Class: NumRu::NetCDFVar

Inherits:
Object
  • Object
show all
Defined in:
lib/netcdf.rb,
lib/netcdf_miss.rb

Constant Summary collapse

@@unpack_type = 
nil

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.new(file, varname, mode = "r", share = false) ⇒ Object Also known as: open 



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# File 'lib/netcdf.rb', line 268

def new(file,varname,mode="r",share=false)
  if(file.is_a?(String))
    file = NetCDF.open(file,mode,share)
  elsif(!file.is_a?(NetCDF))
    raise TypeError, "1st arg must be a NetCDF (file object) or a String (path)"
  end
  file.var(varname)
end

.unpack_type ⇒ Object 



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# File 'lib/netcdf.rb', line 374

def unpack_type
  @@unpack_type
end

.unpack_type=(na_type) ⇒ Object 



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# File 'lib/netcdf.rb', line 377

def unpack_type=(na_type)
  if [NArray::BYTE, NArray::SINT, NArray::INT, 
      NArray::SFLOAT, NArray::FLOAT, nil].include?(na_type)
    @@unpack_type = na_type
  else
    raise ArgumentError, "Arg must be one of NArray::BYTE, NArray::SINT, NArray::INT, NArray::SFLOAT, NArray::FLOAT"
  end
end

Instance Method Details

#[](*a) ⇒ Object 



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# File 'lib/netcdf.rb', line 633

def [](*a)
  if a.length == 0
    return self.get
  end
  a = __rubber_expansion(a)
  first = Array.new
  last = Array.new
  stride = Array.new
  set_stride = false
  a.each{|i|
    if(i.is_a?(Fixnum))
      first.push(i)
      last.push(i)
      stride.push(1)
    elsif(i.is_a?(Range))
      first.push(i.first)
      last.push(i.exclude_end? ? i.last-1 : i.last)
      stride.push(1)
    elsif(i.is_a?(Hash))
      r = (i.to_a[0])[0]
      s = (i.to_a[0])[1]
      if ( !( r.is_a?(Range) ) || ! ( s.is_a?(Integer) ) )
        raise TypeError, "Hash argument must be {a_Range, step}"
      end
      first.push(r.first) 
      last.push(r.exclude_end? ? r.last-1 : r.last)
      stride.push(s)
      set_stride = true
    elsif(i.is_a?(TrueClass))
      first.push(0)
      last.push(-1)
      stride.push(1)
    elsif( i.is_a?(Array) || i.is_a?(NArray))
      a_new = a.dup
      at = a.index(i)
      i = NArray.to_na(i) if i.is_a?(Array)
      for n in 0..i.length-1
        a_new[at] = i[n]..i[n]
        na_tmp = self[*a_new]
        if n==0 then
          k = at
          if at > 0
            a[0..at-1].each{|x| if x.is_a?(Fixnum) then k -= 1 end}
          end
          shape_tmp = na_tmp.shape
          shape_tmp[k] = i.length
          na = na_tmp.class.new(na_tmp.typecode,*shape_tmp)
          index_tmp = Array.new(shape_tmp.length,true)
        end
        index_tmp[k] = n..n
        na[*index_tmp] = na_tmp
      end
      return na
    else
      raise TypeError, "argument must be Fixnum, Range, Hash, TrueClass, Array, or NArray"
    end
  }

  if(set_stride)
    na = self.get({"start"=>first, "end"=>last, "stride"=>stride})
  else
    na = self.get({"start"=>first, "end"=>last})
  end
  shape = na.shape
  (a.length-1).downto(0){ |i|
    shape.delete_at(i) if a[i].is_a?(Fixnum)
  }
  na.reshape!( *shape )
  na
end

#[]=(*a) ⇒ Object 



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# File 'lib/netcdf.rb', line 704

def []=(*a)
  val = a.pop
  a = __rubber_expansion(a)
  first = Array.new
  last = Array.new
  stride = Array.new
  set_stride = false
  a.each{|i|
    if(i.is_a?(Fixnum))
      first.push(i)
      last.push(i)
      stride.push(1)
    elsif(i.is_a?(Range))
      first.push(i.first)
      last.push(i.exclude_end? ? i.last-1 : i.last)
      stride.push(1)
    elsif(i.is_a?(Hash))
      r = (i.to_a[0])[0]
      s = (i.to_a[0])[1]
      if ( !( r.is_a?(Range) ) || ! ( s.is_a?(Integer) ) )
        raise ArgumentError, "Hash argument must be {first..last, step}"
      end
      first.push(r.first) 
      last.push(r.exclude_end? ? r.last-1 : r.last)
      stride.push(s)
      set_stride = true
    elsif(i.is_a?(TrueClass))
      first.push(0)
      last.push(-1)
      stride.push(1)
    elsif(i.is_a?(Array) || i.is_a?(NArray))
      a_new = a.dup
      at = a.index(i)
      i = NArray.to_na(i) if i.is_a?(Array)
      val = NArray.to_na(val) if val.is_a?(Array)
      rank_of_subset = a.dup.delete_if{|v| v.is_a?(Fixnum)}.length
      if val.rank != rank_of_subset
        raise "rank of the rhs (#{val.rank}) is not equal to the rank "+
          "of the subset specified by #{a.inspect} (#{rank_of_subset})"
      end
      k = at
      a[0..at-1].each{|x| if x.is_a?(Fixnum) then k -= 1 end}
      if i.length != val.shape[k]
        raise "length of the #{k+1}-th dim of rhs is incorrect "+
          "(#{i.length} for #{val.shape[k]})"
      end
      index_tmp = Array.new(val.rank,true) if !val.is_a?(Numeric) #==>Array-like
      for n in 0..i.length-1
        a_new[at] = i[n]..i[n]
        if !val.is_a?(Numeric) then
          index_tmp[k] = n..n
          self[*a_new] = val[*index_tmp]
        else
          self[*a_new] = val
        end
      end
      return self
    else
      raise TypeError, "argument must be Fixnum, Range, Hash, TrueClass, Array, or NArray"
    end
  }

  if(set_stride)
    self.put(val, {"start"=>first, "end"=>last, "stride"=>stride})
  else
    self.put(val, {"start"=>first, "end"=>last})
  end
end

#att_names ⇒ Object 



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# File 'lib/netcdf.rb', line 296

def att_names
  num_att=natts()
  names=[]
  for attnum in 0..num_att-1
    obj_Att=id2att(attnum)
    names=names+[obj_Att.name]
  end
  return names
end

#dim_names ⇒ Object 



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# File 'lib/netcdf.rb', line 290

def dim_names
  ary = Array.new()
  dims.each{|dim| ary.push(dim.name)}
  ary
end

#each_att ⇒ Object 



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# File 'lib/netcdf.rb', line 282

def each_att
  num_att=natts()
  for attnum in 0..num_att-1
    obj_Att=id2att(attnum)
    yield(obj_Att)
  end
end

#get_with_miss(*args) ⇒ Object 



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# File 'lib/netcdf_miss.rb', line 8

def get_with_miss(*args)
  __interpret_missing_params if !defined?(@missval)
  data = simple_get(*args)
  if @vmin || @vmax
	if @vmin
	  mask = (data >= @vmin) 
	  mask = mask.and(data <= @vmax) if @vmax
	else
	  mask = (data <= @vmax)
	end
	data = NArrayMiss.to_nam(data, mask)
  elsif @missval	# only missing_value is present.
	mask = (data.ne(@missval)) 
	data = NArrayMiss.to_nam(data, mask)
  end
  data
end

#get_with_miss_and_scaling(*args) ⇒ Object 



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# File 'lib/netcdf_miss.rb', line 26

def get_with_miss_and_scaling(*args)
  __interpret_missing_params if !defined?(@missval)
  data = simple_get(*args)
  if @vmin || @vmax
	if @vmin
	  mask = (data >= @vmin) 
	  mask = mask.and(data <= @vmax) if @vmax
	else
	  mask = (data <= @vmax)
	end
	data = NArrayMiss.to_nam(data, mask)
  elsif @missval	# only missing_value is present.
	mask = (data.ne(@missval))
	data = NArrayMiss.to_nam(data, mask)
  end
  data = unpack( data )
  data
end

#inspect ⇒ Object 



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# File 'lib/netcdf.rb', line 773

def inspect
  'NetCDFVar:'+file.path+'?var='+name
end

#pack(na) ⇒ Object

The put and get methods in the NetCDFVar class



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# File 'lib/netcdf.rb', line 332

def pack(na)
  sf = att('scale_factor')
  ao = att('add_offset')
  if ( sf == nil && ao == nil ) then
    na
  else
    na = NArray.to_na(na) if na.is_a?(Array)
    if sf
      csf = sf.get
      raise NetcdfError,"scale_factor is not a numeric" if csf.is_a?(String)
      raise NetcdfError, "scale_factor is not unique" if csf.length != 1
      raise NetcdfError, "zero scale_factor" if csf[0] == 0
    else
      csf = nil
    end
    if ao
      cao = ao.get
      raise NetcdfError, "add_offset is not a numeric" if cao.is_a?(String)
      raise NetcdfError, "add_offset is not unique" if cao.length != 1
    else
      cao = nil
    end
    if csf and cao
      packed = (na - cao) / csf
    elsif csf
      packed = na / csf
    elsif cao
      packed = na - cao
    end
    if self.typecode <= NArray::LINT
      packed = packed.round
    end
    packed
  end
end

#put_att(attname, val, atttype = nil) ⇒ Object 



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# File 'lib/netcdf.rb', line 306

def put_att(attname,val,atttype=nil)
  put_attraw(attname,val,atttype)
end

#put_with_miss(data, *args) ⇒ Object 



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# File 'lib/netcdf_miss.rb', line 45

def put_with_miss(data, *args)
  if data.is_a?( NArrayMiss )
	__interpret_missing_params if !defined?(@missval)
	if @missval
	  simple_put(data.to_na(@missval), *args)
	else
	  simple_put(data.to_na, *args)
	end
  else
	simple_put(data, *args)
  end
end

#put_with_miss_and_scaling(data, *args) ⇒ Object 



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# File 'lib/netcdf_miss.rb', line 58

def put_with_miss_and_scaling(data, *args)
  if data.is_a?( NArrayMiss )
	__interpret_missing_params if !defined?(@missval)
	if @missval
	  data = pack( data )
	  data = data.to_na(@missval)
	else
	  data = pack( data )
	  data = data.to_na
	end
	simple_put(data, *args)
  else
	scaled_put(data, *args)
  end
end

#scaled_get(hash = nil) ⇒ Object 



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# File 'lib/netcdf.rb', line 421

def scaled_get(hash=nil)
  unpack( simple_get(hash) )
end

#scaled_put(var, hash = nil) ⇒ Object 



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# File 'lib/netcdf.rb', line 368

def scaled_put(var,hash=nil)
  simple_put( pack(var), hash)
end

#shape_current ⇒ Object 



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# File 'lib/netcdf.rb', line 322

def shape_current
  sh = []
  dims.each{|d|
    sh.push(d.length)
  }
  sh
end

#shape_ul0 ⇒ Object 



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# File 'lib/netcdf.rb', line 310

def shape_ul0
  sh = []
  dims.each{|d|
    if d.unlimited? then
      sh.push(0)
    else
      sh.push(d.length)
    end
  }
  sh
end

#simple_get(hash = nil) ⇒ Object Also known as: get 



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# File 'lib/netcdf.rb', line 531

def simple_get(hash=nil)
  t_var = self.vartype
  if hash == nil
    if t_var == "char"
      get_var_char
    elsif t_var == "byte"
      get_var_byte
    elsif t_var == "int16"
      get_var_sint
    elsif t_var == "int32"
      get_var_int
    elsif t_var == "float32"
      get_var_sfloat
    elsif t_var == "float64"
      get_var_float
    else
      raise NetcdfError, "variable type #{t_var} isn't supported in netCDF"
    end
  elsif hash.key?("index")==true
    ind = hash["index"]
    if t_var == "char"
      get_var1_char(ind)
    elsif t_var == "byte"
      get_var1_byte(ind)
    elsif t_var == "int16"
      get_var1_sint(ind)
    elsif t_var == "int32"
      get_var1_int(ind)
    elsif t_var == "float32"
      get_var1_sfloat(ind)
    elsif t_var == "float64"
      get_var1_float(ind)
    else
      raise NetcdfError,"variable type #{t_var} isn't supported in netCDF"
    end
  elsif hash.key?("start")==true
    h_sta = hash["start"]
    h_end = hash["end"]     # can be nill
    h_str = hash["stride"]  # can be nill
    if false && NetCDF.nc4? && h_str && ((xstr=h_str[-1]) != 1)
      # Tentative treatment for the very slow netcdf-4 reading with step.
      # Reading with step is generally slow with NetCDF 4, but it is
      # particularly so for the last (fastest) dimension.
      # Ref: http://www.unidata.ucar.edu/mailing_lists/archives/netcdfgroup/2013/msg00311.html
      h_str[-1] = 1 
      nc4remedy = true
    else
      nc4remedy = false
    end
    if t_var == "char"
      v = get_vars_char(h_sta,h_end,h_str)
    elsif t_var == "byte"
      v = get_vars_byte(h_sta,h_end,h_str)
    elsif t_var == "int16"
      v = get_vars_sint(h_sta,h_end,h_str)
    elsif t_var == "int32"
      v = get_vars_int(h_sta,h_end,h_str)
    elsif t_var == "float32"
      v = get_vars_sfloat(h_sta,h_end,h_str)
    elsif t_var == "float64"
      v = get_vars_float(h_sta,h_end,h_str)
    else
      raise NetcdfError, "variable type #{t_var} isn't supported in netCDF"
    end
    if nc4remedy
      idx = []
      (0...v.shape[-1]).step(xstr){|k| idx.push(k)}
      newshape = v.shape
      newshape[-1] = idx.size
      newv = NMatrix.new(newshape, dtype: v.dtype)
      idx.each_with_index do |iold, inew|
        newv[*[:*]*(v.dim-1), inew] = v[*[:*]*(v.dim-1), iold] # equiv to [false,iold] for narray
      end
      v = newv
      #v = v.slice(idx,*[:*]*(v.dim-1)) # equiv to [idx, false] for narray
    end
    v
  else
    raise ArgumentError,"{'start'}=>{ARRAY} or {'index'}=>{ARRAY} is needed"
  end
end

#simple_put(var, hash = nil) ⇒ Object Also known as: put 



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# File 'lib/netcdf.rb', line 425

def simple_put(var,hash=nil)
  if hash==nil
    if self.vartype == "char"
      put_var_char(var)
    elsif self.vartype == "byte"
      put_var_byte(var)
    elsif self.vartype == "int16"
      put_var_sint(var)
    elsif self.vartype == "int32"
      put_var_int(var)
    elsif self.vartype == "float32"
      put_var_sfloat(var)
    elsif self.vartype == "float64"
      put_var_float(var)
    else 
      raise NetcdfError,"variable type isn't supported in netCDF" 
    end
  elsif hash.key?("index")==true 
    if self.vartype == "char"
      put_var1_char(var,hash["index"])
    elsif self.vartype=="byte"
      put_var1_byte(var,hash["index"])
    elsif self.vartype=="int16"
      put_var1_sint(var,hash["index"])
    elsif self.vartype == "int32"
      put_var1_int(var,hash["index"])
    elsif self.vartype == "float32"
      put_var1_sfloat(var,hash["index"])
    elsif self.vartype == "float64"
      put_var1_float(var,hash["index"])
    else 
      raise NetcdfError,"variable type isn't supported in netCDF"
    end
  elsif hash.key?("start")==true
    if hash.key?("end")==false && hash.key?("stride")==false
      if self.vartype == "char"
        put_vars_char(var,hash["start"],nil,nil)
      elsif self.vartype=="byte"
        put_vars_byte(var,hash["start"],nil,nil)
      elsif self.vartype=="int16"
        put_vars_sint(var,hash["start"],nil,nil)
      elsif self.vartype=="int32"
        put_vars_int(var,hash["start"],nil,nil)
      elsif self.vartype=="float32"
        put_vars_sfloat(var,hash["start"],nil,nil)
      elsif self.vartype=="float64"
        put_vars_float(var,hash["start"],nil,nil)
      else
        raise NetcdfError, "variable type isn't supported in netCDF"
      end
    elsif hash.key?("end")==true && hash.key?("stride") == false
      if self.vartype == "char"
        put_vars_char(var,hash["start"],hash["end"],nil)
      elsif self.vartype=="byte"
        put_vars_byte(var,hash["start"],hash["end"],nil)
      elsif self.vartype=="int16"
        put_vars_sint(var,hash["start"],hash["end"],nil)
      elsif self.vartype=="int32"
        put_vars_int(var,hash["start"],hash["end"],nil)
      elsif self.vartype == "float32"
        put_vars_sfloat(var,hash["start"],hash["end"],nil)
      elsif self.vartype =="float64"
        put_vars_float(var,hash["start"],hash["end"],nil)
      else
        raise NetcdfError, "variable type isn't supported in netCDF"
      end
    elsif hash.key?("end")==false && hash.key?("stride")==true
      if self.vartype == "char"
        put_vars_char(var,hash["start"],nil,hash["stride"])
      elsif self.vartype=="byte"
        put_vars_byte(var,hash["start"],nil,hash["stride"])
      elsif self.vartype=="int16"
        put_vars_sint(var,hash["start"],nil,hash["stride"])
      elsif self.vartype=="int32"
        put_vars_int(var,hash["start"],nil,hash["stride"])
      elsif self.vartype=="float32"
        put_vars_sfloat(var,hash["start"],nil,hash["stride"])
      elsif self.vartype=="float64"
        put_vars_float(var,hash["start"],nil,hash["stride"])
      else
        raise NetcdfError, "variable type isn't supported in netCDF"
      end
    else hash.key?("end")==true && hash.key?("stride")==true
      if self.vartype == "char"
        put_vars_char(var,hash["start"],hash["end"],hash["stride"])
      elsif self.vartype=="byte"
        put_vars_byte(var,hash["start"],hash["end"],hash["stride"])
      elsif self.vartype=="int16"
        put_vars_sint(var,hash["start"],hash["end"],hash["stride"])
      elsif self.vartype=="int32"
        put_vars_int(var,hash["start"],hash["end"],hash["stride"])
      elsif self.vartype=="float32"
        put_vars_sfloat(var,hash["start"],hash["end"],hash["stride"])
      elsif self.vartype=="float64"
        put_vars_float(var,hash["start"],hash["end"],hash["stride"])
      else
        raise NetcdfError, "variable type isn't supported in netCDF"
      end
    end
  else
    raise ArgumentError,"{'start'}=>[ARRAY] or {'index'}=>[ARRAY] is needed"
  end
end

#unpack(na) ⇒ Object 



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# File 'lib/netcdf.rb', line 388

def unpack(na)
  sf = att('scale_factor')
  ao = att('add_offset')
  if ( sf == nil && ao == nil ) then
    na
  else
    if sf
      csf = sf.get
      raise NetcdfError,"scale_factor is not a numeric" if csf.is_a?(String)
      raise NetcdfError, "scale_factor is not unique" if csf.length != 1
      raise NetcdfError, "zero scale_factor" if csf[0] == 0
    else
      csf =nil
    end
    if ao
      cao = ao.get
      raise NetcdfError, "add_offset is not a numeric" if cao.is_a?(String)
      raise NetcdfError, "add_offset is not unique" if cao.length != 1
    else
      cao = nil
    end
    if csf and cao
      una = na * csf + cao  # csf & cao are NArray -> coerced to their types
    elsif csf
      una = na * csf
    elsif cao
      una = na + cao
    end
    una = una.to_type(@@unpack_type) if @@unpack_type
    una
  end
end