gentooboontoo-gphys 0.6.1.3 → 1.3.1.1

data/lib/numru/gphys/varraycomposite.rb

@@ -77,24 +77,31 @@ module NumRu
 
       nvas = varrays.shape
       vrank = nvas.length
-      rank=0
       varrays.each{|va|
-	if va.is_a?(VArray)
+	if !va.nil?
 	  @first_vary = va
-	  @attr = @first_vary.attr
+	  @attr = @first_vary.attr_copy
 	  @name = @first_vary.name
-	  @rank = va.rank
+	  @crank = va.rank   # rank of the component VArrays
 	  break
 	end
       }
-      if vrank > @rank
-	raise ArgumentError, "rank of varrays > rank of the VArray"
-      elsif vrank < @rank
-	(@rank - vrank).times{
-	  varrays = varrays.newdim(vrank)
-	  nvas.push(1)
-	}
-	vrank = @rank
+      if vrank > @crank
+        @rank = vrank       #=>  @rank > @crank
+      else
+	@rank = @crank
+        if vrank < @crank
+          (@crank - vrank).times{
+            varrays = varrays.newdim(vrank)
+            nvas.push(1)
+          }
+          vrank = @crank   # rank of varrays is increased to @crank (==@rank)
+        end
+      end
+      un0 = varrays[0].units
+      for i in 1...varrays.length
+        va = varrays[i]
+        varrays[i] = va.convert_units(un0) if va && va.units != un0
       end
 
       @bound_idx = Array.new     # will be Array of Array
@@ -106,14 +113,24 @@ module NumRu
 	  len=0
 	  varrays[*idx].each{|va|
 	    if !set && va
-	      if !va.is_a?(VArray)
-		raise ArgumentError,"Not a VArray: #{va.inspect}"
-	      end
-	      len = va.shape_current[dim]
+              ### commented out for the duck typing:
+	      #if !va.is_a?(VArray)
+              #  raise ArgumentError,"Not a VArray: #{va.inspect}"
+	      #end
+              if dim < @crank
+                len = va.shape_current[dim]
+              else
+                len = 1
+              end
 	      @bound_idx[dim][i+1] = @bound_idx[dim][i] + len
 	      set=true
 	    elsif va
-	      if va.shape_current[dim] != len
+              if dim < @crank
+                lc = va.shape_current[dim]
+              else
+                lc = 1
+              end
+	      if lc != len
 		raise ArgumentError,"Non-uniformity in the #{i}th element"+
                    " of the #{dim}th dimension (#{va.shape_current[dim]} for #{len})"
 	      end
@@ -148,10 +165,6 @@ module NumRu
       # "bounds=#{@bound_idx.collect{|b| b[1..-2]}.inspect}"
     end
 
-    def ntype
-      @first_vary.ntype
-    end
-
     def shape
       @shape
     end
@@ -169,14 +182,18 @@ module NumRu
       loop_multi_dim_index( @varrays.shape ){|index|
 	vidx = Array.new
 	for d in 0...@rank
-	  vidx[d] = (@bound_idx[d][index[d]])..(@bound_idx[d][index[d]+1]-1)
+          if d < @crank
+            vidx[d] = (@bound_idx[d][index[d]])..(@bound_idx[d][index[d]+1]-1)
+          else
+            vidx[d] = @bound_idx[d][index[d]]
+          end
 	end
 	v = @varrays[*index].val
 	if !val
 	  if NArray===v
-	    val = NArray.new(self.ntype,*@shape)
+	    val = NArray.new(v.typecode,*@shape)
 	  elsif NArrayMiss===v
-	    val = NArrayMiss.new(self.ntype,*@shape)
+	    val = NArrayMiss.new(v.typecode,*@shape)
 	  else
 	    raise TypeError, "Unexpected type #{v.class}"
 	  end
@@ -194,7 +211,11 @@ module NumRu
 	  __check_ary_class(narray)
 	  vidx = Array.new
 	  for d in 0...@rank
-	    vidx[d] = (@bound_idx[d][index[d]])..(@bound_idx[d][index[d]+1]-1)
+            if d < @crank
+              vidx[d] = (@bound_idx[d][index[d]])..(@bound_idx[d][index[d]+1]-1)
+            else
+              vidx[d] = @bound_idx[d][index[d]]
+            end
 	  end
 	  sub=narray[*vidx]
 	end
@@ -224,8 +245,11 @@ module NumRu
       val
     end
 
+#    def ntype
+#      @first_vary.ntype
+#    end
     def ntype
-      __ntype(@first_vary)
+      __ntype(typecode)
     end
 
     def typecode
@@ -287,12 +311,12 @@ module NumRu
       idx.each_with_index{ |ix, dim|
 	size = @bound_idx[dim][-1]
 	imask[dim] = Array.new
-	isub[dim] = Array.new
+	isub[dim] = Array.new if dim < @crank
 	for j in 0...(@bound_idx[dim].length)
 	  match, isb = _imatch( size, ix, @bound_idx[dim][j..j+1] )
 	  if match
 	    imask[dim].push(j)
-	    isub[dim].push(isb) 
+	    isub[dim].push(isb) if dim < @crank
 	  end
 	end
       }
@@ -335,6 +359,11 @@ module NumRu
 	  stp = 1
 	else # Hash
 	  range, stp = index.to_a[0]
+          if stp<=0
+            raise(ArgumentError,"Currently only positive step is supported")
+            # development note: current handling of fst and lst assumes a
+            # positive step
+          end
 	  range = 0..-1 if range==true
 	  fst = range.first
 	  fst += size if fst < 0
@@ -350,11 +379,28 @@ module NumRu
 	  if stp==1
 	    return [true, a..b ]
 	  else
-	    return [true, {(a..b)  => stp} ]
+            len = last-first+1
+            if a<len
+              return [true, {(a..b)  => stp} ]
+            else
+              return [false, nil]
+            end
 	  end
 	else
 	  return [false, nil]
 	end
+      when Array
+        match = false
+        isb = []
+        index.each{ |idx|
+          idx += size if idx < 0
+          if first <= idx && idx <= last
+            match = true
+            isb.push(idx-first)
+          end
+        }
+        isb = nil if isb == []
+        return [match, isb]
       else
 	raise "Unsupported type for indexing: #{index.class}"
       end
@@ -412,4 +458,36 @@ if __FILE__ == $0
   vac.set_att('long_name', 'test data')
   p vac.get_att('long_name')
   p va01.get_att('long_name')
+  p vac.typecode,vac.ntype
+
+  puts "testing rank extension.."
+  va0 = VArray.new( NArray.float(3,2).indgen!,     {"units"=>"m/s"}, 'V' )
+  va1 = VArray.new( NArray.float(3,2).indgen!+100, {"units"=>"m/s"}, 'V' )
+  va2 = VArray.new( NArray.float(3,2).indgen!+200, {"units"=>"m/s"}, 'V' )
+  va3 = VArray.new( NArray.float(3,2).indgen!+300, {"units"=>"m/s"}, 'V' )
+  varrays = NArray.to_na([ [[va0]], [[va1]], [[va2]], [[va3]] ])
+  vac = VArrayComposite.new(varrays)
+  p vac, vac.val
+  if vac[1,1,1].val == 104.0
+    puts "test OK"
+  else
+    raise "test failed"
+  end
+
+  v = vac[0..1,0,{1..-1=>2}].val
+  ans = NArray.to_na( [ [100.0,101.0], [300.0, 301.0] ] )
+  if v==ans
+    puts "test OK"
+  else
+    raise "test failed"
+  end
+
+  vac[-1,true,1..2] = -999.0
+  if vac[-1,true,1..2].val.to_a.flatten.uniq == [-999.0 ] 
+    puts "test OK"
+  else
+    raise "test failed"
+  end
+  #vac.val = NArray.float(3,2,4).random!
+  #p vac.val
 end

data/lib/numru/gphys/varraygrib.rb

@@ -4,6 +4,14 @@
 =end
 
 require "numru/gphys/grib"
+
+### to be made below in the definition of VArrayGrib in order to record
+### whetehr its successfull or not
+#begin
+#  require "numru/grib"
+#rescue LoadError
+#end
+
 require "numru/gphys/varray"
 
 module NumRu
@@ -16,8 +24,50 @@ module NumRu
 =end
   class VArrayGrib < VArray
 
+    begin
+      require "numru/grib"
+      @@rbgribloaded = true
+    rescue LoadError
+      @@rbgribloaded = false
+    end
+
+    @@GribLib = :gphys_grib
+
+    class << self
+      def use_gphys_grib
+        @@GribLib = :gphys_grib
+        set_grib_lib
+      end
+      def use_rb_grib
+        if !@@rbgribloaded
+          raise LoadError, "Loading rb-GRIB has been failed. You probably need to install it."
+        end
+        @@GribLib = :rb_grib
+        set_grib_lib
+      end
+      def grib_lib
+        @@GribLib.dup
+      end
+      def grib
+        @@Grib
+      end
+      def set_grib_lib
+        case @@GribLib
+        when :gphys_grib
+          @@GribDim = GPhys::GribDim
+          @@GribVar = GPhys::GribVar
+          @@Grib = GPhys::Grib
+        when :rb_grib
+          @@GribDim = GribDim
+          @@GribVar = GribVar
+          @@Grib = Grib
+        end
+      end
+    end
+    set_grib_lib
+
     def initialize(aGribVar)
-      if !GribVar===aGribVar && !GribDim===aGribVar
+      if !@@GribVar===aGribVar && !@@GribDim===aGribVar
         raise ArgumentError,"Not a GribVar or GribDim"
       end
       @name = aGribVar.name
@@ -26,9 +76,11 @@ module NumRu
       @ary = aGribVar
       @attr = Attribute.new
       aGribVar.att_names.each{|name|
-        @attr[name] = aGribVar.att(name)
+        val = aGribVar.att(name)
+        val = [val] if val.is_a?(Numeric)
+        @attr[name] = val
       }
-      if GribDim===@ary
+      if @@GribDim===@ary
         class << @ary
           def rank
             return 1
@@ -41,9 +93,9 @@ module NumRu
     end
 
     def inspect
-      if GribVar===@ary
+      if @@GribVar===@ary
         "<'#{@name}' in '#{@ary.file.path}'  [#{@ary.shape.join(", ")}]>"
-      elsif GribDim===@ary
+      elsif @@GribDim===@ary
         "<'#{@name}' in '#{@ary.var.name}'  #{@ary.length}>"
       end
     end
@@ -55,7 +107,7 @@ module NumRu
         v = file.def_var(name)
         dims.length.times{|n|
           d = dims[n]
-          if GribDim===d
+          if @@GribDim===d
             gd = v.def_dim(d.name,n)
             gd.put(d.get)
             d.att_names.each{|name| gd.put_att(name,d.att(name)) }
@@ -80,7 +132,7 @@ module NumRu
       ## < additional class methods > ##
 
       def write(file,vary,dims=nil)
-        Grib===file || raise(ArgumentError,"1st arg: not a Grib")
+        @@Grib===file || raise(ArgumentError,"1st arg: not a Grib")
         VArray===vary || raise(ArgumentError,"2st arg: not a VArray")
         rank = vary.rank
         if !dims
@@ -157,7 +209,7 @@ if $0 == __FILE__
 
   include NumRu
 
-  grib = Grib.open("../../../testdata/T.jan.grib")
+  grib = VArrayGrib.grib.open("../../../testdata/T.jan.grib")
   gv = grib.var("TMP")
 
   va = VArrayGrib.new(gv)
@@ -174,4 +226,14 @@ if $0 == __FILE__
   p va2.shape
   p va2.val
 
+  begin
+    VArrayGrib.use_rb_grib
+    grib = VArrayGrib.grib.open("../../../testdata/T.jan.grib")
+    p grib.var_names
+    gv = grib.var("t")
+    p gv.val
+  rescue LoadError
+    print "...error rescued & test skipped\n\n"
+  end
+
 end

data/lib/numru/gphys/varraygtool3.rb

@@ -0,0 +1,226 @@
+=begin
+=ToDo list
+* Support a temporay attribute (@tmp_attr = Attribute.new)
+=end
+
+require "numru/gphys/gtool3"
+require "numru/gphys/varray"
+
+module NumRu
+
+  ATTR_CF_CONV = {
+    "DSET" => "dataset",
+    "TITLE" => "long_name",
+    "UNIT" => "units",
+    "MISS" => "missing_value"
+#    "ITEM" => nil,       # identical to name
+#    "TIME" => nil,       # treated in the time axis
+#    "DATE" => nil,       # treated in the time axis
+#    "UTIM" => nil,       # treated in the time axis
+#    "TDUR" => nil,       # in Future, should be treaded with cell_* in CF
+#    "CSIGN" => nil,      # will be in history in convination
+#    "CDATE" => nil       # will be in history in convination
+#    "MDATE" => nil,      # will be in history in convination
+#    "MSIGN" =>  nil,     # will be in history in convination
+  }
+
+  class VArrayGtool3 < VArray
+
+    ## < initialization redefined > ##
+
+    def initialize(aGtool3Var)
+      raise ArgumentError,"Not a Gtool3Var" if ! aGtool3Var.is_a?(Gtool3Var)
+      @name = aGtool3Var.name
+      @mapping = nil
+      @varray = nil
+      @ary = aGtool3Var
+      @attr = _attr_conv_to_CF( aGtool3Var.attr )
+    end
+
+    def _attr_conv_to_CF(org)
+      attr = Attribute.new
+      ATTR_CF_CONV.each do |ik,ok|
+        val = org[ik]
+        val = NArray[val] if val.is_a?(Numeric)
+        attr[ok] = val
+      end
+      hist = ""
+      hist += "Created #{org["CDATE"]} by #{org["CSIGN"]}. " if org["CDATE"]
+      hist += "Modifiled #{org["MDATE"]} by #{org["MSIGN"]}. "if org["MDATE"]
+      attr["history"] = hist if hist.length > 0
+      attr
+    end
+    private :_attr_conv_to_CF
+
+    class << self
+      ## < redefined class methods > ##
+
+      #def new2(file, name, ntype, dimensions, attr=nil)
+      #  va = new( file.def_var(name, ntype, dimensions) )
+      #  if attr; attr.each{|key,val| va.attr[key]=val}; end 
+      #  va
+      #end
+      undef new2
+
+      # to make a varray from an axis (except for time)
+      def make_coord(hash)
+        nary = hash.delete(:val)
+        name = hash.delete("ITEM")
+        coord_att_conv!(hash)
+        VArray.new(nary, hash, name)
+      end
+
+      def coord_att_conv!(hash)
+        hash.keys.each do |k|
+          v = hash.delete(k)
+          if (ck=ATTR_CF_CONV[k])   # substitution, not ==
+            v = NArray[v] if v.is_a?(Numeric)
+            if k=="UNIT"
+              case v
+              when "deg"
+                v = "degrees"
+              end
+            end
+            hash[ck] = v
+          elsif k=="STYP" && v
+            if v >= 0
+              hash["positive"] = "up"
+            else
+              hash["positive"] = "down"
+            end
+          end
+        end
+        hash
+      end
+    end
+
+    ## < redefined instance methods > ##
+
+    def val
+      v = @ary.get
+    end
+
+    def val=(narray)
+      @ary.put( __check_ary_class2(narray) )
+      narray
+    end
+
+    # # It is safer not to have the method "shape" to avoid misconfusion of 
+    # # shape_ul0 and shape_current:
+    # def shape
+    #   raise "The shape method is not available. Use shape_ul0 or shape_current instead."
+    # end
+
+    def inspect
+      "<'#{@name}' in '#{@ary.file.path}' #{ntype}#{shape_current.inspect}>"
+    end
+
+    def total
+      len = 1
+      @ary.shape_current.each{|i| len *= i}
+      len
+    end
+    alias length total
+
+    def rank
+      shape_current.length
+    end
+
+#    def reshape!( *args )
+#      raise "cannot reshape a #{class}. Use copy first to make it a VArray with NArray"
+#    end
+    undef reshape!
+
+
+    ## < additional instance methods > ##
+
+    def dim_names
+      @ary.dim_names
+    end
+    def shape_ul0
+      @ary.shape_ul0
+    end
+    def shape_current
+      @ary.shape_current
+    end
+    def file
+      @ary.file
+    end
+
+  end
+
+  class VArrayGtool3Time < VArray
+    def initialize(hash, calendar=nil)
+      @ary = hash.delete(:val)
+      @name = hash.delete("ITEM")
+      @attr = Attribute.new
+      @attr.update( VArrayGtool3.coord_att_conv!(hash) )
+      @attr["calendar"] = calendar if calendar
+      @varray = nil
+      @mapping = nil
+    end
+
+    def inspect
+      "<'#{name}' in '#{@ary.file.path}' #{ntype}#{shape.inspect}>"
+    end
+
+    def val
+      @ary.get
+    end
+  end
+
+
+end
+
+###########################################################
+### < test >
+
+if $0 == __FILE__
+ #  $DEBUG = true
+  include NumRu
+  Gtool3.gtaxdir = File.expand_path("~/dennou/GTAXDIR")
+  path = ARGV[0]
+  varname = ARGV[1] or raise("Need two args")
+
+  file = Gtool3.open(File.expand_path(path))
+  var = file.var(varname)
+  va = VArrayGtool3.new(var)
+
+  p va, va.name
+  p va.dim_names
+  p va.shape_ul0
+  p va.val
+
+  va.att_names.each do |nm|
+    print nm,"\t",va.get_att(nm).inspect,"\n"
+  end
+
+  p va.get_att("long_name")
+
+  print "***************\n"
+  va2 = va[3..9,5..15,0,0]
+  p va2.shape
+  p va2.val
+
+  p va2.get_att("long_name")
+
+  print "****** time *******\n"
+
+  t = VArrayGtool3Time.new(var.axis(-1)["LOC"])
+  p t, t[1..3].val
+  t.att_names.each do |nm|
+    print nm,"\t",va.get_att(nm).inspect,"\n"
+  end
+
+  print "****** lon *******\n"
+
+  xg = var.axis(0)["LOC"]
+  #nm = xg.delete("ITEM)"
+  #na = xg.delete(:val)
+  #x = VArray.new(na, xg, nm)
+  x = VArrayGtool3.make_coord(xg)
+  p x, x[1..3].val
+  x.att_names.each do |nm|
+    print nm,"\t",x.get_att(nm).inspect,"\n"
+  end
+end