gphys 1.5.6 → 1.5.7

data/lib/numru/ggraph.rb

@@ -788,9 +788,9 @@ library if you like.
        "interval"    nil     # contour interval
        "nozero"      nil     # delete zero contour
        "coloring"    false   # set color contours with ud_coloring
-       "clr_min"     13      # (if coloring) minimum color number for the
+       "clr_min"     nil      # (if coloring) minimum color number for the
                              # minimum data values
-       "clr_max"     99      # (if coloring) maximum color number for the
+       "clr_max"     nil      # (if coloring) maximum color number for the
                              # maximum data values
        "help"        false   # show help message if true
        "log"	     nil     # approximately log-scaled levels (by using
@@ -919,6 +919,10 @@ library if you like.
        "color_bar"   false   # Add a color bar: THIS IS ONLY FOR QUICK
                              # LOOK. Use the GGraph::color_bar method explicitly
                              # for full option control
+       "cbunits"     nil     # [nil or true or String] if non nil, shows units
+                             # in color_bar using the specified string or, when
+                             # true, the units of the argument
+                             # using the specified string or, if true, the units of the argument
        "min"         nil     # minimum tone level
        "max"         nil     # maximum tone level
        "nlev"        nil     # number of levels
@@ -1588,6 +1592,7 @@ module NumRu
       ['title',   nil,  'Title of the figure'],
       ['xunits',  nil,  'Units of x axis (if nil, internally determined)'],
       ['yunits',  nil,  'Units of y axis (if nil, internally determined)'],
+      ['format_units', true, 'Format unit expressions for DCL, e.g. m.s-1 -> m s\^{-1}'],
       ['xtickint',  nil,
             'Interval of x axis tickmark (if nil, internally determined)'],
       ['ytickint',  nil,
@@ -1641,16 +1646,27 @@ module NumRu
       ts = [t0,t1].min
       time = UNumeric.new(ts,sunits)
       tstr = time.to_datetime(0.1,calendar)
-      jd0 = tstr.strftime('%Y%m%d').to_i
+      #jd0 = tstr.strftime('%Y%m%d').to_i
       tlen = tun.convert( t1-t0, dayun ).abs
       axtype ||= (tlen < 5) ? 'h' : 'ymd'
       reverse = t1 < t0
+      if axtype == 'h'
+        dh = 0.0
+      else
+        tstr0 = tstr.to_date
+        dh = tstr - tstr0
+        if dh>1e-2  # << 1 な適当な小さな数
+          dh -= 1.0
+          tstr0 += 1.0
+        end
+        tend0 = (tstr+tlen).to_date
+      end
 
       if xax
         unless(reverse)
-          DCL.grswnd(0.0, tlen, window[2], window[3] )
+          DCL.grswnd(dh, tlen+dh, window[2], window[3] )
         else
-          DCL.grswnd(tlen, 0.0, window[2], window[3] )
+          DCL.grswnd(tlen+dh, dh, window[2], window[3] )
         end
         DCL.grstrf
         opts = {'cside'=>side}
@@ -1659,14 +1675,14 @@ module NumRu
         if axtype == 'h'
           DCLExt.datetime_ax(tstr, tstr+tlen, opts )
         else
-          DCLExt.date_ax(tstr, tstr+tlen, opts )
+          DCLExt.date_ax(tstr0, tend0, opts )
           ## DCL.ucxacl(side,jd0,tlen)  #Old: use it again if UCPACK is improved
         end
       else
         unless(reverse)
-          DCL.grswnd(window[0], window[1], 0.0, tlen)
+          DCL.grswnd(window[0], window[1], dh, tlen+dh)
         else
-          DCL.grswnd(window[0], window[1], tlen, 0.0)
+          DCL.grswnd(window[0], window[1], tlen+dh, dh)
         end
         DCL.grstrf
         opts = {'yax'=>true, 'cside'=>side}
@@ -1675,7 +1691,7 @@ module NumRu
         if axtype == 'h'
           DCLExt.datetime_ax(tstr, tstr+tlen, opts )
         else
-          DCLExt.date_ax(tstr, tstr+tlen, opts )
+          DCLExt.date_ax(tstr0, tend0, opts )
           ## DCL.ucyacl(side,jd0,tlen)  #Old: use it again if UCPACK is improved
         end
       end
@@ -1721,6 +1737,7 @@ module NumRu
                 	   opts['xtickint'], opts['xlabelint'])
             end
           else
+            sunits = DCLExt.format_units(sunits) if opts['format_units']
             DCL.uscset('cxttl', (opts['xtitle'] || xai['title']) )
             DCL.uscset('cxunit', sunits)
             DCL.uspset('dxt', opts['xtickint'])  if(opts['xtickint'])
@@ -1760,6 +1777,7 @@ module NumRu
                 	   opts['ytickint'], opts['ylabelint'])
             end
           else
+            sunits = DCLExt.format_units(sunits) if opts['format_units']
             DCL.uscset('cyttl', (opts['ytitle'] || yai['title']) )
             DCL.uscset('cyunit', sunits )
             DCL.uspset('dyt', opts['ytickint'])  if(opts['ytickint'])
@@ -2112,6 +2130,7 @@ module NumRu
       ['step_plot', false, 'If true, draw stair step plot (piecewise constant line plot).'],
       # ['step_extend_ends', false, 'If true, extend both ends of stair step plot.'], # NOT YET IMPLEMENTED
       ['step_position', 0, 'Data point will be at the right corner of each step if negative, center if 0, and left corner if positive.'],
+      ['proc_before_ax', nil, 'Proc (with no argument) to be called just before drawing the axes.'],
       @@data_prep_options
     )
 
@@ -2154,6 +2173,9 @@ module NumRu
       x, y, closer, gp, window = data_prep_1D(gphys, opts)
       if newframe
         fig(x, y, {'window'=>window})
+        if opts['proc_before_ax']
+          opts['proc_before_ax'].call
+        end
         axes_or_map_and_ttl(gp, opts, x, y)
       end
 
@@ -2245,6 +2267,7 @@ module NumRu
       ['legend_vy', nil, '(effective if legend) viewport y value of the legend (Float; or nil for automatic settting)'],
       ['legend_size', nil, '(effective if legend) character size of the legend'],
       ['map_axes', false, '[USE IT ONLY WHEN itr=10 (cylindrical)] If true, draws axes by temprarilly switching to itr=1 and calling GGraph::axes.'],
+      ['proc_before_ax', nil, 'Proc (with no argument) to be called just before drawing the axes.'],
       @@data_prep_options
         )
 
@@ -2275,6 +2298,9 @@ module NumRu
       x, y, closer, gp, window = data_prep_1D(gphys, opts, len1ok: true)
       if newframe
         fig(x, y, {'window'=>window})
+        if opts['proc_before_ax']
+          opts['proc_before_ax'].call
+        end
         axes_or_map_and_ttl(gp, opts, x, y)
       end
       DCL.uumrkz(x.val, y.val, opts['type'], opts['index'], opts['size'])
@@ -2298,8 +2324,8 @@ module NumRu
       ['interval', nil,       'contour interval'],
       ['nozero',   nil,       'delete zero contour'],
       ['coloring', false,     'set color contours with ud_coloring'],
-      ['clr_min',  13,        '(if coloring) minimum color number for the minimum data values'],
-      ['clr_max',  99,       '(if coloring) maximum color number for the maximum data values']
+      ['clr_min',  nil,        '(if coloring) minimum color number for the minimum data values (nil -> uepack parameter icolor1)'],
+      ['clr_max',  nil,       '(if coloring) maximum color number for the maximum data values  (nil -> uepack parameter icolor2)']
     )
     def set_linear_contour_options(options)
       @@linear_contour_options.set(options)
@@ -2497,9 +2523,21 @@ module NumRu
 
     def tone_and_contour(gphys, newframe=true, options=nil)
       options ? copt=@@contour_options.select_existent(options) : copt=nil
-      options ? topt=@@tone_options.select_existent(options) : topt=nil
+      options ? topt=@@tone_options.select_existent(options) : topt=Hash.new
+      topt = @@tone_options.interpret(topt)
+      cbar = topt["color_bar"]
+      topt["color_bar"]=false if cbar  # color bar will be plotted after contour
       tone(gphys, newframe, topt)
       contour(gphys, false, copt)
+      if cbar
+        cbunits = topt['cbunits']
+        cbunits = gphys.units.to_s if cbunits==true
+        if @@used_fullcolor_tone
+          color_bar "units"=>cbunits
+        else
+          color_bar "log"=>topt['log'], "units"=>cbunits
+        end
+      end
     end
 
     @@contour_levels =  Misc::KeywordOptAutoHelp.new(
@@ -2549,6 +2587,7 @@ module NumRu
       ['annotate', true, 'if false, do not put texts on the right margin even when newframe==true'],
       ['map_axes', false, '[USE IT ONLY WHEN itr=10 (cylindrical)] If true, draws axes by temprarilly switching to itr=1 and calling GGraph::axes.'],
       ['keep', false, 'Use the contour levels used previously'],
+      ['proc_before_ax', nil, 'Proc (with no argument) to be called just before drawing the axes.'],
       @@linear_contour_options,
       @@contour_levels,
       @@data_prep_options
@@ -2645,8 +2684,9 @@ module NumRu
       xax, yax, closer, gp = data_prep_2D([gphys], newframe, opts)
       if newframe
         fig(xax, yax)
-      end
-      if newframe
+        if opts['proc_before_ax']
+          opts['proc_before_ax'].call
+        end
         axes_or_map_and_ttl(gp,opts, xax, yax)
       end
       if !opts['keep'] or DCL.udqcln==0
@@ -2776,6 +2816,9 @@ module NumRu
       ['map_axes', false, '[USE IT ONLY WHEN itr=10 (cylindrical)] If true, draws axes by temprarilly switching to itr=1 and calling GGraph::axes.'],
       ['keep', false, 'Use the tone levels and patterns used previously'],
       ['color_bar', false, 'Add a color bar: THIS IS ONLY FOR QUICK LOOK. Use the GGraph::color_bar method explicitly for full option control'],
+      ['cbunits', nil, '[nil or true or String] if non nil, shows units in color_bar using the specified string or, when true, the units of the argument'],
+      ['proc_before_ax', nil, 'Proc (with no argument) to be called just before drawing the axes.'],
+      ['proc_before_tone', nil, 'Proc (with no argument) to be called just before plotting tone.'],
       @@linear_tone_options,
       @@tone_levels,
       @@fullcolor_tone_options,
@@ -2812,6 +2855,10 @@ module NumRu
       if newframe
         fig(xax, yax)
       end
+      if opts['proc_before_tone']
+        opts['proc_before_tone'].call
+      end
+
       DCL.uwsgxa(xax.val) if xax.rank==1
       DCL.uwsgya(yax.val) if yax.rank==1
       if !opts['keep'] or DCL.ueqntl==0
@@ -2857,16 +2904,21 @@ module NumRu
       end
 
       if newframe
+        if opts['proc_before_ax']
+          opts['proc_before_ax'].call
+        end
         axes_or_map_and_ttl(gp,opts, xax, yax)
       end
       DCL.uepset('icolor1', icolor1_bak) if opts['clr_min']
       DCL.uepset('icolor2', icolor2_bak) if opts['clr_max']
 
       if opts['color_bar']
+        cbunits = opts['cbunits']
+        cbunits = gphys.units.to_s if cbunits==true
         if @@used_fullcolor_tone
-          color_bar
+          color_bar "units"=>cbunits
         else
-          color_bar "log"=>opts['log']
+          color_bar "log"=>opts['log'], "units"=>cbunits
         end
       end
       closer.call if closer
@@ -2883,6 +2935,7 @@ module NumRu
       ['size', 0.01, 'marks size'],
       ['map_axes', false, '[USE IT ONLY WHEN itr=10 (cylindrical)] If true, draws axes by temprarilly switching to itr=1 and calling GGraph::axes.'],
       ['correlation', false, 'calculate Pearson\'s correlation coefficient and show it on the bottom margin'],
+      ['proc_before_ax', nil, 'Proc (with no argument) to be called just before drawing the axes.'],
       @@data_prep_options
         )
     ## @@scatter_options.delete("transpose")   # delete is yet to be supported
@@ -2932,6 +2985,9 @@ module NumRu
       y = gpy.data
       if newframe
         fig(x, y)
+        if opts['proc_before_ax']
+          opts['proc_before_ax'].call
+        end
         axes_or_map_and_ttl(gpx, opts, x, y, gpy)
       end
       DCL.uumrkz(x.val, y.val, opts['type'], opts['index'], opts['size'])
@@ -3152,6 +3208,7 @@ module NumRu
       ['keep', false, 'Use the same vector scaling as in the previous call. -- Currently, works only when "flow_vect" is true'],
       ['factor', 1.0, '(Effective only if flow_vect) scaling factor to strech/reduce the arrow lengths'],
       ['unit_vect', false, 'Show the unit vector'],
+      ['uvunits', false, 'units in the unit vector (false: never, true: read from the GPhys; a String: use that'],
       ['max_unit_vect', false, '(Effective only if flow_vect && unit_vect) If true, use the maximum arrows to scale the unit vector; otherwise, normalize in V coordinate.'],
       ['ux_unit', nil, '(If Numeric) length of the x direction unit vector (precedence of this option is lower than max_unit_vect)'],
       ['uy_unit', nil, '(If Numeric) length of the y direction unit vector (precedence of this option is lower than max_unit_vect)'],
@@ -3200,6 +3257,20 @@ module NumRu
 
       oldindex = DCLExt.ug_set_params("index" => opts['index']) if opts['index']
 
+      if opts['unit_vect']
+        if (uvu=opts['uvunits'])
+          case uvu
+          when String
+            un = uvu
+          else
+            raise("fx-fy units miss match") if fx.units != fy.units
+            un = fx.units.to_s
+          end
+          uvopts = {'units'=>un}
+        else
+          uvopts = Hash.new
+        end
+      end
       if opts['flow_itr5']
         if itr_is?(5)
           DCLExt.flow_itr5( fx, fy, opts['factor'], opts['unit_vect'] )
@@ -3218,7 +3289,7 @@ module NumRu
         returnval = { "vfratio"=> @@vfratio, "flenmax"=>@@flenmax }
         if opts['unit_vect']
           len_unit = opts['len_unit'] || @@flenmax
-          DCLExt.unit_vect_single(@@vfratio, len_unit)
+          DCLExt.unit_vect_single(@@vfratio, len_unit, uvopts)
         end
       elsif opts['flow_vect']
         uninfo = DCLExt.flow_vect(fx.val, fy.val, opts['factor'], 1, 1,
@@ -3230,7 +3301,7 @@ module NumRu
             uninfo[2] = opts['ux_unit']  # nil or a Numeric to specify the len 
             uninfo[3] = opts['uy_unit']  # nil or a Numeric to specify the len 
           end
-          DCLExt.unit_vect(*uninfo)
+          DCLExt.unit_vect( *(uninfo+[uvopts]) )
         end
       else
         before=DCLExt.ug_set_params({'lunit'=>true}) if opts['unit_vect']

data/lib/numru/gphys/axis.rb

@@ -630,7 +630,7 @@ module NumRu
 	 end
 
 	 case slicer
-	 when Fixnum
+	 when Integer
 	    pos=@pos[slicer]
 	    cval = ( pos.val.is_a?(Numeric) ? pos.val : pos.val[0] )
 	    units = pos.get_att('units')
@@ -1063,7 +1063,9 @@ module NumRu
 	    @integ_weight = posv.dup
 	    @integ_weight[0] = (posv[1]-posv[0]).abs/2
 	    @integ_weight[-1] = (posv[-1]-posv[-2]).abs/2
-	    @integ_weight[1..-2] = (posv[2..-1] - posv[0..-3]).abs/2
+            if posv.length > 2
+	      @integ_weight[1..-2] = (posv[2..-1] - posv[0..-3]).abs/2
+            end
 	 else
 	    # --- assume that the center values represents the averages ---
 	    bd = @cell_bounds.val

data/lib/numru/gphys/gphys_dim_op.rb

@@ -33,6 +33,7 @@ module NumRu
     #   This parameter is used only when the data have missing.
     #   Minimum number of grid points needed for averaging.
     #   Must be from 1 to len.
+    # * dont_expand (t/f; default: false): true -> keep where missing as missing
     # 
     # RETURN VALUE
     # * a GPhys
@@ -44,7 +45,8 @@ module NumRu
     # * Regardless the na_type of self, double is used for averaging, so:
     # * This method does not support complex numbers.
     # 
-    def running_mean(dim, len_or_wgt=nil, bc=nil, nminvalid=1)
+    def running_mean(dim, len_or_wgt=nil, bc=nil, nminvalid=1,
+                     dont_expand=false)
 
       #< process arguments >
 
@@ -81,9 +83,19 @@ module NumRu
         raise("This method supports only real or integer data")
       end 
       if vi.is_a?(NArrayMiss)
+        omask = vi.get_mask if dont_expand
         vi, missval = nam2na_missval(vi)
         vo = c_running_mean(vi,dim,wgt,bc,missval,nminvalid)
-        vo = NArrayMiss.to_nam(vo, vo.ne(missval) )
+        mask = vo.ne(missval)
+        if dont_expand
+          if (bc ==  BC_TRIM)
+            fst = (len-1)/2    # if odd len/2, if even len/2-1
+            lst = -(len/2) - 1
+            omask = omask[ *([true]*dim + [fst..lst, false]) ]
+          end
+          mask = mask & omask
+        end
+        vo = NArrayMiss.to_nam(vo, mask)
       else
         vo = c_running_mean(vi,dim,wgt,bc)
       end
@@ -134,7 +146,7 @@ module NumRu
     #
     def running_mean_2D(dim1, dim2, len_or_wgt1, len_or_wgt2,
                         bc1=nil, bc2=nil,
-                        nminvalid=1)
+                        nminvalid=1, dont_expand=false)
 
       dim1 = dim_index(dim1)  # to handle String or negative specification
       dim2 = dim_index(dim2)  # to handle String or negative specification
@@ -157,7 +169,7 @@ module NumRu
       vi = self.val
       if vi.is_a?(NArray)
         # Just for convenience.
-        self.running_mean(dim1, len_or_wgt1, bc1, nminvalid).running_mean(dim2, len_or_wgt2, bc2, nminvalid)
+        self.running_mean(dim1, len_or_wgt1, bc1, nminvalid, dont_expand).running_mean(dim2, len_or_wgt2, bc2, nminvalid, dont_expand)
       end
       
       if (vi.typecode > NArray::DFLOAT)
@@ -166,8 +178,12 @@ module NumRu
       if vi.is_a?(NArrayMiss)
         vi, missval = nam2na_missval(vi)
         vo = c_running_mean_2D(vi, dim1,len_or_wgt1,bc1, dim2,len_or_wgt2,bc2,
-                missval, nminvalid)
-        vo = NArrayMiss.to_nam(vo, vo.ne(missval) )
+                               missval, nminvalid)
+        mask = vo.ne(missval)
+        if dont_expand
+          mask = mask & vi.ne(missval)
+        end
+        vo = NArrayMiss.to_nam(vo, mask)
       else
         raise("This method accepts only data with missing. If not, you should apply running_mean twice for dim1 & dim2, respectively")
       end
@@ -225,6 +241,53 @@ module NumRu
 
     #def convolution(dim, g=nil, bc=BC_SIMPLE)
     #end
+
+   
+    # find the positions or the values of y where the values of z crosses zval along dim (using the linear interpolation)
+    # 
+    # * dim [Integer or String]
+    # * y [nil or VArray of float/sfloat] a coordinate variable or a NArray
+    #   having the same shape as self (but data missig is ignored).
+    #   If nil, dim indices are used.
+    # * nth [Integer] 1,2,3,... for the 1st, 2nd, 3rd,... crossing
+    # * descend [true, false, or nil] true: inspect dim indices from the last
+    # * incr [nil, true, or false] nil: any crsossing is detected; true:
+    #   only increasing crossing is detected; false: only decreasing crossing
+    #   is detected
+    #
+    def val_crossing(dim, zval, y: nil, nth: 1, descend: false, incr: nil)
+      z = self.val
+      if z.is_a?(NArrayMiss)
+        mask = z.get_mask
+        z = z.to_na
+      else
+        mask = nil
+      end
+      dim = dim_index(dim)
+      if y.nil?
+        yv = nil
+      elsif y.is_a?(VArray) || y.is_a?(GPhys)
+        y = y.data if y.is_a?(GPhys)
+        yv = y.val
+        if y.is_a?(NArrayMiss)
+          yv = yv.to_na  # ignore missing
+        end
+      else
+        raise("y must be a VArray or GPhys")
+      end
+      yc,ycmk = GPhys.c_val_crossing(z, mask, dim, zval, yv, nth, descend, incr)
+      yc = NArrayMiss.to_nam(yc,ycmk)
+      if y
+        ycva = VArray.new(yc, y, y.name)
+      else
+        ycva = VArray.new(yc, {"units"=>"", "long_name"=>"index"}, "index")
+      end
+      axes = []
+      (0...rank).each{|d|
+        axes.push(axis(d)) if d != dim
+      }
+      GPhys.new( Grid.new(*axes), ycva )
+    end
   end
 
   class VArray

data/lib/numru/gphys/gphys_fft.rb

@@ -526,6 +526,36 @@ module NumRu
       end
     end
 
+    def fft_filter(dim, iwnmin = nil, iwnmax = nil)
+      dim = dim_index(dim)
+      fc = self.fft(false,dim)
+      mask = val.get_mask
+      len = shape[dim]
+      raise("meaningless unless iwnmin or iwnmax is set") if !iwnmin && !iwnmax
+      if iwnmin
+        iwnmin += len if iwnmin<0
+        raise("invalid iwnmin #{iwnmin}") if iwnmin < 0 || iwnmin > len/2
+      end
+      if iwnmax
+        iwnmax += len if iwnmax<0
+        raise("invalid iwnmax #{iwnmax}") if iwnmax < 0 || iwnmax > len/2
+      end
+      if iwnmax && iwnmin
+        raise("iwnmin>iwnmax") if iwnmin>iwnmax
+      end
+      s = [true]*dim
+      if iwnmin
+        fc[ *(s + [0..iwnmin-1,false]) ] = 0.0  if iwnmin >= 1
+        fc[ *(s + [-iwnmin+1..-1,false]) ] = 0.0 if iwnmin > 1
+      end
+      if iwnmax && iwnmax < len/2
+        fc[ *(s + [iwnmax+1..-iwnmax-1,false]) ] = 0.0
+      end
+      filted = fc.fft(true,dim).to_type(self.data.typecode)
+      filted.replace_val( NArrayMiss.to_nam(filted.val, mask) )
+      filted
+    end
+
     def __predefined_coord_units_conversion(coord)
       case coord.units
       when Units["degree"]

data/lib/numru/gphys/gphys_io_common.rb

@@ -25,6 +25,8 @@ module NumRu
 
 	if !files.is_a?(Array)
 	  files = [files]     # put in an Array (if a single File)
+        else
+	  files = files.clone   # will be destroyed by shifting
 	end
 
 	if !loopdims.is_a?(Array)