gphys 1.5.0 → 1.5.1

data/.gitignore

@@ -1,14 +0,0 @@
-*.[oa]
-*~
-*.so
-*.log
-Makefile
-ChangeLog
-/.bundle/
-/.yardoc
-/Gemfile.lock
-/_yardoc/
-/coverage/
-/pkg/
-/spec/reports/
-/tmp/

data/TODO_ep_flux

@@ -1,6 +0,0 @@
-* mathmatical documents
-  * add method reference
-* write tutrial
-  * for user
-    * about precision
-  * for devloper

data/gphys-bigmem.gemspec

@@ -1,44 +0,0 @@
-# coding: utf-8
-lib = File.expand_path('../lib', __FILE__)
-$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
-require 'numru/gphys/version'
-
-Gem::Specification.new do |spec|
-  spec.name          = "gphys-bigmem"
-  spec.version       = NumRu::GPhys::VERSION
-  spec.authors           = ["Takeshi Horinouchi", "Ryo Mizuta",\
-    "Daisuke Tsukahara", "Seiya Nishizawa", "Shin-ichi Takehiro"]
-  spec.email         = ["horinout@ees.hokudai.ac.jp"]
-
-  #if spec.respond_to?(:metadata)
-  #  spec.metadata['allowed_push_host'] = "TODO: Set to 'http://mygemserver.com' to prevent pushes to rubygems.org, or delete to allow pushes to any server."
-  #end
-
-  spec.summary          = %q{A multi-purpose class to handle Gridded Physical quantities}
-  spec.description      = %q{Comprehensive library for self-descriptive gridded physical data (in NetCDF, GrADS, or on memory) with graphics. This version works with Ruby 2.0.}
-  spec.homepage         = 'http://www.gfd-dennou.org/arch/ruby/products/gphys/'
-  spec.licenses       = ["BSD-2-Clause"]
-
-  spec.files         = `git ls-files -z`.split("\x0")
-  spec.bindir        = "bin"
-  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
-  spec.require_paths = ["ext","lib"]
-  spec.test_files    = spec.files.grep(%r{^(test|test_old|sample|testdata)/})
-  spec.extensions << "ext/numru/gphys/extconf.rb"
-
-  spec.post_install_message = "Thanks for installing! You can add extra libraries (i.e., ruby-lapack, rb-grib) to enjoy powerful calculating and handling datasets."
-
-  spec.required_ruby_version = Gem::Requirement.new(">= 1.8")
-
-  spec.add_runtime_dependency(%q<narray-bigmem>)
-  spec.add_runtime_dependency(%q<narray_miss-bigmem>)
-  spec.add_runtime_dependency(%q<numru-misc-bigmem>)
-  spec.add_runtime_dependency(%q<numru-units>, [">= 1.7"])
-  spec.add_runtime_dependency(%q<ruby-netcdf-bigmem>)
-  spec.add_runtime_dependency(%q<ruby-dcl-bigmem>)
-  spec.add_runtime_dependency(%q<ruby-fftw3-bigmem>)
-  #spec.add_runtime_dependency(%q<gsl>, [">= 1.14"])
-  #spec.add_runtime_dependency(%q<rb-gsl>, [">= 1.14"])
-  #spec.add_runtime_dependency(%q<ruby-lapack>, [">= 1.5"])
-  #spec.add_development_dependency(%q<rb-grib>, [">= 0.2.0"])
-end

data/install.rb

@@ -1,130 +0,0 @@
-require 'rbconfig'
-require 'find'
-include Config
-if CONFIG["MINOR"].to_i > 6 then $rb_18 = true else $rb_18 = false end
-if $rb_18
-  require 'fileutils'
-else
-  require 'ftools'
-end
-
-=begin
-$version = CONFIG["MAJOR"]+"."+CONFIG["MINOR"]
-$libdir = File.join(CONFIG["libdir"], "ruby", $version)
-# $archdir = File.join($libdir, CONFIG["arch"])
-$site_libdir = $:.find {|x| x =~ /site_ruby$/}
-if !$site_libdir
-  $site_libdir = File.join($libdir, "site_ruby")
-elsif Regexp.compile($site_libdir) !~ Regexp.quote($version)
-  $site_libdir = File.join($site_libdir, $version)
-end
-
-default_destdir = $site_libdir
-=end
-default_destdir = CONFIG["sitelibdir"]
-
-default_bindir = CONFIG["bindir"]
-
-def install_rb(srcdir, destdir)
-  libdir = "lib"
-  libdir = File.join(srcdir, libdir) if srcdir
-  path = []
-  dir = []
-  Find.find(libdir) do |f|
-    next unless FileTest.file?(f)
-    next if (f = f[libdir.length+1..-1]) == nil
-    next if (/CVS$/ =~ File.dirname(f))
-    path.push f
-    dir |= [File.dirname(f)]
-  end
-  for f in dir
-    next if f == "."
-    next if f == "CVS"
-    if $rb_18
-      FileUtils.makedirs(File.join(destdir, f))
-    else
-      File::makedirs(File.join(destdir, f))
-    end
-  end
-  for f in path
-    next if (/\~$/ =~ f)
-    next if (/^\./ =~ File.basename(f))
-    if $rb_18
-      FileUtils.install(File.join(libdir, f), File.join(destdir, f), {:mode => 0644, :verbose => true})
-    else
-      File::install(File.join(libdir, f), File.join(destdir, f), 0644, true)
-    end
-  end
-end
-
-def install_bin(srcdir, destbindir)
-  localbindir = "bin"
-  localbindir = File.join(srcdir, localbindir) if srcdir
-  path = []
-  dir = []
-  Find.find(localbindir) do |f|
-    next unless FileTest.file?(f)
-    next if (f = f[localbindir.length+1..-1]) == nil
-    next if (/CVS$/ =~ File.dirname(f))
-    path.push f
-    #dir |= [File.dirname(f)]
-  end
-  #for f in dir
-  #  next if f == "."
-  #  next if f == "CVS"
-  #  File::makedirs(File.join(destbindir, f))
-  #end
-  for f in path
-    next if (/\~$/ =~ f)
-    next if (/^\./ =~ File.basename(f))
-    if $rb_18
-      FileUtils.install(File.join(localbindir, f), File.join(destbindir, f), {:mode => 0755, :verbose => true})
-    else
-      File::install(File.join(localbindir, f), File.join(destbindir, f), 0755, true)
-    end
-  end
-end
-
-def ARGV.switch
-  return nil if self.empty?
-  arg = self.shift
-  return nil if arg == '--'
-  if arg =~ /^-(.)(.*)/
-    return arg if $1 == '-'
-    raise 'unknown switch "-"' if $2.index('-')
-    self.unshift "-#{$2}" if $2.size > 0
-    "-#{$1}"
-  else
-    self.unshift arg
-    nil
-  end
-end
-
-def ARGV.req_arg
-  self.shift || raise('missing argument')
-end
-
-destdir = default_destdir
-bindir = default_bindir
-
-begin
-  while switch = ARGV.switch
-    case switch
-    when '-d', '--destdir'
-      destdir = ARGV.req_arg
-    when '-b', '--bindir'
-      bindir = ARGV.req_arg
-    else
-      raise "unknown switch #{switch.dump}"
-    end
-  end
-rescue
-  STDERR.puts $!.to_s
-  STDERR.puts File.basename($0) + 
-    " -d <destdir> -b <bindir>"
-  exit 1
-end    
-
-install_rb(nil, destdir)
-install_bin(nil, bindir)
-

data/sample/cira86_to_nc.rb

@@ -1,122 +0,0 @@
-=begin
-=cira86_to_nc.rb
-
-Read the CIRA86 data file, make corresponding GPhys objects, 
-and write into a NetCDF file.
-
-==Usage
-
-The following will create a NetCDF file 'cira86.nc' under the current 
-directory.
-
-   % ruby cira86_to_nc.rb
-=end
-
-require 'numru/gphys'
-
-#<< read CIRA data >>
-
-file = File.open('../testdata/cira86.dat')
-
-nlat = 17
-nht = 36
-nmon = 12
-cira_miss_val = 999.0
-
-lat, lat_units  = NArray.sfloat(nlat), 'degrees'      # latitude
-ht,  ht_units   = NArray.sfloat(nht), 'km'            # height
-mon, mon_units  = NArray.sfloat(nmon), 'month'        # month
-prs, prs_units  = NArray.sfloat(nht), 'hPa'           # pressure
-temp,temp_units = NArray.sfloat(nht,nlat,nmon), 'K'   # temperature
-gph, gph_units  = NArray.sfloat(nht,nlat,nmon), 'km'  # geopot. height
-west,west_units = NArray.sfloat(nht,nlat,nmon),'m/s'  #eastward(westerly) wind
-
-mon.indgen!.add!(1)      # => 1..12
-lat=(lat.indgen!-8)*10   # => -80,-70,...,80
-
-print "Reading the CIRA86 data file...\n"
-for imon in 0...nmon
-  dummy = file.gets
-  for iht in 0...nht
-    data = file.gets.strip.split(/ +/).collect{|v| v.to_f}
-    ht[iht] = data.shift
-    prs[iht] = data.shift
-    temp[iht,true,imon] = data
-  end
-  dummy = file.gets
-  for iht in 0...nht
-    data = file.gets.strip.split(/ +/).collect{|v| v.to_f}
-    gph[iht,true,imon] = data[2..-1]
-  end
-  dummy = file.gets
-  for iht in 0...nht
-    data = file.gets.strip.split(/ +/).collect{|v| v.to_f}
-    west[iht,true,imon] = data[2..-1]
-  end
-end
-
-temp = temp.transpose(1,0,2)     # => [lat,ht,mon]
-gph  = gph.transpose(1,0,2)      # => [lat,ht,mon]
-west = west.transpose(1,0,2)     # => [lat,ht,mon]
-
-#<< change missing value to a large value >>
-
-gp_miss_val = 2e30
-valid_max = 1e30
-temp[temp.eq(cira_miss_val)] = gp_miss_val
-gph[gph.eq(cira_miss_val)] = gp_miss_val
-west[west.eq(cira_miss_val)] = gp_miss_val
-
-#<< into GPhys >>
-
-include NumRu
-
-lat_ax = Axis.new.set_pos(
-  VArray.new(lat,nil,'lat').set_att('units',lat_units).
-			    set_att('long_name','latitude')
-)
-ht_ax = Axis.new.set_pos(
-  VArray.new(ht,nil,'ht').set_att('units',ht_units).
-			    set_att('long_name','height')
-)
-ht_ax.set_aux('pressure',
-  VArray.new(prs,nil,'prs').set_att('units',prs_units).
-			    set_att('long_name','pressure')
-)
-mon_ax = Axis.new.set_pos(
-  VArray.new(mon,nil,'mon').set_att('units',mon_units).
-			    set_att('long_name','calendar month')
-)
-
-grid = Grid.new(lat_ax, ht_ax, mon_ax)
-
-gp_miss_val = NArray.sfloat(1).fill!(gp_miss_val)
-valid_max = NArray.sfloat(1).fill!(valid_max)
-
-temp_gp = GPhys.new( grid,
-  VArray.new(temp,nil,'temp').set_att('units',temp_units).
-         set_att('long_name','temperature').
-         set_att('valid_max',valid_max).set_att('missing_value',gp_miss_val)
-)
-gph_gp = GPhys.new( grid,
-  VArray.new(gph,nil,'gph').set_att('units',gph_units).
-	 set_att('long_name','geoptential height').
-         set_att('valid_max',valid_max).set_att('missing_value',gp_miss_val)
-)
-west_gp = GPhys.new( grid,
-  VArray.new(west,nil,'west').set_att('units',west_units).
-         set_att('long_name','westerly wind').
-         set_att('valid_max',valid_max).set_att('missing_value',gp_miss_val)
-)
-print "...GPhys created: #{temp_gp.name}, #{gph_gp.name}, #{west_gp.name}\n"
-
-#<<into a NetCDF file>>
-
-ofilename = 'cira86.nc'
-print "Writing into #{ofilename}...\n"
-file = NetCDF.create(ofilename)
-GPhys::NetCDF_IO.write(file,temp_gp)
-GPhys::NetCDF_IO.write(file,gph_gp)
-GPhys::NetCDF_IO.write(file,west_gp)
-file.close
-print "...done\n"

data/sample/druby_cli1.rb

@@ -1,23 +0,0 @@
-# druby_cli1.rb -- a sample dRuby client
-#
-# USAGE
-#   See ./druby_serv1.rb
-
-require "drb/drb"
-require "numru/gphys"
-include NumRu
-
-DRb.start_service
-uri = ARGV.shift || raise("Usage: % #{$0} uri")
-gp = DRbObject.new(nil, uri)
-
-p gp.class, gp.name, gp.rank, gp.length
-p gp.grid.axis(0).pos.name
-
-gps = gp[0,true,true]
-p gps.class, gps.name, gps.rank, gps.length
-p gps.grid.axis(0).pos.name
-
-gpmean = gp[true,true,0].mean(0)
-p gpmean.class, gpmean.name, gpmean.rank, gpmean.length
-p gpmean.grid.axis(0).pos.name

data/sample/druby_cli2.rb

@@ -1,28 +0,0 @@
-# druby_cli2.rb -- a sample dRuby client
-#
-# USAGE
-#   See ./druby_serv2.rb
-
-require "drb/drb"
-require "numru/ggraph"
-include NumRu
-
-DRb.start_service
-uri = ARGV.shift || raise("Usage: % #{$0} uri")
-gp = DRbObject.new(nil, uri)
-
-p gp.class, gp.name, gp.rank, gp.length
-p gp.grid.axis(0).pos.name
-
-gpmean = gp.mean(0)
-p gpmean.class, gpmean.name, gpmean.rank
-
-p ( gpmean_copy = gpmean.copy )
-DCL.gropn(1)
-DCL.sgpset('lfull',true)
-DCL.sgpset('lcntl',false)
-DCL.uzfact(0.7)
-GGraph.set_fig('viewport'=>[0.25,0.7,0.15,0.6], 'itr'=>2 )
-GGraph.contour( gpmean_copy )
-DCL.grcls
-

data/sample/druby_serv1.rb

@@ -1,30 +0,0 @@
-=begin
-=druby_serv1.rb
-
-a sample dRuby server
-
-==USAGE
-
-To start the server:
-
-     % ruby druby_serv1.rb
-
-This will print the address of the server such as
-druby://[hostname]:[port] (For exaple druby://horihost:39391
-
-Then run the client as (if the address is druby://horihost:39391):
-
-     % ruby druby_cli1.rb druby://horihost:39391
-=end
-
-require "drb/drb"
-require "numru/gphys"
-include NumRu
-
-file = NetCDF.open("../testdata/T.jan.nc")
-gp = GPhys::NetCDF_IO.open(file,"T")
-
-DRb.start_service(nil, gp)
-puts 'URI: '+DRb.uri
-puts '[return] to exit'
-gets

data/sample/druby_serv2.rb

@@ -1,51 +0,0 @@
-=begin
-=druby_serv2.rb
-
-a sample dRuby server. The difference from druby_serv1.rb is that
-a couple of methods are added to NArray, which enables us to serialize
-NArray with Marshal.dump. Therefore, a GPhys object can be transferred by 
-value (not by reference) if all the VArray in it is based on NArray.
-This can be done with the copy method of GPhys. See druby_cli2.rb
-for an example.
-
-==USAGE
-
-To start the server:
-
-     % ruby druby_serv2.rb [port]
-
-This will print the address of the server such as
-druby://[hostname]:[port] (For exaple druby://horihost:39391
-
-Then run the client as (if the address is druby://horihost:39391):
-
-     % ruby druby_cli2.rb druby://horihost:39391
-=end
-
-require "drb/drb"
-require "numru/gphys"
-include NumRu
-
-def usage
-  print <<-EOS
-
-  USAGE:
-    % ruby #{$0} [port]
-
-    Here, port (optional) is the port number to assign.
-  EOS
-  raise RuntimeError
-end
-
-port = ARGV.shift
-usage if port && port.to_i.to_s != port
-usage if ARGV.length > 0
-
-file = NetCDF.open("../testdata/T.jan.nc")
-gp = GPhys::NetCDF_IO.open(file,"T")
-
-uri_seed = ( port ? 'druby://:'+port : nil )   # 'druby://:'+port, or nil
-DRb.start_service(uri_seed, gp)
-puts 'URI: '+DRb.uri
-puts '[return] to exit'
-gets