odm/src/ncfuncs.cpp

#define MICHLIB_NOSOURCE
#include "ncfuncs.h"

NCFuncs::CoordNames NCFuncs::GetDNames(const NCFileA& nc)
{
 CoordNames out;
 auto       head = nc.Header();
 for(const auto& dim: head.Dimensions())
 {
  if(dim.Name() == "lon" || dim.Name() == "longitude")
  {
   out.lonname = dim.Name();
   out.nx      = dim.Len();
  }
  if(dim.Name() == "lat" || dim.Name() == "latitude")
  {
   out.latname = dim.Name();
   out.ny      = dim.Len();
  }
  if(dim.Name() == "depth")
  {
   out.depthname = dim.Name();
   out.nz        = dim.Len();
  }
  if(dim.Name() == "time")
  {
   out.timename = dim.Name();
   out.nt       = dim.Len();
  }
 }
 return out;
}

NCFuncs::CoordNames NCFuncs::GetCNames(const NCFileA& nc)
{
 CoordNames out;
 auto       head = nc.Header();
 for(const auto& v: head.Variables()) // Try to define coordinates by attribute standard_name or attribute axis
 {
  auto stname = nc.A<MString>(v.Name(), "standard_name");
  auto axis   = nc.A<MString>(v.Name(), "axis");
  bool islon = false, islat = false, isdepth = false, istime = false;
  if(!(stname || axis)) continue;
  if(stname && stname.Get() == "longitude") islon = true;
  if(stname && stname.Get() == "latitude") islat = true;
  if(stname && stname.Get() == "depth") isdepth = true;
  if(stname && stname.Get() == "time") istime = true;

  if(!out.lonname.Exist() && axis && axis.Get() == "X") islon = true;
  if(!out.latname.Exist() && axis && axis.Get() == "Y") islat = true;
  if(!out.depthname.Exist() && axis && axis.Get() == "Z") isdepth = true;
  if(!out.timename.Exist() && axis && axis.Get() == "T") istime = true;

  if(islon) out.lonname = v.Name();
  if(islat) out.latname = v.Name();
  if(isdepth) out.depthname = v.Name();
  if(istime) out.timename = v.Name();

  if(islon) out.nx = v.Dimensions().size();
  if(islat) out.ny = v.Dimensions().size();
  if(isdepth) out.nz = v.Dimensions().size();
  if(istime) out.nt = v.Dimensions().size();
 }
 return out;
}

void NCFuncs::GetVars(const NCFileA& nc, std::set<MString>& vars)
{
 auto head = nc.Header();
 for(const auto& v: head.Variables())
 {
  auto ret = nc.A<MString>(v.Name(), "standard_name");
  if(!ret) continue;
  if(StName2Name(ret).Exist()) vars.emplace(StName2Name(ret));
 }
 if((vars.contains("ptemp") || vars.contains("temp")) && vars.contains("sal")) vars.emplace("pdens");
 if(vars.contains("ptemp") && vars.contains("sal")) vars.emplace("temp");
 if(vars.contains("temp") && vars.contains("sal")) vars.emplace("ptemp");

 if(vars.contains("u") && vars.contains("v")) vars.emplace("U");
 if(vars.contains("u") && vars.contains("v")) vars.emplace("U2");
 if(vars.contains("ssh")) vars.emplace("ugeo");
 if(vars.contains("ssh")) vars.emplace("vgeo");
}

std::tuple<MDateTime, time_t, bool> NCFuncs::Refdate(const MString& refdate)
{
 MDateTime out;
 time_t    step = 0;

 MString rstr;
 auto    words = michlib::Split_on_words(refdate);
 auto    ci    = words.begin();
 if(ci != words.end())
 {
  if(*ci == "minutes") step = 60;
  if(*ci == "hours") step = 3600;
  if(*ci == "days") step = 3600 * 24;
  ci++;
 }
 if(ci != words.end()) ci++;       // skip "since"
 if(ci != words.end()) rstr = *ci; // Day
 if(ci != words.end()) ci++;
 if(ci != words.end()) rstr += " " + *ci; // Hours
 bool success = out.FromString(rstr);
 return {out, step, success};
}

MString NCFuncs::StName2Name(const MString& stname)
{
 if(stname == "sea_water_potential_temperature") return "ptemp";
 if(stname == "sea_water_temperature") return "temp";
 if(stname == "sea_water_salinity") return "sal";
 if(stname == "ocean_mixed_layer_thickness_defined_by_sigma_theta") return "mld";
 if(stname == "sea_surface_height_above_geoid") return "ssh";
 if(stname == "sea_surface_elevation") return "ssh";
 if(stname == "eastward_sea_water_velocity") return "u";
 if(stname == "northward_sea_water_velocity") return "v";
 if(stname == "surface_geostrophic_eastward_sea_water_velocity") return "u";
 if(stname == "surface_geostrophic_northward_sea_water_velocity") return "v";
 if(stname == "upward_sea_water_velocity") return "w";
 if(stname == "mass_concentration_of_chlorophyll_a_in_sea_water") return "chl";
 if(stname == "mole_concentration_of_nitrate_in_sea_water") return "NO3";
 if(stname == "net_primary_production_of_biomass_expressed_as_carbon_per_unit_volume_in_sea_water") return "prprod";
 if(stname == "mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water") return "Cchl";
 if(stname == "mole_concentration_of_phosphate_in_sea_water") return "PO4";
 if(stname == "mole_concentration_of_silicate_in_sea_water") return "Si";
 return "";
}

MString NCFuncs::Name2StName(const MString& name)
{
 if(name == "ptemp") return "sea_water_potential_temperature";
 if(name == "temp") return "sea_water_temperature";
 if(name == "sal") return "sea_water_salinity";
 if(name == "mld") return "ocean_mixed_layer_thickness_defined_by_sigma_theta";
 if(name == "ssh") return "sea_surface_height_above_geoid";
 if(name == "u") return "eastward_sea_water_velocity";
 if(name == "v") return "northward_sea_water_velocity";
 if(name == "w") return "upward_sea_water_velocity";
 if(name == "chl") return "mass_concentration_of_chlorophyll_a_in_sea_water";
 if(name == "NO3") return "mole_concentration_of_nitrate_in_sea_water";
 if(name == "prprod") return "net_primary_production_of_biomass_expressed_as_carbon_per_unit_volume_in_sea_water";
 if(name == "Cchl") return "mole_concentration_of_phytoplankton_expressed_as_carbon_in_sea_water";
 if(name == "PO4") return "mole_concentration_of_phosphate_in_sea_water";
 if(name == "Si") return "mole_concentration_of_silicate_in_sea_water";
 return "";
}

MString NCFuncs::Name2LongName(const MString& name)
{
 if(name == "ptemp") return "Potential temperature";
 if(name == "temp") return "Temperature";
 if(name == "sal") return "Salinity";
 if(name == "mld") return "Mixed layer depth";
 if(name == "ssh") return "Sea surface height";
 if(name == "u") return "X-velocity";
 if(name == "v") return "Y-velocity";
 if(name == "w") return "Z-velocity";
 if(name == "ugeo") return "Geostrophic eastward velocity from ssh";
 if(name == "vgeo") return "Geostrophic northward velocity from ssh";
 if(name == "chl") return "Concentration of chlorophyll";
 if(name == "NO3") return "Concentration of nitrates";
 if(name == "prprod") return "Primary production";
 if(name == "Cchl") return "Concentration of chlorophyll carbon";
 if(name == "PO4") return "Concentration of phosphates";
 if(name == "Si") return "Concentration of silicates";
 if(name == "U") return "Module of horizontal velocity";
 if(name == "U2") return "Squared horizontal velocity";
 return "";
}

bool NCFuncs::HaveVar(const NCFileA& nc, const MString& vname)
{
 auto head = nc.Header();
 for(const auto& v: head.Variables())
 {
  auto stname = nc.A<MString>(v.Name(), "standard_name");
  if(!stname) continue;
  if(StName2Name(stname) == vname) return true;
 }
 return false;
}