gphys 1.1.1a

data/bin/gpedit

@@ -0,0 +1,228 @@
+#!/usr/bin/env ruby
+=begin
+= NAME
+
+:gpedit:
+   Create or overwrite the attributes of a variable specified by
+   a gtool4-type URL (Only netCDF files are supported).
+  
+= USAGE
+
+  % gpedit [options] path@[varname:var_attr=...][varname|+global_attr]
+
+= EXAMPLES
+
+* Add
+        % gpedit data.nc@temp:units=W/m
+        % gpedit -a data.nc@temp:missing_value=-2.0e20
+        % gpedit --add data.nc@temp+title=\"surface temperature\"
+
+* Delete
+        % gpedit -d data.nc@lon:topology
+        % gpedit --delete data.nc@lon+Conventions
+"
+=  HISTORY
+
+   2010/03/10  Y SASAKI (change help block into RD format)
+   2007/07/18  Y. Morikawa  'gpattr' is renamed to 'gpedit'
+   2006/09/29  Y. Morikawa  A value looks like numeric is treated as a numerical value
+   2005/01/09  Y. Morikawa
+   2005/01/07  D. Tsukahara
+
+
+=end
+##################################################
+#= gpedit
+#== SYNOPSIS
+SYNOPSIS = <<-"SYNOP"
+     Create or overwrite the attributes of a variable specified by
+     a gtool4-type URL (Only netCDF files are supported).
+SYNOP
+
+#== HISTORY
+#
+#   2010/03/10  Y SASAKI (change help block into RD format)
+#   2007/07/18  Y. Morikawa  'gpattr' is renamed to 'gpedit'
+#   2006/09/29  Y. Morikawa  A value looks like numeric is treated as a numerical value
+#   2005/01/09  Y. Morikawa
+#   2005/01/07  D. Tsukahara
+#
+#==USAGE
+URLFMT = "path@[varname:var_attr=...][varname|+global_attr]"
+USAGE = "
+        % #{File.basename(__FILE__)} [options] url
+
+     where the format of the url is
+
+         #{URLFMT}
+"
+#==EXAMPLES
+EXAMPLES = "
+    * Add
+        % #{File.basename(__FILE__)} data.nc@temp:units=W/m
+        % #{File.basename(__FILE__)} -a data.nc@temp:missing_value=-2.0e20
+        % #{File.basename(__FILE__)} --add data.nc@temp+title=\"surface temperature\"
+
+    * Delete
+        % #{File.basename(__FILE__)} -d data.nc@lon:topology
+        % #{File.basename(__FILE__)} --delete data.nc@lon+Conventions
+"
+#
+##################################################
+require "optparse"
+require "numru/netcdf"
+include NumRu
+
+opt = OptionParser.new
+OPTS = {}
+ARGV.options{|opt|
+
+  opt.summary_width = 23
+  opt.summary_indent = ' '*6
+
+  opt.on( '-a', '--add',
+                             "Add attribute (default)."
+         ){|v| OPTS[:add] = v}
+
+  opt.on( '-d', '--delete',
+                             "Delete attribute."
+         ){|v| OPTS[:delete] = v}
+
+  opt.on_tail('-h', '-H', '--help', 
+                             "Show this help message.\n"
+              ){|v| OPTS[:help] = v}
+
+  opt.parse!
+}
+
+## help
+def help(opt)
+  print <<-"EOF"
+
+#{File.basename(__FILE__)}: 
+#{SYNOPSIS}
+  USAGE: #{USAGE}
+  OPTION: \n#{opt.to_a[1..-1].join("")}
+  EXAMPLES:
+    #{EXAMPLES}
+  EOF
+end
+private :help
+
+
+#####################################################
+
+def to_appropriate_type(str)
+  if str =~ /\.|e/i
+    val = str.to_f
+  else
+    val = str.to_i
+  end
+  if val.to_i == 0
+    unless str =~ /^0+((\.0+)?(e\d+)?)?$/i
+      val = str
+    end
+  end
+  return val
+end
+
+def url_error(msg)
+  $stderr.print <<-"EOF"
+
+  Error: invalid URL: #{msg}.
+         Current URL format is 
+  
+           #{URLFMT}
+
+EOF
+  exit 1
+end
+
+def parse_gturl_for_attr(gturl)
+  if /(.*)@(.*)/ =~ gturl
+    file = $1
+    var = $2
+  else
+    url_error "'@' between path & variable is not found"
+  end
+  if /(.*):(.*)/ =~ var
+    var_name = var.split(":")[0]
+    att =      var.split(":")[1]
+    if /(.*)\=(.*)/ =~ att
+      var_att =    att.split("=")[0]
+      global_att = nil
+      att_val  =   to_appropriate_type(var.split("=")[1])
+    elsif OPTS[:delete]
+      var_att =    att
+      global_att = nil
+      att_val =    nil
+    else
+      url_error "'=' between atribute name & value is not found"
+    end
+  elsif /(.*)\+(.*)/ =~ var
+    var_name = var.split("+")[0]
+    att =      var.split("+")[1]
+    if /(.*)\=(.*)/ =~ att
+      var_att =    nil
+      global_att = att.split("=")[0]
+      att_val =    to_appropriate_type(att.split("=")[1])
+    elsif OPTS[:delete]
+      var_att =    nil
+      global_att = att
+      att_val =    nil
+    else
+      url_error "'=' between atribute name & value is not found"
+    end
+  else
+    url_error "':' or '+' between atribute name & value is not found"
+  end
+  if !(att_val) && !OPTS[:delete]
+    url_error "attribute value is not found. you must point out unless delete attribute"
+  end
+  [file, var_name, var_att, global_att, att_val]
+end
+#####################################################
+
+if OPTS[:help] || ARGV.length != 1 then
+  help(opt)
+  exit
+end
+
+gturl = ARGV[0]
+file, var, var_att, global_att, att_val = parse_gturl_for_attr(gturl)
+
+begin
+  nc = NetCDF.new(file, "r")
+  nc.close
+rescue NetcdfSyserr
+  $stderr.print "  Error: " + file + ": " + $!.to_s + "\n"
+  exit 1
+rescue NetcdfNotnc
+  $stderr.print "  Error: " + file + ": " + $!.to_s + "\n"
+  $stderr.print "  \"#{File.basename(__FILE__)}\" supports only netCDF files.\n"
+  exit 1
+end
+
+nc = NetCDF.new(file, "a+")
+if nc.var(var)
+  var = nc.var(var)
+elsif nc.dim(var)
+  var = nc.dim(var)
+end
+nc.redef
+if var.class.to_s == "String"
+  $stderr.print "  Error: #{file}@#{var}: variable is not found.\n"
+  exit 1
+end
+if OPTS[:delete]
+  begin
+    nc.att(global_att).delete       if global_att
+    var.att(var_att).delete         if var_att
+  rescue NoMethodError
+    print "  Warning: " + gturl + " is not exist.\n"
+  end
+else
+  nc.put_att(global_att, att_val) if global_att
+  var.put_att(var_att, att_val)   if var_att
+end
+nc.close

data/bin/gplist

@@ -0,0 +1,68 @@
+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gplist - print out info on GPhys-compatible variables in specified files.
+
+= Usage 
+
+   % gplist [-h] [ FILES... ]
+
+where FILES are plane files (NetCDF, grib, GrADS control..) or directories. 
+If omitted, equivalent to specifing the current directory.
+
+= HISTORY
+
+  2005/05/15  S Takehiro (created)
+  2005/06/21  T Horinouchi (modified to use GDir (non-recursive version))
+  2005/08/10  S Takehiro (utilize internal function for printing help message)
+  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+require "getoptlong"
+
+#---------------------- Option Configuration ----------------------
+parser = GetoptLong.new(
+  ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
+
+begin
+  parser.each do |opt, arg|
+    case opt
+    when "--help"
+      help
+      exit(0)
+    end
+  end
+rescue
+  raise "\n\n"+usage
+end
+
+#------------------------ Do the job ------------------------
+GDir.top='/'
+
+if ARGV.length==0
+  paths = ['.']
+else
+  paths = ARGV
+end
+
+paths.each do |path| 
+  print path,":\n"
+  gdir = GDir.new(File.expand_path(path))
+  # for a plane file:
+  gdir.list_data_v.each{|s| print "  #{s}\n"}
+  # for a directory:
+  gdir.list_dirs.each do |sub|
+    lsv = gdir.dir(sub).list_data_v
+    if lsv.length>0
+      print( (ARGV.length!=0 ? "#{path.sub(/\/+$/,'')}/" : ""), sub, ":\n")
+      lsv.each{|s| print "  #{s}\n"}
+    end
+  end
+end

data/bin/gpmath

@@ -0,0 +1,120 @@
+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gpmath - operating a mathematical function to a GPhys variable. 
+
+= USAGE
+
+  % gpmath [options] path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+
+= OPTIONS
+ 
+:-h,--help
+  print this message. 
+:-f func, --function func
+  function name to operate (optional). 
+  Default function name is $0[2..-1].
+:-n name, --name name
+  name of the output gphys variable (optional).
+:-l name, --longname name
+  long_name attr. of the output gphys variable (optional).
+:-o file, --output file
+  output filename (optional). Default output filename is 'gphys.nc'.
+
+  * Commands which operates mathematical functions to a gphys variable are 
+    successively installed by linking this sciript as a "gp+[math. func. name]".
+
+= HISTORY
+
+  2005/06/21  S Takehiro  (created)
+  2005/07/15  S Takehiro (open_gturl method is used for opening gphys variable)
+  2005/08/10  S Takehiro (utilize internal function for printing help message)
+  2005/08/21  S Takehiro (global attributes copied to the output file)
+  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+require "getoptlong"
+
+#------------------------ Default Settings ------------------------
+Output_default = 'gphys.nc'
+URLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+
+#---------------------- Option Configuration ----------------------
+parser = GetoptLong.new(
+  ["--output",   "-o", GetoptLong::REQUIRED_ARGUMENT],
+  ["--function", "-f", GetoptLong::REQUIRED_ARGUMENT],
+  ["--name",     "-n", GetoptLong::REQUIRED_ARGUMENT],
+  ["--longname", "-l", GetoptLong::REQUIRED_ARGUMENT],
+  ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
+begin
+  parser.each{|opt, arg|
+    case opt
+    when "--output"   then eval "$OPT_output='#{arg}'"
+    when "--function" then eval "$OPT_function='#{arg}'"
+    when "--name"     then eval "$OPT_name='#{arg}'"
+    when "--longname" then eval "$OPT_longname='#{arg}'"
+    when "--help"     then eval "$OPT_help=true"
+    else
+      raise "must not happen"
+    end
+  }
+  rescue GetoptLong::AmbigousOption, GetoptLong::InvalidOption,
+          GetoptLong::MissingArgument, 
+          GetoptLong::NeedlessArgument => err
+    help
+    $srderr.puts err.message
+    exit 1
+end
+
+#------------------------ Help message ------------------------
+if $OPT_help then
+  help
+  exit(0)
+end  
+
+#------------------------ Option check ------------------------
+$OPT_output = Output_default unless $OPT_output
+
+#------------------------ Output file check  --------------------------
+raise "#{$OPT_output} already exists." if FileTest.exist?($OPT_output) 
+outncfile=NetCDF.create($OPT_output)
+
+#------------------------ Open gphys variable ------------------------
+gturl = ARGV[0]
+gphys = GPhys::IO.open_gturl(gturl)
+outncfile.copy_global_att(gphys) # Copy global attributes (only for NetCDF)
+
+#--------------------- evaluate math function  -----------------------
+$OPT_function = File.basename($0)[2..-1] unless $OPT_function
+
+eval <<-EOS
+  gphys = gphys.#{$OPT_function}
+EOS
+
+#--------------------- rename, set attribute  -----------------------
+if $OPT_name
+  gphys.rename($OPT_name)
+else
+  gphys.rename($OPT_function+"_"+gphys.name)
+end
+
+if $OPT_longname
+  gphys.set_att('long_name',$OPT_longname)
+else
+  longname=gphys.get_att('long_name')
+  gphys.set_att('long_name',$OPT_function + " of " + longname) if longname
+end
+
+#---------------------- Output GPhys variable  ------------------------
+GPhys::IO.write( outncfile, gphys )
+NetCDF_Conventions.add_history(outncfile, File.basename($0)+" "+ARGV[0])
+outncfile.close
+
+print File.basename($0) +": "+ARGV[0]+ " is written to #{$OPT_output}.\n"

data/bin/gpmaxmin

@@ -0,0 +1,128 @@
+#!/usr/bin/env ruby
+=begin
+= NAME
+
+gpmaxmin - printing maximum and minimum values of a GPhys variable.
+
+= USAGE
+
+   % gpmaxmin [options] path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+
+= OPTIONS
+
+     -h,      --help     : Print this message. 
+     -n,      --number   : Number of displayed points having max and min values.
+     -a,      --all      : All points are displayed.
+     -i,      --index    : Indicies of max and min points are displayed.
+
+= HISTORY
+
+  2005/05/17  S Takehiro (created)
+  2005/07/15  S Takehiro (open_gturl method is used for opening gphys variable)
+  2005/08/07  S Takehiro (parse_gturl removed)
+  2005/08/10  S Takehiro (locations having max and min values are displayed.
+                          utilize internal function for printing help message.
+                          --all, --index, --number options added.)
+  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2006/03/07  M Nakano (USAGE Typo fixed)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+require "getoptlong"
+
+#------------------------ Default Settings ------------------------
+URLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+print_maxdefault=5
+
+#---------------------- Option Configuration ----------------------
+parser = GetoptLong.new(
+  ["--help",     "-h", GetoptLong::NO_ARGUMENT      ],
+  ["--all",      "-a", GetoptLong::NO_ARGUMENT      ],
+  ["--index",    "-i", GetoptLong::NO_ARGUMENT      ],
+  ["--number",   "-n", GetoptLong::REQUIRED_ARGUMENT])
+begin
+  parser.each{|opt, arg|
+    case opt
+    when "--help" then eval "$OPT_help=true"
+    when "--number" then eval "$OPT_number='#{arg}'"
+    when "--all" then eval "$OPT_all=true"
+    when "--index" then eval "$OPT_index=true"
+    else
+      raise "must not happen"
+    end
+  }
+  rescue GetoptLong::AmbigousOption, GetoptLong::InvalidOption,
+          GetoptLong::MissingArgument, 
+          GetoptLong::NeedlessArgument => err
+    help
+    $srderr.puts err.message
+    exit 1
+end
+
+#------------------------ Help message ------------------------
+if ( $OPT_help )
+  help 
+  exit(0)
+end  
+
+#------------------------ Option check ------------------------
+gturl = ARGV[0]
+gphys = GPhys::IO.open_gturl(gturl)
+print_maxnumber = ($OPT_number.to_i||print_maxdefault)
+
+#-------------------- find max. and min values -----------------------
+maxval = gphys.val.max   # naray-miss class method is implicitly expected 
+minval = gphys.val.min   # naray-miss class method is implicitly expected 
+
+idx1ds = gphys.val.eq(maxval).where
+idxsmax = Array.new
+idx1ds.each do |idx1d|
+  idxsmax.push(idx=Array.new)
+  gphys.shape.each_with_index{|len,d| idx1d,idx[d] = idx1d.divmod(len)}
+end
+
+idx1ds = gphys.val.eq(minval).where
+idxsmin = Array.new
+idx1ds.each do |idx1d|
+  idxsmin.push(idx=Array.new)
+  gphys.shape.each_with_index{|len,d| idx1d,idx[d] = idx1d.divmod(len)}
+end
+
+#---------------------- Output max and min values  ------------------------
+print_maxnumber = idxsmax.length if ( $OPT_all )
+
+print gturl+" : max="+maxval.to_s+", at, \n"
+for i in 0..[print_maxnumber,idxsmax.length].min-1
+  location = Array.new
+  idxsmax[i].each_with_index{|idx,cid|
+    if ($OPT_index) 
+      location.push(gphys.coord(cid).name+"=" + idx.to_s)
+    else
+      location.push(gphys.coord(cid).name+"=" + gphys.coord(cid).val[idx].to_s)
+    end
+  }
+  print " "+ (i+1).to_s + " : "+ location.join(",  ")+"\n"
+end
+print "     ...(total "+idxsmax.length.to_s+" points)...\n" if ( print_maxnumber < idxsmax.length )
+print "\n"
+
+print_maxnumber = idxsmin.length if ( $OPT_all )
+
+print gturl+" : min="+minval.to_s+", at,  \n"
+for i in 0..[print_maxnumber,idxsmin.length].min-1
+  location = Array.new
+  idxsmin[i].each_with_index{|idx,cid|
+    if ($OPT_index) 
+      location.push(gphys.coord(cid).name+"=" + idx.to_s)
+    else
+      location.push(gphys.coord(cid).name+"=" + gphys.coord(cid).val[idx].to_s)
+    end
+  }
+  print " "+ (i+1).to_s + " : "+ location.join(",  ")+"\n"
+end
+print "     ...(total "+idxsmin.length.to_s+" points)...\n" if ( print_maxnumber < idxsmin.length )

data/bin/gpprint

@@ -0,0 +1,60 @@
+#!/usr/bin/env ruby
+
+##################################################
+=begin
+= NAME
+
+gpprint - a command to print the values of a variable specified by a gtool4-type URL. 
+
+= DESCRIPTION
+
+((*gpprint*)) is a command-line tool to print the values of a variable
+specified by a gtool4-type URL. Outputs are comma-separated ascii
+texts with line feeding to avoid long lines and are made to stdout.
+
+= USAGE
+
+     % gpprint url
+ 
+where the format of the url is 
+
+     path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+
+= EXAMPLES
+
+    % gpprint data.nc@temp
+    % gpprint data.nc@temp,lon=135.0
+    % gpprint data.nc@temp,lon=130:150,lat=0
+    % gpprint data.nc@temp,lon=130:150,lat=0:90:2
+
+= HISTORY
+
+  2004/12/14  T Horinouchi (created)
+  2005/01/12  T Horinouchi (document -> in rd)
+  2005/06/15  S Takehiro (set first_dim_length 1 when gp.shape[0] returns nil)
+  2005/08/10  S Takehiro (utilize internal function for printing help message)
+  2005/08/23  S Takehiro (common methods to gp* command moved to gpcommon.rb)
+  2010/03/10  Y SASAKI (change help block into RD format)
+
+=end
+##################################################
+
+require "numru/gphys"
+require "numru/gphys/gpcommon"
+include NumRu
+
+#------------------------ print help message ------------------------
+
+help  if ARGV.length != 1 or /^-+h/ =~ ARGV[0]
+gturl = ARGV[0]
+gp = GPhys::IO.open_gturl(gturl)
+
+new_line_int = 6
+first_dim_len = (gp.shape[0]||1)
+fmt = " %g,"
+i = 1
+gp.val.each do |v| 
+  printf(fmt,v)
+  print "\n" if (i % new_line_int) == 0 or (i % first_dim_len) == 0
+  i += 1
+end