Class: NumRu::NetCDF

Inherits:
Object
  • Object
show all
Defined in:
lib/numru/netcdf.rb,
ext/netcdfraw.c

Constant Summary collapse

Max_Try = 
100
NC_NOWRITE =

Class Constants Definition

INT2FIX(NC_NOWRITE)
NC_WRITE = 
INT2FIX(NC_WRITE)
NC_SHARE = 
INT2FIX(NC_SHARE)
NC_CLOBBER = 
INT2FIX(NC_CLOBBER)
NC_NOCLOBBER = 
INT2FIX(NC_NOCLOBBER)

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.clean_tmpfile(path) ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 72

def clean_tmpfile(path)
	  proc {
	     print "removing ", path, "..." if $DEBUG
	     if File.exist?(path)
		File.unlink(path) 
	     end
	     print "done\n" if $DEBUG
	  }
end

.create(filename, noclobber = false, share = false) ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 49

def NetCDF.create(filename,noclobber=false,share=false)
  case(noclobber)
  when false
	noclobber=NC_CLOBBER
  when true
	noclobber=NC_NOCLOBBER
  else
	raise NetcdfError,"noclobber (2nd argument) must be true or false"
  end
  case(share)
  when false
	share=0
  when true
	share=NC_SHARE
  else
	raise NetcdfError,"share (3rd argument) must be true or false"
  end
  
  cmode=noclobber | share
  nc_create(filename,cmode)
end

.create_tmp(tmpdir = ENV['TMPDIR']||ENV['TMP']||ENV['TEMP']||'.', share = false) ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 84

def NetCDF.create_tmp(tmpdir=ENV['TMPDIR']||ENV['TMP']||ENV['TEMP']||'.', 
 share=false)
   basename = 'temp'
   if $SAFE > 0 and tmpdir.tainted?
	  tmpdir = '.'
   end

   n = 0
   while true
	 begin
tmpname = sprintf('%s/%s%d_%d.nc', tmpdir, basename, $$, n)
unless File.exist?(tmpname)
   netcdf = NetCDF.create(tmpname, true, share)
   ObjectSpace.define_finalizer(netcdf, 
	   NetCDF.clean_tmpfile(tmpname))
   break
end
	 rescue
raise NetcdfError, "cannot generate tempfile `%s'" % tmpname if n >= Max_Try
	 end
	 n += 1
   end
   netcdf
end

.nc_create(filename, cmode) ⇒ Object

rb_define_singleton_method(cNetCDF,“new”,NetCDF_open,2);



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# File 'ext/netcdfraw.c', line 1044

VALUE
NetCDF_create(VALUE mod,VALUE filename,VALUE cmode)
{
  int ncid;
  int status;
  char* c_filename;
  int c_cmode;
  struct Netcdf *ncfile;
  
  Check_Type(filename,T_STRING);
  SafeStringValue(filename);
  c_filename=RSTRING_PTR(filename);
  Check_Type(cmode,T_FIXNUM);
  c_cmode=NUM2INT(cmode);
  
  status = nc_create(c_filename,c_cmode,&ncid);
  if(status != NC_NOERR) NC_RAISE2(status, c_filename);

  ncfile = NetCDF_init(ncid,c_filename);
  return( Data_Wrap_Struct(cNetCDF,0,NetCDF_free,ncfile) );
}

.nc_open(filename, omode) ⇒ Object

The methods of the NetCDF class



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# File 'ext/netcdfraw.c', line 1020

VALUE
NetCDF_open(VALUE mod,VALUE filename,VALUE omode)     
{
  int status;
  int ncid;
  char* c_filename;
  int c_omode;
  struct Netcdf *ncfile;
  VALUE retval;

  Check_Type(filename,T_STRING);
  SafeStringValue(filename);
  c_filename=RSTRING_PTR(filename);
  Check_Type(omode,T_FIXNUM);
  c_omode=NUM2INT(omode);
  
  status = nc_open(c_filename,c_omode,&ncid);
  if(status !=NC_NOERR){NC_RAISE2(status,c_filename);}

  ncfile = NetCDF_init(ncid,c_filename);
  retval = Data_Wrap_Struct(cNetCDF,0,NetCDF_free,ncfile);
  return( retval );
}

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



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# File 'lib/numru/netcdf.rb', line 10

def NetCDF.open(filename,mode="r",share=false)
   call_create=false   # false-> nc_open; true->nc_create
   case(mode)
   when "r","rb"                          # read only
	  mode=NC_NOWRITE
   when "w","w+","wb","w+b"               # overwrite if exits
      call_create=true
	  mode=NC_CLOBBER
   when "a","a+","r+","ab","a+b","r+b"    # append if exits
	  if( File.exists?(filename) )
  mode=NC_WRITE
	  else
  call_create=true   #(nonexsitent --> create)
  mode=NC_CLOBBER
	  end
   else
	  raise NetcdfError, "Mode #{mode} is not supported"
   end
   case(share)
   when false
	  share=0
   when true
	  share=NC_SHARE
   else
	  raise NetcdfError, "We can't use the sharing mode you typed"
   end
   omode = mode | share
   if(!call_create)
	  nc_open(filename,omode)
   else
	  nc_create(filename,omode)
   end
end

Instance Method Details

#==(fileb) ⇒ Object

Redifinition of the “==” and “eql?” methods



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# File 'ext/netcdfraw.c', line 1842

VALUE 
NetCDF_eql(VALUE filea,VALUE fileb)
{
  struct Netcdf *ncfilea;
  struct Netcdf *ncfileb;
  
  if( rb_obj_is_kind_of(fileb, cNetCDF) ){
      Data_Get_Struct(filea,struct Netcdf,ncfilea);
      Data_Get_Struct(fileb,struct Netcdf,ncfileb);
    
      if(ncfilea->ncid == ncfileb->ncid && 
	 strcmp(ncfilea->name,ncfileb->name)==0){
	  return Qtrue;
      } else {
	  return Qfalse;
      }
  } else {
      return Qfalse;
  }
}

#att(att_name) ⇒ Object 



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# File 'ext/netcdfraw.c', line 889

VALUE
NetCDF_att(VALUE file,VALUE att_name)
{
  int ncid;
  int status;
  int attnump;
  char *c_att_name;
  struct Netcdf *Netcdffile;
  struct NetCDFAtt *Netcdf_att;
  VALUE Attribute;

  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;
  Check_Type(att_name,T_STRING);
  c_att_name=RSTRING_PTR(att_name);
  

  status = nc_inq_attid(ncid,NC_GLOBAL,c_att_name,&attnump);
  if(status != NC_NOERR){
    if(status == NC_ENOTATT){
      return(Qnil);
    }
    else{
      NC_RAISE(status);
    }
  }
  
  Netcdf_att = NetCDF_att_init(ncid,NC_GLOBAL,c_att_name);
  
  Attribute = Data_Wrap_Struct(cNetCDFAtt,0,Netcdf_att_free,Netcdf_att);
   
  return Attribute;
}

#att_names ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 205

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

#clone ⇒ Object 



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# File 'ext/netcdfraw.c', line 506

VALUE
NetCDF_clone(VALUE file)
{
    VALUE clone;
    struct Netcdf *nc1, *nc2;

    Data_Get_Struct(file, struct Netcdf, nc1);
    nc2 = NetCDF_init(nc1->ncid, nc1->name);
    clone = Data_Wrap_Struct(cNetCDF, 0, NetCDF_free, nc2);
    CLONESETUP(clone, file);
    return clone;
}

#close ⇒ Object 



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# File 'ext/netcdfraw.c', line 558

VALUE
NetCDF_close(file)
VALUE file;

#def_dim(dim_name, length) ⇒ Object 



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# File 'ext/netcdfraw.c', line 581

VALUE
NetCDF_def_dim(VALUE file,VALUE dim_name,VALUE length)
{
  char* c_dim_name;
  size_t c_length;
  int ncid;
  int dimidp;
  int status;
  struct Netcdf *Netcdffile;
  struct NetCDFDim *Netcdf_dim;
  VALUE Dimension;
  
  rb_secure(4);
  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  
  Check_Type(dim_name,T_STRING);
  c_dim_name=RSTRING_PTR(dim_name);
  c_length=NUM2UINT(length);
  ncid=Netcdffile->ncid;

  status = nc_def_dim(ncid,c_dim_name,c_length,&dimidp);
  if(status !=NC_NOERR) NC_RAISE(status);

  Netcdf_dim = NetCDF_dim_init(ncid,dimidp);

  Dimension = Data_Wrap_Struct(cNetCDFDim,0,NetCDF_dim_free,Netcdf_dim);
  return Dimension;
}

#def_var(var_name, vartype, dimensions) ⇒ Object 



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# File 'ext/netcdfraw.c', line 763

VALUE
NetCDF_def_var(VALUE file,VALUE var_name,VALUE vartype,VALUE dimensions)
{
  int ncid;
  char *c_var_name;
  static int xtype;
  long c_ndims;
  int varidp;
  int dimidp;
  int i=0;
  int status;
  char *c_dim_name;
  int c_dimids[NC_MAX_DIMS];
  struct Netcdf *Netcdffile;
  struct NetCDFVar *Netcdf_var;
  struct NetCDFDim *Netcdf_dim;
  VALUE Var;

  rb_secure(4);
  Check_Type(var_name,T_STRING);
  Check_Type(dimensions,T_ARRAY);

  c_var_name=RSTRING_PTR(var_name);
  c_ndims=RARRAY_LEN(dimensions);
  
  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;

  if (TYPE(vartype) == T_STRING){
      xtype = natype2nctype(RSTRING_PTR(vartype));     
  } else if (TYPE(vartype) == T_FIXNUM){
      xtype = natypecode2nctype(NUM2INT(vartype));     
  } else {
      rb_raise(rb_eNetcdfError,
	       "type specfication must be by a string or nil");
  }

  for(i=0;i<c_ndims;i++){
    switch(TYPE(RARRAY_PTR(dimensions)[c_ndims-1-i])){
    case T_STRING:
      Check_Type(RARRAY_PTR(dimensions)[c_ndims-1-i],T_STRING);
      c_dim_name=StringValueCStr(RARRAY_PTR(dimensions)[c_ndims-1-i]);
      status=nc_inq_dimid(ncid,c_dim_name,&dimidp);
      if(status != NC_NOERR) NC_RAISE(status);
      c_dimids[i]=dimidp;
      break;
    case T_DATA:
      Data_Get_Struct(RARRAY_PTR(dimensions)[c_ndims-1-i],struct NetCDFDim,Netcdf_dim);
      c_dimids[i]=Netcdf_dim->dimid;
      break;
    default:
      rb_raise(rb_eNetcdfError, "No such object of the netCDF dimension class.");
    }
  }
  
  status = nc_def_var(ncid,c_var_name,xtype,c_ndims,c_dimids,&varidp);
  if(status != NC_NOERR) NC_RAISE(status);
  
  Netcdf_var = NetCDF_var_init(ncid,varidp,file);
  
  Var=Data_Wrap_Struct(cNetCDFVar,nc_mark_obj,NetCDF_var_free,Netcdf_var);
  return Var;
}

#def_var_with_dim(name, vartype, shape_ul0, dimnames) ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 114

def def_var_with_dim(name, vartype, shape_ul0, dimnames)
   # Same as def_var but defines dimensions first if needed.
   # Use zero in shape to define an unlimited dimension.
   if (shape_ul0.length != dimnames.length ) then
	  raise ArgumentError, 'lengths of shape and dimnames do not agree'
   end
   dims = []
   dimnames.each_index{ |i|
	  dim = self.dim( dimnames[i] )
	  if ( dim != nil ) then
  # dim exists --> check the length
  if (shape_ul0[i] != dim.length_ul0 ) then
		raise ArgumentError, "dimension length do not agree: #{i}th dim: "+\
		"#{shape_ul0[i]} and #{dim.length_ul0}"
  end
  dims.push(dim)
	  else
  # dim does not exist --> define it
  dims.push( def_dim( dimnames[i], shape_ul0[i] ) )
	  end
   }
   def_var(name, vartype, dims)
end

#define_mode? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'ext/netcdfraw.c', line 989

VALUE 
NetCDF_whether_in_define_mode(VALUE file)
{
  /* returns true if the NetCDF object is currently in the define mode,
             false if in the data mode, and
	     nil if else (possibly the file is read-only, or some other
	     error occurred)
  */
  int ncid;
  int status;
  struct Netcdf *Netcdffile;

  rb_secure(4);
  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;
  status = nc_redef(ncid);
  if(status == NC_EINDEFINE){
    return Qtrue;
  } else if(status == NC_NOERR) {
    /* was in the data mode --> recover the data mode and report false */
    status = nc_enddef(ncid);
    if(status == NC_NOERR) {
      return Qfalse;
    } else {
      return Qnil;
    }
  } else {
    return Qnil;
  }
}

#dim(dim_name) ⇒ Object 



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# File 'ext/netcdfraw.c', line 828

VALUE
NetCDF_dim(VALUE file,VALUE dim_name)
{
  int ncid;
  char *c_dim_name;
  int dimidp;
  int status;
  struct Netcdf *Netcdffile;
  struct NetCDFDim *Netcdf_dim;
  VALUE Dimension;

  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;
  Check_Type(dim_name,T_STRING);
  c_dim_name=RSTRING_PTR(dim_name);
  
  status = nc_inq_dimid(ncid,c_dim_name,&dimidp);
  if(status !=NC_NOERR){
    if(status == NC_EBADDIM){ 
      return(Qnil);  /*2003/08/27 back to orig (from changes on 2003/02/03)*/
    } else{
      NC_RAISE(status);
    }
  }

  Netcdf_dim=NetCDF_dim_init(ncid,dimidp);
  
  Dimension = Data_Wrap_Struct(cNetCDFDim,0,NetCDF_dim_free,Netcdf_dim);
  return Dimension;
}

#dim_names ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 185

def dim_names
  num_dim=ndims()
  names=[]
  for dimid in 0..num_dim-1
	obj_Dim=id2dim(dimid)    
	names=names+[obj_Dim.name]
  end
  return names
end

#dims(names = nil) ⇒ Object

return all if names==nil



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# File 'lib/numru/netcdf.rb', line 163

def dims( names=nil )   # return all if names==nil
   if names == nil
	  dims = (0..ndims()-1).collect{|dimid| id2dim(dimid)}
   else
	  raise TypeError, "names is not an array" if ! names.is_a?(Array)
	  dims = names.collect{|name| dim(name)}
	  raise ArgumentError, "One or more dimensions do not exist" if dims.include?(nil)
   end
   dims
end

#each_att ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 155

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

#each_dim ⇒ Object

Iterators:



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# File 'lib/numru/netcdf.rb', line 139

def each_dim
  num_dim=ndims()    
  for dimid in 0..num_dim-1
	obj_Dim=id2dim(dimid)
	 yield(obj_Dim)
  end
end

#each_var ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 147

def each_var
  num_var=nvars()
  for varid in 0..num_var-1
	obj_Var=id2var(varid)
	yield(obj_Var)
  end
end

#enddef ⇒ Object 



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# File 'ext/netcdfraw.c', line 967

VALUE 
NetCDF_enddef(VALUE file)
{
  int ncid;
  int status;
  struct Netcdf *Netcdffile;

  rb_secure(4);
  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;
  status = nc_enddef(ncid);
  if(status !=NC_NOERR){ 
    if(status == NC_ENOTINDEFINE){
      return Qnil;
    }
    else{
      NC_RAISE(status);
    }
  }
  return Qtrue;
}

#fill(mode) ⇒ Object 



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# File 'ext/netcdfraw.c', line 922

VALUE
NetCDF_fill(VALUE file,VALUE mode)
{
  int ncid;
  int status;
  struct Netcdf *Netcdffile;
  int old_modep;
  
  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid = Netcdffile->ncid;
  if(mode==Qfalse){
    status = nc_set_fill(ncid,NC_NOFILL,&old_modep);
    if(status != NC_NOERR) NC_RAISE(status);
  }
  else if(mode == Qtrue){
    status = nc_set_fill(ncid,NC_FILL,&old_modep);
    if(status != NC_NOERR) NC_RAISE(status);
  }
  else
    rb_raise(rb_eNetcdfError,"Usage:self.fill(true) or self.fill(false)");
  return Qnil;
}

#inspect ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 215

def inspect
  "NetCDF:"+path
end

#natts ⇒ Object 



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# File 'ext/netcdfraw.c', line 1099

VALUE 
NetCDF_natts(VALUE file)
{
  int ncid;
  int nattsp;
  int status;
  VALUE Integer;
  struct Netcdf *ncfile;

  Data_Get_Struct(file,struct Netcdf,ncfile);
  ncid=ncfile->ncid;
  status=nc_inq_natts(ncid,&nattsp);
  if(status != NC_NOERR) NC_RAISE (status);
  Integer = INT2NUM(nattsp);
  return Integer;
}

#ndims ⇒ Object 



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# File 'ext/netcdfraw.c', line 1066

VALUE 
NetCDF_ndims(VALUE file)
{
  int ncid;
  int ndimsp;
  VALUE Integer;
  int status;
  struct Netcdf *ncfile;

  Data_Get_Struct(file,struct Netcdf,ncfile);
  ncid=ncfile->ncid;
  status = nc_inq_ndims(ncid,&ndimsp);
  if(status != NC_NOERR) NC_RAISE (status);
  Integer = INT2NUM(ndimsp);
  return Integer;
}

#nvars ⇒ Object 



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# File 'ext/netcdfraw.c', line 1083

VALUE 
NetCDF_nvars(VALUE file)
{
  int ncid;
  int nvarsp;
  int status;
  VALUE Integer;
  struct Netcdf *ncfile;
  Data_Get_Struct(file,struct Netcdf,ncfile);
  ncid=ncfile->ncid;
  status = nc_inq_nvars(ncid,&nvarsp);
  if(status != NC_NOERR) NC_RAISE (status);
  Integer = INT2NUM(nvarsp);
  return Integer;
}

#path ⇒ Object 



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# File 'ext/netcdfraw.c', line 1160

VALUE
NetCDF_path(VALUE file)
{
  char *path;
  struct Netcdf *ncfile;
  
  Data_Get_Struct(file,struct Netcdf,ncfile);
  path=ncfile->name;
  return(rb_str_new2(path));
}

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



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# File 'lib/numru/netcdf.rb', line 110

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

#put_attraw ⇒ Object

atttype: nil or a String (“string”,“int”,etc). If nil,

the type of attribute is determined from the type of value



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# File 'ext/netcdfraw.c', line 726

VALUE
NetCDF_put_att(VALUE file,VALUE att_name,VALUE value,VALUE atttype)
     /*
      * atttype: nil or a String ("string","int",etc). If nil,
      *          the type of attribute is determined from the type of value
      */
{
    struct Netcdf *ncfile;
    char *name;

    rb_secure(4);
    Data_Get_Struct(file,struct Netcdf,ncfile);
    Check_Type(att_name,T_STRING);
    name = RSTRING_PTR(att_name);

    return( NetCDF_put_att__(ncfile->ncid, name, value, atttype, NC_GLOBAL) );
}

#redef ⇒ Object 



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# File 'ext/netcdfraw.c', line 945

VALUE
NetCDF_redef(VALUE file)
{
  int ncid;
  int status;
  struct Netcdf *Netcdffile;

  rb_secure(4);
  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;
  status = nc_redef(ncid);
  if(status !=NC_NOERR){
    if(status == NC_EINDEFINE){
      return Qnil;
    }
    else{
      NC_RAISE(status);
    }
  }
  return Qtrue;
}

#sync ⇒ Object 



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# File 'ext/netcdfraw.c', line 1145

VALUE
NetCDF_sync(VALUE file)
{
  int ncid;
  int status;
  struct Netcdf *ncfile;

  rb_secure(4);
  Data_Get_Struct(file,struct Netcdf,ncfile);
  ncid=ncfile->ncid;
  status = nc_sync(ncid);
  if(status !=NC_NOERR) NC_RAISE (status);
  return Qnil;
}

#unlimited ⇒ Object 



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# File 'ext/netcdfraw.c', line 1116

VALUE
NetCDF_unlimited(VALUE file)
{
  int ncid;
  int unlimdimidp;
  int status;
  struct Netcdf *ncfile;
  struct NetCDFDim *Netcdf_dim;
  VALUE Dimension;

  Data_Get_Struct(file,struct Netcdf,ncfile);
  ncid=ncfile->ncid;
  status=nc_inq_unlimdim(ncid,&unlimdimidp);
  if(status !=NC_NOERR) NC_RAISE(status);
  
  Netcdf_dim = NetCDF_dim_init(ncid,unlimdimidp);
  
  /* If unlimdimidp=-1,No unlimited dimension is defined in the netCDF dataset */ 
  if(unlimdimidp != -1)
    {
      Dimension = Data_Wrap_Struct(cNetCDFDim,0,NetCDF_dim_free,Netcdf_dim);
      return Dimension;
    }
  else
    {
      return Qnil;
    }
}

#var(var_name) ⇒ Object 



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# File 'ext/netcdfraw.c', line 859

VALUE  
NetCDF_var(VALUE file,VALUE var_name)
{  
  int ncid;
  int status;
  int varidp;
  char *c_var_name;
  struct Netcdf *Netcdffile;
  struct NetCDFVar *Netcdf_var;
  VALUE Variable;

  Data_Get_Struct(file,struct Netcdf,Netcdffile);
  ncid=Netcdffile->ncid;
  Check_Type(var_name,T_STRING);
  c_var_name=RSTRING_PTR(var_name);
  
  status=nc_inq_varid(ncid,c_var_name,&varidp);
  if(status != NC_NOERR){
    if(status == NC_ENOTVAR){
      return(Qnil); /*2003/08/27 back to orig (from changes on 2003/02/03)*/
    } else{ 
      NC_RAISE(status);
    }
  }
  
  Netcdf_var = NetCDF_var_init(ncid,varidp,file);
  Variable = Data_Wrap_Struct(cNetCDFVar,nc_mark_obj,NetCDF_var_free,Netcdf_var);
  return Variable;
}

#var_names ⇒ Object 



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# File 'lib/numru/netcdf.rb', line 195

def var_names
  num_var=nvars()
  names=[]
  for varid in 0..num_var-1
	obj_Var=id2var(varid)
	names=names+[obj_Var.name]
  end
  return names
end

#vars(names = nil) ⇒ Object

return all if names==nil



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# File 'lib/numru/netcdf.rb', line 174

def vars( names=nil )   # return all if names==nil
   if names == nil
	  vars = (0..nvars()-1).collect{ |varid| id2var(varid) }
   else
	  raise TypeError, "names is not an array" if ! names.is_a?(Array)
	  vars = names.collect{|name| var(name)}
	  raise ArgumentError, "One or more variables do not exist" if vars.include?(nil)
   end
   vars
end