,t=1 gtool*.nc
+
+= HISTORY
+
+  2005/08/21  S Takehiro (created)
+  2005/08/23  S Takehiro (common methods to gp* commandmoved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+require "getoptlong"
+
+#------------------------ Default Settings ------------------------
+Output_default = 'gphys.nc'                      # default ouptput file name
+command = File.basename($0)+" "+ARGV.join(' ')   # keep an input command line 
+
+#---------------------- Option Configuration ----------------------
+parser = GetoptLong.new(
+  ["--func",     "-f", GetoptLong::REQUIRED_ARGUMENT],
+  ["--var",      "-v", GetoptLong::REQUIRED_ARGUMENT],
+  ["--output",   "-o", GetoptLong::REQUIRED_ARGUMENT],
+  ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
+begin
+  parser.each{|opt, arg|
+    case opt
+    when "--func" then eval "$OPT_func='#{arg}'"
+    when "--var" then eval "$OPT_var='#{arg}'"
+    when "--output" then eval "$OPT_output='#{arg}'"
+    when "--help" then eval "$OPT_help=true"
+    else
+      raise "must not happen"
+    end
+  }
+  rescue GetoptLong::AmbigousOption, GetoptLong::InvalidOption,
+          GetoptLong::MissingArgument, 
+          GetoptLong::NeedlessArgument => err
+    help
+    $srderr.puts err.message
+    exit 1
+end
+
+#------------------------ Help message ------------------------
+if $OPT_help then
+  help
+  exit(0)
+end  
+
+#------------------------ Option check ------------------------
+$OPT_output ||= Output_default 
+$OPT_func ||= $0.sub(/^gp/,'')
+raise "Operation '#{$OPT_func}' not supported. It should be add,sub,multi or div." unless /(add|sub|multi|div)/ =~ $OPT_func 
+
+unless ARGV[0]
+  help
+  exit 1
+end
+
+#------------------------ Output file check  --------------------------
+raise "#{$OPT_output} already exists." if FileTest.exist?($OPT_output) 
+outncfile=NetCDF.create($OPT_output)
+
+#------------------------ Open gphys variable ------------------------
+# Reading the first Gphys variable
+gturl = ARGV[0]
+gturl = gturl+'@'+$OPT_var if $OPT_var
+gphys = GPhys::IO.open_gturl(gturl)
+print "  Reading #{gturl}\n"
+gphys_aop = gphys.copy
+outncfile.copy_global_att(gphys) # Copy global attributes (only for NetCDF)
+ARGV.shift 
+
+
+# Reading Gphys variables after the first one.
+while ARGV[0] do
+  gturl = ARGV[0]
+  gturl = gturl+'@'+$OPT_var if $OPT_var
+  gphys = GPhys::IO.open_gturl(gturl)
+  print "  Reading #{gturl}\n"
+
+  gphys_aop = gphys_aop + gphys if $OPT_func=="add"
+  gphys_aop = gphys_aop - gphys if $OPT_func=="sub"
+  gphys_aop = gphys_aop * gphys if $OPT_func=="multi"
+  gphys_aop = gphys_aop / gphys if $OPT_func=="div"
+  ARGV.shift 
+end
+
+#---------------------- Output GPhys variable  ------------------------
+GPhys::IO.write( outncfile, gphys_aop )
+NetCDF_Conventions.add_history(outncfile, command) # Exec command written as a history
+outncfile.close
+
+print File.basename($0) +": Output is written to #{$OPT_output}.\n"

data/bin/gpcat

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+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gpcat - Read a variable in multiple NetCDF files, concatenate and write them to a single netcdf file. 
+
+= DESCRIPTION
+
+((*gpcat*)) is command line tools for read a variable in multiple
+  NetCDF files, concatenate and write them to a single netcdf file.
+
+= USAGE
+
+  % gpcat -v VAR [options] FILE1 FILE2...
+
+= OPTIONS
+
+:-h, --help
+   print this message. 
+:-v var, --variable var
+   variable name (required).
+:-s sfmt, --slice sfmt
+   slice,thinnng  (optional).
+:-o file, --output file
+   output filename (optional). Default output filename is 'gphys.nc'.
+                                 
+
+= HISTORY
+
+  2005/05/17  S Takehiro (created)
+  2005/08/10  S Takehiro (utilize internal function for printing help message)
+  2005/08/21  S Takehiro (global attributes copied to the output file)
+  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+require "getoptlong"
+
+
+#-------------------- Slice parameter analysis --------------------
+def parse_slice(arg_slice)
+
+  slice = Hash.new
+  thinning = Hash.new
+  arg_slice_descr = arg_slice.split(/,/)
+#  arg_slice = arg_slice_descr.shift
+  arg_slice_descr.each do |s|
+    if /(.*)=(.*)/ =~ s
+      dimname = $1
+      subset = $2
+      case subset
+      when /(.*):(.*):(.*)/
+        slice[dimname] = ($1.to_f)..($2.to_f)
+        thinning[dimname] = {0..-1,$3.to_i}
+      when /(.*):(.*)/
+        slice[dimname] = ($1.to_f)..($2.to_f)
+      else
+        slice[dimname] = subset.to_f
+      end
+    else
+      raise "invalid slice format\n\n"
+      "slice format: " + SliceFMT
+    end
+  end
+  thinning = nil if thinning.length == 0
+  [slice, thinning]
+end
+
+#------------------------ Default Settings ------------------------
+Output_default = 'gphys.nc'
+SliceFMT = "dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+
+#---------------------- Option Configuration ----------------------
+parser = GetoptLong.new(
+  ["--variable", "-v", GetoptLong::REQUIRED_ARGUMENT],
+  ["--output",   "-o", GetoptLong::REQUIRED_ARGUMENT],
+  ["--slice",    "-s", GetoptLong::REQUIRED_ARGUMENT],
+  ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
+begin
+  parser.each{|opt, arg|
+    case opt
+    when "--variable" then eval "$OPT_var='#{arg}'"
+    when "--output" then eval "$OPT_output='#{arg}'"
+    when "--slice" then eval "$OPT_slice='#{arg}'"
+    when "--help" then eval "$HELP=true"
+    else
+      raise "must not happen"
+    end
+  }
+  rescue GetoptLong::AmbigousOption, GetoptLong::InvalidOption,
+          GetoptLong::MissingArgument, 
+          GetoptLong::NeedlessArgument => err
+    help
+    $srderr.puts err.message
+    exit 1
+end
+
+#------------------------ Help message ------------------------
+if $HELP then
+  help
+  exit(0)
+end  
+
+#------------------------ Option check ------------------------
+unless $OPT_var then 
+  raise "Variable must be set with '-v' or '--var' option."
+end
+
+unless $OPT_output then 
+  $OPT_output = Output_default
+end
+
+slice, thinning = parse_slice($OPT_slice) if $OPT_slice
+
+#------------------------ Output file check  --------------------------
+raise "#{$OPT_output} already exists." if FileTest.exist?($OPT_output) 
+outncfile=NetCDF.create($OPT_output)
+
+#------------------------ Open gphys variable ------------------------
+# Copy global attributes (only for NetCDF file)
+gphys = GPhys::IO.open(ARGV[0],$OPT_var)
+outncfile.copy_global_att(gphys) # Copy global attributes (only for NetCDF)
+
+case ARGV.length
+when 1 then
+  gphys = GPhys::IO.open(ARGV[0],$OPT_var)
+  print "#{$0}: Gphys variable '#{$OPT_var}' in NetCDF file, " + ARGV[0] +", was opened successfully.\n"
+else
+  gphys = GPhys::IO.open(ARGV, $OPT_var)
+  print "#{$0}: GPhys variable '#{$OPT_var}' in NetCDF files, " + ARGV.join(', ') +", was opened successfully.\n"
+end
+
+
+#------------------- Slice/thinning gphys variable --------------------
+gphys = gphys.cut(slice) if slice
+gphys = gphys[thinning]  if thinning
+
+#---------------------- Output GPhys variable  ------------------------
+GPhys::IO.write( outncfile, gphys )
+NetCDF_Conventions.add_history(outncfile, File.basename($0)+" "+ARGV[0])
+outncfile.close
+
+print File.basename($0)+": GPhys variable '#{$OPT_var}' in " + ARGV.join(', ') + ", is written to #{$OPT_output}.\n"

data/bin/gpcut

@@ -0,0 +1,102 @@
+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gpcut - Extract, slicing and thinning a GPhys variable.
+
+= DESCRIPTION
+
+((*gpcut*)) is command line tools for extract, slicing and thinning a GPhys variables.
+
+= USAGE 
+
+   % gpcut [options] path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+
+= OPTIONS
+
+:-h, --help
+  print this message. 
+:-m dim, --mean dim
+   average along dim axis (optional).
+:-o file, --output file
+   output filename (optional). 
+   Default output filename is 'gphys.nc'.
+
+= HISTORY
+
+  2005/05/17  S Takehiro (created)
+  2005/07/15  S Takehiro (open_gturl method is used for opening gphys variable)
+  2005/08/10  S Takehiro (utilize internal function for printing help message)
+  2005/08/21  S Takehiro (global attributes copied to the output file)
+  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+require "getoptlong"
+
+#------------------------ Default Settings ------------------------
+Output_default = 'gphys.nc'
+URLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+
+#---------------------- Option Configuration ----------------------
+parser = GetoptLong.new(
+  ["--mean",     "-m", GetoptLong::REQUIRED_ARGUMENT],
+  ["--output",   "-o", GetoptLong::REQUIRED_ARGUMENT],
+  ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
+begin
+  parser.each{|opt, arg|
+    case opt
+    when "--mean" then eval "$OPT_mean='#{arg}'"
+    when "--output" then eval "$OPT_output='#{arg}'"
+    when "--help" then eval "$OPT_help=true"
+    else
+      raise "must not happen"
+    end
+  }
+  rescue GetoptLong::AmbigousOption, GetoptLong::InvalidOption,
+          GetoptLong::MissingArgument, 
+          GetoptLong::NeedlessArgument => err
+    help
+    $srderr.puts err.message
+    exit 1
+end
+
+#------------------------ Help message ------------------------
+if $OPT_help then
+  help
+  exit(0)
+end  
+
+#------------------------ Option check ------------------------
+$OPT_output = Output_default unless $OPT_output
+
+#------------------------ Output file check  --------------------------
+raise "#{$OPT_output} already exists." if FileTest.exist?($OPT_output) 
+outncfile=NetCDF.create($OPT_output)
+
+#------------------------ Open gphys variable ------------------------
+gturl = ARGV[0]
+gphys = GPhys::IO.open_gturl(gturl)
+outncfile.copy_global_att(gphys) # Copy global attributes (only for NetCDF)
+
+#----------------------- mean along any axis -------------------------
+if ($OPT_mean)
+  dims = ($OPT_mean).split(/\s*,\s*/)
+  dims.each{|dim|
+    dim = dim.to_i if dim.to_i.to_s == dim
+    gphys = gphys.mean(dim)
+  }
+end
+
+
+#---------------------- Output GPhys variable  ------------------------
+GPhys::IO.write( outncfile, gphys )
+NetCDF_Conventions.add_history(outncfile, File.basename($0)+" "+ARGV[0])
+outncfile.close
+
+print File.basename($0) +": "+ARGV[0]+ " is written to #{$OPT_output}.\n"