[219] | 1 | #include "inetcdf4.hpp" |
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[599] | 2 | #include "netCdfInterface.hpp" |
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[782] | 3 | #include "netCdf_cf_constant.hpp" |
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[219] | 4 | |
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| 5 | #include <boost/algorithm/string.hpp> |
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| 6 | |
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[335] | 7 | namespace xios |
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[219] | 8 | { |
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[1491] | 9 | //CINetCDF4::CINetCDF4(const StdString& filename, const ep_lib::MPI_Comm* comm /*= NULL*/, bool multifile /*= true*/, const StdString& timeCounterName /*= "time_counter"*/) |
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| 10 | CINetCDF4::CINetCDF4(const StdString& filename, const ep_lib::MPI_Comm* comm /*= NULL*/, bool multifile /*= true*/, |
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| 11 | bool readMetaDataPar /*= false*/, const StdString& timeCounterName /*= "time_counter"*/) |
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[599] | 12 | { |
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[736] | 13 | // Don't use parallel mode if there is only one process |
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| 14 | if (comm) |
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[599] | 15 | { |
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[736] | 16 | int commSize = 0; |
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[1328] | 17 | ep_lib::MPI_Comm_size(*comm, &commSize); |
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[736] | 18 | if (commSize <= 1) |
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| 19 | comm = NULL; |
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[599] | 20 | } |
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[1491] | 21 | //mpi = comm && !multifile; |
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| 22 | mpi = comm && !multifile && readMetaDataPar; |
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[1328] | 23 | ep_lib::MPI_Info info_null; |
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[736] | 24 | |
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| 25 | // The file format will be detected automatically by NetCDF, it is safe to always set NC_MPIIO |
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| 26 | // even if Parallel NetCDF ends up being used. |
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| 27 | if (mpi) |
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[1362] | 28 | CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *(static_cast<MPI_Comm*>(comm->mpi_comm)), *(static_cast<MPI_Info*>(info_null.mpi_info)), this->ncidp); |
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[1355] | 29 | //CNetCdfInterface::openPar(filename, NC_NOWRITE | NC_MPIIO, *(static_cast<MPI_Comm*>(comm->mpi_comm)), info_null.mpi_info, this->ncidp); |
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[736] | 30 | else |
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| 31 | CNetCdfInterface::open(filename, NC_NOWRITE, this->ncidp); |
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[802] | 32 | |
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| 33 | this->timeCounterName = timeCounterName; |
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[811] | 34 | if (!CNetCdfInterface::isDimExisted(this->ncidp, this->timeCounterName)) this->timeCounterName=this->getUnlimitedDimensionName() ; |
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[825] | 35 | |
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[599] | 36 | } |
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[219] | 37 | |
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[599] | 38 | CINetCDF4::~CINetCDF4(void) |
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| 39 | { /* Nothing to do */ } |
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[219] | 40 | |
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[599] | 41 | //--------------------------------------------------------------- |
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[219] | 42 | |
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[599] | 43 | void CINetCDF4::close(void) |
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| 44 | { |
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[686] | 45 | CNetCdfInterface::close(this->ncidp); |
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[599] | 46 | } |
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[219] | 47 | |
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[599] | 48 | //--------------------------------------------------------------- |
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[219] | 49 | |
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[599] | 50 | int CINetCDF4::getGroup(const CVarPath* const path) |
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| 51 | { |
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| 52 | int retvalue = this->ncidp; |
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| 53 | if (path == NULL) return retvalue; |
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| 54 | CVarPath::const_iterator it = path->begin(), end = path->end(); |
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[219] | 55 | |
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[599] | 56 | for (; it != end; it++) |
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| 57 | { |
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| 58 | const StdString& groupid = *it; |
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[686] | 59 | CNetCdfInterface::inqNcId(retvalue, groupid, retvalue); |
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[599] | 60 | } |
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[219] | 61 | |
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[599] | 62 | return retvalue; |
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| 63 | } |
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[219] | 64 | |
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[599] | 65 | int CINetCDF4::getVariable(const StdString& varname, |
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| 66 | const CVarPath* const path) |
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| 67 | { |
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| 68 | int varid = 0; |
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| 69 | int grpid = this->getGroup(path); |
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[825] | 70 | if (this->hasVariable(varname, path)) |
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| 71 | CNetCdfInterface::inqVarId(grpid, varname, varid); |
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[599] | 72 | return varid; |
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| 73 | } |
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[219] | 74 | |
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[599] | 75 | int CINetCDF4::getDimension(const StdString& dimname, |
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| 76 | const CVarPath* const path) |
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| 77 | { |
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| 78 | int dimid = 0; |
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| 79 | int grpid = this->getGroup(path); |
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[686] | 80 | CNetCdfInterface::inqDimId(grpid, dimname, dimid); |
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[599] | 81 | return dimid; |
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| 82 | } |
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[219] | 83 | |
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[599] | 84 | std::pair<nc_type, StdSize> CINetCDF4::getAttribute(const StdString& attname, |
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| 85 | const StdString* const var, |
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| 86 | const CVarPath* const path) |
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| 87 | { |
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| 88 | std::pair<nc_type, StdSize> retvalue; |
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| 89 | int grpid = this->getGroup(path); |
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[1460] | 90 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[686] | 91 | CNetCdfInterface::inqAtt(grpid, varid, attname, retvalue.first, retvalue.second); |
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[599] | 92 | return retvalue; |
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| 93 | } |
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[219] | 94 | |
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[599] | 95 | int CINetCDF4::getUnlimitedDimension(const CVarPath* const path) |
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| 96 | { |
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| 97 | int dimid = 0; |
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| 98 | int grpid = this->getGroup(path); |
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[686] | 99 | CNetCdfInterface::inqUnLimDim(grpid, dimid); |
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[599] | 100 | return dimid; |
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| 101 | } |
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[219] | 102 | |
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[599] | 103 | StdString CINetCDF4::getUnlimitedDimensionName(const CVarPath* const path) |
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| 104 | { |
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| 105 | int grpid = this->getGroup(path); |
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| 106 | int dimid = this->getUnlimitedDimension(path); |
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[219] | 107 | |
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[686] | 108 | StdString dimname; |
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| 109 | if (dimid != -1) |
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| 110 | CNetCdfInterface::inqDimName(grpid, dimid, dimname); |
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[599] | 111 | return dimname; |
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| 112 | } |
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[219] | 113 | |
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[599] | 114 | //--------------------------------------------------------------- |
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[686] | 115 | |
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[599] | 116 | StdSize CINetCDF4::getNbVertex(const StdString& name, |
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| 117 | const CVarPath* const path) |
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| 118 | { |
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[219] | 119 | |
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[599] | 120 | if (this->isRectilinear(name, path) || |
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| 121 | this->isCurvilinear(name, path)) |
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| 122 | { |
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| 123 | if (this->is3Dim(name, path)) return 8; |
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| 124 | else return 4; |
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| 125 | } |
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| 126 | if (this->isUnstructured(name, path)) |
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| 127 | { |
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| 128 | StdString bound = this->getBoundsId |
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| 129 | (this->getCoordinatesIdList(name, path).back(), path); |
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| 130 | StdString dim = this->getDimensionsList(&bound, path).back(); |
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[686] | 131 | return this->getDimensions(&bound, path)[dim]; |
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[599] | 132 | } |
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| 133 | return size_t(-1); |
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| 134 | } |
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[219] | 135 | |
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[599] | 136 | //--------------------------------------------------------------- |
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[219] | 137 | |
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[599] | 138 | std::list<StdString> CINetCDF4::getGroups(const CVarPath* const path) |
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| 139 | { |
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| 140 | int nbgroup = 0, *groupid = NULL; |
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| 141 | int grpid = this->getGroup(path); |
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| 142 | std::list<StdString> retvalue; |
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[219] | 143 | |
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[686] | 144 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, NULL); |
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[599] | 145 | groupid = new int[nbgroup](); |
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[686] | 146 | CNetCdfInterface::inqGrpIds(grpid, nbgroup, groupid); |
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[219] | 147 | |
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[599] | 148 | for (int i = 0; i < nbgroup; i++) |
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| 149 | { |
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[686] | 150 | StdString fullGrpName; |
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| 151 | CNetCdfInterface::inqGrpFullName(groupid[i], fullGrpName); |
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| 152 | retvalue.push_back(fullGrpName); |
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[599] | 153 | } |
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[219] | 154 | |
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[599] | 155 | delete [] groupid; |
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| 156 | return retvalue; |
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| 157 | } |
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[219] | 158 | |
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[599] | 159 | std::list<StdString> CINetCDF4::getVariables(const CVarPath* const path) |
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| 160 | { |
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| 161 | int nbvar = 0, *varid = NULL; |
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| 162 | int grpid = this->getGroup(path); |
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| 163 | std::list<StdString> retvalue; |
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[219] | 164 | |
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[686] | 165 | CNetCdfInterface::inqVarIds(grpid, nbvar, NULL); |
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[599] | 166 | varid = new int[nbvar](); |
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[686] | 167 | CNetCdfInterface::inqVarIds(grpid, nbvar, varid); |
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[219] | 168 | |
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[599] | 169 | for (int i = 0; i < nbvar; i++) |
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| 170 | { |
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[686] | 171 | StdString varName; |
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| 172 | CNetCdfInterface::inqVarName(grpid, varid[i], varName); |
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| 173 | retvalue.push_back(varName); |
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[599] | 174 | } |
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| 175 | |
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| 176 | delete [] varid; |
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| 177 | return retvalue; |
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| 178 | } |
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| 179 | |
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| 180 | StdSize CINetCDF4::getNbOfTimestep(const CVarPath* const path) |
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| 181 | { |
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[686] | 182 | return this->getDimensions(NULL, path)[this->getUnlimitedDimensionName(path)]; |
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[599] | 183 | } |
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| 184 | |
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| 185 | std::set<StdString> CINetCDF4::getBoundVariables(const CVarPath* const path) |
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| 186 | { |
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| 187 | std::set<StdString> retvalue; |
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| 188 | std::list<StdString> variables = this->getVariables(path); |
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| 189 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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| 190 | for (; it != end; it++) |
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| 191 | { |
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| 192 | const StdString& var = *it; |
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| 193 | if (this->hasBounds(var, path)) |
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| 194 | retvalue.insert(retvalue.end(), this->getBoundsId(var, path)); |
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| 195 | } |
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| 196 | return retvalue; |
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| 197 | } |
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| 198 | |
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| 199 | std::set<StdString> CINetCDF4::getCoordVariables(const CVarPath* const path) |
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| 200 | { |
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| 201 | std::set<StdString> retvalue; |
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| 202 | std::list<StdString> variables = this->getVariables(path); |
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| 203 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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| 204 | for (; it != end; it++) |
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| 205 | { |
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| 206 | const StdString& var = *it; |
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| 207 | std::list<StdString> coords = this->getCoordinatesIdList(var, path); |
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| 208 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
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| 209 | for (; it != end; it++) |
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[219] | 210 | { |
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[599] | 211 | const StdString& coord = *it; |
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| 212 | if (this->hasVariable(coord, path)) |
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| 213 | retvalue.insert(retvalue.end(), coord); |
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[219] | 214 | } |
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[599] | 215 | } |
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| 216 | return retvalue; |
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| 217 | } |
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[219] | 218 | |
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[599] | 219 | std::list<StdString> CINetCDF4::getDimensionsList(const StdString* const var, const CVarPath* const path) |
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| 220 | { |
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| 221 | int nbdim = 0, *dimid = NULL; |
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| 222 | int grpid = this->getGroup(path); |
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[1460] | 223 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[599] | 224 | std::list<StdString> retvalue; |
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[219] | 225 | |
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[1460] | 226 | if (var != NULL && this->hasVariable(*var, path)) |
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[599] | 227 | { |
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[686] | 228 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[599] | 229 | dimid = new int[nbdim](); |
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[686] | 230 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[599] | 231 | } |
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| 232 | else |
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| 233 | { |
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[686] | 234 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[599] | 235 | dimid = new int[nbdim](); |
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[686] | 236 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
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[599] | 237 | } |
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[219] | 238 | |
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[599] | 239 | for (int i = 0; i < nbdim; i++) |
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| 240 | { |
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[686] | 241 | std::string dimname; |
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| 242 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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[599] | 243 | retvalue.push_back(dimname); |
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| 244 | } |
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| 245 | delete [] dimid; |
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[219] | 246 | |
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[599] | 247 | return retvalue; |
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| 248 | } |
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[219] | 249 | |
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[599] | 250 | std::map<StdString, StdSize> CINetCDF4::getDimensions(const StdString* const var, const CVarPath* const path) |
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| 251 | { |
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| 252 | int nbdim = 0, *dimid = NULL; |
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| 253 | int grpid = this->getGroup(path); |
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[1460] | 254 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[599] | 255 | std::map<StdString, StdSize> retvalue; |
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[219] | 256 | |
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[1460] | 257 | if (var != NULL && this->hasVariable(*var, path)) |
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[599] | 258 | { |
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[686] | 259 | CNetCdfInterface::inqVarNDims(grpid, varid, nbdim); |
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[599] | 260 | dimid = new int[nbdim](); |
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[686] | 261 | CNetCdfInterface::inqVarDimId(grpid, varid, dimid); |
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[599] | 262 | } |
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| 263 | else |
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| 264 | { |
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[686] | 265 | CNetCdfInterface::inqDimIds(grpid, nbdim, NULL, 1); |
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[599] | 266 | dimid = new int[nbdim](); |
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[686] | 267 | CNetCdfInterface::inqDimIds(grpid, nbdim, dimid, 1); |
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[599] | 268 | } |
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[219] | 269 | |
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[599] | 270 | for (int i = 0; i < nbdim; i++) |
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| 271 | { |
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[686] | 272 | std::string dimname; |
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| 273 | CNetCdfInterface::inqDimName(grpid, dimid[i], dimname); |
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| 274 | StdSize size = 0; |
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| 275 | CNetCdfInterface::inqDimLen(grpid, dimid[i], size); |
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[219] | 276 | |
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[599] | 277 | retvalue.insert(retvalue.end(), std::make_pair(dimname, size)); |
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| 278 | } |
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| 279 | delete [] dimid; |
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[219] | 280 | |
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[599] | 281 | return retvalue; |
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| 282 | } |
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[219] | 283 | |
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[686] | 284 | std::list<StdString> CINetCDF4::getAttributes(const StdString* const var, const CVarPath* const path) |
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[599] | 285 | { |
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| 286 | int nbatt = 0; |
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| 287 | std::list<StdString> retvalue; |
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| 288 | int grpid = this->getGroup(path); |
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[1460] | 289 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[219] | 290 | |
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[1460] | 291 | if (var != NULL && this->hasVariable(*var, path)) |
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[686] | 292 | CNetCdfInterface::inqVarNAtts(grpid, varid, nbatt); |
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[599] | 293 | else |
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[686] | 294 | CNetCdfInterface::inqNAtts(grpid, nbatt); |
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[219] | 295 | |
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[599] | 296 | for (int i = 0; i < nbatt; i++) |
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| 297 | { |
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[686] | 298 | StdString attname; |
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| 299 | CNetCdfInterface::inqAttName(grpid, varid, i, attname); |
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[599] | 300 | retvalue.push_back(attname); |
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| 301 | } |
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| 302 | return retvalue; |
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| 303 | } |
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[219] | 304 | |
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[599] | 305 | int CINetCDF4::getAttributeId(const StdString& name, |
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| 306 | const StdString* const var, |
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| 307 | const CVarPath* const path) |
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| 308 | { |
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| 309 | int retvalue = 0; |
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| 310 | std::list<StdString> atts = this->getAttributes(var, path); |
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| 311 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
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| 312 | for (; it != end; it++) |
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| 313 | { |
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| 314 | const StdString& attname = *it; |
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[782] | 315 | if (attname.compare(0, name.size(), name) == 0) |
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[599] | 316 | return retvalue; |
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| 317 | retvalue++; |
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| 318 | } |
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| 319 | return -1; |
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| 320 | } |
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[219] | 321 | |
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[599] | 322 | //--------------------------------------------------------------- |
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[219] | 323 | |
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[599] | 324 | bool CINetCDF4::hasMissingValue(const StdString& name, |
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| 325 | const CVarPath* const path) |
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| 326 | { |
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[686] | 327 | return (this->hasAttribute("missing_value", &name, path) || this->hasAttribute("_FillValue", &name, path)); |
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[599] | 328 | } |
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[219] | 329 | |
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[599] | 330 | bool CINetCDF4::hasAttribute(const StdString& name, |
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| 331 | const StdString* const var , |
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| 332 | const CVarPath* const path) |
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| 333 | { |
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| 334 | std::list<StdString> atts = this->getAttributes(var, path); |
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| 335 | std::list<StdString>::const_iterator it = atts.begin(), end = atts.end(); |
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| 336 | for (; it != end; it++) |
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| 337 | { |
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| 338 | const StdString& attname = *it; |
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[782] | 339 | if (attname.compare(0, name.size(), name) == 0) return true; |
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[599] | 340 | } |
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| 341 | return false; |
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| 342 | } |
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[219] | 343 | |
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[599] | 344 | bool CINetCDF4::hasVariable(const StdString& name, |
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| 345 | const CVarPath* const path) |
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| 346 | { |
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| 347 | std::list<StdString> variables = this->getVariables(path); |
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| 348 | std::list<StdString>::const_iterator it = variables.begin(), end = variables.end(); |
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| 349 | for (; it != end; it++) |
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| 350 | { |
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| 351 | const StdString& varname = *it; |
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[825] | 352 | if ((varname.compare(0, name.size(), name) == 0) && (0 != name.size())) return true; |
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[599] | 353 | } |
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| 354 | return false; |
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| 355 | } |
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[219] | 356 | |
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[599] | 357 | bool CINetCDF4::hasCoordinates(const StdString& name, |
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| 358 | const CVarPath* const path) |
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| 359 | { |
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[782] | 360 | return this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path); |
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[599] | 361 | } |
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[219] | 362 | |
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[599] | 363 | bool CINetCDF4::hasBounds(const StdString& name, |
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| 364 | const CVarPath* const path) |
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| 365 | { |
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[782] | 366 | return this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path); |
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[599] | 367 | } |
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[219] | 368 | |
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[599] | 369 | bool CINetCDF4::hasTemporalDim(const CVarPath* const path) |
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| 370 | { |
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[802] | 371 | std::list<StdString> dims = this->getDimensionsList(NULL, path); |
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| 372 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
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[599] | 373 | } |
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[219] | 374 | |
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[599] | 375 | //--------------------------------------------------------------- |
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[219] | 376 | |
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[686] | 377 | template <class T> |
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| 378 | std::vector<T> CINetCDF4::getAttributeValue(const StdString& name, |
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| 379 | const StdString* const var, |
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| 380 | const CVarPath* const path) |
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| 381 | { |
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| 382 | int grpid = this->getGroup(path); |
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[1460] | 383 | int varid = (var != NULL && this->hasVariable(*var, path)) ? this->getVariable(*var, path) : NC_GLOBAL; |
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[686] | 384 | std::pair<nc_type , StdSize> attinfos = this->getAttribute(name, var, path); |
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| 385 | std::vector<T> retvalue(attinfos.second); |
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| 386 | nc_type type = CNetCdfInterface::getNcType<T>(); |
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| 387 | if (attinfos.first != type) |
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| 388 | ERROR("CINetCDF4::getAttributeValue<T>(name, var, path)", |
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| 389 | << "[ name : " << name |
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| 390 | << ", type requested :" << attinfos.first |
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| 391 | << ", type stored : " << type << "]" |
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| 392 | << " Invalid type !"); |
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| 393 | CNetCdfInterface::getAttType(grpid, varid, name.c_str(), &retvalue[0]); |
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| 394 | return retvalue; |
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[599] | 395 | } |
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[219] | 396 | |
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[686] | 397 | template std::vector<double> CINetCDF4::getAttributeValue(const StdString& name, |
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| 398 | const StdString* const var, |
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| 399 | const CVarPath* const path); |
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| 400 | template std::vector<float> CINetCDF4::getAttributeValue(const StdString& name, |
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| 401 | const StdString* const var, |
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| 402 | const CVarPath* const path); |
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| 403 | template std::vector<int> CINetCDF4::getAttributeValue(const StdString& name, |
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| 404 | const StdString* const var, |
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| 405 | const CVarPath* const path); |
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| 406 | template std::vector<char> CINetCDF4::getAttributeValue(const StdString& name, |
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| 407 | const StdString* const var, |
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| 408 | const CVarPath* const path); |
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[219] | 409 | |
---|
[599] | 410 | StdString CINetCDF4::getAttributeValue(const StdString& name, |
---|
| 411 | const StdString* const var, |
---|
| 412 | const CVarPath* const path) |
---|
| 413 | { |
---|
[686] | 414 | std::vector<char> data = this->getAttributeValue<char>(name, var, path); |
---|
[219] | 415 | |
---|
[686] | 416 | return StdString(data.begin(), data.end()); |
---|
[599] | 417 | } |
---|
[219] | 418 | |
---|
[686] | 419 | template <class T> |
---|
| 420 | T CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path) |
---|
[599] | 421 | { |
---|
| 422 | if (this->hasAttribute("missing_value", &name, path)) |
---|
[686] | 423 | return this->getAttributeValue<T>("missing_value", &name, path)[0]; |
---|
[599] | 424 | if (this->hasAttribute("_FillValue", &name, path)) |
---|
[686] | 425 | return this->getAttributeValue<T>("_FillValue", &name, path)[0]; |
---|
[599] | 426 | return 0; |
---|
| 427 | } |
---|
[219] | 428 | |
---|
[686] | 429 | template double CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
| 430 | template float CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
| 431 | template int CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
| 432 | template char CINetCDF4::getMissingValue(const StdString& name, const CVarPath* const path); |
---|
[219] | 433 | |
---|
[599] | 434 | //--------------------------------------------------------------- |
---|
[219] | 435 | |
---|
[599] | 436 | std::list<StdString> CINetCDF4::getCoordinatesIdList(const StdString& name, const CVarPath* const path) |
---|
| 437 | { |
---|
| 438 | std::list<StdString> retvalue; |
---|
| 439 | StdString value = this->getCoordinatesId(name, path); |
---|
[219] | 440 | |
---|
[599] | 441 | boost::split(retvalue, value, boost::is_any_of(" ")); |
---|
[219] | 442 | |
---|
[599] | 443 | std::list<StdString>::iterator it = retvalue.begin(), end = retvalue.end(); |
---|
| 444 | for (; it != end; it++) |
---|
| 445 | { |
---|
| 446 | StdString& coord = *it; |
---|
| 447 | coord.assign(coord.data()); |
---|
| 448 | } |
---|
| 449 | return retvalue; |
---|
| 450 | } |
---|
[219] | 451 | |
---|
[599] | 452 | StdString CINetCDF4::getCoordinatesId(const StdString& name, const CVarPath* const path) |
---|
| 453 | { |
---|
| 454 | StdString retvalue; |
---|
[782] | 455 | if (this->hasAttribute(CCFKeywords::XIOS_CF_coordinates, &name, path)) |
---|
[599] | 456 | { |
---|
[782] | 457 | return this->getAttributeValue(CCFKeywords::XIOS_CF_coordinates, &name, path); |
---|
[599] | 458 | } |
---|
| 459 | else |
---|
| 460 | { |
---|
| 461 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
---|
| 462 | std::list<StdString>::const_iterator it = dims.begin(), end = dims.end(); |
---|
| 463 | for (; it != end; it++) |
---|
[219] | 464 | { |
---|
[599] | 465 | const StdString& value = *it; |
---|
| 466 | retvalue.append(value).push_back(' '); |
---|
[219] | 467 | } |
---|
[599] | 468 | retvalue.erase(retvalue.end() - 1) ; |
---|
| 469 | } |
---|
[219] | 470 | |
---|
[599] | 471 | return retvalue; |
---|
| 472 | } |
---|
| 473 | |
---|
| 474 | StdString CINetCDF4::getBoundsId(const StdString& name, |
---|
| 475 | const CVarPath* const path) |
---|
| 476 | { |
---|
| 477 | StdString retvalue; |
---|
[782] | 478 | if (this->hasAttribute(CCFKeywords::XIOS_CF_bounds, &name, path)) |
---|
| 479 | retvalue = this->getAttributeValue(CCFKeywords::XIOS_CF_bounds, &name, path); |
---|
[599] | 480 | return retvalue; |
---|
| 481 | } |
---|
| 482 | |
---|
| 483 | //--------------------------------------------------------------- |
---|
| 484 | |
---|
| 485 | bool CINetCDF4::isBound(const StdString& name, |
---|
| 486 | const CVarPath* const path) |
---|
| 487 | { |
---|
| 488 | std::set<StdString> bounds = this->getBoundVariables(path); |
---|
| 489 | return (bounds.find(name) != bounds.end()); |
---|
| 490 | } |
---|
| 491 | |
---|
| 492 | bool CINetCDF4::isCoordinate(const StdString& name, |
---|
| 493 | const CVarPath* const path) |
---|
| 494 | { |
---|
| 495 | std::set<StdString> coords = this->getCoordVariables(path); |
---|
| 496 | return (coords.find(name) != coords.end()); |
---|
| 497 | } |
---|
| 498 | |
---|
[1463] | 499 | /* |
---|
[599] | 500 | bool CINetCDF4::isRectilinear(const StdString& name, const CVarPath* const path) |
---|
| 501 | { |
---|
[1460] | 502 | std::list<StdString> varCoords = this->getCoordinatesIdList(name, path); |
---|
[1462] | 503 | std::list<StdString>::const_iterator it = varCoords.begin(), end = varCoords.end(); |
---|
| 504 | for (; it != end; it++) |
---|
| 505 | { |
---|
| 506 | const StdString& coord = *it; |
---|
| 507 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path)) |
---|
| 508 | { |
---|
| 509 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
| 510 | if ((dimvar.size() == 1) && (dimvar.find(coord) != dimvar.end())) |
---|
| 511 | continue; |
---|
| 512 | else |
---|
| 513 | return false; |
---|
| 514 | } |
---|
| 515 | } |
---|
| 516 | return true; |
---|
| 517 | } |
---|
[1463] | 518 | */ |
---|
[1462] | 519 | |
---|
[1463] | 520 | bool CINetCDF4::isRectilinear(const StdString& name, const CVarPath* const path) |
---|
[1462] | 521 | { |
---|
| 522 | std::list<StdString> varCoords = this->getCoordinatesIdList(name, path); |
---|
[1460] | 523 | std::list<StdString> varDims = this->getDimensionsList(&name, path); |
---|
| 524 | std::list<StdString>::const_iterator it = varCoords.begin(), end = varCoords.end(); |
---|
| 525 | std::set<StdString> varDims1D; |
---|
| 526 | |
---|
| 527 | // Firstly, loop over coordinate list |
---|
[599] | 528 | for (; it != end; it++) |
---|
| 529 | { |
---|
| 530 | const StdString& coord = *it; |
---|
[1460] | 531 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) ) |
---|
[219] | 532 | { |
---|
[1460] | 533 | std::map<StdString, StdSize> coordDims = this->getDimensions(&coord, path); |
---|
| 534 | for (std::map<StdString, StdSize>::const_iterator itTmp = coordDims.begin(); itTmp != coordDims.end(); itTmp++) |
---|
| 535 | { |
---|
| 536 | varDims.remove(itTmp->first); |
---|
| 537 | } |
---|
| 538 | if (this->isLonOrLat(coord, path) && coordDims.size() == 1) |
---|
| 539 | { |
---|
| 540 | varDims1D.insert(coordDims.begin()->first); |
---|
[599] | 541 | continue; |
---|
[1460] | 542 | } |
---|
[219] | 543 | } |
---|
[599] | 544 | } |
---|
[1460] | 545 | // Secondly, loop over remaining dimensions |
---|
| 546 | for (it= varDims.begin(); it != varDims.end(); it++) |
---|
| 547 | { |
---|
| 548 | const StdString& coord = *it; |
---|
| 549 | std::map<StdString, StdSize> coordDims = this->getDimensions(&coord, path); |
---|
| 550 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) ) |
---|
| 551 | { |
---|
| 552 | if (this->isLonOrLat(coord, path) && coordDims.size() == 1) |
---|
| 553 | { |
---|
| 554 | varDims1D.insert(coordDims.begin()->first); |
---|
| 555 | continue; |
---|
| 556 | } |
---|
| 557 | } |
---|
| 558 | } |
---|
| 559 | |
---|
| 560 | return (varDims1D.size() == 2); |
---|
[599] | 561 | } |
---|
[219] | 562 | |
---|
[1463] | 563 | |
---|
[599] | 564 | bool CINetCDF4::isCurvilinear(const StdString& name, const CVarPath* const path) |
---|
| 565 | { |
---|
| 566 | if (this->isRectilinear(name, path) || !this->hasCoordinates(name, path)) |
---|
| 567 | return false; |
---|
| 568 | |
---|
[782] | 569 | bool isCurVi = true; |
---|
| 570 | unsigned int nbLonLat = 0; |
---|
[599] | 571 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 572 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 573 | for (; it != end; it++) |
---|
| 574 | { |
---|
| 575 | const StdString& coord = *it; |
---|
[1460] | 576 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) && this->isLonOrLat(coord, path)) |
---|
[219] | 577 | { |
---|
[599] | 578 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
[782] | 579 | if (2 == dimvar.size()) ++nbLonLat; |
---|
[219] | 580 | } |
---|
[599] | 581 | } |
---|
[782] | 582 | if (2 != nbLonLat) isCurVi = false; |
---|
| 583 | |
---|
| 584 | return isCurVi; |
---|
[599] | 585 | } |
---|
[219] | 586 | |
---|
[599] | 587 | bool CINetCDF4::isUnstructured(const StdString& name, const CVarPath* const path) |
---|
| 588 | { |
---|
| 589 | if (this->isRectilinear(name, path) || |
---|
| 590 | this->isCurvilinear(name, path) || |
---|
| 591 | !this->hasCoordinates(name, path)) |
---|
| 592 | return false; |
---|
[948] | 593 | else return true ; |
---|
| 594 | |
---|
| 595 | // check this part above |
---|
[599] | 596 | StdString dimname = this->getDimensionsList(&name, path).back(); |
---|
[219] | 597 | |
---|
[599] | 598 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 599 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 600 | for (; it != end; it++) |
---|
| 601 | { |
---|
| 602 | const StdString& coord = *it; |
---|
[1460] | 603 | if (this->hasVariable(coord, path) && !this->isTemporal(coord, path) && this->isLonOrLat(coord, path)) |
---|
[219] | 604 | { |
---|
[599] | 605 | std::map<StdString, StdSize> dimvar = this->getDimensions(&coord, path); |
---|
| 606 | if ((dimvar.size() == 1) && |
---|
| 607 | (dimvar.find(dimname) != dimvar.end())) |
---|
| 608 | continue; |
---|
| 609 | else |
---|
| 610 | return false; |
---|
| 611 | } |
---|
| 612 | } |
---|
[219] | 613 | |
---|
[599] | 614 | return true; |
---|
| 615 | } |
---|
[219] | 616 | |
---|
[599] | 617 | bool CINetCDF4::isUnknown(const StdString& name, const CVarPath* const path) |
---|
| 618 | { |
---|
| 619 | return !(this->isRectilinear(name, path) || this->isCurvilinear(name, path) || this->isUnstructured(name, path)); |
---|
| 620 | } |
---|
[219] | 621 | |
---|
[599] | 622 | bool CINetCDF4::isTemporal(const StdString& name, const CVarPath* const path) |
---|
| 623 | { |
---|
[802] | 624 | std::list<StdString> dims = this->getDimensionsList(&name, path); |
---|
| 625 | return (std::find(dims.begin(), dims.end(), timeCounterName) != dims.end()); |
---|
[599] | 626 | } |
---|
[219] | 627 | |
---|
[599] | 628 | bool CINetCDF4::is3Dim(const StdString& name, const CVarPath* const path) |
---|
| 629 | { |
---|
| 630 | int i = 0; |
---|
| 631 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 632 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 633 | for (; it != end; it++) |
---|
| 634 | { |
---|
| 635 | const StdString& coord = *it; |
---|
| 636 | if (this->hasVariable(coord, path)) |
---|
[219] | 637 | { |
---|
[599] | 638 | if (this->isTemporal(coord, path)) |
---|
| 639 | continue; |
---|
| 640 | i++; |
---|
[219] | 641 | } |
---|
[599] | 642 | else |
---|
[219] | 643 | { |
---|
[782] | 644 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
| 645 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
[599] | 646 | continue; |
---|
| 647 | i++; |
---|
[219] | 648 | } |
---|
[599] | 649 | } |
---|
| 650 | return (i == 3); |
---|
| 651 | } |
---|
[219] | 652 | |
---|
[599] | 653 | bool CINetCDF4::isCellGrid(const StdString& name, const CVarPath* const path) |
---|
| 654 | { |
---|
| 655 | if (this->isCoordinate(name, path)) |
---|
| 656 | { |
---|
[686] | 657 | return this->hasBounds(name, path); |
---|
[599] | 658 | } |
---|
| 659 | else |
---|
| 660 | { |
---|
| 661 | std::list<StdString> coords = this->getCoordinatesIdList(name, path); |
---|
| 662 | std::list<StdString>::const_iterator it = coords.begin(), end = coords.end(); |
---|
| 663 | for (; it != end; it++) |
---|
[219] | 664 | { |
---|
[599] | 665 | const StdString& coord = *it; |
---|
| 666 | if (this->hasVariable(coord, path)) |
---|
| 667 | { |
---|
| 668 | if (this->isTemporal(coord, path)) |
---|
| 669 | continue; |
---|
| 670 | if (this->isCellGrid(coord, path)) |
---|
| 671 | continue; |
---|
| 672 | return false; |
---|
| 673 | } |
---|
| 674 | else |
---|
| 675 | { |
---|
[782] | 676 | StdString unlimitedDimName = this->getUnlimitedDimensionName(); |
---|
| 677 | if (coord.compare(0, unlimitedDimName.size(), unlimitedDimName) == 0) |
---|
[599] | 678 | continue; |
---|
| 679 | return false; |
---|
| 680 | } |
---|
[219] | 681 | } |
---|
[599] | 682 | } |
---|
[219] | 683 | |
---|
[599] | 684 | return true; |
---|
| 685 | } |
---|
[219] | 686 | |
---|
[599] | 687 | //--------------------------------------------------------------- |
---|
[219] | 688 | |
---|
[599] | 689 | std::list<StdString> CINetCDF4::getDataVariables(bool _is3D, bool _isRecti, |
---|
| 690 | bool _isCurvi, bool _isUnstr, |
---|
| 691 | bool _isCellData, bool _isTemporal, |
---|
| 692 | const CVarPath* const path) |
---|
| 693 | { |
---|
| 694 | std::list<StdString> retvalue; |
---|
| 695 | std::list<StdString> allvars = this->getVariables(path); |
---|
| 696 | std::set<StdString> allcoords = this->getCoordVariables(path); |
---|
[219] | 697 | |
---|
[599] | 698 | std::list<StdString>::const_iterator it = allvars.begin(), end = allvars.end(); |
---|
| 699 | for (; it != end; it++) |
---|
| 700 | { |
---|
| 701 | const StdString& var = *it; |
---|
| 702 | if (this->isCoordinate(var, path)) continue; |
---|
[219] | 703 | |
---|
[599] | 704 | if (!_isRecti && this->isRectilinear(var, path)) continue; |
---|
| 705 | if (!_isCurvi && this->isCurvilinear(var, path)) continue; |
---|
| 706 | if (!_isUnstr && this->isUnstructured(var, path)) continue; |
---|
[219] | 707 | |
---|
[599] | 708 | if (!_isTemporal && this->isTemporal(var, path)) continue; |
---|
| 709 | if (!_is3D && this->is3Dim(var, path)) continue; |
---|
| 710 | if (!_isCellData && this->isCellGrid(var, path)) continue; |
---|
[219] | 711 | |
---|
[599] | 712 | if (this->isUnknown(var, path)) continue; |
---|
[219] | 713 | |
---|
[599] | 714 | retvalue.push_back(var); |
---|
| 715 | } |
---|
| 716 | return retvalue; |
---|
| 717 | } |
---|
[219] | 718 | |
---|
[599] | 719 | //--------------------------------------------------------------- |
---|
[219] | 720 | |
---|
[599] | 721 | void CINetCDF4::getDataInfo(const StdString& var, const CVarPath* const path, StdSize record, |
---|
| 722 | std::vector<StdSize>& sstart, std::vector<StdSize>& scount, StdSize& array_size, |
---|
| 723 | const std::vector<StdSize>* start /*= NULL*/, const std::vector<StdSize>* count /*= NULL*/) |
---|
| 724 | { |
---|
| 725 | std::list<StdString> dimlist = this->getDimensionsList(&var, path); |
---|
| 726 | std::map<StdString, StdSize> dimmap = this->getDimensions(&var, path); |
---|
| 727 | std::list<StdString>::iterator it = dimlist.begin(); |
---|
| 728 | if (this->isTemporal(var, path)) |
---|
| 729 | { |
---|
| 730 | if (record != UNLIMITED_DIM) |
---|
| 731 | sstart.push_back(record); |
---|
| 732 | else |
---|
| 733 | sstart.push_back(0); |
---|
| 734 | scount.push_back(1); |
---|
| 735 | it++; |
---|
| 736 | } |
---|
| 737 | for (int i = 0; it != dimlist.end(); it++, i++) |
---|
| 738 | { |
---|
| 739 | if (start && count) |
---|
[219] | 740 | { |
---|
[599] | 741 | sstart.push_back((*start)[i]); |
---|
| 742 | scount.push_back((*count)[i]); |
---|
| 743 | array_size *= (*count)[i]; |
---|
[219] | 744 | } |
---|
[599] | 745 | else |
---|
[219] | 746 | { |
---|
[599] | 747 | sstart.push_back(0); |
---|
| 748 | scount.push_back(dimmap[*it]); |
---|
| 749 | array_size *= dimmap[*it]; |
---|
[219] | 750 | } |
---|
[599] | 751 | } |
---|
| 752 | } |
---|
[219] | 753 | |
---|
[686] | 754 | template <class T> |
---|
| 755 | void CINetCDF4::getData(CArray<T, 1>& data, const StdString& var, |
---|
[599] | 756 | const CVarPath* const path, StdSize record) |
---|
| 757 | { |
---|
| 758 | std::vector<StdSize> start, count; |
---|
| 759 | int grpid = this->getGroup(path); |
---|
| 760 | int varid = this->getVariable(var, path); |
---|
| 761 | StdSize array_size = 1; |
---|
| 762 | this->getDataInfo(var, path, record, start, count, array_size); |
---|
| 763 | data.resize(array_size); |
---|
[686] | 764 | CNetCdfInterface::getVaraType(grpid, varid, &start[0], &count[0], data.dataFirst()); |
---|
[599] | 765 | } |
---|
[219] | 766 | |
---|
[599] | 767 | template <> |
---|
[686] | 768 | void CINetCDF4::getData(CArray<int, 1>& data, const StdString& var, |
---|
| 769 | const CVarPath* const path, StdSize record); |
---|
| 770 | template <> |
---|
[599] | 771 | void CINetCDF4::getData(CArray<double, 1>& data, const StdString& var, |
---|
[686] | 772 | const CVarPath* const path, StdSize record); |
---|
[599] | 773 | template <> |
---|
| 774 | void CINetCDF4::getData(CArray<float, 1>& data, const StdString& var, |
---|
[686] | 775 | const CVarPath* const path, StdSize record); |
---|
[219] | 776 | |
---|
[599] | 777 | //--------------------------------------------------------------- |
---|
| 778 | |
---|
| 779 | StdString CINetCDF4::getLonCoordName(const StdString& varname, |
---|
| 780 | const CVarPath* const path) |
---|
| 781 | { |
---|
[825] | 782 | StdString lonName; |
---|
[782] | 783 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
[599] | 784 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
[782] | 785 | itbList = clist.begin(); iteList = clist.end(); |
---|
| 786 | for (itList = itbList; itList != iteList; ++itList) |
---|
| 787 | { |
---|
| 788 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
| 789 | { |
---|
| 790 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
| 791 | if (CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit)) |
---|
[825] | 792 | { |
---|
| 793 | lonName = *itList; |
---|
| 794 | return lonName; |
---|
| 795 | } |
---|
[782] | 796 | } |
---|
| 797 | } |
---|
[825] | 798 | return lonName; |
---|
[599] | 799 | } |
---|
| 800 | |
---|
| 801 | StdString CINetCDF4::getLatCoordName(const StdString& varname, |
---|
| 802 | const CVarPath* const path) |
---|
| 803 | { |
---|
[825] | 804 | StdString latName; |
---|
[782] | 805 | std::list<StdString>::const_iterator itbList, itList, iteList; |
---|
[599] | 806 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
---|
[782] | 807 | itbList = clist.begin(); iteList = clist.end(); |
---|
| 808 | for (itList = itbList; itList != iteList; ++itList) |
---|
| 809 | { |
---|
| 810 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &(*itList), path)) |
---|
| 811 | { |
---|
| 812 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &(*itList), path); |
---|
| 813 | if (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit)) |
---|
[825] | 814 | { |
---|
| 815 | latName = *itList; |
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| 816 | return latName; |
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| 817 | } |
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[782] | 818 | } |
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| 819 | } |
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[825] | 820 | return latName; |
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[599] | 821 | } |
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| 822 | |
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| 823 | StdString CINetCDF4::getVertCoordName(const StdString& varname, |
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| 824 | const CVarPath* const path) |
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| 825 | { |
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| 826 | if (!this->is3Dim(varname, path)) return ""; |
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| 827 | std::list<StdString> clist = this->getCoordinatesIdList(varname, path); |
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| 828 | if (this->hasCoordinates(varname, path)) |
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[686] | 829 | return *(++(++clist.begin())); |
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[599] | 830 | else |
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[686] | 831 | return *(++(++clist.rbegin())); |
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[599] | 832 | } |
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[1460] | 833 | |
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| 834 | bool CINetCDF4::isLonOrLat(const StdString& varname, const CVarPath* const path) |
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| 835 | { |
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| 836 | if (this->hasAttribute(CCFKeywords::XIOS_CF_units, &varname, path)) |
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| 837 | { |
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| 838 | StdString unit = this->getAttributeValue(CCFKeywords::XIOS_CF_units, &varname, path); |
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| 839 | return (CCFConvention::XIOS_CF_Latitude_units.end() != CCFConvention::XIOS_CF_Latitude_units.find(unit) |
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| 840 | || CCFConvention::XIOS_CF_Longitude_units.end() != CCFConvention::XIOS_CF_Longitude_units.find(unit)); |
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| 841 | } |
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| 842 | } |
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| 843 | |
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[335] | 844 | } // namespace xios |
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