nc_io_compound_types.cc

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/* Copyright (C) 2003-2012 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 "config.h"

#ifdef ENABLE_NETCDF

#include <cstring>

#include "arts.h"
#include "nc_io.h"
#include "nc_io_types.h"

//=== GasAbsLookup ==========================================================


void nca_read_from_file(const int ncid, GasAbsLookup& gal, const Verbosity&) {
  nca_get_data_ArrayOfArrayOfSpeciesTag(ncid, "species", gal.species, true);
  if (!gal.species.nelem())
    throw runtime_error("No species found in lookup table file!");

  nca_get_data_ArrayOfIndex(
      ncid, "nonlinear_species", gal.nonlinear_species, true);
  nca_get_data_Vector(ncid, "f_grid", gal.f_grid, true);
  nca_get_data_Vector(ncid, "p_grid", gal.p_grid, true);
  nca_get_data_Matrix(ncid, "vmrs_ref", gal.vmrs_ref, true);
  nca_get_data_Vector(ncid, "t_ref", gal.t_ref, true);
  nca_get_data_Vector(ncid, "t_pert", gal.t_pert, true);
  nca_get_data_Vector(ncid, "nls_pert", gal.nls_pert, true);
  nca_get_data_Tensor4(ncid, "xsec", gal.xsec, true);
}


void nca_write_to_file(const int ncid,
                       const GasAbsLookup& gal,
                       const Verbosity&) {
  int retval;

  int species_strings_varid;
  int species_count_varid;

  ArrayOfIndex species_count(gal.species.nelem());
  Index species_max_strlen = 0;
  char* species_strings = NULL;

  if (gal.species.nelem()) {
    long species_total_nelems = 0;
    for (Index nspecies = 0; nspecies < gal.species.nelem(); nspecies++) {
      Index nspecies_nelem = gal.species[nspecies].nelem();
      species_total_nelems += nspecies_nelem;
      species_count[nspecies] = nspecies_nelem;

      for (ArrayOfSpeciesTag::const_iterator it = gal.species[nspecies].begin();
           it != gal.species[nspecies].end();
           it++)
        if (it->Name().nelem() > species_max_strlen)
          species_max_strlen = it->Name().nelem();
    }
    species_max_strlen++;

    species_strings = new char[species_total_nelems * species_max_strlen];
    memset(species_strings, 0, species_total_nelems * species_max_strlen);

    Index str_i = 0;
    for (ArrayOfArrayOfSpeciesTag::const_iterator it1 = gal.species.begin();
         it1 != gal.species.end();
         it1++)
      for (ArrayOfSpeciesTag::const_iterator it2 = it1->begin();
           it2 != it1->end();
           it2++) {
        memccpy(&species_strings[str_i],
                it2->Name().c_str(),
                0,
                species_max_strlen);
        str_i += species_max_strlen;
      }

    species_count_varid =
        nca_def_ArrayOfIndex(ncid, "species_count", species_count);

    int species_strings_ncdims[2];
    nca_def_dim(ncid,
                "species_strings_nelem",
                species_total_nelems,
                &species_strings_ncdims[0]);
    nca_def_dim(ncid,
                "species_strings_length",
                species_max_strlen,
                &species_strings_ncdims[1]);
    nca_def_var(ncid,
                "species_strings",
                NC_CHAR,
                2,
                &species_strings_ncdims[0],
                &species_strings_varid);
  } else {
    throw runtime_error("Current lookup table contains no species!");
  }

  // Define dimensions and variables
  int nonlinear_species_varid =
      nca_def_ArrayOfIndex(ncid, "nonlinear_species", gal.nonlinear_species);
  int f_grid_varid = nca_def_Vector(ncid, "f_grid", gal.f_grid);
  int p_grid_varid = nca_def_Vector(ncid, "p_grid", gal.p_grid);
  int vmrs_ref_varid = nca_def_Matrix(ncid, "vmrs_ref", gal.vmrs_ref);
  int t_ref_varid = nca_def_Vector(ncid, "t_ref", gal.t_ref);
  int t_pert_varid = nca_def_Vector(ncid, "t_pert", gal.t_pert);
  int nls_pert_varid = nca_def_Vector(ncid, "nls_pert", gal.nls_pert);
  int xsec_varid = nca_def_Tensor4(ncid, "xsec", gal.xsec);

  if ((retval = nc_enddef(ncid))) nca_error(retval, "nc_enddef");

  // Write variables
  nca_put_var_ArrayOfIndex(ncid, species_count_varid, species_count);
  if (gal.species.nelem()) {
    if ((retval =
             nc_put_var_text(ncid, species_strings_varid, species_strings)))
      nca_error(retval, "nc_put_var");
  }

  delete[] species_strings;

  nca_put_var_ArrayOfIndex(
      ncid, nonlinear_species_varid, gal.nonlinear_species);
  nca_put_var_Vector(ncid, f_grid_varid, gal.f_grid);
  nca_put_var_Vector(ncid, p_grid_varid, gal.p_grid);
  nca_put_var_Matrix(ncid, vmrs_ref_varid, gal.vmrs_ref);
  nca_put_var_Vector(ncid, t_ref_varid, gal.t_ref);
  nca_put_var_Vector(ncid, t_pert_varid, gal.t_pert);
  nca_put_var_Vector(ncid, nls_pert_varid, gal.nls_pert);
  nca_put_var_Tensor4(ncid, xsec_varid, gal.xsec);
}

//   Dummy funtion for groups for which
//   IO function have not yet been implemented

#define TMPL_NC_READ_WRITE_FILE_DUMMY(what)                                   \
  void nca_write_to_file(const int, const what&, const Verbosity&) {          \
    throw runtime_error("NetCDF support not yet implemented for this type!"); \
  }                                                                           \
  void nca_read_from_file(const int, what&, const Verbosity&) {               \
    throw runtime_error("NetCDF support not yet implemented for this type!"); \
  }

TMPL_NC_READ_WRITE_FILE_DUMMY(Agenda)

//==========================================================================

// Undefine the macro to avoid it being used anywhere else
#undef TMPL_NC_READ_WRITE_FILE_DUMMY

#endif /* ENABLE_NETCDF */