gentooboontoo-gphys 0.6.1.3 → 1.3.1.1

data/lib/numru/gphys/version.rb

@@ -0,0 +1,3 @@
+class GPhys
+  VERSION = "1.3.1.1"
+end

data/sample/druby_cli1.rb

@@ -4,6 +4,8 @@
 #   See ./druby_serv1.rb
 
 require "drb/drb"
+require "numru/gphys"
+include NumRu
 
 DRb.start_service
 uri = ARGV.shift || raise("Usage: % #{$0} uri")

data/sample/druby_cli2.rb

@@ -17,10 +17,6 @@ p gp.grid.axis(0).pos.name
 gpmean = gp.mean(0)
 p gpmean.class, gpmean.name, gpmean.rank
 
-class NArray
-  def self._load(o) to_na(*Marshal::load(o)).ntoh end
-end
-
 p ( gpmean_copy = gpmean.copy )
 DCL.gropn(1)
 DCL.sgpset('lfull',true)
@@ -30,5 +26,3 @@ GGraph.set_fig('viewport'=>[0.25,0.7,0.15,0.6], 'itr'=>2 )
 GGraph.contour( gpmean_copy )
 DCL.grcls
 
-print "\nThe following will be a DRbObject rather than GPhys since the size is too large\n(see druby_serv2.rb):\n"
-p ( gpcopy = gp.copy )

data/sample/druby_serv2.rb

@@ -41,19 +41,6 @@ port = ARGV.shift
 usage if port && port.to_i.to_s != port
 usage if ARGV.length > 0
 
-class NArray
-  DUMP_SIZE_LIMIT = 5000
-  def self._load(o) to_na(*Marshal::load(o)).ntoh end
-  def _dump(limit) 
-    if size <= DUMP_SIZE_LIMIT
-      Marshal::dump([hton.to_s, typecode, *shape]) 
-    else
-      raise "size of the NArray (#{size}) is too large to dump "+
-            "(limit: #{DUMP_SIZE_LIMIT})"
-    end
-  end
-end
-
 file = NetCDF.open("../testdata/T.jan.nc")
 gp = GPhys::NetCDF_IO.open(file,"T")
 

data/sample/ncep_theta_coord.rb

@@ -0,0 +1,79 @@
+# = Sample program to use GPhys#interpolation by using NCEP reanalysis data
+#
+# USAGE 
+# 
+#   % ruby ncep_theta_coord.rb [data_directory [varname [year [day_of_yr_from0]]]]
+# 
+# COMMAND-LINE OPTIONS
+# 
+# * data_directory : directory where the NCEP data situated -- by default
+#   an existing OPeNDAP directory is specified -- so it should work, 
+#   though it may be slow for network data transfer.
+# * others : you can guess -- see the source code.
+#
+# DESCRIPTION
+#
+# Here are two samples: one is a simple interpolation along a coordinate
+# and the other is a coordinate transformation from pressure to potential
+# temperature (isentropic coordinate).
+ 
+require "numru/ggraph"
+include NumRu
+
+
+dir = ARGV[0] || "http://db-dods.rish.kyoto-u.ac.jp/cgi-bin/nph-dods/ncep/ncep.reanalysis.dailyavgs/pressure"
+
+vname = ARGV[1] || "uwnd"   # name of the variable to be interpolated
+
+year = ARGV[2] || 2008
+iday = ( ARGV[3] || 0 ).to_i  # day of the year
+
+
+xsel = 0
+temp = GPhys::IO.open(dir+"/air.#{year}.nc","air")[xsel,false,2..-1,iday]
+gp = GPhys::IO.open(dir+"/#{vname}.#{year}.nc",vname)[xsel,false,2..-1,iday]
+
+prs = temp.axis("level").to_gphys
+p00 =  UNumeric[1000.0, "millibar"]
+kappa = 2.0 / 7.0
+pfact = (prs/p00)**(-kappa)
+
+theta = temp * pfact
+theta.name = "theta"
+theta.long_name = "potential theta"
+
+gp.set_assoc_coords([theta])
+
+tht_crd = VArray.new( NArray[300.0,350.0, 400.0, 500.0, 700.0, 800.0] ).rename("theta")
+gp_ontht = gp.interpolate("level"=>tht_crd)
+
+p_crd = VArray.new( NArray[25.0, 15.0] ).rename("level")
+p_crd.units = "hPa"
+gp_onp = gp.interpolate(p_crd)   # 1D: same as interpolate("level"=>p_crd)
+
+DCL.swpset('iwidth',800)
+DCL.swpset('iheight',800)
+
+DCL.gropn(1)
+DCL.sgpset('isub', 96)      # control character of subscription: '_' --> '`'
+DCL.glpset('lmiss',true)
+DCL.sldiv('y',2,2)
+
+GGraph::set_fig "itr"=>2
+
+GGraph::tone_and_contour theta[false],true,"int"=>50
+GGraph::color_bar
+
+GGraph::tone_and_contour gp[false],true
+GGraph::color_bar
+
+GGraph::set_fig "itr"=>1
+
+GGraph::tone_and_contour gp_onp[false],true,"keep"=>true
+GGraph::color_bar
+
+GGraph::tone_and_contour gp_ontht[false],true,"keep"=>true
+GGraph::color_bar
+
+
+DCL.grcls

data/test/eof_slp.rb

@@ -0,0 +1,28 @@
+require "numru/gphys"
+require "numru/ganalysis"
+require "numru/ggraph"
+include NumRu
+
+slp = GPhys::IO.open("slp.mon.mean.nc","slp") # ftp://ftp.cdc.noaa.gov/Datasets/ncep.reanalysis.derived/surface/slp.mon.mean.nc
+slp = slp.cut("lat"=>30..90) # 北緯30度以北のデータを使用する
+slp = slp[{0..-1,4},{0..-1,2},true] # 経度, 緯度について4, 2点おきに読む
+                                    # 計算時間を速めるため（∴不要）
+nt = slp.shape[2]
+mon = NArray.sint(12,nt/12).indgen #=> [ [0,1,..,11], [12,13,..,23], .. ]
+mon = mon[[0,1,11],true] # [0,1,11]: Jan,Feb,Dec (use [0] to include only Jan)
+mon = mon.reshape!(mon.total) # to 1D (list of months to use)
+slp = slp[true,true,mon] # 12,1,2月のデータを切取り
+
+vec,val = slp.eof("time","norder"=>2) # EOF第2モードまで計算する
+
+DCL::gropn(4)
+GGraph.set_fig("itr"=>32)
+eof = vec[true,true,0]
+if eof.cut("lat"=>90).mean > 0
+  eof = -eof # 北極における値がが負になるようにする
+end
+GGraph.tone(eof, true, "min"=>-7.0, "max"=>7.0)
+GGraph.contour(eof,false, "min"=>-7.0, "max"=>7.0)
+GGraph.map("coast_world"=>true)
+
+DCL::grcls

data/test/test_multibitIO.rb

@@ -0,0 +1,19 @@
+require "numru/gphys"
+include NumRu
+path = "../mltbit.dat"
+mbio = MultibitIO.new("mltbit.dat")
+
+10000.times{|i|
+ na = mbio.read2D(12, 15, 100,100, 1,9,2, 1,7,3, nil, nil,
+                        nil, nil)
+ p(na) if i==0
+ na = mbio.read2D(12, 15, 100,100, 
+                        nil,nil,nil, 1,5,2, [0,5,3],nil, 0.1, 1000.0)
+ p(na) if i==0
+
+ na = mbio.read2D(12, 15, 100,100, 
+                        nil,nil,nil, nil,nil,nil, [0,5,3],[90,80,5], nil, nil)
+ p(na) if i==0
+}
+
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: gentooboontoo-gphys
 version: !ruby/object:Gem::Version 
-  version: 0.6.1.3
+  version: 1.3.1.1
 platform: ruby
 authors: 
 - Takeshi Horinouchi
@@ -56,7 +56,7 @@ dependencies:
   type: :runtime
   version_requirements: *id004
 - !ruby/object:Gem::Dependency 
-  name: gentooboontoo-ruby-netcdf
+  name: ruby-netcdf
   prerelease: false
   requirement: &id005 !ruby/object:Gem::Requirement 
     requirements: 
@@ -66,15 +66,55 @@ dependencies:
   type: :runtime
   version_requirements: *id005
 - !ruby/object:Gem::Dependency 
-  name: gentooboontoo-ruby-fftw3
+  name: ruby-dcl
   prerelease: false
   requirement: &id006 !ruby/object:Gem::Requirement 
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: "0.4"
+        version: 1.6.1
   type: :runtime
   version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: ruby-fftw3
+  prerelease: false
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0.3"
+  type: :runtime
+  version_requirements: *id007
+- !ruby/object:Gem::Dependency 
+  name: gsl
+  prerelease: false
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "1.14"
+  type: :runtime
+  version_requirements: *id008
+- !ruby/object:Gem::Dependency 
+  name: ruby-lapack
+  prerelease: false
+  requirement: &id009 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "1.5"
+  type: :runtime
+  version_requirements: *id009
+- !ruby/object:Gem::Dependency 
+  name: rb-grib
+  prerelease: false
+  requirement: &id010 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.2.0
+  type: :development
+  version_requirements: *id010
 description: a multi-purpose class to handle Gridded Physical quantities.
 email: 
 - julien.sanchez@gmail.com
@@ -92,49 +132,65 @@ executables:
 - grads2nc_with_gphys
 - gpmath
 - gpcut
-extensions: []
-
+extensions: 
+- ext/extconf.rb
 extra_rdoc_files: []
 
 files: 
 - lib/numru/htdir.rb
-- lib/numru/vizshot.rb
+- lib/numru/ganalysis/covariance.rb
+- lib/numru/ganalysis/planet.rb
+- lib/numru/ganalysis/histogram.rb
+- lib/numru/ganalysis/met.rb
+- lib/numru/ganalysis/eof.rb
 - lib/numru/gphys.rb
 - lib/numru/gdir_connect_ftp-like.rb
 - lib/numru/ggraph_on_merdional_section.rb
 - lib/numru/derivative.rb
+- lib/numru/ganalysis.rb
 - lib/numru/gdir.rb
 - lib/numru/ggraph.rb
-- lib/numru/dclext_datetime_ax.rb
 - lib/numru/gphys/gphys_io_common.rb
 - lib/numru/gphys/unumeric.rb
 - lib/numru/gphys/attributenetcdf.rb
+- lib/numru/gphys/interpolate.rb
 - lib/numru/gphys/gphys_io.rb
 - lib/numru/gphys/grid.rb
 - lib/numru/gphys/gphys_fft.rb
 - lib/numru/gphys/gphys.rb
 - lib/numru/gphys/gphys_grads_io.rb
+- lib/numru/gphys/narray_ext.rb
 - lib/numru/gphys/grib_params.rb
+- lib/numru/gphys/gphys_gtool3_io.rb
 - lib/numru/gphys/gphys_nusdas_io.rb
+- lib/numru/gphys/gphys_hdfeos5_io.rb
 - lib/numru/gphys/coordtransform.rb
 - lib/numru/gphys/varraygrads.rb
 - lib/numru/gphys/grads_gridded.rb
 - lib/numru/gphys/subsetmapping.rb
 - lib/numru/gphys/grib.rb
+- lib/numru/gphys/mdstorage.rb
 - lib/numru/gphys/netcdf_convention.rb
 - lib/numru/gphys/derivative.rb
 - lib/numru/gphys/varraycomposite.rb
 - lib/numru/gphys/coordmapping.rb
 - lib/numru/gphys/varraynetcdf.rb
 - lib/numru/gphys/gphys_netcdf_io.rb
+- lib/numru/gphys/assoccoords.rb
+- lib/numru/gphys/varraygtool3.rb
 - lib/numru/gphys/varraygrib.rb
 - lib/numru/gphys/varraynusdas.rb
 - lib/numru/gphys/gpcommon.rb
 - lib/numru/gphys/ep_flux.rb
 - lib/numru/gphys/gphys_grib_io.rb
+- lib/numru/gphys/varrayhdfeos5.rb
+- lib/numru/gphys/gtool3.rb
 - lib/numru/gphys/varray.rb
 - lib/numru/gphys/attribute.rb
+- lib/numru/gphys/version.rb
 - lib/numru/gphys/axis.rb
+- lib/numru/dclext.rb
+- lib/numru/dcl_mouse.rb
 - bin/gpprint
 - bin/gpcat
 - bin/gplist
@@ -149,6 +205,7 @@ files:
 - bin/gpmath
 - bin/gpcut
 - ChangeLog
+- doc/dclext.html
 - doc/gdir_client.html
 - doc/ggraph.html
 - doc/gphys_grib_io.html
@@ -476,6 +533,11 @@ files:
 - doc/axis.html
 - doc/gdir.html
 - doc/varray.html
+- ext/multibitIO.c
+- ext/interpo.c
+- ext/ext_coord.c
+- ext/ext_init.c
+- LICENSE.txt
 - README
 - sample/ggraph_mapfit-axes_dr002687.rb
 - sample/druby_serv2.rb
@@ -483,19 +545,25 @@ files:
 - sample/ep_flux/demo_NCEP_2.rb
 - sample/ep_flux/demo_NCEP_3.rb
 - sample/ep_flux/demo_NCEP_1.rb
+- sample/ncep_theta_coord.rb
 - sample/druby_cli1.rb
 - sample/druby_serv1.rb
 - sample/map_projection.rb
 - sample/druby_cli2.rb
 - sample/cira86_to_nc.rb
 - test/test_ep_flux.rb
+- test/mltbit.dat
+- test/test_multibitIO.rb
+- test/eof_slp.rb
 - testdata/T.jan.packed.withmiss.nc
 - testdata/T.jan.ctl
 - testdata/T.jan.dat
 - testdata/T.jan.nc
 - testdata/T.jan.grib
 - testdata/UV.jan.nc
+- testdata/assoc_crds.nc
 - testdata/cira86.dat
+- ext/extconf.rb
 homepage: https://github.com/gentooboontoo/gentooboontoo-gphys
 licenses: 
 - Ruby
@@ -525,3 +593,6 @@ specification_version: 4
 summary: GPhys fork compatible with Rubygems
 test_files: 
 - test/test_ep_flux.rb
+- test/mltbit.dat
+- test/test_multibitIO.rb
+- test/eof_slp.rb

data/lib/numru/dclext_datetime_ax.rb

@@ -1,220 +0,0 @@
-require "numru/dcl"
-require "numru/misc"
-require "date"      # needs ruby >= 1.8 for DateTime class
-
-
-module NumRu
-  module DCLExt
-
-    module_function
-
-    @@datetime_ax_options = Misc::KeywordOptAutoHelp.new(
-      ['yax', false, 'true => y-axis, false => x-axis'],
-      ['cside', nil, '"b", "t", "l", "r", nil (=>left/bottom), or false (=>right/top)'],
-      ['dtick1', 1, 'small tick interval in hours'],
-      ['dtick2', nil, 'large tick (with hour labels) interval in hours'],
-      ['year', false, 'true => add year to date label'],
-      ['month', true, 'true => add month to date label']
-    )
-
-    def datetime_ax(date_from, date_to, options=nil)
-      # date_from [a DateTime] : start on this date&time
-      # date_to [a DateTime]   : end on this date&time
-
-      opt = @@datetime_ax_options.interpret(options)
-
-      yax = opt['yax']
-      xax = !yax
-      if xax
-	xy='x'
-      else
-	xy='y'
-      end
-
-      if opt['cside']
-	cside = opt['cside']
-      elsif opt['cside'].nil?
-	if xax
-	  cside='b'
-	else
-	  cside='l'
-	end
-      else
-	if xax
-	  cside='t'
-	else
-	  cside='r'
-	end
-      end
-
-      if opt['year']
-	datefmt = '%Y/%m/%d'
-      elsif opt['month']
-	datefmt = '%m/%d'
-      else
-	datefmt = '%d'
-      end
-
-      # < window parameters >
-
-      ux1,ux2,uy1,uy2 = DCL.sgqwnd
-      if xax
-	u1, u2 = ux1, ux2
-      else
-	u1, u2 = uy1, uy2
-      end
-
-      loffset_save = DCL.uzpget('loffset')
-      xyfact_save = DCL.uzpget(xy+'fact')
-      xyoffset_save = DCL.uzpget(xy+'offset')
-
-      tu1 = date_from.day_fraction.to_f
-      range_day = date_to - date_from    # time btwn start and end (in days)
-      tu2 = tu1 + range_day
-
-      # < axis in hours >
-
-      DCL.uzpset('loffset',true)
-
-      DCL.uzpset(xy+'fact',24.0)
-      DCL.uzpset(xy+'offset',(tu1-u1)*24)
-
-      dtick1 = opt['dtick1']
-      if opt['dtick2']
-	dtick2 = opt['dtick2']
-      else
-	if range_day >= 4
-	  dtick2 = 24
-	elsif range_day >= 2
-	  dtick2 = 12
-	elsif range_day >= 1
-	  dtick2 = 6
-	elsif range_day >= 0.5
-	  dtick2 = 3
-	elsif range_day >= 0.25
-	  dtick2 = 2
-	else
-	  dtick2 = 1
-	end
-      end
-
-      str_hour = (tu1*24).ceil
-      end_hour = (tu2*24).floor
-      tick1=Array.new
-      tick2=Array.new
-      labels=Array.new
-      h1 = str_hour + (-str_hour % dtick1)
-      (h1..end_hour).step(dtick1){|i| tick1.push(i)}
-      h2 = str_hour + (-str_hour % dtick2)
-      (h2..end_hour).step(dtick2) do |i|
-	tick2.push(i)
-	labels.push((i%24).to_s)
-      end
-      if xax
-	DCL.uxaxlb(cside, tick1, tick2, labels, 2)
-      else
-	irotl_save = DCL.uzpget('irotly'+cside)
-	icent_save = DCL.uzpget('icenty'+cside)
-	DCL.uzpset('irotly'+cside,1)
-	DCL.uzpset('icenty'+cside,0)
-	DCL.uyaxlb(cside, tick1, tick2, labels, 2)
-      end
-
-      # < labels in days >
-
-      if DCL.uzpget('label'+xy+cside)
-	DCL.uzpset(xy+'fact',1.0)
-	DCL.uzpset(xy+'offset',0.0)
-
-	str_day = tu1.floor
-	end_day = tu2.floor
-	pos=Array.new
-	labels=Array.new
-	(str_day..end_day).step(1) do |i|
-	  u = i.to_f + 0.5 + (u1- tu1)
-	  u = (u1+u+0.5)/2 if u < u1
-	  u = (u2+u-0.5)/2 if u > u2
-	  pos.push(u)
-	  str = (date_from+i).strftime(datefmt)
-	  str.sub!(/^0/,'') if !opt['year'] && opt['month']
-	  labels.push(str)
-	end
-
-        if xax
-	  DCL.uxsaxz(cside,DCL.uzpget('roffx'+cside))
-	  DCL.uxplbl(cside,1,pos,labels,10)
-	else
-	  DCL.uysaxz(cside,DCL.uzpget('roffy'+cside))
-	  DCL.uyplbl(cside,1,pos,labels,10)
-	#  DCL.uzpset('irotly'+cside,irotl_save)
-	#  DCL.uzpset('icenty'+cside,icent_save)
-	end
-
-      end
-
-      if xax
-      else
-	DCL.uzpset('irotly'+cside,irotl_save)
-	DCL.uzpset('icenty'+cside,icent_save)
-      end
-
-      # < to finish >
-
-      DCL.uzpset('loffset',loffset_save)
-      DCL.uzpset(xy+'fact',xyfact_save)
-      DCL.uzpset(xy+'offset',xyoffset_save)
-
-    end
-  end
-end
-
-
-######## test program ######
-
-if $0 == __FILE__
-  
-  include NumRu
-
-  iws = (ARGV[0] || (puts ' WORKSTATION ID (I)  ? ;'; DCL.sgpwsn; gets)).to_i
-  DCL.swpset('ldump',true) if iws==4
-  DCL.gropn iws
-  DCL.sldiv('y',2,1)
-  
-  date_from = DateTime.parse('2005-06-30 17:00')
-  date_to = DateTime.parse('2005-07-01 5:00')
-  date_from2 = DateTime.parse('2005-06-29 17:00')
-  date_to2 = DateTime.parse('2005-07-02 5:00')
-
-  any_offst = 10
-
-  DCL.grfrm
-  DCL.grswnd(0.0, date_to-date_from, any_offst, date_to2-date_from2+any_offst)
-  DCL.grsvpt(0.2, 0.8, 0.2, 0.8)
-  DCL.grstrn(1)
-  DCL.grstrf
-  DCLExt.datetime_ax(date_from,  date_to,                 'year'=>true)
-  DCLExt.datetime_ax(date_from,  date_to, 'cside'=>'t',   'year'=>true)
-  DCLExt.datetime_ax(date_from2, date_to2, 'yax'=>true)
-  DCLExt.datetime_ax(date_from2, date_to2, 'yax'=>true, 'cside'=>'r')
-  DCL.uxsttl('b','TIME AND DATE',0.0)
-  DCL.uysttl('l','TIME AND DATE',0.0)
-
-  DCL.grfrm
-  DCL.grswnd(0.0, date_to-date_from, 0, date_to2-date_from2)
-  DCL.grsvpt(0.2, 0.8, 0.2, 0.8)
-  DCL.grstrn(1)
-  DCL.grstrf
-  DCL.uzpset('inner',-1)
-  DCLExt.datetime_ax(date_from,  date_to,               'dtick2'=>2)
-  DCLExt.datetime_ax(date_from,  date_to, 'cside'=>'t', 'dtick2'=>2)
-  DCL.uzpset('inner',1)
-  DCLExt.datetime_ax(date_from2, date_to2, 'yax'=>true, 
-                     'dtick1'=>2, 'dtick2'=>24)
-  DCLExt.datetime_ax(date_from2, date_to2, 'yax'=>true, 'cside'=>'r',
-                     'dtick1'=>2, 'dtick2'=>24)
-  DCL.uxsttl('b','TIME AND DATE',0.0)
-  DCL.uysttl('l','TIME AND DATE',0.0)
-
-  DCL.grcls
-
-end