gphys 1.1.1 → 1.2.2

data/bin/gpvect

@@ -13,7 +13,7 @@ The first command form is for only vector field plotting.
 
 where the format of the gturl is
 
-     path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+     path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
 
 The command loads two gphys variables in each time and draws 
 vector field whose x and y components are the first and the second argument, 
@@ -100,6 +100,9 @@ gturl_x gturl_y.
 :--mean <dim>:
   mean along axis <dim>. 
 
+:--eddy <dim>:
+  deviation from mean along axis <dim>. 
+
 :--m, --map <map_type>:
   plot map. itr number must be set.  this option is neglect if itr
   number is 1-4.  abailable map type is coast_world, border_world,
@@ -150,6 +153,9 @@ gturl_x gturl_y.
 :--patterns:
   set each patterns for tone plot. 
 
+:--tonf:
+  use tonf instead of tone.
+
 :--nocolorbar:
   do not draw color bar
 
@@ -178,7 +184,7 @@ gturl_x gturl_y.
 
 :--max_unit_vect:
   (Effective only if flow_vect && unit_vect) use the maximum arrows to
-  scale the unit vector
+s  scale the unit vector
 
 ==EXAMPLES
 
@@ -203,6 +209,8 @@ For the second command format,
   2010/03/10  Y SASAKI (change help block into RD 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)
+
 =end
 #################################################
 require "getoptlong"        # for option_parse
@@ -215,7 +223,7 @@ include NumRu
 ## Default param.
 
 VIEWPORT = [0.15,0.85,0.2,0.55]
-URLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+URLfmt = "path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
 
 #####################################################
 def GGraph::annotate(str_ary)
@@ -397,7 +405,8 @@ def draw(gp, gpux, gpuy, draw_flag)
                 "annotate"=>$annotate,
                 "transpose"=>$OPT_exch,
                 "levels"=>$OPT_slevels,
-                "patterns"=>$OPT_patterns
+                "patterns"=>$OPT_patterns,
+                "tonf"=>$OPT_tonf
                 )
     GGraph.contour(gp,
 		   false,
@@ -414,7 +423,8 @@ def draw(gp, gpux, gpuy, draw_flag)
                 "annotate"=>$annotate,
                 "transpose"=>$OPT_exch,
                 "levels"=>$OPT_slevels,
-                "patterns"=>$OPT_patterns
+                "patterns"=>$OPT_patterns,
+                "tonf"=>$OPT_tonf
                 )
     vnewframe = false
 
@@ -555,6 +565,7 @@ parser.set_options(
                    ['--reverse',                  GetoptLong::NO_ARGUMENT],
                    ['--Gr',                       GetoptLong::NO_ARGUMENT],
                    ['--mean',                     GetoptLong::REQUIRED_ARGUMENT],
+                   ['--eddy',                     GetoptLong::REQUIRED_ARGUMENT],
                    ['--map',                      GetoptLong::REQUIRED_ARGUMENT],
                    ['--m',                        GetoptLong::NO_ARGUMENT],
                    ['--scalar',                   GetoptLong::NO_ARGUMENT],
@@ -572,6 +583,7 @@ parser.set_options(
                    ['--clevels',                  GetoptLong::REQUIRED_ARGUMENT],
                    ['--slevels',                  GetoptLong::REQUIRED_ARGUMENT],
                    ['--patterns',                  GetoptLong::REQUIRED_ARGUMENT],
+                   ['--tonf',                     GetoptLong::NO_ARGUMENT],
                    ['--nocolorbar',               GetoptLong::NO_ARGUMENT],
                    ['--nozero',                   GetoptLong::NO_ARGUMENT],
                    ###    vector option    ###
@@ -677,6 +689,17 @@ while ARGV[0] do
     }
   end
 
+## deviation from mean along any axis
+  if ($OPT_eddy)
+    dims = ($OPT_eddy).split(/\s*,\s*/)
+    dims.each{|dim|
+      dim = dim.to_i if dim.to_i.to_s == dim
+      gp = gp.eddy(dim)
+      gpux = gpux.eddy(dim)
+      gpuy = gpuy.eddy(dim)
+    }
+  end
+
   # set title
   if !$OPT_title && $OPT_scalar
     gpnm   = gp.data.get_att('long_name')   || gp.name

data/bin/gpview

@@ -19,7 +19,7 @@ The first command form is
 
 where the format of the gturl is
 
-    path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
+    path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]
 
 The second commnad form is 
 
@@ -77,7 +77,6 @@ if you want to know more description, please read
 
 :--animate/anim <dim>:
   plot animation along <dim>. <dim> must be name of dimension. 
-                           
 
 :--alternate, --Ga: 
   enable to backing store.
@@ -97,6 +96,9 @@ if you want to know more description, please read
 :--mean <dim>:
   mean along axis <dim>. 
 
+:--eddy <dim>:
+  deviation from mean along axis <dim>. 
+
 :--m, --map <map_type>: 
   plot map. itr number must be set.  this option is neglect if itr
   number is 1-4.  abailable map type is coast_world, border_world,
@@ -107,6 +109,15 @@ if you want to know more description, please read
   <math_func> should be a math function with one argument 
   such as log10, sqrt, sin, etc.
 
+:--time_ax [nil|false|h|ymd]: 
+  specify type of calendar-type time axis: 
+    nil   (=> auto slection)
+    false (=> do not use the time axis even if 
+              the units of the axis is a time one with since field)
+    "h"   (=> like nil, but always use the hour-resolving datetime_ax method
+              in dclext_datetime_ax.rb)
+    "ymd" (=> like "h" but for y-m-d type using DCL.uc[xy]acl)
+
 
 == LINE/MARK OPTIONS
 
@@ -172,6 +183,9 @@ if you want to know more description, please read
 :--patterns:           
   set each patterns for tone plot. 
 
+:--tonf:
+  use tonf instead of tone.
+
 :--nocolorbar:         
   do not draw color bar
 
@@ -195,6 +209,7 @@ For a single GPhys variable,
     % gpview --overplot=3 --anim t data.nc@temp,lon=0
     % gpview --mark data.nc@temp,lon=0,lat=0
     % gpview --operation log10 data.nc@temp,lon=0
+    % gpview --time_ax false data.nc@temp,lon=0,lat=0
 
 For multiple GPhys variables, 
     % gpview data1.nc@temp data2.nc@temp
@@ -238,6 +253,9 @@ For multiple GPhys variables,
   2008/12/14  S Takehiro (option --mark implemented)
   2010/03/10  Y SASAKI (change help block into RD format)
   2011/01/14  T Tanigawa && S Takehiro (option --operation implemented)
+  2011/11/04  S Takehiro (option --time_ax implemented)
+  2011/11/20  S Takehiro (option --eddy implemented)
+  2012/02/19  S Takehiro (description for gturl format updated)
 
 =end
 #################################################
@@ -251,7 +269,7 @@ include NumRu
 ## Default param.
 
 VIEWPORT = [0.15,0.85,0.2,0.55]
-URLfmt = "path@varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
+URLfmt = "path[@|/]varname[,dimname=pos1[:pos2[:thinning_intv]][,dimname=...]]"
 
 #####################################################
 def GGraph::annotate(str_ary)
@@ -389,6 +407,12 @@ def draw_setup(gp)
     GGraph::set_map(map_type=>true)
   end
 
+  # time axis 
+  if ($OPT_time_ax)
+    $OPT_time_ax = false if $OPT_time_ax == "false"
+    GGraph.set_axes('time_ax'=>$OPT_time_ax)
+  end
+
   return draw_flag
 
 end
@@ -464,7 +488,8 @@ def draw(gp, draw_flag)
                 "annotate"=>$annotate,
                 "transpose"=>$OPT_exch,
                 "levels"=>$OPT_slevels,
-                "patterns"=>$OPT_patterns
+                "patterns"=>$OPT_patterns,
+                "tonf"=>$OPT_tonf
                 )
     GGraph.contour(gp, 
 		   false,
@@ -479,7 +504,8 @@ def draw(gp, draw_flag)
                 "annotate"=>$annotate,
                 "transpose"=>$OPT_exch,
                 "levels"=>$OPT_slevels,
-                "patterns"=>$OPT_patterns
+                "patterns"=>$OPT_patterns,
+                "tonf"=>$OPT_tonf
                 )
   when "noshade"
     mj = DCL.udpget('indxmj')
@@ -587,9 +613,11 @@ parser.set_options(
                    ['--reverse',                  GetoptLong::NO_ARGUMENT],
                    ['--Gr',                       GetoptLong::NO_ARGUMENT],
                    ['--mean',                     GetoptLong::REQUIRED_ARGUMENT],
+                   ['--eddy',                     GetoptLong::REQUIRED_ARGUMENT],
                    ['--map',                      GetoptLong::REQUIRED_ARGUMENT],
                    ['--m',                        GetoptLong::NO_ARGUMENT],
                    ['--operation',                GetoptLong::REQUIRED_ARGUMENT],
+                   ['--time_ax',                  GetoptLong::REQUIRED_ARGUMENT],
                    ###     line/mark option    ###
                    ['--line',                     GetoptLong::NO_ARGUMENT],
                    ['--mark',                     GetoptLong::NO_ARGUMENT],
@@ -610,6 +638,7 @@ parser.set_options(
                    ['--clevels',                  GetoptLong::REQUIRED_ARGUMENT],
                    ['--slevels',                  GetoptLong::REQUIRED_ARGUMENT],
                    ['--patterns',                 GetoptLong::REQUIRED_ARGUMENT],
+                   ['--tonf',                     GetoptLong::NO_ARGUMENT],
                    ['--nocolorbar',               GetoptLong::NO_ARGUMENT],
                    ['--nozero',                   GetoptLong::NO_ARGUMENT],
                    ['--help',                     GetoptLong::NO_ARGUMENT]
@@ -683,6 +712,15 @@ while ARGV[0] do
     }
   end
 
+## deviation from mean along any axis
+  if ($OPT_eddy)
+    dims = ($OPT_eddy).split(/\s*,\s*/)
+    dims.each{|dim|
+      dim = dim.to_i if dim.to_i.to_s == dim
+      gp = gp.eddy(dim)
+    }
+  end
+
 ## operation of a mathematical function
   if ($OPT_operation)
     eval "gp = gp.#{$OPT_operation}"

data/extconf.rb

@@ -8,11 +8,10 @@ def install_dirs
 end
 
 #dir_config('narray',$sitearchdir,$sitearchdir)
-hoge = Gem::GemPathSearcher.new.find("narray")
-narray_fullname = hoge.full_name
-narray_installpath = hoge.installation_path
-narray_include = "#{narray_installpath}/gems/#{narray_fullname}/"
-narray_lib = "#{narray_installpath}/gems/#{narray_fullname}/"
+gem_home=(`gem environment GEM_HOME`).chomp
+narray_dir = Dir.glob("#{gem_home}/gems/narray-*").sort[-1]
+narray_include = narray_dir
+narray_lib = narray_dir
 dir_config('narray',narray_include,narray_lib)
 
 if ( ! ( have_header("narray.h") && have_header("narray_config.h") ) ) then
@@ -39,4 +38,4 @@ if /cygwin|mingw/ =~ RUBY_PLATFORM
   end    
 end
 
-create_makefile("numru/gphys_ext")
+create_makefile("gphys_ext")

data/gphys.gemspec

@@ -0,0 +1,34 @@
+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "gphys"
+  gem.version       = GPhys::VERSION
+  gem.authors           = ["Takeshi Horinouchi", "Ryo Mizuta",\
+    "Daisuke Tsukahara", "Seiya Nishizawa", "Shin-ichi Takehiro"]
+  gem.email         = ["eriko@gfd-dennou.org"]
+  gem.description      = %q{comprehensive library for self-descriptive gridded physical data (in NetCDF, GrADS, or on memory) with graphicsgraphicsgraphicsgraphics.}
+  gem.summary          = %q{a multi-purpose class to handle Gridded Physical quantities}
+  gem.homepage         = 'http://www.gfd-dennou.org/arch/ruby/products/gphys/'
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+  gem.extensions << "extconf.rb"
+
+  gem.required_ruby_version = Gem::Requirement.new(">= 1.8")
+
+  gem.add_runtime_dependency(%q<narray>, [">= 0.5.7"])
+  gem.add_runtime_dependency(%q<numru-misc>, [">= 0.1.0"])
+  gem.add_runtime_dependency(%q<numru-units>, [">= 1.7"])
+  gem.add_runtime_dependency(%q<narray_miss>, [">= 1.2.4"])
+  gem.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
+  gem.add_runtime_dependency(%q<ruby-dcl>, [">= 1.6.1"])
+  gem.add_runtime_dependency(%q<ruby-fftw3>, [">= 0.3"])
+  gem.add_runtime_dependency(%q<gsl>, [">= 1.14"])
+  gem.add_runtime_dependency(%q<ruby-lapack>, [">= 1.5"])
+  gem.add_runtime_dependency(%q<rb-grib>, [">= 0.2.0"])
+end

data/interpo.c

@@ -14,12 +14,13 @@
 #endif
 
 static VALUE
-interpo_do(obj, shape_to, idxmap, val_from, missval)
+interpo_do(obj, shape_to, idxmap, val_from, missval, extrapo)
      VALUE obj;
      VALUE shape_to; // [Array] shape of the new grid
      VALUE idxmap;   // [Array] index mapping
      VALUE val_from; // [NArray] values to be interpolated
      VALUE missval;  // [nil or Float] missing value if Float
+     VALUE extrapo; // [false/true] whether to extrapolate
 {
     VALUE val_to;
     VALUE chk , ary;
@@ -33,12 +34,13 @@ interpo_do(obj, shape_to, idxmap, val_from, missval)
     double *pt, *pf;
     int nomiss;
     double vmiss;
+    int extr;
     size_t i, it, kf, j, k, l;
     int *mtyp;
     size_t *dm, *dm2, *dm2f, *dm3, *dm3f, *dm4, *dm4f;
     int **di, nid, nic;
     double **df, *f, a;
-    size_t *idf, idfc, *idt;
+    int *idf, idfc, *idt;
 
     // check arguments
 
@@ -76,7 +78,10 @@ interpo_do(obj, shape_to, idxmap, val_from, missval)
     nomiss = (missval == Qnil);
     if (!nomiss){
 	vmiss = NUM2DBL(missval);
+    } else {
+	vmiss = -999.0;   // dummy to avoid compiler warning (not used)
     }
+    extr = (extrapo != Qfalse);  // false -> 0(false); else -> true
 
     // read argument (idxmap) 
 
@@ -139,8 +144,8 @@ interpo_do(obj, shape_to, idxmap, val_from, missval)
 
     // do interpolation
 
-    idt  = ALLOCA_N(size_t, rankt);
-    idf  = ALLOCA_N(size_t, rankf);
+    idt  = ALLOCA_N(int, rankt);
+    idf  = ALLOCA_N(int, rankf);
 
     for(it=0; it<lent; it++){
 	l = it;
@@ -193,6 +198,10 @@ interpo_do(obj, shape_to, idxmap, val_from, missval)
 	    k = 0;
 	    for(j=0; j<rankf; j++){
 		idfc = idf[j];
+                if(!extr && idfc<0){
+                    pt[it] = vmiss;
+                    break;
+                }
 		if(mtyp[j]>0){
                     if ( (l>>k)%2 && idfc<shf[j]-1 ){
                         idfc += 1;
@@ -202,13 +211,16 @@ interpo_do(obj, shape_to, idxmap, val_from, missval)
 		kf += idfc*cshf;
 		cshf *= shf[j];
 	    }
+            if (!nomiss && pt[it] == vmiss) {break;}
 	    if (nomiss || pf[kf] != vmiss){
 		pt[it] += a*pf[kf];
 	    } else {
 		pt[it] = vmiss;
 		break;
 	    }
+            //printf("$$$$ %d %f %f\n",it, a, pf[kf]);
 	}
+        //printf("//// %d %f\n",it, pt[it]);
     }
 
     // finish
@@ -217,32 +229,39 @@ interpo_do(obj, shape_to, idxmap, val_from, missval)
 }
 
 static void
-__interpo_find_loc_1D(N, P, n, p, ids, f)
+__interpo_find_loc_1D(N, P, n, p, vmiss, extr, ids, f)
      double *P, *p;   // INPUT
      size_t N, n;     // INPUT
+     double vmiss;    // INPUT
+     int extr;        // INPUT
      int *ids;        // OUTPUT
      double *f;       // OUTPUT
 {
-    size_t i, j, il, ir;
+    size_t j;
+    int i, il, ir;
     int down;
 
     // first time finding : use a simple looping 
     j = 0;
     for(i=0; i<n-1; i++){
-	if ( (p[i]-P[j])*(P[j]-p[i+1]) >= 0 ){
+	if ( p[i] != vmiss && p[i+1] != vmiss && 
+             (p[i]-P[j])*(P[j]-p[i+1]) >= 0 ){
 	    break;
 	}
     }
     if (i<n-1){
 	// found
 	ids[j] = i;
-    } else {
+    } else if (extr) {
 	// not found --> to be extrapolated
 	if ( (P[j]-p[0])*(p[0]-p[n-1]) >= 0 ){
 	    ids[j] = i = 0;
 	} else {
 	    ids[j] = i = n-2;
 	}
+    } else {
+        ids[j] = -999999;   // a negative value
+        i = 0;
     }
     f[j] = (p[i]-P[j])/(p[i]-p[i+1]);
 
@@ -254,41 +273,50 @@ __interpo_find_loc_1D(N, P, n, p, ids, f)
 	    if ( (p[i]-P[j])*(P[j]-p[i+1]) >= 0 ) {
 		break;
 	    } else {
-		if ( il>0 && ( down || ir==n-1 )  ){
+		if ( il>0 && ( down || ir==n-2 )  ){
 		    il--;
 		    i = il;
 		    down = 0; // false
-		} else if ( ir<n-1 && ( !down || il==0 ) ){
+		} else if ( ir<n-2 && ( !down || il==0 ) ){
 		    ir++;
 		    i = ir;
 		    down = 1; // true
 		} else {
-		    // not found --> to be extrapolated
-		    if ( (P[j]-p[0])*(p[0]-p[n-1]) >= 0 ){
-			i = 0;
-		    } else {
-			i = n-2;
+		    // not found
+                    if (extr) {
+                        // to be extrapolated
+                        if ( (P[j]-p[0])*(p[0]-p[n-1]) >= 0 ){
+                            i = 0;
+                        } else {
+                            i = n-2;
+                        }
+                    } else {
+                        i = -999999;  // a negative value (changed to 0 below)
 		    }
 		    break;
 		}
 	    }
 	}
 	ids[j] = i;
+        if(i<0){i = 0; down = 0;}
 	f[j] = (p[i]-P[j])/(p[i]-p[i+1]);
     }
 }
 
 static VALUE
-interpo_find_loc_1D(obj, X, x)
+interpo_find_loc_1D(obj, X, x, missval, extrapo)
      VALUE obj;
      VALUE X; // [NArray(1D)] coordinate values onto which interpolation is made
      VALUE x; // [NArray(1D)] coordinate values of original data
+     VALUE missval; // [Float] missing value in x
+     VALUE extrapo; // [false/true] whether to extrapolate
 {
     VALUE na_ids, na_f;
     VALUE chk;
     size_t N, n;
     struct NARRAY *na;
-    double *P, *p;
+    double *P, *p, vmiss;
+    int extr;
     int *ids;
     double *f;
     int shape[1];  // could be size_t if NArray is changed
@@ -311,6 +339,10 @@ interpo_find_loc_1D(obj, X, x)
     n = na->total;
     p = (double *)NA_PTR(na, 0);
 
+    vmiss = NUM2DBL(missval);
+
+    extr = (extrapo != Qfalse);  // false -> 0(false); else -> true
+
     // prepare output NArrays
 
     shape[0] = N;
@@ -323,7 +355,7 @@ interpo_find_loc_1D(obj, X, x)
 
     // Do the job
 
-    __interpo_find_loc_1D(N, P, n, p, ids, f);
+    __interpo_find_loc_1D(N, P, n, p, vmiss, extr, ids, f);
 
     // Return
 
@@ -333,17 +365,20 @@ interpo_find_loc_1D(obj, X, x)
 /* To apply interpo_find_loc_1D multi-dimensionally 
  */
 static VALUE
-interpo_find_loc_1D_MD(obj, X, x, dimc)
+interpo_find_loc_1D_MD(obj, X, x, dimc, missval, extrapo)
      VALUE obj;
      VALUE X; // [NArray(1D)] coordinate values onto which interpolation is made
      VALUE x; // [NArray(multi-D)] coordinate values of original data
      VALUE dimc; // [Integer] the dimension in x except which mapping has been set
+     VALUE missval; // [Float] missing value in x
+     VALUE extrapo; // [false/true] whether to extrapolate
 {
     VALUE na_ids, na_f;
     VALUE chk;
     size_t N, n1;
     struct NARRAY *na;
-    double *P, *p, *p1;
+    double *P, *p, *p1, vmiss;
+    int extr;
     int *ids, *ids1;
     double *f, *f1;
     int *shr;  // shape of the result (could be size_t if NArray is changed)
@@ -370,6 +405,10 @@ interpo_find_loc_1D_MD(obj, X, x, dimc)
 
     dmc = NUM2INT( dimc ); 
 
+    vmiss = NUM2DBL(missval);
+
+    extr = (extrapo != Qfalse);  // false -> 0(false); else -> true
+
     x = na_cast_object(x, NA_DFLOAT);
     GetNArray(x, na);
     p = (double *)NA_PTR(na, 0);
@@ -458,7 +497,7 @@ interpo_find_loc_1D_MD(obj, X, x, dimc)
 
 	// find loc in 1D
 
-	__interpo_find_loc_1D(N, P, n1, p1, ids1, f1);
+	__interpo_find_loc_1D(N, P, n1, p1, vmiss, extr, ids1, f1);
 
 	// substitute ids1 and f1 (1D) into ids and f (multi-D)
  
@@ -486,10 +525,10 @@ init_gphys_interpo()
     // rb_require("narray");  // it does not work
     mNumRu = rb_define_module("NumRu");
     cGPhys = rb_define_class_under(mNumRu, "GPhys", rb_cObject);
-    rb_define_private_method(cGPhys, "c_interpo_find_loc_1D", interpo_find_loc_1D, 2);
-    rb_define_private_method(cGPhys, "c_interpo_find_loc_1D_MD", interpo_find_loc_1D_MD, 3);
+    rb_define_private_method(cGPhys, "c_interpo_find_loc_1D", interpo_find_loc_1D, 4);
+    rb_define_private_method(cGPhys, "c_interpo_find_loc_1D_MD", interpo_find_loc_1D_MD, 5);
 
-    rb_define_private_method(cGPhys, "c_interpo_do", interpo_do, 4);
+    rb_define_private_method(cGPhys, "c_interpo_do", interpo_do, 5);
 
     // to make "find loc" methods available outside GPhys as class methods
     rb_define_singleton_method(cGPhys, "interpo_find_loc_1D", interpo_find_loc_1D, 2);

data/lib/gphys.rb

@@ -0,0 +1,2 @@
+require "version"
+require "numru/gphys.rb