gphys 1.2.2.1 → 1.4.3

data/LICENSE.txt

@@ -1,22 +1,34 @@
-Copyright (c) 2012 Eriko Nishimoto
+GPhys is copyrighted free software by Takeshi Horinouchi and
+GFD Dennou Club (http://www.gfd-dennou.org/).
 
-MIT License
+Copyright 2003-2015 (C) Takeshi Horinouchi and GFD Dennou Club
+(http://www.gfd-dennou.org/) All rights reserved.
 
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+   1. Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+   2. Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in
+      the documentation and/or other materials provided with the
+      distribution.
+
+THIS SOFTWARE IS PROVIDED BY GFD DENNOU CLUB AND CONTRIBUTORS ``AS IS'' 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GFD DENNOU CLUB OR
+CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The views and conclusions contained in the software and documentation
+are those of the authors and should not be interpreted as representing
+official policies, either expressed or implied, of Takeshi Horinouchi
+and GFD Dennou Club.

data/Rakefile

@@ -1 +1,2 @@
 require "bundler/gem_tasks"
+

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "gphys"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/gpcat

@@ -21,6 +21,12 @@ gpcat - Read a variable in multiple NetCDF files, concatenate and write them to
    variable name (required).
 :-s sfmt, --slice sfmt
    slice,thinnng  (optional).
+:-m axis --mean axis
+   mean along axis (optional)
+:-d axis --stddev axis
+   stddev along axis (optional)
+:-e axis --eddy axis
+   eddy along axis  (optional)
 :-o file, --output file
    output filename (optional). Default output filename is 'gphys.nc'.
                                  
@@ -32,6 +38,8 @@ gpcat - Read a variable in multiple NetCDF files, concatenate and write them to
   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)
+  2014/03/10  S Takehiro (big fix for ruby 1.9)
+  2015/02/03  S Takehiro (option --mean, --stddev, --eddy added)
 
 =end
 
@@ -41,7 +49,6 @@ include NumRu
 
 require "getoptlong"
 
-
 #-------------------- Slice parameter analysis --------------------
 def parse_slice(arg_slice)
 
@@ -56,7 +63,7 @@ def parse_slice(arg_slice)
       case subset
       when /(.*):(.*):(.*)/
         slice[dimname] = ($1.to_f)..($2.to_f)
-        thinning[dimname] = {0..-1,$3.to_i}
+        thinning[dimname] = {0..-1=>$3.to_i}
       when /(.*):(.*)/
         slice[dimname] = ($1.to_f)..($2.to_f)
       else
@@ -80,6 +87,9 @@ parser = GetoptLong.new(
   ["--variable", "-v", GetoptLong::REQUIRED_ARGUMENT],
   ["--output",   "-o", GetoptLong::REQUIRED_ARGUMENT],
   ["--slice",    "-s", GetoptLong::REQUIRED_ARGUMENT],
+  ["--mean",     "-m", GetoptLong::REQUIRED_ARGUMENT],
+  ["--stddev",   "-d", GetoptLong::REQUIRED_ARGUMENT],
+  ["--eddy",     "-e", GetoptLong::REQUIRED_ARGUMENT],
   ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
 begin
   parser.each{|opt, arg|
@@ -87,6 +97,9 @@ begin
     when "--variable" then eval "$OPT_var='#{arg}'"
     when "--output" then eval "$OPT_output='#{arg}'"
     when "--slice" then eval "$OPT_slice='#{arg}'"
+    when "--mean" then eval "$OPT_mean='#{arg}'"
+    when "--stddiv" then eval "$OPT_stddev='#{arg}'"
+    when "--eddy" then eval "$OPT_eddy='#{arg}'"
     when "--help" then eval "$HELP=true"
     else
       raise "must not happen"
@@ -140,6 +153,34 @@ end
 gphys = gphys.cut(slice) if slice
 gphys = gphys[thinning]  if thinning
 
+#------------------- mean/eddy gphys variable --------------------
+## mean along any axis
+if ($OPT_mean)
+  dims_mean = ($OPT_mean).split(/\s*,\s*/)
+  dims_mean = dims_mean.map{|dim| dim.to_i.to_s == dim ? dim.to_i : dim}
+  dims_mean.each{|dim|
+    gphys = gphys.mean(dim)
+  }
+end
+
+## standard deviation along any axis
+if ($OPT_stddev)
+  dims_stddev = ($OPT_stddev).split(/\s*,\s*/)
+  dims_stddev = dims_stddev.map{|dim| dim.to_i.to_s == dim ? dim.to_i : dim}
+  dims_stddev.each{|dim|
+    gphys = gphys.stddev(dim)
+  }
+end
+ 
+## deviation from mean along any axis
+if ($OPT_eddy)
+  dims_eddy = ($OPT_eddy).split(/\s*,\s*/)
+  dims_eddy = dims_eddy.map{|dim| dim.to_i.to_s == dim ? dim.to_i : dim}
+  dims_eddy.each{|dim|
+    gphys = gphys.eddy(dim)
+  }
+end
+
 #---------------------- Output GPhys variable  ------------------------
 GPhys::IO.write( outncfile, gphys )
 NetCDF_Conventions.add_history(outncfile, File.basename($0)+" "+ARGV[0])

data/bin/gpcut

@@ -18,6 +18,8 @@ gpcut - Extract, slicing and thinning a GPhys variable.
   print this message. 
 :-m dim, --mean dim
    average along dim axis (optional).
+:-e dim, --eddy dim:
+  deviation from mean along dim axis (optional). 
 :-o file, --output file
    output filename (optional). 
    Default output filename is 'gphys.nc'.
@@ -31,6 +33,7 @@ gpcut - Extract, slicing and thinning a GPhys variable.
   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)
   2012/02/19  S Takehiro (description for gturl format updated)
+  2014/04/23  S Takehiro (add --eddy option)
 
 =end
 
@@ -47,12 +50,14 @@ URLfmt = "path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
 #---------------------- Option Configuration ----------------------
 parser = GetoptLong.new(
   ["--mean",     "-m", GetoptLong::REQUIRED_ARGUMENT],
+  ['--eddy',     "-e", GetoptLong::REQUIRED_ARGUMENT],
   ["--output",   "-o", GetoptLong::REQUIRED_ARGUMENT],
   ["--help",     "-h", GetoptLong::NO_ARGUMENT      ])
 begin
   parser.each{|opt, arg|
     case opt
     when "--mean" then eval "$OPT_mean='#{arg}'"
+    when "--eddy" then eval "$OPT_eddy='#{arg}'"
     when "--output" then eval "$OPT_output='#{arg}'"
     when "--help" then eval "$OPT_help=true"
     else
@@ -86,6 +91,7 @@ gphys = GPhys::IO.open_gturl(gturl)
 outncfile.copy_global_att(gphys) # Copy global attributes (only for NetCDF)
 
 #----------------------- mean along any axis -------------------------
+## mean along any axis
 if ($OPT_mean)
   dims = ($OPT_mean).split(/\s*,\s*/)
   dims.each{|dim|
@@ -94,6 +100,16 @@ if ($OPT_mean)
   }
 end
 
+## deviation from mean along any axis
+if ($OPT_eddy)
+  dims_eddy = ($OPT_eddy).split(/\s*,\s*/)
+  dims_eddy = dims_eddy.map{|dim| dim.to_i.to_s == dim ? dim.to_i : dim}
+  dims_eddy.each{|dim|
+    dim = dim.to_i if dim.to_i.to_s == dim
+    gphys = gphys.eddy(dim)
+  }
+end
+
 
 #---------------------- Output GPhys variable  ------------------------
 GPhys::IO.write( outncfile, gphys )

data/bin/gpvect

@@ -111,6 +111,13 @@ gturl_x gturl_y.
 :--scalar:
   plot scaler field (contour,tone)
 
+:-xx:yyyy=value:
+  specify Dennou Club Library internal variable. 
+  'xx' is a package name prefix of DCL (eg. sg=>sgpack).
+  'yy' is a variable name of DCL.
+  'value' is a value of the DCL variable.
+
+
 ===CONTOUR/TONE OPTIONS
 
 :--shade:            
@@ -153,8 +160,13 @@ gturl_x gturl_y.
 :--patterns:
   set each patterns for tone plot. 
 
-:--tonf:
-  use tonf instead of tone.
+:--tone [a|e|f|b|c]:
+  set tone subroutine:
+    a (=> tone routine is selected automatically depending on the datasize)
+    e (=> DCL.uetone is used)
+    f (=> DCL.uetonf is used)
+    b (=> DCL.uetonb is used)
+    c (=> DCL.uetonc is used)
 
 :--nocolorbar:
   do not draw color bar
@@ -162,19 +174,21 @@ gturl_x gturl_y.
 :--nozero:
   do not draw zero contour
 
+:--udsfmt [strings]:
+  change contour label format. see UDCNTR/DCL manual for the format.
+
+
 ===VECTOR OPTIONS
 
 :--noflow_vect:
   DCL::ugvect is used.
 
 :--xintv <xintv>:
-  (Effective only if flow_vect) interval of data sampling in x
-                            
+  interval of data sampling in x
 
 :--yintv <yintv>:
-  (Effective only if flow_vect) interval of data sampling in y
+  interval of data sampling in y
                             
-
 :--factor <factor>:
   (Effective only if flow_vect) scaling factor to strech/reduce the
   arrow lengths
@@ -184,7 +198,22 @@ gturl_x gturl_y.
 
 :--max_unit_vect:
   (Effective only if flow_vect && unit_vect) use the maximum arrows to
-s  scale the unit vector
+  scale the unit vector
+
+:--ux_unit <value>:
+  (Effective only if flow_vect) length of the x direction unit vector 
+  (precedence of this option is lower than max_unit_vect)
+
+:--uy_unit <value>:
+  (Effective only if flow_vect) length of the y direction unit vector 
+  (precedence of this option is lower than max_unit_vect)
+
+:--xscale <value>:
+  (Effective only if noflow_vect) scaling of the x direction vector 
+
+:--yscale <value>:
+  (Effective only if noflow_vect) scaling of the y direction vector 
+
 
 ==EXAMPLES
 
@@ -210,6 +239,12 @@ For the second command format,
   2010/07/16  Y SASAKI (option --clrmap implemented)
   2011/07/29  S Takehiro (option --clrmap fixed)
   2012/02/19  S Takehiro (description for gturl format updated)
+  2012/07/28  S Takehiro (option --ux_unit, --uy_unit, --xscale, --yscale
+                          implemented)
+  2014/02/21  Y Naito && S Takehiro (implement DCL internal variable setting,
+                                     add option --udsfmt)
+  2014/02/23  S Takehiro (option --tonf is changed to --tone)
+  2014/03/10  Y Kawai && S Takehiro (setting labels for contours)
 
 =end
 #################################################
@@ -305,6 +340,7 @@ def draw_setup(gp)
                                     'max' => ( max_srange  || max_range )
                                  )
   if ( $OPT_clevels || $OPT_levels )
+    $OPT_label=($OPT_clevels || $OPT_levels).split(',')
     $OPT_clevels=($OPT_clevels || $OPT_levels).split(',').map!{|v| v.to_f }
   end
 
@@ -386,6 +422,32 @@ def draw_setup(gp)
     $max_unit_vect = false 
   end
 
+  if ($OPT_ux_unit)
+    $ux_unit = $OPT_ux_unit.to_f
+  else
+    $ux_unit = nil
+  end
+
+  if ($OPT_uy_unit)
+    $uy_unit = $OPT_uy_unit.to_f
+  else
+    $uy_unit = nil
+  end
+
+  if ($OPT_xscale)
+    xscale = $OPT_xscale.to_f
+    DCL.ugpset('LNRMAL',false)
+    vx_unit=DCL.ugpget('VXUNIT')
+    DCL.ugpset('XFACT1',vx_unit/xscale)
+  end
+
+  if ($OPT_yscale)
+    yscale = $OPT_yscale.to_f
+    DCL.ugpset('LNRMAL',false)
+    vy_unit=DCL.ugpget('VYUNIT')
+    DCL.ugpset('YFACT1',vy_unit/yscale)
+  end
+
   $xintv=($OPT_xintv||1).to_i
   $yintv=($OPT_yintv||1).to_i
   $factor=($OPT_factor||1).to_f
@@ -406,13 +468,17 @@ def draw(gp, gpux, gpuy, draw_flag)
                 "transpose"=>$OPT_exch,
                 "levels"=>$OPT_slevels,
                 "patterns"=>$OPT_patterns,
-                "tonf"=>$OPT_tonf
+                "auto"=>$auto,
+                "tonf"=>$tonf,
+                "tonb"=>$tonb,
+                "tonc"=>$tonc
                 )
     GGraph.contour(gp,
 		   false,
 		   "transpose"=>$OPT_exch,
 		   "levels"=>$OPT_clevels,
-		   "nozero"=>$OPT_nozero
+		   "nozero"=>$OPT_nozero,
+                   "label"=>$OPT_label
 		   )
     vnewframe = false
 
@@ -424,7 +490,10 @@ def draw(gp, gpux, gpuy, draw_flag)
                 "transpose"=>$OPT_exch,
                 "levels"=>$OPT_slevels,
                 "patterns"=>$OPT_patterns,
-                "tonf"=>$OPT_tonf
+                "auto"=>$auto,
+                "tonf"=>$tonf,
+                "tonb"=>$tonb,
+                "tonc"=>$tonc
                 )
     vnewframe = false
 
@@ -438,7 +507,8 @@ def draw(gp, gpux, gpuy, draw_flag)
                    "annotate"=>$annotate,
 		   "transpose"=>$OPT_exch,
                    "levels"=>$OPT_clevels,
-		   "nozero"=>$OPT_nozero
+		   "nozero"=>$OPT_nozero,
+                   "label"=>$OPT_label
                    )
     vnewframe = false
 
@@ -459,7 +529,9 @@ def draw(gp, gpux, gpuy, draw_flag)
                   "yintv"=>$yintv,
                   "factor"=>$factor,
                   "unit_vect"=>$unit_vect,
-                  "max_unit_vect"=>$max_unit_vect
+                  "max_unit_vect"=>$max_unit_vect,
+                  "ux_unit"=>$ux_unit, 
+                  "uy_unit"=>$uy_unit
                   )
   else
     GGraph.vector(gpux, gpuy, newframe=vnewframe,
@@ -471,7 +543,9 @@ def draw(gp, gpux, gpuy, draw_flag)
                   "yintv"=>$yintv,
                   "factor"=>$factor,
                   "unit_vect"=>$unit_vect,
-                  "max_unit_vect"=>$max_unit_vect
+                  "max_unit_vect"=>$max_unit_vect,
+                  "ux_unit"=>$ux_unit, 
+                  "uy_unit"=>$uy_unit
                   )
    end
 
@@ -536,10 +610,60 @@ def __split_range(range)
   return min, max
 end
 
+def check_dclopts
+
+  indices = []
+    ARGV.each_index{|i|
+    if /^-(.)(.):(.*)=(.*)/ =~ ARGV[i]
+      indices << i
+    end
+    }
+
+  dclopts = []
+    indices.reverse_each{|i|
+    dclopts << ARGV[i]
+    ARGV.slice!(i)
+    }
+
+  dclopts.each{|opt|
+    pkg = opt[1..2]
+    name = opt[4..-1].split('=')[0]
+    value = opt[4..-1].split('=')[1]
+    dcl_set_params(pkg,name,value)
+  }
+  
+end
+
+def dcl_set_params(pkg,name,value)
+
+  set = 'stx'
+  case name
+  when /^c/i
+    eval( "DCL.#{pkg}c#{set}(name,value.to_s)" )
+  when /^l/i
+    if /(.*)(T|t)(.*)/ =~ value
+      eval( "DCL.#{pkg}l#{set}(name,true)" )
+    else
+    if /(.*)(F|f)(.*)/ =~ value
+      eval( "DCL.#{pkg}l#{set}(name,false)" )
+    else
+      raise "value of logical parameter must include 't' or 'f'"
+    end
+    end
+  when /^[i-n]/i
+    eval( "DCL.#{pkg}i#{set}(name,value.to_i)" )
+  else
+    eval( "DCL.#{pkg}r#{set}(name,value.to_f)" )
+  end
+  
+end
 
 #####################################################
 ###++++++           Main Routine            ++++++###
 
+## options for DCL
+check_dclopts
+
 ## parse options
 parser = GetoptLong.new
 parser.set_options(
@@ -583,7 +707,8 @@ parser.set_options(
                    ['--clevels',                  GetoptLong::REQUIRED_ARGUMENT],
                    ['--slevels',                  GetoptLong::REQUIRED_ARGUMENT],
                    ['--patterns',                  GetoptLong::REQUIRED_ARGUMENT],
-                   ['--tonf',                     GetoptLong::NO_ARGUMENT],
+                   ['--tone',                     GetoptLong::REQUIRED_ARGUMENT],
+                   ['--udsfmt',                   GetoptLong::REQUIRED_ARGUMENT],
                    ['--nocolorbar',               GetoptLong::NO_ARGUMENT],
                    ['--nozero',                   GetoptLong::NO_ARGUMENT],
                    ###    vector option    ###
@@ -593,6 +718,10 @@ parser.set_options(
                    ['--factor',                    GetoptLong::REQUIRED_ARGUMENT],
                    ['--unit_vect',              GetoptLong::NO_ARGUMENT],
                    ['--max_unit_vect',          GetoptLong::NO_ARGUMENT],
+                   ['--ux_unit',                    GetoptLong::REQUIRED_ARGUMENT],
+                   ['--uy_unit',                    GetoptLong::REQUIRED_ARGUMENT],
+                   ['--xscale',                    GetoptLong::REQUIRED_ARGUMENT],
+                   ['--yscale',                    GetoptLong::REQUIRED_ARGUMENT],
                    ['--help',                     GetoptLong::NO_ARGUMENT]
 #                   ['--version',                  GetoptLong::NO_ARGUMENT]  # to be defined
                    )
@@ -628,12 +757,35 @@ else
   $colorbar = true
 end
 
+if ($OPT_tone) 
+  case $OPT_tone
+  when "a"
+    $auto, $tonf, $tona, $toneb, $tonec = true,false,false,false
+  when "e"
+    $auto, $tonf, $tona, $toneb, $tonec = false,false,false,false
+  when "f"
+    $auto, $tonf, $tona, $toneb, $tonec = false,true,false,false
+  when "b"
+    $auto, $tonf, $tona, $toneb, $tonec = false,false,true,false
+  when "c"
+    $auto, $tonf, $tona, $toneb, $tonec = false,false,false,true
+  else
+    raise "The value of option --tone should be 'a','e','f','b' or 'c'."
+  end
+else
+  $auto, $tonf, $tona, $toneb, $tonec = true,false,false,false
+end
+
 ## decide VIEWPORT
 $VIEWPORT = set_vpsize( VIEWPORT, ($OPT_aspect||2.0) )
 
 ## tune the size of axis parameters.
 DCL.uzfact(0.7)
 
+## set the format of contour labels.
+udsfmt = ($OPT_udsfmt||DCL.udqfmt())
+DCL.udsfmt(udsfmt)
+
 ## draw figure
 loopdim   = ( $OPT_animate || $OPT_anim ) 
 loopdim = loopdim.to_i if loopdim.to_i.to_s == loopdim
@@ -641,7 +793,7 @@ loopdim = loopdim.to_i if loopdim.to_i.to_s == loopdim
 ## set colormap
 DCL.sgscmn($OPT_clrmap||1)
 ## open work station
-DCL.gropn($OPT_wsn||1)
+DCL.gropn($OPT_wsn||4)
 
 ## open netcdf variables