nc_io.cc

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/* Copyright (C) 2012 Oliver Lemke <olemke@core-dump.info>
 
   This program is free software; you can redistribute it and/or modify it
   under the terms of the GNU General Public License as published by the
   Free Software Foundation; either version 2, or (at your option) any
   later version.
 
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
 
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307,
   USA. */
 
 
//   File description
 
#include "arts.h"
 
#ifdef ENABLE_NETCDF
 
#include "nc_io.h"
#include "nc_io_types.h"
#include "file.h"
#include "messages.h"
#include "exceptions.h"
 
 
//   Default file name
 
 
void nca_filename(String& filename, const String&  varname)
{
  if ("" == filename)
    {
      extern const String out_basename;
      filename = out_basename + "." + varname + ".nc";
    }
}
 
 
 
 
void nca_filename_with_index(String&       filename,
                             const Index&  file_index,
                             const String& varname)
{
  if ("" == filename)
    {
      extern const String out_basename;
      ostringstream os;
      os << out_basename << "." << varname << "." << file_index << ".nc";
      filename = os.str();
    }
  else
    {
      ostringstream os;
      os << filename << "." << file_index << ".nc";
      filename = os.str();
    }
}
 
 
 
template<typename T>
void nca_read_from_file(const String&    filename,
                        T&               type,
                        const Verbosity& verbosity)
{
  CREATE_OUT2;
  
  String efilename = expand_path(filename);
  
  out2 << "  Reading " << efilename << '\n';
 
#pragma omp critical(netcdf__critical_region)
    {
  int ncid;
  if (nc_open(efilename.c_str(), NC_NOWRITE, &ncid))
    {
      ostringstream os;
      os << "Error reading file: " << efilename << endl;
      throw runtime_error(os.str());
    }
 
  try
    {
      nca_read_from_file(ncid, type, verbosity);
    }
  catch (runtime_error e)
    {
      ostringstream os;
      os << "Error reading file: " << efilename << endl;
      os << e.what() << endl;
      throw runtime_error(os.str());
    }
 
  nc_close(ncid);
    }
}
 
 
 
template<typename T>
void nca_write_to_file(const String&    filename,
                       const T&         type,
                       const Verbosity& verbosity)
{
  CREATE_OUT2;
  
  String efilename = add_basedir(filename);
  
  out2 << "  Writing " << efilename << '\n';
 
#pragma omp critical(netcdf__critical_region)
    {
  int ncid;
  if (nc_create(efilename.c_str(), NC_CLOBBER, &ncid))
    {
      ostringstream os;
      os << "Error writing file: " << efilename << endl;
      throw runtime_error(os.str());
    }
 
  try
    {
      nca_write_to_file(ncid, type, verbosity);
    }
  catch (runtime_error e)
    {
      ostringstream os;
      os << "Error writing file: " << efilename << endl;
      os << e.what() << endl;
      throw runtime_error(os.str());
    }
 
  nc_close(ncid);
    }
}
 
 
 
void nca_def_dim(const int ncid, const String& name, const Index nelem, int* ncdim)
{
  int retval;
  if ((retval = nc_def_dim(ncid, name.c_str(), nelem, ncdim)))
    nca_error(retval, "nc_def_dim");
}
 
 
 
void nca_def_var(const int ncid, const String& name, const nc_type type, const int ndims,
                 const int* dims, int* varid)
{
  int retval;
  if ((retval = nc_def_var(ncid, name.c_str(), type, ndims, dims, varid)))
    nca_error(retval, "nc_def_var");
}
 
 
 
int nca_def_ArrayOfIndex(const int ncid, const String& name, const ArrayOfIndex& a)
{
  int ncdims[1], varid;
  if (a.nelem())
    {
      nca_def_dim(ncid, name+"_nelem", a.nelem(), &ncdims[0]);
      nca_def_var(ncid, name, NC_INT, 1, &ncdims[0], &varid);
    }
  else
    varid = -1;
  
  return varid;
}
 
 
 
int nca_def_Vector(const int ncid, const String& name, const Vector& v)
{
  int ncdims[1], varid;
  if (v.nelem())
    {
      nca_def_dim(ncid, name+"_nelem", v.nelem(), &ncdims[0]);
      nca_def_var(ncid, name, NC_DOUBLE, 1, &ncdims[0], &varid);
    }
  else
    varid = -1;
  
  return varid;
}
 
 
 
int nca_def_Matrix(const int ncid, const String& name, const Matrix& m)
{
  int ncdims[2], varid;
  if (m.nrows() && m.ncols())
    {
      nca_def_dim(ncid, name+"_nrows", m.nrows(), &ncdims[0]);
      nca_def_dim(ncid, name+"_ncols", m.ncols(), &ncdims[1]);
      nca_def_var(ncid, name, NC_DOUBLE, 2, &ncdims[0], &varid);
    }
  else
    varid = -1;
  
  return varid;
}
 
 
 
int nca_def_Tensor4(const int ncid, const String& name, const Tensor4& t)
{
  int ncdims[4], varid;
  if (t.nbooks() && t.npages() && t.nrows() && t.ncols())
    {
      nca_def_dim(ncid, name+"_nbooks", t.nbooks(), &ncdims[0]);
      nca_def_dim(ncid, name+"_npages", t.npages(), &ncdims[1]);
      nca_def_dim(ncid, name+"_nrows", t.nrows(), &ncdims[2]);
      nca_def_dim(ncid, name+"_ncols", t.ncols(), &ncdims[3]);
      nca_def_var(ncid, name, NC_DOUBLE, 4, &ncdims[0], &varid);
    }
  else
    varid = -1;
  
  return varid;
}
 
 
 
Index nc_get_dim(const int ncid, const String& name, const bool noerror)
{
  int retval, dimid;
  size_t ndim;
  if ((retval = nc_inq_dimid(ncid, name.c_str(), &dimid)))
    {
      if (!noerror) nca_error(retval, "nc_inq_ndims("+name+")");
      else return 0;
    }
  if ((retval = nc_inq_dimlen(ncid, dimid, &ndim)))
    {
      if (!noerror) nca_error(retval, "nc_inq_dimlen("+name+")");
      else return 0;
    }
  
  return (Index)ndim;
}
 
 
 
void nca_get_data_int(const int ncid, const String& name, int* data)
{
  int retval, varid;
  if ((retval = nc_inq_varid(ncid, name.c_str(), &varid)))
    nca_error(retval, "nc_inq_varid("+name+")");
  if ((retval = nc_get_var_int(ncid, varid, data)))
    nca_error(retval, "nc_get_var("+name+")");
}
 
 
 
void nca_get_data_long(const int ncid, const String& name, long* data)
{
  int retval, varid;
  if ((retval = nc_inq_varid(ncid, name.c_str(), &varid)))
    nca_error(retval, "nc_inq_varid("+name+")");
  if ((retval = nc_get_var_long(ncid, varid, data)))
    nca_error(retval, "nc_get_var("+name+")");
}
 
 
 
void nca_get_data_double(const int ncid, const String& name, Numeric* data)
{
  int retval, varid;
  if ((retval = nc_inq_varid(ncid, name.c_str(), &varid)))
    nca_error(retval, "nc_inq_varid("+name+")");
  if ((retval = nc_get_var_double(ncid, varid, data)))
    nca_error(retval, "nc_get_var("+name+")");
}
 
 
 
void nca_get_dataa_double(const int ncid, const String& name,
                          size_t start, size_t count, Numeric* data)
{
  int retval, varid;
  if ((retval = nc_inq_varid(ncid, name.c_str(), &varid)))
    nca_error(retval, "nc_inq_varid("+name+")");
  if ((retval = nc_get_vara_double(ncid, varid, &start, &count, data)))
    nca_error(retval, "nc_get_var("+name+")");
}
 
 
 
void nca_get_data_text(const int ncid, const String& name, char* data)
{
  int retval, varid;
  if ((retval = nc_inq_varid(ncid, name.c_str(), &varid)))
    nca_error(retval, "nc_inq_varid("+name+")");
  if ((retval = nc_get_var_text(ncid, varid, data)))
    nca_error(retval, "nc_get_var("+name+")");
}
 
 
 
void nca_get_data_ArrayOfIndex(const int ncid, const String& name, ArrayOfIndex& aoi,
                               const bool noerror)
{
  Index nelem = nc_get_dim(ncid, name+"_nelem", noerror);
  aoi.resize(nelem);
  if (nelem)
    {
      Index* ind_arr = new Index[nelem];
      nca_get_data_long(ncid, name, ind_arr);
      Index i = 0;
      for (ArrayOfIndex::iterator it = aoi.begin(); it != aoi.end(); it++, i++)
        *it = ind_arr[i];
    }
}
 
 
 
void nca_get_data_ArrayOfArrayOfSpeciesTag(const int                 ncid,
                                           const String&             name,
                                           ArrayOfArrayOfSpeciesTag& aast,
                                           const bool                noerror)
{
  ArrayOfIndex species_count;
  nca_get_data_ArrayOfIndex(ncid, name+"_count", species_count, noerror);
  aast.resize(species_count.nelem());
  if (species_count.nelem())
    {
      Index species_strings_nelem = nc_get_dim(ncid, name+"_strings_nelem", noerror);
      Index species_strings_length = nc_get_dim(ncid, name+"_strings_length", noerror);
      char* species_strings = new char[species_strings_nelem*species_strings_length];
      if (species_count.nelem()) nca_get_data_text(ncid, name+"_strings", species_strings);
 
      Index si = 0;
      for (Index i = 0; i < species_count.nelem(); i++)
        {
          aast[i].resize(0);
          for (Index j = 0; j < species_count[i]; j++)
            {
              aast[i].push_back(SpeciesTag(&species_strings[si]));
              si += species_strings_length;
            }
        }
    
      delete[] species_strings;
    }
}
 
 
 
void nca_get_data_Vector(const int ncid, const String& name, Vector& v, const bool noerror)
{
  Index nelem = nc_get_dim(ncid, name+"_nelem", noerror);
  v.resize(nelem);
  if (nelem) nca_get_data_double(ncid, name, v.get_c_array());
}
 
 
 
void nca_get_data_Matrix(const int ncid, const String& name, Matrix& m, const bool noerror)
{
  Index nrows = nc_get_dim(ncid, name+"_nrows", noerror);
  Index ncols = nc_get_dim(ncid, name+"_ncols", noerror);
  m.resize(nrows, ncols);
  if (nrows && ncols) nca_get_data_double(ncid, name, m.get_c_array());
}
 
 
 
void nca_get_data_Tensor4(const int ncid, const String& name, Tensor4& t, const bool noerror)
{
  Index nbooks = nc_get_dim(ncid, name+"_nbooks", noerror);
  Index npages = nc_get_dim(ncid, name+"_npages", noerror);
  Index nrows = nc_get_dim(ncid, name+"_nrows", noerror);
  Index ncols = nc_get_dim(ncid, name+"_ncols", noerror);
  t.resize(nbooks, npages, nrows, ncols);
  if (nbooks && npages && nrows && ncols) nca_get_data_double(ncid, name, t.get_c_array());
}
 
 
 
bool nca_put_var_ArrayOfIndex(const int ncid, const int varid, const ArrayOfIndex& a)
{
  bool fail = true;
  if (a.nelem())
    {
      Index* ind_arr = new Index[a.nelem()];
      for (Index i = 0; i < a.nelem(); i++)
        ind_arr[i] = a[i];
 
      int retval;
      if ((retval = nc_put_var_long(ncid, varid, ind_arr)))
        nca_error(retval, "nc_put_var");
 
      delete[] ind_arr;
      fail = false;
    }
  return fail;
}
 
 
 
bool nca_put_var_Vector(const int ncid, const int varid, const Vector& v)
{
  bool fail = true;
  if (v.nelem())
    {
      int retval;
      if ((retval = nc_put_var_double(ncid, varid, v.get_c_array())))
        nca_error(retval, "nc_put_var");
    }
  return fail;
}
 
 
 
bool nca_put_var_Matrix(const int ncid, const int varid, const Matrix& m)
{
  bool fail = true;
  if (m.nrows() && m.ncols())
    {
      int retval;
      if ((retval = nc_put_var_double(ncid, varid, m.get_c_array())))
        nca_error(retval, "nc_put_var");
    }
  return fail;
}
 
 
 
bool nca_put_var_Tensor4(const int ncid, const int varid, const Tensor4& t)
{
  bool fail = true;
  if (t.nbooks() && t.npages() && t.nrows() && t.ncols())
    {
      int retval;
      if ((retval = nc_put_var_double(ncid, varid, t.get_c_array())))
        nca_error(retval, "nc_put_var");
    }
  return fail;
}
 
 
void nca_error(const int e, const String s)
{
  ostringstream os;
  os << "NetCDF error: " << s << ", " << e;
  throw runtime_error(os.str());
}
 
 
// We can't do the instantiation at the beginning of this file, because the
// implementation of nca_write_to_file and nca_read_from_file have to be known.
 
#include "nc_io_instantiation.h"
 
#endif /* ENABLE_NETCDF */