gphys 1.1.1a

data/lib/numru/gphys/gphys_grads_io.rb

@@ -0,0 +1,212 @@
+require "numru/gphys/gphys"
+require "numru/gphys/varraygrads"
+
+=begin
+=module NumRu::GPhys::GrADS_IO
+
+helps read/write GrADS-formatted data
+
+==Module functions
+---is_a_GrADS?(filename)
+    test whether the file is a GrADS control file.
+
+    ARGUMENTS
+    * filename (String): filename to test.
+
+    RETURN VALUE
+    * true/false
+
+---open(file, varname)
+    GPhys constructor from GrADS.
+
+    ARGUMENTS
+    * file (GrADS_Gridded or String): file to read. If string,
+      it must be the name (path) of a GrADS control file. 
+    * varname (String): name of the varible in the file, for which
+      a GPhys object is constructed.
+
+    RETURN VALUE
+    * a GPhys
+
+    EXAMPLE
+    * Suppose that you have a file T.jan.ctl in the currentdirectly,
+      and it contains a variable "T". The following creates a GPhys
+      object representing the variable in the file.
+
+        require "numru/gphys"
+        include GPhys
+        temp = GPhys::GrADS_IO.open("T.jan.ctl","T")
+
+---write(file, gphys, name=nil)
+
+    writes a GPhys object into a GrADS file. -- !!only 4D data is supported!!
+
+---var_names(file)
+    ARGUMENTS
+    * file (GrADS_Gridded or String): if string,
+      it must be the name (path) of a GrADS control file.
+
+    RETURN VALUE
+    * names of variables (Array): this return the names of variables
+      which the file has.
+
+---var_names_except_coordinates(file)
+    same as var_names
+
+=end
+
+module NumRu
+  class GPhys
+
+    module GrADS_IO
+
+      module_function
+
+      def is_a_GrADS?(filename)
+        file = nil
+        begin
+          file = File.open(filename)
+          str = file.read(4)
+        ensure
+          file.close if file
+        end
+        return str=="DSET"
+      end
+
+      def open(file, varname)
+        if file.is_a?(String)
+          file = GrADS_Gridded.open(file)
+        elsif ! file.is_a?(GrADS_Gridded)
+          raise ArgumentError, "1st arg must be a GrADS_Gridded or a file name"
+        end
+
+        grvar = file.var(varname)
+        data = VArrayGrADS.new(grvar)
+
+#        axposnames = [ "lon", "lat", "lev", "time" ]
+        axposnames = [ "x", "y", "z", "t" ]
+        rank = 4
+        bare_index = [ false ] * rank # will be true if coord var is not found
+
+        axes = Array.new
+        for i in 0...rank
+          axpos = VArrayGrADS.new( file.var(axposnames[i]) )[0...data.shape_current[i]]
+
+          cell_center = true
+          cell = false
+
+          axis = Axis.new(cell,bare_index[i])
+          if !cell
+            axis.set_pos( axpos )
+          else
+            if cell_center
+              if varray_cell_bounds
+                axis.set_cell(axpos, varray_cell_bounds).set_pos_to_center
+              else
+                p "cell bounds are guessed"
+                axis.set_cell_guess_bounds(axpos).set_pos_to_center
+              end
+            else  # then it is cell_bounds
+              if varray_cell_center
+                axis.set_cell(varray_cell_center, axpos).set_pos_to_bounds
+              else
+                p "cell center is guessed"
+                axis.set_cell_guess_center(axpos).set_pos_to_bounds
+              end
+            end
+          end
+          
+          #p "yet-to-be-defined: method to define aux coord vars"
+          
+          axes[i] = axis
+        end
+
+        grid = Grid.new( *axes )
+
+        GPhys.new(grid,data)
+      end
+
+      def write(file, gphys, name=nil)
+        if file.is_a?(String)
+          file = GrADS_Gridded.open(file,"w")
+        elsif ! file.is_a?(GrADS_Gridded)
+          raise ArgumentError, "1st arg must be a GrADS_Gridded or a file name"
+        end
+        if( ! file.dset )
+          bfname = file.path.gsub(/\.ctl/,"")+".dat"
+          while( File.exist?(bfname) )
+            bfname = bfname + "_"
+          end
+          file.dset = bfname
+        end
+        VArrayGrADS.write_control(file, gphys)
+        VArrayGrADS.write_binary(file, gphys.data)
+      end
+
+      def var_names(file)
+        opened = false
+        case file
+        when String
+          file = GrADS_Gridded.open(file,"r")
+        when GrADS_Gridded
+          opened = true
+        else
+          raise ArgumentError, "arg must be a GrADS_Gridded or a file name"
+        end
+        var_names = file.var_names
+        file.close unless opened
+        return var_names
+      end
+      def var_names_except_coordinates(file)
+        var_names(file)
+      end
+
+    end
+  end
+end
+
+######################################################
+if $0 == __FILE__
+   include NumRu
+
+   begin
+     file = GrADS_Gridded.open("../../testdata/T.jan.ctl")
+   rescue
+     file = GrADS_Gridded.open("../../../testdata/T.jan.ctl")
+   end
+   temp = GPhys::GrADS_IO.open(file,"T")
+   p temp.name, temp.shape_current
+   temp2 = temp[true,true,2,0]
+   p temp2.name, temp2.shape_current
+
+   temp_xmean = temp.average(0)
+   p temp.val
+
+   temp_edy = ( temp - temp_xmean )
+   p '$$$',temp_edy.name,temp_edy.val[0,true,true,0]
+   p '@@@',temp
+   p '///',temp.copy
+   p '+++',temp2
+
+   puts "\n** test write (tmp.nc) **"
+   require "numru/gphys/gphys_netcdf_io"
+   file2 = NetCDF.create('tmp.nc')
+   p v = temp_edy.axis(0).pos[0..-2].copy.rename('lonlon')
+   temp_edy.axis(0).set_aux('test',v)
+   temp_edy.axis(0).set_aux('test2',(v/2).rename('lonlon2'))
+   temp_edy.axis(0).set_aux('test2',(v/2).rename('lonlon3')[0..-2])
+   GPhys::NetCDF_IO.write(file2,temp_edy)
+   file2.close
+   file3 = NetCDF.create('tmp2.nc')
+   GPhys::NetCDF_IO.write(file3,temp_xmean)
+   file3.close
+
+   puts "\n** test write (tmp.ctl) **"
+   file1 = GrADS_Gridded.create("tmp.ctl")
+   file1.put_att("big_endian",true)
+   file1.put_att("dset","tmp.dr")
+   file1.put_att("title","test control file")
+   file1.put_att("undef",-999.0)
+   GPhys::GrADS_IO.write(file1,temp_edy)
+
+end

data/lib/numru/gphys/gphys_grib_io.rb

@@ -0,0 +1,214 @@
+require "numru/gphys/gphys"
+require "numru/gphys/varraygrib"
+
+=begin
+=module NumRu::GPhys::Grib_IO
+
+helps read Grib-formatted data
+
+==Module functions
+---is_a_Grib? filename)
+    test whether the file is a Grib file.
+
+    ARGUMENTS
+    * filename (String): filename to test.
+
+    RETURN VALUE
+    * true/false
+
+---open(file, varname)
+    GPhys constructor from Grib.
+
+    ARGUMENTS
+    * file (Grib or String): file to read. If string,
+      it must be the name (path) of a Grib file. 
+    * varname (String): name of the varible in the file, for which
+      a GPhys object is constructed.
+
+    RETURN VALUE
+    * a GPhys
+
+    EXAMPLE
+    * Suppose that you have a file temp in the currentdirectly,
+      and it contains a variable "T". The following creates a GPhys
+      object representing the variable in the file.
+
+        require "numru/gphys"
+        include GPhys
+        temp = GPhys::Grib_IO.open("temp","T")
+
+---write(file, gphys, name_dummy=nil)
+
+    Write a GPhys into a Grib file. The whole data under the GPhys 
+    (such as coordinate vars) are written self-descriptively.
+
+    ARGUMENTS
+    * file (Grib): the Grib file to write in. Must be writable of course.
+    * gphys (GPhys): the GPhys to write.
+    * name_dummy (nil) : Unused in this module; Just for consistency with others.
+
+    RETURN VALUE
+    * nil
+
+---var_names(file)
+    ARGUMENTS
+    * file (Grib or String): if string,
+      it must be the name (path) of a Grib file.
+
+    RETURN VALUE
+    * names of variables (Array): this return the names of variables
+      which the file has.
+
+---var_names_except_coordinates(file)
+    * same as var_names
+
+=end
+
+module NumRu
+  class GPhys
+
+    module Grib_IO
+
+      module_function
+
+      def is_a_Grib?(filename)
+        Grib.is_a_Grib?(filename)
+      end
+
+      def open(file, varname)
+        if file.is_a?(String)
+          file = Grib.open(file)
+        elsif ! Grib===file
+          raise ArgumentError, "1st arg must be a Grib or a file name"
+        end
+
+        var = file.var(varname)
+        var.nil? && raise("variable '#{varname}' not found in '#{file.path}'")
+        data = VArrayGrib.new(var)
+
+        rank = data.rank
+        bare_index = [ false ] * rank # will be true if coord var is not found
+
+
+        axes = Array.new
+        var_names = file.var_names
+        for i in 0...rank
+          dim = var.dim(i)
+          val = dim.get
+          if Array===val && val.length!=1
+            bare_index[i] = true
+          end
+          axpos = VArrayGrib.new( dim )
+          cell_center = true
+          cell = false
+
+          axis = Axis.new(cell,bare_index[i])
+          if !cell
+            axis.set_pos( axpos )
+          else
+            if cell_center
+              if varray_cell_bounds
+                axis.set_cell(axpos, varray_cell_bounds).set_pos_to_center
+              else
+                p "cell bounds are guessed"
+                axis.set_cell_guess_bounds(axpos).set_pos_to_center
+              end
+            else  # then it is cell_bounds
+              if varray_cell_center
+                axis.set_cell(varray_cell_center, axpos).set_pos_to_bounds
+              else
+                p "cell center is guessed"
+                axis.set_cell_guess_center(axpos).set_pos_to_bounds
+              end
+            end
+          end
+          if Array===val && val.length!=1
+            val[1..-1].each{|hash|
+              va = 
+	      va = VArray.new(hash["value"],nil,hash["name"])
+	      hash.each{|k,v|
+		next if k=="value"||k=="name"
+		va.put_att(k,v)
+              }
+              axis.set_aux(hash["name"],va)
+            }
+          end
+          
+          #p "yet-to-be-defined: method to define aux coord vars"
+          
+          axes[i] = axis
+        end
+
+        grid = Grid.new( *axes )
+
+        GPhys.new(grid,data)
+      end
+
+      def write(file, gphys, name_dummy=nil)
+        dims = Array.new
+        gphys.rank.times{|n|
+          dims[n] = gphys.coord(n)
+        }
+        VArrayGrib.write(file,gphys.data,dims)
+        nil
+      end
+
+      def var_names(file)
+        opened = false
+        case file
+        when String
+          file = Grib.open(file)
+        when Grib
+          opened = true
+        else
+          raise ArgumentError, "arg must be a Grib or a file name"
+        end
+        var_names = file.var_names
+        file.close unless opened
+        return var_names
+      end
+      def var_names_except_coordinates(file)
+	var_names(file)
+      end
+
+
+    end
+  end
+end
+
+######################################################
+if $0 == __FILE__
+  include NumRu
+  require "numru/gphys/gphys_netcdf_io"
+
+  temp = GPhys::Grib_IO.open("../../../testdata/T.jan.grib","TMP")
+  p temp.name, temp.shape_current
+  temp2 = temp[true,true,2]
+  p temp2.name, temp2.shape_current
+
+  temp_xmean = temp.average(0)
+  p temp.val
+
+  temp_edy = ( temp - temp_xmean )
+  p '$$$',temp_edy.name,temp_edy.val[0,true,true]
+  p '@@@',temp
+  p '///',temp.copy
+  p '+++',temp2
+
+  puts "\n** test convert (T.jan.nc to tmp.grib) **"
+  temp3 = GPhys::NetCDF_IO.open("../../../testdata/T.jan.nc","T")
+  file = Grib.create("tmp.grib")
+  GPhys::Grib_IO.write(file,temp3)
+  file.close
+
+  puts "\n** test compare (T.jan.nc and tmp.grib) **"
+  temp4 = GPhys::Grib_IO.open("tmp.grib","TMP")
+  p temp3.val
+  p temp4.val
+  print "max    => #{temp3.max}, and #{temp4.max}\n"
+  print "min    => #{temp3.min}, and #{temp4.min}\n"
+  print "mean   => #{temp3.mean}, and #{temp4.mean}\n"
+  print "stddev => #{temp3.stddev}, and #{temp4.stddev}\n"
+
+
+end

data/lib/numru/gphys/gphys_gtool3_io.rb

@@ -0,0 +1,162 @@
+require "numru/gphys/gphys"
+require "numru/gphys/varraygtool3"
+
+=begin
+=module NumRu::GPhys::Gtool3_IO
+
+helps read/write Gtool3-formatted data
+
+==Module functions
+---is_a_Gtool3?(filename)
+    test whether the file is a Gtool3 control file.
+
+    ARGUMENTS
+    * filename (String): filename to test.
+
+    RETURN VALUE
+    * true/false
+
+---open(file, varname)
+    GPhys constructor from Gtool3.
+
+    ARGUMENTS
+    * file (Gtool3 or String): file to read. If string,
+      it must be the name (path) of a Gtool3 control file. 
+    * varname (String): name of the varible in the file, for which
+      a GPhys object is constructed.
+
+    RETURN VALUE
+    * a GPhys
+
+    EXAMPLE
+    * Suppose that you have a file T.jan.ctl in the currentdirectly,
+      and it contains a variable "T". The following creates a GPhys
+      object representing the variable in the file.
+
+        require "numru/gphys"
+        include GPhys
+        temp = GPhys::Gtool3_IO.open("T.jan.ctl","T")
+
+#---write(file, gphys, name=nil)
+#
+#    writes a GPhys object into a Gtool3 file. -- !!only 4D data is supported!!
+
+---var_names(file)
+    ARGUMENTS
+    * file (Gtool3 or String): if string,
+      it must be the name (path) of a Gtool3 control file.
+
+    RETURN VALUE
+    * names of variables (Array): this return the names of variables
+      which the file has.
+
+---var_names_except_coordinates(file)
+    same as var_names
+
+=end
+
+module NumRu
+  class GPhys
+
+    module Gtool3_IO
+
+      module_function
+
+      @@default_calendar = nil  #  e.g., "360_day"
+      def default_calendar=(cal)
+        @@default_calendar = cal
+      end
+      def default_calendar
+        @@default_calendar
+      end
+
+      def is_a_Gtool3?(filename)
+        Gtool3.is_a_Gtool3?(filename)
+      end
+
+      def open(file, varname)
+        if file.is_a?(String)
+          file = Gtool3.open(file)
+        elsif ! file.is_a?(Gtool3)
+          raise ArgumentError, "1st arg must be a Gtool3 or a file name"
+        end
+
+        var = file.var(varname)
+        data = VArrayGtool3.new(var)
+
+        axes = Array.new
+        for i in 0...var.rank
+          gax = var.axis(i)
+          gloc = gax["LOC"]
+          if gloc["ITEM"]=="time"
+            loc = VArrayGtool3Time.new(gloc, @@default_calendar)
+          else
+            loc = VArrayGtool3.make_coord(gloc)
+          end
+#          if (gwgt = gax("WGT"))
+#            wgt = VArray.new(gwgt.delete(:val), gwgt, gwgt.delete("ITEM"))
+#            cell_center = true
+#            cell = true
+#          else
+            cell = false
+#          end
+
+          axis = Axis.new(cell,false)
+          if !cell
+            axis.set_pos( loc )
+          end
+          
+          axes[i] = axis
+        end
+
+        grid = Grid.new( *axes )
+
+        GPhys.new(grid,data)
+      end
+
+#      def write(file, gphys, name=nil)
+#      end
+
+      def var_names(file)
+        opened = false
+        case file
+        when String
+          file = Gtool3.open(file,"r")
+        when Gtool3
+          opened = true
+        else
+          raise ArgumentError, "arg must be a Gtool3 or a file name"
+        end
+        var_names = file.var_names
+        file.close unless opened
+        return var_names
+      end
+      def var_names_except_coordinates(file)
+        var_names(file)
+      end
+
+    end
+  end
+end
+
+######################################################
+if $0 == __FILE__
+  include NumRu
+  Gtool3.gtaxdir = File.expand_path("~/dennou/GTAXDIR")
+  file = ARGV[0]
+  varname = ARGV[1] or raise("Need two args")
+
+  gp = GPhys::Gtool3_IO.open(file,varname)
+  GPhys::Gtool3_IO.default_calendar = "360_day"
+
+  p gp 
+  p gp[false,0].val
+  p gp[false,0,0].copy
+  print "\n****\n"
+  gp.att_names.each{|k| print k,"   ",gp.get_att(k),"\n"}
+  print "\n******\n"
+  p gp.coord(0).name
+  gp.coord(0).att_names.each{|k| print k,"   ",gp.get_att(k),"\n"}
+  p gp.coord(-1).name
+  gp.coord(-1).att_names.each{|k| print k,"   ",gp.get_att(k),"\n"}
+end