xml_io_basic_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 "absorptionlines.h"
#include "arts.h"
#include "debug.h"
#include "isotopologues.h"
#include "messages.h"
#include "quantum_numbers.h"
#include "xml_io.h"
#include <algorithm>
#include <vector>
 
//   Overloaded functions for reading/writing data from/to XML stream
 
//=== JacobianTarget ==================================================================
 
 
void xml_read_from_stream(istream& is_xml,
                          JacobianTarget& jt,
                          bifstream* pbifs,
                          const Verbosity& verbosity) {
  ArtsXMLTag tag(verbosity);
 
  tag.read_from_stream(is_xml);
  tag.check_name("JacobianTarget");
  
  // Type information
  String typestr, subtypestr;
  tag.get_attribute_value("Type", typestr);
  tag.get_attribute_value("SubType", subtypestr);
  jt.TargetType(typestr);
  jt.TargetSubType(subtypestr);
  
  if (jt.needQuantumIdentity()) {
    String qid;
    tag.get_attribute_value("id", qid);
    jt.qid = QuantumIdentifier(qid);
  }
 
  if (jt.needArrayOfSpeciesTag()) {
    String key;
    tag.get_attribute_value("species", key);
    jt.species_array_id = ArrayOfSpeciesTag(key);
  }
 
  if (jt.needString()) {
    tag.get_attribute_value("string_key", jt.string_id);
  }
  
  if (pbifs) {
    *pbifs >> jt.perturbation;
    if (pbifs->fail()) {
      xml_data_parse_error(tag, "");
    }
  } else {
    is_xml >> double_imanip() >> jt.perturbation;
    if (is_xml.fail()) {
      xml_data_parse_error(tag, "");
    }
  }
 
  tag.read_from_stream(is_xml);
  tag.check_name("/JacobianTarget");
  
  ARTS_USER_ERROR_IF (not jt.TargetSubTypeOK(),
    "Bad input: ", typestr, " or ", subtypestr, '\n', "\tCannot be interpreted as a type or substype...\n")
}
 
 
void xml_write_to_stream(ostream& os_xml,
                         const JacobianTarget& jt,
                         bofstream* pbofs,
                         const String& name,
                         const Verbosity& verbosity) {
  ArtsXMLTag open_tag(verbosity);
  ArtsXMLTag close_tag(verbosity);
 
  os_xml << '\n';
  open_tag.set_name("JacobianTarget");
  if (name.length()) open_tag.add_attribute("name", name);
  
  // Type information
  open_tag.add_attribute("Type", jt.TargetType());
  open_tag.add_attribute("SubType", jt.TargetSubType());
  
  if (jt.needQuantumIdentity()) {
    open_tag.add_attribute("id", var_string(jt.qid));
  }
 
  if (jt.needArrayOfSpeciesTag()) {
    open_tag.add_attribute("species", jt.species_array_id.Name());
  }
 
  if (jt.needString()) {
    open_tag.add_attribute("string_key", jt.string_id);
  }
  open_tag.write_to_stream(os_xml);
 
  if (pbofs)
    *pbofs << jt.perturbation;
  else
    os_xml << ' ' << jt.perturbation << ' ';
 
  close_tag.set_name("/JacobianTarget");
  close_tag.write_to_stream(os_xml);
  os_xml << '\n';
}
 
//=== Rational =========================================================
 
 
void xml_read_from_stream(istream& is_xml,
                          Rational& rational,
                          bifstream* pbifs,
                          const Verbosity& verbosity) {
  ArtsXMLTag tag(verbosity);
 
  tag.read_from_stream(is_xml);
  tag.check_name("Rational");
 
  if (pbifs) {
    *pbifs >> rational;
    if (pbifs->fail()) {
      xml_data_parse_error(tag, "");
    }
  } else {
    is_xml >> rational;
    if (is_xml.fail()) {
      xml_data_parse_error(tag, "");
    }
  }
 
  tag.read_from_stream(is_xml);
  tag.check_name("/Rational");
}
 
 
void xml_write_to_stream(ostream& os_xml,
                         const Rational& rational,
                         bofstream* pbofs,
                         const String& name,
                         const Verbosity& verbosity) {
  ArtsXMLTag open_tag(verbosity);
  ArtsXMLTag close_tag(verbosity);
 
  open_tag.set_name("Rational");
  if (name.length()) open_tag.add_attribute("name", name);
 
  open_tag.write_to_stream(os_xml);
 
  if (pbofs)
    *pbofs << rational;
  else
    os_xml << ' ' << rational << ' ';
 
  close_tag.set_name("/Rational");
  close_tag.write_to_stream(os_xml);
  os_xml << '\n';
}
 
//=== TransmissionMatrix ================================================================
 
 
void xml_read_from_stream(istream& is_xml,
                          TransmissionMatrix& tm,
                          bifstream* pbifs,
                          const Verbosity& verbosity) {
  ArtsXMLTag tag(verbosity);
  Index stokes_dim, nf;
 
  tag.read_from_stream(is_xml);
  tag.check_name("TransmissionMatrix");
 
  tag.get_attribute_value("Stokes", stokes_dim);
  tag.get_attribute_value("Freqs", nf);
  tm = TransmissionMatrix(nf, stokes_dim);
  if (pbifs) {
    *pbifs >> tm;
    if (pbifs->fail()) {
      ostringstream os;
      os << "TransmissionMatrix has wrong dimensions";
      xml_data_parse_error(tag, os.str());
    }
  } else {
    is_xml >> tm;
    if (is_xml.fail()) {
      ostringstream os;
      os << "TransmissionMatrix has wrong dimensions";
      xml_data_parse_error(tag, os.str());
    }
  }
 
  tag.read_from_stream(is_xml);
  tag.check_name("/TransmissionMatrix");
}
 
 
void xml_write_to_stream(ostream& os_xml,
                         const TransmissionMatrix& tm,
                         bofstream* pbofs,
                         const String& name,
                         const Verbosity& verbosity) {
  ArtsXMLTag open_tag(verbosity);
  ArtsXMLTag close_tag(verbosity);
 
  open_tag.set_name("TransmissionMatrix");
  if (name.length()) open_tag.add_attribute("name", name);
  open_tag.add_attribute("Stokes", tm.stokes_dim);
  open_tag.add_attribute("Freqs", tm.Frequencies());
 
  open_tag.write_to_stream(os_xml);
  os_xml << '\n';
 
  xml_set_stream_precision(os_xml);
  if (pbofs)
    *pbofs << tm;
  else
    os_xml << tm;
 
  close_tag.set_name("/TransmissionMatrix");
  close_tag.write_to_stream(os_xml);
 
  os_xml << '\n';
}
 
//=== RadiationVector ================================================================
 
 
void xml_read_from_stream(istream& is_xml,
                          RadiationVector& rv,
                          bifstream* pbifs,
                          const Verbosity& verbosity) {
  ArtsXMLTag tag(verbosity);
  Index stokes_dim, nf;
 
  tag.read_from_stream(is_xml);
  tag.check_name("RadiationVector");
 
  tag.get_attribute_value("Stokes", stokes_dim);
  tag.get_attribute_value("Freqs", nf);
  rv = RadiationVector(nf, stokes_dim);
  if (pbifs) {
    *pbifs >> rv;
    if (pbifs->fail()) {
      ostringstream os;
      os << "RadiationVector has wrong dimensions";
      xml_data_parse_error(tag, os.str());
    }
  } else {
    is_xml >> rv;
    if (is_xml.fail()) {
      ostringstream os;
      os << "RadiationVector has wrong dimensions";
      xml_data_parse_error(tag, os.str());
    }
  }
 
  tag.read_from_stream(is_xml);
  tag.check_name("/RadiationVector");
}
 
 
void xml_write_to_stream(ostream& os_xml,
                         const RadiationVector& rv,
                         bofstream* pbofs,
                         const String& name,
                         const Verbosity& verbosity) {
  ArtsXMLTag open_tag(verbosity);
  ArtsXMLTag close_tag(verbosity);
 
  open_tag.set_name("RadiationVector");
  if (name.length()) open_tag.add_attribute("name", name);
  open_tag.add_attribute("Stokes", rv.stokes_dim);
  open_tag.add_attribute("Freqs", rv.Frequencies());
 
  open_tag.write_to_stream(os_xml);
  os_xml << '\n';
 
  xml_set_stream_precision(os_xml);
  if (pbofs)
    *pbofs << rv;
  else
    os_xml << rv;
 
  close_tag.set_name("/RadiationVector");
  close_tag.write_to_stream(os_xml);
 
  os_xml << '\n';
}
 
//=== Time ================================================================
 
 
void xml_read_from_stream(istream& is_xml,
                          Time& t,
                          bifstream* pbifs [[maybe_unused]],
                          const Verbosity& verbosity) {
  ArtsXMLTag tag(verbosity);
  
  tag.read_from_stream(is_xml);
  tag.check_name("Time");
  
  Index version;
  tag.get_attribute_value("version", version);
  ARTS_USER_ERROR_IF (version not_eq 1,
                      "Your version of ARTS can only handle version 1 of Time");
  
  is_xml >> t;
  if (is_xml.fail()) {
    xml_data_parse_error(tag, "Time is poorly formatted");
  }
 
  tag.read_from_stream(is_xml);
  tag.check_name("/Time");
}
 
 
void xml_write_to_stream(ostream& os_xml,
                         const Time& t,
                         bofstream* pbofs [[maybe_unused]],
                         const String&,
                         const Verbosity& verbosity) {
  ArtsXMLTag open_tag(verbosity);
  ArtsXMLTag close_tag(verbosity);
 
  open_tag.set_name("Time");
  open_tag.add_attribute("version", t.Version());
  open_tag.write_to_stream(os_xml);
 
  xml_set_stream_precision(os_xml);
  
  os_xml << ' ' << t << ' ';
 
  close_tag.set_name("/Time");
  close_tag.write_to_stream(os_xml);
  os_xml << '\n';
}
 
//=== AbsorptionLines ================================================================
 
 
void xml_read_from_stream(istream& is_xml,
                          AbsorptionLines& al,
                          bifstream* pbifs,
                          const Verbosity& verbosity) {
  static_assert(AbsorptionLines::version == 2, "The reading routine expects version 1 of the absorption lines data type to work");
  
  ArtsXMLTag tag(verbosity);
  
  tag.read_from_stream(is_xml);
  tag.check_name("AbsorptionLines");
  
  Index version;
  if (tag.has_attribute("version")) {
    tag.get_attribute_value("version", version);
  } else {
    version = 0;
  }
 
  ARTS_USER_ERROR_IF(
      AbsorptionLines::version < version,
      "The version of this catalog is too new.  You need to upgrade ARTS to use it.")
 
  ARTS_USER_ERROR_IF(
      version < AbsorptionLines::version - 1 or
          (pbifs and version not_eq AbsorptionLines::version),
      "Using descoped version of the catalog; version: ",
      version,
      '\n',
      "We only ever support limited number of versions. Your compilation supports versions ",
      AbsorptionLines::version,
      " and ",
      AbsorptionLines::version - 1,
      " in ascii but only version ",
      AbsorptionLines::version,
      " in binary\n\n",
      "To update from versions, please check-out the following branch, compile, and save your catalog again (as ascii):\n"
      "0 to 1: 3b6565fb93702308c4cdd660ec63c71d63dcaf26\n"
      "1 to 2: Current version\n")
 
  // Number of lines
  Index nlines;
  tag.get_attribute_value("nlines", nlines);
  
  // Identity of the lines (Changes between versions)
  QuantumIdentifier id;
  if (version == 2) {
    String id_str;
    tag.get_attribute_value("id", id_str);
    id = QuantumIdentifier(id_str);
  } else if (version == 1) {
    String spec;
    tag.get_attribute_value("species", spec);
 
    Index spec_ind = Species::find_species_index(spec);
    ARTS_USER_ERROR_IF(spec_ind < 0, "Bad species index for: ", spec)
    id.isotopologue_index = spec_ind;
  }
  
  // Cutoff type
  String s_cutoff;
  tag.get_attribute_value("cutofftype", s_cutoff);
  const Absorption::CutoffType cutoff = Absorption::toCutoffTypeOrThrow(s_cutoff);
  
  // Mirroring type
  String s_mirroring;
  tag.get_attribute_value("mirroringtype", s_mirroring);
  const Absorption::MirroringType mirroring = Absorption::toMirroringTypeOrThrow(s_mirroring);
  
  // Line population type
  String s_population;
  tag.get_attribute_value("populationtype", s_population);
  const Absorption::PopulationType population = Absorption::toPopulationTypeOrThrow(s_population);
  
  // Normalization type
  String s_normalization;
  tag.get_attribute_value("normalizationtype", s_normalization);
  const Absorption::NormalizationType normalization = Absorption::toNormalizationTypeOrThrow(s_normalization);
  
  // Shape type
  String s_lineshapetype;
  tag.get_attribute_value("lineshapetype", s_lineshapetype);
  const LineShape::Type lineshapetype = LineShape::toTypeOrThrow(s_lineshapetype);
  
  Numeric T0;
  tag.get_attribute_value("T0", T0);
  
  Numeric cutofffreq;
  tag.get_attribute_value("cutofffreq", cutofffreq);
  
  Numeric linemixinglimit;
  tag.get_attribute_value("linemixinglimit", linemixinglimit);
  
  Quantum::Number::LocalState meta_localstate;
  String localquanta_str;
  tag.get_attribute_value("localquanta", localquanta_str);
  const Index nlocal = Quantum::Number::count_items(localquanta_str);
  Array<QuantumNumberType> qn_key;
  for (Index i = 0; i < nlocal; i++)
    qn_key.push_back(
        Quantum::Number::toType(Quantum::Number::items(localquanta_str, i)));
  ARTS_USER_ERROR_IF(
      std::any_of(qn_key.begin(),
                  qn_key.end(),
                  [](auto& qn) {
                    return Quantum::Number::common_value_type(
                               Quantum::Number::common_value_type(qn),
                               Quantum::Number::ValueType::H) not_eq
                           Quantum::Number::ValueType::H;
                  }),
      "Quantum number list contains a string type, this is not allowed: [",
      qn_key,
      ']')
  meta_localstate.set_unsorted_qns(qn_key);
 
  if (version == 1) {
    String uid, lid;
    tag.get_attribute_value("upperglobalquanta", uid);
    tag.get_attribute_value("lowerglobalquanta", lid);
    id.val = Quantum::Number::ValueList(uid, lid);
  }
  
  ArrayOfSpecies broadeningspecies;
  bool selfbroadening;
  bool bathbroadening;
  tag.get_attribute_value("broadeningspecies", broadeningspecies, selfbroadening, bathbroadening);
  if (selfbroadening) broadeningspecies.front() = id.Species();
  
  String temperaturemodes;
  tag.get_attribute_value("temperaturemodes", temperaturemodes);
  auto metamodel = LineShape::MetaData2ModelShape(temperaturemodes);
 
  al = AbsorptionLines(selfbroadening, bathbroadening,
                       nlines, cutoff, mirroring,
                       population, normalization,
                       lineshapetype, T0, cutofffreq,
                       linemixinglimit, id,
                       broadeningspecies, meta_localstate, metamodel);
  
  if (pbifs) {
    al.read(*pbifs);
     if (pbifs->fail()) {
       ostringstream os;
       os << "AbsorptionLines has wrong dimensions";
       xml_data_parse_error(tag, os.str());
     }
  } else {
    is_xml >> al;
    if (is_xml.fail()) {
      ostringstream os;
      os << "AbsorptionLines has wrong dimensions";
      xml_data_parse_error(tag, os.str());
    }
  }
 
  // Finalize the sorting because we have to
  for (auto& line: al.lines) line.localquanta.val.finalize();
 
  tag.read_from_stream(is_xml);
  tag.check_name("/AbsorptionLines");
 
  CREATE_OUT3;
  if (out3.sufficient_priority_screen()) {
    if (not al.quantumidentity.good()) {
      out3 << "Bad data in absorption band " << al.MetaData() << '\n';
    }
    for (auto& line : al.lines) {
      if (not line.localquanta.good()) {
        out3 << "Bad data in absorption band " << al.MetaData() << '\n'
             << "Line: " << line << '\n';
      }
    }
  }
}
 
 
void xml_write_to_stream(ostream& os_xml,
                         const AbsorptionLines& al,
                         bofstream* pbofs,
                         const String&,
                         const Verbosity& verbosity) {
  ArtsXMLTag open_comment_tag(verbosity);
  ArtsXMLTag close_comment_tag(verbosity);
  open_comment_tag.set_name("comment");
  open_comment_tag.write_to_stream(os_xml);
  os_xml << al.MetaData();
  close_comment_tag.set_name("/comment");
  close_comment_tag.write_to_stream(os_xml);
  os_xml << '\n';
 
  ArtsXMLTag open_tag(verbosity);
  ArtsXMLTag close_tag(verbosity);
 
  open_tag.set_name("AbsorptionLines");
  open_tag.add_attribute("version", al.version);
  open_tag.add_attribute("id", var_string(al.quantumidentity));
  open_tag.add_attribute("nlines", al.NumLines());
  open_tag.add_attribute("cutofftype", Absorption::toString(al.cutoff));
  open_tag.add_attribute("mirroringtype", Absorption::toString(al.mirroring));
  open_tag.add_attribute("populationtype", Absorption::toString(al.population));
  open_tag.add_attribute("normalizationtype", Absorption::toString(al.normalization));
  open_tag.add_attribute("lineshapetype", LineShape::toString(al.lineshapetype));
  open_tag.add_attribute("T0", al.T0);
  open_tag.add_attribute("cutofffreq", al.cutofffreq);
  open_tag.add_attribute("linemixinglimit", al.linemixinglimit);
 
  const String localquanta_str =
      al.NumLines() ? al.lines.front().localquanta.keys() : "";
  open_tag.add_attribute("localquanta", localquanta_str);
 
  open_tag.add_attribute("broadeningspecies", al.broadeningspecies, al.selfbroadening, al.bathbroadening);
  open_tag.add_attribute("temperaturemodes", al.LineShapeMetaData());
 
  open_tag.write_to_stream(os_xml);
  os_xml << '\n';
 
  xml_set_stream_precision(os_xml);
  if (pbofs)
    al.write(*pbofs);
  else
    os_xml << al;
 
  close_tag.set_name("/AbsorptionLines");
  close_tag.write_to_stream(os_xml);
 
  os_xml << '\n';
}
 
//   Dummy funtion for groups for which
//   IO function have not yet been implemented
 
// FIXME: These should be implemented, sooner or later...
 
void xml_read_from_stream(istream&,
                          Timer&,
                          bifstream* /* pbifs */,
                          const Verbosity&) {
  ARTS_USER_ERROR_IF(true, "Method not implemented!");
}
 
void xml_write_to_stream(ostream&,
                         const Timer&,
                         bofstream* /* pbofs */,
                         const String& /* name */,
                         const Verbosity&) {
  ARTS_USER_ERROR_IF(true, "Method not implemented!");
}