gphys 1.1.1 → 1.2.2

data/lib/numru/gphys/assoccoords.rb

@@ -55,18 +55,34 @@ module NumRu
       @groups = Hash.new    # axnames => assoc coord names
       assoc_crds.each do |gp|
         pushed = false
+        axnames_sv = acnames_sv = nil
         @groups.each do | axnames, acnames |
           a = gp.axnames
           if (axnames - a).length < axnames.length   # included?
-            axnames.concat(a).uniq!
-            acnames.push(gp.name)
+            unless pushed
+              # first time in this loop
+              axnames.concat(a).uniq!
+              acnames.push(gp.name)
+              axnames_sv = axnames
+              acnames_sv = acnames
+            else
+              # second or greater time in this loop --> need merger to the first
+              @groups.delete(axnames)
+              axnames_sv.concat(axnames).uniq!
+              acnames_sv.concat(acnames).uniq!
+            end
             pushed = true
-            break
+            #break  # <-- old code; this doesn't work
           end
         end
         @groups[ gp.axnames ] = [gp.name] if !pushed  # new group
       end
 
+      # < sort keys in @groups in the order of original axes >
+      # -- though its necesity was not originally supposed, but...
+      @groups.each_key do |axnames|
+        axnames.replace( @axnames - (@axnames - axnames) )
+      end
     end
 
     attr_reader :assoc_crds, :axnames, :axlens

data/lib/numru/gphys/axis.rb

@@ -823,7 +823,7 @@ module NumRu
       end
 
       def cyclic_extendible?
-	@pos.axis_cyclic?
+	@pos.axis_cyclic_extendible?
       end
 
       #########  private methods ####################################

data/lib/numru/gphys/coordmapping.rb

@@ -278,9 +278,9 @@ if $0 == __FILE__
    puts "<<forward>>"
    p p,q,r
    puts "<<inverse>>"
-   p *mp.inverse_map(p,q,r)
+   p( *mp.inverse_map(p,q,r))
    puts "<<map grid>>"
    x = y = NArray[0.0, 1.0]
    z = NArray[0.0,1.0,2.0]
-   p *mp.map_grid(x,y,z)
+   p( *mp.map_grid(x,y,z))
 end

data/lib/numru/gphys/derivative.rb

@@ -82,6 +82,9 @@ module NumRu
     def threepoint_O2nd_deriv(*args)
       Derivative::threepoint_O2nd_deriv(self,*args)
     end
+    def deriv2nd(*args)
+      Derivative::deriv2nd(self,*args)
+    end
 
     module Derivative
 
@@ -93,15 +96,19 @@ module NumRu
 
       module_function
 
-      def threepoint_O2nd_deriv(gp, dim, bc=LINEAR_EXT, altcoord=nil)
-        __deriv(gp, dim, bc, altcoord, "threepoint_O2nd_deriv")
+      def threepoint_O2nd_deriv(gp, dim, bc=CYCLIC_OR_LINEAR, altcoord=nil)
+        __deriv(gp, dim, bc, altcoord, "threepoint_O2nd_deriv",1)
+      end
+
+      def cderiv(gp, dim, bc=CYCLIC_OR_LINEAR, altcoord=nil)
+        __deriv(gp, dim, bc, altcoord, "cderiv",1)
       end
 
-      def cderiv(gp, dim, bc=LINEAR_EXT, altcoord=nil)
-        __deriv(gp, dim, bc, altcoord, "cderiv")
+      def deriv2nd(gp, dim, bc=CYCLIC_OR_LINEAR, altcoord=nil)
+        __deriv(gp, dim, bc, altcoord, "deriv2nd",2)
       end
 
-      def __deriv(gp,dim,bc, altcoord, dtype="cderiv")
+      def __deriv(gp,dim,bc, altcoord, dtype="cderiv", deriv_order=1)
         if bc == CYCLIC_OR_LINEAR
           bc = ( gp.axis(dim).cyclic_extendible? ? CYCLIC_EXT : LINEAR_EXT )
         end
@@ -127,22 +134,39 @@ module NumRu
           n_dgpdx = NumRu::Derivative::cderiv(n_data,n_x,dim,bc)
         when "threepoint_O2nd_deriv"
           n_dgpdx = NumRu::Derivative::threepoint_O2nd_deriv(n_data,n_x,dim,bc) 
+        when "deriv2nd"
+          n_dgpdx = NumRu::Derivative::deriv2nd(n_data,n_x,dim,bc)
         else
           raise ArgumentError, "Unsupported derivative type :'#{dtype}'"
         end
-        name = "d#{gp.name}_d#{v_x.name}"                      # ex. "dT_dx"
-	v_dgpdx = VArray.new(n_dgpdx, gp.data, name)           # make varray 
+        case deriv_order
+        when 1
+          name = "d#{gp.name}_d#{v_x.name}"                      # ex. "dT_dx"
+        when 2
+          name = "d2#{gp.name}_d#{v_x.name}2"                   # ex. "d2T_dx2"
+        end
+ 	v_dgpdx = VArray.new(n_dgpdx, gp.data, name)           # make varray 
 	g_dgpdx = GPhys.new( gp.grid_copy, v_dgpdx )           # make gphys 
 
         # <<set attribute>>
 	u_data = v_data.units
         u_x = v_x.units
-	g_dgpdx.units = u_data/u_x                             # set units
-	if v_data.get_att('long_name') && v_x.get_att('long_name')
-	  long_name = "d_#{v_data.get_att('long_name')}_d_#{v_x.get_att('long_name')}"
-	else
-	  long_name = name
-	end
+        case deriv_order
+        when 1
+          g_dgpdx.units = u_data/u_x                             # set units
+          if v_data.get_att('long_name') && v_x.get_att('long_name')
+            long_name = "d_#{v_data.get_att('long_name')}_d_#{v_x.get_att('long_name')}"
+          else
+            long_name = name
+          end
+        when 2
+          g_dgpdx.units = u_data/u_x**2                         # set units
+          if v_data.get_att('long_name') && v_x.get_att('long_name')
+            long_name = "d2(#{v_data.get_att('long_name')})_d(#{v_x.get_att('long_name')})2"
+          else
+            long_name = name
+          end
+        end
 	g_dgpdx.data.set_att("long_name",long_name)            # set long_name
 	return g_dgpdx
       end
@@ -277,6 +301,20 @@ if $0 == __FILE__
     show_attr(gp, deriv)
   end
 
+  def test5(x1, dim_or_dimname)
+    f1 = sin(x1)
+    gp1 = make_gp1D(f1, x1)
+    deriv = GPhys::Derivative::deriv2nd(gp1, dim_or_dimname)
+    dfdx1 = deriv.data.val
+    dfdx2 = -sin(x1)
+    p(dfdx1) if $VERBOSE
+    diff = (dfdx1 - dfdx2)[1..-2].abs
+    err = diff.mean
+    print "dfdx - kaiseki_kai (except boundary): "
+    print err, "\t", diff.max,"\n"
+    err
+  end
+
   ## main routine of test ---------------------------------------------
 
   [0, "lon"].each do |dim|
@@ -303,6 +341,11 @@ if $0 == __FILE__
     er2 = test2( gen_z2(21), dim )
     print "error change from nx=11->21: ", er2/er1,"\n"
 
+    print "**** equally spaced grid (2nd deriv) ****\n"
+    er1 = test5( gen_x(11), dim )
+    er2 = test5( gen_x(21), dim )
+    print "error change from nx=11->21: ", er2/er1,"\n"
+    
   end
   
   print "**************      multi-D     *************\n"

data/lib/numru/gphys/gphys.rb

@@ -409,7 +409,13 @@
     ((|You know what it is.|))
 
 ---shape_coerce(other)
-    Like ((<coerce>)), but just changes shape without changing numeric type.
+    Like ((<coerce>)), but just changes shape without changing numeric type
+    by possibly inserting dimensions whose lengths are one (i.e.,
+    without changeing the total length of data).
+
+---shape_coerce_full(other)
+    Similar to ((<shape_coerce>)) but to return the gphyses having  
+    really the same shape with possible expansion by replication.
 
 ---transpose(*dims)
     Transpose.
@@ -767,6 +773,16 @@ module NumRu
 	 end
       end
 
+      def shape_coerce_full(other)
+        o, s = shape_coerce(other)
+        if o.length < s.length
+          o = GPhys.new( s.grid, o + NArray.new(o.typecode,*s.shape) )
+        elsif o.length > s.length
+          s = GPhys.new( o.grid, s + NArray.new(s.typecode,*o.shape) )
+        end
+        [o, s]
+      end
+
       def transpose(*dims)
 	grid = @grid.transpose(*dims)
 	data = @data.transpose(*dims)

data/lib/numru/gphys/gphys_grads_io.rb

@@ -80,17 +80,18 @@ module NumRu
           raise ArgumentError, "1st arg must be a GrADS_Gridded or a file name"
         end
 
-        grvar = file.var(varname)
+        grvar = GrADSVar.new(file,varname,true,false)
         data = VArrayGrADS.new(grvar)
 
-#        axposnames = [ "lon", "lat", "lev", "time" ]
-        axposnames = [ "x", "y", "z", "t" ]
-        rank = 4
+        shape_current = grvar.shape_current
+        dimnames = grvar.dim_names
+        rank = dimnames.length
         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]]
+          grvar = GrADSVar.new(file,dimnames[i],false,true)
+          axpos = VArrayGrADS.new(grvar)[0...shape_current[i]]
 
           cell_center = true
           cell = false

data/lib/numru/gphys/gphys_grib_io.rb

@@ -72,13 +72,13 @@ module NumRu
       module_function
 
       def is_a_Grib?(filename)
-        Grib.is_a_Grib?(filename)
+        VArrayGrib.grib.is_a_Grib?(filename)
       end
 
       def open(file, varname)
         if file.is_a?(String)
-          file = Grib.open(file)
-        elsif ! Grib===file
+          file = VArrayGrib.grib.open(file)
+        elsif ! VArrayGrib.grib===file
           raise ArgumentError, "1st arg must be a Grib or a file name"
         end
 
@@ -157,8 +157,8 @@ module NumRu
         opened = false
         case file
         when String
-          file = Grib.open(file)
-        when Grib
+          file = VArrayGrib.grib.open(file)
+        when VArrayGrib.grib
           opened = true
         else
           raise ArgumentError, "arg must be a Grib or a file name"
@@ -197,7 +197,7 @@ if $0 == __FILE__
 
   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")
+  file = VArrayGrib.grib.create("tmp.grib")
   GPhys::Grib_IO.write(file,temp3)
   file.close
 

data/lib/numru/gphys/gphys_io.rb

@@ -61,11 +61,11 @@ For example, (('GPhys::IO.open(file, name)')) simply calls
 ---parse_gturl(gturl)
     Parses GTOOL4-type URLs to specify path, variable name,
     and optionally subsets, whose format is 
-    (('path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'))
+    (('path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'))
 
     ARGUMENTS
     * gturl (String) GTOOL4 URL, whose format is
-      (('path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'))
+      (('path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]'))
 
     RETURN VALUES
     * An Array consisting of [file, var, slice, cut_slice, thinning], where
@@ -116,6 +116,15 @@ module NumRu
     module IO
       module_function
 
+      ## switches for io libraries
+      # switch grib library
+      def use_gphys_grib
+        VArrayGrib.use_gphys_grib
+      end
+      def use_rb_grib
+        VArrayGrib.use_rb_grib
+      end
+
       ## // module functions to be defined in specific IO modules -->
       def open(file, varname)
 	file2specific_module(file)::open(file, varname)
@@ -158,9 +167,16 @@ module NumRu
                      GTOOL3 => GPhys::Gtool3_IO}
       @@file_class = {NETCDF => NetCDF,
                      GRADS => GrADS_Gridded,
-                     GRIB => Grib,
+                     #GRIB => VArrayGrib.grib, # Hash is not dynamic: see below
                      NUSDAS => NuSDaS,
                      GTOOL3 => Gtool3}
+      def @@file_class.[](key)
+        if key == GRIB
+          VArrayGrib.grib
+        else
+          super
+        end
+      end
       @@nc_pattern = [/\.nc$/]
       @@grad_pattern = [/\.ctl$/]
       @@grib_pattern = [/\.grib$/, /\.grb$/]
@@ -181,7 +197,7 @@ module NumRu
 	  return NETCDF
 	when GrADS_Gridded
 	  return GRADS
-	when Grib
+	when VArrayGrib.grib
 	  return GRIB
         when NuSDaS
           return NUSDAS
@@ -260,14 +276,17 @@ module NumRu
         file2specific_module(file).var_names_except_coordinates(file)
       end
 
-      GTURLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+      GTURLfmt = "path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
 
       def parse_gturl(gturl)
 	if /(.*)@(.*)/ =~ gturl
 	  file = $1
 	  var = $2
+        elsif /(.*)\/(.*)/ =~ gturl
+          file = $1
+          var = $2
 	else
-	  raise "invalid URL: '@' between path & variable is not found\n\n" + 
+	  raise "invalid URL: '[@|/]' between path & variable is not found\n\n" + 
 	         "URL format: " + GTURLfmt
 	end
 	if /,/ =~ var

data/lib/numru/gphys/grads_gridded.rb

@@ -1215,56 +1215,58 @@ EOS
 
  class GrADSVar
 
-  def initialize(file,varname)
+  def initialize(file,varname,varonly=false,dimonly=false)
     @varname = varname
 
     if file.is_a?(String)
       file = GrADS_Gridded.open(file)
-    elsif ! file.is_a?(GrADS_Gridded)
+    elsif !file.is_a?(GrADS_Gridded)
       raise ArgumentError, "1st arg must be a GrADS_Gridded or a file name"
     end
     @ctl = file  # control file name
-#    @ctl = ctl
-
-    @idim = -1
-    for i in 0...@ctl.dimensions.length
-#      p @ctl.dimensions[i][:name]
-      if @varname == @ctl.dimensions[i][:name]
-        @idim = i
-      end
-    end
 
     @attr = NumRu::Attribute.new
-    if( @idim != -1 )
-      @dimensions = [ @ctl.dimensions[@idim] ]
-      @rank = 1
-      @attr[:name] = @dimensions[0][:name]
-      @attr[:long_name] = @dimensions[0][:description]
-      @attr[:units] = @dimensions[0][:units]
-      if @attr[:long_name] == "time" && @ctl.get_att("365_day_calendar") == true
-        @attr[:calendar] = "365_day"
-      end
 
-      @shape = [@dimensions[0][:len]]
-    else
+    found = false
+    if !dimonly
       @dimensions = @ctl.dimensions
       @rank = @dimensions.length
-      found = false
-      for i in 0...@ctl.variables.length
-        if @varname == @ctl.variables[i][:name]
-          @attr[:long_name] = @ctl.variables[i][:description]
-          @attr[:nlev] = @ctl.variables[i][:nlev].to_s
+      @ctl.variables.each do |var|
+        if @varname == var[:name]
+          @idim = -1
+          @attr[:long_name] = var[:description]
+          @attr[:nlev] = var[:nlev].to_s
 
           @shape = [@dimensions[0][:len],@dimensions[1][:len],
                     @dimensions[2][:len],@dimensions[3][:len]]
-          @shape[2] = @ctl.variables[i][:nlev].to_i if( @ctl.variables[i][:nlev] )
+          @shape[2] = var[:nlev].to_i if( var[:nlev] )
 
           @attr[:missing_value] = NArray.sfloat(1).fill!(@ctl.undef)
           found = true
         end
       end
-      raise "variable #{@varname} is not found" if !found
     end
+
+    if !found && !varonly
+      @ctl.dimensions.each_with_index do |dim,i|
+        if @varname == dim[:name]
+          @idim = i
+          @dimensions = [ dim ]
+          @rank = 1
+          @attr[:name] = dim[:name]
+          @attr[:long_name] = dim[:description]
+          @attr[:units] = dim[:units]
+          if @attr[:long_name] == "time" && @ctl.get_att("365_day_calendar") == true
+            @attr[:calendar] = "365_day"
+          end
+
+          @shape = [dim[:len]]
+          found = true
+        end
+      end
+    end
+
+    raise "variable #{@varname} is not found" if !found
   end
 
   attr_accessor (:rank)

data/lib/numru/gphys/grib.rb

@@ -31,6 +31,7 @@ end
 ## <---/
 
 module NumRu
+class GPhys
   module GribUtils
     require "numru/gphys/grib_params"
     private
@@ -230,7 +231,7 @@ module NumRu
           len = file.read(3).to_uint3
           bds = GribBDS.new(obj,file.pos,len)
           obj.bds = bds
-          file.seek(len-3,IO::SEEK_CUR)
+          file.seek(len-3,::IO::SEEK_CUR)
 
           es = GribES.new(obj,file.read(4))
           unless es.grib?
@@ -1020,14 +1021,14 @@ module NumRu
       private
       def oct4
         return @oct4 if @oct4
-        @sgm.file.seek(@pos, IO::SEEK_SET)
+        @sgm.file.seek(@pos, ::IO::SEEK_SET)
         @oct4 = @sgm.file.read(1).to_uint1
         return @oct4
       end
       def oct14
         return nil if flag4==0
         return @oct14 if @oct14
-        @sgm.file.seek(@pos+10, IO::SEEK_SET)
+        @sgm.file.seek(@pos+10, ::IO::SEEK_SET)
         @oct14 = @sgm.file.read(1).to_uint1
         return @oct14
       end
@@ -1070,7 +1071,7 @@ module NumRu
         ebu = (8-(eb&7))/nstep unless ebu==0
         eb = (eb+7)/8
         return NArray.sfloat(0) if eb==sb
-        file.seek(pos+sb,IO::SEEK_SET)
+        file.seek(pos+sb,::IO::SEEK_SET)
         str = file.read(eb-sb)
         return get_bits(str,nstep,nbits,sbu,ebu,NArray::SFLOAT)
       end
@@ -1183,19 +1184,19 @@ module NumRu
       end
       def offset
         return @offset if @offset
-        @sgm.file.seek(@pos+3, IO::SEEK_SET)
+        @sgm.file.seek(@pos+3, ::IO::SEEK_SET)
         @offset = float_value(@sgm.file.read(4))
         return @offset
       end
       def efactor
         return @efactor if @efactor
-        @sgm.file.seek(@pos+1, IO::SEEK_SET)
+        @sgm.file.seek(@pos+1, ::IO::SEEK_SET)
         @efactor = 2.0**str2int2( @sgm.file.read(2) )
         return @efactor
       end
       def value(shape,*arg)
         nbits_unuse = oct4&15
-        @sgm.file.seek(@pos+7, IO::SEEK_SET)
+        @sgm.file.seek(@pos+7, ::IO::SEEK_SET)
         nbits_pack = @sgm.file.read(1).to_uint1
         if (nbits_pack%8) == 0
           nstep = 8
@@ -1280,7 +1281,7 @@ module NumRu
         else
           raise "not defined yet"
           n1 = @file.read(2).to_uint2
-          @sgm.file.seek(1, IO::SEEK_CUR)
+          @sgm.file.seek(1, ::IO::SEEK_CUR)
           str = @sgm.file.read(6)
           n2 = str.to_uint2
           p1 = str.to_uint2(2)
@@ -1406,6 +1407,8 @@ module NumRu
         return defined?(is) && is
       end
       def open(fname)
+        #warn "This grib library is obsoleted."
+        #warn "Use http://ruby.gfd-dennou.org/products/rb-grib/ instead."
         f = Grib.new(fname,"r")
         mbio = NumRu::MultibitIO.new(fname)
         f.parse(mbio)
@@ -1427,7 +1430,7 @@ module NumRu
       while true
         @file.read(1)=="\000" && next
         @file.eof? && break
-        @file.seek(-1, IO::SEEK_CUR)
+        @file.seek(-1, ::IO::SEEK_CUR)
         sgm = GribSegment.parse(@file, mbio)
         return nil unless sgm
         name = sgm.pds.sname
@@ -2015,6 +2018,7 @@ module NumRu
   end
 
 end
+end
 
 
 #####################################################