gfdnavi 1.3.0.0

data/data/samples/jmadata/MSM-P/2006/0101.nc.yml

@@ -0,0 +1,13 @@
+description:
+    Derived from the http://davis.rish.kyoto-u.ac.jp/arch/jmadata/data/gpv/netcdf/MSM-P/2006/.
+contains:
+  temp:
+    missing_value: 999.0e+0
+    gfdnavi:
+      draw_parameters:
+        tone_contour: false
+        tone_max: 5
+        tone_min: -5
+      user: root
+  %:
+    remark: number of grid points are significantly reduced by thinning.

data/data/samples/jmadata/MSM-P/2006/010[1-3].nc.yml

@@ -0,0 +1,2 @@
+--- 
+remark: This is a vertual united file

data/data/samples/jmadata/MSM-P/2006/skip_data.rb

@@ -0,0 +1,96 @@
+#!/usr/bin/env ruby
+require "optparse"
+require "numru/gphys"
+include NumRu
+
+opt = OptionParser.new
+OPTS = {}
+ARGV.options{|opt|
+  opt.on( '-o=VAL', '--output=VAL',
+          "Output file"
+          ){|v| OPTS[:output] = v.gsub(/^=/, '')}
+
+  opt.on( '-s=VAL', '--skip=VAL',
+          "Skip interval 
+                                     (ex. \"10,5,8,0\". 0 is not skipped)"
+          ){|v| OPTS[:skip] = v.gsub(/^=/, '')}
+
+  opt.on( '--copy-dims=VAL',
+          "Copy dimensions additionally
+                                     (ex. \"ref_time,lon_weight\")"
+          ){|v| OPTS[:copy_dims] = v.gsub(/^=/, '')}
+
+  opt.on_tail('-h', '-H', '--help', 
+              "This help message is output"
+              ){|v| OPTS[:help] = v}
+  opt.parse!
+}
+
+if OPTS[:help] || !(OPTS[:output]) || ARGV.size < 1 || !(OPTS[:skip])
+  print <<-"EOF"
+
+  #{File.basename($0.to_s)}:
+
+    USAGE: #{File.basename($0.to_s)} [options] input_url -o output_file -s skip_interval
+
+    OPTION: \n#{opt.to_a[1..-1].join("")}
+    EOF
+    exit
+end
+
+#=== �e��ݒ�
+input_url = ARGV[0]
+output_file = OPTS[:output]
+skip_intervals = OPTS[:skip].split(',')
+skip_intervals.collect!{|skipchar|
+  skipint = skipchar.to_i
+  if skipint > 0
+    skipint
+  else
+    1
+  end
+}
+copy_dims = []
+copy_dims = OPTS[:copy_dims].split(',') if OPTS[:copy_dims]
+
+#=== �ǂݍ���, �������݃t�@�C���̃I�[�v��
+gphys = GPhys::IO.open_gturl(input_url)
+outfile = NetCDF.create(output_file)
+
+#=== ��摮���R�s�[
+gphys.data.file.each_att{|att|
+  outfile.put_att(att.name, att.get)
+}
+
+#=== �f�[�^�̊Ԉ��� (�[�����Ƃ͍l����)
+reduced_size_array = Array.new(gphys.rank)
+gphys.rank.times{ |dim_index|
+  dim_size = gphys.coord(dim_index).val.size
+  interval = skip_intervals[dim_index] || 1
+  if dim_size < interval
+    reduced_size_array[dim_index] = 0
+    next
+  elsif interval == 1
+    reduced_size_array[dim_index] = 0..-1
+    next
+  end
+  reduced_size = dim_size / interval
+  reduced_size_array[dim_index] = Array.new(reduced_size)
+  reduced_size.times{|n| reduced_size_array[dim_index][n] = n*interval}
+}
+
+gphys = gphys[*reduced_size_array]
+
+#=== �t�@�C���o��
+if File.exist?(output_file)
+  print "  *** MESSAGE *** \"#{output_file}\" is overwritten.\n"
+end
+GPhys::NetCDF_IO.write(outfile, gphys)
+
+#=== �lj��̎����ϐ������o��
+copy_dims.each{|dim|
+  gphys_dim = GPhys::IO.open_gturl(input_url.sub(/@\w+$/, "@#{dim}"))
+  GPhys::NetCDF_IO.write_grid(outfile, gphys_dim)
+}
+
+outfile.close

data/data/samples/jmadata/MSM-P/2006/skip_data.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+for nc in `ls orig/????.nc` ; do
+    new_file=`basename $nc`
+    echo "$nc -> $new_file"
+    ruby skip_data.rb $nc@temp -o $new_file -s 10,10,2 --copy-dims=ref_time
+done

data/data/samples/reanalysis.SIGEN

@@ -0,0 +1,8 @@
+Subject:	�ĉ�̓f�[�^
+Maintainer:	�X�� ����
+Description:	
+Note:		
+Update:		2006/09/12  
+
+����
+	2006/09/12  �X�� ����  

data/data/samples/reanalysis/era40.SIGEN

@@ -0,0 +1,8 @@
+Subject:        ERA40 �ĉ�̓f�[�^
+Maintainer:     ���V�@����
+Description:    ERA �Ō��J����Ă���ĉ�̓f�[�^
+Note:
+Update:         2007/01/26
+
+����	
+	2007/01/26  ���V�@����

data/data/samples/reanalysis/era40.yml

@@ -0,0 +1,2 @@
+gfdnavi:
+  downloadable: false

data/data/samples/reanalysis/era40/t.jan.nc.yml

@@ -0,0 +1 @@
+--- {}

data/data/samples/reanalysis/ncep.SIGEN

@@ -0,0 +1,9 @@
+Subject:        NCEP �ĉ�̓f�[�^
+Maintainer:     �X�� ����
+Description:    �č��‹��\���Z���^�[ (NCEP) �Ō��J����Ă���
+		�ĉ�̓f�[�^
+Note:
+Update:         2006/09/13
+
+����	
+	2006/09/13  �X�� ����

data/data/samples/reanalysis/ncep/T.jan.100hPa.png.yml

@@ -0,0 +1,43 @@
+--- 
+gfdnavi: 
+  vizshot: |
+    --- !ruby/object:NumRu::VizShot 
+    plots: 
+    - :file: /samples/reanalysis/ncep/T.jan.nc
+      :cut: 
+        lon: !ruby/range 
+          begin: 0.0
+          end: 350.0
+          excl: false
+        level: 1000.0
+        lat: !ruby/range 
+          begin: 90.0
+          end: -90.0
+          excl: false
+      log: false
+      :tone: true
+      :var: T
+      :color_bar: true
+      :contour: true
+      :method: :tone_cont
+    set: 
+      :tone: 
+        tonf: true
+      :fig: 
+        itr: 1
+        viewport: 
+        - 0.2
+        - 0.8
+        - 0.2
+        - 0.8
+      :admin: 
+        :ydiv: 1
+        :basename: temp
+        :iwidth: 550
+        :iheight: 550
+        :xdiv: 1
+  user: root
+  references: 
+  - name: draw
+    path: /samples/reanalysis/ncep/T.jan.nc/T
+description: Longitude-latitude cross section of climatorogy temperature in January

data/data/samples/reanalysis/ncep/T.jan.zonal_mean.nc.yml

@@ -0,0 +1,8 @@
+--- 
+contains: 
+  T_mean: 
+    gfdnavi: 
+      references: 
+      - name: analyze
+        path: /samples/reanalysis/ncep/T.jan.nc/T
+    analysis: mean calculated from T

data/data/samples/reanalysis/ncep/T.jan_only_root.nc.yml

@@ -0,0 +1,4 @@
+test: test
+gfdnavi:
+  user: root
+  other_mode: 0

data/data/samples/reanalysis/ncep/UV.jan.nc.yml

@@ -0,0 +1,10 @@
+title: ncep climatology
+description: 
+    Derived from the ncep reanalysis climatology data.
+contains:
+  U:
+    long_name: Zonal Wind
+  V:
+    long_name: Merional Wind
+  %:
+    remark: number of grid points are significantly reduced by thinning.

data/data/samples/reanalysis/ncep/UV.jan.nc.yml.ja

@@ -0,0 +1,11 @@
+title: �č��‹��\���Z���^�[ (NCEP) / �č�������C�����Z���^�[ (NCAR)
+       �ĉ�̓f�[�^����̋C��l
+comments: ���̃f�[�^��, �I���W�i���f�[�^���Ԉ����������̂ł�.
+#contains:
+#  U:
+#    ������: ������
+#    �����l: -9.96921e+36f
+#  V:
+#    ������: �q�ߖʕ�
+#  *:
+#    remark: number of grid points are significantly reduced by thinning.

data/data/samples/sonde_operational.yml

@@ -0,0 +1,5 @@
+title: operation radiosonde data archive
+
+description: 
+    Archive of operational radiosonde data transmitted originally
+    through WMO's GTS network.

data/data/samples/sonde_operational/std_plev.yml

@@ -0,0 +1,12 @@
+title: starndard pressure level data
+
+creator: N. Hashiguchi, RISH, Kyoto Univ.
+
+description:
+    The raw data obtained from NCEP were screened
+    with an algorithm suitable for the tropical conditions.
+    The files archived here contains data only at the
+    standard pressure levels.
+
+    See http://dss.ucar.edu/datasets/ds353.4/ for more
+    info on the original data.

data/db/NetCDFparser.rb

@@ -0,0 +1,406 @@
+#
+# NetCDF�t�@�C����gfdnavi�f�[�^�x�[�X�ɓo�^����
+# ���߂̃N���X
+#
+class NetCDFparser
+
+  def initialize(file,rw="r",topdir="/",quiet=false)
+    @filename=file
+    @rw=rw
+    @io=NetCDF.open(@filename,@rw)
+    @temporal_rangeinfo={}
+    @spatial_rangeinfo={}
+#    @topdir=File.expand_path(topdir)
+    @topdir=File.expand_path(GFDNAVI_DATA_PATH)
+    @quiet=quiet
+   
+    #�ܓx�o�x���Ԃ̑��������i�b��I�ɒ������j
+    @varname={}
+    @varname["longitude"]=["lon","longitude"]
+    @varname["latitude"]=["lat","latitude"]
+    @varname["time"]=["time"]
+  end
+
+  def close
+    @io.close
+  end 
+
+  # �t�@�C��@filename���f�[�^�x�[�X�ɓo�^����
+  def regist 
+    regist_directory(@filename)
+    regist_globalattributes
+
+    find_spatial_variables("longitude")
+    find_spatial_variables("latitude")
+    find_temporal_variable
+
+    @io.each_var do |var|    
+      vardb=regist_variable(var)
+    end
+  end
+
+  #�t�@�C������directories�e�[�u���ɓo�^����
+  def regist_directory(fname)
+    @dir = Directory.new
+    @dir.name = File.basename(fname)
+    @dir.path = File.expand_path(fname).sub(/^#{@topdir}\//,'/')
+    pdir=Directory.find(:first, :conditions => "path=\"#{File.dirname(File.expand_path(fname))}\"")
+    if pdir==nil 
+       #pdir=regist_directory(File.dirname(fname))
+       print "WARNING: #{File.dirname(File.expand_path(fname))} is not found in Directory table.\n"
+    else
+       @dir.parent_id = pdir.id
+       @dir.save
+    end
+    if !@quiet
+      print "Directory #{@dir.name} is registered (id=#{@dir.id}).\n"
+    end
+  end
+
+  #�t�@�C���̃O���[�o������directory�ɑ΂���L�[���[�h�����Ƃ���
+  #keyword_attributes�e�[�u���ɓo�^����
+  def regist_globalattributes
+    @io.each_att do |att|
+       key = KeywordAttribute.new
+       key.directory = @dir
+       key.name=att.name
+       key.data_type=att.atttype
+       key.value=att.get.to_s
+       key.save
+    end
+  end
+
+  #�evariable�̃L�[���[�h������keyword_attributes�e�[�u���ɓo�^����
+  def regist_keyword_attributes(var,vardb)
+     var.each_att do |att|
+       key = KeywordAttribute.new
+       key.variable=vardb
+       key.name = att.name
+       key.data_type = att.atttype
+       key.value = att.get.to_s
+       key.save
+     end
+  end
+
+  #nc�t�@�C�����Œ�`����Ă��鎞�ԑ��������o��
+  #@temporal_rangeinfo�ɂ���Ă���
+  #@temporal_rangeinfo�̓n�b�V���e�[�u���̑��d�z��
+  #  @temporal_rangeinfo[varname][type]
+  #    varname:������
+  #    type:{"start_time","end_time","ndims"}������
+  #         ndims�͑����̎�����
+  def find_temporal_variable
+    @varname["time"].each do |v|
+      var=@io.var(v)
+      if var!=nil then
+        if var.ndims==0 then
+          start_time=end_time=var.get()[0]
+        elsif var.ndims==1 then
+          timearray=var.get()
+          start_time = timearray.min()
+          end_time = timearray.max()
+        else
+         print "Error: time attribute' dimensions cannot be more than 2.\n"
+         return
+        end
+        unit=var.att("units").get
+        if unit!=nil then
+          start_time=parse_time_since(start_time,unit)
+          end_time=parse_time_since(end_time,unit)
+        end
+        info={}
+        info["ndims"]=var.ndims
+        info["start_time"]=start_time
+        info["end_time"]=end_time
+        @temporal_rangeinfo[v]=info
+      end
+    end
+  end
+
+  #nc�t�@�C�����Œ�`����Ă����ԑ��������o��
+  #@spatial_rangeinfo�ɂ���Ă���
+  # @spatial_rangeinfo[category][varname][type]
+  #    category:{"longitude","latitude"}�̂����ꂩ
+  #�@�@varname:������
+  #    type:{"var","range"}�̂����ꂩ������
+  #      "var"�F�������̂���
+  #�@�@�@"range"�F�����l�̂Ƃ肤��͈͂̔z��
+  #          [[min_0,max_0],...,[min_n,max_n]]
+  def find_spatial_variables(category)
+    ranges = Array.new
+    @varname[category].each do |v|
+      var=@io.var(v)
+      if var!=nil then
+         unit=var.att("units").get
+         if var.ndims<2 then
+           #point or grid
+           values=var.get()
+           ranges.push([spunit_convert(category,values.min,unit),spunit_convert(category,values.max,unit)])
+         elsif var.ndims()==2 then
+           #swath
+           dnum=Array.new()
+           each_dim do |d|
+             dnum.push(d.length_u10())
+           end
+           i=0
+           interval=dnum[0]
+           while i<dnum[1]-1 do
+             endpoint=i+interval
+             if endpoint>=dnum[1] then
+               endpoint=dnum[1]-1
+             end
+             var.get({"start"=>[0,i],"end"=>[dnum[0]-1,endpoint]})
+             values.sort()
+             ranges.push([spunit_convert(category,values.first,unit),spunit_convert(category,values.last,unit)])
+             i=endpoint
+           end
+         end
+         if @spatial_rangeinfo[category]==nil
+           @spatial_rangeinfo[category]={}
+         end
+         if @spatial_rangeinfo[category][v]==nil
+           @spatial_rangeinfo[category][v]={}
+         end
+         @spatial_rangeinfo[category][v]["var"]=var
+         @spatial_rangeinfo[category][v]["range"]=ranges
+     end
+     #check gloval attributes
+     att=@io.att(v)
+     if att!=nil then
+       @spatial_rangeinfo[category][v]["var"]=att
+       @spatial_rangeinfo[category][v]["range"]=[[att.get,att.get]]
+     end
+   end
+ end
+ 
+ #spunit_convert(category,value,unit)
+ def spunit_convert(category,value,unit)
+   if unit!=nil
+     if category=="latitude"
+        if unit!="degree_east"
+           ud_to=Units.new('degree_east')
+           ud_from=Units.new(unit)
+           value=ud_from.convert(value,ud_to)
+        end
+     elsif category="longitude" 
+        if unit!="degree_north"
+           ud_to=Units.new('degree_north')
+           ud_from=Units.new(unit)
+           value=ud_from.convert(value,ud_to)
+        end       
+     end
+   end
+   return value
+ end
+
+ #variable����variables�e�[�u���ɓo�^����
+ def regist_variable(var)
+   vardb = Variable.new
+   vardb.path = "#{@dir.path}"+'@'+"#{var.name}"
+   vardb.name = var.name
+   vardb.directory = @dir
+   unless vardb.save
+     $stderr.print vardb.errors.full_messages.join(", "), "\n"
+   end
+      
+   regist_spatial_attributes(var,vardb)
+   regist_temporal_attribute(var,vardb)
+   regist_keyword_attributes(var,vardb)
+
+   if !@quiet
+     print "Variable #{vardb.path} is registered (id=#{vardb.id})\n"
+   end
+ end
+
+ #variable�̎��ԏ���variables�e�[�u���ɒlj�����
+ def regist_temporal_attribute(var,vardb)
+  if @io.dim(var.name)!=nil then
+    return
+  end
+  dnames=var.dim_names
+  dnames.each do |dname|
+   if @temporal_rangeinfo[dname]!=nil then
+     vardb.starttime=@temporal_rangeinfo[dname]["start_time"]
+     vardb.endtime=@temporal_rangeinfo[dname]["end_time"]     
+     vardb.save
+     return
+   end
+  end
+  @temporal_rangeinfo.each_value do |rangeinfo|
+   if rangeinfo["ndims"]==0 then
+     vardb.starttime=rangeinfo["start_time"]
+     vardb.endtime=rangeinfo["end_time"]
+     vardb.save  
+     return
+   end
+  end
+ end
+
+ #variable�̋�ԏ���spatial_attribute�ɓo�^����
+ def regist_spatial_attributes(var,vardb)
+  #�������p�̃f�[�^�Z�b�g�������ꍇ�͓o�^���Ȃ�
+  @io.each_dim do |d|
+     if d.name==var.name
+       return
+     end
+  end
+  
+  if var.dims==0 then
+    #0�����̏ꍇ��Dir��KeywordAttribute�ɂ��Ă��܂�
+    keyattr=KeywordAttribute.new
+    keyattr.directory=@dir
+    keyattr.name=var.name
+    keyattr.data_type=var.vartype
+    keyattr.value=var.value
+    keyattr.save
+  end
+
+  lon=get_spatial_rangeinfo_by_dims("longitude",var)
+  lat=get_spatial_rangeinfo_by_dims("latitude",var)
+  #(1) lon,lat�Ƃ��Ɏ�����Ȃ� 
+  if lon==nil && lat==nil then 
+    lon0th=get_spatial_rangeinfo_by_ndims("longitude",0)
+    lat0th=get_spatial_rangeinfo_by_ndims("latitude",0)
+    if lon0th!=nil && lat0th!=nil then
+      #(1-a) lon,lat�Ƃ��ɂO�����̑��������遨point�^
+      add_spatial_attribute(vardb,lon0th["range"][0],lat0th["range"][0])
+      return
+    elsif lon0th!=nil then
+      #(1-b) lon,lat�̂ǂ��炩���O�����̑�����grid�^
+      add_spatial_attribute(vardb,lon0th["range"][0],[-90,90])
+      return
+    elsif lat0th!=nil then
+      add_spatial_attribute(vardb,[0,360],lat0th["range"][0])
+      return
+    end
+    #(1-c) lon,lat��1�����ł��̎����f�[�^�Z�b�g�̎��Ɠ�����point�^
+    lon1st=get_spatial_rangeinfo_by_ndims("longitude",1)
+    lat1st=get_spatial_rangeinfo_by_ndims("latitude",1)
+    if lon1st!=nil && lat1st!=nil && be_present_in(lon1st["var"].dims,var.dims) && be_present_in(lat1st["var"].dims,var.dims) then 
+       i=0
+       lon1st["range"].each do |l|
+         add_spatial_attribute(vardb,l,lat1st["range"][i])
+         i+=1 
+       end
+    end
+    #(1-d) lon,lat��2�����ł��̎����f�[�^�Z�b�g�̎��Ɠ�����swath�^
+    lon2nd=get_spatial_rangeinfo_by_ndims("longitude",2)
+    lat2nd=get_spatial_rangeinfo_by_ndims("latitude",2)
+    if lon2nd!=nil && lat2nd!=nil && be_present_in(lon2nd["var"].dims,var.dims) && be_present_in(lat2nd["var"],var.dims) then
+       i=0
+         lon2nd["range"].each do |range|
+         add_spatial_attribute(vardb,range,lat2nd["range"][i])
+         i+=1
+       end
+       return
+    end
+  #(2) latitude����
+  elsif lon==nil
+    lon0th=get_spatial_rangeinfo_by_ndims("longitude",0)
+    if lon0th!=nil
+      add_spatial_attribute(vardb,lon0th["range"][0],lat["range"][0])
+    else
+      add_spatial_attribute(vardb,[0,360],lat["range"][0])
+    end
+  #(3) longitude����
+  elsif lat==nil
+    lat0th=get_spatial_rangeinfo_by_ndims("latitude",0)
+    if lat0th!=nil
+      add_spatial_attribute(vardb,lon["range"][0],lat0th["range"][0])
+    else
+      add_spatial_attribute(vardb,lon["range"][0],[-90,90])
+    end
+  #(4) longitude,latitude�Ƃ��Ɏ�
+  else
+    add_spatial_attribute(vardb,lon["range"][0],lat["range"][0])
+  end 
+ end
+
+ #@spatial_rangeinfo�ɂ����ԑ����̃��X�g����
+ #��������ndims�ł�����̂����o��
+ #�o�͂����̂̓n�b�V���e�[�u��
+ # rangeinfo[type]
+ #   type: "var","range"�̂����ꂩ
+ def get_spatial_rangeinfo_by_ndims(category,ndims)
+  @spatial_rangeinfo[category].each_value do |info|
+      if info["var"].ndims==ndims then
+         return info
+      end
+    end
+    return
+ end
+
+ #@spatial_rangeinfo�ɂ����ԑ����̃��X�g����
+ #������var�ł�����͈̂̔͏������o��
+ #�o�͂����̂̓n�b�V���e�[�u��
+ # rangeinfo[type]
+ #   type: "var","range"�̂����ꂩ
+ def get_spatial_rangeinfo_by_dims(category,var)
+    @spatial_rangeinfo[category].each_key do |v|
+      dims=var.dims
+      dims.each do |d|
+        if d.name==v then
+         return @spatial_rangeinfo[category][v] 
+        end
+      end  
+    end
+    return
+ end
+
+ #dimb�̒���dima�̗v�f���S���͂����Ă�����true
+ #�����łȂ����false��Ԃ�
+ def be_present_in(dima,dimb)
+  i=0; j=0; 
+  while i<dima.size do
+   flg=false
+   while j<dimb.size do
+    if dima[i].name==dimb[j].name
+      flg=true
+    end
+    j+=1
+   end
+   if flg==false then
+     return false
+   end
+   i+=1
+  end
+  return true
+ end
+
+ #spatial_attributes�e�[�u���ւ̒lj�
+ def add_spatial_attribute(var,lon,lat)
+  sp=SpatialAttribute.new
+  sp.variable=var
+  sp.longitude_lb=lon[0]
+  sp.longitude_rt=lon[1]
+  sp.latitude_lb=lat[0]
+  sp.latitude_rt=lat[1]
+  sp.save
+ end
+
+ #udunits�\���ɂ�鎞��time�ƒP��units�̒l��
+ #�f�[�^�x�[�X��DateTime�^�ŔF���ł���`�ɂ���
+ def parse_time_since(time, units)
+  if /(\w+) since (.*)/ =~ units
+    units = $1
+    since = $2
+  else
+    raise ArgumentError, 
+          "units '#{units}' is not in the expected form: units since date&time"
+  end
+  case units
+  when /^s$/i,/^sec/i
+    time = time/86400.0
+  when /^min/i
+    time = time/1440.0
+  when /^h$/i,/^hour/i
+    time = time/24.0
+  when /^day/i
+  else
+    raise ArgumentError, "Sorry, #{units} is not supported. Is it a time unit?"
+  end
+  eps = 1e-7   # adjuster to avoid unwanted round off
+  DateTime.parse(since) + ( time + eps )
+end
+
+end