cdo 1.0.2 → 1.0.3

data/ChangeLog

@@ -1,3 +1,7 @@
 1.0.0 2011-12-14: initial version 
 1.0.1 2011-12-15: bugix release
 1.0.2 2012-01-11: return NetCDF/NArray (optional)
+1.0.3 2012-01-17: bugfix for NArray return values
+		  remove chainCall method - can be replaced by setting :in
+		  speed up by reuse operator list instead of computing it
+		  every time

data/gemspec

@@ -2,7 +2,7 @@ require 'rubygems'
 
 spec = Gem::Specification.new do |s|
   s.name              = "cdo"
-  s.version           = '1.0.2'
+  s.version           = '1.0.3'
   s.platform          = Gem::Platform::RUBY
   s.files             = ["lib/cdo.rb"] + ["gemspec","COPYING","README.rdoc","ChangeLog"]
   s.test_file         = "test/test_cdo.rb"

data/lib/cdo.rb

@@ -16,15 +16,35 @@ require 'pp'
 # CDO calling mechnism
 module Cdo
   State = {
-    :debug => false,
-    :returnArray => false
+    :debug       => false,
+    :returnArray => false,
+    :operators   => []
   }
   @@CDO = ENV['CDO'].nil? ? '/usr/bin/cdo' : ENV['CDO']
 
-  # Only operators with documentation are accessible vie the build-in help.
-  # Other have to be added manually
-  @@undocumentedOperators = %w[geopotheight pressure_fl pressure_hl]
-  @@addOperators          = %w[boundaryLevels thicknessOfLevels]
+  # Since cdo-1.5.4 undocumented operators are given with the -h option. For
+  # earlier version, they have to be provided manually
+  @@undocumentedOperators = %w[anomaly beta boxavg change_e5lsm change_e5mask
+    change_e5slm chisquare chvar cloudlayer cmd com command complextorect
+    covar0 covar0r daycount daylogs del29feb delday delete deltap deltap_fl
+    delvar diffv divcoslat dumplogo dumplogs duplicate eca_r1mm enlargegrid
+    ensrkhistspace ensrkhisttime eof3d eof3dspatial eof3dtime export_e5ml
+    export_e5res fc2gp fc2sp fillmiss fisher fldcovar fldrms fourier fpressure
+    gather gengrid geopotheight ggstat ggstats globavg gp2fc gradsdes
+    gridverify harmonic hourcount hpressure ifs2icon import_e5ml import_e5res
+    import_obs imtocomplex infos infov interpolate intgrid intgridbil
+    intgridtraj intpoint isosurface lmavg lmean lmmean lmstd log lsmean
+    meandiff2test mergegrid mod moncount monlogs mrotuv mrotuvb mulcoslat ncode
+    ncopy nmltest normal nvar outputbounds outputboundscpt outputcenter
+    outputcenter2 outputcentercpt outputkey outputtri outputvector outputvrml
+    pardup parmul pinfo pinfov pressure_fl pressure_hl read_e5ml remapcon1
+    remapdis1 retocomplex scalllogo scatter seascount select selgridname
+    seloperator selvar selzaxisname setrcaname setvar showvar sinfov smemlogo
+    snamelogo sort sortcode sortlevel sortname sorttaxis sorttimestamp sortvar
+    sp2fc specinfo spectrum sperclogo splitvar stimelogo studentt template1
+    template2 test test2 testdata thinout timcount timcovar tinfo transxy trms
+    tstepcount vardes vardup varmul varquot2test varrms vertwind write_e5ml
+    writegrid writerandom yearcount]
 
   private
   def Cdo.call(cmd)
@@ -48,34 +68,38 @@ module Cdo
     end
     cmd << "#{ofile}"
     call(cmd)
-    if State[:returnArray] or returnArray
+    if returnArray or State[:returnArray]
+      Cdo.loadCdf unless State[:returnArray]
       return NetCDF.open(ofile)
     else
       return ofile
     end
   end
+  def Cdo.loadCdf
+    begin
+      require "numru/netcdf"
+      include NumRu
+    rescue LoadError
+      warn "Could not load ruby's netcdf bindings. Please install it."
+      raise
+    end
+  end
 
   public
-  def Cdo.Debug=(value)
+  def Cdo.debug=(value)
     State[:debug] = value
   end
-  def Cdo.Debug
+  def Cdo.debug
     State[:debug]
   end
-  def Cdo.returnArray=(value)
+  def Cdo.setReturnArray(value=true)
     if value
-      begin
-        require "numru/netcdf"
-        include NumRu
-        State[:returnArray] = true
-
-      rescue LoadError
-        warn "Could not load ruby's netcdf bindings. Please install it."
-        raise
-      end
-    else
-      State[:returnArray] = value
+      Cdo.loadCdf
     end
+    State[:returnArray] = value
+  end
+  def Cdo.unsetReturnArray
+    setReturnArray(false)
   end
   def Cdo.returnArray
     State[:returnArray]
@@ -92,44 +116,30 @@ module Cdo
     end
   end
   def Cdo.setCdo(cdo)
-    puts "Will use #{cdo} instead of #@@CDO" if Cdo.Debug
+    puts "Will use #{cdo} instead of #@@CDO" if Cdo.debug
     @@CDO = cdo
+    Cdo.getOperators(true)
   end
 
-  def Cdo.getOperators
+  def Cdo.getOperators(force=false)
+    # Do NOT compute anything, if it is not required
+    return State[:operators] unless (State[:operators].empty? or force)
+
     cmd       = @@CDO + ' 2>&1'
     help      = IO.popen(cmd).readlines.map {|l| l.chomp.lstrip}
     if 5 >= help.size
       warn "Operators could not get listed by running the CDO binary (#{@@CDO})"
-      pp help if Cdo.Debug
+      pp help if Cdo.debug
       exit
-    else
-      help[help.index("Operators:")+1].split
-    end
-  end
-
-  # Call an operator chain without checking opeartors
-  def Cdo.chainCall(chain,*args)
-    io = args.find {|a| a.class == Hash}
-    args.delete_if {|a| a.class == Hash}
-
-    chain   = chain.strip
-    firstOp = chain
-    firstOp = chain[0...[chain.index(','),chain.index(' ')].min] unless chain.index(',').nil?
-    firstOp = firstOp[1..-1] if firstOp[0] == '-'
-    if /(info|show|griddes)/.match(firstOp)
-      Cdo.run(" #{chain} #{io[:in]} ",$stdout)
-    else
-      opts = args.empty? ? '' : ',' + args.reject {|a| a.class == Hash}.join(',')
-      Cdo.run(" #{chain}#{opts} #{io[:in]} ",io[:out],io[:options])
     end
+    State[:operators] = (help[help.index("Operators:")+1].split + @@undocumentedOperators).uniq
   end
 
   def Cdo.method_missing(sym, *args, &block)
     # args is expected to look like [opt1,...,optN,:in => iStream,:out => oStream] where
     # iStream could be another CDO call (timmax(selname(Temp,U,V,ifile.nc))
     puts "Operator #{sym.to_s} is called" if State[:debug]
-    if getOperators.include?(sym.to_s) or @@undocumentedOperators.include?(sym.to_s)
+    if getOperators.include?(sym.to_s)
       io = args.find {|a| a.class == Hash}
       args.delete_if {|a| a.class == Hash}
       if /(diff|info|show|griddes)/.match(sym)
@@ -160,7 +170,7 @@ module Cdo
     bound_levels = Cdo.boundaryLevels(args)
     delta_levels    = []
     bound_levels.each_with_index {|v,i| 
-      next if i == 0
+      next if 0 == i
       delta_levels << v - bound_levels[i-1]
     }
     delta_levels
@@ -172,6 +182,7 @@ module MyTempfile
   require 'tempfile'
   @@_tempfiles           = []
   @@persistent_tempfiles = false
+  @@N                    = 10000000
   def MyTempfile.setPersist(value)
     @@persistent_tempfiles = value
   end
@@ -181,7 +192,7 @@ module MyTempfile
       @@_tempfiles << t
       t.path
     else
-      t = "_"+rand(10000000).to_s
+      t = "_"+rand(@@N).to_s
       @@_tempfiles << t
       t
     end

data/test/test_cdo.rb

@@ -28,9 +28,12 @@ class TestCdo < Test::Unit::TestCase
   end
 
   def test_getOperators
-    %w[for random stdatm info showlevel sinfo remap mask topo thicknessOfLevels].each {|op|
-      assert(Cdo.getOperators.include?(op),"Operator '#{op}' not found") unless op == "thicknessOfLevels"
-      assert(Cdo.respond_to?(op),"Operator '#{op}' not found") if op == "thicknessOfLevels"
+    %w[for random stdatm info showlevel sinfo remap geopotheight mask topo thicknessOfLevels].each {|op|
+      if ["thicknessOfLevels"].include?(op)
+        assert(Cdo.respond_to?(op),"Operator '#{op}' not found")
+      else
+        assert(Cdo.getOperators.include?(op))
+      end
     }
   end
   def test_info
@@ -39,7 +42,6 @@ class TestCdo < Test::Unit::TestCase
 
     info = Cdo.sinfo(:in => "-stdatm,0")
     assert_equal("File format: GRIB",info[0])
-
   end
   def test_args
     #Cdo.Debug = true
@@ -73,7 +75,7 @@ class TestCdo < Test::Unit::TestCase
   def test_chain
     ofile     = MyTempfile.path
     #Cdo.Debug = true
-    Cdo.chainCall("-setname,veloc -copy",:in => "-random,r1x1",:out => ofile,:options => "-f nc")
+    Cdo.setname('veloc',:in => " -copy -random,r1x1",:out => ofile,:options => "-f nc")
     assert_equal(["veloc"],Cdo.showname(:in => ofile))
   end
 
@@ -94,25 +96,26 @@ class TestCdo < Test::Unit::TestCase
                  Cdo.thicknessOfLevels(:in => ofile))
   end
 
-  def test_returnArray
-    ofile = MyTempfile.path
-    vals = Cdo.stdatm(25,100,250,500,875,1400,2100,3000,4000,5000,:out => ofile,:options => "-f nc")
-    assert_equal(ofile,vals)
-    Cdo.returnArray = true
-    vals = Cdo.stdatm(25,100,250,500,875,1400,2100,3000,4000,5000,:out => ofile,:options => "-f nc")
-    assert_equal(["lon","lat","level","P","T"],vals.var_names)
-    assert_equal(276,vals.var("T").get.flatten.mean.floor)
-    Cdo.returnArray = false
-  end
   def test_combine
     ofile0, ofile1 = MyTempfile.path, MyTempfile.path
     Cdo.fldsum(:in => Cdo.stdatm(25,100,250,500,875,1400,2100,3000,4000,5000,:options => "-f nc"),:out => ofile0)
     ofile1 = Cdo.fldsum(:in => "-stdatm,25,100,250,500,875,1400,2100,3000,4000,5000",:options => "-f nc")
-    Cdo.returnArray = true
+    Cdo.setReturnArray(true)
     diff = Cdo.sub(:in => [ofile0,ofile1].join(' '),:out => MyTempfile.path).var('T').get
     assert_equal(0.0,diff.min)
     assert_equal(0.0,diff.max)
-    Cdo.returnArray = false
+    Cdo.setReturnArray(false)
+  end
+
+  def test_returnArray
+    ofile = MyTempfile.path
+    vals = Cdo.stdatm(25,100,250,500,875,1400,2100,3000,4000,5000,:out => ofile,:options => "-f nc")
+    assert_equal(ofile,vals)
+    Cdo.setReturnArray
+    vals = Cdo.stdatm(25,100,250,500,875,1400,2100,3000,4000,5000,:out => ofile,:options => "-f nc")
+    assert_equal(["lon","lat","level","P","T"],vals.var_names)
+    assert_equal(276,vals.var("T").get.flatten.mean.floor)
+    Cdo.unsetReturnArray
   end
   def test_simple_returnArray
     ofile0, ofile1 = MyTempfile.path, MyTempfile.path
@@ -121,6 +124,26 @@ class TestCdo < Test::Unit::TestCase
     assert_equal(1013.25,sum.min)
     test_returnArray
   end
+
+  def test_thickness
+    levels            = "25 100 250 500 875 1400 2100 3000 4000 5000".split
+    targetThicknesses = [50.0,  100.0,  200.0,  300.0,  450.0,  600.0,  800.0, 1000.0, 1000.0, 1000.0]
+    assert_equal(targetThicknesses, Cdo.thicknessOfLevels(:in => "-selname,T -stdatm,#{levels.join(',')}"))
+  end
+
+  if 'thingol' == `hostname`.chomp  then
+    def test_verticalLevels
+      iconpath = "/home/ram/src/git/icon/grids"
+      # check, if a given input files has vertival layers of a given thickness array
+      targetThicknesses = [50.0,  100.0,  200.0,  300.0,  450.0,  600.0,  800.0, 1000.0, 1000.0, 1000.0]
+      ifile = [iconpath,"ts_phc_annual-iconR2B04-L10_50-1000m.nc"].join('/')
+      assert_equal(["25 100 250 500 875 1400 2100 3000 4000 5000",
+                   "25 100 250 500 875 1400 2100 3000 4000 5000"],Cdo.showlevel(:in => ifile))
+      thicknesses = Cdo.thicknessOfLevels(:in => ifile)
+      assert_equal(targetThicknesses,thicknesses)
+    end
+  end
+
 end
 
 #  # Calling simple operators
@@ -162,12 +185,6 @@ end
 #             end
 #  Cdo.send(operator,var,:in => @ifile, :out => varfile)
 #  
-#  # For chaining operators, there is a special method:
-#  Cdo.chainCall("-setname,veloc -copy",:in => ifile,:out => ofile,:options => "-f nc")
-#  #   another example with 3 operators and a different hash syntax
-#  C_R          = 287.05
-#  Cdo.chainCall("setname,#{rho} -divc,#{C_R} -div",in: [pressureFile,temperatureFile].join(' '), out: densityFile)
-#  
 #  # Pass an array for operators with multiple options:
 #  #   Perform conservative remapping with pregenerated weights
 #  Cdo.remap([gridfile,weightfile],:in => copyfile,:out => outfile)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cdo
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-11 00:00:00.000000000 Z
+date: 2012-01-17 00:00:00.000000000 Z
 dependencies: []
 description: Easy access to the Climate Data operators
 email: stark.dreamdetective@gmail.com