Class: NumRu::GPhys

Inherits:
Object
  • Object
show all
Includes:
Misc::MD_Iterators
Defined in:
lib/numru/ganalysis/fitting.rb,
lib/numru/gphys/grib.rb,
lib/numru/gphys/gphys.rb,
lib/numru/ganalysis/eof.rb,
lib/numru/ganalysis/met.rb,
lib/numru/gphys/ep_flux.rb,
lib/numru/gphys/version.rb,
lib/numru/gphys/gphys_io.rb,
lib/numru/ganalysis/log_p.rb,
lib/numru/gphys/gphys_fft.rb,
lib/numru/gphys/derivative.rb,
lib/numru/gphys/interpolate.rb,
lib/numru/gphys/gphys_dim_op.rb,
lib/numru/ganalysis/histogram.rb,
lib/numru/gphys/gphys_grib_io.rb,
lib/numru/ganalysis/covariance.rb,
lib/numru/gphys/coordtransform.rb,
lib/numru/gphys/gphys_grads_io.rb,
lib/numru/gphys/gphys_gtool3_io.rb,
lib/numru/gphys/gphys_io_common.rb,
lib/numru/gphys/gphys_netcdf_io.rb,
lib/numru/gphys/gphys_nusdas_io.rb,
lib/numru/gphys/gphys_hdfeos5_io.rb,
ext/numru/gphys/dim_op.c,
ext/numru/gphys/interpo.c,
ext/numru/gphys/quad_mesh_sample.c

Overview

GPhys extension with GAnalysis::Fitting

Defined Under Namespace

Modules: Derivative, EP_Flux, GrADS_IO, GribUtils, Grib_IO, Gtool3_IO, HE5_IO, IO, IO_Common, NetCDF_IO, NuSDaS_IO Classes: Grib, GribDim, GribVar

Constant Summary collapse

VERSION =

Add subsubminor version while under development; remove it and advance version to release

"1.5.6"
COS_TAPER_SP_FACTOR = 
1.0 / 0.875
BC_SIMPLE =

enum in convol_filter.c

10
BC_CYCLIC =

enum in convol_filter.c

11
BC_TRIM =

enum in convol_filter.c

12
@@fft_forward = 
-1
@@fft_backward = 
1
@@fft_ignore_missing = 
false
@@fft_missing_replace_val = 
nil
@@interpo_previous_cutter = 
nil
@@interpo_previous_modifier = 
nil
@@interpo_missval =

NC_FILL_DOUBLE/FLOAT ~15*2^119

9.9692099683868690e+36
@@interpo_extrapolation = 
false
@@default_missval =

NC_FILL_DOUBLE/FLOAT ~15*2^119

9.9692099683868690e+36

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(grid, data) ⇒ GPhys

Returns a new instance of GPhys.



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# File 'lib/numru/gphys/gphys.rb', line 584

def initialize(grid, data)
	 #raise ArgumentError,"1st arg not a Grid" if ! grid.is_a?(Grid)
	 #raise ArgumentError,"2nd arg not a VArray" if ! data.is_a?(VArray)
	 if ( grid.shape_current != data.shape_current )
	    raise ArgumentError, "Shapes of grid and data do not agree. " +
  "#{grid.shape_current.inspect} vs #{data.shape_current.inspect}"
	 end
	 @grid = grid
	 @data = data
end

Instance Attribute Details

#data ⇒ Object (readonly)

Returns the value of attribute data.



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# File 'lib/numru/gphys/gphys.rb', line 595

def data
  @data
end

#grid ⇒ Object (readonly)

Returns the value of attribute grid.



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# File 'lib/numru/gphys/gphys.rb', line 595

def grid
  @grid
end

Class Method Details

.c_bin_mean(*args) ⇒ Object 



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# File 'ext/numru/gphys/dim_op.c', line 853

static VALUE
bin_mean(int argc, VALUE *argv, VALUE self)
{
    bin_mean_sum(argc, argv, self, 1);
}

.c_bin_sum(*args) ⇒ Object 



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# File 'ext/numru/gphys/dim_op.c', line 859

static VALUE
bin_sum(int argc, VALUE *argv, VALUE self)
{
    bin_mean_sum(argc, argv, self, 0);
}

.c_cap_by_boundary ⇒ Object

cap_by_boundary : Cap (insert) a NArray with boundary values

Restriction; data alignment is restricted so that the beginning of the out data is always valid (within the domain). To ensure it, it should be either zcrd is increasing and upper==true or zcrd is decreasing and upper==false.

RETURN VALUES

fe: f capped by the boundary values. The dimension zdim is

extended by 1; i.e., f[:,nz,:] --> fe[:,nz+1,:], where ":" respresent
arbitrary number of dimensions. The elements of fe are equal to
those of f where inside the domain (simple copies), and they are equal
to the elements of fs at the bondary (simple copies if fs is given;
if not, guessed by interpolation or naive extension).

ze: grid points of fe along zdim. It is a mixture of zcrd and zs;

it is zcrd inside the domain (where f is copied), and it is zs
at the boundary (where fs is copied).
Same shape as fe.

nze: The number of valid data along zdim of fe. Shaped as ze,

according to the notation above. For example, when fe is 4D and
zdim==2, fe[i,j,k,l] is valid for k = 0,1,...,nze[i,j,l]-1,
where the boundary is at nze[i,j,l]-1. Thus, nze is always
smaller than or equal to the length of zdim of fe (which is nz+1)



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# File 'ext/numru/gphys/dim_op.c', line 1235

static VALUE
cap_by_boundary(obj, f, zdim, zcrd, upper, zb, fb)
VALUE obj;

.c_cell_integ_irreg ⇒ Object

cell_integ_irreg: trapezoidal numerical integration over coordinate cells, supporting irregular grid

Description

Suppose a multi-dimensional NArray f, where colon represents any number of dimensions, and k is the “z” dimension along which integration is made. We write its real space representation as f(z; x), where x symbolically represents all of the independent variables other than z, and for simplicity, we further write it as f(z).

z is sampled at z_k, k=0,1,…,nzbound-1. This method allows z_k to be defined for each z column, so it requires a multi-D NArray argument z (having the same shape as f). Optionally, nzbound can also vary as nzbound. If, instead, nil is given to nzbound, the entire z grid is used; nzbound is set to f.shape(zdim).

We define the integration of f as

           {    \int_za^zb f(z) dz,  when za<=zb,
I(za,zb) = {
           {   -\int_za^zb f(z) dz,  otherwise.

In other words, our integration is always made from the smaller end to the greater end.

In the normal use case (when w is given nil), we define the cell integration as,

I(-\infty, zc_0), I(zc_0, zc_1), I(zc_1, zc_2),...,

The cell boundaries zc_m (m=0,1,..) are specified by the 1D NArray argument “ccell”; ccell must be aligned in the increasing order.

This method allows coordinate transformation by specifying another coordinate variable w (having the same shape as f). In this case, the ccell argument specifies a coordinate with respect to w: wc_m (m=0,1,…; wc_m must be in the increasing order). The integration is still taken with respect to z, so the cell integration is expressed as

I(-\infty, z(wc_0)), I(z(wc_0), z(wc_1)), I(z(wc_1), z(wc_2)),...,

The grid values z and w do not have to be monotonic; the numerical integration properly treats the contribution from multiple ranges along k. Mathematically, the coordinate-transferred integration over the w bin (-infty, wc] is expressed as

\int_-\infty^+\infty H(wc-w(z)) f(z) dz,

where H is the Heaviside function. The normal use case (without w) is simply when w is z itself, which is exploited in implementation.



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# File 'ext/numru/gphys/dim_op.c', line 1002

static VALUE
cell_integ_irreg(obj, f, z, zdim, nzbound, ccell, w)
VALUE obj;

.c_cum_integ_irreg ⇒ Object

cum_integ_irreg : similar to cell_integ_irreg but it sums up along the axis. – This method acutually uses cell_integ_irreg and make sumation.



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# File 'ext/numru/gphys/dim_op.c', line 1191

static VALUE
cum_integ_irreg(obj, f, z, zdim, nzbound, ccell, w)
VALUE obj;

.c_running_mean(*args) ⇒ Object 



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# File 'ext/numru/gphys/dim_op.c', line 320

static VALUE
running_mean(int argc, VALUE *argv, VALUE self)
{
    VALUE vi;    // mandatory 1st arg; input NArray
    VALUE dim;   // mandatory 2nd arg; Integer 
    VALUE wgt;   // mandatory 3rd arg; weight 1D NArray
    VALUE bc;    // mandatory 4th arg; boundary condition (Integer class const)
    VALUE missv=Qnil; // optional 5th arg; if present(Float) vi may have missing
    int nminvalid=1;     // optional 6th arg; miminum count of non-missing vales
    int with_miss;
    struct NARRAY *na;
    na_shape_t *shi, wlen;
    na_shape_t n0, n1, n2;
    double *zi, *w, zmiss;
    int d, i, rank, ibc;
    VALUE vo;
    na_shape_t *sho, n1o;
    double *zo;

    // < process arguments >

    if ( argc<4 || argc>6 ) { rb_raise(rb_eArgError,"Need 4 to 6 arguments"); }
    vi  = argv[0];
    dim = argv[1];
    wgt = argv[2];
    bc  = argv[3];
    with_miss = (argc > 4) && (!NIL_P(argv[4]));
    if ( with_miss ) { missv = argv[4]; }
    if ( argc == 6) {
	nminvalid = NUM2INT( argv[5] );
    }

    //   1st arg
    if (!IsNArray(vi)) { rb_raise(rb_eArgError,"1st arg must be a NArray"); }
    vi = na_cast_object(vi, NA_DFLOAT);
    rank = NA_RANK(vi);
    zi = NA_PTR_TYPE(vi, double *);
    GetNArray(vi, na);
    shi = na->shape;

    //   2nd arg
    d = NUM2INT( dim );

    //   3rd arg
    if (!IsNArray(wgt)) {rb_raise(rb_eArgError,"3rd arg must be a 1D NArray");}
    if (NA_RANK(wgt)!=1) {rb_raise(rb_eArgError,"3rd arg must be a 1D NArray");}
    wgt = na_cast_object(wgt, NA_DFLOAT);
    wlen = NA_TOTAL(wgt);
    w = NA_PTR_TYPE(wgt, double *);

    //   4th arg
    ibc = NUM2INT( bc );

    //   5th arg
    if ( with_miss ) { zmiss = NUM2DBL(missv); }

    //   6th arg
    if (nminvalid > wlen) {rb_raise(rb_eArgError,"nminvalid > filtering length");}

    // < shape as 3D >

    n1 = shi[d];   // length of the dim to filter
    if (wlen >= n1) {rb_raise(rb_eArgError,"filter len >= len of the dim");}

    n0 = n2 = 1;
    for (i=0; i<d; i++) {
	n0 *= shi[i];   // total lengths of dims before d
    }
    for (i=d+1; i<rank; i++) {
	n2 *= shi[i];   // total lengths of dims after d
    }

    // < initialize the NArray to ruturn >

    n1o = convol_result_length(n1, wlen, ibc);

    sho = ALLOCA_N(int, rank);
    for(i=0; i<rank; i++){
	sho[i] = ( i!=d ? shi[i] : n1o );
    }

    vo = na_make_object(NA_DFLOAT, rank, sho, cNArray);
    GetNArray(vo, na);
    na_clear_data(na);
    zo = NA_PTR_TYPE(vo, double *);

    // < do the job >
    if ( with_miss ) {
	running_mean_miss(zi,n0,n1,n2, w,wlen, ibc, zmiss, nminvalid, zo);
    } else {
	running_mean_nomiss(zi,n0,n1,n2, w,wlen, ibc, zo);
    }

    return vo;
}

.c_running_mean_2D ⇒ Object 



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# File 'ext/numru/gphys/dim_op.c', line 518

static VALUE
running_mean_2D(obj, vi, dim1, len_or_wgt1, bc1, dim2, len_or_wgt2, bc2,
            missv, nminvalid)
VALUE obj;

.concat(gpary, axis_or_ary, name = nil, attr = nil) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1342

def GPhys.concat(gpary, axis_or_ary, name=nil, attr=nil)
  #< interpret gpary (1st arg) >
  gpary = NArray.to_na(gpary) if gpary.is_a?(Array)
  if !gpary.is_a?(NArray) || gpary.rank != 1
    raise(ArgumentError,"1st arg must be a 1D NArray or Array of GPhys")
  end
  len = gpary.length

  #< interpret axis_or_ary (2nd arg) and make an Axis if not >
  case axis_or_ary
  when Axis
    ax = axis_or_ary
    if ax.length != len
      raise(ArgumentError,"length mismatch #{len} vs #{ax.length}")
    end
  else
    ary = axis_or_ary   # must be an NArray or Array
    ary = NArray.to_na(ary).to_f if ary.is_a?(Array)
    if !ary.is_a?(NArray) || ary.rank != 1
      raise(ArgumentError,
        "If not an Axis, 2nd arg must be 1D NArray or Array of float")
    end
    if ary.length != len
      raise(ArgumentError,"length mismatch #{len} vs #{ary.length}")
    end
    if name.nil?
      raise(ArgumentError,
         "3rd arg (name) is needed if the 2nd arg is not an Axis") 
    end
    va = VArray.new(ary, attr, name)
    ax = Axis.new().set_pos(va)
  end

  #< new grid >
  grid = gpary[0].grid.insert_axis(-1,ax)  # insert_axis: non-destructive

  #< join VArrays >
  ds = gpary.collect{|gp| gp.data}
  gpary[0].rank.times{ds.newdim!(0)}   # for VArrayComposite.new
  data = VArrayComposite.new(ds)

  #< result >
  GPhys.new(grid, data)
end

.each_along_dims(gphyses, loopdims) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1045

def self.each_along_dims(gphyses, loopdims)
	if !gphyses.is_a?(Array)
	  gphyses = [gphyses]     # put in an Array (if a single GPhys)
	end
	gp = gphyses[0]

	if !loopdims.is_a?(Array)
	  loopdims = [loopdims]  # put in an Array (if a single Integer/String)
	end
	if loopdims.length == 0
	  #raise ArgumentError, "No loop dimension is specified "+
	  #  " -- In that case, you don't need this iterator."

	  return yield(*gphyses)  # trivial case supported just for generality
	end

	#if loopdims.min<0 || loopdims.max>=gp.rank
	#  raise ArguemntError,"Invalid dims #{loopdims.inspect} for #{gp.rank}D array"
	#end

	loopdimids = Array.new
	loopdimnames = Array.new
	loopdims.each{|d|
	  case d
	  when Integer
	    if d < 0
 d += gp.rank
	    end
	    loopdimids.push( d )
	    loopdimnames.push( gp.axis(d).name )
	  when String
	    loopdimids.push( gp.dim_index(d) )
	    loopdimnames.push( d )
	  else
	    raise ArgumentError,"loopdims must consist of Integer and/or String"
	  end
	}

	sh = Array.new
	len = 1
	loopdimids.each{|i|
	  sh.push(gp.shape[i])
	  len *= gp.shape[i]
	}

	gphyses.each do |g|
	  for i in 1...gphyses.length
	    loopdimnames.each_with_index do |nm,i|
 if !g.axnames.include?( nm )
		raise ArgumentError,"#{i+1}-th GPhys do not have dim '#{nm}'"
 end
 if g.coord(nm).length != sh[i]
		raise ArgumentError,"loop dimensions must have the same lengths(#{nm}; #{sh[i]} vs #{g.coord(nm).length})"
 end
	    end
	  end
	end

	to_return = nil

	cs = [1]
	(1...sh.length).each{|i| cs[i] = sh[i-1]*cs[i-1]}
	idx_hash = Hash.new
	for i in 0...len do
	  loopdimnames.each_with_index{|d,j| 
	    idx_hash[d] = ((i/cs[j])%sh[j])..((i/cs[j])%sh[j]) # rank preserved
	  }
	  subs = gphyses.collect{|g| g[idx_hash] }
	  results = yield(*subs)
	  if results.is_a?(Array)  # then it must consist of GPhys objects
	    if i == 0
 to_return = results_whole = Array.new
 for j in 0...results.length
		rs = results[j]
		grid = rs.grid_copy
		loopdimnames.each{|nm|
		  # replaces with original axes (full length)
		  if !grid.axnames.include?( nm )
raise "Dimension '#{nm}' has been eliminated. "+
                    "You must keep all loop dimensions." 
		  end
		  grid.set_axis(nm,gphyses[0].axis(nm))
		}
		if ( (vtst=rs.data[0..0,false].val).respond_to?(:set_mask) )
             # DEVELOPPER'S NOTE (2006/08/15 horinout). 
             # Here, [0..0,false] is to take the minimum subset,
             # and respond_to?(:set_mask) is used to check whether
             # the data array is compatible to NArrayMiss
		  vary = VArray.new(NArrayMiss.new(vtst.typecode, *grid.shape), 
  rs.data)
		else
		  vary = VArray.new(NArray.new(vtst.typecode, *grid.shape), rs.data)
		end
		results_whole.push( self.new( grid, vary ) )
 end
	    end
	    for j in 0...results.length
 rs = results[j]
 results_whole[j][idx_hash] = rs.data
	    end
	  else
	    to_return = nil
	  end
	end
	return to_return

end

.extrapolation=(extrapo) ⇒ Object

Change the behavior of the interpolation methods to extrapolate outside the grid coverage.

ARGUMENTS

  • extrapo : true or false — the default behaviour is false (not to extrapolate), so use this method if you want to set it to true.



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# File 'lib/numru/gphys/interpolate.rb', line 28

def self.extrapolation=(extrapo)
  @@interpo_extrapolation = extrapo
end

.fft_ignore_missing(ignore = true, replace_val = nil) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 331

def self.fft_ignore_missing( ignore=true, replace_val=nil )
  @@fft_ignore_missing = ignore 
  @@fft_missing_replace_val = replace_val
end

.interpo_find_loc_1D ⇒ Object

to make “find loc” methods available outside GPhys as class methods



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# File 'ext/numru/gphys/interpo.c', line 311

static VALUE
interpo_find_loc_1D(obj, X, x, missval, extrapo)
VALUE obj;

.interpo_find_loc_1D_MD ⇒ Object

To apply interpo_find_loc_1D multi-dimensionally



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# File 'ext/numru/gphys/interpo.c', line 372

static VALUE
interpo_find_loc_1D_MD(obj, X, x, dimc, missval, extrapo)
VALUE obj;

.join(gpary, ignore_overlap = false, no_sort = false) ⇒ Object

Join multiple GPhys objects (not need for any pre-ordering).

ARGUMENT

  • gpnarray [Array (or 1D NArray) of GPhys]



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# File 'lib/numru/gphys/gphys.rb', line 1298

def GPhys.join(gpary, ignore_overlap=false, no_sort=false)

  #< initialization with the first GPhys object >

  gp = gpary[0]
  rank = gp.rank
  gpstore = MDStorage.new(rank)
  gpstore[ *Array.new(rank, 0) ] = gp     # first element
  x0s = (0...rank).collect{|d| 
    pos = gp.axis(d).pos
    x0 = UNumeric[ pos.val[0], pos.units ]
    [ x0 ]   # first values of each coordinate
  }

  #< scan the coordiantes of the remaining GPhys objects >
  for k in 1...gpary.length
    gp = gpary[k]
    idx = Array.new
    for d in 0...rank
      pos = gp.axis(d).pos
      x0 = UNumeric[ pos.val[0], pos.units ]
      i = x0s[d].index(x0)  
      if i.nil?
        x0s[d].push(x0)
        i = x0s[d].length-1
      end
      idx.push(i)
    end
    gpstore[*idx] = gp
  end

  if !ignore_overlap && gpstore.count_non_nil != gpary.length
    raise(ArgumentError,"Cannot uniquely locate one or more objects; some overlap in the grids?")
  end

  gpnary = gpstore.to_na

  #< Sort along dimensions to join >
  gpnary = __sort_gpnary(gpnary) unless no_sort

  #< Join! >
  self.join_md_nocheck(gpnary)
end

.join_md(gpnary, no_sort = false) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1226

def GPhys.join_md(gpnary, no_sort=false)
  #< Check >

  if !gpnary.is_a?(NArray)
    raise(ArgumentError,"Input must be an NArray of GPhys") 
  end
  arank = gpnary.rank      # rank of the input NArray
  ashape = gpnary.shape
  rank = gpnary[0].rank    

  #< Reshape and transpose gpnary if needed >

  #  / find dimmensions to join /
  dimmap = Array.new
  for i in 0...arank
    if ashape[i] > 1   # join needed
      sel = Array.new(arank, 0)   # [0,0,...,0]
      gp0 = gpnary[ *sel ]
      sel[i] = 1
      gp1 = gpnary[ *sel ]   # [0,..,0,1,0,...,0]
      for d in 0...rank
        c0 = gp0.coord(d)[0]
        c1 = gp1.coord(d)[0]
        if c0.val != c1.convert_units(c0.units).val
          dimmap[i] = d   # dimension to join (found)
          break
        end
        raise("Corresponding dim is not found for #{i}") if d==rank-1
      end
    else
      dimmap[i] = nil   # no need to join this dimension
    end
  end
  if (x=dimmap-[nil]).length != x.uniq.length
    raise "Dimensions to join cannot be determined uniquely"
  end

  #  / "solo" dimensions (dimensions no need to join) /
  sdims = (0...rank).collect{|d| d} - dimmap
  for i in 0...arank
    if dimmap[i].nil?
      dimmap[i] = sdims.shift    # assign dimensions orderly to 
                                 # minimize the need to transpose
    end
  end
  sdims.each do |d|
    dimmap.insert(d,d)           # assign dimensions orderly to 
    gpnary = gpnary.newdim(d)    # minimize the need to transpose
  end
  #   now, gpnary.rank == rank

  #  / transpose gpnary if needed /
  if dimmap != (0...rank).collect{|d| d}
    imap = Array.new
    dimmap.each_with_index do |d,j|
      imap[j] = d
    end
    gpnary = gpnary.transpose(*imap)
  end

  #< Sort along dimensions to join >
  gpnary = __sort_gpnary(gpnary) unless no_sort

  #< Join! >
  self.join_md_nocheck(gpnary)
end

.join_md_nocheck(gpnary) ⇒ Object

join multiple GPhys objects #######



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# File 'lib/numru/gphys/gphys.rb', line 1187

def GPhys.join_md_nocheck(gpnary)
  #< check >
  if !gpnary.is_a?(NArray)
    raise(ArgumentError,"Input must be an NArray of GPhys") 
  end
  rank = gpnary.rank

  #< axes >
  gp0 = gpnary[0]

  axes = Array.new
  for d in 0...rank
    if gpnary.shape[d] > 1  # --> join axes
      sel = [0]*d + [true] + [0]*(rank-d-1)   # [0,..0,true,0,...0]
      axs = gpnary[*sel].collect{|gp| gp.axis(d)}   # axes along d-th dim
      ax = Axis.join(axs)
    else
      ax = gp0.axis(d)
    end
    axes.push(ax)
  end

  #< grid >
  grid = Grid.new(*axes)
  if gp0.assoc_coords
    assoc_coords = gp0.assoccoordnames.collect do |aname|
      GPhys.join( gpnary.collect{|gp| gp.assoc_coord_gphys(aname)}, true,
                  true )
    end
    grid.set_assoc_coords(assoc_coords)
  end

  #< data >
  data = VArrayComposite.new( gpnary.collect{|gp| gp.data} )

  #< new gphys >
  GPhys.new(grid, data)
end

.quad_mesh_sample(z_na, si_na, ri_na, p_na, q_na, misval_f) ⇒ Object 



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# File 'ext/numru/gphys/quad_mesh_sample.c', line 357

VALUE rb_quad_mesh_sample(VALUE obj, VALUE z_na, VALUE si_na, VALUE ri_na,
                       VALUE p_na, VALUE q_na, VALUE misval_f)
{
  VALUE zg_na;
  int ns, nr, nx, ny;
  int *si, *ri; 
  double *p, *q, misval, *z, *zg;
  struct NARRAY *na;
  na_shape_t sh[2];

  GetNArray( na_cast_object(z_na, NA_DFLOAT), na);
  ns = na->shape[0];  
  nr = na->shape[1];  
  z = (double *) NA_PTR(na, 0);

  GetNArray( na_cast_object(si_na, NA_DFLOAT), na);
  nx = na->shape[0];
  ny = na->shape[1];
  si = NA_PTR_TYPE(si_na, int *);
  ri = NA_PTR_TYPE(ri_na, int *);
  p = NA_PTR_TYPE(p_na, double *);
  q = NA_PTR_TYPE(q_na, double *);
  misval = NUM2DBL( misval_f ); 

  sh[0] = (na_shape_t) nx;
  sh[1] = (na_shape_t) ny;
  zg_na = na_make_object(NA_DFLOAT, 2, sh, cNArray);
  zg = NA_PTR_TYPE(zg_na, double *);

  quad_mesh_sample(ns, nr, z, nx, ny, si, ri, p, q, misval, zg);

  return zg_na;
}

.quad_mesh_sample_init ⇒ Object

(in)



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# File 'ext/numru/gphys/quad_mesh_sample.c', line 292

VALUE rb_quad_mesh_sample_init(VALUE obj, VALUE x_na, VALUE y_na, // (in)
                        VALUE nx_i, VALUE x0_f, VALUE dx_f,     // (in)
                        VALUE ny_i, VALUE y0_f, VALUE dy_f,     // (in)
                        VALUE misval_f )     // (in)
{
  VALUE si_na, ri_na, p_na, q_na;  // (out)
  int ns, nr, nx, ny, rank;
  double *x, *y;
  double x0, dx, y0, dy, misval;
  int handle_miss;
  int *si, *ri;
  double *p, *q;
  struct NARRAY *na;
  na_shape_t sh[2];

  if (!IsNArray(x_na)) rb_raise(rb_eTypeError, "1st arg (x) must be an NArray");
  if (!IsNArray(y_na)) rb_raise(rb_eTypeError, "2nd arg (y) must be an NArray");

  rank = NA_RANK(x_na);
  if (rank != 2) rb_raise(rb_eArgError, "rank of x is not 2");
  rank = NA_RANK(y_na);
  if (rank != 2) rb_raise(rb_eArgError, "rank of x is not 2");

  GetNArray( na_cast_object(x_na, NA_DFLOAT), na);
  ns = na->shape[0];  
  nr = na->shape[1];  
  x = (double *) NA_PTR(na, 0);

  GetNArray( na_cast_object(y_na, NA_DFLOAT), na);
  if ( ns != na->shape[0] || nr != na->shape[1])
    rb_raise(rb_eArgError, "shapes of x and y do not agree");
  y = (double *) NA_PTR(na, 0);

  nx = NUM2INT( nx_i ); 
  ny = NUM2INT( ny_i ); 
  x0 = NUM2DBL( x0_f ); 
  dx = NUM2DBL( dx_f ); 
  y0 = NUM2DBL( y0_f ); 
  dy = NUM2DBL( dy_f ); 

  handle_miss = misval_f != Qnil;
  if (handle_miss) {
    misval = NUM2DBL( misval_f ); 
  } else {
    misval_f = 0.0; // just to avoid non-nitialization
  } 

  sh[0] = (na_shape_t) nx;
  sh[1] = (na_shape_t) ny;
  si_na = na_make_object(NA_LINT, 2, sh, cNArray);
  si = NA_PTR_TYPE(si_na, int *);
  ri_na = na_make_object(NA_LINT, 2, sh, cNArray);
  ri = NA_PTR_TYPE(ri_na, int *);
  p_na = na_make_object(NA_DFLOAT, 2, sh, cNArray);
  p = NA_PTR_TYPE(p_na, double *);
  q_na = na_make_object(NA_DFLOAT, 2, sh, cNArray);
  q = NA_PTR_TYPE(q_na, double *);

  quad_mesh_sample_init(ns, nr, x, y, nx, x0, dx, ny, y0, dy, // (in)
                     handle_miss, misval, // (in)
                     si, ri, p, q);

  return rb_ary_new3(4, si_na, ri_na, p_na, q_na);
}

Instance Method Details

#[](*slicer) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 678

def [](*slicer)
	 if slicer.length==1 && slicer[0].is_a?(Hash) && 
	    slicer[0].keys[0].is_a?(String)
	   slicer = __process_hash_slicer(slicer[0])
	 else
	   slicer = __rubber_expansion( slicer )
	 end
	 self.class.new( @grid[*slicer], @data[*slicer] )
end

#[]=(*args) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 688

def []=(*args)
	 val = args.pop
	 slicer = args
	 if slicer.length==1 && slicer[0].is_a?(Hash) && 
	    slicer[0].keys[0].is_a?(String)
	   slicer = __process_hash_slicer(slicer[0])
	 else
	   slicer = __rubber_expansion( slicer )
	 end
	 val = val.data if val.respond_to?(:grid) #.is_a?(GPhys)
	 @data[*slicer] = val
end

#add_lost_axes(lost) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 770

def add_lost_axes( lost )
  @grid.add_lost_axes( lost )
  self
end

#assoc_coord_gphys(name) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 759

def assoc_coord_gphys(name)
	@grid.assoc_coord_gphys(name)
end

#assoc_coords ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 798

def assoc_coords
  @grid.assoc_coords
end

#assoc_coords=(assoc_coords) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 795

def assoc_coords=(assoc_coords)
  @grid.assoc_coords=assoc_coords
end

#assoccoordnames ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 789

def assoccoordnames
  @grid.assoccoordnames
end

#att_names ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 635

def att_names
	@data.att_names
end

#axis(i) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 753

def axis(i)
	@grid.axis(i)
end

#axnames ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 744

def axnames
	 @grid.axnames
end

#bin_mean(dim, len, nminvalid = 1) ⇒ Object

Binning along a dimension (mean)

The values are averaged every “len” grids; unlike running_mean the number of grids is reduced to 1/len. Currently, the only available boundary condition is BC_TRIM.

ARGUMENTS

  • dim (Integer or String) : the dimension

  • len (Integer): length of the bin

  • nminvalid (Integer; optional; defualt=1): Effective only for data with missing. Minimum number of grid points needed for averaging (1 to len).

RETURN VALUE

  • a GPhys



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# File 'lib/numru/gphys/gphys_dim_op.rb', line 194

def bin_mean(dim, len, nminvalid=1)
  dim = dim_index(dim)  # to handle String or negative specification
  GPhys.new( grid.binning(dim, len), data.bin_mean(dim, len, nminvalid) )
end

#bin_sum(dim, len, nminvalid = 1) ⇒ Object

Binning along a dimension (summation)

Similar to bin_mean, but the values are simply summed without averaging

ARGUMENTS

  • dim (Integer or String) : the dimension

  • len (Integer): length of the bin

  • nminvalid (Integer; optional; defualt=1): Effective only for data with missing. Minimum number of grid points needed for averaging (1 to len).

RETURN VALUE

  • a GPhys



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# File 'lib/numru/gphys/gphys_dim_op.rb', line 212

def bin_sum(dim, len, nminvalid=1)
  dim = dim_index(dim)  # to handle String or negative specification
  GPhys.new( grid.binning(dim, len), data.bin_sum(dim, len, nminvalid) ) 
end

#cderiv(*args) ⇒ Object 



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# File 'lib/numru/gphys/derivative.rb', line 91

def cderiv(*args)
  Derivative::cderiv(self,*args)
end

#coerce(other) ⇒ Object

<– For graphics



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# File 'lib/numru/gphys/gphys.rb', line 848

def coerce(other)
	case other
  when Numeric, Array, NArrayMiss
    c_other = UNumeric::Num2Coerce.new( other )
  else
    raise "Cannot coerse #{other.class}"
  end
	[c_other, self]
end

#convert_units(to) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 662

def convert_units(to)
	# ==NOTE: 
	#    * VArray#convert_units does not copy data if to == @data.units
	#    * @grid is shared with self (no duplication)
  #    Thus, use GPhys#copy to separate all sub-objects (deep clone).
	data = @data.convert_units(to)  
	self.class.new(@grid, data)
end

#coord(i) ⇒ Object Also known as: coordinate 



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# File 'lib/numru/gphys/gphys.rb', line 756

def coord(i)
	@grid.coord(i)
end

#coord_data_reverse(axname, pos) ⇒ Object

Reverse the main data (i.e., the dependent variable) and one of the coordinates (an independent variable) through interpolation.

Returns a GPhys in which the main data is the specfied coordinate (argument: axname) sampled at specified locations (argument: pos) in terms of the main data of self. The main data of self is expected to be quai-monotonic with respect to the specfied coordinate.

ARGUMENTS

  • axname [String] : one of the names of the axes (i.e. main coordinates. Auxiliary coordinates are not supported as the target.)

  • pos [NArray] : grid locations. For example, if the current data is potential temperature theta, pos consists of the theta levels to make sampling.

RETURN VALUE

  • a GPhys



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# File 'lib/numru/gphys/interpolate.rb', line 231

def coord_data_reverse(axname,pos)
  gp = self.axis(axname).to_gphys
  gp = self.shape_coerce_full(gp)[0]   # conform the shape to that of self
  gp = GPhys.new( gp.grid.copy, gp.data )  # copy grid to avoid side effect
                                           # on the grid of self
  gp.set_assoc_coords([self])
  pos = NArray[*pos].to_type(NArray::FLOAT) if pos.is_a?(Array)
  newcrd = VArray.new(pos,self.data,self.name)  # succeeds the attributes
  gp.interpolate(axname=>newcrd)
end

#coordnames ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 777

def coordnames
  @grid.coordnames
end

#coordtransform(coordmapping, axes_to, *dims) ⇒ Object 



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# File 'lib/numru/gphys/coordtransform.rb', line 41

def coordtransform( coordmapping, axes_to, *dims )

  rankmp = coordmapping.rank

  #< check arguments >
  if axes_to.length != rankmp
    raise ArgumentError,
      "length of axes_to must be equal to the rank of coordmapping"
  end
  if self.rank == rankmp
    dims = (0...rankmp).collect{|i| i}
  elsif self.rank < rankmp
    raise ArgumentError,"rank of coordmapping is greater than self.rank"
  elsif dims.length != rankmp
    raise ArguemntError,
      "# of dimensions speficied is not equal to the rank of coordmapping"
  elsif dims != dims.sort
    raise ArguementErroor,"dims must be in the increasing order"
  end

  #< get grid points >
  vt = coordmapping.map_grid( *dims.collect{|d| axes_to[d].pos.val} )
  x = dims.collect{|d| self.grid.axis(d).pos.val}
  #< prepare the output object >
  axes = (0...self.rank).collect{|i| grid.axis(i)}
  dims.each_with_index{|d,j| axes[d]=axes_to[j]}
  grid_to = Grid.new( *axes )
  vnew = VArray.new( NArray.new( self.data.ntype, *grid_to.shape ),
                    self.data, self.name )

  #< do interpolation (so far only 2D is supported) >
  case dims.length
  when 2
    if !HAVE_NUMRU_SSL2

      p "interpolation without SSL2"
#         raise "Sorry, so far I need SSL2 (ruby-ssl2)"
      self.each_subary_at_dims_with_index( *dims ){ |fxy,idx|

        wgts = Array.new
        idxs = Array.new

        for d in 0..dims.length-1
          wgt = vt[d].dup.fill!(-1.0)
          idx0 = vt[d].dup.to_i.fill!(-1)
          idx1 = idx0.dup.fill!(x[d].length)

          xsort = x[d].sort
          xsortindex = x[d].sort_index
          for i in 0..x[d].length-1
            idx0[ xsort[i] <= vt[d] ] = xsortindex[i]
            idx1[ xsort[-1-i] >= vt[d] ] = xsortindex[-1-i]
          end

          # where idx0=idx1
          wgt[ idx0.eq(idx1) ] = 1.0

          # where vt[d] < x[d].min
          wgt[ idx0 <= -1 ] = 1.0
          idx0[ idx0 <= -1 ] = 0

          # where vt[d] > x[d].max
          wgt[ idx1 >= x[d].length ] = 0.0
          idx1[ idx1 >= x[d].length ] = x[d].length-1

          # normal points
          mask = wgt.eq(-1.0)
          wgt[mask] = (vt[d][mask]-x[d][idx0[mask]])/(x[d][idx1[mask]]-x[d][idx0[mask]])

          wgts.push(wgt)
          idxs[d*2] = idx0
          idxs[d*2+1] = idx1

        end

        case dims.length
#            when 1
#              f =   fxy.data.val[idxs[0]]*(1-wgts[0]) + 
#                    fxy.data.val[idxs[1]]*wgts[0]
#              f = f.to_na if( f.class.to_s == "NArrayMiss" )
        when 2
          lx = fxy.shape[0]
          f =   ( fxy.data.val[idxs[0]+idxs[2]*lx]*(1-wgts[0]) + 
                  fxy.data.val[idxs[1]+idxs[2]*lx]*wgts[0]
                ) * (1-wgts[1]) + 
                ( fxy.data.val[idxs[0]+idxs[3]*lx]*(1-wgts[0]) + 
                  fxy.data.val[idxs[1]+idxs[3]*lx]*wgts[0] 
                ) * wgts[1]
          f = f.to_na if( f.class.to_s == "NArrayMiss" )
        else
          raise "Sorry, #{v.length}D interpolation is yet to be supported"
        end

        if(idx==false)
          vnew[] = f
        else
          vnew[*idx] = f
        end
      }

    else
      ix=iy=0
      m=3
      self.each_subary_at_dims_with_index( *dims ){ |fxy,idx|
        c,xt = SSL2.bicd3(x[0],x[1],fxy.val,m)
        begin
          ix,iy,f = SSL2.bifd3(x[0],x[1],m,c,xt,0,vt[0],ix,0,vt[1],iy)
        rescue
          $stderr.print "Interpolation into", vt[0].inspect, vt[1].inspect
          raise $!
        end
        vnew[*idx] = f
      }
    end
  else
    raise "Sorry, #{v.length}D interpolation is yet to be supported"
  end

  #< finish >
  GPhys.new( grid_to, vnew )
end

#copy ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 603

def copy
	 # deep clone onto memory
	 self.class.new( @grid.copy, @data.copy )
end

#correlation(other, *dims) ⇒ Object 



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# File 'lib/numru/ganalysis/covariance.rb', line 93

def correlation(other, *dims)
  GAnalysis.correlation(self, other, *dims)
end

#cos_taper(*dims) ⇒ Object

Spectral factor for the cosine taper. Specta should be multiplied by this.



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# File 'lib/numru/gphys/gphys_fft.rb', line 339

def cos_taper(*dims)
  if dims.length < 1
	raise ArgumentError,'You have to specify one or more dimensions'
  end
  dims.sort!.uniq!
  val = self.data.val
  dims.each{|dim|
	dim = dim_index(dim) if dim.is_a?(String)
	dim += rank if dim < 0
	raise ArgumentError,"dim #{dim} does not exist" if dim<0 || dim>rank
    nx = shape[dim]
	wgt = NArray.float(nx).fill!(1)
    x = 10.0 / nx * (NArray.float(nx).indgen!+0.5) 
	wskl = x.lt(1).where
	wskr = x.gt(9).where
	wgt[wskl] = 0.5*( 1.0 - NMath::cos(Math::PI*x[wskl]) )
	wgt[wskr] = 0.5*( 1.0 - NMath::cos(Math::PI*x[wskr]) )
	wgt.reshape!( *([1]*dim + [nx] + [1]*(rank-dim-1)) )
	val = val*wgt
  }
  to_ret = self.copy
  to_ret.data.val = val
  to_ret
end

#covariance(other, *dims) ⇒ Object 



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# File 'lib/numru/ganalysis/covariance.rb', line 89

def covariance(other, *dims)
  GAnalysis.covariance(self, other, *dims)
end

#cut(*args) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 712

def cut( *args )
  if has_assoccoord? && args.length==1 && ((spec=args[0]).is_a?(Hash)) &&
      ( acnms = (spec.keys & assoccoordnames ) ).length > 0
    acspec = Hash.new
    acnms.each{|nm| acspec[nm] = spec.delete(nm)}
    grid, sl = @grid.cut_assoccoord(acspec)
    gphys = self.class.new( grid, self.data[*sl] )
  else
    gphys = self
  end
	newgrid, slicer = gphys.grid.cut( *args )
	self.class.new( newgrid, gphys.data[ *slicer ] )
end

#cut_rank_conserving(*args) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 726

def cut_rank_conserving( *args )
	newgrid, slicer = @grid.cut_rank_conserving( *args )
	self.class.new( newgrid, @data[ *slicer ] )
end

#cyclic_ext(dim_or_dimname) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1024

def cyclic_ext(dim_or_dimname)
  # Cyclic extention to push the first element after the last element
  # if appropriate. (by using the cut method)

  ax = axis(dim_or_dimname)
  if ax.cyclic_extendible? 
    modulo = ax.modulo
    v = ax.pos.val
    v0 = v[0]
    eps = 1e-2/ax.length
    if v0 < v[-1]  # increasing
      v1 = v0 + modulo*(1+eps)
    else
      v1 = v0 - modulo*(1+eps)
    end
    return self.cut(ax.name=>v0..v1)
  else
    return self 
  end
end

#cyclic_ext_with_modulo(dim_or_dimname, modulo) ⇒ Object

Old version of cyclic_ext



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# File 'lib/numru/gphys/gphys.rb', line 998

def cyclic_ext_with_modulo(dim_or_dimname, modulo)
	# Cyclic extention to push the first element after the last element
  # if appropriate.

	vx = coord(dim_or_dimname)
	return self if vx.length <= 1

	vvx = vx.val
	width = (vvx[-1] - vvx[0]).abs
	dx = width / (vx.length-1)
	eps = 1e-4
	modulo = modulo.abs
	extendible = ( ((width+dx) - modulo).abs < eps*modulo )

	if extendible
	  dim = @grid.dim_index(dim_or_dimname)
	  newgp = self.copy[false, [0...vx.length, 0], *([true]*(rank-1-dim))]
	  vx = newgp.coord(dim).copy
	  vx[-1] = vx[-1].val + modulo
	  newgp.axis(dim).set_pos(vx)
	  return newgp
	else
	  return self
	end
end

#dcl_fig_cut(dimx, dimy, ux, uy) ⇒ Object

Interpolation on the DCL window (automatic iso-interval interpolation along a poly line that can be drawn in the current viewport of the DCL window). Used in mouse_cut.

ARGUMENTS

  • dimx [Integer or String] : specifies the dimension corresponding to the UX coordinate. (Here, the UX coordinate is the X coordinate of the DCL’s USER coordinate. For exapmle, longitude if map projection.)

  • dimy [Integer or String] : specifies the dimension corresponding to the UY coordinate. (Here, the UY coordinate is the Y coordinate of the DCL’s USER coordinate. For exapmle, latitude if map projection.)

  • ux [Array] : x values in terms of the UX coordinate

  • uy [Array] : y values in terms of the UY coordinate Lengths of ux and uy must be the same and greter or equal to 2.



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# File 'lib/numru/gphys/interpolate.rb', line 89

def dcl_fig_cut(dimx,dimy,ux,uy)
  len = ux.length
  raise("ux and uy must be arrays with the (same) length >= 2") if len<=1
  raise("ux's len (#{len}) != uy's len (#{uy.length})") if uy.length != len
  vx=Array.new; vy=Array.new
  for i in 0...len
    vx[i],vy[i] = NumRu::DCL.stftrf(ux[i],uy[i]) 
  end
  kx = Array.new
  ky = Array.new
  cut = [true]*rank
  for i in 0...len
    cut[dimx] = ux[i]
    cut[dimy] = uy[i]
    dummy, sl = grid.cut(*cut)
    kx[i] = sl[dimx]
    ky[i] = sl[dimy]
  end
  ndiv = Array.new
  ndsum = [0]
  for i in 0...len-1
    ndiv[i] = Math.sqrt( (kx[i+1]-kx[i])**2 + (ky[i+1]-ky[i])**2).to_i
    ndiv[i] += 1 if i==len-2
    ndsum.push ndsum[-1] + ndiv[i]   # 0, ndiv[0], ndiv[0]+ndiv[1], ...
  end
  ndtot = ndsum[-1]
  vxdiv = NArray.float(ndtot)
  vydiv = NArray.float(ndtot)
  for i in 0...len-1
    if i!=len-2
      a = NArray.float(ndiv[i]).indgen / ndiv[i]
    else
      a = NArray.float(ndiv[i]).indgen / (ndiv[i]-1)
    end
    vxdiv[ndsum[i]...ndsum[i+1]] = (1.0-a)*vx[i] + a*vx[i+1]
    vydiv[ndsum[i]...ndsum[i+1]] = (1.0-a)*vy[i] + a*vy[i+1]
  end
  uxdiv = NArray.float(ndtot)
  uydiv = NArray.float(ndtot)
  for i in 0...ndtot
    uxdiv[i], uydiv[i] = DCL.stitrf(vxdiv[i], vydiv[i])
  end
  cx = coord(dimx)
  xcrd = VArray.new(uxdiv, cx, cx.name)
  cy = coord(dimy)
  ycrd = VArray.new(uydiv, cy, cy.name)
  if (vxdiv[-1]-vxdiv[0]).abs > (vydiv[-1]-vydiv[0]).abs
    cutter = [xcrd,ycrd]  # x will be the main coord var if not map proj
    crd = xcrd
  else
    cutter = [ycrd,xcrd]  # x will be the main coord var if not map proj
    crd = ycrd
  end
  axnm = crd.name
  itr = DCL.sgqtrn
  if itr>=10 and itr<=40
    newcrd = __sp_dist(xcrd,ycrd)
    modifier = Proc.new{|gp|
      newax = Axis.new.set_pos(newcrd)
      gp.grid.set_axis(axnm,newax)
      g = Grid.new( newax )
      gxcrd = GPhys.new(g,xcrd)
      gycrd = GPhys.new(g,ycrd)
      gp.set_assoc_coords([gxcrd, gycrd])
      gp
    }
  else
    modifier = nil
  end
  @@interpo_previous_cutter = cutter
  @@interpo_previous_modifier = modifier

  # < do the job >

  gpnew = interpolate(cutter)
  gpnew = modifier[gpnew] if modifier
  gpnew
end

#del_att(name) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 645

def del_att(name)
	@data.del_att(name)
	self
end

#deriv2nd(*args) ⇒ Object 



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# File 'lib/numru/gphys/derivative.rb', line 97

def deriv2nd(*args)
  Derivative::deriv2nd(self,*args)
end

#detrend(*dims) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 364

def detrend(*dims)
  if dims.length < 1
	raise ArgumentError,'You have to specify one or more dimensions'
  end
  dims.sort!.uniq!
  val = self.data.val
  dims.each{|dim|
	dim = dim_index(dim) if dim.is_a?(String)
	dim += rank if dim < 0
	raise ArgumentError,"dim #{dim} does not exist" if dim<0 || dim>rank
	if val.is_a?(NArray)
	  x = self.coord(dim).val
	  x.reshape!( *([1]*dim + [x.length] + [1]*(rank-dim-1)) )
	  vmean = val.mean(dim)
	  vxmean = (val*x).mean(dim)
	  xmean = x.mean(dim)
	  x2mean = (x*x).mean(dim)
	  denom = x2mean-xmean**2
	  if denom != 0
 a = (vxmean - vmean*xmean)/denom
 b = (vmean*x2mean - vxmean*xmean)/denom
	  else
 a = 0
 b = vmean
	  end
	elsif val.is_a?(NArrayMiss)
	  x = self.coord(dim).val
	  x.reshape!( *([1]*dim + [x.length] + [1]*(rank-dim-1)) )
	  x = NArrayMiss.to_nam( NArray.new(x.typecode, *val.shape) + x,
 val.get_mask ) 
	  vmean = val.mean(dim)
	  vxmean = (val*x).mean(dim)
	  xmean = x.mean(dim)
	  x2mean = (x*x).mean(dim)
	  denom = x2mean-xmean**2
	  meq0 = denom.eq(0).to_na(0)    # ==0 and not masked
	  mne0 = denom.ne(0).to_na(0)    # !=0 and not masked
      denom.set_mask(mne0)    # only nonzero part will be used to divide:
	  a = (vxmean - vmean*xmean)/denom
	  b = (vmean*x2mean - vxmean*xmean)/denom
	  a[meq0] = 0
	  b[meq0] = vmean[meq0]
	end
	a.newdim!(dim) if !a.is_a?(Numeric)
	b.newdim!(dim) if !b.is_a?(Numeric)
	val = val - a*x-b
  }
  to_ret = self.copy
  to_ret.data.val = val
  to_ret
end

#dim_index(dimname) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 774

def dim_index( dimname )
	 @grid.dim_index( dimname )
end

#eddy(*dim) ⇒ Object

Basic numerical operations that are not defined on the VArray level



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# File 'lib/numru/gphys/gphys.rb', line 804

def eddy(*dim)
  self - self.mean(*dim)
end

#eof(*args) ⇒ Object 



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# File 'lib/numru/ganalysis/eof.rb', line 235

def eof(*args)
  GAnalysis.eof(self, *args)
end

#fft(backward = false, *dims) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 416

def fft(backward=false, *dims)
  fftw3 = false
  if defined?(FFTW3)
	fftw3 = true
  elsif !defined?(FFTW)
	raise "Both FFTW3 and FFTW are not installed."
  end
  if backward==true
	dir = @@fft_backward
  elsif !backward
	dir = @@fft_forward
  else
	raise ArgumentError,"1st arg must be true or false (or, equivalenty, nil)"
  end

  # <FFT>

  gfc = self.copy  # make a deep clone
  if fftw3
	val = gfc.data.val
	if @@fft_ignore_missing and val.is_a?(NArrayMiss)
	  if @@fft_missing_replace_val
 val = val.to_na(@@fft_missing_replace_val)
	  else
 val = val.to_na 
	  end
    elsif val.is_a?(NArrayMiss) && val.count_invalid == 0
      val = val.to_na 
	end
	fcoef = FFTW3.fft( val, dir, *dims )
  else
	# --> always FFT for all dimensions
	if dims.length == 0
	  raise ArgumentError,
 "dimension specification is available only if FFTW3 is installed"
	end
	val = gfc.data.val
	if @@fft_ignore_missing and val.is_a?(NArrayMiss)
	  if @@fft_missing_replace_val
 val = val.to_na(@@fft_missing_replace_val)
	  else
 val = val.to_na 
	  end
    elsif val.is_a?(NArrayMiss) && val.count_invalid == 0
      val = val.to_na 
	end
	fcoef = FFTW.fftw( val, dir )
  end
  if dir == @@fft_forward
	if dims.length == 0
	  fcoef = fcoef / fcoef.length.to_f   # normalized if forward FT
	else
	  sh = fcoef.shape
	  len = 1
	  dims.each{|d|
 raise ArgumentError, "dimension out of range" if sh[d] == nil
 len *= sh[d]
      }
	  fcoef = fcoef / len
    end
  end
  gfc.data.replace_val( fcoef )

  # <coordinate variables>
  for i in 0...gfc.rank
	if dims.length == 0 || dims.include?(i) || dims.include?(i+rank)
	  __predefined_coord_units_conversion(gfc.coord(i))
	  cv = gfc.coord(i).val
	  n = cv.length
	  clen = (cv.max - cv.min) * n / (n-1)
	  wn = (2*Math::PI/clen) * NArray.new(cv.typecode,cv.length).indgen!.to_f
	  if (!backward)
 gfc.coord(i).set_att('origin_in_real_space',cv[0..0])
	  else 
 if ( org = gfc.coord(i).get_att('origin_in_real_space') )
   wn += org[0]
   ###gfc.coord(i).del_att('origin_in_real_space')
 end
	  end
	  gfc.coord(i).replace_val(wn)
	  gfc.coord(i).units = gfc.coord(i).units**(-1)
	  __coord_name_conversion(gfc.coord(i), backward)
	end
  end

  # <fini>
  gfc
end

#fft_deriv(dim) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 505

def fft_deriv(dim)
  tp = self.data.typecode
  fc = self.fft(false,dim)
  wn = fc.coord(dim)
  k = wn.val.to_type(NArray::Complex)
  n = k.length
  n2a = (n-1)/2
  n2b = [n/2 + 1, n-1].min  # min to avoid error if n=2 (though meaningless)
  kmx = k[-1]+k[1]
  ik = NArray.complex(n)
  ik[0..n2a] = k[0..n2a]*Complex::I
  ik[n2b..-1] = (k[n2b..-1]-kmx) * Complex::I
  dim.times{ik.newdim!(0)}
  (self.rank-dim-1).times{ik.newdim!(-1)}
  fc.replace_val(fc.val*ik)
  deriv = fc.fft(true,dim)
  deriv.units = deriv.units * wn.units
  if tp >= NArray::SCOMPLEX
    deriv
  else
    deriv.real
  end
end

#first1D ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 817

def first1D
	raise "rank less than 1" if rank < 1
	self[true,*([0]*(rank-1))]
end

#first1Dreally ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 843

def first1Dreally
  firstNDreally(1)
end

#first2D ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 813

def first2D
	raise "rank less than 2" if rank < 2
	self[true,true,*([0]*(rank-2))]
end

#first2Dreally ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 840

def first2Dreally
  firstNDreally(2)
end

#first3D ⇒ Object

For graphics –>



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# File 'lib/numru/gphys/gphys.rb', line 809

def first3D
	raise "rank less than 3" if rank < 3
	self[true,true,true,*([0]*(rank-3))]
end

#first3Dreally ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 837

def first3Dreally
  firstNDreally(3)
end

#firstNDreally(nd) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 821

def firstNDreally(nd)
  sh = shape_current
  n = 0
  sel = sh.map do |len|
    if len > 1 && n < nd
      n += 1
      true
    else
      0
    end
  end
  if n<nd
    raise "Invalid shape #{sh} (not really #{nd}D or greater): # of dims with len>1 is fewer than #{nd}"
  end
  self[*sel]
end

#get_att(name) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 638

def get_att(name)
	@data.get_att(name)
end

#grid_copy ⇒ Object

protected :grid # protection is lifted



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# File 'lib/numru/gphys/gphys.rb', line 598

def grid_copy
	# deep clone of the grid
	@grid.copy
end

#has_assoccoord?(*arg) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/numru/gphys/gphys.rb', line 783

def has_assoccoord?(*arg)
  @grid.has_assoccoord?(*arg)
end

#has_axis?(name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/numru/gphys/gphys.rb', line 780

def has_axis?(name)
  @grid.has_axis?(name)
end

#has_coord?(name) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/numru/gphys/gphys.rb', line 786

def has_coord?(name)
  @grid.has_coord?(name)
end

#histogram(opts = Hash.new) ⇒ Object Also known as: histogram1D 



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# File 'lib/numru/ganalysis/histogram.rb', line 155

def histogram(opts=Hash.new)
  GAnalysis.histogram(self, opts)
end

#inspect ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 608

def inspect
  "<#{self.class} grid=#{@grid.inspect}\n   data=#{@data.inspect}>"
end

#interpolate(*coords) ⇒ Object

Wide-purpose multi-dimensional linear interpolation

This method supports interpolation regarding combinations of 1D and 2D coordinate variables. For instance, suppose self is 4D with coordinates named [“x”, “y”, “z”, “t”] and associated coordinates “sigma” (“sigma” is 1D and its axis is “z”), “p”, “q” (“p” and “q” are 2D having the coordinates “x” and “y”). You can make interpolation by specifying 1D VArrays whose names are among “x”, “y”, “z”, “t”, “sigma”, “p”, “q”. You can also use a Hash like => 1.0 to specify a single point along the “x” coordinate.

If the units of the target coordinate and the current coordinate are different, a converstion was made so that slicing is made correctly, as long as the two units are comvertible; if the units are not convertible, it is just warned.

If you specify only “x”, “y”, and “t” coordinates for interpolation, the remaining coordinates “z” is simply retained. So the result will be 4 dimensional with coordinates named [“x”, “y”, “z”, “t”], but the lengths of “x”, “y”, and “t” dimensions are changed according to the specification. Note that the result could be 3-or-smaller dimensional – see below.

Suppose you have two 1D VArrays, xnew and ynew, having names “x” and “y”, respectively, and the lengths of xnew and the ynew are the same. Then, you can give an array of the two, [xnew, ynew], for coord0 as

gp_int = gp_org.interpolate( [xnew, ynew] )

(Here, gp_org represents a GPhys object, and the return value pointed by gp_int is also a GPhys.) In this case, the 1st dimension of the result (gp_int) will be sampled at the points [xnew,ynew], [xnew,ynew], [xnew,ynew], …, while the 2nd and the third dimensions are “z” and “t” (no interpolation). This way, the rank of the result will be reduced from that of self.

If you instead give xnew to coord0 and ynew to coord1 as 

gp_int = gp_org.interpolate( xnew, ynew )

The result will be 4-dimensional with the first coordinate sampled at xnew, xnew, xnew,… and the second coordinate sampled at ynew, ynew, ynew,…

You can also cut regarding 2D coordinate variable as

gp_int = gp_org.interpolate( pnew, qnew )
gp_int = gp_org.interpolate( xnew, qnew )
gp_int = gp_org.interpolate( [pnew, qnew] )
gp_int = gp_org.interpolate( [xnew, qnew] )

In any case, the desitination VArrays such as xnew ynew pnew qnew must be one-dimensional.

Note that

gp_int = gp_org.interpolate( qnew )

fails (exception raised), since it is ambiguous. If you tempted to do so, perhaps what you want is covered by the following special form:

As a special form, you can specify a particular dimension like this:

gp_int = gp_org.interpolate( "x"=>pnew )

Here, interpolation along “x” is made, while other axes are retained. This is useful if pnew corresponds to a multi-D coordinate variable where there are two or more corresponding axes (otherwise, this special form is not needed.)

See the test part at the end of this file for more examples.

LIMITATION

Currently associated coordinates expressed by 3D or greater dimensional arrays are not supported.

Computational efficiency of pure two-dimensional coordinate support should be improved by letting C extensions cover deeper and improving the search algorithm for grid (which is usually ordered quasi-regularly).

COVERAGE

Extrapolation is covered for 1D coordinates, but only interpolation is covered for 2D coordinates (which is limited by gt2dlib in DCL – exception will be raised if you specify a grid point outside the original 2D grid points.).

MATHEMATICAL SPECIFICATION

The multi-dimensional linear interpolation is done by supposing a (hyper-) “rectangular” grid, where each dimension is independently sampled one-dimensionally. In case of interpolation along two dimensional coordinates such as “p” and “q” in the example above, a mapping from a rectangular grid is assumed, and the corresponding points in the rectangular grid is solved inversely (currently by using gt2dlib in DCL).

For 1D and 2D cases, linear interpolations may be expressed as

1D:  zi = (1-a)*z0 + a*z1
2D:  zi = (1-a)*(1-b)*z00 + a*(1-b)*z10 + (1-a)*b*z01 + a*b*z11

This method is extended to arbitrary number of dimensions. Thus, if the number of dimensions to interpolate is S, then 2**S grid points are used for each interpolation (8 points for 3D, 16 points for 4D,…). Thus, the linearity of this interpolation is only along each dimension, not over the whole dimensionality.

USAGE

interpolate(coord0, coord1, ...)

ARGUMENTS

  • coord0, coord1,… [ 1D VArray, or Array of 1D VArray, or a 1-element Hash as => slice_loc_value(Numeric) ] : locations to which interpolation is made. Names of all the VArray’s in the arguments must exist among the names of the coordinates of self (including associated coordinates), since the dimension finding is made in terms of coordinate names. If an argument is an Array of VArray’s, the first VArray will become the main coordinate variable, and the rest will be associated coordinates.

  • SPECIAL CASE

    You can specfify a one-element Hash as the only argument such as

    gphys.interpolate("x"=>varray)

    where varray is a coordinate onto which interpolation is made. This is espcially useful if varray is multi-D. If varray’s name “p” (name of a 2D coordnate var), for example, you can interpolate only regarding “x” by retaining other axes. If varray is 1-diemnsional, the same thing can be done simply by 

    gphys.interpolate(varray)

    since the corresponding 1D coordinate is found aotomatically.

RETURN VALUE

  • a GPhys



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# File 'lib/numru/gphys/interpolate.rb', line 389

def interpolate(*coords)
  coords, org_coords, org_dims, newgrid = _interpo_match_coords(coords)
  crdmap = _interpo_reorder_2crdmap(coords, org_coords, org_dims)
  idxmap = _interpo_find_position(crdmap)

  z = val
  if z.is_a?(NArrayMiss)
    missval = ( (a=get_att('_FillValue')) ? a[0] : nil ) || 
              ( (a=get_att('missing_value')) ? a[0] : nil ) || 
              @@interpo_missval
    z = z.to_na(missval)
    input_nomiss = false
  else
    input_nomiss = true
    if @@interpo_extrapolation
      missval = nil
    else
      missval = @@interpo_missval
    end
  end

  na = c_interpo_do(newgrid.shape, idxmap, z, missval,
                    @@interpo_extrapolation)   # [C-extension]

  if !input_nomiss || !@@interpo_extrapolation
    mask = na.ne(missval)
    if !input_nomiss || mask.min == 0
      na = NArrayMiss.to_nam_no_dup(na,mask)
    end
  end

  va = VArray.new(na, data, name)

  ret = GPhys.new(newgrid, va)
  ret.grid.set_lost_axes(self.lost_axes)
  ret
end

#least_square_fit(functions, ensemble_dims = nil, indep_dims = nil) ⇒ Object 



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# File 'lib/numru/ganalysis/fitting.rb', line 476

def least_square_fit(functions, ensemble_dims=nil, indep_dims=nil)

  #< preparation >

  no_fitting_dims = Array.new
  if ensemble_dims
    ensemble_dims = ensemble_dims.collect{|d| @grid.dim_index(d)}
    no_fitting_dims += ensemble_dims
  end
  if indep_dims
    indep_dims = indep_dims.collect{|d| @grid.dim_index(d)}
    no_fitting_dims += indep_dims
  end
  fitting_dims = (0...rank).collect{|i| i} - no_fitting_dims
  grid_locs = fitting_dims.collect{|d| coord(d).val}
  data = self.val

  #< fitting >
  c, bf, diff = GAnalysis::Fitting.least_square_fit(data, grid_locs, 
                                      functions, ensemble_dims, indep_dims)

  #< make a GPhys of the best fit >

  if !ensemble_dims
    grid = self.grid
  else
    axes = Array.new
    (0...rank).each{|d| 
      axes.push(self.axis(d)) unless ensemble_dims.include?(d)
    }
    grid = Grid.new(*axes)
    shape = bf.shape
    ensemble_dims.sort.reverse_each{|d| shape.delete_at(d)}
    bf = bf.reshape(*shape)
  end

  va = VArray.new(bf, self.data, self.name)
  bf = GPhys.new(grid, va)

  [c, bf, diff]
end

#logp_coord_p2z(pdim = nil) ⇒ Object

Convert the pressure coordinate in self to log-pressure height (after duplicating self)

Return value: a GPhys



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# File 'lib/numru/ganalysis/log_p.rb', line 84

def logp_coord_p2z(pdim=nil)
  pdim = GAnalysis::Met.find_prs_d(self) if !pdim
  p = self.coord(pdim)
  z = GAnalysis::LogP.p2z(p)
  ax = self.axis(pdim).copy
  ax.set_pos(z)
  ax.name = z.name
  grid = self.grid.copy.set_axis(pdim, ax)
  GPhys.new(grid,self.data)
end

#long_name ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 671

def long_name
	@data.long_name
end

#long_name=(long_name) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 674

def long_name=(long_name)
	@data.long_name= long_name
end

#lost_axes ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 763

def lost_axes
	 @grid.lost_axes
end

#marshal_dump ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1176

def marshal_dump
  [@data.copy, @grid.copy]
end

#marshal_load(ary) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1180

def marshal_load(ary)
  @data = ary[0]
  @grid = ary[1]
end

#mask(mask) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1164

def mask(mask)
  mask = mask.to_na(0) if mask.is_a?(NArrayMiss)
  v = self.val
  if v.is_a?(NArrayMiss)
    v.set_mask( v.get_mask & mask )
  else
    v = NArrayMiss.to_nam(v,mask)
  end        
  self.copy.replace_val(v)
end

#mask!(mask) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 1153

def mask!(mask)
  mask = mask.to_na(0) if mask.is_a?(NArrayMiss)
  v = self.val
  if v.is_a?(NArrayMiss)
    v.set_mask( v.get_mask & mask )
  else
    v = NArrayMiss.to_nam(v,mask)
  end        
  self.replace_val(v)
end

#mouse_cut(dimx, dimy, num = 2, line_type = 1, line_index = 1) ⇒ Object

Makes a subset interactively by specifying a (poly-)line on the DCL viewport

ARGUMENTS

  • dimx {String] : name of number (0,1,..) of the dimension corresponding to the X coordinate in the current window of DCL

  • dimy {String] : name of number (0,1,..) of the dimension corresponding to the Y coordinate in the current window of DCL

  • num {Integer] : the number of points along the (poly-)line (2 or greater – if 2, a single line segment; if 3 or more, a poly-line)

RETURN VALUE

  • a GPhys



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# File 'lib/numru/gphys/interpolate.rb', line 45

def mouse_cut(dimx, dimy, num=2, line_type=1, line_index=1)

  # < preparation >

  dimx = dim_index(dimx)
  dimy = dim_index(dimy)

  rundef = DCL.glpget("rundef")
  line = nil
  while(true)
    puts "\n*** Waiting for mouse click. Click #{num} points in the current viewport."
    line = DCLMouseLine.new(num)
    if line.ux.include?(rundef)
      puts "** The points specified include one(s) outside the U window. Do it again."
    else
      break
    end
  end
  line.draw(line_type, line_index)
  vx = line.vx
  vy = line.vy
  ux = line.ux
  uy = line.uy
  gpnew = dcl_fig_cut(dimx,dimy,ux,uy)
  [gpnew, line]
end

#mouse_cut_repeat ⇒ Object

Interpolation onto grid points specified by the previous call of GPhys#mouse_cut



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# File 'lib/numru/gphys/interpolate.rb', line 169

def mouse_cut_repeat
  if @@interpo_previous_cutter.nil?
    raise("You must first use GPhys#mouse_cut. This method repeats it") 
  end
  gpnew = interpolate(@@interpo_previous_cutter)
  gpnew = @@interpo_previous_modifier[gpnew] if @@interpo_previous_modifier
  gpnew
end

#name ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 612

def name
	 data.name
end

#name=(nm) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 615

def name=(nm)
	 data.name=nm
end

#ntype ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 651

def ntype
	@data.ntype
end

#phase_velocity(kdim, fdim, kconv, fconv, kf0_is_c0 = true, no_kfreorder = false) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 757

def phase_velocity(kdim,fdim,kconv,fconv,kf0_is_c0=true,no_kfreorder=false)
  kax = self.axis(kdim)
  fax = self.axis(fdim)
  kax.pos = kax.pos*kconv if kconv
  fax.pos = fax.pos*fconv if fconv
  cunits = fax.pos.units / kax.pos.units

  f = fax.pos.val
  k = kax.pos.val
  nk = k.length
  nf = f.length
  if no_kfreorder
    k[nk/2+1..-1] = -k[nk/2+1..-1][-1..0]+k[nk/2]
    f[nf/2+1..-1] = -f[nf/2+1..-1][-1..0]+f[nf/2]
  end
  f = -f
  cp = f.newdim(0) / k.newdim(1) #cp[kdim,fdim]
  jf0 = f.eq(0).where[0]  # where f==0
  jk0 = k.eq(0).where[0]  # where k==0
  if kf0_is_c0
    cp[jk0,jf0] = 0.0       # treat k=f=0 as stationary (c=0)
  else
    cp[jk0,jf0] = 1.0/0.0   # not to count k=f=0 component at all (c=infty)
  end

  [cp, cunits]
end

#phase_velocity_binning(kdim, fdim, cbins, kconv = nil, fconv = nil) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 673

def phase_velocity_binning(kdim, fdim, cbins, kconv=nil, fconv=nil)

  # < process arguments >

  case cbins
  when Hash 
    min = cbins["min"] ||raise(ArgumentError,"a Hash cbins must have 'min'")
    max = cbins["max"] ||raise(ArgumentError,"a Hash cbins must have 'max'")
    int = cbins["int"] ||raise(ArgumentError,"a Hash cbins must have 'int'")
    cbins = Array.new
    eps = int.abs*1e-6   # epsilon to deal with float steps
    (min.to_f..(max.to_f+eps)).step(int){|c| cbins.push(c)}
    cbins = NArray.to_na(cbins)
  when Array
    cbins = NArray.to_na(cbins)
  when NArray
  else
    raise ArgumentError, "cbins must be a Hash or Array or NArray"
  end

  kdim = dim_index(kdim) if kdim.is_a?(String)
  kdim += rank if kdim < 0
  fdim = dim_index(fdim) if fdim.is_a?(String)
  fdim += rank if fdim < 0

  # < sort along wavenumber/freuqency axis >

  pw = self.spect_zero_centering(kdim).spect_one_sided(fdim)

  # < process axes >

  cp, cunits = pw.phase_velocity(kdim,fdim,kconv,fconv,false)

  vcbins = VArray.new(cbins, {"units"=>cunits.to_s, 
                "long_name"=>"phase velocity bounds"}, "cbounds")
  vccent = VArray.new( (cbins[0..-2] + cbins[1..-1])/2, 
                {"units"=>cunits.to_s, "long_name"=>"phase velocity"}, "c")
  axc = Axis.new(true).set_cell(vccent, vcbins).set_pos_to_center
  axes = [axc]   # the first dimension will be "c"
  gr = pw.grid
  (0...pw.rank).each do |d|
    if d!=kdim && d!=fdim
      axes.push(gr.axis(d))
    end
  end
  newgrid = Grid.new(*axes)

  nk = pw.shape[kdim]
  nf = pw.shape[fdim]
  cp.reshape!(nk*nf)

  # < reorder input data >

  dimorder = (0...pw.rank).collect{|i| i}
  dimorder.delete(fdim)
  dimorder.unshift(fdim)
  dimorder.delete(kdim)
  dimorder.unshift(kdim)   # --> [kdim, fdim, the other dims...]
  sh = pw.shape
  reshape = [nk*nf]
  (0...rank).each{|i| reshape.push(sh[i]) if i!=fdim && i!=kdim}
  pwv = pw.val.transpose(*dimorder).reshape(*reshape)  
                           # --> [ combined k&fdim, the other dims...]

  # < binning >

  shc = newgrid.shape
  pwc = NArray.new(pwv.typecode, *shc)    # will have no missing data
  nc = axc.length
  for jc in 0...nc
    w = (cp.gt(cbins[jc]) & cp.lt(cbins[jc+1])).where
    pwc[jc,false] += pwv[w,false].sum(0) if w.length>0
    w = (cp.eq(cbins[jc])).where
    pwc[jc,false] += pwv[w,false].sum(0)/2 if w.length>0  # half from bdry
    w = (cp.eq(cbins[jc+1])).where
    pwc[jc,false] += pwv[w,false].sum(0)/2 if w.length>0  # half from bdry
  end

  vpwc = VArray.new(pwc,pw.data,pw.name)
  gpwc = GPhys.new(newgrid,vpwc)

  gpwc
end

#phase_velocity_binning_iso_norml(kdim, fdim, cmin, cmax, cint, kconv = nil, fconv = nil) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 665

def phase_velocity_binning_iso_norml(kdim, fdim, cmin, cmax, cint, 
                               kconv=nil, fconv=nil)
  cbins = {"min"=>cmin,"max"=>cmax,"int"=>cint}
  pwc = phase_velocity_binning(kdim, fdim, cbins, kconv, fconv)
  fact = UNumeric[int, pwc.coord(0).units]
  pwc/fact
end

#phase_velocity_filter(xdim, tdim, cmin = nil, cmax = nil, xconv = nil, tconv = nil, remove_xtmean = false) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/numru/gphys/gphys_fft.rb', line 628

def phase_velocity_filter(xdim, tdim, cmin=nil, cmax=nil, xconv=nil, tconv=nil, remove_xtmean=false)
  raise(ArgumentError,"need at least cmin or cmax") if !(cmin || cmax)


  xdim = dim_index(xdim) if xdim.is_a?(String)
  xdim += rank if xdim < 0
  tdim = dim_index(tdim) if tdim.is_a?(String)
  tdim += rank if tdim < 0
  fc = self.fft(nil,xdim,tdim)
  
  kdim = xdim
  fdim = tdim
  kconv = ( xconv ? 1.0/xconv : nil )
  fconv = ( tconv ? 1.0/tconv : nil )
  cp, = fc.phase_velocity(kdim,fdim,kconv,fconv,!remove_xtmean,true)

  fcv = fc.val
  nk = fc.shape[kdim]
  nf = fc.shape[fdim]
  sel = [true]*fc.rank
  for jf in 0...nf
    for jk in 0...nk
      c = cp[jk,jf]
      if ( cmin && c<cmin or cmax && c>cmax)
        sel[kdim]=jk
        sel[fdim]=jf
        fcv[*sel] = 0.0
      end
    end
  end
  fc.replace_val(fcv)
  gp = fc.fft(true,xdim,tdim)
  gp = gp.real if (self.typecode <= NArray::FLOAT)
  GPhys.new(self.grid_copy, gp.data)
            #^ use the original grid, since units may have changed
end

#rank ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 747

def rank
	@grid.rank
end

#rank_len_ne_1 ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 750

def rank_len_ne_1
	(shape_current - [1]).length
end

#rawspect2powerspect(*dims) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 612

def rawspect2powerspect(*dims)
  # developpers memo: Needs Units conversion.
  factor = nil
  dims.each{|dim|
	ax = self.coord(dim)
	dwn = UNumeric.new( ((ax[-1].val - ax[0].val)/(ax.length - 1)).abs,
   ax.units )
    if !factor
	  factor = dwn**(-1)
	else
	  factor = factor / dwn.to_f
	end
  }
  self * factor
end

#regrid(to) ⇒ Object

Interpolate to conform the grid to a target GPhys object

ARGUMENTS

  • to [GPhys] : the target gphys

RETURN VALUE

  • a GPhys



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# File 'lib/numru/gphys/interpolate.rb', line 208

def regrid(to)
  coords = to.axnames.collect{|nm| to.coord(nm)}
  interpolate(*coords)
end

#rename(nm) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 618

def rename(nm)
	data.name=nm
	self
end

#replace_val(v) ⇒ Object

Raises:

  • (ArgumentError) 


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# File 'lib/numru/gphys/gphys.rb', line 629

def replace_val(v)
	 raise(ArgumentError,"Shape miss-match") if @grid.shape != v.shape
	 @data.replace_val(v)
	 self
end

#running_mean(dim, len_or_wgt = nil, bc = nil, nminvalid = 1) ⇒ Object

Running mean along a dimension (with optional weight specification).

ARGUMENTS

  • dim (Integer or String) : the dimension

  • len_or_wgt : If Integer, specifies the length; if 1D NArray, specifies the weight (e.g., NArray[1.0, 2.0, 1.0] for the 1-2-1 smooting)

  • bc (Integer; optional) : Specify one of the following:

    • nil (default) : choose BC_SIMPLE or BC_CYCLIC automatically

    • GPhys::BC_SIMPLE : Averaging is truncated at the boundaries (the number of grid points used is reduced near the boundaries). The shape of the object is conserved.

    • GPhys::BC_CYCLIC : Cyclic boundary condition. Shape conserved.

    • GPhys::BC_TRIM : Grids near the boundaries are trimmed to secure the number of grid points to average. Shape not conserved; length along the dim is reduced by (len-1).

  • nminvalid (Integer; optional; default=1): This parameter is used only when the data have missing. Minimum number of grid points needed for averaging. Must be from 1 to len.

RETURN VALUE

  • a GPhys

REMARK AND LIMITATION

  • If the length of the running mean is even number, fewer grid points are used from the “left” side; e.g., If len is 6, result is a mean over self..self.

  • Regardless the na_type of self, double is used for averaging, so:

  • This method does not support complex numbers.



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# File 'lib/numru/gphys/gphys_dim_op.rb', line 47

def running_mean(dim, len_or_wgt=nil, bc=nil, nminvalid=1)

  #< process arguments >

  dim = dim_index(dim)  # to handle String or negative specification

  if bc.nil?
    if axis(dim).cyclic_extendible?
      bc=BC_CYCLIC
    else
      bc=BC_SIMPLE
    end
  end

  case len_or_wgt
  when nil
    raise ArgumentError, "You need to specify the length (Integer) or the weight (1D NArray) as the 2nd argument"
  when Integer
    # len_or_wgt is a length
    len = len_or_wgt  
    wgt = NArray.float(len).fill!(1.0)
  else
    # len_or_wgt is a weight
    wgt = len_or_wgt
    if (!wgt.respond_to?(:rank) || wgt.rank != 1)
      raise ArgumentError, "wgt: expect a 1D NArray(-like obj)"
    end
    len = wgt.length
  end

  #< calc running mean >

  vi = self.val
  if (vi.typecode > NArray::DFLOAT)
    raise("This method supports only real or integer data")
  end 
  if vi.is_a?(NArrayMiss)
    vi, missval = nam2na_missval(vi)
    vo = c_running_mean(vi,dim,wgt,bc,missval,nminvalid)
    vo = NArrayMiss.to_nam(vo, vo.ne(missval) )
  else
    vo = c_running_mean(vi,dim,wgt,bc)
  end

  #< grid >

  if (bc ==  BC_TRIM)
    fst = (len-1)/2    # if odd len/2, if even len/2-1
    lst = -(len/2) - 1 
    grid = self.grid[ *([true]*dim + [fst..lst, false]) ]
  else
    grid = self.grid
  end

  #< result >
  vvo = VArray.new( vo, self.data, self.name )  # Inherit name & attrs
  GPhys.new( grid, vvo )

end

#running_mean_2D(dim1, dim2, len_or_wgt1, len_or_wgt2, bc1 = nil, bc2 = nil, nminvalid = 1) ⇒ Object

Running mean along two dimensions (with optional weight specification).

This method would be needed for data with missing. If the data has no missing, you should apply running_mean consecutively along the two dimensions you want, which will be faster and efficient.

However, if the data have missing, the results are not the same. That’s why this method is needed.

ARGUMENTS

  • dim1 (Integer or String) : a dimension to apply the running mean

  • dim2 (Integer or String) : another dimension to apply the running mean (dim1 must be smaller than dim2)

  • len_or_wgt1 : If Integer, specifies the length of running mean for dim1. If 1D NArray, it specifies the weight (e.g., NArray[1.0, 2.0, 1.0] for the 1-2-1 smoothing)

  • len_or_wgt2 : as len_or_wgt1 but for dim2.

  • bc1 (Integer or nil; optional) : Specify one of the following for dim1:

    • nil : choose BC_SIMPLE or BC_CYCLIC automatically

    • GPhys::BC_SIMPLE : Averaging is truncated at the boundaries (the number of grid points used is reduced near the boundaries). The shape of the object is conserved.

    • GPhys::BC_CYCLIC : Cyclic boundary condition. Shape conserved.

  • bc2 : as bc1 but for dim2.

  • nminvalid (Integer; optional; default=1): Minimum number of grid points needed to define the running mean (it is the number of valid data in the 2-dimensional tile).



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# File 'lib/numru/gphys/gphys_dim_op.rb', line 135

def running_mean_2D(dim1, dim2, len_or_wgt1, len_or_wgt2,
                    bc1=nil, bc2=nil,
                    nminvalid=1)

  dim1 = dim_index(dim1)  # to handle String or negative specification
  dim2 = dim_index(dim2)  # to handle String or negative specification

  if bc1.nil?
    if axis(dim1).cyclic_extendible?
      bc1=BC_CYCLIC
    else
      bc1=BC_SIMPLE
    end
  end
  if bc2.nil?
    if axis(dim2).cyclic_extendible?
      bc2=BC_CYCLIC
    else
      bc2=BC_SIMPLE
    end
  end

  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)
  end
  
  if (vi.typecode > NArray::DFLOAT)
    raise("This method supports only real or integer data")
  end 
  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) )
  else
    raise("This method accepts only data with missing. If not, you should apply running_mean twice for dim1 & dim2, respectively")
  end

  vvo = VArray.new( vo, self.data, self.name )  # Inherit name & attrs
  GPhys.new( self.grid, vvo )
end

#set_assoc_coords(assoc_crds) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 792

def set_assoc_coords(assoc_crds)
  @grid.set_assoc_coords(assoc_crds)
end

#set_att(name, val) ⇒ Object Also known as: put_att 



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# File 'lib/numru/gphys/gphys.rb', line 641

def set_att(name, val)
	@data.set_att(name, val)
	self
end

#set_lost_axes(lost) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 766

def set_lost_axes( lost )
  @grid.set_lost_axes( lost )
  self
end

#shape_coerce(other) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 858

def shape_coerce(other)
	 #
	 # for binary operations
	 #
	 if self.rank == other.rank
	    # nothing to do
	    [other, self]
	 else
	    if self.rank < other.rank
  shorter = self
  longer = other
  i_am_the_shorter = true
	    else
  shorter = other
  longer = self 
  i_am_the_shorter = false
	    end
	    reshape_args = 
  __shape_matching( shorter.shape_current, longer.shape_current, 
				shorter.axnames, longer.axnames )
	    shorter = shorter.data.copy.reshape!(*reshape_args)
	    ##def shorter.data; self; end  # singular method!
	    if i_am_the_shorter
  [longer, shorter]
	    else
  [shorter, longer]
	    end
	 end
end

#shape_coerce_full(other) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 888

def shape_coerce_full(other)
  o, s = shape_coerce(other)
  if o.length < s.length
    o = self.class.new( s.grid, o + NArray.new(o.typecode,*s.shape) )
  elsif o.length > s.length
    s = self.class.new( o.grid, s + NArray.new(s.typecode,*o.shape) )
  end
  [o, s]
end

#shape_current ⇒ Object Also known as: shape 



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# File 'lib/numru/gphys/gphys.rb', line 992

def shape_current
	 @data.shape_current
end

#spect_one_sided(dim) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 601

def spect_one_sided(dim)
  dim = dim + self.rank if dim<0
  len = self.shape[dim]
  b = self[ *([true]*dim + [0..len/2,false]) ] * 2
  b[*([true]*dim + [0,false])] = b[*([true]*dim + [0,false])] / 2
  if (self.shape[dim] % 2) == 0  # --> even number
    b[*([true]*dim + [-1,false])] = b[*([true]*dim + [-1,false])] / 2
  end
  b
end

#spect_zero_centering(dim) ⇒ Object 



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# File 'lib/numru/gphys/gphys_fft.rb', line 587

def spect_zero_centering(dim)
  dim = dim + self.rank if dim<0
  len = self.shape[dim]
  b = self[ *( [true]*dim + [[(len+1)/2..len-1,0..len/2],false] ) ].copy
  s1 = [true]*dim + [0, false]
  s2 = [true]*dim + [-1, false]
  if (len % 2) == 0   #--> even number
    b[*s1] = b[*s1]/2      # the ends are duplicated --> halved
    b[*s2] = b[*s1]
  end
  b.coord(dim)[0..len/2-1] = -b.coord(dim)[len/2+1..-1].val[-1..0]
  b
end

#threepoint_O2nd_deriv(*args) ⇒ Object 



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# File 'lib/numru/gphys/derivative.rb', line 94

def threepoint_O2nd_deriv(*args)
  Derivative::threepoint_O2nd_deriv(self,*args)
end

#transpose(*dims) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 898

def transpose(*dims)
	grid = @grid.transpose(*dims)
	data = @data.transpose(*dims)
	self.class.new( grid, data )
end

#units ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 655

def units
	@data.units
end

#units=(units) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 658

def units=(units)
	@data.units= units
end

#val ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 623

def val
	 @data.val
end

#val=(v) ⇒ Object 



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# File 'lib/numru/gphys/gphys.rb', line 626

def val=(v)
	 @data.val= v
end