Module: NumRu::GPhys::IO

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

Constant Summary collapse

NETCDF =

// file type selctor –>

"NETCDF"
GRADS = 
"GRADS"
GRIB = 
"GRIB"
NUSDAS = 
"NUSDAS"
He5 = 
"He5"
GTOOL3 = 
"GTOOL3"
GTURLfmt = 
"path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
@@iomdl = 
{NETCDF => GPhys::NetCDF_IO,
GRADS => GPhys::GrADS_IO,
GRIB => GPhys::Grib_IO,
NUSDAS => GPhys::NuSDaS_IO,
GTOOL3 => GPhys::Gtool3_IO}
@@file_class = 
{NETCDF => NetCDF,
GRADS => GrADS_Gridded,
#GRIB => VArrayGrib.grib, # Hash is not dynamic: see below
NUSDAS => NuSDaS,
GTOOL3 => Gtool3}
@@nc_pattern = 
[/\.nc$/]
@@grad_pattern = 
[/\.ctl$/]
@@grib_pattern = 
[/\.grib$/, /\.grb$/]
@@nus_pattern = 
[/\.nus$/]
@@has_he5 = 
defined?(HE5)
@@he5_pattern = 
[/\.he5$/]

Class Method Summary collapse

Class Method Details

.[](key) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 272

def @@file_class.[](key)
  if key == GRIB
    VArrayGrib.grib
  else
    super
  end
end

.each_along_dims_write(gphyses, files, *loopdims, &block) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 241

def each_along_dims_write(gphyses, files, *loopdims, &block)

	files = [files] if !files.is_a?(Array)
	files.each do |fl|
	  if fl.is_a?(NetCDF)
	    NetCDF_Conventions.add_history(fl, "#{File.basename($0)}")
	  end
	end

	IO_Common::each_along_dims_write(gphyses, files, loopdims, 
file2specific_module(files), &block)
end

.file2file_class(file) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 341

def file2file_class(file)
	@@file_class[ file2type(file) ]
end

.file2specific_module(file) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 337

def file2specific_module(file)
	@@iomdl[ file2type(file) ]
end

.file2type(file) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 291

def file2type(file)
 	case file
	when Array, NArray
	  return file2type(file[0])   # inspect the first element (ignoring the rest)
	when NetCDF
	  return NETCDF
	when GrADS_Gridded
	  return GRADS
	when VArrayGrib.grib
	  return GRIB
  when NuSDaS
    return NUSDAS
  when Gtool3
    return GTOOL3
	when *@@nc_pattern
	  return NETCDF
	when *@@grad_pattern
	  return GRADS
	when *@@grib_pattern
    return GRIB
  when *@@nus_pattern
    return NUSDAS
	when String
	  return NETCDF if /^http:\/\// =~ file   # assume a DODS URL
    raise ArgumentError, "File not found: #{file}" unless File.exist?(file)
    return NETCDF if NetCDF_IO.is_a_NetCDF?(file)
    return GRADS if GrADS_IO.is_a_GrADS?(file)
    return GRIB if Grib_IO.is_a_Grib?(file)
    return NUSDAS if NuSDaS_IO.is_a_NuSDaS?(file)
    return GTOOL3 if Gtool3_IO.is_a_Gtool3?(file)
	end
  if @@has_he5
    case file
    when HE5, HE5Sw
      return He5
    when *@@he5_pattern
      return He5
    when String
      return He5   if HE5_IO.is_a_HE5?(file)
    end
  end
  raise "cannot specify the file type of \""+ file + \
        "\"; maybe unsupported format."
  return nil
end

.open(file, varname) ⇒ Object

// module functions to be defined in specific IO modules –>



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# File 'lib/numru/gphys/gphys_io.rb', line 186

def open(file, varname)
  case file
  when Array, NArray, Regexp
    open_multi(file, varname)
  else
    file2specific_module(file)::open(file, varname)
  end
end

.open_gturl(gturl) ⇒ Object

def parse_gturl



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# File 'lib/numru/gphys/gphys_io.rb', line 458

def open_gturl(gturl)
	file, var, slice, cut_slice, thinning = GPhys::IO.parse_gturl(gturl)
  if var.is_a?(Array)
    raise "This method treats a gturl of a single GPhys object. " +
       "Use open_multi_gturl to treat a gturl of multiple objects."
  end
  gp = GPhys::IO.open(file,var)
	gp = gp[slice] if slice
	gp = gp.cut(cut_slice) if cut_slice
	gp = gp[thinning] if thinning
	gp
end

.open_multi(files, varname) ⇒ Object 



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

def open_multi(files, varname)
  case files
  when Array
    GPhys.join( files.collect{|f| open(f,varname)} )
  when NArray
    GPhys.join_md( files.collect{|f| open(f,varname)} )
  when Regexp
    GPhys.join_md( regexp2files(files).collect{|f| open(f,varname)} )
  end
end

.open_multi_gturl(gturl) ⇒ Object

def open_gturl



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# File 'lib/numru/gphys/gphys_io.rb', line 471

def open_multi_gturl(gturl)
	files, vars, slice, cut_slice, thinning = GPhys::IO.parse_gturl(gturl)
  vars = [vars] unless vars.is_a?(Array)
  gp_array = Array.new
  vars.each do |v|
    begin 
      gps = [ GPhys::IO.open(files,v) ]   # opened as a single GPhys
    rescue ArgumentError 
      if files.is_a?(Array)
        # gturl may designate multiple GPhys objects
        gps = files.collect{|f| gp = GPhys::IO.open(f,v) }
      else
        raise $!    # it must have been a real error
      end
    end
    gp_array += gps
  end
  gp_array.map!{|gp|
    gp = gp[slice] if slice
    gp = gp.cut(cut_slice) if cut_slice
    gp = gp[thinning] if thinning
    gp
  }
  gp_array
end

.parse_gturl(gturl) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 380

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" + 
    "URL format: " + GTURLfmt
	end
  if /[\*\?]/ =~ file ## match file names if wildcard expression included.
    raise "\n Any files did not match the given expression: \""+file+\
          "\" \n" if Dir[file].empty?
    file = Dir[file].sort
  elsif (!File.exist?(file))
    raise "File specified by gturl \"#{gturl}\" was not found"
  end
	if /,/ =~ var
	  slice = Hash.new
	  cut_slice = Hash.new
	  thinning = Hash.new
	  var_descr = var.split(/,/)
	  var = var_descr.shift
	  var_descr.each do |s|
	    if /(.*)=(.*)/ =~ s
 dimname = $1
 subset = $2
 case subset
 when /\^(.*):(.*):(.*)/
		slice[dimname] = ($1.to_i)..($2.to_i)
		thinning[dimname] = {(0..-1) => $3.to_i}
 when /\^(.*):(.*)/
		slice[dimname] = ($1.to_i)..($2.to_i)
 when /\^(.*)/
		slice[dimname] = $1.to_i
 when /(.*):(.*):(.*)/
		cut_slice[dimname] = ($1.to_f)..($2.to_f)
		thinning[dimname] = {(0..-1) => $3.to_i}
 when /(.*):(.*)/
		cut_slice[dimname] = ($1.to_f)..($2.to_f)
 else
		cut_slice[dimname] = subset.to_f
 end
	    else
 raise "invalid URL: variable subset specification error\n\n" + 
		"URL format: " + GTURLfmt
	    end
	  end
	  slice = nil if slice.length == 0
	  cut_slice = nil if cut_slice.length == 0
	  thinning = nil if thinning.length == 0
	else
	  slice = nil
	  cut_slice = nil
	  thinning = nil
	end
  if /[\*\?]/ =~ var ## match var names if wildcard expression included.
    var_reg = var.gsub("*",".*").gsub("?",".") # convert to regular exp.
    case file
    when String
      vars = GPhys::IO.var_names_except_coordinates(file)
    when Array
      vars_t = file.collect{|f| GPhys::IO.var_names_except_coordinates(f)}
      vars = vars_t.flatten.uniq
    end
    vars_matched = vars.select{|v| v.match(/#{var_reg}/)}
    if (vars_matched.empty?) 
      raise "\n Any variables in \"#{file}\" did not match the given 
      expression: \"#{var}\".\n Included variable(s): #{vars.join(", ")}."
    end
    # put the variable name by String if the number of matched variable is
    # one, otherwise by Array of Strings.
    var = vars_matched.length == 1 ? vars_matched[0] : vars_matched 
  end
	[file, var, slice, cut_slice, thinning]
end

.regexp2files(pat) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 206

def regexp2files( pat )
  if  /^(.*)\\?\/(.*)$/ =~ (pat.source)
    d=$1
    f=$2
    dir = d.gsub(/\\/,'') + '/'
    pat = Regexp.new(f)
  else
    dir = './'
  end
  flstore = MDStorage.new(1)
  lbs = Array.new
  Dir.open(dir).each do |fn| 
    if pat =~ fn
      raise(ArgumentError,"has no capture; need one or more") if $1.nil?
      idx = Array.new
      Regexp.last_match.captures.each_with_index{|lb,i|
        flstore.add_dim if flstore.rank == i   # rank smaller by 1 -> add
        lbs[i] = Array.new if lbs[i].nil?
        idx.push( lbs[i].index(lb) || lbs[i].push(lb) && lbs[i].length-1 )
      }
      flstore[*idx] = NetCDF.open(dir+fn)
    end
  end
  flstore.to_na
end

.str2gphys(str) ⇒ Object

def open_multi_gturl



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# File 'lib/numru/gphys/gphys_io.rb', line 497

def str2gphys(str)

  case str
  when /^https?:\/\//
    file_tester = Proc.new{|fname| NetCDF.open(fname) rescue false}
  when
    file_tester = Proc.new{|fname| File.exists?(fname)}
  end
  fname = str; vname = nil   # initial value
  while fname
    if file_tester.call(fname)
      break
    else
      if /(.*)\/([^\/]+)/ =~ fname
        fname = $1
        if vname.nil?
          vname = $2
        else
          vname = $2 + "/" + vname
        end
      else
        raise "Not found: #{str}"
      end
    end
  end
  if vname.nil?
    vns = var_names_except_coordinates(fname)
    if vns.length==1
      vname=vns.first 
    else
      raise "#{str} has multiple variables #{vns.inspect}. Specify one."
    end
  end
  open(fname,vname)
end

.use_gphys_grib ⇒ Object

switches for io libraries switch grib library



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# File 'lib/numru/gphys/gphys_io.rb', line 178

def use_gphys_grib
  VArrayGrib.use_gphys_grib
end

.use_rb_grib ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 181

def use_rb_grib
  VArrayGrib.use_rb_grib
end

.var_names(file) ⇒ Object

<– file type selctor //



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# File 'lib/numru/gphys/gphys_io.rb', line 371

def var_names(file)
  file2specific_module(file).var_names(file)
end

.var_names_except_coordinates(file) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 374

def var_names_except_coordinates(file)
  file2specific_module(file).var_names_except_coordinates(file)
end

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



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# File 'lib/numru/gphys/gphys_io.rb', line 232

def write(file, gphys, name=nil)
	file2specific_module(file)::write(file, gphys, name)
end

.write_grid(file, grid_or_gphys) ⇒ Object 



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# File 'lib/numru/gphys/gphys_io.rb', line 236

def write_grid(file, grid_or_gphys)
	# usually not needed (internally called by write)
	file2specific_module(file)::write_grid(file, grid_or_gphys)
end