Module: NumRu::GPhys::HE5_IO

Defined in:
lib/numru/gphys/gphys_hdfeos5_io.rb

Constant Summary collapse

PredefCoordNames = 
["Time","Longitude","Latitude","Colatitude"]
@@predef_gdcoords =

^ In the order of precedence

[/^altitude$/i, /^altitude/i, /^pressure$/i, /^wavelength$/i, /^wavelength/i,/^wavenumber$/i, /^wavenumber/i, /^time$/i,/time$/i]
@@predef_zacoords =

^ In the order of precedence

[/^latitude$/i, /^latitude/i, /^altitude$/i, /^altitude/i, /^pressure$/i, /^wavelength$/i, /^wavelength/i,/^wavenumber$/i, /^wavenumber/i, /^time$/i, /time$/i, /^solarzenithangle$/i, /^solarzenithangle/i]

Class Method Summary collapse

Class Method Details

.__convertTime(axisname) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 228

def __convertTime( axisname )
  # Convert Geo Location Field "Time" or "LocalTime"
#	if axisname.name == "Time" ||  axisname.name == "LocalTime"
#          axisname.val.each{|ax|
#            stun = axisname.units.to_s
#            since = DateTime.parse("1993-01-01 00:00:00+00:00")
#            tun = Units[stun]
#            sec = tun.convert( ax, Units['seconds'] ).round + 1e-1
#            datetime = since + (sec/86400.0)
#            ax =datetime.strftime("%Y-%m-%d %H:%M:%S")
#          }
#p axisname[0].val
#        end
end

.__files2varray(files, varname, dim = nil, gd_flag = nil, ntype = nil) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 243

def __files2varray( files, varname, dim=nil, gd_flag=nil, ntype=nil )
	if files.is_a?(HE5Sw)
	  # Single file. Returns a VArrayHE5SwField. dim is ignored.
	  file = files
	  var = file.var(varname)
	  raise "variable '#{varname}' not found in #{file}" if !var
	  if ntype != nil && gd_flag == 1
      VArrayHE5SwField.new2( var , varname, ntype,  dim)
	  elsif ntype != nil && gd_flag == 0
      VArrayHE5SwField.new3( file, varname, ntype,  dim)
	  else
      VArrayHE5SwField.new( var )
    end
  elsif files.is_a?(HE5Gd)
	  # Single file. Returns a VArrayHE5GdField. dim is ignored. 
	  file = files
	  var = file.var(varname)
	  raise "variable '#{varname}' not found in #{file}" if !var
	  if ntype != nil && gd_flag == 1
      VArrayHE5GdField.new2( var , varname, ntype,  dim)
	  else
      VArrayHE5GdField.new( var )
    end
  elsif files.is_a?(HE5Za)
	  # Single file. Returns a VArrayHE5ZaField. dim is ignored. 
	  file = files
	  var = file.var(varname)
	  raise "variable '#{varname}' not found in #{file}" if !var
	  if ntype != nil && gd_flag == 1
      VArrayHE5ZaField.new2( var , varname, ntype,  dim)
	  else
      VArrayHE5ZaField.new( var )
    end
	elsif files.is_a?(NArray)
	  # Suppose that files is a NArray of HDF-EOS5. Returns a VArrayCompsite.
	  if dim.is_a?(Integer) && dim>=0 && dim<files.rank
	    files = files[ *([0]*dim+[true]+[0]*(files.rank-dim-1)) ]
	  end
	  varys = NArray.object( *files.shape )
	  for i in 0...files.length
	    var = files[i].var( varname )
      ntype = var.ntype
      ntype = var.dim
	    raise "variable '#{varname}' not found in #{files[i].path}" if !var
  if ntype != nil && gd_flag == 1     # For Data Field
        varys[i] = VArrayHE5SwField.new2( var , varname, ntype,  dim)
	    elsif ntype != nil && gd_flag == 0  # For Geo Location Field
        varys[i] = VArrayHE5SwField.new3( file, varname, ntype,  dim)
	    else
        varys[i] = VArrayHE5SwField.new( var )
      end
	  end
	  if files.length != 1
	    VArrayComposite.new( varys )
	  else
	    varys[0]
	  end
	else
	  raise TypeError, "not a HDF-EOS5 or NArray"
	end
end

.__interpret_files(files, varname) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 305

def __interpret_files( files, varname )
  gridtype = nil  # --> "swath", "grid", "za", ....
	case files
	when HE5, String
    files   = HE5.open(files) if files.is_a?(String)
    dirname, varname, = varname.split(/\//)

    if files.has_swath?
      swath = files.swath(dirname) or raise("Can't find a swath named #{dirname}")
      he5var0 = swath.var( varname )
      gridtype = 'swath'
    elsif files.has_grid?
      grid = files.grid(dirname) or raise("Can't find a grid named #{dirname}")
      he5var0 = grid.var( varname )
      gridtype = 'grid'
    elsif files.has_za?
      za = files.zonal(dirname) or raise("Can't find a zonal average named #{dirname}")
      he5var0 = za.var( varname )
      gridtype = 'za'
    else
      raise "Sorry. Currenly, only the Swath type is supported"
    end
	when HE5Sw
	  he5var0 = files.var( varname )
    gridtype = 'swath'
	when HE5Gd
	  he5var0 = files.var( varname )
    gridtype = 'grid'
  # when Regexp 
	else
	  raise TypeError, "argument files: not a HDF-EOS5, String, NArray, or Array"
	end
	[files, he5var0, varname, gridtype]
end

.__make_field_one_dimension(aHE5GdField, dim_index) ⇒ Object

dim_index に関して実質1次元の変数ならば VArray を返す。そうでなければ nil を返す。



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 479

def __make_field_one_dimension(aHE5GdField, dim_index)
  rank = aHE5GdField.rank
  indexes = Array.new
  seps = (2**(-23).to_f) * 10
  deps = Float::EPSILON * 10 # (2**(-52).to_f) * 10
  permissible_diff = case aHE5GdField.simple_get.typecode
                     when NArray::SFLOAT, NArray::SCOMPLEX then seps
                     when NArray::DFLOAT, NArray::DCOMPLEX then deps
                     else 0
                     end

  for i in 0...rank do
    indexes.push(i) unless i == dim_index
  end
  mn = aHE5GdField.simple_get.min(*indexes)
  mx = aHE5GdField.simple_get.max(*indexes)
  maxdiff = (mx - mn).max
  maxval = ((mx1=mx.max)>(mx2=-mn.min)) ? mx1 : mx2        

  is_zero = (maxdiff/maxval <= permissible_diff)

  unless is_zero
    return nil 
  else
    ary = Array.new
    for j in 0...rank do
      if j == dim_index
        ary.push(true)
      else
        ary.push(0)
      end
    end
    return VArrayHE5GdField.new(aHE5GdField).[](*ary)
  end
end

.__make_gd_axes(var0, grid, data) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 340

def __make_gd_axes(var0, grid, data)
  dim_names = var0.dim_names # 次元の名前
  unlocated_dim_names = var0.dim_names # まだ軸の決まっていない次元の名前
  unused_var_names = grid.var_names
  axes = Array.new

  # (#1) HDF-EOS5 standard rule.
  ["Longitude", "Latitude"].each do |provided_varname|
    unlocated_dim_names.each do |dim_nm|
      if (vary = __make_field_one_dimension(grid.var(provided_varname), dim_names.index(dim_nm)))
        axes.push(Axis.new().set_pos(vary))
        unlocated_dim_names.delete(dim_nm)
        unused_var_names.delete(provided_varname)
        break
      end
    end
  end
  if unused_var_names.include?("Longitude") || unused_var_names.include?("Latitude")
    raise("Sorry. Truely multidimensional longitudes/latitudes are yet to be supported. (2-dimensional lon/lat data that are actually one dimensional are supported.)")
  end

  # (#2) Empirical rule (from EOS-AURA, MLS, etc)
  # (#2-1) 軸が未確定の次元に対し、次元名と一致する名前を持つ1次元変数を座標変数として採用する
  unlocated_dim_names.each do |dim_nm|
    if unused_var_names.include?(dim_nm)
      vary = __files2varray( grid, dim_nm)
      if vary.rank == 1
        axes.push(Axis.new().set_pos(vary))
        unlocated_dim_names.delete(dim_nm)
        unused_var_names.delete(dim_nm)
      end
    end
  end

  # (#2-2) 軸が未確定の次元に対し、その次元を使って定義されている1次元変数を座標変数として採用する
  # (a) select variables match to Regexp. 
  @@predef_gdcoords.each do |reg_exp|
    unlocated_dim_names.each do |dim_nm|
      # get candidates
      candidate_var_names = Array.new
      unused_var_names.each do |var_nm|
        var = grid.var(var_nm)
        if reg_exp =~ var_nm && var.dim_names.include?(dim_nm)
          candidate_var_names.push(var_nm)
        end
      end
      
      # permute the candidates in order of length.
      candidate_var_names = candidate_var_names.sort {|a, b| a.length <=> b.length}
      candidate_var_names.each do |candidate|
        vary = __files2varray(grid, candidate)
        if vary.rank == 1
          axes.push(Axis.new().set_pos(vary))
          unlocated_dim_names.delete(dim_nm)
          unused_var_names.delete(candidate)
        end
        break if unlocated_dim_names.length == 0
      end
    end
  end

  # (#2-3) 座標変数はファイル中にないものとみなし，
  # ダミーとして 0,1,2,... が割り当てられるようにする．
  unlocated_dim_names.each do |dim_nm|
    nary_length = data.shape_current[dim_names.index(dim_nm)]
    nary = NArray[0...nary_length]
    vary = VArray.new(nary).rename(dim_nm + "_dummy")
    axis = Axis.new(false, true)
    axis.set_pos(vary)
    axes.push(axis)
  end

  return axes
end

.__make_za_axes(var0, za, data) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 416

def __make_za_axes(var0, za, data)
  dim_names = var0.dim_names # 次元の名前
  unlocated_dim_names = var0.dim_names # まだ軸の決まっていない次元の名前
  unused_var_names = za.var_names
  axes = Array.new

  # (#1) HDF-EOS5 standard rule is none.
  # (#2) Empirical rule (from EOS-AURA, MLS, etc)
  # (#2-1) 次元名と一致する名前を持つ1次元変数を座標変数として採用する
  unlocated_dim_names.each do |dim_nm|
    if unused_var_names.include?(dim_nm)
      vary = __files2varray( za, dim_nm)
      if vary.rank == 1
        axes.push(Axis.new().set_pos(vary))
        unlocated_dim_names.delete(dim_nm)
        unused_var_names.delete(dim_nm)
      end
    end
  end

  # (#2-2) 軸が未確定の次元に対し、その次元を使って定義されている1次元変数を座標変数として採用する
  # (a) select variables match to Regexp. 
  @@predef_zacoords.each do |reg_exp|
    unlocated_dim_names.each do |dim_nm|
      # get candidates
      candidate_var_names = Array.new
      unused_var_names.each do |var_nm|
        var = za.var(var_nm)
        if reg_exp =~ var_nm && var.dim_names.include?(dim_nm)
          candidate_var_names.push(var_nm)
        end
      end
      
      # permute the candidates in order of length.
      candidate_var_names = candidate_var_names.sort {|a, b| a.length <=> b.length}
      candidate_var_names.each do |candidate|
        vary = __files2varray(za, candidate)
        if vary.rank == 1
          axes.push(Axis.new().set_pos(vary))
          unlocated_dim_names.delete(dim_nm)
          unused_var_names.delete(candidate)
        end
        break if unlocated_dim_names.length == 0
      end
    end
  end

  # (#2-3) 座標変数はファイル中にないものとみなし，
  # ダミーとして 0,1,2,... が割り当てられるようにする．
  unlocated_dim_names.each do |dim_nm|
    nary_length = data.shape_current[dim_names.index(dim_nm)]
    nary = NArray[0...nary_length]
    vary = VArray.new(nary).rename(dim_nm + "_dummy")
    axis = Axis.new(false, true)
    axis.set_pos(vary)
    axes.push(axis)
  end

  return axes
end

._gd_open(var0, varname) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 146

def _gd_open(var0, varname)
  #< make axes >
  grid = var0.grid
  data = __files2varray( grid, varname )
  axes = __make_gd_axes(var0, grid, data)

  #< make grid >
  new_grid = Grid.new( *axes )

  #< make gphys >
  GPhys.new(new_grid,data)
end

._sw_open(var0, varname) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 65

def _sw_open(var0, varname)
  swath = var0.swath
  	data = __files2varray( swath, varname )
	rank = data.rank
  dim_names = var0.dim_names

  #< coordiante varables >

  geo_names = swath.geo_names  # geolocation varables
  coords = Array.new(rank)
  assoccoords = Array.new

  proc = Proc.new{|nm|
    vdns = swath.var(nm).dim_names
    if vdns.length==1 && (dim=dim_names.index(vdns[0])) && !coords[dim]
      coords[dim] = __files2varray( swath, nm)
    elsif ( (vdns - dim_names).length==0 )  # all dims are covered
      dimids = vdns.collect{|s| dim_names.index(s)}
      assoccoords.push( [dimids, __files2varray( swath, nm)] )
    end
  }

  # (first precedence) Predefined coordinate variable names
  PredefCoordNames.each do |nm|
    proc.call(nm) if geo_names.delete(nm)  # if included, delete and call
  end

  # (second precedence) Variables having the same name as a dimension
  dim_names.each do |nm|
    proc.call(nm) if geo_names.delete(nm)  # if included, delete and call
  end

  # (else)
  geo_names.each do |nm|
    proc.call(nm) if  swath.geo(nm).ntype != "char"
  end

=begin
  # if no geolocation variable was found for a dim, search variables too
  if coords.include?(nil)
    swath.var_names.each do |nm|
      vdns = swath.var(nm).dim_names
      if vdns.length==1 && (dim=dim_names.index(vdns[0])) && !coords[dim]
        coords[dim] = __files2varray( swath, nm)
      end
      break if !coords.include?(nil)
    end
  end
=end

  #< make axes >
  axes = Array.new
  coords.each_with_index do |crd, dim|
    if crd
      axis = Axis.new
      axis.set_pos( crd )
    else
      axis = Axis.new(false, true)
      dimnm = dim_names[dim]
      len = data.shape_current[dim]
      axis.set_pos( VArray.new(NArray.float(len).indgen!).rename(dimnm) )
    end
    axes.push( axis )
  end

  #< make grid >
  grid = Grid.new( *axes )

  if assoccoords.length > 0
    assoccoords.collect! do |dimids, vary|
      acgrid = Grid.new( *(dimids.collect{|dim| axes[dim]}) )
      gphys = GPhys.new(acgrid, vary)
    end
    grid.set_assoc_coords( assoccoords )
  end

  #< make gphys >
  GPhys.new(grid,data)
end

._za_open(var0, varname) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 160

def _za_open(var0, varname)
  #< make axes >
  za = var0.za

  data = __files2varray( za, varname )
  axes = __make_za_axes(var0, za, data)

  #< make grid >
  new_za = Grid.new( *axes )

  #< make gphys >
  GPhys.new(new_za,data)
end

.add_predef_gdcoords(regexp) ⇒ Object

^ In the order of precedence

Raises:

  • (ArgumentError) 


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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 22

def self.add_predef_gdcoords(regexp)
  raise ArgumentError, "arg must be a regexp" unless regexp.is_a?(Regexp)
  @@predef_gdcoords.push(regexp)
end

.add_predef_zacoords(regexp) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 31

def self.add_predef_zacoords(regexp)
  raise ArgumentError, "arg must be a regexp" unless regexp.is_a?(Regexp)
  @@predef_gdcoords.push(regexp)
end

.is_a_HE5?(filename) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 40

def is_a_HE5?(filename)
  file = nil
  begin
    file = File.open(filename,"rb")
    str = file.read(4)
  ensure
    file.close if file
  end
  return str=="\211HDF"
end

.open(files, varname) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 51

def open(files, varname)
	files, var0, varname, gridtype = __interpret_files( files, varname )
  case gridtype
  when "swath"
    _sw_open(var0, varname)
  when "grid"
    _gd_open(var0, varname)
  when "za"
    _za_open(var0, varname)
  else
    raise "Sorry. Currently, only the Swath type is supported"
  end
end

.predef_gdcoords ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 27

def self.predef_gdcoords
  @@predef_gdcoords
end

.predef_zacoords ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 36

def self.predef_zacoords
  @@predef_gdcoords
end

.var_names(files) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 195

def var_names(files)
  case files
  when HE5
    file = files
    opened = true
  when String
    file = HE5.open(files)
    opened = false
  else
    raise ArgumentError, "arg must be a HDF-EOS5 or a file name"
  end
  raise "file must be a HDF-EOS5 swath filed" if !file.has_swath?()
  swathlist=file.swath_names()
  varnames=[]
  for i in 0..swathlist.size-1
    sfile=file.swath(swathlist[i])
    sfile.var_names.each{|name|
      f, var, varname, gridtype = __interpret_files( sfile, name )
      if var.rank>1 || var.name!=var.dim_names[0]
        varnames.push(swathlist[i]+"/"+name)
      end
    }
    sfile.closed           # close Swath field
  end
  file.close unless opened # close Swath field & close HDF-EOS5 file
  return varnames
end

.var_names_except_coordinates(files) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 223

def var_names_except_coordinates(files)
  var_names(files)
end

.write(file, gphys, name = nil) ⇒ Object 



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# File 'lib/numru/gphys/gphys_hdfeos5_io.rb', line 175

def write(file, gphys, name=nil)
  name = gphys.name if name.nil?
  dims = Array.new
  gphys.rank.times{|n|
    dims[n] = gphys.coord(n)
  }

  case file
  when HE5Sw
    VArrayHE5SwField.write(file,gphys.data,name,dims)
  when HE5Gd
    VArrayHE5GdField.write(file,gphys.data,name,dims)
  when HE5Za
  else
    raise ArgumentError, "arg must be a HE5Sw, a HE5Gd or a HE5Za"
  end

  nil
end